From 4787d4f8dc4e441d53350a2ae666665f19faeb38 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:00:22 +0300 Subject: [PATCH 001/142] docs on extending junifer (WIP) --- docs/extending/index.rst | 18 ++++++++++++++++++ docs/index.rst | 1 + 2 files changed, 19 insertions(+) create mode 100644 docs/extending/index.rst diff --git a/docs/extending/index.rst b/docs/extending/index.rst new file mode 100644 index 000000000..ce25d63bd --- /dev/null +++ b/docs/extending/index.rst @@ -0,0 +1,18 @@ +.. include:: ../links.inc + +Extending junifer +================= + +While we aim to provide as many datasets and markers as possible, we are also +interested in allowing users to extend the functionality with their own +datagrabbers, preprocessing, markers, etc. + +This does not mean that the new functinality will have to be included in +junifer before the user can use them. Instead, the user can simply +create a new python file, code the desired functionality and use it with +junifer. This is the first step towards including the new functionality in +the junifer package. + +In this section we will show how to extend junifer, by creating new +datagrabbers, preprocessing and markers, following the _junifer_ way. + diff --git a/docs/index.rst b/docs/index.rst index cef0f0606..5eb8c8a72 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -21,6 +21,7 @@ enabling others to extend it easily. installation understanding/index.rst builtin + extending/index.rst auto_examples/index.rst api/index.rst contribution -- 2.52.0 From d4000e8a7e64e993c6d99c5c41c3ac3088ea4521 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:19:11 +0300 Subject: [PATCH 002/142] update --- docs/extending/datagrabber.rst | 0 docs/extending/index.rst | 11 ++++++++++- 2 files changed, 10 insertions(+), 1 deletion(-) create mode 100644 docs/extending/datagrabber.rst diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst new file mode 100644 index 000000000..e69de29bb diff --git a/docs/extending/index.rst b/docs/extending/index.rst index ce25d63bd..dcd38bb7e 100644 --- a/docs/extending/index.rst +++ b/docs/extending/index.rst @@ -14,5 +14,14 @@ junifer. This is the first step towards including the new functionality in the junifer package. In this section we will show how to extend junifer, by creating new -datagrabbers, preprocessing and markers, following the _junifer_ way. +datagrabbers, preprocessing and markers, following the *junifer* way. + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + datagrabber + .. datareader + .. marker + .. storage \ No newline at end of file -- 2.52.0 From c476969bcfe342c428ede6414fdcc02b28800e21 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:28:06 +0300 Subject: [PATCH 003/142] typo --- docs/extending/index.rst | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/extending/index.rst b/docs/extending/index.rst index dcd38bb7e..e14714c6d 100644 --- a/docs/extending/index.rst +++ b/docs/extending/index.rst @@ -22,6 +22,3 @@ datagrabbers, preprocessing and markers, following the *junifer* way. :caption: Contents: datagrabber - .. datareader - .. marker - .. storage \ No newline at end of file -- 2.52.0 From f9a7c5af203e296aab55f96bee22a1b2b7931519 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:41:18 +0300 Subject: [PATCH 004/142] now? --- docs/extending/datagrabber.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst index e69de29bb..acb7b4b5f 100644 --- a/docs/extending/datagrabber.rst +++ b/docs/extending/datagrabber.rst @@ -0,0 +1,4 @@ +Creating datagrabbers +===================== + +Datagrabbers are created by... \ No newline at end of file -- 2.52.0 From 7381b691d928e173c0ba7d5a077eebde1e08cfd8 Mon Sep 17 00:00:00 2001 From: Fede Date: Sun, 23 Oct 2022 14:10:54 +0300 Subject: [PATCH 005/142] fixing the doc and consistency --- docs/api/api.rst | 10 + docs/contribution.rst | 6 +- docs/extending/datagrabber.rst | 271 +++++++++++++++++- docs/extending/index.rst | 4 +- docs/links.inc | 1 + docs/understanding/data.rst | 7 +- docs/understanding/datagrabber.rst | 5 +- docs/understanding/index.rst | 2 + docs/understanding/marker.rst | 6 +- docs/understanding/storage.rst | 2 + examples/run_datagrabber_bids_datalad.py | 6 +- .../tests/test_datagrabber_utils.py | 12 +- junifer/datagrabber/tests/test_multiple.py | 12 +- .../datagrabber/tests/test_pattern_datalad.py | 24 +- .../datareader/tests/test_default_reader.py | 18 +- 15 files changed, 338 insertions(+), 48 deletions(-) diff --git a/docs/api/api.rst b/docs/api/api.rst index b1a96e243..106a4e309 100644 --- a/docs/api/api.rst +++ b/docs/api/api.rst @@ -2,6 +2,16 @@ API Functions ^^^^^^^^^^^^^^ +Main API functions +------------------ + .. automodule:: junifer.api :members: :imported-members: + +Decorators +---------- + +.. automodule:: junifer.api.decorators + :members: + :imported-members: diff --git a/docs/contribution.rst b/docs/contribution.rst index 47e646bd0..b510c6a4a 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -175,10 +175,10 @@ texts. # The BIDS datagrabber requires three parameters: the types of data we want, # the specific pattern that matches each type, and the variables that will be # replaced int he patterns. - types = ["T1w", "bold"] + types = ["T1w", "BOLD"] patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } replacements = ["subject"] ############################################################################### @@ -204,7 +204,7 @@ texts. ############################################################################### # Another feature of the datagrabber is the ability to get a specific # element by its name. In this case, we index `sub-01` and we get the file - # paths for the two types of data we want (T1w and bold). + # paths for the two types of data we want (T1w and BOLD). with PatternDataladDataGrabber( rootdir=rootdir, types=types, diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst index acb7b4b5f..3ee2bc871 100644 --- a/docs/extending/datagrabber.rst +++ b/docs/extending/datagrabber.rst @@ -1,4 +1,271 @@ -Creating datagrabbers +.. include:: ../links.inc + +.. _extending_datagrabbers: + +Creating DataGrabbers ===================== -Datagrabbers are created by... \ No newline at end of file +DataGrabbers are the first step of the pipeline. It's purpose is to interpret +the structure of a dataset and provide two specific functionalities: + +1) Given an *element*, provide the path to each kind of data available for this + element (e.g. the path to the T1 image, the path to the T2 image, etc.) +2) Provide the list of *elements* available in the dataset. + +In this section, we will see how to create a datagrabber for a dataset. Basic +aspects of datagrabbers are covedered in the +:ref:`Understanding DataGrabbers ` section. + +.. _extending_datagrabbers_think: + +Step 1: Think about the element +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Like with any programming-related task, the first step is to think. When +creating a DataGrabber, we need to first define what an *element* is. +The *element* should be the smallest unit of data that can be processed. That +is, for each element, there should be a set of data that can be processed, but +only one of each *data type* (see :ref:`data_types`). + +For example, if we have a dataset from an fMRI study in which: + +a) both T1w and fMRI was acquired +b) 20 subjects went through a experiment twice +c) the experiment included resting-stage fMRI and a task named *stroop* + +then the *element* should be composed of 3 items: + +* ``subject``: The subject IDs, e.g. `sub001`, `sub002`, ... `sub020` +* ``session``: The sesion number, e.g. `ses1`, `ses2` +* ``task``: The task performed, e.g. `rest`, `stroop` + +If any of this items were not part of the element, then we will have more than +one ``T1w`` and/or ``BOLD`` image for each subject, which is not allowed. + +Importantly, nothing prevents that one image is part of two different elements. +For example, it is usually the case that the ``T1w`` image is not acquired for +each task, but once in the entire session. So in this case, the ``T1w`` image +for the element (``sub001``, ``ses1``, ``rest``) will be the same as the +``T1w`` image for the element (``sub001``, ``ses1``, ``stroop``). + +We will now continue this section using as an example, a dataset in BIDS format +in which each 9 subjects (`sub-01` to `sub-09`) were scanned each in 3 +sessions (`ses-01`, `ses-02`, `ses-03`) and each session included a `T1w` and +a `BOLD` image (resting-state), except for `ses-03` which was only anatomical. + +Step 2: Think about the dataset's structure +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Now that we have our element defined, we need to think about the structure of +the dataset. Mainly, because the structure of the dataset will determine how +the DataGrabber needs to be implemented. + +Junifer provides an abstract class to deal with datasets that can be thought in +terms of *patterns*. A *pattern* is a string that contains placeholders that are +replaced by the actual values of the element. In our BIDS example, the path +to the T1w image of subject `sub-01` and session `ses-01`, relative to the +dataset location, is ``sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz``. By +replacing ``sub-01`` with ``sub-02``, we can obtain the T1w image of the first +session of the second subject. Indeed, the path to the T1w images can be +expressed as a pattern: + +``{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz`` + +where ``{subject}`` is the replacement for the subject id and ``{session}}`` +is the replacement for the session id. + +Since it is a BIDS dataaset, the same happens with the BOLD images. The path to +the BOLD images can be expressed as a pattern: + +``{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz`` + + +This will be the norm in most of the datasets. If your dataset can be expressed +in terms of patterns, then follow :ref:`extending_datagrabbers_pattern`. +Otherwise, we recommend that you take time to re-think about your dataset +structure and why it does not have clear *patterns*. Feel free to open a +discussion in the `junifer Discussions`_ page. Most probably we can help you +get your dataset in order. + +If there is no other way, then you can follow :ref:`extending_datagrabbers_base` +to create a DataGrabber from scratch. + + +.. _extending_datagrabbers_pattern: + +Option A: Extending from PatternDataGrabber +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +The :py:class:`~junifer.datagrabber.PatternDataGrabber` class is an +abstract class that has the functionality of understanding patterns embeded +in it. + +Before creating the datagrabber, we need to define 3 variables: + +* ``types``: A list with the available :ref:`data_types` in our dataset +* ``patterns``: A dictionary that specifies the pattern for each data type. +* ``replacements``: A list indicating which of the elements in the patterns + should be replaced by the values of the element. + +For example, in our BIDS example, the variables will be: + +.. code-block:: python + + types = ["T1w", "BOLD"] + patterns = { + "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", + "BOLD": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz", + } + replacements = ["subject", "session"] + + +An additional fourth variable is the ``datadir``, which should be the path to +where the dataset is located. For example, if the dataset is located in +``/data/project/test/data``, then ``datadir`` should be +``/data/project/test/data``. Or, if we want to allow the user to specify the +location of the dataset, we can expose the variable in the constructor, as in +this example + +With this defined, we can now create our datagrabber, we will name it +``ExampleBIDSDataGrabber``: + + +.. code-block:: python + + from junifer.datagrabber.pattern import PatternDataGrabber + + class ExampleBIDSDataGrabber(PatternDataGrabber): + + def __init__(self, datadir): + types = ["T1w", "BOLD"] + patterns = { + "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", + "BOLD": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz", + } + replacements = ["subject", "session"] + super().__init__( + datadir=datadir, + types=types, + patterns=patterns, + replacements=replacements) + + +Our datagrabber is ready to be used by junifer. However, it is still unknown +to the library. We need to register it in the library. To do so, we need to +use the :py:func:`~junifer.api.decorators.register_datagrabber` decorator. + + +.. code-block:: python + + from junifer.datagrabber.pattern import PatternDataGrabber + from junifer.api.decorators import register_datagrabber + + + @register_datagrabber + class ExampleBIDSDataGrabber(PatternDataGrabber): + + def __init__(self, datadir): + types = ["T1w", "BOLD"] + patterns = { + "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", + "BOLD": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz", + } + replacements = ["subject", "session"] + super().__init__( + datadir=datadir, + types=types, + patterns=patterns, + replacements=replacements) + + +Now, we can use our datagrabber in junifer, by setting the ``datagrabber`` kind +in the yaml file to ``ExampleBIDSDataGrabber``. Remember that we still need to +set the ``datadir``. + +.. code-block:: yaml + + datagrabber: + kind: ExampleBIDSDataGrabber + datadir: /data/project/test/data + + +Optional: Using datalad +----------------------- + +If you are using datalad, you can use the +:py:class:`~junifer.datagrabber.PatternDataladDataGrabber` instead of the +:py:class:`~junifer.datagrabber.PatternDataGrabber`. This class will also +interpret patterns, but will also use datalad to `clone` and `get` the data. + +The main difference between the two is that the ``datadir`` is not the actual +location of the dataset, but the location where the dataset will be cloned. It +can now be ``None``, which means that the data will be downloaded to a +temporary directory. To set the location of the dataset, you can use the +``uri`` argument in the constructor. Additionally, a ``rootdir`` argument can +be used to specify the path to the root directory of the dataset after doing +``datalad clone`` + +In the example, the dataset is hosted in gin +(``https://gin.g-node.org/juaml/datalad-example-bids``). + +When we clone this dataset, we will see the following structure: + +.. code-block:: + + . + └── example_bids_ses + ├── sub-01 + │ ├── ses-01 + │ ├── ses-02 + │ └── ses-03 + ├── sub-02 + │ ├── ses-01 + │ ├── ses-02 + │ └── ses-03 + ├── sub-03 + ... + +So the patterns will start after ``example_bids_ses``. This is our ``rootdir``. + +Now we have our 2 additional variables: + +.. code-block:: python + + uri = "https://gin.g-node.org/juaml/datalad-example-bids" + rootdir = "example_bids_ses" + + +And we can create our datagrabber: + + +.. code-block:: python + + from junifer.datagrabber.pattern import PatternDataladDataGrabber + from junifer.api.decorators import register_datagrabber + + + @register_datagrabber + class ExampleBIDSDataGrabber(PatternDataladDataGrabber): + + def __init__(self): + types = ["T1w", "BOLD"] + patterns = { + "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", + "BOLD": "{subject}/{session}/func/{subject}_{session}_task-rest_bold.nii.gz", + } + replacements = ["subject", "session"] + uri = "https://gin.g-node.org/juaml/datalad-example-bids" + rootdir = "example_bids_ses" + super().__init__( + datadir=None, + uri=uri, + rootdir=rootdir, + types=types, + patterns=patterns, + replacements=replacements) + + +.. _extending_datagrabbers_base: + +Option B: Extending from BaseDataGrabber +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ \ No newline at end of file diff --git a/docs/extending/index.rst b/docs/extending/index.rst index e14714c6d..3706e914e 100644 --- a/docs/extending/index.rst +++ b/docs/extending/index.rst @@ -1,5 +1,7 @@ .. include:: ../links.inc +.. _extending: + Extending junifer ================= @@ -18,7 +20,7 @@ datagrabbers, preprocessing and markers, following the *junifer* way. .. toctree:: - :maxdepth: 2 + :maxdepth: 1 :caption: Contents: datagrabber diff --git a/docs/links.inc b/docs/links.inc index 47d3ad6a4..6f8d31de1 100644 --- a/docs/links.inc +++ b/docs/links.inc @@ -25,6 +25,7 @@ .. _`Github`: https://github.com/ .. _`junifer Github`: https://github.com/juaml/junifer +.. _`junifer Discussions`: https://github.com/juaml/junifer/discussions .. _`Wikipedia`: https://wikipedia.org diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index 1010720a8..ba50af255 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -1,5 +1,7 @@ .. include:: ../links.inc +.. _understanding_data_object: + The Data Object =============== @@ -16,7 +18,7 @@ The second level of keys are the actual data. So far, there are two keys used: - ``path``: path to the file containing the data. - ``data``: the data loaded in memory. -The :ref:`datagrabber` step will only fill the ``path`` value. +The :ref:`datagrabbers` step will only fill the ``path`` value. The ``data`` value will be filled by the :ref:`datareader` step, if it is one of the possible file types that the datareader can read. @@ -38,6 +40,9 @@ Data types * - ``BOLD`` - BOLD image (4D) - Preprocessed/Denoised BOLD image (fmriprep output) + * - ``BOLD_confounds`` + - BOLD image confounds (CSV/TSV file) + - Confounds that can be applied to the BOLD image. * - ``VBM_GM`` - VBM Gray Matter segmentation (3D) - CAT output (`m0wp1` images) diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index ed27cc606..da9dc0481 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -1,11 +1,10 @@ .. include:: ../links.inc -.. _datagrabber: +.. _datagrabbers: Data Grabber ============ - Description ^^^^^^^^^^^ A datagrabber is an object that can provide datasets you want to junifer. @@ -14,7 +13,7 @@ Of course, datagrabbers are not only possible for Datalad but any origin of a da It is intended to use them as context managers. If you are interested in just using already provided datagrabbers please go to :doc:`../builtin`. If you want to implement your own Data Grabbers you need to inherit from different types of -Data Grabbers we already provide. +Data Grabbers we already provide (see :ref:`extending_datagrabbers`). Typical Data Grabbers ^^^^^^^^^^^^^^^^^^^^^ diff --git a/docs/understanding/index.rst b/docs/understanding/index.rst index e24c92883..df2627f36 100644 --- a/docs/understanding/index.rst +++ b/docs/understanding/index.rst @@ -1,5 +1,7 @@ .. include:: ../links.inc +.. _understanding: + Understanding junifer ===================== diff --git a/docs/understanding/marker.rst b/docs/understanding/marker.rst index 3bf018ba7..02446016f 100644 --- a/docs/understanding/marker.rst +++ b/docs/understanding/marker.rst @@ -1,4 +1,6 @@ .. include:: ../links.inc -Marker -====== +.. _markers: + +Markers +======= diff --git a/docs/understanding/storage.rst b/docs/understanding/storage.rst index ef296e1d4..1da80a289 100644 --- a/docs/understanding/storage.rst +++ b/docs/understanding/storage.rst @@ -1,4 +1,6 @@ .. include:: ../links.inc +.. _storage: + Storage ======= diff --git a/examples/run_datagrabber_bids_datalad.py b/examples/run_datagrabber_bids_datalad.py index eb14892a6..727fc5178 100644 --- a/examples/run_datagrabber_bids_datalad.py +++ b/examples/run_datagrabber_bids_datalad.py @@ -23,10 +23,10 @@ configure_logging(level="INFO") # The BIDS datagrabber requires three parameters: the types of data we want, # the specific pattern that matches each type, and the variables that will be # replaced int he patterns. -types = ["T1w", "bold"] +types = ["T1w", "BOLD"] patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } replacements = ["subject"] ############################################################################### @@ -52,7 +52,7 @@ with PatternDataladDataGrabber( ############################################################################### # Another feature of the datagrabber is the ability to get a specific # element by its name. In this case, we index `sub-01` and we get the file -# paths for the two types of data we want (T1w and bold). +# paths for the two types of data we want (T1w and BOLD). with PatternDataladDataGrabber( rootdir=rootdir, types=types, diff --git a/junifer/datagrabber/tests/test_datagrabber_utils.py b/junifer/datagrabber/tests/test_datagrabber_utils.py index c26e4be97..4b203a718 100644 --- a/junifer/datagrabber/tests/test_datagrabber_utils.py +++ b/junifer/datagrabber/tests/test_datagrabber_utils.py @@ -19,7 +19,7 @@ def test_validate_types() -> None: with pytest.raises(TypeError, match="must be a list of strings"): validate_types([1]) # type: ignore - validate_types(["T1w", "bold"]) + validate_types(["T1w", "BOLD"]) def test_validate_replacements() -> None: @@ -31,7 +31,7 @@ def test_validate_replacements() -> None: patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } with pytest.raises(TypeError, match="must be a list of strings"): @@ -42,7 +42,7 @@ def test_validate_replacements() -> None: wrong_patterns = { "T1w": "{subject}/anat/_T1w.nii.gz", - "bold": "{session}/func/_task-rest_bold.nii.gz", + "BOLD": "{session}/func/_task-rest_bold.nii.gz", } with pytest.raises(ValueError, match="At least one pattern"): @@ -53,7 +53,7 @@ def test_validate_replacements() -> None: def test_validate_patterns() -> None: """Test validation of patterns.""" - types = ["T1w", "bold"] + types = ["T1w", "BOLD"] with pytest.raises(TypeError, match="must be a dict"): validate_patterns(types, "wrong") # type: ignore @@ -74,12 +74,12 @@ def test_validate_patterns() -> None: patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } wrongpatterns = { "T1w": "{subject}/anat/{subject}*.nii", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } with pytest.raises(ValueError, match="following a replacement"): diff --git a/junifer/datagrabber/tests/test_multiple.py b/junifer/datagrabber/tests/test_multiple.py index 5e1298d3a..c7113986c 100644 --- a/junifer/datagrabber/tests/test_multiple.py +++ b/junifer/datagrabber/tests/test_multiple.py @@ -27,7 +27,7 @@ def test_multiple() -> None: "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", } pattern2 = { - "bold": "{subject}/{session}/func/" + "BOLD": "{subject}/{session}/func/" "{subject}_{session}_task-rest_bold.nii.gz", } dg1 = PatternDataladDataGrabber( @@ -41,7 +41,7 @@ def test_multiple() -> None: dg2 = PatternDataladDataGrabber( rootdir=rootdir, uri=repo_uri, - types=["bold"], + types=["BOLD"], patterns=pattern2, replacements=replacements, ) @@ -50,7 +50,7 @@ def test_multiple() -> None: types = dg.get_types() assert "T1w" in types - assert "bold" in types + assert "BOLD" in types expected_subs = [ (f"sub-{i:02d}", f"ses-{j:02d}") @@ -64,7 +64,7 @@ def test_multiple() -> None: data = dg[("sub-01", "ses-01")] assert "T1w" in data - assert "bold" in data + assert "BOLD" in data meta = dg.get_meta() assert "class" in meta @@ -85,7 +85,7 @@ def test_multiple_no_intersection() -> None: "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", } pattern2 = { - "bold": "{subject}/{session}/func/" + "BOLD": "{subject}/{session}/func/" "{subject}_{session}_task-rest_bold.nii.gz", } dg1 = PatternDataladDataGrabber( @@ -99,7 +99,7 @@ def test_multiple_no_intersection() -> None: dg2 = PatternDataladDataGrabber( rootdir=rootdir, uri=repo_uri2, - types=["bold"], + types=["BOLD"], patterns=pattern2, replacements=replacements, ) diff --git a/junifer/datagrabber/tests/test_pattern_datalad.py b/junifer/datagrabber/tests/test_pattern_datalad.py index 7cacf7b60..3397d9582 100644 --- a/junifer/datagrabber/tests/test_pattern_datalad.py +++ b/junifer/datagrabber/tests/test_pattern_datalad.py @@ -45,11 +45,11 @@ def test_bids_PatternDataladDataGrabber(tmp_path: Path) -> None: """ # Define types - types = ["T1w", "bold"] + types = ["T1w", "BOLD"] # Define patterns patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } # Define replacements replacements = ["subject"] @@ -75,8 +75,8 @@ def test_bids_PatternDataladDataGrabber(tmp_path: Path) -> None: assert t_sub["T1w"]["path"] == ( dg.datadir / f"{elem}/anat/{elem}_T1w.nii.gz" ) - assert "path" in t_sub["bold"] - assert t_sub["bold"]["path"] == ( + assert "path" in t_sub["BOLD"] + assert t_sub["BOLD"]["path"] == ( dg.datadir / f"{elem}/func/{elem}_task-rest_bold.nii.gz" ) @@ -104,11 +104,11 @@ def test_bids_PatternDataladDataGrabber_datadir(tmp_path: Path) -> None: """ # Define types - types = ["T1w", "bold"] + types = ["T1w", "BOLD"] # Define patterns patterns = { "T1w": "{subject}/anat/{subject}_T1w.nii.gz", - "bold": "{subject}/func/{subject}_task-rest_bold.nii.gz", + "BOLD": "{subject}/func/{subject}_task-rest_bold.nii.gz", } # Define replacements replacements = ["subject"] @@ -118,7 +118,7 @@ def test_bids_PatternDataladDataGrabber_datadir(tmp_path: Path) -> None: datadir = "dataset" # use string and not absolute path patterns = { "T1w": "example_bids/{subject}/anat/{subject}_T*w.nii.gz", - "bold": "example_bids/{subject}/func/{subject}_task-rest_*.nii.gz", + "BOLD": "example_bids/{subject}/func/{subject}_task-rest_*.nii.gz", } with PatternDataladDataGrabber( uri=repo_uri, @@ -134,18 +134,18 @@ def test_bids_PatternDataladDataGrabber_datadir(tmp_path: Path) -> None: assert t_sub["T1w"]["path"] == ( dg.datadir / f"{elem}/anat/{elem}_T1w.nii.gz" ) - assert "path" in t_sub["bold"] - assert t_sub["bold"]["path"] == ( + assert "path" in t_sub["BOLD"] + assert t_sub["BOLD"]["path"] == ( dg.datadir / f"{elem}/func/{elem}_task-rest_bold.nii.gz" ) def test_bids_PatternDataladDataGrabber_session(): """Test a subject and session-based BIDS datalad datagrabber.""" - types = ["T1w", "bold"] + types = ["T1w", "BOLD"] patterns = { "T1w": "{subject}/{session}/anat/{subject}_{session}_T1w.nii.gz", - "bold": "{subject}/{session}/func/" + "BOLD": "{subject}/{session}/func/" "{subject}_{session}_task-rest_bold.nii.gz", } replacements = ["subject", "session"] @@ -162,7 +162,7 @@ def test_bids_PatternDataladDataGrabber_session(): rootdir = "example_bids_ses" # repo_commit = _testing_dataset['example_bids_ses']['id'] - # With T1W and bold, only 2 sessions are available + # With T1W and BOLD, only 2 sessions are available with PatternDataladDataGrabber( rootdir=rootdir, uri=repo_uri, diff --git a/junifer/datareader/tests/test_default_reader.py b/junifer/datareader/tests/test_default_reader.py index a645844ce..4ebf61b34 100644 --- a/junifer/datareader/tests/test_default_reader.py +++ b/junifer/datareader/tests/test_default_reader.py @@ -42,7 +42,7 @@ def test_meta() -> None: nib_data_path = Path(nib_testing.data_path) t_path = nib_data_path / "example4d.nii.gz" - input = {"bold": {"path": t_path}} + input = {"BOLD": {"path": t_path}} output = reader.fit_transform(input) assert "meta" in output assert "datareader" in output["meta"] @@ -67,23 +67,23 @@ def test_read_nifti(fname: str) -> None: t_path = nib_data_path / fname - input = {"bold": {"path": t_path}} + input = {"BOLD": {"path": t_path}} output = reader.fit_transform(input) assert isinstance(output, dict) - assert "bold" in output - assert isinstance(output["bold"], dict) - assert "path" in output["bold"] - assert "data" in output["bold"] + assert "BOLD" in output + assert isinstance(output["BOLD"], dict) + assert "path" in output["BOLD"] + assert "data" in output["BOLD"] - read_img = output["bold"]["data"] + read_img = output["BOLD"]["data"] t_read_img = nib.load(t_path) assert_array_equal(read_img.get_fdata(), t_read_img.get_fdata()) - input = {"bold": {"path": t_path.as_posix()}} + input = {"BOLD": {"path": t_path.as_posix()}} output2 = reader.fit_transform(input) - assert output["bold"]["path"] == output2["bold"]["path"] + assert output["BOLD"]["path"] == output2["BOLD"]["path"] def test_read_unknown() -> None: -- 2.52.0 From 081d57a16b8775ad1e41b3438dcc9db1a5c21fa8 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:02:18 +0300 Subject: [PATCH 006/142] update action title --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 607f88c94..c973a7359 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -1,4 +1,4 @@ -name: Build docs and preview PR +name: Build and preview docs on: push: -- 2.52.0 From 3c12717658ec5a7ab3ad30d7e6a6f608db93e95b Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:07:00 +0300 Subject: [PATCH 007/142] Avoid running tests if only docs changed --- .github/workflows/ci.yml | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f16b24d64..462a7267b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,6 +1,12 @@ name: Run Tests -on: [push, pull_request] +on: + push: + paths-ignore: + - 'docs/**' + pull_request: + paths-ignore: + - 'docs/**' jobs: run-tests: -- 2.52.0 From a57979a3525c0eec08726eb29f89f94fa64e131c Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 22 Oct 2022 14:17:41 +0300 Subject: [PATCH 008/142] fix the source dir for the preview --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c973a7359..2ea66c5f8 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -51,4 +51,4 @@ jobs: if: github.event_name == 'pull_request' uses: rossjrw/pr-preview-action@v1 with: - source-dir: docs/_build \ No newline at end of file + source-dir: docs/_build/main \ No newline at end of file -- 2.52.0 From 607c0b49f50b0ff0e83629921c4cbc9157bc88b8 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Sun, 23 Oct 2022 09:54:19 +0200 Subject: [PATCH 009/142] feature: add selftest command for junifer --- junifer/api/cli.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/junifer/api/cli.py b/junifer/api/cli.py index a5888ccbd..6c1575976 100644 --- a/junifer/api/cli.py +++ b/junifer/api/cli.py @@ -5,6 +5,9 @@ # License: AGPL import pathlib +import subprocess +import sys +from pathlib import Path from typing import Dict, List, Union import click @@ -216,3 +219,16 @@ def wtf(long_: bool) -> None: "environment": _get_environment_information(long_=long_), } click.echo(yaml.dump(report, sort_keys=False)) + + +@cli.command() +def selftest() -> None: + """Selftest command for CLI.""" + subprocess.run( + ["pytest", "-vvv"], + stdin=subprocess.DEVNULL, + stdout=sys.stdout, + stderr=subprocess.STDOUT, + cwd=Path(__file__).parent.parent.parent.absolute(), + check=True, + ) -- 2.52.0 From ce2414ece25a99c5c91acefe3c697c6387612736 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 11:54:19 +0200 Subject: [PATCH 010/142] update: make junifer selftest take argument for specific sub-package tests --- junifer/api/cli.py | 71 +++++++++++++++++++++++++++++++++++++++------- 1 file changed, 61 insertions(+), 10 deletions(-) diff --git a/junifer/api/cli.py b/junifer/api/cli.py index 6c1575976..fb8656dd0 100644 --- a/junifer/api/cli.py +++ b/junifer/api/cli.py @@ -222,13 +222,64 @@ def wtf(long_: bool) -> None: @cli.command() -def selftest() -> None: - """Selftest command for CLI.""" - subprocess.run( - ["pytest", "-vvv"], - stdin=subprocess.DEVNULL, - stdout=sys.stdout, - stderr=subprocess.STDOUT, - cwd=Path(__file__).parent.parent.parent.absolute(), - check=True, - ) +@click.argument("subpkg", type=str) +def selftest(subpkg: str) -> None: + """Selftest command for CLI. + + Parameters + ---------- + subpkg : {"all", "api", "configs", "data", "datagrabber", "datareader", + "markers", "pipeline", "preprocess", "storage", "testing", "utils", + "stats"} + The sub-package to run tests for. + + Raises + ------ + click.BadArgumentUsage + If `subpkg` is invalid. + + """ + sub_packages = [ + "all", + "api", + "configs", + "data", + "datagrabber", + "datareader", + "markers", + "pipeline", + "preprocess", + "storage", + "testing", + "tests", + "utils", + ] + if subpkg not in sub_packages: + raise click.BadArgumentUsage( + f"Invalid value for argument `subpkg`: {subpkg}. " + f"Should be one of {sub_packages}" + ) + + if subpkg == "all": + completed_process = subprocess.run( + ["pytest", "-vvv"], + stdin=subprocess.DEVNULL, + stdout=sys.stdout, + stderr=subprocess.STDOUT, + cwd=Path(__file__).parent.parent.parent.absolute(), + check=False, + ) + else: + completed_process = subprocess.run( + ["pytest", f"junifer/{subpkg}", "-vvv"], + stdin=subprocess.DEVNULL, + stdout=sys.stdout, + stderr=subprocess.STDOUT, + cwd=Path(__file__).parent.parent.parent.absolute(), + check=False, + ) + + if completed_process.returncode == 0: + click.secho("Successful.", fg="green") + else: + click.secho("Failure.", fg="red") -- 2.52.0 From 1d249a57826b478b79ca34beb5a0cf2bc91567ad Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 11:54:56 +0200 Subject: [PATCH 011/142] update: add tests for junifer selftest --- junifer/api/tests/test_cli.py | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/junifer/api/tests/test_cli.py b/junifer/api/tests/test_cli.py index e2259c581..8e90dc765 100644 --- a/junifer/api/tests/test_cli.py +++ b/junifer/api/tests/test_cli.py @@ -11,7 +11,7 @@ import pytest import yaml from click.testing import CliRunner -from junifer.api.cli import collect, run, wtf +from junifer.api.cli import collect, run, selftest, wtf # Create click test runner @@ -84,3 +84,19 @@ def test_wtf_long() -> None: wtf_result = runner.invoke(wtf, "--long") # Check assert wtf_result.exit_code == 0 + + +def test_selftest_invalid_arg() -> None: + """Test selftest failure for invalid argument value.""" + # Invoke selftest command + selftest_result = runner.invoke(selftest, "abyss") + # Check + assert selftest_result.exit_code == 2 + + +def test_selftest() -> None: + """Test selftest.""" + # Invoke selftest command + selftest_result = runner.invoke(selftest, "tests") + # Check; will result in 1 due to I/O descriptor manipulation + assert selftest_result.exit_code == 1 -- 2.52.0 From 5af3d290bc92e3a6a9264b4d06135620c96dbaab Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 09:30:12 +0300 Subject: [PATCH 012/142] Run tests only when needed --- .github/workflows/ci-docs.yml | 14 ++++++++++++++ .github/workflows/ci.yml | 8 ++++---- 2 files changed, 18 insertions(+), 4 deletions(-) create mode 100644 .github/workflows/ci-docs.yml diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml new file mode 100644 index 000000000..4f3ebe172 --- /dev/null +++ b/.github/workflows/ci-docs.yml @@ -0,0 +1,14 @@ +name: Run Tests + +on: + push: + paths-ignore: + - 'junifer/**' + pull_request: + paths-ignore: + - 'junifer/**' +jobs: + build: + runs-on: ubuntu-latest + steps: + - run: 'echo "No build required"' diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 462a7267b..f6de392e4 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,11 +2,11 @@ name: Run Tests on: push: - paths-ignore: - - 'docs/**' + paths: + - 'junifer/**' pull_request: - paths-ignore: - - 'docs/**' + paths: + - 'junifer/**' jobs: run-tests: -- 2.52.0 From e12fc9097e1523f768d52f846f4dc36265a3da9b Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 09:34:00 +0300 Subject: [PATCH 013/142] Need to pass in all 3 python versions --- .github/workflows/ci-docs.yml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 4f3ebe172..8e4b8f743 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -8,7 +8,11 @@ on: paths-ignore: - 'junifer/**' jobs: - build: + run-tests: runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + python-version: ['3.8', '3.9', '3.10'] steps: - run: 'echo "No build required"' -- 2.52.0 From 9a151c1aa0c72225fe1d1782cca21990569e9e1e Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 10:00:19 +0300 Subject: [PATCH 014/142] Success if no upload --- codecov.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/codecov.yml b/codecov.yml index 307c497ca..c521faebf 100644 --- a/codecov.yml +++ b/codecov.yml @@ -13,7 +13,7 @@ coverage: patch: default: if_ci_failed: failure - if_no_uploads: error + if_no_uploads: success if_not_found: success target: 95.0 project: -- 2.52.0 From 7ddb4c0ace32b998f74b681db46a79f8f53451e9 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 13:53:20 +0200 Subject: [PATCH 015/142] update: add junifer logo in README and docs index --- README.md | 2 ++ docs/images/junifer_logo.png | Bin 0 -> 62081 bytes docs/index.rst | 4 ++++ 3 files changed, 6 insertions(+) create mode 100644 docs/images/junifer_logo.png diff --git a/README.md b/README.md index 5ba79f77c..9f89a61c9 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +![Junifer logo](docs/images/junifer_logo.png) + # junifer - JUelich NeuroImaging FEature extractoR ![PyPI](https://img.shields.io/pypi/v/junifer?style=flat-square) diff --git 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zwpv&0zIb6hKKEwcBYngv9Cvud!SFGeIP85ITGWNKDN4?_1yVcj@bbAvQ=H4~Dnd`n zr03}C%(GF709JH4UhOwe4cuIS?^f6?h7q+$mYRq3GyV#=6Rs>>_Qk+U&Lk(d zacV6r$1*%Q92?UPUf_D_OSai%-I)d^Lf9AbFav*aAt+^345q&kz*26wt`@BZJIk-9 zByg9x^`caR6KX)Ned!$0W&ZeX)5q}-#;3{0R)3_1{*XJdbhJUG^50A0#oj|hJ= z2Udpx$kyWWD>-*_>C7rGBW7@UMyd0 z8@eI;foe1xquXoEvNq&V`dUGab=kRI6JTvvW265*qt259|qw literal 0 HcmV?d00001 diff --git a/docs/index.rst b/docs/index.rst index 5eb8c8a72..5d77b0a21 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,5 +1,9 @@ .. include:: links.inc +.. image:: images/junifer_logo.png + :width: 300px + :alt: junifer logo + Welcome to junifer's documentation! =================================== -- 2.52.0 From 4a0a874d31beaf8591259bbdbf8304ebc86d38e4 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 15:13:41 +0200 Subject: [PATCH 016/142] docs: correct typo in builtin.rst --- docs/builtin.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/builtin.rst b/docs/builtin.rst index d1e04d007..e49cc6393 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -14,7 +14,7 @@ Data Grabbers - Open with registration - Restricted - Type/config: this should mention weather the class is built-in in the + Type/config: this should mention whether the class is built-in in the core of junifer or needs to be imported from a specific configuration in the `junifer.configs` module. -- 2.52.0 From 92c62d5a4f6b6b5e0749e79e5ca7f13c97be8d08 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 15:14:31 +0200 Subject: [PATCH 017/142] docs: fix class paths and config for available datagrabbers --- docs/builtin.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/builtin.rst b/docs/builtin.rst index e49cc6393..10649f5ce 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -47,7 +47,7 @@ Available - Built-in - In Progress - :gh:`4` - * - :class:`junifer.configs.juseless.JuselessDataladUKBVBM` + * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladUKBVBM` - UKB VBM dataset preprocessed with CAT. Available for Juseless only. - Restricted - ``junifer.configs.juseless`` @@ -56,7 +56,7 @@ Available * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladCamCANVBM` - CamCAN VBM dataset preprocessed with CAT. Available for Juseless only. - Restricted - - ``junifer.configs.juseless.datagrabbers`` + - ``junifer.configs.juseless`` - Done - 0.0.1 * - :class:`junifer.datagrabber.DataladAOMICID1000` @@ -77,7 +77,7 @@ Available - Built-in - Done - 0.0.1 - * - :class:`junifer.configs.juseless.JuselessDataladAOMICVBM` + * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICVBM` - AOMIC VBM dataset. Available for Juseless only. - Restricted - ``junifer.configs.juseless`` @@ -86,7 +86,7 @@ Available * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM` - `IXI VBM dataset `_. Available for Juseless only. - Restricted - - ``junifer.configs.juseless.datagrabbers`` + - ``junifer.configs.juseless`` - Done - 0.0.1 -- 2.52.0 From 4d0beef5f22ae31acfa36a5aea5ecbae1687a400 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 15:16:49 +0200 Subject: [PATCH 018/142] docs: add FunctionalConnectivitySpheres to available markers --- docs/builtin.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/builtin.rst b/docs/builtin.rst index 10649f5ce..19ef11d07 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -154,6 +154,10 @@ Available - Spherical aggregation using mean - Done - 0.0.1 + * - :class:`junifer.markers.FunctionalConnectivitySpheres` + - Perform spherical aggregation and compute functional connectivity + - Done + - 0.0.1 * - :class:`junifer.markers.RSSETSMarker` - Compute root sum of squares of edgewise timeseries - Done -- 2.52.0 From 78dd22b7989ce8eb781f7e68d4172499bffb2e32 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 17:37:40 +0200 Subject: [PATCH 019/142] docs: improve data.rst --- docs/understanding/data.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index ba50af255..8b47142db 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -9,7 +9,7 @@ Description ^^^^^^^^^^^ This is the *object* that traverses the steps of the pipeline. It is indeed a -dictionary of dictionaries. The first level of keys are the :ref:`data_types` +dictionary of dictionaries. The first level of keys are the :ref:`data types ` and a special key named ``meta`` that contains all the information on the data object including source and previous transformation steps. @@ -18,8 +18,8 @@ The second level of keys are the actual data. So far, there are two keys used: - ``path``: path to the file containing the data. - ``data``: the data loaded in memory. -The :ref:`datagrabbers` step will only fill the ``path`` value. -The ``data`` value will be filled by the :ref:`datareader` step, if it is one of the possible file types +The :ref:`DataGrabber ` step will only fill the ``path`` value. +The ``data`` value will be filled by the :ref:`DataReader ` step, if it is one of the possible file types that the datareader can read. .. _data_types: -- 2.52.0 From 19d4a9aba48a081f73cc5e55e759534c7c0200b6 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 17:38:23 +0200 Subject: [PATCH 020/142] docs: add preprocess.rst --- docs/understanding/index.rst | 1 + docs/understanding/preprocess.rst | 4 ++++ 2 files changed, 5 insertions(+) create mode 100644 docs/understanding/preprocess.rst diff --git a/docs/understanding/index.rst b/docs/understanding/index.rst index df2627f36..0cc074d01 100644 --- a/docs/understanding/index.rst +++ b/docs/understanding/index.rst @@ -26,5 +26,6 @@ julearn_). data datagrabber datareader + preprocess marker storage diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst new file mode 100644 index 000000000..39c1ba0fd --- /dev/null +++ b/docs/understanding/preprocess.rst @@ -0,0 +1,4 @@ +.. include:: ../links.inc + +Preprocess +========== -- 2.52.0 From 4dc57f262a766c517ef394a5ad65596e33d15128 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 24 Oct 2022 17:39:17 +0200 Subject: [PATCH 021/142] docs: update title of datagrabber.rst and datareader.rst --- docs/understanding/datagrabber.rst | 4 ++-- docs/understanding/datareader.rst | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index da9dc0481..8f5ba3a35 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -2,8 +2,8 @@ .. _datagrabbers: -Data Grabber -============ +DataGrabber +=========== Description ^^^^^^^^^^^ diff --git a/docs/understanding/datareader.rst b/docs/understanding/datareader.rst index 8a3521efd..0aec04547 100644 --- a/docs/understanding/datareader.rst +++ b/docs/understanding/datareader.rst @@ -2,5 +2,5 @@ .. _datareader: -Data Reader -=========== +DataReader +========== -- 2.52.0 From a6e05b2e6e7e0f2b6273447aa8da7395433a0dee Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 08:50:46 +0200 Subject: [PATCH 022/142] docs: improve installation.rst --- docs/installation.rst | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index 90209b8e5..f52e13d1c 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -9,14 +9,14 @@ Requirements junifer is compatible with `Python`_ >= 3.8 and requires the following packages: -* click>=8.1.3,<8.2 -* numpy>=1.22,<1.23 -* datalad>=0.15.4,<0.18 -* pandas>=1.4.0,<1.5 -* nibabel>=3.2.0,<4.1 -* nilearn>=0.9.0,<1.0 -* sqlalchemy>=1.4.27,<= 1.5.0 -* pyyaml>=5.1.2,<7.0 +* ``click>=8.1.3,<8.2`` +* ``numpy>=1.22,<1.23`` +* ``datalad>=0.15.4,<0.18`` +* ``pandas>=1.4.0,<1.5`` +* ``nibabel>=3.2.0,<4.1`` +* ``nilearn>=0.9.0,<1.0`` +* ``sqlalchemy>=1.4.27,<= 1.5.0`` +* ``pyyaml>=5.1.2,<7.0`` Depending on the installation method, these packages might be installed automatically. -- 2.52.0 From a03aa67ccac30689bfd244d93f79689786a64caf Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 09:06:17 +0200 Subject: [PATCH 023/142] docs: correct article in understanding/index.rst --- docs/understanding/index.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/understanding/index.rst b/docs/understanding/index.rst index 0cc074d01..808bf141a 100644 --- a/docs/understanding/index.rst +++ b/docs/understanding/index.rst @@ -6,7 +6,7 @@ Understanding junifer ===================== Before you start, you should understand how junifer works. Junifer is a -tool conceived to extract features from neuroimaging data in a easy-to-use +tool conceived to extract features from neuroimaging data in an easy-to-use manner, with minimal coding and minimal user expertise in the internal aspects. Unlike other tools like FSL, SPM, AFNI, etc., junifer is not a toolbox to -- 2.52.0 From a5c11a8ebe71e32d6a3ada2793e94b0b2f84c46e Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 09:09:09 +0200 Subject: [PATCH 024/142] docs: improve understanding/data.rst --- docs/understanding/data.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index 8b47142db..f59b6dc4e 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -22,13 +22,15 @@ The :ref:`DataGrabber ` step will only fill the ``path`` value. The ``data`` value will be filled by the :ref:`DataReader ` step, if it is one of the possible file types that the datareader can read. +A point to note is that you never directly interact with the *data object* but it's important to know where and how the object is being manipulated to reason about your pipeine. + .. _data_types: Data types ^^^^^^^^^^ -.. list-table:: Built-in data types - :widths: 30 80 40 +.. list-table:: + :widths: auto :header-rows: 1 * - Name -- 2.52.0 From 9e7044bea87ff1808f8473f523a70b6e27004168 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 10:49:53 +0200 Subject: [PATCH 025/142] docs: improve datagrabber.rst --- docs/understanding/data.rst | 2 +- docs/understanding/datagrabber.rst | 73 ++++++++++++++++-------------- 2 files changed, 39 insertions(+), 36 deletions(-) diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index f59b6dc4e..a97483a1f 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -1,6 +1,6 @@ .. include:: ../links.inc -.. _understanding_data_object: +.. _data_object: The Data Object =============== diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index 8f5ba3a35..dd743b6df 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -7,44 +7,47 @@ DataGrabber Description ^^^^^^^^^^^ -A datagrabber is an object that can provide datasets you want to junifer. -For example, a DataladDataGrabber can provide data from a Datalad dataset to junifer. -Of course, datagrabbers are not only possible for Datalad but any origin of a dataset. -It is intended to use them as context managers. -If you are interested in just using already provided datagrabbers please go to :doc:`../builtin`. -If you want to implement your own Data Grabbers you need to inherit from different types of -Data Grabbers we already provide (see :ref:`extending_datagrabbers`). -Typical Data Grabbers -^^^^^^^^^^^^^^^^^^^^^ -In this section we will showcase different types of datagrabber classes you might want to use -to implement your own datagrabbers for your own data. +The ``DataGrabber`` is an object that can provide an interface to datasets you want to work with in junifer. +Every concrete implementation of a datagrabber is aware of a particular dataset's structure and thus allows +you to fetch specific elements of interest from the dataset. It adds the ``path`` key to each :ref:`data type ` +in the :ref:`Data object `. -.. list-table:: Data Grabbers Type - :widths: 25 35 +Datagrabbers are intended to be used as context managers. When used within a context, a datagrabber takes care +of any pre and post steps for interacting with the dataset, for example, downloading and cleaning up. As the interface +is consistent, you always use the same procedure to interact with the datagrabber. + +For example, a concrete implementation of :class:`junifer.datagrabber.DataladDataGrabber` can provide junifer +with data from a Datalad dataset. Of course, datagrabbers are not only meant to work with Datalad datasets but +any dataset. + +If you are interested in using already provided datagrabbers please go to :doc:`../builtin`. And, if you want +to implement your own datagrabber, you need to provide concrete implementations of base classes already +provided. + +Base classes +^^^^^^^^^^^^ +In this section, we showcase different abstract base classes you might want to use to implement your own datagrabber. + +.. list-table:: + :widths: auto :header-rows: 1 * - Name - Description - * - :py:class:`~junifer.datagrabber.base.BaseDataGrabber` - - | An abstract class providing you an interface to implement for you own datagrabber. - | This is not intedent to be used in general. - | Instead you should use the DataladDataGrabber or PatternDataGrabber if possible. - | You have to at least implement the ``get_elements`` method, but most of the time - | you should also overwrite other existing methods like ``__enter__`` and ``__exit__``. - * - :py:class:`~junifer.datagrabber.pattern.PatternDataGrabber` - - | Implements some functionality to help you to define the pattern of the dataset you want to get. - | E.g. you know that T1 images are found in a directory following this pattern - | inside of the dataset "{subject}/anat/{subject}_T1w.nii.gz". - | Now you can provide this to the PatternDataGrabber - | and it will be able to get the image to junifer. - * - :py:class:`~junifer.datagrabber.datalad_base.DataladDataGrabber` - - | Implements some functionality specific to basic usage of Datalad datasets. - | This mostly takes care of the ``__enter__`` and ``__exit__`` methods to clone your Datalad dataset - | and remove it on ``__exit__``. - | This means that even if your code fails inside of the context of the - | datagrabber the DataladDataGrabber cleans up the created Datalad directories. - * - :py:class:`~junifer.datagrabber.pattern_datalad.PatternDataladDataGrabber` - - | Combination of PatternDataGrabber and DataladDataGrabber. - | Probably the class you are looking for when using Datalad. - + * - :class:`junifer.datagrabber.BaseDataGrabber` + - | The abstract base class providing you an interface to implement your own datagrabber. + | You should try to avoid using this directly and instead use + | :class:`junifer.datagrabber.PatternDataGrabber` or :class:`junifer.datagrabber.DataladDataGrabber`. + | To build your own custom *low-level* datagrabber, you need to at least implement the ``get_elements`` method, + | but most of the time you should also override other existing methods like ``__enter__`` and ``__exit__``. + * - :class:`junifer.datagrabber.PatternDataGrabber` + - | It implements functionality to help you define the pattern of the dataset you want to get. For example, + | you know that T1 images are found in a directory following this pattern ``{subject}/anat/{subject}_T1w.nii.gz`` + | inside of the dataset. Now you can provide this to the **PatternDataGrabber** and it will be able to get the file. + * - :class:`junifer.datagrabber.DataladDataGrabber` + - | It implements functionality to deal with Datalad datasets. Specifically, the ``__enter__`` and ``__exit__`` methods + | take care of cloning and removing the Datalad dataset. + * - :class:`junifer.datagrabber.PatternDataladDataGrabber` + - | It is a combination of :class:`junifer.datagrabber.PatternPatternDataGrabber` and + | :class:`junifer.datagrabber.DataladDataGrabber`. This is probably the class you are looking for when using Datalad. -- 2.52.0 From 0cfb2868dc3ffc5052d14e208a3a28a4af1fb367 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 11:57:49 +0200 Subject: [PATCH 026/142] docs: add content in datareader.rst --- docs/understanding/datareader.rst | 40 +++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/docs/understanding/datareader.rst b/docs/understanding/datareader.rst index 0aec04547..774f402db 100644 --- a/docs/understanding/datareader.rst +++ b/docs/understanding/datareader.rst @@ -4,3 +4,43 @@ DataReader ========== + +Description +^^^^^^^^^^^ + +The ``DataReader`` is an object that is responsible for actually reading data files in junifer. +It reads the value of the key ``path`` for each :ref:`data type ` in the :ref:`Data object ` +and loads them to memory. After reading the data into memory, it adds the key ``data`` to the same level as ``path`` +and the value is the actual data in the memory. + +Datareaders are meant to be used inside the datagrabber context but you can operate on them outside the context as long +as the actual data is in the memory and the Python runtime has not garbage-collected it. + +For data formats not supported by junifer yet, you can either make your own ``DataReader`` or open an issue on +`junifer Github`_ and we can help you out. + +Currently supported file-formats +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +We already provide a concrete implementation :class:`junifer.datareader.DefaultDataReader` which knows how to +read the following file formats: + +.. list-table:: + :widths: auto + :header-rows: 1 + + * - File extension + - File type + - Description + * - ``.nii`` + - NIfTI (uncompressed) + - Uncompressed NIfTI + * - ``.nii.gz`` + - NIfTI (compressed) + - Compressed NIfTI + * - ``.csv`` + - CSV + - Comma-separated values file + * - ``.tsv`` + - TSV + - Tab-separated values file -- 2.52.0 From a142e2947f6ddd1b0c89118d80db4b65181718ae Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 13:00:23 +0200 Subject: [PATCH 027/142] docs: add missing comma in datagrabber.rst --- docs/understanding/datagrabber.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index dd743b6df..800c3f896 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -21,7 +21,7 @@ For example, a concrete implementation of :class:`junifer.datagrabber.DataladDat with data from a Datalad dataset. Of course, datagrabbers are not only meant to work with Datalad datasets but any dataset. -If you are interested in using already provided datagrabbers please go to :doc:`../builtin`. And, if you want +If you are interested in using already provided datagrabbers, please go to :doc:`../builtin`. And, if you want to implement your own datagrabber, you need to provide concrete implementations of base classes already provided. -- 2.52.0 From 9d281c35dffe8123ed4ec69d357fb957f3ce6e44 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 13:00:41 +0200 Subject: [PATCH 028/142] docs: add content in marker.rst --- docs/understanding/marker.rst | 23 ++++++++++++++++++++--- 1 file changed, 20 insertions(+), 3 deletions(-) diff --git a/docs/understanding/marker.rst b/docs/understanding/marker.rst index 02446016f..915f8ed99 100644 --- a/docs/understanding/marker.rst +++ b/docs/understanding/marker.rst @@ -1,6 +1,23 @@ .. include:: ../links.inc -.. _markers: +.. _marker: -Markers -======= +Marker +====== + +Description +^^^^^^^^^^^ + +The ``Marker`` is an object that is responsible for feature extraction. It primarily operates on data loaded +in memory by :ref:`datareader ` and stored in the ``data`` key of each :ref:`data type ` +in the :ref:`Data object `. In some cases, it can also operate on pre-processed data as obtained +from the :ref:`Preprocess ` step of the pipeline. It is important to note that this pre-process is +not similar to pre-processing done by tools like FSL, SPM, AFNI, etc. . For example, one can perform confound +removal on loaded data and then perform feature extraction. + +Markers are meant to be used inside the datagrabber context but you can operate on them outside the context as long +as the actual data is in the memory and the Python runtime has not garbage-collected it. + +If you are interested in using already provided markers, please go to :doc:`../builtin`. And, if you want to implement +your own marker, you need to provide concrete implementation of :class:`junifer.markers.BaseMarker`. Specifically, you +need to override ``get_output_kind``, ``store`` and ``compute`` methods. -- 2.52.0 From b23c4411daf30ee23cf0d1fbbf01fa2c5bb3638f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 13:00:56 +0200 Subject: [PATCH 029/142] docs: add preprocess link --- docs/understanding/preprocess.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index 39c1ba0fd..2e0ff2efa 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -1,4 +1,6 @@ .. include:: ../links.inc +.. _preprocess: + Preprocess ========== -- 2.52.0 From 8007b737d8d750588d497802648d36cb59b4de7a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 14:19:04 +0200 Subject: [PATCH 030/142] docs: add content in storage.rst --- docs/understanding/storage.rst | 35 ++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/docs/understanding/storage.rst b/docs/understanding/storage.rst index 1da80a289..c409809b0 100644 --- a/docs/understanding/storage.rst +++ b/docs/understanding/storage.rst @@ -4,3 +4,38 @@ Storage ======= + +Description +^^^^^^^^^^^ + +The ``Storage`` is an object that is responsible for storing extracted features as computed from :ref:`Marker ` +step of the pipeline. If the pipeline is provided with a ``storage-like`` object, the extracted features are stored via +that object else they are kept in memory. + +Storage is meant to be used inside the datagrabber context but you can operate on them outside the context as long +as the processed data is in the memory and the Python runtime has not garbage-collected it. + +The :ref:`Markers ` are responsible for defining what *storage kind* (``matrix``, ``table``, ``timeseries``) +they support for which :ref:`data type ` by overriding its ``store`` method. The storage object in turn +declares and provides implementation for specific *storage kind*. For example, :class:`junifer.storage.SQLiteFeatureStorage` +supports saving ``matrix``, ``table`` and ``timeseries`` via ``store_matrix``, ``store_table`` and ``store_timeseries`` +methods respectively. + +For storage interfaces not supported by junifer yet, you can either make your own ``Storage`` by providing a concrete +implementation of :class:`junifer.storage.BaseFeatureStorage` or open an issue on `junifer Github`_ and we can help you out. + +Currently supported storage interfaces +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. list-table:: + :widths: auto + :header-rows: 1 + + * - Storage class + - File extension + - File type + - Storage kinds + * - :class:`junifer.storage.SQLiteFeatureStorage` + - ``.db`` + - SQLite + - ``matrix``, ``table``, ``timeseries`` -- 2.52.0 From 0f3a95648b205f06ef13ff216a44176146de006a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 14:27:37 +0200 Subject: [PATCH 031/142] docs: add content in preprocess.rst --- docs/understanding/preprocess.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index 2e0ff2efa..eea630214 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -4,3 +4,12 @@ Preprocess ========== + +Description +^^^^^^^^^^^ + +The ``Preprocess`` step of the pipeline is meant for pre-processing before or after :ref:`Marker ` step +depending on the use-case. For example, you might want to perform confound removal on ``BOLD`` data before +feature extraction. + +This step is still under development and is an optional one for the pipeline to work. -- 2.52.0 From 1749e198586760e41250beee3d473305ada51f47 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 14:34:20 +0200 Subject: [PATCH 032/142] docs: cleanup conf.py --- docs/conf.py | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index a6ba15330..fd12b8dcd 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -64,9 +64,19 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # a list of builtin themes. # html_theme = "sphinx_rtd_theme" - -html_sidebars = {"**": ["globaltoc.html", "sourcelink.html", "searchbox.html"]} - +html_theme_options = { + "display_version": True, + "style_external_links": True, + "logo_only": True, +} +html_sidebars = { + "**": [ + "globaltoc.html", + "sourcelink.html", + "searchbox.html", + ] +} +html_logo = "./images/junifer_logo.png" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, -- 2.52.0 From 47221240fbed1b7d8ab9787457d796bc6f7f5f30 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 15:49:08 +0200 Subject: [PATCH 033/142] update: complete type annotations for DefaultDataReader --- junifer/datareader/default.py | 37 +++++++++++++++++++++++------------ 1 file changed, 24 insertions(+), 13 deletions(-) diff --git a/junifer/datareader/default.py b/junifer/datareader/default.py index ac6b72b3e..8aaec4e9a 100644 --- a/junifer/datareader/default.py +++ b/junifer/datareader/default.py @@ -5,7 +5,7 @@ # License: AGPL from pathlib import Path -from typing import Dict, List +from typing import Dict, List, Optional import nibabel as nib import pandas as pd @@ -32,48 +32,59 @@ _readers["TSV"] = {"func": pd.read_csv, "params": {"sep": "\t"}} class DefaultDataReader(PipelineStepMixin): """Mixin class for default data reader.""" - # TODO: complete type annotations def validate_input(self, input: List[str]) -> None: """Validate input. Parameters ---------- - input + input : list of str + The input to the pipeline step. The list must contain the + available Junifer Data dictionary keys. """ # Nothing to validate, any input is fine pass - # TODO: complete type annotations - def get_output_kind(self, input): + def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. Parameters ---------- - input + input : list of str + The input to the reader. The list must contain the + available Junifer Data dictionary keys. + + Returns + ------- + list of str + The updated list of output kinds, as reading possibilities. """ # It will output the same kind of data as the input return input - # TODO: complete type annotations - def fit_transform(self, input, params=None) -> Dict: + def fit_transform( + self, + input: Dict[str, Dict], + params: Optional[Dict] = None, + ) -> Dict: """Fit and transform. Parameters ---------- - input - params + input : dict + The Junifer Data object. + params : dict, optional + Extra parameters for data types (default None). Returns ------- dict + The processed output as dictionary. The "data" key is added to + each data type dictionary except "meta". """ # For each kind of data, try to read it - - # out is the same, but with the 'data' key set in - # each kind dictionary, except for meta out = input.copy() if params is None: params = {} -- 2.52.0 From d03e4caa8ff992fb095a2bab76cc39b37cc5333d Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 13:53:04 +0300 Subject: [PATCH 034/142] Another attempt at codecov checks --- .github/workflows/ci-docs.yml | 12 ++++++++++++ .github/workflows/ci.yml | 2 ++ codecov.yml | 7 ++++++- 3 files changed, 20 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 8e4b8f743..690d48312 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -16,3 +16,15 @@ jobs: python-version: ['3.8', '3.9', '3.10'] steps: - run: 'echo "No build required"' + - name: Create mock coverage.xml file + run: | + echo '' > coverage.xml + echo ' ' >> coverage.xml + if: matrix.python-version == 3.9 + - name: Upload mock coverage to Codecov + uses: codecov/codecov-action@v3 + with: + token: ${{ secrets.CODECOV_TOKEN }} + fail_ci_if_error: true + flags: mock + if: success() && matrix.python-version == 3.9 \ No newline at end of file diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f6de392e4..bafa35419 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -42,4 +42,6 @@ jobs: uses: codecov/codecov-action@v3 with: token: ${{ secrets.CODECOV_TOKEN }} + fail_ci_if_error: true + flags: junifer if: success() && matrix.python-version == 3.9 diff --git a/codecov.yml b/codecov.yml index c521faebf..b21e58149 100644 --- a/codecov.yml +++ b/codecov.yml @@ -16,10 +16,15 @@ coverage: if_no_uploads: success if_not_found: success target: 95.0 + flags: + - junifer + - mock project: default: false library: if_ci_failed: failure if_no_uploads: error if_not_found: success - target: 90.0 \ No newline at end of file + target: 90.0 + flags: + - junifer -- 2.52.0 From 969422d82dd5cac79eff15fd9c167cabb35a45db Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 14:02:25 +0300 Subject: [PATCH 035/142] Missing one parameter --- codecov.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/codecov.yml b/codecov.yml index b21e58149..90c9d8c60 100644 --- a/codecov.yml +++ b/codecov.yml @@ -12,6 +12,7 @@ coverage: status: patch: default: + flag_coverage_not_uploaded_behavior: pass if_ci_failed: failure if_no_uploads: success if_not_found: success -- 2.52.0 From e73006ea0e9d57139b8d6913e8189ce00579294e Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 14:10:15 +0300 Subject: [PATCH 036/142] Update mock coverage.xml --- .github/workflows/ci-docs.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 690d48312..397e45402 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -19,7 +19,15 @@ jobs: - name: Create mock coverage.xml file run: | echo '' > coverage.xml - echo ' ' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '/home/runner/work/junifer/junifer' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml if: matrix.python-version == 3.9 - name: Upload mock coverage to Codecov uses: codecov/codecov-action@v3 -- 2.52.0 From 019d7adf2faeed03f1388f7b4c62a196ef751b45 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 14:24:05 +0300 Subject: [PATCH 037/142] tabs --- .github/workflows/ci-docs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 397e45402..4b04aea4a 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -21,8 +21,8 @@ jobs: echo '' > coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml - echo '/home/runner/work/junifer/junifer' >> coverage.xml - echo '' >> coverage.xml + echo '/home/runner/work/junifer/junifer' >> coverage.xml + echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml -- 2.52.0 From c1133c3ac3c64f1c04d9e23be76ab988775efd52 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 14:30:04 +0300 Subject: [PATCH 038/142] Better mock file --- .github/workflows/ci-docs.yml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 4b04aea4a..4a4cadc03 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -25,6 +25,25 @@ jobs: echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo 'line number="11" hits="1"/>' >> coverage.xml + echo 'line number="12" hits="1"/>' >> coverage.xml + echo 'line number="13" hits="1"/>' >> coverage.xml + echo 'line number="14" hits="1"/>' >> coverage.xml + echo 'line number="15" hits="1"/>' >> coverage.xml + echo 'line number="16" hits="1"/>' >> coverage.xml + echo 'line number="17" hits="1"/>' >> coverage.xml + echo 'line number="18" hits="1"/>' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml + echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml -- 2.52.0 From 62d62146c9c479e5186c87a058594c2f10217262 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 14:31:46 +0300 Subject: [PATCH 039/142] Maybe create a file --- .github/workflows/ci-docs.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 4a4cadc03..f154033ab 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -18,6 +18,8 @@ jobs: - run: 'echo "No build required"' - name: Create mock coverage.xml file run: | + mkdir junifer + touch junifer/__init__.py echo '' > coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml -- 2.52.0 From 949f16a2d1e9ddcc9c815e1c1a01de31832193a7 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 15:24:54 +0300 Subject: [PATCH 040/142] Checking another coverage config --- .github/workflows/ci-docs.yml | 23 +++++------------- codecov.yml | 46 ++++++++++++++++++++--------------- 2 files changed, 33 insertions(+), 36 deletions(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index f154033ab..b573c46f9 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -18,31 +18,20 @@ jobs: - run: 'echo "No build required"' - name: Create mock coverage.xml file run: | - mkdir junifer - touch junifer/__init__.py + mkdir docs + touch docs/conf.py echo '' > coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml - echo '/home/runner/work/junifer/junifer' >> coverage.xml + echo '/home/runner/work/docs/docs' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml - echo '' >> coverage.xml + echo '' >> coverage.xml echo '' >> coverage.xml - echo '' >> coverage.xml + echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml - echo '' >> coverage.xml - echo '' >> coverage.xml - echo '' >> coverage.xml - echo 'line number="11" hits="1"/>' >> coverage.xml - echo 'line number="12" hits="1"/>' >> coverage.xml - echo 'line number="13" hits="1"/>' >> coverage.xml - echo 'line number="14" hits="1"/>' >> coverage.xml - echo 'line number="15" hits="1"/>' >> coverage.xml - echo 'line number="16" hits="1"/>' >> coverage.xml - echo 'line number="17" hits="1"/>' >> coverage.xml - echo 'line number="18" hits="1"/>' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml @@ -55,5 +44,5 @@ jobs: with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true - flags: mock + flags: docs if: success() && matrix.python-version == 3.9 \ No newline at end of file diff --git a/codecov.yml b/codecov.yml index 90c9d8c60..17e51fd9a 100644 --- a/codecov.yml +++ b/codecov.yml @@ -10,22 +10,30 @@ comment: # this is a top-level key coverage: status: - patch: - default: - flag_coverage_not_uploaded_behavior: pass - if_ci_failed: failure - if_no_uploads: success - if_not_found: success - target: 95.0 - flags: - - junifer - - mock - project: - default: false - library: - if_ci_failed: failure - if_no_uploads: error - if_not_found: success - target: 90.0 - flags: - - junifer + project: off + patch: off + +flag_management: + default_rules: + carryforward: true + individual_flags: + - name: junifer + paths: + - junifer/ + statuses: + - type: project + target: 90% + threshold: 1% + - type: patch + target: 95% + threshold: 1% + - name: docs + paths: + - docs/ + statuses: + - type: project + target: 100% + threshold: 1% + - type: patch + target: 95% + threshold: 1% \ No newline at end of file -- 2.52.0 From 2eec2a36f9a9ddabed61c8431d06440726ca942e Mon Sep 17 00:00:00 2001 From: Fede Date: Tue, 25 Oct 2022 10:09:11 +0300 Subject: [PATCH 041/142] fix latest.inc syntax --- docs/changes/latest.inc | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 43fa05c80..65bb46db0 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -19,15 +19,15 @@ Current (0.0.0.dev) Enhancements ~~~~~~~~~~~~ +- Created a the repository based on the mockup by `Fede Raimondo`_. + - Implemented SPM Auditory testing datagrabber X (:gh:`52` by `Fede Raimondo`_). -- Created a the repository based on the mockup by by `Fede Raimondo`_. - - Added comments to datalad grabber and changed to use datalad-clone instead of - datalad-install (:gh: `55` by `Benjamin Poldrack`_). + datalad-install (:gh:`55` by `Benjamin Poldrack`_). -- Added an example how to use junifer and julearn (:gh: `40` by `Leonard Sasse_`, - `Nicolas Nieto_`, and `Sami Hamdan_`) in one pipeline to extract features +- Added an example how to use junifer and julearn (:gh:`40` by `Leonard Sasse`_, + `Nicolas Nieto`_, and `Sami Hamdan`_) in one pipeline to extract features and do machine learning. - Implement matrix storage in SQliteFeatureStorage (:gh:`42` by `Fede Raimondo`_). @@ -35,8 +35,8 @@ Enhancements - Marker for functional connectivity using an atlas (:gh:`41` by `Amir Omidvarnia`_ and `Kaustubh R. Patil`_). -- Added documentation for the datagrabbers (by `Leonard Sasse_`, - `Nicolas Nieto_`, and `Sami Hamdan_`). +- Added documentation for the datagrabbers (by `Leonard Sasse`_, + `Nicolas Nieto`_, and `Sami Hamdan`_). - Implement coordinate register, list and load (:gh:`11` by `Fede Raimondo`_). @@ -46,23 +46,25 @@ Enhancements - Added support to access other input in the data object in the `compute` method (by `Fede Raimondo`_). -- Implemented the edge time series RSS marker (:gh: `51` by `Leonard Sasse`_, +- Implemented the edge time series RSS marker (:gh:`51` by `Leonard Sasse`_, `Nicolas Nieto`_, `Sami Hamdan`_). - Implement SphereAggregation marker (by `Fede Raimondo`_). - Implement PIOP1 and PIOP2 AOMIC datasets and refactor AOMICID1000 slightly - (:gh: `94` by `Leonard Sasse`_) + (:gh:`94` by `Leonard Sasse`_) -- Implement a JuselessDataladCamCANVBM datagrabber class (:gh: `99` by `Leonard Sasse`_) +- Implement a JuselessDataladCamCANVBM datagrabber class (:gh:`99` by `Leonard Sasse`_) -- Implement IXI CAT output datagrabber for juseless (:gh: `48` by `Leonard Sasse`_). +- Implement IXI CAT output datagrabber for juseless (:gh:`48` by `Leonard Sasse`_). -- Upgrade storage interface for storage-like objects (:gh: `84` by `Synchon Mandal`_). +- Upgrade storage interface for storage-like objects (:gh:`84` by `Synchon Mandal`_). -- Add missing type annotations (:gh: `74` by `Synchon Mandal`_). +- Add missing type annotations (:gh:`74` by `Synchon Mandal`_). -- Add ``junifer wtf`` to report environment details (:gh: `33` by `Synchon Mandal`_). +- Add ``junifer wtf`` to report environment details (:gh:`33` by `Synchon Mandal`_). + +- Add ``junifer selftest`` to report environment details (:gh:`9` by `Synchon Mandal`_). Bugs ~~~~ -- 2.52.0 From 4f379ce930a3d14acdcab548488a39b153c36b71 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 15:27:44 +0300 Subject: [PATCH 042/142] Fix this again --- docs/changes/latest.inc | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 65bb46db0..d93244cbb 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -19,6 +19,7 @@ Current (0.0.0.dev) Enhancements ~~~~~~~~~~~~ + - Created a the repository based on the mockup by `Fede Raimondo`_. - Implemented SPM Auditory testing datagrabber X (:gh:`52` by `Fede Raimondo`_). -- 2.52.0 From 6e55faa87dd88bf9b0b71a5b84b95551785583a9 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 15:41:11 +0300 Subject: [PATCH 043/142] trigger codecov --- junifer/datagrabber/base.py | 1 - 1 file changed, 1 deletion(-) diff --git a/junifer/datagrabber/base.py b/junifer/datagrabber/base.py index 7e49d9313..a9f5a2a1a 100644 --- a/junifer/datagrabber/base.py +++ b/junifer/datagrabber/base.py @@ -59,7 +59,6 @@ class BaseDataGrabber(ABC): for elem in self.get_elements(): yield elem - # TODO: element does nothing, check def __getitem__(self, element: Union[str, Tuple]) -> Dict[str, Dict]: """Enable indexing support. -- 2.52.0 From 82c427e94781115b7de896ff6e8a0d2655ddd711 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 16:50:59 +0300 Subject: [PATCH 044/142] Refactor markers --- docs/changes/latest.inc | 2 ++ examples/run_compute_parcel_mean.py | 2 +- junifer/markers/__init__.py | 2 +- junifer/markers/base.py | 34 +++++++++++++++---- junifer/markers/ets_rss.py | 17 ++++++++-- .../markers/functional_connectivity_atlas.py | 16 +++++++-- .../functional_connectivity_spheres.py | 13 ++++++- .../{parcel.py => parcel_aggregation.py} | 15 ++++++-- junifer/markers/sphere_aggregation.py | 13 +++++-- .../test_functional_connectivity_atlas.py | 2 +- junifer/markers/tests/test_markers_base.py | 12 +++++-- junifer/markers/tests/test_parcel.py | 2 +- scratch/test_niftimasker.py | 2 +- 13 files changed, 106 insertions(+), 26 deletions(-) rename junifer/markers/{parcel.py => parcel_aggregation.py} (94%) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index d93244cbb..0319a32d3 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -67,6 +67,8 @@ Enhancements - Add ``junifer selftest`` to report environment details (:gh:`9` by `Synchon Mandal`_). +- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the marker can be computed on the input data types (by `Fede Raimondo`_) + Bugs ~~~~ diff --git a/examples/run_compute_parcel_mean.py b/examples/run_compute_parcel_mean.py index 1f76a88f2..32da018f1 100644 --- a/examples/run_compute_parcel_mean.py +++ b/examples/run_compute_parcel_mean.py @@ -12,7 +12,7 @@ License: BSD 3 clause import nilearn -from junifer.markers.parcel import ParcelAggregation +from junifer.markers.parcel_aggregation import ParcelAggregation from junifer.utils import configure_logging diff --git a/junifer/markers/__init__.py b/junifer/markers/__init__.py index 6fcc780b9..39004824b 100644 --- a/junifer/markers/__init__.py +++ b/junifer/markers/__init__.py @@ -9,5 +9,5 @@ from .collection import MarkerCollection from .ets_rss import RSSETSMarker from .functional_connectivity_atlas import FunctionalConnectivityAtlas from .functional_connectivity_spheres import FunctionalConnectivitySpheres -from .parcel import ParcelAggregation +from .parcel_aggregation import ParcelAggregation from .sphere_aggregation import SphereAggregation diff --git a/junifer/markers/base.py b/junifer/markers/base.py index 12227ce79..d8f71d2b6 100644 --- a/junifer/markers/base.py +++ b/junifer/markers/base.py @@ -30,14 +30,36 @@ class BaseMarker(ABC, PipelineStepMixin): """ def __init__( - self, on: Union[List[str], str], name: Optional[str] = None + self, + on: Optional[Union[List[str], str]] = None, + name: Optional[str] = None, ) -> None: """Initialize the class.""" + if on is None: + on = self.get_valid_inputs() if not isinstance(on, list): on = [on] - self._valid_inputs = on self.name = self.__class__.__name__ if name is None else name + if any(x not in self.get_valid_inputs() for x in on): + wrong_on = [x for x in on if x not in self.get_valid_inputs()] + raise ValueError(f"{self.name} cannot be computed on {wrong_on}") + self._on = on + + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + raise_error( + msg="Concrete classes need to implement get_valid_inputs().", + klass=NotImplementedError, + ) + def get_meta(self, kind: str) -> Dict: """Get metadata. @@ -74,11 +96,11 @@ class BaseMarker(ABC, PipelineStepMixin): If the input does not have the required data. """ - if not any(x in input for x in self._valid_inputs): + if not any(x in input for x in self._on): raise_error( "Input does not have the required data." f"\t Input: {input}" - f"\t Required (any of): {self._valid_inputs}" + f"\t Required (any of): {self._on}" ) @abstractmethod @@ -157,7 +179,7 @@ class BaseMarker(ABC, PipelineStepMixin): def fit_transform( self, input: Dict[str, Dict], - storage: "BaseFeatureStorage" = None, + storage: Optional["BaseFeatureStorage"] = None, ) -> Dict: """Fit and transform. @@ -177,7 +199,7 @@ class BaseMarker(ABC, PipelineStepMixin): """ out = {} meta = input.get("meta", {}) - for kind in self._valid_inputs: + for kind in self._on: if kind in input.keys(): logger.info(f"Computing {kind}") t_input = input[kind] diff --git a/junifer/markers/ets_rss.py b/junifer/markers/ets_rss.py index 668773201..d0fd50c15 100644 --- a/junifer/markers/ets_rss.py +++ b/junifer/markers/ets_rss.py @@ -13,7 +13,7 @@ import numpy as np from ..api.decorators import register_marker from ..utils import logger from .base import BaseMarker -from .parcel import ParcelAggregation +from .parcel_aggregation import ParcelAggregation from .utils import _ets @@ -43,12 +43,23 @@ class RSSETSMarker(BaseMarker): self, atlas: str, aggregation_method: str = "mean", - name: str = None, + name: Optional[str] = None, ) -> None: """Initialize the class.""" self.atlas = atlas self.aggregation_method = aggregation_method - super().__init__(on=["BOLD"], name=name) + super().__init__(name=name) + + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + return ["BOLD"] def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. diff --git a/junifer/markers/functional_connectivity_atlas.py b/junifer/markers/functional_connectivity_atlas.py index 4a84f215c..ef0e2deb6 100644 --- a/junifer/markers/functional_connectivity_atlas.py +++ b/junifer/markers/functional_connectivity_atlas.py @@ -12,7 +12,7 @@ from sklearn.covariance import EmpiricalCovariance from ..api.decorators import register_marker from ..utils import logger from .base import BaseMarker -from .parcel import ParcelAggregation +from .parcel_aggregation import ParcelAggregation if TYPE_CHECKING: @@ -65,13 +65,23 @@ class FunctionalConnectivityAtlas(BaseMarker): self.cor_method_params = ( {} if cor_method_params is None else cor_method_params ) - on = ["BOLD"] # default to nilearn behavior self.cor_method_params["empirical"] = self.cor_method_params.get( "empirical", False ) - super().__init__(on=on, name=name) + super().__init__(name=name) + + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + return ["BOLD"] def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. diff --git a/junifer/markers/functional_connectivity_spheres.py b/junifer/markers/functional_connectivity_spheres.py index e65a6f10b..44c9f1dae 100644 --- a/junifer/markers/functional_connectivity_spheres.py +++ b/junifer/markers/functional_connectivity_spheres.py @@ -79,7 +79,18 @@ class FunctionalConnectivitySpheres(BaseMarker): "empirical", False ) - super().__init__(on=["BOLD"], name=name) + super().__init__(name=name) + + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + return ["BOLD"] def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. diff --git a/junifer/markers/parcel.py b/junifer/markers/parcel_aggregation.py similarity index 94% rename from junifer/markers/parcel.py rename to junifer/markers/parcel_aggregation.py index b4c64a150..c75816fe0 100644 --- a/junifer/markers/parcel.py +++ b/junifer/markers/parcel_aggregation.py @@ -38,7 +38,7 @@ class ParcelAggregation(BaseMarker): :func:`junifer.stats.get_aggfunc_by_name`. on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} or list of the options, optional - The kind of data to apply the marker to. If None, will work on all + The data types to apply the marker to. If None, will work on all available data (default None). name : str, optional The name of the marker. If None, will use the class name (default @@ -58,10 +58,19 @@ class ParcelAggregation(BaseMarker): self.atlas = atlas self.method = method self.method_params = {} if method_params is None else method_params - if on is None: - on = ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] super().__init__(on=on, name=name) + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] + def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. diff --git a/junifer/markers/sphere_aggregation.py b/junifer/markers/sphere_aggregation.py index e25478c52..fde777a9b 100644 --- a/junifer/markers/sphere_aggregation.py +++ b/junifer/markers/sphere_aggregation.py @@ -69,10 +69,19 @@ class SphereAggregation(BaseMarker): self.method = method self.method_params = {} if method_params is None else method_params - if on is None: - on = ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] super().__init__(on=on, name=name) + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] + def get_output_kind(self, input: List[str]) -> List[str]: """Get output kind. diff --git a/junifer/markers/tests/test_functional_connectivity_atlas.py b/junifer/markers/tests/test_functional_connectivity_atlas.py index 4b14b17c1..33e38127f 100644 --- a/junifer/markers/tests/test_functional_connectivity_atlas.py +++ b/junifer/markers/tests/test_functional_connectivity_atlas.py @@ -14,7 +14,7 @@ from numpy.testing import assert_array_almost_equal, assert_array_equal from junifer.markers.functional_connectivity_atlas import ( FunctionalConnectivityAtlas, ) -from junifer.markers.parcel import ParcelAggregation +from junifer.markers.parcel_aggregation import ParcelAggregation from junifer.storage import SQLiteFeatureStorage diff --git a/junifer/markers/tests/test_markers_base.py b/junifer/markers/tests/test_markers_base.py index 12d0b583e..22057696f 100644 --- a/junifer/markers/tests/test_markers_base.py +++ b/junifer/markers/tests/test_markers_base.py @@ -12,13 +12,16 @@ from junifer.markers.base import BaseMarker def test_base_marker_abstractness() -> None: """Test BaseMarker is abstract base class.""" with pytest.raises(TypeError, match=r"abstract"): - BaseMarker(on=["BOLD"]) + BaseMarker(on=["BOLD"]) # type: ignore -def test_base_datagrabber_subclassing() -> None: +def test_base_marker_subclassing() -> None: """Test proper subclassing of BaseMarker.""" # Create concrete class class MyBaseMarker(BaseMarker): + def get_valid_inputs(self): + return ["BOLD", "T1w"] + def get_output_kind(self, input): return ["timeseries"] @@ -32,6 +35,9 @@ def test_base_datagrabber_subclassing() -> None: def store(self, kind, out, storage): return super().store(kind=kind, out=out, storage=storage) + with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"): + MyBaseMarker(on=["BOLD", "T2w"]) + # Create input for marker input_ = { "meta": {"datagrabber": "dg", "element": "elem", "datareader": "dr"}, @@ -54,7 +60,7 @@ def test_base_datagrabber_subclassing() -> None: # Check no implementation check with pytest.raises(NotImplementedError): - marker.store(kind="kind", out="out", storage="storage") + marker.store(kind="kind", out="out", storage="storage") # type: ignore # Check attributes assert marker.name == "MyBaseMarker" diff --git a/junifer/markers/tests/test_parcel.py b/junifer/markers/tests/test_parcel.py index 4098bd59c..74518b279 100644 --- a/junifer/markers/tests/test_parcel.py +++ b/junifer/markers/tests/test_parcel.py @@ -12,7 +12,7 @@ from nilearn.maskers import NiftiLabelsMasker, NiftiMasker from numpy.testing import assert_array_almost_equal, assert_array_equal from scipy.stats import trim_mean -from junifer.markers.parcel import ParcelAggregation +from junifer.markers.parcel_aggregation import ParcelAggregation def test_ParcelAggregation_input_output() -> None: diff --git a/scratch/test_niftimasker.py b/scratch/test_niftimasker.py index db7fcd0a2..2cd9c86ed 100644 --- a/scratch/test_niftimasker.py +++ b/scratch/test_niftimasker.py @@ -43,7 +43,7 @@ for t_v in sorted(np.unique(atlas_values)): manual.append(t_values) -from junifer.markers.parcel import ParcelAggregation +from junifer.markers.parcel_aggregation import ParcelAggregation marker = ParcelAggregation(atlas='Schaefer100x7', method='mean') input = dict(VBM_GM=dict(data=img)) -- 2.52.0 From 64b459715b2704f0e3c7edbbe8e2f33acfdf47ff Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 26 Oct 2022 17:51:05 +0300 Subject: [PATCH 045/142] Increase coverage --- junifer/markers/tests/test_markers_base.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/junifer/markers/tests/test_markers_base.py b/junifer/markers/tests/test_markers_base.py index 22057696f..220d3dbfe 100644 --- a/junifer/markers/tests/test_markers_base.py +++ b/junifer/markers/tests/test_markers_base.py @@ -47,6 +47,10 @@ def test_base_marker_subclassing() -> None: }, } marker = MyBaseMarker(on=["BOLD"]) + + with pytest.raises(ValueError, match="not have the required data"): + marker.validate_input(["T1w"]) + output = marker.fit_transform(input=input_) # process # Check output assert "BOLD" in output -- 2.52.0 From 464de2264e4c428979a9c5d62811c4917222659a Mon Sep 17 00:00:00 2001 From: Felix Hoffstaedter Date: Tue, 13 Sep 2022 13:24:58 +0200 Subject: [PATCH 046/142] add grabber for local VBM AOMIC 1000 dataset --- junifer/configs/juseless/juseless.py | 75 ++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 junifer/configs/juseless/juseless.py diff --git a/junifer/configs/juseless/juseless.py b/junifer/configs/juseless/juseless.py new file mode 100644 index 000000000..cc26f55e1 --- /dev/null +++ b/junifer/configs/juseless/juseless.py @@ -0,0 +1,75 @@ +"""Provide class for juseless datalad datagrabber.""" + +# Authors: Federico Raimondo +# Leonard Sasse +# Synchon Mandal +# License: AGPL + +from pathlib import Path +from typing import Union + +from ..api.decorators import register_datagrabber +from ..datagrabber import PatternDataladDataGrabber + + +@register_datagrabber +class JuselessDataladUKBVBM(PatternDataladDataGrabber): + """Juseless UKB VBM DataGrabber class. + + Implements a DataGrabber to access the UKB VBM data in Juseless. + + Parameters + ----------- + datadir : str or pathlib.Path, optional + The directory where the datalad dataset will be cloned. If None, + the datalad dataset will be cloned into a temporary directory + (default None). + + """ + + def __init__(self, datadir: Union[str, Path, None] = None) -> None: + """Initialize the class.""" + uri = "ria+http://ukb.ds.inm7.de#~cat_m0wp1" + rootdir = "m0wp1" + types = ["VBM_GM"] + replacements = ["subject", "session"] + patterns = {"VBM_GM": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz"} + super().__init__( + types=types, + datadir=datadir, + uri=uri, + rootdir=rootdir, + replacements=replacements, + patterns=patterns, + ) + +@register_datagrabber +class JuselessDataladAOMICVBM(PatternDataladDataGrabber): + """Juseless AOMIC VBM DataGrabber class. + + Implements a DataGrabber to access the AOMIC VBM data in Juseless. + + Parameters + ----------- + datadir : str or pathlib.Path, optional + The directory where the datalad dataset will be cloned. If None, + the datalad dataset will be cloned into a temporary directory + (default None). + + """ + + def __init__(self, datadir: Union[str, Path, None] = None) -> None: + """Initialize the class.""" + uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097_ReproVBM" + rootdir = "" + types = ["VBM_GM"] + replacements = ["subject"] + patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} + super().__init__( + types=types, + datadir=datadir, + uri=uri, + rootdir=rootdir, + replacements=replacements, + patterns=patterns, + ) -- 2.52.0 From d0c3be45450c59e43672a5041cdce40ef29d0990 Mon Sep 17 00:00:00 2001 From: Felix Hoffstaedter Date: Thu, 15 Sep 2022 21:17:23 +0200 Subject: [PATCH 047/142] fix missing space and uri too long is problematic: copied symlink with short name --- junifer/configs/juseless/juseless.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/junifer/configs/juseless/juseless.py b/junifer/configs/juseless/juseless.py index cc26f55e1..90843ea94 100644 --- a/junifer/configs/juseless/juseless.py +++ b/junifer/configs/juseless/juseless.py @@ -43,6 +43,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber): patterns=patterns, ) + @register_datagrabber class JuselessDataladAOMICVBM(PatternDataladDataGrabber): """Juseless AOMIC VBM DataGrabber class. @@ -60,11 +61,11 @@ class JuselessDataladAOMICVBM(PatternDataladDataGrabber): def __init__(self, datadir: Union[str, Path, None] = None) -> None: """Initialize the class.""" - uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097_ReproVBM" - rootdir = "" + uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" + rootdir = "{subject}/mri" types = ["VBM_GM"] replacements = ["subject"] - patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} + patterns = {"VBM_GM": "m0wp1sub-{subject}_T1w.nii.gz"} super().__init__( types=types, datadir=datadir, -- 2.52.0 From 764fadd2fdc411907b30eac2f8c356a814ac37cc Mon Sep 17 00:00:00 2001 From: Felix Hoffstaedter Date: Tue, 13 Sep 2022 13:24:58 +0200 Subject: [PATCH 048/142] add grabber for local VBM AOMIC 1000 dataset --- junifer/configs/juseless/juseless.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/configs/juseless/juseless.py b/junifer/configs/juseless/juseless.py index 90843ea94..937ca0aac 100644 --- a/junifer/configs/juseless/juseless.py +++ b/junifer/configs/juseless/juseless.py @@ -61,11 +61,11 @@ class JuselessDataladAOMICVBM(PatternDataladDataGrabber): def __init__(self, datadir: Union[str, Path, None] = None) -> None: """Initialize the class.""" - uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" - rootdir = "{subject}/mri" + uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097_ReproVBM" + rootdir = "" types = ["VBM_GM"] replacements = ["subject"] - patterns = {"VBM_GM": "m0wp1sub-{subject}_T1w.nii.gz"} + patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} super().__init__( types=types, datadir=datadir, -- 2.52.0 From 0a167245f878771e740377f95f6a7f79a48f6f8f Mon Sep 17 00:00:00 2001 From: Felix Hoffstaedter Date: Thu, 15 Sep 2022 21:17:23 +0200 Subject: [PATCH 049/142] fix missing space and uri too long is problematic: copied symlink with short name --- junifer/configs/juseless/juseless.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/configs/juseless/juseless.py b/junifer/configs/juseless/juseless.py index 937ca0aac..90843ea94 100644 --- a/junifer/configs/juseless/juseless.py +++ b/junifer/configs/juseless/juseless.py @@ -61,11 +61,11 @@ class JuselessDataladAOMICVBM(PatternDataladDataGrabber): def __init__(self, datadir: Union[str, Path, None] = None) -> None: """Initialize the class.""" - uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097_ReproVBM" - rootdir = "" + uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" + rootdir = "{subject}/mri" types = ["VBM_GM"] replacements = ["subject"] - patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} + patterns = {"VBM_GM": "m0wp1sub-{subject}_T1w.nii.gz"} super().__init__( types=types, datadir=datadir, -- 2.52.0 From fac94378839ea28b8f1ed68ad2320725eca905d6 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Oct 2022 13:05:31 +0200 Subject: [PATCH 050/142] refactor: move JuselessDataladAOMICID1000VBM to separate module --- .../configs/juseless/datagrabbers/__init__.py | 3 + .../juseless/datagrabbers/aomic_id1000_vbm.py | 41 ++++++++++ junifer/configs/juseless/juseless.py | 76 ------------------- 3 files changed, 44 insertions(+), 76 deletions(-) create mode 100644 junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py delete mode 100644 junifer/configs/juseless/juseless.py diff --git a/junifer/configs/juseless/datagrabbers/__init__.py b/junifer/configs/juseless/datagrabbers/__init__.py index 421ec09fa..5c9ceb50a 100644 --- a/junifer/configs/juseless/datagrabbers/__init__.py +++ b/junifer/configs/juseless/datagrabbers/__init__.py @@ -1,8 +1,11 @@ """Provide imports for datagrabbers sub-package.""" # Authors: Federico Raimondo +# Leonard Sasse +# Synchon Mandal # License: AGPL from .ukb_vbm import JuselessDataladUKBVBM from .camcan_vbm import JuselessDataladCamCANVBM from .ixi_vbm import JuselessDataladIXIVBM +from .aomic_id1000_vbm import JuselessDataladAOMICID1000VBM diff --git a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py new file mode 100644 index 000000000..4d1532180 --- /dev/null +++ b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py @@ -0,0 +1,41 @@ +"""Provide class for AOMIC1000 VBM juseless datalad datagrabber.""" + +# Authors: Felix Hoffstaedter +# Synchon Mandal +# License: AGPL + +from pathlib import Path +from typing import Union + +from ..api.decorators import register_datagrabber +from ..datagrabber import PatternDataladDataGrabber + + +@register_datagrabber +class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber): + """Juseless AOMICID1000 VBM DataGrabber class. + + Implements a DataGrabber to access the AOMICID1000 VBM data in Juseless. + + Parameters + ----------- + datadir : str or pathlib.Path, optional + The directory where the datalad dataset will be cloned. If None, + the datalad dataset will be cloned into a temporary directory + (default None). + + """ + + def __init__(self, datadir: Union[str, Path, None] = None) -> None: + """Initialize the class.""" + uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" + types = ["VBM_GM"] + replacements = ["subject"] + patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} + super().__init__( + types=types, + datadir=datadir, + uri=uri, + replacements=replacements, + patterns=patterns, + ) diff --git a/junifer/configs/juseless/juseless.py b/junifer/configs/juseless/juseless.py deleted file mode 100644 index 90843ea94..000000000 --- a/junifer/configs/juseless/juseless.py +++ /dev/null @@ -1,76 +0,0 @@ -"""Provide class for juseless datalad datagrabber.""" - -# Authors: Federico Raimondo -# Leonard Sasse -# Synchon Mandal -# License: AGPL - -from pathlib import Path -from typing import Union - -from ..api.decorators import register_datagrabber -from ..datagrabber import PatternDataladDataGrabber - - -@register_datagrabber -class JuselessDataladUKBVBM(PatternDataladDataGrabber): - """Juseless UKB VBM DataGrabber class. - - Implements a DataGrabber to access the UKB VBM data in Juseless. - - Parameters - ----------- - datadir : str or pathlib.Path, optional - The directory where the datalad dataset will be cloned. If None, - the datalad dataset will be cloned into a temporary directory - (default None). - - """ - - def __init__(self, datadir: Union[str, Path, None] = None) -> None: - """Initialize the class.""" - uri = "ria+http://ukb.ds.inm7.de#~cat_m0wp1" - rootdir = "m0wp1" - types = ["VBM_GM"] - replacements = ["subject", "session"] - patterns = {"VBM_GM": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz"} - super().__init__( - types=types, - datadir=datadir, - uri=uri, - rootdir=rootdir, - replacements=replacements, - patterns=patterns, - ) - - -@register_datagrabber -class JuselessDataladAOMICVBM(PatternDataladDataGrabber): - """Juseless AOMIC VBM DataGrabber class. - - Implements a DataGrabber to access the AOMIC VBM data in Juseless. - - Parameters - ----------- - datadir : str or pathlib.Path, optional - The directory where the datalad dataset will be cloned. If None, - the datalad dataset will be cloned into a temporary directory - (default None). - - """ - - def __init__(self, datadir: Union[str, Path, None] = None) -> None: - """Initialize the class.""" - uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" - rootdir = "{subject}/mri" - types = ["VBM_GM"] - replacements = ["subject"] - patterns = {"VBM_GM": "m0wp1sub-{subject}_T1w.nii.gz"} - super().__init__( - types=types, - datadir=datadir, - uri=uri, - rootdir=rootdir, - replacements=replacements, - patterns=patterns, - ) -- 2.52.0 From 0857d780c0eba13f930f942cfc5bfe11411d77ec Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Oct 2022 13:06:16 +0200 Subject: [PATCH 051/142] update: add juseless test for JuselessDataladAOMICID1000VBM --- .../tests/test_aomic_id1000_vbm.py | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py diff --git a/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py new file mode 100644 index 000000000..1da9ccdd6 --- /dev/null +++ b/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py @@ -0,0 +1,32 @@ +"""Provide tests for AOMICID1000 VBM juseless datagrabber.""" + +# Authors: Felix Hoffstaedter +# Synchon Mandal +# License: AGPL + +import socket + +import pytest + +from junifer.configs.juseless.datagrabbers import JuselessDataladAOMICID1000VBM +from junifer.utils.logging import configure_logging + + +# Check if the test is running on juseless +if socket.gethostname() != "juseless": + pytest.skip("These tests are only for juseless", allow_module_level=True) + +configure_logging(level="DEBUG") + + +def test_juselessdataladaomicid1000vbm_datagrabber() -> None: + """Test datalad AOMICID1000VBM datagrabber.""" + with JuselessDataladAOMICID1000VBM() as dg: + all_elements = dg.get_elements() + test_element = all_elements[0] + out = dg[test_element] + assert "VBM_GM" in out + assert ( + out["VBM_GM"]["path"].name == f"m0wp1sub-{test_element}_T1w.nii.gz" + ) + assert out["VBM_GM"]["path"].exists() -- 2.52.0 From 58360e01a1a27184677e5b7357eba6d49dcc9171 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Oct 2022 13:18:30 +0200 Subject: [PATCH 052/142] fix: correct imports for aomic_id1000_vbm.py --- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py index 4d1532180..1db4d8b17 100644 --- a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +++ b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py @@ -7,8 +7,8 @@ from pathlib import Path from typing import Union -from ..api.decorators import register_datagrabber -from ..datagrabber import PatternDataladDataGrabber +from ....api.decorators import register_datagrabber +from ....datagrabber import PatternDataladDataGrabber @register_datagrabber -- 2.52.0 From e6355457fecc6c57ba9a550d30fa9848b616dd68 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 12:28:56 +0200 Subject: [PATCH 053/142] update: update URI and pattern for JuselessDataladAOMICID1000VBM --- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py index 1db4d8b17..3fba4e07e 100644 --- a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +++ b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py @@ -28,10 +28,12 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber): def __init__(self, datadir: Union[str, Path, None] = None) -> None: """Initialize the class.""" - uri = "ria+file:///data/project/infrasound/dataladstore#~ds003097" + uri = "https://gin.g-node.org/felixh/ds003097_ReproVBM" types = ["VBM_GM"] replacements = ["subject"] - patterns = {"VBM_GM": "{subject}/mri/m0wp1sub-{subject}_T1w.nii.gz"} + patterns = { + "VBM_GM": "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz", + } super().__init__( types=types, datadir=datadir, -- 2.52.0 From d0a4b1c61dbb0d830afd9648b403abc4c4d2675e Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 25 Oct 2022 12:29:30 +0200 Subject: [PATCH 054/142] fix: correct pattern for JuselessDataladAOMICID1000VBM test --- .../juseless/datagrabbers/tests/test_aomic_id1000_vbm.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py index 1da9ccdd6..fad38837f 100644 --- a/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py +++ b/junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py @@ -27,6 +27,7 @@ def test_juselessdataladaomicid1000vbm_datagrabber() -> None: out = dg[test_element] assert "VBM_GM" in out assert ( - out["VBM_GM"]["path"].name == f"m0wp1sub-{test_element}_T1w.nii.gz" + out["VBM_GM"]["path"].name + == f"mwp1sub-{test_element}_run-2_T1w.nii.gz" ) assert out["VBM_GM"]["path"].exists() -- 2.52.0 From 97c6eb3936f3e939f9d76db5fca44ca7e49e1c4a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 09:35:03 +0200 Subject: [PATCH 055/142] chore: add Felix to contributors.inc --- docs/changes/contributors.inc | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/changes/contributors.inc b/docs/changes/contributors.inc index 46ee5aaaa..4e81f0aa2 100644 --- a/docs/changes/contributors.inc +++ b/docs/changes/contributors.inc @@ -8,3 +8,4 @@ .. _Xuan Li: https://github.com/xuanli-ac .. _Sami Hamdan: https://github.com/samihamdan .. _Nicolas Nieto: https://github.com/N-Nieto +.. _Felix Hoffstaedter: https://github.com/FeHoff -- 2.52.0 From abcf2f5af0061acc9628f97d7e51e41775508954 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 09:35:16 +0200 Subject: [PATCH 056/142] chore: update latest.inc --- docs/changes/latest.inc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 0319a32d3..900393c2f 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -69,6 +69,8 @@ Enhancements - Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the marker can be computed on the input data types (by `Fede Raimondo`_) +- Implement JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID 1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_ and `Synchon Mandal`_) + Bugs ~~~~ -- 2.52.0 From e81d7615d721e87a1dabe256bb2caf10475a48cb Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 30 Sep 2022 10:31:10 +0200 Subject: [PATCH 057/142] update: add script for HCP1200 test data generation in Gin --- tools/create_hcp1200_example_dataset.py | 74 +++++++++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 tools/create_hcp1200_example_dataset.py diff --git a/tools/create_hcp1200_example_dataset.py b/tools/create_hcp1200_example_dataset.py new file mode 100644 index 000000000..4aa4044ea --- /dev/null +++ b/tools/create_hcp1200_example_dataset.py @@ -0,0 +1,74 @@ +"""Script to generate example dataset for HCP1200.""" + +# Authors: Synchon Mandal +# License: AGPL + +from itertools import product +from tempfile import TemporaryDirectory +from pathlib import Path + +import datalad.api as dl + + +# Set destination URL +DST = "git@gin.g-node.org:/juaml/datalad-example-hcp1200.git" + + +if __name__ == "__main__": + + with TemporaryDirectory() as tmpdir: + # Convert str to Path + tmpdir_path = Path(tmpdir) + # Set base directory + basedir = tmpdir_path / "example_hcp1200" + # Create new datalad dataset + dataset = dl.create(path=str(basedir.absolute())) + # Generate subject directories + for sub in range(1, 10): + subdir = basedir / f"sub-{sub:02d}" + # Create subject directory + subdir.mkdir() + + for (task, phase_encoding) in product( + [ + "REST1", + "REST2", + "SOCIAL", + "WM", + "RELATIONAL", + "EMOTION", + "LANGUAGE", + "GAMBLING", + "MOTOR", + ], + ["LR", "RL"], + ): + # Proper formatting of task name + if "REST" in task: + new_task = f"rfMRI_{task}" + else: + new_task = f"tfMRI_{task}" + # Set subject data directory + sub_datadir = ( + subdir + / "MNINonLinear" + / "Results" + / f"{new_task}_{phase_encoding}" + ) + # Create subject data directory + sub_datadir.mkdir(parents=True) + # Set subject data file + sub_datafile = ( + sub_datadir + / f"{new_task}_{phase_encoding}_hp2000_clean.nii.gz" + ) + # Create subject data file + with open(sub_datafile, "w") as f: + f.write("placeholder") + + # Save datalad dataset + dataset.save(recursive=True) + # Add datalad sibling + dataset.siblings(action="add", name="gin", url=DST) + # Push dataset to sibling + dataset.push(to="gin", force="all") -- 2.52.0 From aca638cbb4521a0ccc9f04ca7663db2113a18250 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 30 Sep 2022 10:31:54 +0200 Subject: [PATCH 058/142] update: add test for DataladHCP1200() datagrabber --- junifer/datagrabber/tests/test_hcp.py | 41 +++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 junifer/datagrabber/tests/test_hcp.py diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py new file mode 100644 index 000000000..81673c6eb --- /dev/null +++ b/junifer/datagrabber/tests/test_hcp.py @@ -0,0 +1,41 @@ +"""Provide tests for HCP1200.""" + +# Authors: Synchon Mandal +# License: AGPL + +from junifer.datagrabber.hcp import DataladHCP1200 +from junifer.utils import configure_logging + + +URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200" + + +def test_dataladhcp1200_datagrabber() -> None: + """Test datalad HCP1200 datagrabber.""" + configure_logging(level="DEBUG") + dg = DataladHCP1200() + # Set URI to Gin + dg.uri = URI + # Set correct root directory + dg._rootdir = "." + with dg: + # Get all elements + all_elements = dg.get_elements() + # Get test element + test_element = all_elements[0] + # Get test element data + out = dg[test_element] + # Asserts data type + assert "BOLD" in out + # Assert data file name + assert out["BOLD"]["path"].name == "rfMRI_REST1_LR_hp2000_clean.nii.gz" + # Assert data file path exists + assert out["BOLD"]["path"].exists() + # Assert data file path is a file + assert out["BOLD"]["path"].is_file() + # Assert metadata + assert "meta" in out + meta = out["meta"] + assert "element" in meta + assert "subject" in meta["element"] + assert test_element[0] == meta["element"]["subject"] -- 2.52.0 From 6a614d01b155780b3f4b645290f44dc72bee00c4 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 30 Sep 2022 10:37:55 +0200 Subject: [PATCH 059/142] chore: update latest.inc --- docs/changes/latest.inc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 900393c2f..496cbfc5a 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -71,6 +71,8 @@ Enhancements - Implement JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID 1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_ and `Synchon Mandal`_) +- Add test for DataladHCP1200 datagrabber (:gh: `93` by `Synchon Mandal`_). + Bugs ~~~~ -- 2.52.0 From 33abb48b1a7eb334a999bf8a3545963d8327d930 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Mon, 10 Oct 2022 10:32:48 +0200 Subject: [PATCH 060/142] update: parametrize test for DataladHCP1200 datagrabber --- junifer/datagrabber/tests/test_hcp.py | 54 +++++++++++++++++++++++++-- 1 file changed, 50 insertions(+), 4 deletions(-) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index 81673c6eb..d32238766 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -3,6 +3,10 @@ # Authors: Synchon Mandal # License: AGPL +from typing import Optional + +import pytest + from junifer.datagrabber.hcp import DataladHCP1200 from junifer.utils import configure_logging @@ -10,10 +14,52 @@ from junifer.utils import configure_logging URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200" -def test_dataladhcp1200_datagrabber() -> None: - """Test datalad HCP1200 datagrabber.""" +@pytest.mark.parametrize( + "tasks, phase_encodings, expected_path_name", + [ + (None, None, "rfMRI_REST1_LR_hp2000_clean.nii.gz"), + ("REST1", "LR", "rfMRI_REST1_LR_hp2000_clean.nii.gz"), + ("REST1", "RL", "rfMRI_REST1_RL_hp2000_clean.nii.gz"), + ("REST2", "LR", "rfMRI_REST2_LR_hp2000_clean.nii.gz"), + ("REST2", "RL", "rfMRI_REST2_RL_hp2000_clean.nii.gz"), + ("SOCIAL", "LR", "tfMRI_SOCIAL_LR_hp2000_clean.nii.gz"), + ("SOCIAL", "RL", "tfMRI_SOCIAL_RL_hp2000_clean.nii.gz"), + ("WM", "LR", "tfMRI_WM_LR_hp2000_clean.nii.gz"), + ("WM", "RL", "tfMRI_WM_RL_hp2000_clean.nii.gz"), + ("RELATIONAL", "LR", "tfMRI_RELATIONAL_LR_hp2000_clean.nii.gz"), + ("RELATIONAL", "RL", "tfMRI_RELATIONAL_RL_hp2000_clean.nii.gz"), + ("EMOTION", "LR", "tfMRI_EMOTION_LR_hp2000_clean.nii.gz"), + ("EMOTION", "RL", "tfMRI_EMOTION_RL_hp2000_clean.nii.gz"), + ("LANGUAGE", "LR", "tfMRI_LANGUAGE_LR_hp2000_clean.nii.gz"), + ("LANGUAGE", "RL", "tfMRI_LANGUAGE_RL_hp2000_clean.nii.gz"), + ("GAMBLING", "LR", "tfMRI_GAMBLING_LR_hp2000_clean.nii.gz"), + ("GAMBLING", "RL", "tfMRI_GAMBLING_RL_hp2000_clean.nii.gz"), + ("MOTOR", "LR", "tfMRI_MOTOR_LR_hp2000_clean.nii.gz"), + ("MOTOR", "RL", "tfMRI_MOTOR_RL_hp2000_clean.nii.gz"), + ], +) +def test_dataladhcp1200_datagrabber( + tasks: Optional[str], + phase_encodings: Optional[str], + expected_path_name: str, +) -> None: + """Test datalad HCP1200 datagrabber. + + Parameters + ---------- + tasks : str + The parametrized tasks. + phase_encodings : str + The parametrized phase encodings. + expected_path_name : str + The parametrized expected path name. + + """ configure_logging(level="DEBUG") - dg = DataladHCP1200() + dg = DataladHCP1200( + tasks=tasks, + phase_encodings=phase_encodings, + ) # Set URI to Gin dg.uri = URI # Set correct root directory @@ -28,7 +74,7 @@ def test_dataladhcp1200_datagrabber() -> None: # Asserts data type assert "BOLD" in out # Assert data file name - assert out["BOLD"]["path"].name == "rfMRI_REST1_LR_hp2000_clean.nii.gz" + assert out["BOLD"]["path"].name == expected_path_name # Assert data file path exists assert out["BOLD"]["path"].exists() # Assert data file path is a file -- 2.52.0 From c4a0bdc50dd8a0bd1e08a41beb0e537ee8e90e28 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 11:08:03 +0200 Subject: [PATCH 061/142] update: add support for checking file existence in PatternDataGrabber --- junifer/datagrabber/pattern.py | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/junifer/datagrabber/pattern.py b/junifer/datagrabber/pattern.py index bf5fd1cef..34b9f43d1 100644 --- a/junifer/datagrabber/pattern.py +++ b/junifer/datagrabber/pattern.py @@ -32,6 +32,8 @@ class PatternDataGrabber(BaseDataGrabber): `{subject}` in the pattern will be replaced by the indexed element. replacements: list of str Replacements in the patterns for each item in the "element" tuple. + check_file_existence : bool, optional + Whether to check if file exists while accessing (default False). datadir : str or pathlib.Path The directory where the data is / will be stored. **kwargs @@ -48,6 +50,7 @@ class PatternDataGrabber(BaseDataGrabber): types: List[str], patterns: Dict[str, str], replacements: List[str], + check_file_existence: bool = False, **kwargs, ) -> None: """Initialize the class.""" @@ -65,6 +68,7 @@ class PatternDataGrabber(BaseDataGrabber): logger.debug(f"\treplacements = {replacements}") self.patterns = patterns self.replacements = replacements + self.check_file_existence = check_file_existence def _replace_patterns_regex( self, pattern: str @@ -170,11 +174,12 @@ class PatternDataGrabber(BaseDataGrabber): t_out = t_matches[0] else: t_out = self.datadir / t_replace - if not t_out.exists() and not t_out.is_symlink(): - raise_error( - f"Cannot access {t_type} for {element}: " - f"File {t_out} does not exist" - ) + if self.check_file_existence: + if not t_out.exists() and not t_out.is_symlink(): + raise_error( + f"Cannot access {t_type} for {element}: " + f"File {t_out} does not exist" + ) out[t_type] = {"path": t_out} # Meta here is element and types out["meta"]["element"] = dict(zip(self.replacements, element)) -- 2.52.0 From 885fa3562cca742db55c9f0d4c55dcf7a8d244bb Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 11:08:35 +0200 Subject: [PATCH 062/142] chore: docstring fix in PatternDataGrabber --- junifer/datagrabber/pattern.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/datagrabber/pattern.py b/junifer/datagrabber/pattern.py index 34b9f43d1..7375e81c4 100644 --- a/junifer/datagrabber/pattern.py +++ b/junifer/datagrabber/pattern.py @@ -30,7 +30,7 @@ class PatternDataGrabber(BaseDataGrabber): Patterns for each type of data as a dictionary. The keys are the types and the values are the patterns. Each occurrence of the string `{subject}` in the pattern will be replaced by the indexed element. - replacements: list of str + replacements : list of str Replacements in the patterns for each item in the "element" tuple. check_file_existence : bool, optional Whether to check if file exists while accessing (default False). -- 2.52.0 From a5ec5f32d1f42aa7c86363a0848fc3ae5645935d Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 17:58:48 +0200 Subject: [PATCH 063/142] update: add check_file_existence argument in DataladHCP1200 --- junifer/datagrabber/hcp.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/junifer/datagrabber/hcp.py b/junifer/datagrabber/hcp.py index 9db59031b..700ebb95b 100644 --- a/junifer/datagrabber/hcp.py +++ b/junifer/datagrabber/hcp.py @@ -174,6 +174,8 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): phase_encodings : {"LR", "RL"} or list of the options, optional HCP phase encoding directions. If None, both will be used (default None). + check_file_existence : bool, optional + Whether to check if file exists while accessing (default False). **kwargs Keyword arguments passed to superclass. @@ -184,6 +186,7 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): datadir: Union[str, Path, None] = None, tasks: Union[str, List[str], None] = None, phase_encodings: Union[str, List[str], None] = None, + check_file_existence: bool = False, **kwargs, ) -> None: """Initialize the class.""" @@ -196,6 +199,7 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): datadir=datadir, tasks=tasks, phase_encodings=phase_encodings, + check_file_existence=check_file_existence, uri=uri, rootdir=rootdir, ) -- 2.52.0 From d5f3879be712516c0a073fa0cdf91f181585f2b0 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 18:24:24 +0200 Subject: [PATCH 064/142] chore: update latest.inc --- docs/changes/latest.inc | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 496cbfc5a..21aba6c49 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -81,3 +81,7 @@ Bugs API changes ~~~~~~~~~~~ + +- Add new argument ``check_file_existence`` for PatternDataGrabber which allows skipping actual file existence check. + This is needed for datagrabbers which extend from PatternDataGrabber and DataladDataGrabber and have one or more + Datalad subdatasets inside the dataset, for example, DataladHCP1200. \ No newline at end of file -- 2.52.0 From 0e93cc5b5846c6a45dbf20253ca169a4d53176ba Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 18:52:47 +0200 Subject: [PATCH 065/142] fix: add check_file_existence argument for test_PatternDataGrabber_errors --- junifer/datagrabber/tests/test_pattern.py | 1 + 1 file changed, 1 insertion(+) diff --git a/junifer/datagrabber/tests/test_pattern.py b/junifer/datagrabber/tests/test_pattern.py index 472934d2c..61e6c416b 100644 --- a/junifer/datagrabber/tests/test_pattern.py +++ b/junifer/datagrabber/tests/test_pattern.py @@ -103,6 +103,7 @@ def test_PatternDataGrabber_errors(tmp_path: Path) -> None: "anat": "anat/{subject}_{session}_ses.nii", }, replacements=["subject", "session"], + check_file_existence=True, ) with pytest.raises(ValueError, match="element length must be"): -- 2.52.0 From ef138bdef51287645892fa18f01c217eced4ca31 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 18:54:37 +0200 Subject: [PATCH 066/142] update: add correct iterator test for DataladHCP1200 tests --- junifer/datagrabber/tests/test_hcp.py | 61 +++++++++++++++++++++++++-- 1 file changed, 58 insertions(+), 3 deletions(-) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index d32238766..b02f68981 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -39,9 +39,9 @@ URI = "https://gin.g-node.org/juaml/datalad-example-hcp1200" ], ) def test_dataladhcp1200_datagrabber( - tasks: Optional[str], - phase_encodings: Optional[str], - expected_path_name: str, + tasks: Optional[str], + phase_encodings: Optional[str], + expected_path_name: str, ) -> None: """Test datalad HCP1200 datagrabber. @@ -85,3 +85,58 @@ def test_dataladhcp1200_datagrabber( assert "element" in meta assert "subject" in meta["element"] assert test_element[0] == meta["element"]["subject"] + + +@pytest.mark.parametrize( + "tasks, phase_encodings", + [ + ("REST1", "LR"), + ("REST1", "RL"), + ("REST2", "LR"), + ("REST2", "RL"), + ("SOCIAL", "LR"), + ("SOCIAL", "RL"), + ("WM", "LR"), + ("WM", "RL"), + ("RELATIONAL", "LR"), + ("RELATIONAL", "RL"), + ("EMOTION", "LR"), + ("EMOTION", "RL"), + ("LANGUAGE", "LR"), + ("LANGUAGE", "RL"), + ("GAMBLING", "LR"), + ("GAMBLING", "RL"), + ("MOTOR", "LR"), + ("MOTOR", "RL"), + ], +) +def test_dataladhcp1200_datagrabber_iterator( + tasks: Optional[str], + phase_encodings: Optional[str], +) -> None: + """Test datalad HCP1200 datagrabber iterator. + + Parameters + ---------- + tasks : str + The parametrized tasks. + phase_encodings : str + The parametrized phase encodings. + + """ + configure_logging(level="DEBUG") + dg = DataladHCP1200( + tasks=tasks, + phase_encodings=phase_encodings, + ) + # Set URI to Gin + dg.uri = URI + # Set correct root directory + dg._rootdir = "." + with dg: + # Get all elements + all_elements = dg.get_elements() + # Check only specified task and phase encoding are found + for element in all_elements: + assert element[1] == tasks + assert element[2] == phase_encodings -- 2.52.0 From f3ec4eedbd2cd3b28683089cb3beadb190ee8635 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:13:00 +0200 Subject: [PATCH 067/142] chore: rename test for DataladHCP1200 single access --- junifer/datagrabber/tests/test_hcp.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index b02f68981..adf8d1740 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -110,11 +110,11 @@ def test_dataladhcp1200_datagrabber( ("MOTOR", "RL"), ], ) -def test_dataladhcp1200_datagrabber_iterator( +def test_dataladhcp1200_datagrabber_single_access( tasks: Optional[str], phase_encodings: Optional[str], ) -> None: - """Test datalad HCP1200 datagrabber iterator. + """Test datalad HCP1200 datagrabber single access. Parameters ---------- -- 2.52.0 From f593fbcb46a56ccebbab10210aa263a4d8b98fbc Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:13:28 +0200 Subject: [PATCH 068/142] update: add test for DataladHCP1200 multiple access --- junifer/datagrabber/tests/test_hcp.py | 39 +++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index adf8d1740..257b32602 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -140,3 +140,42 @@ def test_dataladhcp1200_datagrabber_single_access( for element in all_elements: assert element[1] == tasks assert element[2] == phase_encodings + + +@pytest.mark.parametrize( + "tasks, phase_encodings", + [ + (["REST1", "REST2"], ["LR", "RL"]), + (["REST1", "REST2"], None), + ], +) +def test_dataladhcp1200_datagrabber_multi_access( + tasks: Optional[str], + phase_encodings: Optional[str], +) -> None: + """Test datalad HCP1200 datagrabber multiple access. + + Parameters + ---------- + tasks : str + The parametrized tasks. + phase_encodings : str + The parametrized phase encodings. + + """ + configure_logging(level="DEBUG") + dg = DataladHCP1200( + tasks=["REST1", "REST2"], + phase_encodings=["LR", "RL"], + ) + # Set URI to Gin + dg.uri = URI + # Set correct root directory + dg._rootdir = "." + with dg: + # Get all elements + all_elements = dg.get_elements() + # Check only specified task and phase encoding are found + for element in all_elements: + assert element[1] in ["REST1", "REST2"] + assert element[2] in ["LR", "RL"] -- 2.52.0 From c48a93790866b0036bc67577fb4ac8705653b24f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:14:15 +0200 Subject: [PATCH 069/142] update: add test for DataladHCP1200 multi access with single task --- junifer/datagrabber/tests/test_hcp.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index 257b32602..6e538aa67 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -179,3 +179,23 @@ def test_dataladhcp1200_datagrabber_multi_access( for element in all_elements: assert element[1] in ["REST1", "REST2"] assert element[2] in ["LR", "RL"] + + +def test_dataladhcp1200_datagrabber_multi_access_task_simple() -> None: + """Test datalad HCP1200 datagrabber simple multiple access for task.""" + configure_logging(level="DEBUG") + dg = DataladHCP1200( + tasks="REST1", + phase_encodings=["LR", "RL"], + ) + # Set URI to Gin + dg.uri = URI + # Set correct root directory + dg._rootdir = "." + with dg: + # Get all elements + all_elements = dg.get_elements() + # Check only specified task and phase encoding are found + for element in all_elements: + assert element[1] == "REST1" + assert element[2] in ["LR", "RL"] -- 2.52.0 From a5d106596bbb1610806d3343bd80c7dc7c02cf9a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:14:44 +0200 Subject: [PATCH 070/142] update: add test for DataladHCP1200 multiple access with single phase encoding --- junifer/datagrabber/tests/test_hcp.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index 6e538aa67..e83e23a5b 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -199,3 +199,23 @@ def test_dataladhcp1200_datagrabber_multi_access_task_simple() -> None: for element in all_elements: assert element[1] == "REST1" assert element[2] in ["LR", "RL"] + + +def test_dataladhcp1200_datagrabber_multi_access_phase_simple() -> None: + """Test datalad HCP1200 datagrabber simple multiple access for phase.""" + configure_logging(level="DEBUG") + dg = DataladHCP1200( + tasks=["REST1", "REST2"], + phase_encodings="LR", + ) + # Set URI to Gin + dg.uri = URI + # Set correct root directory + dg._rootdir = "." + with dg: + # Get all elements + all_elements = dg.get_elements() + # Check only specified task and phase encoding are found + for element in all_elements: + assert element[1] in ["REST1", "REST2"] + assert element[2] == "LR" -- 2.52.0 From 3eb427ca9119ff0279a5b5795020fcae27220705 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:15:10 +0200 Subject: [PATCH 071/142] update: add test for DataladHCP1200 incorrect access of tasks --- junifer/datagrabber/tests/test_hcp.py | 31 +++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index e83e23a5b..bf54fe430 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -219,3 +219,34 @@ def test_dataladhcp1200_datagrabber_multi_access_phase_simple() -> None: for element in all_elements: assert element[1] in ["REST1", "REST2"] assert element[2] == "LR" + + +@pytest.mark.parametrize( + "tasks, phase_encodings", + [ + ("FOO", ["LR", "RL"]), + ("FOO", "RL"), + (["FOO", "BAR"], ["LR", "RL"]), + (["FOO", "BAR"], "LR"), + ], +) +def test_dataladhcp1200_datagrabber_incorrect_access_task( + tasks: Optional[str], + phase_encodings: Optional[str], +) -> None: + """Test datalad HCP1200 datagrabber incorrect access for task. + + Parameters + ---------- + tasks : str + The parametrized tasks. + phase_encodings : str + The parametrized phase encodings. + + """ + configure_logging(level="DEBUG") + with pytest.raises(ValueError, match="not a valid HCP-YA fMRI task input"): + _ = DataladHCP1200( + tasks=tasks, + phase_encodings=phase_encodings, + ) -- 2.52.0 From aaaf954dd12fd3cb2aac13b2bee65d385e91e5b1 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 27 Oct 2022 21:15:32 +0200 Subject: [PATCH 072/142] update: add test for DataladHCP1200 incorrect access for phase encodings --- junifer/datagrabber/tests/test_hcp.py | 31 +++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/junifer/datagrabber/tests/test_hcp.py b/junifer/datagrabber/tests/test_hcp.py index bf54fe430..9b6275314 100644 --- a/junifer/datagrabber/tests/test_hcp.py +++ b/junifer/datagrabber/tests/test_hcp.py @@ -250,3 +250,34 @@ def test_dataladhcp1200_datagrabber_incorrect_access_task( tasks=tasks, phase_encodings=phase_encodings, ) + + +@pytest.mark.parametrize( + "tasks, phase_encodings", + [ + ("REST1", ["FOO", "BAR"]), + ("REST1", "FOO"), + (["REST1", "REST2"], ["FOO", "BAR"]), + (["REST1", "REST2"], "BAR"), + ], +) +def test_dataladhcp1200_datagrabber_incorrect_access_phase( + tasks: Optional[str], + phase_encodings: Optional[str], +) -> None: + """Test datalad HCP1200 datagrabber incorrect access for phase. + + Parameters + ---------- + tasks : str + The parametrized tasks. + phase_encodings : str + The parametrized phase encodings. + + """ + configure_logging(level="DEBUG") + with pytest.raises(ValueError, match="not a valid HCP-YA phase encoding"): + _ = DataladHCP1200( + tasks=tasks, + phase_encodings=phase_encodings, + ) -- 2.52.0 From 4255bc5adc03bf39e8cc2e79312821b958b1977a Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 09:04:54 +0200 Subject: [PATCH 073/142] update: remove check_file_existence argument from DataladHCP1200 --- junifer/datagrabber/hcp.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/junifer/datagrabber/hcp.py b/junifer/datagrabber/hcp.py index 700ebb95b..9db59031b 100644 --- a/junifer/datagrabber/hcp.py +++ b/junifer/datagrabber/hcp.py @@ -174,8 +174,6 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): phase_encodings : {"LR", "RL"} or list of the options, optional HCP phase encoding directions. If None, both will be used (default None). - check_file_existence : bool, optional - Whether to check if file exists while accessing (default False). **kwargs Keyword arguments passed to superclass. @@ -186,7 +184,6 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): datadir: Union[str, Path, None] = None, tasks: Union[str, List[str], None] = None, phase_encodings: Union[str, List[str], None] = None, - check_file_existence: bool = False, **kwargs, ) -> None: """Initialize the class.""" @@ -199,7 +196,6 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): datadir=datadir, tasks=tasks, phase_encodings=phase_encodings, - check_file_existence=check_file_existence, uri=uri, rootdir=rootdir, ) -- 2.52.0 From c0a92b5f547cc412971c7d5c9ea64ea501af5748 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 12:08:45 +0200 Subject: [PATCH 074/142] update: replace check_file_existence argument with skip_file_check property for PatternDataGrabber --- junifer/datagrabber/pattern.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/junifer/datagrabber/pattern.py b/junifer/datagrabber/pattern.py index 7375e81c4..11e727cd6 100644 --- a/junifer/datagrabber/pattern.py +++ b/junifer/datagrabber/pattern.py @@ -32,8 +32,6 @@ class PatternDataGrabber(BaseDataGrabber): `{subject}` in the pattern will be replaced by the indexed element. replacements : list of str Replacements in the patterns for each item in the "element" tuple. - check_file_existence : bool, optional - Whether to check if file exists while accessing (default False). datadir : str or pathlib.Path The directory where the data is / will be stored. **kwargs @@ -50,7 +48,6 @@ class PatternDataGrabber(BaseDataGrabber): types: List[str], patterns: Dict[str, str], replacements: List[str], - check_file_existence: bool = False, **kwargs, ) -> None: """Initialize the class.""" @@ -68,7 +65,11 @@ class PatternDataGrabber(BaseDataGrabber): logger.debug(f"\treplacements = {replacements}") self.patterns = patterns self.replacements = replacements - self.check_file_existence = check_file_existence + + @property + def skip_file_check(self) -> bool: + """Skip file check existence.""" + return False def _replace_patterns_regex( self, pattern: str @@ -174,7 +175,7 @@ class PatternDataGrabber(BaseDataGrabber): t_out = t_matches[0] else: t_out = self.datadir / t_replace - if self.check_file_existence: + if not self.skip_file_check: if not t_out.exists() and not t_out.is_symlink(): raise_error( f"Cannot access {t_type} for {element}: " -- 2.52.0 From 64ad95f34605d297976dd7483fd78721fbb41269 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 12:09:15 +0200 Subject: [PATCH 075/142] fix: correct test for PatternDataGrabber --- junifer/datagrabber/tests/test_pattern.py | 1 - 1 file changed, 1 deletion(-) diff --git a/junifer/datagrabber/tests/test_pattern.py b/junifer/datagrabber/tests/test_pattern.py index 61e6c416b..472934d2c 100644 --- a/junifer/datagrabber/tests/test_pattern.py +++ b/junifer/datagrabber/tests/test_pattern.py @@ -103,7 +103,6 @@ def test_PatternDataGrabber_errors(tmp_path: Path) -> None: "anat": "anat/{subject}_{session}_ses.nii", }, replacements=["subject", "session"], - check_file_existence=True, ) with pytest.raises(ValueError, match="element length must be"): -- 2.52.0 From 11da30cb045061fc3114bc8baff2217344728fbc Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 28 Oct 2022 12:09:38 +0200 Subject: [PATCH 076/142] update: implement skip_file_check property for DataladHCP1200 --- junifer/datagrabber/hcp.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/junifer/datagrabber/hcp.py b/junifer/datagrabber/hcp.py index 9db59031b..90e975a2a 100644 --- a/junifer/datagrabber/hcp.py +++ b/junifer/datagrabber/hcp.py @@ -199,3 +199,8 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): uri=uri, rootdir=rootdir, ) + + @property + def skip_file_check(self) -> bool: + """Skip file check existence.""" + return True -- 2.52.0 From e8fb156f696b29eb064f75f3a11e3f88eb2ffd5c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:52:51 +0100 Subject: [PATCH 077/142] update: support Python 3.11 in tox.ini --- tox.ini | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tox.ini b/tox.ini index a7c187bb9..0cb26f786 100644 --- a/tox.ini +++ b/tox.ini @@ -1,12 +1,13 @@ [tox] -envlist = isort, black, flake8, test, coverage, codespell, py3{8,9,10} +envlist = isort, black, flake8, test, coverage, codespell, py3{8,9,10,11} isolated_build = true [gh-actions] python = 3.8: py38 - 3.9: coverage - 3.10: py310 + 3.9: py39 + 3.10: coverage + 3.11: py311 [testenv] skip_install = false -- 2.52.0 From 4301d3897b2ccefcab7df63a5dc9e87d34e06f9b Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:53:24 +0100 Subject: [PATCH 078/142] update: support Python 3.11 for ci-docs.yml --- .github/workflows/ci-docs.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index b573c46f9..3bbea84b2 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -1,6 +1,6 @@ name: Run Tests -on: +on: push: paths-ignore: - 'junifer/**' @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.8', '3.9', '3.10'] + python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - run: 'echo "No build required"' - name: Create mock coverage.xml file @@ -38,11 +38,11 @@ jobs: echo '' >> coverage.xml echo '' >> coverage.xml echo '' >> coverage.xml - if: matrix.python-version == 3.9 + if: matrix.python-version == 3.10 - name: Upload mock coverage to Codecov uses: codecov/codecov-action@v3 with: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true flags: docs - if: success() && matrix.python-version == 3.9 \ No newline at end of file + if: success() && matrix.python-version == 3.10 \ No newline at end of file -- 2.52.0 From 57d24f78de25f15de66dc6df6749a347f0a016e0 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:53:45 +0100 Subject: [PATCH 079/142] update: support Python 3.11 for ci.yml --- .github/workflows/ci.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bafa35419..22c99514d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,6 +1,6 @@ name: Run Tests -on: +on: push: paths: - 'junifer/**' @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ['3.8', '3.9', '3.10'] + python-version: ['3.8', '3.9', '3.10', '3.11'] steps: - name: Set up system @@ -44,4 +44,4 @@ jobs: token: ${{ secrets.CODECOV_TOKEN }} fail_ci_if_error: true flags: junifer - if: success() && matrix.python-version == 3.9 + if: success() && matrix.python-version == 3.10 -- 2.52.0 From 87783caa58f064b1caab929ec6629829ae0049a8 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:54:26 +0100 Subject: [PATCH 080/142] update: use Python 3.10 for docs-preview.yml --- .github/workflows/docs-preview.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index 2ea66c5f8..b51c8063f 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -24,10 +24,10 @@ jobs: steps: - name: Checkout source uses: actions/checkout@v2 - - name: Set up Python 3.9 uses: actions/setup-python@v2 + - name: Set up Python 3.10 with: - python-version: 3.9 + python-version: 3.10 - name: Check for sudo shell: bash run: | -- 2.52.0 From 3e9752f668df16e04a08920f76e67883932a4981 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:55:00 +0100 Subject: [PATCH 081/142] chore: use actions/checkout@v3 for docs-preview.yml --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index b51c8063f..ecb40ed94 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -23,8 +23,8 @@ jobs: steps: - name: Checkout source - uses: actions/checkout@v2 uses: actions/setup-python@v2 + uses: actions/checkout@v3 - name: Set up Python 3.10 with: python-version: 3.10 -- 2.52.0 From 1122c3f8d24e85a9ee47a985b562c44dcb598646 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:55:20 +0100 Subject: [PATCH 082/142] chore: use actions/setup-python@v4 for docs-preview.yml --- .github/workflows/docs-preview.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index ecb40ed94..c2796165b 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -23,9 +23,9 @@ jobs: steps: - name: Checkout source - uses: actions/setup-python@v2 uses: actions/checkout@v3 - name: Set up Python 3.10 + uses: actions/setup-python@v4 with: python-version: 3.10 - name: Check for sudo -- 2.52.0 From e04fc7a6f32487f5488a5a7aee11e33260cb701d Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:56:07 +0100 Subject: [PATCH 083/142] update: use Python 3.10 for docs.yml --- .github/workflows/docs.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 344982d0e..0f11b17e2 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -3,10 +3,10 @@ name: Build and publish docs on: push: # Sequence of patterns matched against refs/heads - branches: + branches: - main # Sequence of patterns matched against refs/tags - tags: + tags: - v* jobs: @@ -21,10 +21,10 @@ jobs: with: # require all of history to see all tagged versions' docs fetch-depth: 0 - - name: Set up Python 3.9 uses: actions/setup-python@v2 + - name: Set up Python 3.10 with: - python-version: 3.9 + python-version: 3.10 - name: Check for sudo shell: bash run: | -- 2.52.0 From de9357264205664f375a39dc0628f3f5998e8424 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:56:47 +0100 Subject: [PATCH 084/142] chore: use actions/checkout@v3 for docs.yml --- .github/workflows/docs.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index 0f11b17e2..ab270bbd1 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -17,7 +17,7 @@ jobs: steps: - name: Checkout source - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: # require all of history to see all tagged versions' docs fetch-depth: 0 @@ -44,7 +44,7 @@ jobs: - name: Checkout gh-pages # As we already did a deploy of gh-pages above, it is guaranteed to be there # so check it out so we can selectively build docs below - uses: actions/checkout@v2 + uses: actions/checkout@v3 with: ref: gh-pages path: docs/_build -- 2.52.0 From 01ae2364b7b71f885ca4d2fc19cda642db7426f6 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:56:59 +0100 Subject: [PATCH 085/142] chore: use actions/setup-python@v4 for docs.yml --- .github/workflows/docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index ab270bbd1..eb42d4c1f 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -21,8 +21,8 @@ jobs: with: # require all of history to see all tagged versions' docs fetch-depth: 0 - uses: actions/setup-python@v2 - name: Set up Python 3.10 + uses: actions/setup-python@v4 with: python-version: 3.10 - name: Check for sudo -- 2.52.0 From 613a00f6362cf0ec2f10ed903b7a3d592d99568c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:57:09 +0100 Subject: [PATCH 086/142] update: use Python 3.11 for lint.yml --- .github/workflows/lint.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index edf01ba2e..e129f0af8 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -11,7 +11,7 @@ jobs: fail-fast: false matrix: os: [ubuntu-latest] - python-version: ['3.10'] + python-version: ['3.11'] steps: - uses: actions/checkout@v3 -- 2.52.0 From 35d846c189d30482f742e1f1a4d275362006b684 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:57:34 +0100 Subject: [PATCH 087/142] update: use Python 3.10 for pypi.yml --- .github/workflows/pypi.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 0ffc75efa..9765bf70b 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -13,12 +13,12 @@ jobs: - uses: actions/checkout@master with: fetch-depth: 0 - - name: Set up Python 3.8 uses: actions/setup-python@v1 + - name: Set up Python 3.10 with: - python-version: 3.8 + python-version: 3.10 - name: Install build - run: + run: pip install build - name: Build a binary wheel and a source tarball run: -- 2.52.0 From ed53828e20dc2b6125e4e7a08a6004e5cd981e8d Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 10:57:57 +0100 Subject: [PATCH 088/142] chore: use actions/setup-python@v4 for pypi.yml --- .github/workflows/pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 9765bf70b..8b0b97555 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -13,8 +13,8 @@ jobs: - uses: actions/checkout@master with: fetch-depth: 0 - uses: actions/setup-python@v1 - name: Set up Python 3.10 + uses: actions/setup-python@v4 with: python-version: 3.10 - name: Install build -- 2.52.0 From 7a2e3604422af557b5514500dc24369c2fa1d7b6 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 11:02:03 +0100 Subject: [PATCH 089/142] fix: add missing quotes in docs.yml and docs-preview.yml --- .github/workflows/docs-preview.yml | 2 +- .github/workflows/docs.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/docs-preview.yml b/.github/workflows/docs-preview.yml index c2796165b..9025eb8af 100644 --- a/.github/workflows/docs-preview.yml +++ b/.github/workflows/docs-preview.yml @@ -27,7 +27,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v4 with: - python-version: 3.10 + python-version: '3.10' - name: Check for sudo shell: bash run: | diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml index eb42d4c1f..e7ed4c66a 100644 --- a/.github/workflows/docs.yml +++ b/.github/workflows/docs.yml @@ -24,7 +24,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v4 with: - python-version: 3.10 + python-version: '3.10' - name: Check for sudo shell: bash run: | -- 2.52.0 From 4b6560e451c09fdbe19bb15bd0d72e8fa651cd51 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 12:59:15 +0200 Subject: [PATCH 090/142] BUMP pandas and numpy versions --- pyproject.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index e425e4e5a..7d1905270 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -39,9 +39,9 @@ classifiers = [ ] dependencies = [ "click>=8.1.3,<8.2", - "numpy>=1.22,<1.23", + "numpy>=1.22,<1.24", "datalad>=0.15.4,<0.18", - "pandas>=1.4.0,<1.5", + "pandas>=1.4.0,<1.6", "nibabel>=3.2.0,<4.1", "nilearn>=0.9.0,<1.0", "sqlalchemy>=1.4.27,<= 1.5.0", -- 2.52.0 From 858bcf8343fbd466a054bdbbb6d4af36576ebd2d Mon Sep 17 00:00:00 2001 From: LeSasse Date: Wed, 2 Nov 2022 09:59:16 +0100 Subject: [PATCH 091/142] fixing get_elements for aomic piop2 by imposing user-specified constraints; adding some tests --- junifer/datagrabber/aomic/piop2.py | 17 +++++++++++++++++ junifer/datagrabber/aomic/tests/test_piop2.py | 5 +++++ 2 files changed, 22 insertions(+) diff --git a/junifer/datagrabber/aomic/piop2.py b/junifer/datagrabber/aomic/piop2.py index a11ea2e61..0802e7429 100644 --- a/junifer/datagrabber/aomic/piop2.py +++ b/junifer/datagrabber/aomic/piop2.py @@ -119,3 +119,20 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber): patterns=patterns, replacements=replacements, ) + + def get_elements(self): + """Implement fetching list of elements in the dataset. + + Returns + ------- + elements : list + The list of elements that can be grabbed in the dataset after + imposing constraints based on specified tasks. + """ + all_elements = super().get_elements() + constrained_elements = [] + for el in all_elements: + if el[1] in self.tasks: + constrained_elements.append(el) + + return constrained_elements diff --git a/junifer/datagrabber/aomic/tests/test_piop2.py b/junifer/datagrabber/aomic/tests/test_piop2.py index ed448709f..a1b8850d0 100644 --- a/junifer/datagrabber/aomic/tests/test_piop2.py +++ b/junifer/datagrabber/aomic/tests/test_piop2.py @@ -28,6 +28,11 @@ def test_aomic_piop2_datagrabber() -> None: with dg: all_elements = dg.get_elements() + + if task_param == "restingstate": + for el in all_elements: + assert el[1] == "restingstate" + test_element = all_elements[0] sub, task = test_element -- 2.52.0 From 4eb98e10fddac7730c243cc2b363cce3016c8b52 Mon Sep 17 00:00:00 2001 From: LeSasse Date: Wed, 2 Nov 2022 10:03:05 +0100 Subject: [PATCH 092/142] adding entry to latest --- docs/changes/latest.inc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 21aba6c49..b51cb5645 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -79,6 +79,8 @@ Bugs - Fix a bug in which a PatternDatagrabber would now work with relative `datadir` paths. (:gh:`96` by `Leonard Sasse`_, fixed in :gh:`98` by `Fede Raimondo`_). +- Fix a bug in which AOMIC PIOP2 datagrabber did not use user input to constrain elements based on tasks (:gh: `105` by `Leonard Sasse`_) + API changes ~~~~~~~~~~~ -- 2.52.0 From eb87039e5a1edc220fb57c55e92f62d05ab89dc3 Mon Sep 17 00:00:00 2001 From: LeSasse Date: Wed, 2 Nov 2022 10:15:58 +0100 Subject: [PATCH 093/142] change to list comprehension --- junifer/datagrabber/aomic/piop2.py | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/junifer/datagrabber/aomic/piop2.py b/junifer/datagrabber/aomic/piop2.py index 0802e7429..6aeb056c5 100644 --- a/junifer/datagrabber/aomic/piop2.py +++ b/junifer/datagrabber/aomic/piop2.py @@ -130,9 +130,4 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber): imposing constraints based on specified tasks. """ all_elements = super().get_elements() - constrained_elements = [] - for el in all_elements: - if el[1] in self.tasks: - constrained_elements.append(el) - - return constrained_elements + return [x for x in all_elements if x[1] in self.tasks] -- 2.52.0 From 970db8308e4caf66e54ccbd65dee714a057f5193 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 2 Nov 2022 13:53:53 +0100 Subject: [PATCH 094/142] docs: update numpy and pandas version constraints in installation.rst --- docs/installation.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index f52e13d1c..c2f9f0e38 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -10,9 +10,9 @@ Requirements junifer is compatible with `Python`_ >= 3.8 and requires the following packages: * ``click>=8.1.3,<8.2`` -* ``numpy>=1.22,<1.23`` +* ``numpy>=1.22,<1.24`` * ``datalad>=0.15.4,<0.18`` -* ``pandas>=1.4.0,<1.5`` +* ``pandas>=1.4.0,<1.6`` * ``nibabel>=3.2.0,<4.1`` * ``nilearn>=0.9.0,<1.0`` * ``sqlalchemy>=1.4.27,<= 1.5.0`` -- 2.52.0 From a8918abcdfdc2598255d2fe2240fb8e0cf1c8930 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 11:08:45 +0100 Subject: [PATCH 095/142] chore: rename test_parcel.py to test_parcel_aggregation.py --- .../markers/tests/{test_parcel.py => test_parcel_aggregation.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename junifer/markers/tests/{test_parcel.py => test_parcel_aggregation.py} (100%) diff --git a/junifer/markers/tests/test_parcel.py b/junifer/markers/tests/test_parcel_aggregation.py similarity index 100% rename from junifer/markers/tests/test_parcel.py rename to junifer/markers/tests/test_parcel_aggregation.py -- 2.52.0 From 4c63c15b7a3b814e0f2d54655bb0ad19cf949148 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 22:02:50 +0200 Subject: [PATCH 096/142] fix sphinx refs --- docs/api/configs.rst | 9 +++ docs/api/data.rst | 6 ++ docs/api/index.rst | 16 ++++- docs/api/pipeline.rst | 7 +++ docs/api/stats.rst | 7 +++ docs/conf.py | 58 ++++++++++++++++++- docs/understanding/datagrabber.rst | 2 +- junifer/data/atlases.py | 32 +--------- junifer/data/coordinates.py | 3 - junifer/datagrabber/base.py | 2 +- junifer/datagrabber/multiple.py | 2 +- .../markers/functional_connectivity_atlas.py | 6 +- .../functional_connectivity_spheres.py | 7 ++- junifer/markers/sphere_aggregation.py | 2 +- junifer/stats.py | 6 +- junifer/storage/sqlite.py | 6 +- 16 files changed, 120 insertions(+), 51 deletions(-) create mode 100644 docs/api/configs.rst create mode 100644 docs/api/data.rst create mode 100644 docs/api/pipeline.rst create mode 100644 docs/api/stats.rst diff --git a/docs/api/configs.rst b/docs/api/configs.rst new file mode 100644 index 000000000..2a5fe7455 --- /dev/null +++ b/docs/api/configs.rst @@ -0,0 +1,9 @@ +Configs +^^^^^^^ + +Juseless +-------- + +.. automodule:: junifer.configs.juseless + :members: + :imported-members: diff --git a/docs/api/data.rst b/docs/api/data.rst new file mode 100644 index 000000000..eb65e86dc --- /dev/null +++ b/docs/api/data.rst @@ -0,0 +1,6 @@ +Data +^^^^ + +.. automodule:: junifer.data + :members: + :imported-members: diff --git a/docs/api/index.rst b/docs/api/index.rst index 4a16b9f78..9bcdf98ad 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -14,7 +14,6 @@ Pipeline Elements markers storage - Utilities ^^^^^^^^^ @@ -22,6 +21,19 @@ Utilities :maxdepth: 2 :caption: Contents: + data + stats + pipeline api utils - testing \ No newline at end of file + testing + + +Configs +^^^^^^^ + +.. toctree:: + :maxdepth: 2 + :caption: Contents: + + configs diff --git a/docs/api/pipeline.rst b/docs/api/pipeline.rst new file mode 100644 index 000000000..95aaa477b --- /dev/null +++ b/docs/api/pipeline.rst @@ -0,0 +1,7 @@ + +Pipeline +^^^^^^^^ + +.. automodule:: junifer.pipeline + :members: + :imported-members: diff --git a/docs/api/stats.rst b/docs/api/stats.rst new file mode 100644 index 000000000..3fed0b1ed --- /dev/null +++ b/docs/api/stats.rst @@ -0,0 +1,7 @@ + +Stats +^^^^^ + +.. automodule:: junifer.stats + :members: + :imported-members: diff --git a/docs/conf.py b/docs/conf.py index fd12b8dcd..ec3a03f12 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -23,6 +23,20 @@ from pathlib import Path curdir = Path(__file__).parent sys.path.append((curdir / "sphinxext").as_posix()) + +paths_to_add = [ + "junifer/configs/juseless", +] + +for t_path in paths_to_add: + t_path = (curdir.parent / t_path).resolve().as_posix() + sys.path.insert(0, t_path) + + +# sys.path.insert( +# 1, (curdir.parent / "junifer" / "configs" / "juseless").resolve() +# ) + # -- Project information ----------------------------------------------------- project = "junifer" @@ -38,6 +52,7 @@ author = "Fede Raimondo" # ones. extensions = [ "sphinx.ext.autodoc", # include documentation from docstrings + "sphinx_autodoc_typehints", # include type hints from docstrings "sphinx.ext.autosummary", # generate autodoc summaries "sphinx.ext.doctest", # test snippets in the documentation "sphinx.ext.intersphinx", # link to other projects’ documentation @@ -57,6 +72,42 @@ templates_path = ["_templates"] # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +nitpicky = True + +nitpick_ignore_regex = [ + ("py:class", "numpy._typing.*"), + ("py:obj", "trimboth"), # python 3.11 error + ("py:obj", "tmean"), # python 3.11 error + ("py:obj", "subclass"), # python 3.11 error + ("py:class", "typing.Any"), # python 3.11 error + # ('py:class', 'numpy.typing.ArrayLike') +] + +# numpydoc_validation_checks = { +# "all", +# "GL01", +# "GL02", +# "GL03", +# "ES01", +# "SA01", +# "EX01", +# } +numpydoc_xref_param_type = True +numpydoc_xref_aliases = { + "Path": "pathlib.Path", + "Nifti1Image": "nibabel.nifti1.Nifti1Image", + "Nifti2Image": "nibabel.nifti2.Nifti2Image", + "Engine": "sqlalchemy.engine.Engine", +} +numpydoc_xref_ignore = { + "of", + "shape", + "optional", + "or", + "the", + "options", + "function" +} # -- Options for HTML output ------------------------------------------------- @@ -85,10 +136,15 @@ html_static_path = [] # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { - "python": ("https://docs.python.org/", None), + "python": ("https://docs.python.org/3/", None), "sklearn": ("https://scikit-learn.org/stable", None), "nilearn": ("https://nilearn.github.io/stable/", None), "julearn": ("https://juaml.github.io/julearn/main", None), + "nibabel": ("https://nipy.org/nibabel/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "numpy": ("https://numpy.org/doc/stable/", None), + "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None), + "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None), } sphinx_gallery_conf = { diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index 800c3f896..3411e40f1 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -49,5 +49,5 @@ In this section, we showcase different abstract base classes you might want to u - | It implements functionality to deal with Datalad datasets. Specifically, the ``__enter__`` and ``__exit__`` methods | take care of cloning and removing the Datalad dataset. * - :class:`junifer.datagrabber.PatternDataladDataGrabber` - - | It is a combination of :class:`junifer.datagrabber.PatternPatternDataGrabber` and + - | It is a combination of :class:`junifer.datagrabber.PatternDataladDataGrabber` and | :class:`junifer.datagrabber.DataladDataGrabber`. This is probably the class you are looking for when using Datalad. diff --git a/junifer/data/atlases.py b/junifer/data/atlases.py index 9b9bfc3b3..1968ced5a 100644 --- a/junifer/data/atlases.py +++ b/junifer/data/atlases.py @@ -101,7 +101,6 @@ def register_atlas( ValueError If the atlas name is already registered and overwrite is set to False or if the atlas name is a built-in atlas. - """ # Check for attempt of overwriting built-in atlases if name in _available_atlases: @@ -134,7 +133,6 @@ def list_atlases() -> List[str]: ------- list of str A list with all available atlases. - """ return sorted(_available_atlases.keys()) @@ -174,28 +172,6 @@ def load_atlas( path_only : bool, optional If True, the atlas image will not be loaded (default False). - Extra Parameters - ---------------- - Use to specify atlas specific keyword arguments. - - - Schaefer : - n_rois : {100, 200, 300, 400, 500, 600, 700, 800, 900, 1000} - Granularity of atlas to be used. - yeo_network : {7, 17}, optional - Number of yeo networks to use (default 7). - - Tian : - scale : {1, 2, 3, 4} - Scale of atlas (defines granularity). - space : {"MNI6thgeneration", "MNInonlinear2009cAsym"}, optional - Space of atlas (default "MNI6thgeneration"). (For more information - see https://github.com/yetianmed/subcortex) - magneticfield : {"3T", "7T"}, optional - Magnetic field (default "3T"). - - SUIT : - space : {"MNI", "SUIT"}, optional - Space of atlas (default "MNI"). (For more information - see http://www.diedrichsenlab.org/imaging/suit.htm). - Returns ------- niimg-like object or None @@ -204,7 +180,6 @@ def load_atlas( Atlas labels. pathlib.Path File path to the atlas image. - """ # Invalid atlas name if name not in _available_atlases: @@ -261,7 +236,7 @@ def _retrieve_atlas( higher than the desired one. By default, will load the highest one (default None). - Extra Parameters + Other Parameters ---------------- **kwargs Use to specify atlas specific keyword arguments. @@ -295,7 +270,6 @@ def _retrieve_atlas( ------ ValueError If the atlas name is invalid. - """ if atlas_dir is None: atlas_dir = Path().home() / "junifer" / "data" / "atlas" @@ -343,7 +317,6 @@ def _closest_resolution( ------- float The closest valid resolution. - """ # Convert list of int to numpy.ndarray if not isinstance(valid_resolution, np.ndarray): @@ -396,7 +369,6 @@ def _retrieve_schaefer( ValueError If invalid value is provided for `n_rois` or `yeo_networks` or if there is a problem fetching the atlas. - """ logger.info("Atlas parameters:") logger.info(f"\tn_rois: {n_rois}") @@ -503,7 +475,6 @@ def _retrieve_tian( ValueError If invalid value is provided for `scale` or `magneticfield` or `space` or if there is a problem fetching the atlas. - """ # show atlas parameters to user logger.info("Atlas parameters:") @@ -655,7 +626,6 @@ def _retrieve_suit( ValueError If invalid value is provided for `space` or if there is a problem fetching the atlas. - """ logger.info("Atlas parameters:") logger.info(f"\tspace: {space}") diff --git a/junifer/data/coordinates.py b/junifer/data/coordinates.py index 29bd969c4..8d6ef224e 100644 --- a/junifer/data/coordinates.py +++ b/junifer/data/coordinates.py @@ -68,7 +68,6 @@ def register_coordinates( overwrite : bool, optional If True, overwrite an existing list of coordinates with the same name. Does not apply to built-in coordinates (default False). - """ if name in _available_coordinates: if isinstance(_available_coordinates[name], Path): @@ -114,7 +113,6 @@ def list_coordinates() -> List[str]: ------- list of str A list with all available coordinates names. - """ return sorted(_available_coordinates.keys()) @@ -133,7 +131,6 @@ def load_coordinates(name: str) -> Tuple[ArrayLike, List[str]]: The coordinates. list of str The names of the VOIs. - """ if name not in _available_coordinates: raise_error(f"Coordinates {name} not found.") diff --git a/junifer/datagrabber/base.py b/junifer/datagrabber/base.py index a9f5a2a1a..5c42b9727 100644 --- a/junifer/datagrabber/base.py +++ b/junifer/datagrabber/base.py @@ -30,7 +30,6 @@ class BaseDataGrabber(ABC): ---------- datadir : pathlib.Path The directory where the data is / will be stored. - """ def __init__(self, types: List[str], datadir: Union[str, Path]) -> None: @@ -124,6 +123,7 @@ class BaseDataGrabber(ABC): Returns ------- str + The element keys. """ return "element" diff --git a/junifer/datagrabber/multiple.py b/junifer/datagrabber/multiple.py index 606fc82bc..885ea5388 100644 --- a/junifer/datagrabber/multiple.py +++ b/junifer/datagrabber/multiple.py @@ -19,7 +19,7 @@ class MultipleDataGrabber(BaseDataGrabber): Parameters ---------- - datagrabbers : list of datagrabbers + datagrabbers : list of BaseDataGrabber The datagrabbers to use to fetch data using. **kwargs Keyword arguments passed to superclass. diff --git a/junifer/markers/functional_connectivity_atlas.py b/junifer/markers/functional_connectivity_atlas.py index ef0e2deb6..c35d571ba 100644 --- a/junifer/markers/functional_connectivity_atlas.py +++ b/junifer/markers/functional_connectivity_atlas.py @@ -36,10 +36,12 @@ class FunctionalConnectivityAtlas(BaseMarker): :func:`junifer.stats.get_aggfunc_by_name` (default None). cor_method : str, optional The method to perform correlation using. Check valid options in - :func:`nilearn.connectome.ConnectivityMeasure` (default "covariance"). + :external:class:`nilearn.connectome.ConnectivityMeasure` + (default "covariance"). cor_method_params : dict, optional Parameters to pass to the correlation function. Check valid options in - :func:`nilearn.connectome.ConnectivityMeasure` (default None). + :external:class:`nilearn.connectome.ConnectivityMeasure` + (default None). name : str, optional The name of the marker. If None, will use the class name (default None). diff --git a/junifer/markers/functional_connectivity_spheres.py b/junifer/markers/functional_connectivity_spheres.py index 44c9f1dae..16ae49037 100644 --- a/junifer/markers/functional_connectivity_spheres.py +++ b/junifer/markers/functional_connectivity_spheres.py @@ -27,7 +27,7 @@ class FunctionalConnectivitySpheres(BaseMarker): ---------- coords : str The name of the coordinates list to use. See - :mod:`junifer.data.coordinates` for options. + :func:`junifer.data.list_coordinates` for options. radius : float, optional The radius of the sphere in mm. If None, the signal will be extracted from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker` @@ -40,10 +40,11 @@ class FunctionalConnectivitySpheres(BaseMarker): The parameters to pass to the aggregation method (default None). cor_method : str, optional The method to perform correlation using. Check valid options in - :func:`nilearn.connectome.ConnectivityMeasure` (default "covariance"). + :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` + (default "covariance"). cor_method_params : dict, optional Parameters to pass to the correlation function. Check valid options in - :func:`nilearn.connectome.ConnectivityMeasure` (default None). + :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` (default None). name : str, optional The name of the marker. By default, it will use KIND_FunctionalConnectivitySpheres where KIND is the kind of data it diff --git a/junifer/markers/sphere_aggregation.py b/junifer/markers/sphere_aggregation.py index fde777a9b..ee477280f 100644 --- a/junifer/markers/sphere_aggregation.py +++ b/junifer/markers/sphere_aggregation.py @@ -26,7 +26,7 @@ class SphereAggregation(BaseMarker): ---------- coords: str The name of the coordinates list to use. See - :mod:`junifer.data.coordinates` for options. + :func:`junifer.data.list_coordinates` for options. radius: float, optional The radius of the sphere in mm. If None, the signal will be extracted from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker` diff --git a/junifer/stats.py b/junifer/stats.py index 30f910ac2..f108d977f 100644 --- a/junifer/stats.py +++ b/junifer/stats.py @@ -4,7 +4,6 @@ # Synchon Mandal # License: AGPL -from functools import partial from typing import Any, Callable, Dict, Optional import numpy as np @@ -37,8 +36,8 @@ def get_aggfunc_by_name( ------- function Respective function with `func_params` parameter set. - """ + from functools import partial # local import to avoid sphinx error # check validity of names _valid_func_names = {"winsorized_mean", "mean", "std", "trim_mean"} if func_params is None: @@ -65,6 +64,8 @@ def get_aggfunc_by_name( ) logger.info(f"Limits for winsorized mean are set to {limits}.") # partially interpret func_params + + func = partial(winsorized_mean, **func_params) elif name == "mean": func = np.mean @@ -100,7 +101,6 @@ def winsorized_mean( numpy.ndarray Winsorized mean of the inputted data with the winsorize settings applied as specified in win_params. - """ win_dat = winsorize(data, axis=axis, **win_params) win_mean = win_dat.mean(axis=axis) diff --git a/junifer/storage/sqlite.py b/junifer/storage/sqlite.py index 80a3fb1cd..daac3e810 100644 --- a/junifer/storage/sqlite.py +++ b/junifer/storage/sqlite.py @@ -88,7 +88,9 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage): # Set upsert self._upsert = upsert - def get_engine(self, meta: Optional[Dict] = None) -> "Engine": + def get_engine( + self, meta: Optional[Dict] = None + ) -> "Engine": """Get engine. Parameters @@ -98,7 +100,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage): Returns ------- - sqlalchemy.Engine + sqlalchemy.engine.Engine The sqlalchemy engine. """ -- 2.52.0 From f407d8ca149b123e71f2f1b8ea984800aa8eb75c Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:23:33 +0200 Subject: [PATCH 097/142] fix for many things in the documentation, but mostly references --- docs/_static/css/custom.css | 6 ++++ docs/api/configs.rst | 7 +++-- docs/api/data.rst | 12 ++++++-- docs/api/stats.rst | 1 - docs/builtin.rst | 12 ++++---- docs/conf.py | 28 +++++++++++++------ .../juseless/datagrabbers/aomic_id1000_vbm.py | 3 +- .../juseless/datagrabbers/camcan_vbm.py | 3 +- .../configs/juseless/datagrabbers/ixi_vbm.py | 3 +- .../configs/juseless/datagrabbers/ukb_vbm.py | 3 +- junifer/data/atlases.py | 2 +- junifer/datagrabber/aomic/id1000.py | 1 - junifer/datagrabber/aomic/piop1.py | 3 +- junifer/datagrabber/aomic/piop2.py | 3 +- junifer/datagrabber/base.py | 1 - junifer/datagrabber/datalad_base.py | 11 ++++---- junifer/datagrabber/hcp.py | 8 ++---- junifer/datagrabber/multiple.py | 4 +-- junifer/datagrabber/pattern.py | 19 ++++--------- junifer/datagrabber/pattern_datalad.py | 8 +++--- junifer/markers/base.py | 4 +-- junifer/markers/collection.py | 3 +- junifer/markers/ets_rss.py | 5 ++-- .../markers/functional_connectivity_atlas.py | 8 ++---- .../functional_connectivity_spheres.py | 9 +++--- junifer/markers/parcel_aggregation.py | 6 ++-- junifer/markers/sphere_aggregation.py | 18 ++++++------ junifer/stats.py | 4 +-- junifer/storage/base.py | 3 +- junifer/storage/pandas_base.py | 3 +- junifer/storage/sqlite.py | 5 ++-- junifer/testing/datagrabbers.py | 2 -- tox.ini | 1 + 33 files changed, 96 insertions(+), 113 deletions(-) create mode 100644 docs/_static/css/custom.css diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css new file mode 100644 index 000000000..f3f55faed --- /dev/null +++ b/docs/_static/css/custom.css @@ -0,0 +1,6 @@ +.wy-table-responsive table td, .wy-table-responsive table th { + white-space: nowrap; +} +.wy-table-responsive table td a.reference.internal { + overflow-wrap: normal; +} diff --git a/docs/api/configs.rst b/docs/api/configs.rst index 2a5fe7455..372ab36c8 100644 --- a/docs/api/configs.rst +++ b/docs/api/configs.rst @@ -4,6 +4,7 @@ Configs Juseless -------- -.. automodule:: junifer.configs.juseless - :members: - :imported-members: +.. automodule:: junifer.configs.juseless.datagrabbers + :members: + :imported-members: + :special-members: None diff --git a/docs/api/data.rst b/docs/api/data.rst index eb65e86dc..e9b417e73 100644 --- a/docs/api/data.rst +++ b/docs/api/data.rst @@ -1,6 +1,14 @@ Data ^^^^ -.. automodule:: junifer.data +Atlases +------- + +.. automodule:: junifer.data.atlases + :members: + +Coordinates +----------- + +.. automodule:: junifer.data.coordinates :members: - :imported-members: diff --git a/docs/api/stats.rst b/docs/api/stats.rst index 3fed0b1ed..c55efb8a6 100644 --- a/docs/api/stats.rst +++ b/docs/api/stats.rst @@ -4,4 +4,3 @@ Stats .. automodule:: junifer.stats :members: - :imported-members: diff --git a/docs/builtin.rst b/docs/builtin.rst index 19ef11d07..e6ff0b880 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -45,8 +45,8 @@ Available - `HCP OpenAccess dataset `_ - Open with registration - Built-in - - In Progress - - :gh:`4` + - Done + - 0.0.1 * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladUKBVBM` - UKB VBM dataset preprocessed with CAT. Available for Juseless only. - Restricted @@ -77,12 +77,12 @@ Available - Built-in - Done - 0.0.1 - * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICVBM` - - AOMIC VBM dataset. Available for Juseless only. + * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladAOMICID1000VBM` + - AOMIC ID1000 VBM dataset. Available for Juseless only. - Restricted - ``junifer.configs.juseless`` - - In Progress - - :gh:`57` + - Done + - 0.0.1 * - :class:`junifer.configs.juseless.datagrabbers.JuselessDataladIXIVBM` - `IXI VBM dataset `_. Available for Juseless only. - Restricted diff --git a/docs/conf.py b/docs/conf.py index ec3a03f12..2f23a215c 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -24,13 +24,13 @@ curdir = Path(__file__).parent sys.path.append((curdir / "sphinxext").as_posix()) -paths_to_add = [ - "junifer/configs/juseless", -] +# paths_to_add = [ +# "junifer/configs/juseless", +# ] -for t_path in paths_to_add: - t_path = (curdir.parent / t_path).resolve().as_posix() - sys.path.insert(0, t_path) +# for t_path in paths_to_add: +# t_path = (curdir.parent / t_path).resolve().as_posix() +# sys.path.insert(0, t_path) # sys.path.insert( @@ -52,7 +52,6 @@ author = "Fede Raimondo" # ones. extensions = [ "sphinx.ext.autodoc", # include documentation from docstrings - "sphinx_autodoc_typehints", # include type hints from docstrings "sphinx.ext.autosummary", # generate autodoc summaries "sphinx.ext.doctest", # test snippets in the documentation "sphinx.ext.intersphinx", # link to other projects’ documentation @@ -106,9 +105,14 @@ numpydoc_xref_ignore = { "or", "the", "options", - "function" + "function", + "object" } +autoclass_content = "class" +autodoc_typehints = "description" +autodoc_typehints_description_target = "documented" + # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for @@ -132,7 +136,13 @@ html_logo = "./images/junifer_logo.png" # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = [] +html_static_path = ['_static'] + +# These paths are either relative to html_static_path +# or fully qualified paths (eg. https://...) +html_css_files = [ + 'css/custom.css', +] # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { diff --git a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py index 3fba4e07e..0de6fe1f3 100644 --- a/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +++ b/junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py @@ -18,7 +18,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber): Implements a DataGrabber to access the AOMICID1000 VBM data in Juseless. Parameters - ----------- + ---------- datadir : str or pathlib.Path, optional The directory where the datalad dataset will be cloned. If None, the datalad dataset will be cloned into a temporary directory @@ -27,7 +27,6 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber): """ def __init__(self, datadir: Union[str, Path, None] = None) -> None: - """Initialize the class.""" uri = "https://gin.g-node.org/felixh/ds003097_ReproVBM" types = ["VBM_GM"] replacements = ["subject"] diff --git a/junifer/configs/juseless/datagrabbers/camcan_vbm.py b/junifer/configs/juseless/datagrabbers/camcan_vbm.py index 15be14d32..602f90b64 100644 --- a/junifer/configs/juseless/datagrabbers/camcan_vbm.py +++ b/junifer/configs/juseless/datagrabbers/camcan_vbm.py @@ -19,7 +19,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber): Implements a DataGrabber to access the CamCAN VBM data in Juseless. Parameters - ----------- + ---------- datadir : str or pathlib.Path, optional The directory where the datalad dataset will be cloned. If None, the datalad dataset will be cloned into a temporary directory @@ -28,7 +28,6 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber): """ def __init__(self, datadir: Union[str, Path, None] = None) -> None: - """Initialize the class.""" uri = ( "ria+http://cat_12.5.ds.inm7.de" "#a139b26a-8406-11ea-8f94-a0369f287950" diff --git a/junifer/configs/juseless/datagrabbers/ixi_vbm.py b/junifer/configs/juseless/datagrabbers/ixi_vbm.py index 8941795ae..88774898f 100644 --- a/junifer/configs/juseless/datagrabbers/ixi_vbm.py +++ b/junifer/configs/juseless/datagrabbers/ixi_vbm.py @@ -20,7 +20,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber): Implements a DataGrabber to access the IXI VBM data in Juseless. Parameters - ----------- + ---------- datadir : str or pathlib.Path, optional The directory where the datalad dataset will be cloned. If None, the datalad dataset will be cloned into a temporary directory @@ -36,7 +36,6 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber): datadir: Union[str, Path, None] = None, sites: Union[str, List[str], None] = None, ) -> None: - """Initialize the class.""" uri = ( "ria+http://cat_12.5.ds.inm7.de" "#b7107c52-8408-11ea-89c6-a0369f287950" diff --git a/junifer/configs/juseless/datagrabbers/ukb_vbm.py b/junifer/configs/juseless/datagrabbers/ukb_vbm.py index f54f9fea2..24a1fbd61 100644 --- a/junifer/configs/juseless/datagrabbers/ukb_vbm.py +++ b/junifer/configs/juseless/datagrabbers/ukb_vbm.py @@ -19,7 +19,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber): Implements a DataGrabber to access the UKB VBM data in Juseless. Parameters - ----------- + ---------- datadir : str or pathlib.Path, optional The directory where the datalad dataset will be cloned. If None, the datalad dataset will be cloned into a temporary directory @@ -28,7 +28,6 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber): """ def __init__(self, datadir: Union[str, Path, None] = None) -> None: - """Initialize the class.""" uri = "ria+http://ukb.ds.inm7.de#~cat_m0wp1" rootdir = "m0wp1" types = ["VBM_GM"] diff --git a/junifer/data/atlases.py b/junifer/data/atlases.py index 1968ced5a..e84920287 100644 --- a/junifer/data/atlases.py +++ b/junifer/data/atlases.py @@ -174,7 +174,7 @@ def load_atlas( Returns ------- - niimg-like object or None + Nifti1Image or None Loaded atlas image. list of str Atlas labels. diff --git a/junifer/datagrabber/aomic/id1000.py b/junifer/datagrabber/aomic/id1000.py index 64da05fe5..250a78594 100644 --- a/junifer/datagrabber/aomic/id1000.py +++ b/junifer/datagrabber/aomic/id1000.py @@ -34,7 +34,6 @@ class DataladAOMICID1000(PatternDataladDataGrabber): datadir: Union[str, Path, None] = None, **kwargs, ) -> None: - """Initialize the class.""" # The types of data types = [ "BOLD", diff --git a/junifer/datagrabber/aomic/piop1.py b/junifer/datagrabber/aomic/piop1.py index 7bd9683c1..1453f8878 100644 --- a/junifer/datagrabber/aomic/piop1.py +++ b/junifer/datagrabber/aomic/piop1.py @@ -41,7 +41,6 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber): tasks: Union[str, List[str], None] = None, **kwargs, ) -> None: - """Initialize the class.""" # The types of data types = [ "BOLD", @@ -162,7 +161,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber): Returns ------- - elements : list of str + list of str The list of subjects in the dataset. """ diff --git a/junifer/datagrabber/aomic/piop2.py b/junifer/datagrabber/aomic/piop2.py index 6aeb056c5..c773932fd 100644 --- a/junifer/datagrabber/aomic/piop2.py +++ b/junifer/datagrabber/aomic/piop2.py @@ -40,7 +40,6 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber): tasks: Union[str, List[str], None] = None, **kwargs, ) -> None: - """Initialize the class.""" # The types of data types = [ "BOLD", @@ -125,7 +124,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber): Returns ------- - elements : list + list The list of elements that can be grabbed in the dataset after imposing constraints based on specified tasks. """ diff --git a/junifer/datagrabber/base.py b/junifer/datagrabber/base.py index 5c42b9727..ef5cc3ec7 100644 --- a/junifer/datagrabber/base.py +++ b/junifer/datagrabber/base.py @@ -33,7 +33,6 @@ class BaseDataGrabber(ABC): """ def __init__(self, types: List[str], datadir: Union[str, Path]) -> None: - """Initialize the class.""" # Validate types validate_types(types) # Convert str to Path diff --git a/junifer/datagrabber/datalad_base.py b/junifer/datagrabber/datalad_base.py index 918d5dc17..2377736ba 100644 --- a/junifer/datagrabber/datalad_base.py +++ b/junifer/datagrabber/datalad_base.py @@ -46,17 +46,17 @@ class DataladDataGrabber(BaseDataGrabber): Removes the datalad dataset from the `datadir`. This method is called automatically when the datagrabber is used within a context. + See Also + -------- + BaseDataGrabber + For the abstract base class of any datagrabber. + Notes ----- By itself, this class is still abstract as the `__getitem__` method relies on the parent class `BaseDataGrabber.__getitem__` which is not yet implemented. This class is intended to be used as a superclass of a class with multiple inheritance. - - See Also - -------- - BaseDataGrabber - """ def __init__( @@ -66,7 +66,6 @@ class DataladDataGrabber(BaseDataGrabber): uri: Optional[str] = None, **kwargs, ): - """Initialize the class.""" if datadir is None: logger.warning("`datadir` is None, creating a temporary directory") # Create temporary directory diff --git a/junifer/datagrabber/hcp.py b/junifer/datagrabber/hcp.py index 90e975a2a..a65307055 100644 --- a/junifer/datagrabber/hcp.py +++ b/junifer/datagrabber/hcp.py @@ -40,7 +40,6 @@ class HCP1200(PatternDataGrabber): phase_encodings: Union[str, List[str], None] = None, **kwargs, ) -> None: - """Initialize the class.""" # All tasks all_tasks = [ "REST1", @@ -139,12 +138,12 @@ class HCP1200(PatternDataGrabber): return out def get_elements(self) -> List: - """Implement fetching list of subjects in the dataset. + """Implement fetching list of elements in the dataset. Returns ------- - elements : list of str - The list of subjects in the dataset. + list + The list of elements in the dataset. """ subjects = [x.name for x in self.datadir.iterdir() if x.is_dir()] @@ -186,7 +185,6 @@ class DataladHCP1200(DataladDataGrabber, HCP1200): phase_encodings: Union[str, List[str], None] = None, **kwargs, ) -> None: - """Initialize the class.""" uri = ( "https://github.com/datalad-datasets/" "human-connectome-project-openaccess.git" diff --git a/junifer/datagrabber/multiple.py b/junifer/datagrabber/multiple.py index 885ea5388..bb1799364 100644 --- a/junifer/datagrabber/multiple.py +++ b/junifer/datagrabber/multiple.py @@ -23,11 +23,9 @@ class MultipleDataGrabber(BaseDataGrabber): The datagrabbers to use to fetch data using. **kwargs Keyword arguments passed to superclass. - """ def __init__(self, datagrabbers: List[BaseDataGrabber], **kwargs) -> None: - """Initialize the class.""" # TODO: Check datagrabbers consistency # - same element keys # - no overlapping types @@ -73,7 +71,7 @@ class MultipleDataGrabber(BaseDataGrabber): Returns ------- - elements : list + list The list of elements that can be grabbed in the dataset. It corresponds to the elements that are present in all the related datagrabbers. diff --git a/junifer/datagrabber/pattern.py b/junifer/datagrabber/pattern.py index 11e727cd6..e67bcb573 100644 --- a/junifer/datagrabber/pattern.py +++ b/junifer/datagrabber/pattern.py @@ -7,6 +7,7 @@ import re from typing import Dict, List, Tuple, Union +from pathlib import Path import numpy as np @@ -34,13 +35,6 @@ class PatternDataGrabber(BaseDataGrabber): Replacements in the patterns for each item in the "element" tuple. datadir : str or pathlib.Path The directory where the data is / will be stored. - **kwargs - Keyword arguments passed to superclass. - - See Also - -------- - BaseDataGrabber - """ def __init__( @@ -48,9 +42,8 @@ class PatternDataGrabber(BaseDataGrabber): types: List[str], patterns: Dict[str, str], replacements: List[str], - **kwargs, + datadir: Union[str, Path], ) -> None: - """Initialize the class.""" # Validate patterns validate_patterns(types=types, patterns=patterns) @@ -59,7 +52,7 @@ class PatternDataGrabber(BaseDataGrabber): # Validate replacements validate_replacements(replacements=replacements, patterns=patterns) - super().__init__(types=types, **kwargs) + super().__init__(types=types, datadir=datadir) logger.debug("Initializing PatternDataGrabber") logger.debug(f"\tpatterns = {patterns}") logger.debug(f"\treplacements = {replacements}") @@ -195,10 +188,8 @@ class PatternDataGrabber(BaseDataGrabber): Returns ------- - elements : list - The list of elements that can be grabbed in the dataset. Each - element is a subject in the BIDS database. - + list + The list of elements that can be grabbed in the dataset. """ elements = None diff --git a/junifer/datagrabber/pattern_datalad.py b/junifer/datagrabber/pattern_datalad.py index 07e5e296d..dc4d4b570 100644 --- a/junifer/datagrabber/pattern_datalad.py +++ b/junifer/datagrabber/pattern_datalad.py @@ -34,9 +34,10 @@ class PatternDataladDataGrabber(DataladDataGrabber, PatternDataGrabber): See Also -------- - DataladDataGrabber - PatternDataGrabber - + DataladDataGrabber: + Base class for data fetching via Datalad. + PatternDataGrabber: + Base class for pattern-based data fetching. """ def __init__( @@ -45,7 +46,6 @@ class PatternDataladDataGrabber(DataladDataGrabber, PatternDataGrabber): patterns: Dict[str, str], **kwargs, ) -> None: - """Initialize the class.""" # Validate patterns validate_patterns(types=types, patterns=patterns) diff --git a/junifer/markers/base.py b/junifer/markers/base.py index d8f71d2b6..accdc0861 100644 --- a/junifer/markers/base.py +++ b/junifer/markers/base.py @@ -34,7 +34,6 @@ class BaseMarker(ABC, PipelineStepMixin): on: Optional[Union[List[str], str]] = None, name: Optional[str] = None, ) -> None: - """Initialize the class.""" if on is None: on = self.get_valid_inputs() if not isinstance(on, list): @@ -52,8 +51,7 @@ class BaseMarker(ABC, PipelineStepMixin): Returns ------- list of str - The list of data types that can be used as input for this marker - + The list of data types that can be used as input for this marker. """ raise_error( msg="Concrete classes need to implement get_valid_inputs().", diff --git a/junifer/markers/collection.py b/junifer/markers/collection.py index 4fe2a0f33..6688a02cb 100644 --- a/junifer/markers/collection.py +++ b/junifer/markers/collection.py @@ -41,7 +41,6 @@ class MarkerCollection: preprocessing: Optional[PipelineStepMixin] = None, storage: Optional[BaseFeatureStorage] = None, ): - """Initialize the class.""" # Check that the markers have different names marker_names = [m.name for m in markers] if len(set(marker_names)) != len(marker_names): @@ -62,7 +61,7 @@ class MarkerCollection: Parameters ---------- - input + input : dict The input data to fit the pipeline on. Should be the output of indexing the DataGrabber with one element. diff --git a/junifer/markers/ets_rss.py b/junifer/markers/ets_rss.py index d0fd50c15..8b1bdac38 100644 --- a/junifer/markers/ets_rss.py +++ b/junifer/markers/ets_rss.py @@ -29,7 +29,7 @@ class RSSETSMarker(BaseMarker): ---------- atlas : str The name of the atlas. Check valid options by calling - :func:`junifer.data.list_atlases`. + :func:`junifer.data.atlases.list_atlases`. aggregation_method : str, optional The method to perform aggregation using. Check valid options in :func:`junifer.stats.get_aggfunc_by_name` (default "mean"). @@ -45,7 +45,6 @@ class RSSETSMarker(BaseMarker): aggregation_method: str = "mean", name: Optional[str] = None, ) -> None: - """Initialize the class.""" self.atlas = atlas self.aggregation_method = aggregation_method super().__init__(name=name) @@ -56,7 +55,7 @@ class RSSETSMarker(BaseMarker): Returns ------- list of str - The list of data types that can be used as input for this marker + The list of data types that can be used as input for this marker. """ return ["BOLD"] diff --git a/junifer/markers/functional_connectivity_atlas.py b/junifer/markers/functional_connectivity_atlas.py index c35d571ba..ed4f908a3 100644 --- a/junifer/markers/functional_connectivity_atlas.py +++ b/junifer/markers/functional_connectivity_atlas.py @@ -27,7 +27,7 @@ class FunctionalConnectivityAtlas(BaseMarker): ---------- atlas : str The name of the atlas. Check valid options by calling - :func:`junifer.data.list_atlases`. + :func:`junifer.data.atlases.list_atlases`. agg_method : str, optional The method to perform aggregation using. Check valid options in :func:`junifer.stats.get_aggfunc_by_name` (default "mean"). @@ -45,7 +45,6 @@ class FunctionalConnectivityAtlas(BaseMarker): name : str, optional The name of the marker. If None, will use the class name (default None). - """ def __init__( @@ -57,7 +56,6 @@ class FunctionalConnectivityAtlas(BaseMarker): cor_method_params: Optional[Dict] = None, name: Optional[str] = None, ) -> None: - """Initialize the class.""" self.atlas = atlas self.agg_method = agg_method self.agg_method_params = ( @@ -80,8 +78,7 @@ class FunctionalConnectivityAtlas(BaseMarker): Returns ------- list of str - The list of data types that can be used as input for this marker - + The list of data types that can be used as input for this marker. """ return ["BOLD"] @@ -98,7 +95,6 @@ class FunctionalConnectivityAtlas(BaseMarker): ------- list of str The updated list of output kinds, as storage possibilities. - """ outputs = ["matrix"] return outputs diff --git a/junifer/markers/functional_connectivity_spheres.py b/junifer/markers/functional_connectivity_spheres.py index 16ae49037..fd08e2ecb 100644 --- a/junifer/markers/functional_connectivity_spheres.py +++ b/junifer/markers/functional_connectivity_spheres.py @@ -27,7 +27,7 @@ class FunctionalConnectivitySpheres(BaseMarker): ---------- coords : str The name of the coordinates list to use. See - :func:`junifer.data.list_coordinates` for options. + :func:`junifer.data.coordinates.list_coordinates` for options. radius : float, optional The radius of the sphere in mm. If None, the signal will be extracted from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker` @@ -44,7 +44,8 @@ class FunctionalConnectivitySpheres(BaseMarker): (default "covariance"). cor_method_params : dict, optional Parameters to pass to the correlation function. Check valid options in - :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` (default None). + :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` + (default None). name : str, optional The name of the marker. By default, it will use KIND_FunctionalConnectivitySpheres where KIND is the kind of data it @@ -62,7 +63,6 @@ class FunctionalConnectivitySpheres(BaseMarker): cor_method_params: Optional[Dict] = None, name: Optional[str] = None, ) -> None: - """Initialize the class.""" self.coords = coords self.radius = radius if radius is None or radius <= 0: @@ -88,8 +88,7 @@ class FunctionalConnectivitySpheres(BaseMarker): Returns ------- list of str - The list of data types that can be used as input for this marker - + The list of data types that can be used as input for this marker. """ return ["BOLD"] diff --git a/junifer/markers/parcel_aggregation.py b/junifer/markers/parcel_aggregation.py index c75816fe0..465394039 100644 --- a/junifer/markers/parcel_aggregation.py +++ b/junifer/markers/parcel_aggregation.py @@ -29,7 +29,7 @@ class ParcelAggregation(BaseMarker): ---------- atlas : str The name of the atlas. Check valid options by calling - :func:`junifer.data.list_atlases`. + :func:`junifer.data.atlases.list_atlases`. method : str The method to perform aggregation using. Check valid options in :func:`junifer.stats.get_aggfunc_by_name`. @@ -43,7 +43,6 @@ class ParcelAggregation(BaseMarker): name : str, optional The name of the marker. If None, will use the class name (default None). - """ def __init__( @@ -54,7 +53,6 @@ class ParcelAggregation(BaseMarker): on: Union[List[str], str, None] = None, name: Optional[str] = None, ) -> None: - """Initialize the class.""" self.atlas = atlas self.method = method self.method_params = {} if method_params is None else method_params @@ -66,7 +64,7 @@ class ParcelAggregation(BaseMarker): Returns ------- list of str - The list of data types that can be used as input for this marker + The list of data types that can be used as input for this marker. """ return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] diff --git a/junifer/markers/sphere_aggregation.py b/junifer/markers/sphere_aggregation.py index ee477280f..9909caa84 100644 --- a/junifer/markers/sphere_aggregation.py +++ b/junifer/markers/sphere_aggregation.py @@ -24,28 +24,27 @@ class SphereAggregation(BaseMarker): Parameters ---------- - coords: str + + coords : str The name of the coordinates list to use. See - :func:`junifer.data.list_coordinates` for options. - radius: float, optional + :func:`junifer.data.coordinates.list_coordinates` for options. + radius : float, optional The radius of the sphere in mm. If None, the signal will be extracted from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker` for more information (default None). - method: str, optional + method : str, optional The aggregation method to use. See :func:`junifer.stats.get_aggfunc_by_name` for more information (default "mean"). - method_params: dict, optional + method_params : dict, optional The parameters to pass to the aggregation method (default None). - on: list of str, optional + on : list of str, optional The kind of data to apply the marker to. By default, will work on all available data (default None). name : str, optional The name of the marker. By default, it will use KIND_SphereAggregation where KIND is the kind of data it was applied to (default None). - """ - def __init__( self, coords: str, @@ -55,7 +54,6 @@ class SphereAggregation(BaseMarker): on: Optional[List[str]] = None, name: Optional[str] = None, ) -> None: - """Initialize the class.""" self.coords = coords self.radius = radius @@ -77,7 +75,7 @@ class SphereAggregation(BaseMarker): Returns ------- list of str - The list of data types that can be used as input for this marker + The list of data types that can be used as input for this marker. """ return ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"] diff --git a/junifer/stats.py b/junifer/stats.py index f108d977f..aba64ff4f 100644 --- a/junifer/stats.py +++ b/junifer/stats.py @@ -64,8 +64,6 @@ def get_aggfunc_by_name( ) logger.info(f"Limits for winsorized mean are set to {limits}.") # partially interpret func_params - - func = partial(winsorized_mean, **func_params) elif name == "mean": func = np.mean @@ -94,7 +92,7 @@ def winsorized_mean( The axis to calculate winsorized mean on (default None). **win_params : dict Dictionary containing the keyword arguments for the winsorize function. - E.g. {'limits': [0.1, 0.1]} + E.g. ``{'limits': [0.1, 0.1]}``. Returns ------- diff --git a/junifer/storage/base.py b/junifer/storage/base.py index 16513ba7c..29a19b51c 100644 --- a/junifer/storage/base.py +++ b/junifer/storage/base.py @@ -37,7 +37,6 @@ class BaseFeatureStorage(ABC): storage_types: Union[List[str], str], single_output: bool = False, ) -> None: - """Initialize the class.""" self.uri = uri if not isinstance(storage_types, list): storage_types = [storage_types] @@ -49,7 +48,7 @@ class BaseFeatureStorage(ABC): Returns ------- - meta : dict + dict The metadata as a dictionary. """ diff --git a/junifer/storage/pandas_base.py b/junifer/storage/pandas_base.py index eaa2a0a32..da9b5f2b1 100644 --- a/junifer/storage/pandas_base.py +++ b/junifer/storage/pandas_base.py @@ -30,14 +30,13 @@ class PandasBaseFeatureStorage(BaseFeatureStorage): See Also -------- - BaseFeatureStorage + BaseFeatureStorage : The base class for feature storage. """ def __init__( self, uri: Union[str, Path], single_output: bool = False, **kwargs ) -> None: - """Initialize the class.""" super().__init__(uri=uri, single_output=single_output, **kwargs) def _meta_row(self, meta: Dict, meta_md5: str) -> pd.DataFrame: diff --git a/junifer/storage/sqlite.py b/junifer/storage/sqlite.py index daac3e810..3acb1fa34 100644 --- a/junifer/storage/sqlite.py +++ b/junifer/storage/sqlite.py @@ -47,7 +47,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage): See Also -------- - PandasBaseFeatureStorage + PandasBaseFeatureStorage : The base class for Pandas-based feature storage. """ @@ -58,7 +58,6 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage): upsert: str = "update", **kwargs: str, ) -> None: - """Initialize the class.""" # Check upsert argument value if upsert not in ["update", "ignore"]: raise_error( @@ -568,7 +567,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage): Parameters ---------- - data: dict + data : dict The timeseries data to store. meta : dict The metadata as a dictionary. diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index f591fc4b4..af247c6c7 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -17,7 +17,6 @@ class OasisVBMTestingDatagrabber(BaseDataGrabber): """DataGrabber for Oasis VBM testing data.""" def __init__(self) -> None: - """Initialize the class.""" # Create temporary directory datadir = tempfile.mkdtemp() # Define types @@ -75,7 +74,6 @@ class SPMAuditoryTestingDatagrabber(BaseDataGrabber): """ def __init__(self) -> None: - """Initialize the class.""" # Create temporary directory datadir = tempfile.mkdtemp() # Define types diff --git a/tox.ini b/tox.ini index 0cb26f786..f4a6f3e17 100644 --- a/tox.ini +++ b/tox.ini @@ -95,6 +95,7 @@ max-line-length = 79 extend-ignore = B024 # abstract class with no abstract methods D202 + D107 # missing docstring in __init__, incompatible with numpydoc E201 # whitespace after ‘(’ E202 # whitespace before ‘)’ E203 # whitespace before ‘,’, ‘;’, or ‘:’ -- 2.52.0 From e41b0dbf0c0be77b5a06e6c99e042863e3376cf9 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:27:58 +0200 Subject: [PATCH 098/142] Flake --- junifer/markers/sphere_aggregation.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/markers/sphere_aggregation.py b/junifer/markers/sphere_aggregation.py index 9909caa84..c54ca0368 100644 --- a/junifer/markers/sphere_aggregation.py +++ b/junifer/markers/sphere_aggregation.py @@ -24,7 +24,6 @@ class SphereAggregation(BaseMarker): Parameters ---------- - coords : str The name of the coordinates list to use. See :func:`junifer.data.coordinates.list_coordinates` for options. @@ -45,6 +44,7 @@ class SphereAggregation(BaseMarker): The name of the marker. By default, it will use KIND_SphereAggregation where KIND is the kind of data it was applied to (default None). """ + def __init__( self, coords: str, -- 2.52.0 From a18a1cc243582e43df2c58531e3f2b712692935b Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:29:37 +0200 Subject: [PATCH 099/142] Fix CI --- .github/workflows/pypi.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pypi.yml b/.github/workflows/pypi.yml index 8b0b97555..902c7ccd8 100644 --- a/.github/workflows/pypi.yml +++ b/.github/workflows/pypi.yml @@ -16,7 +16,7 @@ jobs: - name: Set up Python 3.10 uses: actions/setup-python@v4 with: - python-version: 3.10 + python-version: '3.10' - name: Install build run: pip install build -- 2.52.0 From 90b607024be1025634fe1d6f484176e8e285e1b1 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:38:18 +0200 Subject: [PATCH 100/142] Fix stats docs --- docs/api/index.rst | 6 +++--- docs/conf.py | 1 + junifer/stats.py | 18 +++++++++++++----- 3 files changed, 17 insertions(+), 8 deletions(-) diff --git a/docs/api/index.rst b/docs/api/index.rst index 9bcdf98ad..cb1209325 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -5,7 +5,7 @@ Pipeline Elements ^^^^^^^^^^^^^^^^^ .. toctree:: - :maxdepth: 2 + :maxdepth: 3 :caption: Contents: datagrabbers @@ -18,7 +18,7 @@ Utilities ^^^^^^^^^ .. toctree:: - :maxdepth: 2 + :maxdepth: 3 :caption: Contents: data @@ -33,7 +33,7 @@ Configs ^^^^^^^ .. toctree:: - :maxdepth: 2 + :maxdepth: 3 :caption: Contents: configs diff --git a/docs/conf.py b/docs/conf.py index 2f23a215c..b0c4f7c91 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -155,6 +155,7 @@ intersphinx_mapping = { "numpy": ("https://numpy.org/doc/stable/", None), "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None), "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None), + "scipy": ("https://docs.scipy.org/doc/scipy/", None), } sphinx_gallery_conf = { diff --git a/junifer/stats.py b/junifer/stats.py index aba64ff4f..964e6a7a5 100644 --- a/junifer/stats.py +++ b/junifer/stats.py @@ -23,13 +23,16 @@ def get_aggfunc_by_name( name : str Name to identify the function. Currently supported names and corresponding functions are: - - 'winsorized_mean' -> scipy.stats.mstats.winsorize - - 'mean' -> numpy.mean - - 'std' -> numpy.std - - 'trim_mean' -> scipy.stats.trim_mean + + * ``winsorized_mean`` -> + :external+scipy:func:`scipy.stats.mstats.winsorize` + * ``mean`` -> :external+numpy:func:`numpy.mean` + * ``std`` -> :external+numpy:func:`numpy.std` + * ``trim_mean`` -> :external+scipy:func:`scipy.stats.trim_mean` + func_params : dict, optional Parameters to pass to the function. - E.g. for 'winsorized_mean': func_params = {'limits': [0.1, 0.1]} + E.g. for `winsorized_mean`: ``func_params = {'limits': [0.1, 0.1]}`` (default None). Returns @@ -99,6 +102,11 @@ def winsorized_mean( numpy.ndarray Winsorized mean of the inputted data with the winsorize settings applied as specified in win_params. + + See Also + -------- + scipy.stats.mstats.winsorize : + The winsorize function used in this function. """ win_dat = winsorize(data, axis=axis, **win_params) win_mean = win_dat.mean(axis=axis) -- 2.52.0 From f23a717247980080a835b79fd9e1aadfc08c8713 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:50:02 +0200 Subject: [PATCH 101/142] more fixes --- docs/api/data.rst | 7 ++----- docs/api/index.rst | 4 ++-- docs/api/pipeline.rst | 7 +++++++ docs/conf.py | 3 ++- junifer/api/__init__.py | 2 +- 5 files changed, 14 insertions(+), 9 deletions(-) diff --git a/docs/api/data.rst b/docs/api/data.rst index e9b417e73..d6b0d857b 100644 --- a/docs/api/data.rst +++ b/docs/api/data.rst @@ -1,14 +1,11 @@ -Data -^^^^ - Atlases -------- +^^^^^^^ .. automodule:: junifer.data.atlases :members: Coordinates ------------ +^^^^^^^^^^^ .. automodule:: junifer.data.coordinates :members: diff --git a/docs/api/index.rst b/docs/api/index.rst index cb1209325..2325c485f 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -5,7 +5,7 @@ Pipeline Elements ^^^^^^^^^^^^^^^^^ .. toctree:: - :maxdepth: 3 + :maxdepth: 2 :caption: Contents: datagrabbers @@ -18,7 +18,7 @@ Utilities ^^^^^^^^^ .. toctree:: - :maxdepth: 3 + :maxdepth: 2 :caption: Contents: data diff --git a/docs/api/pipeline.rst b/docs/api/pipeline.rst index 95aaa477b..7142b0e6e 100644 --- a/docs/api/pipeline.rst +++ b/docs/api/pipeline.rst @@ -5,3 +5,10 @@ Pipeline .. automodule:: junifer.pipeline :members: :imported-members: + +Registry +^^^^^^^^ + +.. automodule:: junifer.pipeline.registry + :members: + :imported-members: diff --git a/docs/conf.py b/docs/conf.py index b0c4f7c91..ff53dc79a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -106,7 +106,8 @@ numpydoc_xref_ignore = { "the", "options", "function", - "object" + "object", + "class" } autoclass_content = "class" diff --git a/junifer/api/__init__.py b/junifer/api/__init__.py index bb976649a..e36a4f6e8 100644 --- a/junifer/api/__init__.py +++ b/junifer/api/__init__.py @@ -5,5 +5,5 @@ # License: AGPL from .cli import cli -from .functions import run, collect +from .functions import run, collect, queue from . import decorators -- 2.52.0 From 609489f7850321a344cdde1870483a9357228ac9 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 00:55:40 +0200 Subject: [PATCH 102/142] Update doc dependencies --- pyproject.toml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 7d1905270..a5b1b7b6d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,11 +61,11 @@ junifer = "junifer.api.cli:cli" dev = ["tox"] docs = [ "seaborn>=0.11.2,<0.12", - "Sphinx>=5.0.2,<5.1", - "sphinx-gallery>=0.10.1,<0.11", - "sphinx-rtd-theme>=1.0.0,<1.1", + "Sphinx>=5.3.0,<5.4", + "sphinx-gallery>=0.11.0,<0.12", + "sphinx-rtd-theme>=1.1.0,<1.2", "sphinx-multiversion>=0.2.4,<0.3", - "numpydoc>=1.4.0,<1.5", + "numpydoc>=1.5.0,<1.6", "julearn==0.2.5" ] -- 2.52.0 From 0c5f96eebe436b2bdf6cc8516c0a4a3ecc06e36d Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 08:43:54 +0200 Subject: [PATCH 103/142] Remove :external: --- junifer/markers/functional_connectivity_atlas.py | 5 ++--- junifer/markers/functional_connectivity_spheres.py | 6 ++---- junifer/stats.py | 9 ++++----- 3 files changed, 8 insertions(+), 12 deletions(-) diff --git a/junifer/markers/functional_connectivity_atlas.py b/junifer/markers/functional_connectivity_atlas.py index ed4f908a3..ffbe8ee40 100644 --- a/junifer/markers/functional_connectivity_atlas.py +++ b/junifer/markers/functional_connectivity_atlas.py @@ -36,12 +36,11 @@ class FunctionalConnectivityAtlas(BaseMarker): :func:`junifer.stats.get_aggfunc_by_name` (default None). cor_method : str, optional The method to perform correlation using. Check valid options in - :external:class:`nilearn.connectome.ConnectivityMeasure` + :class:`nilearn.connectome.ConnectivityMeasure` (default "covariance"). cor_method_params : dict, optional Parameters to pass to the correlation function. Check valid options in - :external:class:`nilearn.connectome.ConnectivityMeasure` - (default None). + :class:`nilearn.connectome.ConnectivityMeasure` (default None). name : str, optional The name of the marker. If None, will use the class name (default None). diff --git a/junifer/markers/functional_connectivity_spheres.py b/junifer/markers/functional_connectivity_spheres.py index fd08e2ecb..d29f4ff9f 100644 --- a/junifer/markers/functional_connectivity_spheres.py +++ b/junifer/markers/functional_connectivity_spheres.py @@ -40,12 +40,10 @@ class FunctionalConnectivitySpheres(BaseMarker): The parameters to pass to the aggregation method (default None). cor_method : str, optional The method to perform correlation using. Check valid options in - :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` - (default "covariance"). + :class:`nilearn.connectome.ConnectivityMeasure` (default "covariance"). cor_method_params : dict, optional Parameters to pass to the correlation function. Check valid options in - :external+nilearn:class:`nilearn.connectome.ConnectivityMeasure` - (default None). + :class:`nilearn.connectome.ConnectivityMeasure` (default None). name : str, optional The name of the marker. By default, it will use KIND_FunctionalConnectivitySpheres where KIND is the kind of data it diff --git a/junifer/stats.py b/junifer/stats.py index 964e6a7a5..caef7ad96 100644 --- a/junifer/stats.py +++ b/junifer/stats.py @@ -24,11 +24,10 @@ def get_aggfunc_by_name( Name to identify the function. Currently supported names and corresponding functions are: - * ``winsorized_mean`` -> - :external+scipy:func:`scipy.stats.mstats.winsorize` - * ``mean`` -> :external+numpy:func:`numpy.mean` - * ``std`` -> :external+numpy:func:`numpy.std` - * ``trim_mean`` -> :external+scipy:func:`scipy.stats.trim_mean` + * ``winsorized_mean`` -> :func:`scipy.stats.mstats.winsorize` + * ``mean`` -> :func:`numpy.mean` + * ``std`` -> :func:`numpy.std` + * ``trim_mean`` -> :func:`scipy.stats.trim_mean` func_params : dict, optional Parameters to pass to the function. -- 2.52.0 From 61577d30c21b0394a5d85db1e70a89928dccce01 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 10:56:12 +0200 Subject: [PATCH 104/142] Fix comments + furo template --- docs/Makefile | 2 +- docs/_static/css/custom.css | 13 ++++++++- docs/_static/js/custom.js | 14 ++++++++++ docs/_templates/versions copy.html | 25 +++++++++++++++++ docs/_templates/versions.html | 44 ++++++++++++++---------------- docs/conf.py | 22 ++++++++++----- junifer/stats.py | 2 +- pyproject.toml | 2 +- 8 files changed, 90 insertions(+), 34 deletions(-) create mode 100644 docs/_static/js/custom.js create mode 100644 docs/_templates/versions copy.html diff --git a/docs/Makefile b/docs/Makefile index 48bb6ad18..4e5d3141d 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?="-W" +SPHINXOPTS ?="" SPHINXBUILD ?= sphinx-multiversion SOURCEDIR = . BUILDDIR ?= _build diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index f3f55faed..149083b3d 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -2,5 +2,16 @@ white-space: nowrap; } .wy-table-responsive table td a.reference.internal { - overflow-wrap: normal; + overflow-wrap: normal; } + +/* Style the button that is used to open and close the collapsible content */ +.version-select { + cursor: pointer; +} + +/* Style the collapsible content. Note: hidden by default */ +#versions { + display: none; + overflow: hidden; +} \ No newline at end of file diff --git a/docs/_static/js/custom.js b/docs/_static/js/custom.js new file mode 100644 index 000000000..c661f2221 --- /dev/null +++ b/docs/_static/js/custom.js @@ -0,0 +1,14 @@ +var coll = document.getElementsByClassName("version-select"); +var i; + +for (i = 0; i < coll.length; i++) { + coll[i].addEventListener("click", function() { + this.classList.toggle("active"); + var content = this.nextElementSibling; + if (content.style.display === "block") { + content.style.display = "none"; + } else { + content.style.display = "block"; + } + }); +} \ No newline at end of file diff --git a/docs/_templates/versions copy.html b/docs/_templates/versions copy.html new file mode 100644 index 000000000..d8299d1ca --- /dev/null +++ b/docs/_templates/versions copy.html @@ -0,0 +1,25 @@ +{% if versions %} +
+

+ Other Versions +

+ +
+{% endif %} diff --git a/docs/_templates/versions.html b/docs/_templates/versions.html index 476c8d195..08b7d02bf 100644 --- a/docs/_templates/versions.html +++ b/docs/_templates/versions.html @@ -1,27 +1,25 @@ -{%- if current_version %} -
- - Other Versions - v: {{ current_version.name }} - - -
- {%- if versions.tags %} -
-
Tags
- {%- for item in versions.tags %} -
{{ item.name }}
- {%- endfor %} -
- {%- endif %} - {%- if versions.branches %} -
-
Branches
+{% if versions %} +
+

+ Other Versions +

+
+ {% if versions.branches %} + {{ _('Branches') }} +
- {%- endif %} + + {% endif %} + {% if versions.tags %} + {{ _('Tags') }} + + {% endif %}
-{%- endif %} \ No newline at end of file +{% endif %} diff --git a/docs/conf.py b/docs/conf.py index ff53dc79a..a4b807212 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -119,17 +119,21 @@ autodoc_typehints_description_target = "documented" # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # -html_theme = "sphinx_rtd_theme" +html_theme = "furo" html_theme_options = { - "display_version": True, - "style_external_links": True, - "logo_only": True, + # "display_version": True, + # "style_external_links": True, + # "logo_only": True, } html_sidebars = { "**": [ - "globaltoc.html", - "sourcelink.html", - "searchbox.html", + "sidebar/scroll-start.html", + "sidebar/brand.html", + "sidebar/search.html", + "sidebar/navigation.html", + "versions.html" + "sidebar/ethical-ads.html", + "sidebar/scroll-end.html", ] } html_logo = "./images/junifer_logo.png" @@ -145,6 +149,10 @@ html_css_files = [ 'css/custom.css', ] +html_js_files = [ + 'js/custom.js', +] + # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { "python": ("https://docs.python.org/3/", None), diff --git a/junifer/stats.py b/junifer/stats.py index caef7ad96..4e2fa18ac 100644 --- a/junifer/stats.py +++ b/junifer/stats.py @@ -31,7 +31,7 @@ def get_aggfunc_by_name( func_params : dict, optional Parameters to pass to the function. - E.g. for `winsorized_mean`: ``func_params = {'limits': [0.1, 0.1]}`` + E.g. for ``winsorized_mean``: ``func_params = {'limits': [0.1, 0.1]}`` (default None). Returns diff --git a/pyproject.toml b/pyproject.toml index a5b1b7b6d..24ab26d5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ docs = [ "seaborn>=0.11.2,<0.12", "Sphinx>=5.3.0,<5.4", "sphinx-gallery>=0.11.0,<0.12", - "sphinx-rtd-theme>=1.1.0,<1.2", + "furo>=2022.9.29,<2023.0.0", "sphinx-multiversion>=0.2.4,<0.3", "numpydoc>=1.5.0,<1.6", "julearn==0.2.5" -- 2.52.0 From 8b23a2120adf4d98b3af497a234b5ba3ed13b99b Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 10:57:15 +0200 Subject: [PATCH 105/142] Revert back this change --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index 4e5d3141d..120e641c3 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?="" +SPHINXOPTS ?="-D" SPHINXBUILD ?= sphinx-multiversion SOURCEDIR = . BUILDDIR ?= _build -- 2.52.0 From a87cbbf837927ff013c183d7196d503e6b0fc7ba Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 10:57:49 +0200 Subject: [PATCH 106/142] typo --- docs/conf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index a4b807212..0c24b4887 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -131,7 +131,7 @@ html_sidebars = { "sidebar/brand.html", "sidebar/search.html", "sidebar/navigation.html", - "versions.html" + "versions.html", "sidebar/ethical-ads.html", "sidebar/scroll-end.html", ] -- 2.52.0 From 671a4f6d12ca9de27e029461ea25d9f7eb75200e Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 10:58:07 +0200 Subject: [PATCH 107/142] another typo --- docs/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/Makefile b/docs/Makefile index 120e641c3..48bb6ad18 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?="-D" +SPHINXOPTS ?="-W" SPHINXBUILD ?= sphinx-multiversion SOURCEDIR = . BUILDDIR ?= _build -- 2.52.0 From ee2ee43d7e3c0d784553ecc98b99f99567d38685 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 11:43:40 +0200 Subject: [PATCH 108/142] Remove rtd theme extension --- docs/conf.py | 21 +-------------------- 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 0c24b4887..a07a086a1 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -23,20 +23,6 @@ from pathlib import Path curdir = Path(__file__).parent sys.path.append((curdir / "sphinxext").as_posix()) - -# paths_to_add = [ -# "junifer/configs/juseless", -# ] - -# for t_path in paths_to_add: -# t_path = (curdir.parent / t_path).resolve().as_posix() -# sys.path.insert(0, t_path) - - -# sys.path.insert( -# 1, (curdir.parent / "junifer" / "configs" / "juseless").resolve() -# ) - # -- Project information ----------------------------------------------------- project = "junifer" @@ -57,7 +43,6 @@ extensions = [ "sphinx.ext.intersphinx", # link to other projects’ documentation "sphinx.ext.mathjax", # math support for HTML outputs in Sphinx "sphinx_gallery.gen_gallery", # HTML gallery of examples - "sphinx_rtd_theme", # RTD theme "sphinx_multiversion", # self-hosted versioned documentation "numpydoc", # support for NumPy style docstrings "gh_substitutions", # custom GitHub substitutions @@ -120,11 +105,7 @@ autodoc_typehints_description_target = "documented" # a list of builtin themes. # html_theme = "furo" -html_theme_options = { - # "display_version": True, - # "style_external_links": True, - # "logo_only": True, -} + html_sidebars = { "**": [ "sidebar/scroll-start.html", -- 2.52.0 From c56a39ffd6e30e26da0233f77aa8a19b4df226e1 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 12:02:33 +0200 Subject: [PATCH 109/142] cleanup + fix tables + fix search index --- docs/Makefile | 2 +- docs/_static/css/custom.css | 6 +++--- docs/_templates/versions copy.html | 25 ------------------------- 3 files changed, 4 insertions(+), 29 deletions(-) delete mode 100644 docs/_templates/versions copy.html diff --git a/docs/Makefile b/docs/Makefile index 48bb6ad18..a58f174d8 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS ?="-W" +SPHINXOPTS ?="-W" "-E" SPHINXBUILD ?= sphinx-multiversion SOURCEDIR = . BUILDDIR ?= _build diff --git a/docs/_static/css/custom.css b/docs/_static/css/custom.css index 149083b3d..518a7e367 100644 --- a/docs/_static/css/custom.css +++ b/docs/_static/css/custom.css @@ -1,7 +1,7 @@ -.wy-table-responsive table td, .wy-table-responsive table th { - white-space: nowrap; +.table-wrapper.colwidths-auto table td, .table-wrapper.colwidths-auto table th { + white-space: nowrap; } -.wy-table-responsive table td a.reference.internal { +.table-wrapper.colwidths-auto table td a.reference.internal { overflow-wrap: normal; } diff --git a/docs/_templates/versions copy.html b/docs/_templates/versions copy.html deleted file mode 100644 index d8299d1ca..000000000 --- a/docs/_templates/versions copy.html +++ /dev/null @@ -1,25 +0,0 @@ -{% if versions %} -
-

- Other Versions -

- -
-{% endif %} -- 2.52.0 From 7822cbbef4648ad71e8de4d78e3c0ff0bcdf071b Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 12:25:18 +0200 Subject: [PATCH 110/142] Changes requested --- docs/conf.py | 3 ++- junifer/datagrabber/multiple.py | 2 +- junifer/markers/functional_connectivity_atlas.py | 10 +++++----- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index a07a086a1..8df7856aa 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -92,7 +92,8 @@ numpydoc_xref_ignore = { "options", "function", "object", - "class" + "class", + "objects" } autoclass_content = "class" diff --git a/junifer/datagrabber/multiple.py b/junifer/datagrabber/multiple.py index bb1799364..ac4370102 100644 --- a/junifer/datagrabber/multiple.py +++ b/junifer/datagrabber/multiple.py @@ -19,7 +19,7 @@ class MultipleDataGrabber(BaseDataGrabber): Parameters ---------- - datagrabbers : list of BaseDataGrabber + datagrabbers : list of datagrabber-like objects The datagrabbers to use to fetch data using. **kwargs Keyword arguments passed to superclass. diff --git a/junifer/markers/functional_connectivity_atlas.py b/junifer/markers/functional_connectivity_atlas.py index ffbe8ee40..4f542cbb4 100644 --- a/junifer/markers/functional_connectivity_atlas.py +++ b/junifer/markers/functional_connectivity_atlas.py @@ -14,7 +14,6 @@ from ..utils import logger from .base import BaseMarker from .parcel_aggregation import ParcelAggregation - if TYPE_CHECKING: from junifer.storage import BaseFeatureStorage @@ -121,10 +120,11 @@ class FunctionalConnectivityAtlas(BaseMarker): dict The computed result as dictionary. The following data will be included in the dictionary: - - data: functional connectivity matrix as a numpy.ndarray. - - row_names: row names as a list - - col_names: column names as a list - - matrix_kind: the kind of matrix (tril, triu or full) + + * data: functional connectivity matrix as a numpy.ndarray. + * row_names: row names as a list + * col_names: column names as a list + * matrix_kind: the kind of matrix (tril, triu or full) """ pa = ParcelAggregation( -- 2.52.0 From 553be9bea288965a75a8e68efa3cf65eea724ee8 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 12:42:07 +0200 Subject: [PATCH 111/142] Fix latest.inc --- docs/changes/latest.inc | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index b51cb5645..112e44300 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -71,7 +71,9 @@ Enhancements - Implement JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID 1000 VBM from juseless (:gh:`57` by `Felix Hoffstaedter`_ and `Synchon Mandal`_) -- Add test for DataladHCP1200 datagrabber (:gh: `93` by `Synchon Mandal`_). +- Add test for DataladHCP1200 datagrabber (:gh:`93` by `Synchon Mandal`_). + +- Change documentation template to furo. Fix references and standardize documentation (:gh:`114` by `Fede Raimondo`_). Bugs ~~~~ @@ -79,7 +81,7 @@ Bugs - Fix a bug in which a PatternDatagrabber would now work with relative `datadir` paths. (:gh:`96` by `Leonard Sasse`_, fixed in :gh:`98` by `Fede Raimondo`_). -- Fix a bug in which AOMIC PIOP2 datagrabber did not use user input to constrain elements based on tasks (:gh: `105` by `Leonard Sasse`_) +- Fix a bug in which AOMIC PIOP2 datagrabber did not use user input to constrain elements based on tasks (:gh:`105` by `Leonard Sasse`_) API changes ~~~~~~~~~~~ -- 2.52.0 From 654b80a0e2478662aed8d48b18d7b5d9263bc546 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:54:37 +0100 Subject: [PATCH 112/142] chore: standardize sphinx section header ordering in docs/api --- docs/api/api.rst | 3 +-- docs/api/configs.rst | 4 ++-- docs/api/data.rst | 4 ++-- docs/api/datagrabbers.rst | 4 ++-- docs/api/datareaders.rst | 5 ++--- docs/api/index.rst | 7 +++---- docs/api/markers.rst | 3 +-- docs/api/pipeline.rst | 5 ++--- docs/api/preprocessing.rst | 3 +-- docs/api/stats.rst | 3 +-- docs/api/storage.rst | 3 +-- docs/api/testing.rst | 3 +-- docs/api/utils.rst | 3 +-- 13 files changed, 20 insertions(+), 30 deletions(-) diff --git a/docs/api/api.rst b/docs/api/api.rst index 106a4e309..449232516 100644 --- a/docs/api/api.rst +++ b/docs/api/api.rst @@ -1,6 +1,5 @@ - API Functions -^^^^^^^^^^^^^^ +============= Main API functions ------------------ diff --git a/docs/api/configs.rst b/docs/api/configs.rst index 372ab36c8..e237fa772 100644 --- a/docs/api/configs.rst +++ b/docs/api/configs.rst @@ -1,10 +1,10 @@ Configs -^^^^^^^ +======= Juseless -------- .. automodule:: junifer.configs.juseless.datagrabbers - :members: + :members: :imported-members: :special-members: None diff --git a/docs/api/data.rst b/docs/api/data.rst index d6b0d857b..2975fe12c 100644 --- a/docs/api/data.rst +++ b/docs/api/data.rst @@ -1,11 +1,11 @@ Atlases -^^^^^^^ +======= .. automodule:: junifer.data.atlases :members: Coordinates -^^^^^^^^^^^ +=========== .. automodule:: junifer.data.coordinates :members: diff --git a/docs/api/datagrabbers.rst b/docs/api/datagrabbers.rst index 974bd303b..8556ab5f0 100644 --- a/docs/api/datagrabbers.rst +++ b/docs/api/datagrabbers.rst @@ -1,5 +1,5 @@ -Data Grabbers -^^^^^^^^^^^^^ +DataGrabbers +============ .. automodule:: junifer.datagrabber :members: diff --git a/docs/api/datareaders.rst b/docs/api/datareaders.rst index 3dee2aa11..28e3d7e62 100644 --- a/docs/api/datareaders.rst +++ b/docs/api/datareaders.rst @@ -1,6 +1,5 @@ - -Data Readers -^^^^^^^^^^^^ +DataReaders +=========== .. automodule:: junifer.datareader :members: diff --git a/docs/api/index.rst b/docs/api/index.rst index 2325c485f..4abc5afa7 100644 --- a/docs/api/index.rst +++ b/docs/api/index.rst @@ -2,7 +2,7 @@ API Reference ============= Pipeline Elements -^^^^^^^^^^^^^^^^^ +----------------- .. toctree:: :maxdepth: 2 @@ -15,7 +15,7 @@ Pipeline Elements storage Utilities -^^^^^^^^^ +--------- .. toctree:: :maxdepth: 2 @@ -28,9 +28,8 @@ Utilities utils testing - Configs -^^^^^^^ +------- .. toctree:: :maxdepth: 3 diff --git a/docs/api/markers.rst b/docs/api/markers.rst index 7c6a34b8d..b9e995b4c 100644 --- a/docs/api/markers.rst +++ b/docs/api/markers.rst @@ -1,6 +1,5 @@ - Markers -^^^^^^^ +======= .. automodule:: junifer.markers :members: diff --git a/docs/api/pipeline.rst b/docs/api/pipeline.rst index 7142b0e6e..1a9b691f4 100644 --- a/docs/api/pipeline.rst +++ b/docs/api/pipeline.rst @@ -1,13 +1,12 @@ - Pipeline -^^^^^^^^ +======== .. automodule:: junifer.pipeline :members: :imported-members: Registry -^^^^^^^^ +======== .. automodule:: junifer.pipeline.registry :members: diff --git a/docs/api/preprocessing.rst b/docs/api/preprocessing.rst index 571bc7b6e..036fddb53 100644 --- a/docs/api/preprocessing.rst +++ b/docs/api/preprocessing.rst @@ -1,6 +1,5 @@ - Pre-processing -^^^^^^^^^^^^^^ +============== .. automodule:: junifer.preprocess :members: diff --git a/docs/api/stats.rst b/docs/api/stats.rst index c55efb8a6..e2243f729 100644 --- a/docs/api/stats.rst +++ b/docs/api/stats.rst @@ -1,6 +1,5 @@ - Stats -^^^^^ +===== .. automodule:: junifer.stats :members: diff --git a/docs/api/storage.rst b/docs/api/storage.rst index 4e785ce60..3b442b4ea 100644 --- a/docs/api/storage.rst +++ b/docs/api/storage.rst @@ -1,6 +1,5 @@ - Storage -^^^^^^^ +======= .. automodule:: junifer.storage :members: diff --git a/docs/api/testing.rst b/docs/api/testing.rst index 0220bd917..0e25f04b3 100644 --- a/docs/api/testing.rst +++ b/docs/api/testing.rst @@ -1,6 +1,5 @@ - Testing -^^^^^^^ +======= .. automodule:: junifer.testing.datagrabbers :members: diff --git a/docs/api/utils.rst b/docs/api/utils.rst index 999a180d3..ad7755127 100644 --- a/docs/api/utils.rst +++ b/docs/api/utils.rst @@ -1,6 +1,5 @@ - Utils -^^^^^ +===== .. automodule:: junifer.utils :members: -- 2.52.0 From 7a2922f4ddf41333f9e149a96f1690026e73594c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:55:26 +0100 Subject: [PATCH 113/142] chore: standardize sphinx section header ordering for docs/understanding --- docs/understanding/data.rst | 4 ++-- docs/understanding/datagrabber.rst | 5 +++-- docs/understanding/datareader.rst | 4 ++-- docs/understanding/marker.rst | 2 +- docs/understanding/preprocess.rst | 2 +- docs/understanding/storage.rst | 4 ++-- 6 files changed, 11 insertions(+), 10 deletions(-) diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index a97483a1f..a109d9955 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -6,7 +6,7 @@ The Data Object =============== Description -^^^^^^^^^^^ +----------- This is the *object* that traverses the steps of the pipeline. It is indeed a dictionary of dictionaries. The first level of keys are the :ref:`data types ` @@ -27,7 +27,7 @@ A point to note is that you never directly interact with the *data object* but i .. _data_types: Data types -^^^^^^^^^^ +---------- .. list-table:: :widths: auto diff --git a/docs/understanding/datagrabber.rst b/docs/understanding/datagrabber.rst index 3411e40f1..93d7a059c 100644 --- a/docs/understanding/datagrabber.rst +++ b/docs/understanding/datagrabber.rst @@ -6,7 +6,7 @@ DataGrabber =========== Description -^^^^^^^^^^^ +----------- The ``DataGrabber`` is an object that can provide an interface to datasets you want to work with in junifer. Every concrete implementation of a datagrabber is aware of a particular dataset's structure and thus allows @@ -26,7 +26,8 @@ to implement your own datagrabber, you need to provide concrete implementations provided. Base classes -^^^^^^^^^^^^ +------------ + In this section, we showcase different abstract base classes you might want to use to implement your own datagrabber. .. list-table:: diff --git a/docs/understanding/datareader.rst b/docs/understanding/datareader.rst index 774f402db..4fffd0d7b 100644 --- a/docs/understanding/datareader.rst +++ b/docs/understanding/datareader.rst @@ -6,7 +6,7 @@ DataReader ========== Description -^^^^^^^^^^^ +----------- The ``DataReader`` is an object that is responsible for actually reading data files in junifer. It reads the value of the key ``path`` for each :ref:`data type ` in the :ref:`Data object ` @@ -20,7 +20,7 @@ For data formats not supported by junifer yet, you can either make your own ``Da `junifer Github`_ and we can help you out. Currently supported file-formats -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +-------------------------------- We already provide a concrete implementation :class:`junifer.datareader.DefaultDataReader` which knows how to read the following file formats: diff --git a/docs/understanding/marker.rst b/docs/understanding/marker.rst index 915f8ed99..749275f20 100644 --- a/docs/understanding/marker.rst +++ b/docs/understanding/marker.rst @@ -6,7 +6,7 @@ Marker ====== Description -^^^^^^^^^^^ +----------- The ``Marker`` is an object that is responsible for feature extraction. It primarily operates on data loaded in memory by :ref:`datareader ` and stored in the ``data`` key of each :ref:`data type ` diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index eea630214..420de2bb7 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -6,7 +6,7 @@ Preprocess ========== Description -^^^^^^^^^^^ +----------- The ``Preprocess`` step of the pipeline is meant for pre-processing before or after :ref:`Marker ` step depending on the use-case. For example, you might want to perform confound removal on ``BOLD`` data before diff --git a/docs/understanding/storage.rst b/docs/understanding/storage.rst index c409809b0..25ceed0b3 100644 --- a/docs/understanding/storage.rst +++ b/docs/understanding/storage.rst @@ -6,7 +6,7 @@ Storage ======= Description -^^^^^^^^^^^ +----------- The ``Storage`` is an object that is responsible for storing extracted features as computed from :ref:`Marker ` step of the pipeline. If the pipeline is provided with a ``storage-like`` object, the extracted features are stored via @@ -25,7 +25,7 @@ For storage interfaces not supported by junifer yet, you can either make your ow implementation of :class:`junifer.storage.BaseFeatureStorage` or open an issue on `junifer Github`_ and we can help you out. Currently supported storage interfaces -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +-------------------------------------- .. list-table:: :widths: auto -- 2.52.0 From a0d542b1388afbb7569e1e87512249416e26e53e Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:56:11 +0100 Subject: [PATCH 114/142] chore: standardize sphinx section header ordering for docs/builtin --- docs/builtin.rst | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/docs/builtin.rst b/docs/builtin.rst index e6ff0b880..35ab80796 100644 --- a/docs/builtin.rst +++ b/docs/builtin.rst @@ -4,8 +4,8 @@ Pipeline steps and atlases ========================== -Data Grabbers -^^^^^^^^^^^^^ +DataGrabbers +------------ .. Provide a list of the DataGrabbers that are implemented or planned. @@ -29,7 +29,7 @@ Data Grabbers following syntax: :gh:`` Available ---------- +~~~~~~~~~ .. list-table:: :widths: auto @@ -92,7 +92,7 @@ Available Planned -------- +~~~~~~~ .. list-table:: :widths: auto @@ -116,23 +116,23 @@ Planned Markers -^^^^^^^ +------- .. Provide a list of the Markers that are implemented or planned. - State: this should indicate the state of the dataset. Valid options are + State: this should indicate the state of the marker. Valid options are - Planned - In Progress - Done Version added: If the status is "Done", the Junifer version in which the - dataset was added. Else, a link to the Github issue or pull request - implementing the dataset. Links to github can be added by using the + marker was added. Else, a link to the Github issue or pull request + implementing the marker. Links to github can be added by using the following syntax: :gh:`` Available ---------- +~~~~~~~~~ .. list-table:: :widths: auto @@ -165,7 +165,7 @@ Available Planned -------- +~~~~~~~ .. list-table:: :widths: auto @@ -195,10 +195,15 @@ Planned Atlases -^^^^^^^ +------- + +.. + Provide a list of the Atlases that are implemented or planned. + + Version added: The Junifer version in which the atlas was added. Available ---------- +~~~~~~~~~ ======== ================= ================================================================================= ============= ==================================================== Name Options Keys Version added Publication @@ -225,7 +230,7 @@ TIAN ``scale``, | ``TianxS1x3TxMNI6thgeneration``, ``TianxS1x3TxMNI Planned -------- +~~~~~~~ ================= ============================================================================== Name Publication -- 2.52.0 From 01ec5cb274a23c3f253b323916ffad9443c7686f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:56:29 +0100 Subject: [PATCH 115/142] chore: remove extra line in docs/contribution --- docs/contribution.rst | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/contribution.rst b/docs/contribution.rst index b510c6a4a..8a5d369c1 100644 --- a/docs/contribution.rst +++ b/docs/contribution.rst @@ -5,7 +5,6 @@ Contributing to junifer ======================= - Setting up the local development environment -------------------------------------------- -- 2.52.0 From 22ccde1f82d847cda2b1fb5f328814a6f43c5a16 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:57:44 +0100 Subject: [PATCH 116/142] chore: standardize sphinx section header ordering for docs/faq --- docs/faq.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/faq.rst b/docs/faq.rst index aed46d33b..a9bc63b14 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -4,12 +4,12 @@ FAQs ==== How do I contribute to junifer? -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +------------------------------- Please follow the :ref:`contribution guidelines `. How do I set up VSCode for contribution? -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +---------------------------------------- The :ref:`contribution guidelines ` apply in general when using VSCode as your IDE as well. -- 2.52.0 From dadc4c910e4c3c05ad191ef949ef56b60a336f90 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:57:55 +0100 Subject: [PATCH 117/142] chore: standardize sphinx section header ordering for docs/maintaining --- docs/maintaining.rst | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/maintaining.rst b/docs/maintaining.rst index 91b463067..5ea1bd14c 100644 --- a/docs/maintaining.rst +++ b/docs/maintaining.rst @@ -4,7 +4,8 @@ Maintaining =========== Versioning -^^^^^^^^^^ +---------- + Version numbers are as follows: *MAJOR.MINOR.MICRO*. Additionally, development version append *devN* where N is the distance (in commits) to the last release. @@ -20,9 +21,10 @@ version "X.Y.Z". Additionally, for every push to main, it will be published as pre-release to TestPypi. Releasing a new version -^^^^^^^^^^^^^^^^^^^^^^^ +----------------------- + Once the milestone is reached (all issues closed), it is time to do a new -release. +release. 1. Open a PR to update documentation: - `docs/changes/latest.inc` should now be renamed to the version to be @@ -54,4 +56,4 @@ release. .. code-block:: bash - git push origin vX.Y.Z \ No newline at end of file + git push origin vX.Y.Z -- 2.52.0 From 9f2836f4dae4f856e1c0f2f7ef41a6c2aefcf9b0 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 17:58:02 +0100 Subject: [PATCH 118/142] chore: standardize sphinx section header ordering for docs/installation --- docs/installation.rst | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index c2f9f0e38..53622ccb7 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -5,7 +5,7 @@ Installing junifer Requirements -^^^^^^^^^^^^ +------------ junifer is compatible with `Python`_ >= 3.8 and requires the following packages: @@ -21,7 +21,8 @@ junifer is compatible with `Python`_ >= 3.8 and requires the following packages: Depending on the installation method, these packages might be installed automatically. Installation -^^^^^^^^^^^^ +------------ + Depending on your use-case, junifer can be installed differently: * Install the :ref:`install_latest_release`. This is the most suitable approach @@ -36,7 +37,7 @@ Either way, we strongly recommend using `virtual environments `_, like so: @@ -48,6 +49,6 @@ Use ``pip`` to install julearn from `PyPI `_, like so: .. _install_development_git: Local Git repository --------------------- +~~~~~~~~~~~~~~~~~~~~ Follow the `detailed contribution guidelines `_. -- 2.52.0 From 825365f3192879d5f235d5e0786584ae9bc6d2e3 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 3 Nov 2022 20:41:06 +0100 Subject: [PATCH 119/142] fix: current unix timestamp in milliseconds for ci-docs.yml --- .github/workflows/ci-docs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci-docs.yml b/.github/workflows/ci-docs.yml index 3bbea84b2..997dca0f8 100644 --- a/.github/workflows/ci-docs.yml +++ b/.github/workflows/ci-docs.yml @@ -21,7 +21,7 @@ jobs: mkdir docs touch docs/conf.py echo '' > coverage.xml - echo '' >> coverage.xml + echo '' >> coverage.xml echo '' >> coverage.xml echo '/home/runner/work/docs/docs' >> coverage.xml echo '' >> coverage.xml -- 2.52.0 From ea6976eee5c73ea50f46bf5dd0292181312db095 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 27 Oct 2022 00:01:58 +0300 Subject: [PATCH 120/142] Confound removal WIP --- junifer/preprocess/__init__.py | 2 +- junifer/preprocess/confounds.py | 351 +++++++---- junifer/preprocess/tests/test_confounds.py | 588 +++++++++--------- junifer/testing/datagrabbers.py | 94 ++- .../tests/test_oasisvmbtesting_datagrabber.py | 29 + .../test_partlycloudytesting_datagrabber.py | 40 ++ 6 files changed, 705 insertions(+), 399 deletions(-) create mode 100644 junifer/testing/tests/test_oasisvmbtesting_datagrabber.py create mode 100644 junifer/testing/tests/test_partlycloudytesting_datagrabber.py diff --git a/junifer/preprocess/__init__.py b/junifer/preprocess/__init__.py index b7016a59d..532763ce5 100644 --- a/junifer/preprocess/__init__.py +++ b/junifer/preprocess/__init__.py @@ -4,4 +4,4 @@ # Leonard Sasse # License: AGPL -from .confounds import BaseConfoundRemover +from .confounds import FMRIPrepConfoundRemover diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index f61f29644..fe121c386 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -5,7 +5,7 @@ # Synchon Mandal # License: AGPL -from typing import TYPE_CHECKING, Dict, List, Optional, Union +from typing import TYPE_CHECKING, Dict, List, Optional, Union, Tuple, Any import numpy as np import pandas as pd @@ -21,8 +21,8 @@ if TYPE_CHECKING: from nibabel import MGHImage, Nifti1Image, Nifti2Image -class BaseConfoundRemover(PipelineStepMixin): - """Base class for confound removal. +class FMRIPrepConfoundRemover(PipelineStepMixin): + """Class for confound removal. Read confound files and select columns according to a pre-defined strategy. @@ -46,8 +46,8 @@ class BaseConfoundRemover(PipelineStepMixin): (default None). spike : float, optional If None, no spike regressor is added. If spike is a float, it will - add a spike regressor for every point at which FD exceeds the - specified float (default None). + add a spike regressor for every point at which framewise displacement + exceeds the specified float (default None). detrend : bool, Optional If True, detrending will be applied on timeseries (before confound removal) (default True). @@ -147,7 +147,7 @@ class BaseConfoundRemover(PipelineStepMixin): If the input does not have the required data. """ - _required_inputs = ["BOLD", "confounds"] + _required_inputs = ["BOLD", "BOLD_confounds"] if any(x not in input for x in _required_inputs): raise_error( msg="Input does not have the required data. \n" @@ -175,51 +175,178 @@ class BaseConfoundRemover(PipelineStepMixin): # Does not add any new keys return input - # TODO: complete type annotations - def _pick_confounds(self, input): + def _pick_confounds(self, input: Dict[str, Any]) -> pd.DataFrame: """Select relevant confounds from the specified file.""" - to_select = [] - confounds_df = input["data"] - confounds_spec = input["names"]["spec"] - # for every confound there is a derivative - # and for every confound + derivative there should be squares - derivatives_to_compute = input["names"].get("derivatives", {}) - squares_to_compute = input["names"].get("squares", {}) - spike_name = input["names"]["spike"] - # Get all the column names according to the strategy - for comp, param in self.strategy.items(): - to_select.extend(confounds_spec[comp][param]) + confounds_format = input["format"] + if confounds_format == "adhoc": + self._map_adhoc_to_fmriprep(input) + elif confounds_format != "fmriprep": + raise ValueError(f"Invalid confounds format {confounds_format}") + + processed_spec = self._process_fmriprep_spec(input) + + ( + to_select, + squares_to_compute, + derivatives_to_compute, + spike_name, + ) = processed_spec + # Copy the confounds + out_df = input["data"].copy() # Add derivatives if needed - to_compute = [x in derivatives_to_compute.keys() for x in to_select] - out_df = confounds_df.copy() - if any(to_compute): - for t_dst, t_src in derivatives_to_compute.items(): - out_df[t_dst] = np.append( # type: ignore - np.diff(out_df[t_src]), 0 - ) # type: ignore + for t_dst, t_src in derivatives_to_compute.items(): + out_df[t_dst] = np.append(np.diff(out_df[t_src]), 0) # Add squares (of base confounds and derivatives) if needed - to_compute = [x in squares_to_compute.keys() for x in to_select] - if any(to_compute): - for t_dst, t_src in squares_to_compute.items(): - out_df[t_dst] = out_df[t_src] ** 2 - out_df = out_df[to_select] + for t_dst, t_src in squares_to_compute.items(): + out_df[t_dst] = out_df[t_src] ** 2 # add binary spike regressor if needed at given threshold if self.spike is not None: - fd = confounds_df[spike_name].copy() + fd = out_df[spike_name].copy() fd.loc[fd > self.spike] = 1 fd.loc[fd != 1] = 0 out_df["spike"] = fd + to_select.append("spike") + # Now pick all the relevant confounds + out_df = out_df[to_select] return out_df + def _process_fmriprep_spec( + self, input: Dict[str, Any] + ) -> Tuple[List, Dict, Dict, str]: + """Process the fmpriprep format spec from the specified file. + + Based on the strategy, find the relevant column names in the dataframe, + as well as the required squared and derivatives to compute. + + Parameters + ---------- + input : dict + Dictionary containing the following keys: + - path: path to the confounds file + - data: the confounds file loaded in memory (dataframe) + - format: format of the confounds file (must be "fmriprep") + + Returns + ------- + to_select : list of str + List of confounds to select from the confounds file, based on the + strategy + squares_to_compute : dict[str, str] + Dictionary containing the missing power2 confounds to compute + (keys) and the corresponding confounds to square (values) + derivatives_to_compute : dict[str, str] + Dictionary containing the missing derivatives confounds to compute + (keys) and the corresponding confounds to compute the derivative + from (values) + spike_name : str + Name of the confound to use for spike detection + + """ + confounds_df = input["data"] + available_vars = confounds_df.columns + + # This function should build this 3 variables + to_select = [] # the list of confounds to select + squares_to_compute = {} # the dictionary of missing squares + derivatives_to_compute = {} # the dictionary of missing derivatives + + basics = { + "motion": [ + "trans_x", + "trans_y", + "trans_z", + "rot_x", + "rot_y", + "rot_z", + ], + "wm_csf": ["csf", "white_matter"], + "global_signal": ["global_signal"], + } + + for t_kind, t_strategy in self.strategy.items(): + t_basics = basics[t_kind] + + if any(x not in available_vars for x in t_basics): + missing = [x for x in t_basics if x not in available_vars] + raise ValueError( + "Invalid confounds file. Missing basic confounds: " + f"{missing}. " + "Check if this file is really an fmriprep confounds file. " + "You can also modify the confound removal strategy." + ) + + to_select.extend(t_basics) + + if t_strategy in ["power2", "full"]: + for x in t_basics: + x_2 = f"{x}_power2" + to_select.append(x_2) + if x_2 not in available_vars: + squares_to_compute[x_2] = x + + if t_strategy in ["derivatives", "full"]: + for x in t_basics: + x_derivative = f"{x}_derivative1" + to_select.append(x_derivative) + if x_derivative not in available_vars: + derivatives_to_compute[x_derivative] = x + if t_strategy == "full": + x_derivative_2 = f"{x_derivative}_power2" + to_select.append(x_derivative_2) + if x_derivative_2 not in available_vars: + squares_to_compute[x_derivative_2] = x_derivative + spike_name = "framewise_displacement" + + out = to_select, squares_to_compute, derivatives_to_compute, spike_name + return out + + def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]): + """Map the adhoc format to the fmpriprep format spec. + + Based on the spec, map the column names to match the fmriprep format. + + This method modifies the dataframe in place. + + Parameters + ---------- + input : dict + Dictionary containing the following keys: + - path: path to the confounds file + - data: the confounds file loaded in memory (dataframe) + - format: format of the confounds file (must be "adhoc") + """ + + confounds_df = input["data"] + + # This is an + confounds_mapping = input["mappings"] + + # Check that all the required columns are present + missing = [ + x + for x in confounds_mapping.keys() + if x not in confounds_df.columns + ] + + if len(missing) is not None: + raise ValueError( + "Invalid confounds file. Missing columns: " + f"{missing}. " + "Check if this file matches the adhoc specification for " + "this dataset." + ) + + # Rename the columns + confounds_df.rename(columns=confounds_mapping, inplace=True) + def _remove_confounds( self, bold_img: "Nifti1Image", confounds_df: pd.DataFrame ) -> Union["Nifti1Image", "Nifti2Image", "MGHImage", List]: - """Remove confounds from the BOLD data.""" """Remove confounds from the BOLD image. Parameters @@ -267,19 +394,18 @@ class BaseConfoundRemover(PipelineStepMixin): return clean_bold - # TODO: complete type annotations - def _validate_data(self, input): + def _validate_data(self, input: Dict[str, Any]): """Validate input data.""" # Bold must be 4D niimg check_niimg_4d(input["BOLD"]["data"]) # Confounds must be a dataframe - if not isinstance(input["confounds"]["data"], pd.DataFrame): + if not isinstance(input["BOLD_confounds"]["data"], pd.DataFrame): raise_error( - "confounds data must be a pandas dataframe", ValueError + "Confounds data must be a pandas dataframe", ValueError ) - confound_df = input["confounds"]["data"] + confound_df = input["BOLD_confounds"]["data"] bold_img = input["BOLD"]["data"] if bold_img.get_fdata().shape[3] != len(confound_df): raise_error( @@ -308,95 +434,96 @@ class BaseConfoundRemover(PipelineStepMixin): # 'full', [(list of columns)]} # } - # Check the columns in the dataframe - conf_spec = input["confounds"]["names"]["spec"] - if any(x not in conf_spec.keys() for x in self._valid_components): - raise_error( - "All of the component types must be in the confounds data " - "object `spec`. Please check your datagrabber.", - ValueError, - ) + # # Check the columns in the dataframe + # conf_spec = input["confounds"]["names"]["spec"] + # if any(x not in conf_spec.keys() for x in self._valid_components): + # raise_error( + # "All of the component types must be in the confounds data " + # "object `spec`. Please check your datagrabber.", + # ValueError, + # ) - if any( - x not in v.keys() - for x in self._valid_confounds - for v in conf_spec.values() - ): - raise_error( - "All of the confound types must be in the confounds data " - "object `spec`. Please check your datagrabber.", - ValueError, - ) + # if any( + # x not in v.keys() + # for x in self._valid_confounds + # for v in conf_spec.values() + # ): + # raise_error( + # "All of the confound types must be in the confounds data " + # "object `spec`. Please check your datagrabber.", + # ValueError, + # ) - spike_name = input["confounds"]["names"]["spike"] + # spike_name = input["confounds"]["names"]["spike"] - derivatives_to_compute = input["confounds"]["names"].get( - "derivatives", {} - ) - if not (isinstance(derivatives_to_compute, dict)): - raise_error( - 'input["confounds"]["names"]["derivatives"] ' - "must be a dictionary. Please check your datagrabber", - ValueError, - ) + # derivatives_to_compute = input["confounds"]["names"].get( + # "derivatives", {} + # ) + # if not (isinstance(derivatives_to_compute, dict)): + # raise_error( + # 'input["confounds"]["names"]["derivatives"] ' + # "must be a dictionary. Please check your datagrabber", + # ValueError, + # ) - if any( - not (isinstance(k, str) or isinstance(v, str)) - for k, v in derivatives_to_compute.items() - ): - raise_error( - 'input["confounds"]["names"]["derivatives"] ' - "must be a dictionary with string keys and values. " - "Please check your datagrabber", - ValueError, - ) + # if any( + # not (isinstance(k, str) or isinstance(v, str)) + # for k, v in derivatives_to_compute.items() + # ): + # raise_error( + # 'input["confounds"]["names"]["derivatives"] ' + # "must be a dictionary with string keys and values. " + # "Please check your datagrabber", + # ValueError, + # ) - missing_derivatives = [ - x - for x in derivatives_to_compute.values() - if x not in confound_df.columns - ] - if len(missing_derivatives) > 0: - raise_error( - "Some of the derivatives to calculate are not in the confounds" - f" dataframe: {missing_derivatives}." - "Please check your data " - f'({input["confounds"]["path"].as_posix()}) ' - "and the datagrabber.", - ValueError, - ) + # missing_derivatives = [ + # x + # for x in derivatives_to_compute.values() + # if x not in confound_df.columns + # ] + # if len(missing_derivatives) > 0: + # raise_error( + # "Some of the derivatives to calculate are not in the " + # "confounds" + # f" dataframe: {missing_derivatives}." + # "Please check your data " + # f'({input["confounds"]["path"].as_posix()}) ' + # "and the datagrabber.", + # ValueError, + # ) - t_conf_spec = { - k: input["confounds"]["names"]["spec"][k][v] - for k, v in self.strategy.items() - } + # t_conf_spec = { + # k: input["confounds"]["names"]["spec"][k][v] + # for k, v in self.strategy.items() + # } - column_names = set([x for y in t_conf_spec.values() for x in y]) - column_names.add(spike_name) + # column_names = set([x for y in t_conf_spec.values() for x in y]) + # column_names.add(spike_name) - missing_columns = [ - x - for x in column_names - if x not in confound_df.columns - and x not in derivatives_to_compute.keys() - ] + # missing_columns = [ + # x + # for x in column_names + # if x not in confound_df.columns + # and x not in derivatives_to_compute.keys() + # ] - if len(missing_columns) > 0: - raise_error( - "Some of the columns in the confound spec are not in the " - f"confounds dataframe: {missing_columns}. " - "Please check your data " - f'({input["confounds"]["path"].as_posix()}) ' - "and the datagrabber.", - ValueError, - ) + # if len(missing_columns) > 0: + # raise_error( + # "Some of the columns in the confound spec are not in the " + # f"confounds dataframe: {missing_columns}. " + # "Please check your data " + # f'({input["confounds"]["path"].as_posix()}) ' + # "and the datagrabber.", + # ValueError, + # ) # TODO: complete type annotations def fit_transform(self, input): """Fit and transform.""" self._validate_data(input) bold_img = input["BOLD"]["data"] - confounds_df = self._pick_confounds(input["confounds"]) + confounds_df = self._pick_confounds(input["BOLD_confounds"]) input["BOLD"]["data"] = self._remove_confounds(bold_img, confounds_df) # TODO: Update meta diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 8050e1d2d..2dfe9a8f4 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -5,343 +5,361 @@ # Synchon Mandal # License: AGPL -import random -import string -from pathlib import Path -from typing import Tuple -import numpy as np -import pandas as pd -from nibabel import Nifti1Image -from nilearn._utils.niimg_conversions import check_niimg_4d - -from junifer.preprocess.confounds import BaseConfoundRemover +from numpy.testing import assert_array_equal, assert_raises +from junifer.preprocess.confounds import FMRIPrepConfoundRemover +from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber +from junifer.datareader import DefaultDataReader # Set RNG seed for reproducibility -np.random.seed(1234567) +# np.random.seed(1234567) -def generate_conf_name( - size: int = 6, chars: str = string.ascii_uppercase + string.digits -) -> str: - """Generate configuration name.""" - return "".join(random.choice(chars) for _ in range(size)) +# def generate_conf_name( +# size: int = 6, chars: str = string.ascii_uppercase + string.digits +# ) -> str: +# """Generate configuration name.""" +# return "".join(random.choice(chars) for _ in range(size)) -def _simu_img() -> Tuple[Nifti1Image, Nifti1Image]: - # Random 4D volume with 100 time points - vol = 100 + 10 * np.random.randn(5, 5, 2, 100) - img = Nifti1Image(vol, np.eye(4)) - # Create an nifti image with the data, and corresponding mask - mask = Nifti1Image(np.ones([5, 5, 2]), np.eye(4)) - return img, mask +# def _simu_img() -> Tuple[Nifti1Image, Nifti1Image]: +# # Random 4D volume with 100 time points +# vol = 100 + 10 * np.random.randn(5, 5, 2, 100) +# img = Nifti1Image(vol, np.eye(4)) +# # Create an nifti image with the data, and corresponding mask +# mask = Nifti1Image(np.ones([5, 5, 2]), np.eye(4)) +# return img, mask -# TODO: split the tests -def test_baseconfoundremover() -> None: - """Test BaseConfoundRemover.""" - # Generate a simulated BOLD img - siimg, simsk = _simu_img() +def test_FMRIPrepConfoundRemover_allpresent() -> None: + """Test FMRIPrepConfoundRemover with all confounds present.""" - # generate random confound dataframe with Felix's column naming + # need reader for the data + reader = DefaultDataReader() + # All strategies full, no spike + confound_remover = FMRIPrepConfoundRemover() - motion_basic = [f"RP.{i}" for i in range(1, 7)] - motion_power2 = [f"RP^2.{i}" for i in range(1, 7)] - motion_derivatives = [f"DRP.{i}" for i in range(1, 7)] - motion_full = [f"DRP^2.{i}" for i in range(1, 7)] + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + orig_bold = input["BOLD"]["data"].get_fdata().copy() + output = confound_remover.fit_transform(input) + trans_bold = output["BOLD"]["data"].get_fdata() + # Transformation is in place + assert_array_equal(trans_bold, input["BOLD"]["data"].get_fdata()) - wm_csf_basic = ["WM", "CSF"] - wm_csf_power2 = ["WM^2", "CSF^2"] - wm_csf_derivatives = ["DWM", "DCSF"] - wm_csf_full = ["DWM^2", "DCSF^2"] + # Data should have the same shape + assert orig_bold.shape == trans_bold.shape + assert_raises( + AssertionError, assert_array_equal, orig_bold, trans_bold + ) - gs_basic = ["GS"] - gs_power2 = ["GS^2"] - gs_derivatives = ["DGS"] - gs_full = ["DGS^2"] - confound_column_names = [] +# # TODO: split the tests +# def test_baseconfoundremover() -> None: +# """Test BaseConfoundRemover.""" +# # Generate a simulated BOLD img +# siimg, simsk = _simu_img() - confound_column_names.append("FD") # spike +# # generate random confound dataframe with Felix's column naming - confound_column_names.extend(motion_basic) - confound_column_names.extend(motion_power2) - confound_column_names.extend(motion_derivatives) - confound_column_names.extend(motion_full) +# motion_basic = [f"RP.{i}" for i in range(1, 7)] +# motion_power2 = [f"RP^2.{i}" for i in range(1, 7)] +# motion_derivatives = [f"DRP.{i}" for i in range(1, 7)] +# motion_full = [f"DRP^2.{i}" for i in range(1, 7)] - confound_column_names.extend(wm_csf_basic) - confound_column_names.extend(wm_csf_power2) - confound_column_names.extend(wm_csf_derivatives) - confound_column_names.extend(wm_csf_full) +# wm_csf_basic = ["WM", "CSF"] +# wm_csf_power2 = ["WM^2", "CSF^2"] +# wm_csf_derivatives = ["DWM", "DCSF"] +# wm_csf_full = ["DWM^2", "DCSF^2"] - confound_column_names.extend(gs_basic) - confound_column_names.extend(gs_power2) - confound_column_names.extend(gs_derivatives) - confound_column_names.extend(gs_full) +# gs_basic = ["GS"] +# gs_power2 = ["GS^2"] +# gs_derivatives = ["DGS"] +# gs_full = ["DGS^2"] - # add some random irrelevant confounds - for _ in range(10): - confound_column_names.append(generate_conf_name()) +# confound_column_names = [] - np.random.shuffle(confound_column_names) - n_cols = len(confound_column_names) - confounds_df = pd.DataFrame( - np.random.randint(0, 100, size=(100, n_cols)), - columns=confound_column_names, - ) +# confound_column_names.append("FD") # spike - # Generate spec from Felix's column naming - spec = { - "motion": { - "basic": motion_basic, - "power2": motion_basic + motion_power2, - "derivatives": motion_basic + motion_derivatives, - "full": motion_basic - + motion_derivatives - + motion_power2 - + motion_full, - }, - "wm_csf": { - "basic": wm_csf_basic, - "power2": wm_csf_basic + wm_csf_power2, - "derivatives": wm_csf_basic + wm_csf_derivatives, - "full": wm_csf_basic - + wm_csf_derivatives - + wm_csf_power2 - + wm_csf_full, - }, - "global_signal": { - "basic": gs_basic, - "power2": gs_basic + gs_power2, - "derivatives": gs_basic + gs_derivatives, - "full": gs_basic + gs_derivatives + gs_power2 + gs_full, - }, - } +# confound_column_names.extend(motion_basic) +# confound_column_names.extend(motion_power2) +# confound_column_names.extend(motion_derivatives) +# confound_column_names.extend(motion_full) - # generate a junifer pipeline data object dictionary - input_data_obj = {} - input_data_obj["meta"] = {} - input_data_obj["BOLD"] = {} - input_data_obj["BOLD"]["data"] = siimg - input_data_obj["confounds"] = {} - input_data_obj["confounds"]["path"] = Path("/test.df") - input_data_obj["confounds"]["data"] = confounds_df - input_data_obj["confounds"]["names"] = {} - input_data_obj["confounds"]["names"]["spec"] = spec - input_data_obj["confounds"]["names"]["spike"] = "FD" +# confound_column_names.extend(wm_csf_basic) +# confound_column_names.extend(wm_csf_power2) +# confound_column_names.extend(wm_csf_derivatives) +# confound_column_names.extend(wm_csf_full) - # generate confound removal strategies with varying numbers of parameters +# confound_column_names.extend(gs_basic) +# confound_column_names.extend(gs_power2) +# confound_column_names.extend(gs_derivatives) +# confound_column_names.extend(gs_full) - # Test #1: 36 params, no derivatives to compute, no spike - # 36 params - strat1 = {"motion": "full", "wm_csf": "full", "global_signal": "full"} +# # add some random irrelevant confounds +# for _ in range(10): +# confound_column_names.append(generate_conf_name()) - cr = BaseConfoundRemover( - strategy=strat1, spike=None, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# np.random.shuffle(confound_column_names) +# n_cols = len(confound_column_names) +# confounds_df = pd.DataFrame( +# np.random.randint(0, 100, size=(100, n_cols)), +# columns=confound_column_names, +# ) - assert "BOLD" in out_type +# # Generate spec from Felix's column naming +# spec = { +# "motion": { +# "basic": motion_basic, +# "power2": motion_basic + motion_power2, +# "derivatives": motion_basic + motion_derivatives, +# "full": motion_basic +# + motion_derivatives +# + motion_power2 +# + motion_full, +# }, +# "wm_csf": { +# "basic": wm_csf_basic, +# "power2": wm_csf_basic + wm_csf_power2, +# "derivatives": wm_csf_basic + wm_csf_derivatives, +# "full": wm_csf_basic +# + wm_csf_derivatives +# + wm_csf_power2 +# + wm_csf_full, +# }, +# "global_signal": { +# "basic": gs_basic, +# "power2": gs_basic + gs_power2, +# "derivatives": gs_basic + gs_derivatives, +# "full": gs_basic + gs_derivatives + gs_power2 + gs_full, +# }, +# } - # Check if the input data is valid - cr._validate_data(input_data_obj) +# # generate a junifer pipeline data object dictionary +# input_data_obj = {} +# input_data_obj["meta"] = {} +# input_data_obj["BOLD"] = {} +# input_data_obj["BOLD"]["data"] = siimg +# input_data_obj["confounds"] = {} +# input_data_obj["confounds"]["path"] = Path("/test.df") +# input_data_obj["confounds"]["data"] = confounds_df +# input_data_obj["confounds"]["names"] = {} +# input_data_obj["confounds"]["names"]["spec"] = spec +# input_data_obj["confounds"]["names"]["spike"] = "FD" - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 36 - assert all(x in t_df.columns for x in motion_basic) - assert all(x in t_df.columns for x in motion_power2) - assert all(x in t_df.columns for x in motion_derivatives) - assert all(x in t_df.columns for x in motion_full) - assert all(x in t_df.columns for x in wm_csf_basic) - assert all(x in t_df.columns for x in wm_csf_power2) - assert all(x in t_df.columns for x in wm_csf_derivatives) - assert all(x in t_df.columns for x in wm_csf_full) - assert all(x in t_df.columns for x in gs_basic) - assert all(x in t_df.columns for x in gs_power2) - assert all(x in t_df.columns for x in gs_derivatives) - assert all(x in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" not in t_df.columns +# # generate confound removal strategies with varying numbers of parameters - # Test #2: 24 params, no derivatives to compute, no spike - # 24 params - strat2 = { - "motion": "full", - } +# # Test #1: 36 params, no derivatives to compute, no spike +# # 36 params +# strat1 = {"motion": "full", "wm_csf": "full", "global_signal": "full"} - cr = BaseConfoundRemover( - strategy=strat2, spike=None, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# cr = BaseConfoundRemover( +# strategy=strat1, spike=None, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) - assert "BOLD" in out_type +# assert "BOLD" in out_type - # Check if the input data is valid - cr._validate_data(input_data_obj) +# # Check if the input data is valid +# cr._validate_data(input_data_obj) - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 24 - assert all(x in t_df.columns for x in motion_basic) - assert all(x in t_df.columns for x in motion_power2) - assert all(x in t_df.columns for x in motion_derivatives) - assert all(x in t_df.columns for x in motion_full) - assert all(x not in t_df.columns for x in wm_csf_basic) - assert all(x not in t_df.columns for x in wm_csf_power2) - assert all(x not in t_df.columns for x in wm_csf_derivatives) - assert all(x not in t_df.columns for x in wm_csf_full) - assert all(x not in t_df.columns for x in gs_basic) - assert all(x not in t_df.columns for x in gs_power2) - assert all(x not in t_df.columns for x in gs_derivatives) - assert all(x not in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" not in t_df.columns +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 36 +# assert all(x in t_df.columns for x in motion_basic) +# assert all(x in t_df.columns for x in motion_power2) +# assert all(x in t_df.columns for x in motion_derivatives) +# assert all(x in t_df.columns for x in motion_full) +# assert all(x in t_df.columns for x in wm_csf_basic) +# assert all(x in t_df.columns for x in wm_csf_power2) +# assert all(x in t_df.columns for x in wm_csf_derivatives) +# assert all(x in t_df.columns for x in wm_csf_full) +# assert all(x in t_df.columns for x in gs_basic) +# assert all(x in t_df.columns for x in gs_power2) +# assert all(x in t_df.columns for x in gs_derivatives) +# assert all(x in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" not in t_df.columns - # Test #3: 9 params, no derivatives to compute, no spike - strat3 = {"motion": "basic", "wm_csf": "basic", "global_signal": "basic"} +# # Test #2: 24 params, no derivatives to compute, no spike +# # 24 params +# strat2 = { +# "motion": "full", +# } - cr = BaseConfoundRemover( - strategy=strat3, spike=None, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# cr = BaseConfoundRemover( +# strategy=strat2, spike=None, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) - assert "BOLD" in out_type +# assert "BOLD" in out_type - # Check if the input data is valid - cr._validate_data(input_data_obj) +# # Check if the input data is valid +# cr._validate_data(input_data_obj) - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 9 - assert all(x in t_df.columns for x in motion_basic) - assert all(x not in t_df.columns for x in motion_power2) - assert all(x not in t_df.columns for x in motion_derivatives) - assert all(x not in t_df.columns for x in motion_full) - assert all(x in t_df.columns for x in wm_csf_basic) - assert all(x not in t_df.columns for x in wm_csf_power2) - assert all(x not in t_df.columns for x in wm_csf_derivatives) - assert all(x not in t_df.columns for x in wm_csf_full) - assert all(x in t_df.columns for x in gs_basic) - assert all(x not in t_df.columns for x in gs_power2) - assert all(x not in t_df.columns for x in gs_derivatives) - assert all(x not in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" not in t_df.columns +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 24 +# assert all(x in t_df.columns for x in motion_basic) +# assert all(x in t_df.columns for x in motion_power2) +# assert all(x in t_df.columns for x in motion_derivatives) +# assert all(x in t_df.columns for x in motion_full) +# assert all(x not in t_df.columns for x in wm_csf_basic) +# assert all(x not in t_df.columns for x in wm_csf_power2) +# assert all(x not in t_df.columns for x in wm_csf_derivatives) +# assert all(x not in t_df.columns for x in wm_csf_full) +# assert all(x not in t_df.columns for x in gs_basic) +# assert all(x not in t_df.columns for x in gs_power2) +# assert all(x not in t_df.columns for x in gs_derivatives) +# assert all(x not in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" not in t_df.columns - # Test #4: 6 params, no derivatives to compute, no spike - strat4 = { - "motion": "basic", - } - cr = BaseConfoundRemover( - strategy=strat4, spike=None, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# # Test #3: 9 params, no derivatives to compute, no spike +# strat3 = {"motion": "basic", "wm_csf": "basic", "global_signal": "basic"} - assert "BOLD" in out_type +# cr = BaseConfoundRemover( +# strategy=strat3, spike=None, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) - # Check if the input data is valid - cr._validate_data(input_data_obj) +# assert "BOLD" in out_type - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 6 - assert all(x in t_df.columns for x in motion_basic) - assert all(x not in t_df.columns for x in motion_power2) - assert all(x not in t_df.columns for x in motion_derivatives) - assert all(x not in t_df.columns for x in motion_full) - assert all(x not in t_df.columns for x in wm_csf_basic) - assert all(x not in t_df.columns for x in wm_csf_power2) - assert all(x not in t_df.columns for x in wm_csf_derivatives) - assert all(x not in t_df.columns for x in wm_csf_full) - assert all(x not in t_df.columns for x in gs_basic) - assert all(x not in t_df.columns for x in gs_power2) - assert all(x not in t_df.columns for x in gs_derivatives) - assert all(x not in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" not in t_df.columns +# # Check if the input data is valid +# cr._validate_data(input_data_obj) - # Test #5: 2 params, no derivatives to compute, no spike - strat5 = { - "wm_csf": "basic", - } - cr = BaseConfoundRemover( - strategy=strat5, spike=None, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 9 +# assert all(x in t_df.columns for x in motion_basic) +# assert all(x not in t_df.columns for x in motion_power2) +# assert all(x not in t_df.columns for x in motion_derivatives) +# assert all(x not in t_df.columns for x in motion_full) +# assert all(x in t_df.columns for x in wm_csf_basic) +# assert all(x not in t_df.columns for x in wm_csf_power2) +# assert all(x not in t_df.columns for x in wm_csf_derivatives) +# assert all(x not in t_df.columns for x in wm_csf_full) +# assert all(x in t_df.columns for x in gs_basic) +# assert all(x not in t_df.columns for x in gs_power2) +# assert all(x not in t_df.columns for x in gs_derivatives) +# assert all(x not in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" not in t_df.columns - assert "BOLD" in out_type +# # Test #4: 6 params, no derivatives to compute, no spike +# strat4 = { +# "motion": "basic", +# } +# cr = BaseConfoundRemover( +# strategy=strat4, spike=None, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) - # Check if the input data is valid - cr._validate_data(input_data_obj) +# assert "BOLD" in out_type - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 2 - assert all(x not in t_df.columns for x in motion_basic) - assert all(x not in t_df.columns for x in motion_power2) - assert all(x not in t_df.columns for x in motion_derivatives) - assert all(x not in t_df.columns for x in motion_full) - assert all(x in t_df.columns for x in wm_csf_basic) - assert all(x not in t_df.columns for x in wm_csf_power2) - assert all(x not in t_df.columns for x in wm_csf_derivatives) - assert all(x not in t_df.columns for x in wm_csf_full) - assert all(x not in t_df.columns for x in gs_basic) - assert all(x not in t_df.columns for x in gs_power2) - assert all(x not in t_df.columns for x in gs_derivatives) - assert all(x not in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" not in t_df.columns +# # Check if the input data is valid +# cr._validate_data(input_data_obj) - out = cr.fit_transform(input_data_obj) - check_niimg_4d(out["BOLD"]["data"]) - # TODO: check meta +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 6 +# assert all(x in t_df.columns for x in motion_basic) +# assert all(x not in t_df.columns for x in motion_power2) +# assert all(x not in t_df.columns for x in motion_derivatives) +# assert all(x not in t_df.columns for x in motion_full) +# assert all(x not in t_df.columns for x in wm_csf_basic) +# assert all(x not in t_df.columns for x in wm_csf_power2) +# assert all(x not in t_df.columns for x in wm_csf_derivatives) +# assert all(x not in t_df.columns for x in wm_csf_full) +# assert all(x not in t_df.columns for x in gs_basic) +# assert all(x not in t_df.columns for x in gs_power2) +# assert all(x not in t_df.columns for x in gs_derivatives) +# assert all(x not in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" not in t_df.columns - # Test #6: 12 params, derivatives to compute, spike - to_select = [ - x for x in confounds_df.columns if x not in motion_derivatives - ] - no_d_df = confounds_df[to_select] - input_data_obj["confounds"]["data"] = no_d_df +# # Test #5: 2 params, no derivatives to compute, no spike +# strat5 = { +# "wm_csf": "basic", +# } +# cr = BaseConfoundRemover( +# strategy=strat5, spike=None, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) - derivatives = {f"D{x}": x for x in motion_basic} +# assert "BOLD" in out_type - input_data_obj["confounds"]["names"]["derivatives"] = derivatives +# # Check if the input data is valid +# cr._validate_data(input_data_obj) - strat6 = { - "motion": "derivatives", - } - cr = BaseConfoundRemover( - strategy=strat6, spike=0.75, mask_img=simsk, t_r=0.75 - ) - cr.validate_input(list(input_data_obj.keys())) - out_type = cr.get_output_kind(list(input_data_obj.keys())) +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 2 +# assert all(x not in t_df.columns for x in motion_basic) +# assert all(x not in t_df.columns for x in motion_power2) +# assert all(x not in t_df.columns for x in motion_derivatives) +# assert all(x not in t_df.columns for x in motion_full) +# assert all(x in t_df.columns for x in wm_csf_basic) +# assert all(x not in t_df.columns for x in wm_csf_power2) +# assert all(x not in t_df.columns for x in wm_csf_derivatives) +# assert all(x not in t_df.columns for x in wm_csf_full) +# assert all(x not in t_df.columns for x in gs_basic) +# assert all(x not in t_df.columns for x in gs_power2) +# assert all(x not in t_df.columns for x in gs_derivatives) +# assert all(x not in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" not in t_df.columns - assert "BOLD" in out_type +# out = cr.fit_transform(input_data_obj) +# check_niimg_4d(out["BOLD"]["data"]) +# # TODO: check meta - # Check if the input data is valid - cr._validate_data(input_data_obj) +# # Test #6: 12 params, derivatives to compute, spike +# to_select = [ +# x for x in confounds_df.columns if x not in motion_derivatives +# ] +# no_d_df = confounds_df[to_select] +# input_data_obj["confounds"]["data"] = no_d_df - # Check that the confounds are picked correctly: - t_df = cr._pick_confounds(input_data_obj["confounds"]) - assert len(t_df.columns) == 13 - assert all(x in t_df.columns for x in motion_basic) - assert all(x not in t_df.columns for x in motion_power2) - assert all(x in t_df.columns for x in motion_derivatives) - assert all(x not in t_df.columns for x in motion_full) - assert all(x not in t_df.columns for x in wm_csf_basic) - assert all(x not in t_df.columns for x in wm_csf_power2) - assert all(x not in t_df.columns for x in wm_csf_derivatives) - assert all(x not in t_df.columns for x in wm_csf_full) - assert all(x not in t_df.columns for x in gs_basic) - assert all(x not in t_df.columns for x in gs_power2) - assert all(x not in t_df.columns for x in gs_derivatives) - assert all(x not in t_df.columns for x in gs_full) - assert "FD" not in t_df.columns - assert "spike" in t_df.columns +# derivatives = {f"D{x}": x for x in motion_basic} + +# input_data_obj["confounds"]["names"]["derivatives"] = derivatives + +# strat6 = { +# "motion": "derivatives", +# } +# cr = BaseConfoundRemover( +# strategy=strat6, spike=0.75, mask_img=simsk, t_r=0.75 +# ) +# cr.validate_input(list(input_data_obj.keys())) +# out_type = cr.get_output_kind(list(input_data_obj.keys())) + +# assert "BOLD" in out_type + +# # Check if the input data is valid +# cr._validate_data(input_data_obj) + +# # Check that the confounds are picked correctly: +# t_df = cr._pick_confounds(input_data_obj["confounds"]) +# assert len(t_df.columns) == 13 +# assert all(x in t_df.columns for x in motion_basic) +# assert all(x not in t_df.columns for x in motion_power2) +# assert all(x in t_df.columns for x in motion_derivatives) +# assert all(x not in t_df.columns for x in motion_full) +# assert all(x not in t_df.columns for x in wm_csf_basic) +# assert all(x not in t_df.columns for x in wm_csf_power2) +# assert all(x not in t_df.columns for x in wm_csf_derivatives) +# assert all(x not in t_df.columns for x in wm_csf_full) +# assert all(x not in t_df.columns for x in gs_basic) +# assert all(x not in t_df.columns for x in gs_power2) +# assert all(x not in t_df.columns for x in gs_derivatives) +# assert all(x not in t_df.columns for x in gs_full) +# assert "FD" not in t_df.columns +# assert "spike" in t_df.columns diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index af247c6c7..0bff71f10 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -5,6 +5,7 @@ # License: AGPL import tempfile +from pathlib import Path from typing import Dict, List import nibabel as nib @@ -39,7 +40,7 @@ class OasisVBMTestingDatagrabber(BaseDataGrabber): """ out = super().__getitem__(element) i_sub = int(element.split("-")[1]) - 1 - out["VBM_GM"] = {"path": self._dataset.gray_matter_maps[i_sub]} + out["VBM_GM"] = {"path": Path(self._dataset.gray_matter_maps[i_sub])} # Set the element accordingly out["meta"]["element"] = {"subject": element} return out @@ -120,3 +121,94 @@ class SPMAuditoryTestingDatagrabber(BaseDataGrabber): # Set the element accordingly out["meta"]["element"] = {"subject": element} return out + + +class PartlyCloudyTestingDataGrabber(BaseDataGrabber): + """DataGrabber for Partly Cloudy dataset. + + Wrapper for nilearn.datasets.fetch_partly_cloudy + + + Parameters + ---------- + reduce_confounds : bool, optional + If True, the returned confounds only include 6 motion parameters, + mean framewise displacement, signal from white matter, csf, and + 6 anatomical compcor parameters. This selection only serves the + purpose of having realistic examples. Depending on your research + question, other confounds might be more appropriate. + If False, returns all :term:`fMRIPrep` confounds. + Default=True. + + age_group : str, optional + Default='both'. Which age group to fetch + - 'adults' = fetch adults only (n=33, ages 18-39) + - 'child' = fetch children only (n=122, ages 3-12) + - 'both' = fetch full sample (n=155) + """ + + def __init__(self, reduce_confounds=True, age_group="both") -> None: + """Initialize the class.""" + datadir = tempfile.mkdtemp() + # Define types + types = ["BOLD", "BOLD_confounds"] + self.reduce_confounds = reduce_confounds + self.age_group = age_group + super().__init__(types=types, datadir=datadir) + + def __enter__(self) -> "PartlyCloudyTestingDataGrabber": + """Implement context entry. + + Returns + ------- + PartlyCloudyTestingDataGrabber + + """ + self._dataset = datasets.fetch_development_fmri( + n_subjects=10, + reduce_confounds=self.reduce_confounds, + age_group=self.age_group, + ) + return self + + def get_elements(self) -> List[str]: + """Get elements. + + Returns + ------- + list of str + List of elements that can be grabbed. + + """ + return [f"sub-{x:02d}" for x in list(range(1, 11))] + + def __getitem__(self, element: str) -> Dict: + """Implement indexing support. + + Parameters + ---------- + element : str + The element to retrieve. + + Returns + ------- + dict + The data along with the metadata. + + """ + out = super().__getitem__(element) + i_sub = int(element.split("-")[1]) - 1 + out["BOLD"] = {"path": Path(self._dataset["func"][i_sub])} + conf_format = "adhoc" if self.reduce_confounds else "fmriprep" + + out["BOLD_confounds"] = { + "path": Path(self._dataset["confounds"][i_sub]), + "format": conf_format, + } + # if self.reduce_confounds: + # spec = { + + # } + # Set the element accordingly + out["meta"]["element"] = {"subject": element} + return out diff --git a/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py new file mode 100644 index 000000000..9129b93c0 --- /dev/null +++ b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py @@ -0,0 +1,29 @@ +"""Provide tests for SPM Auditory datagrabber.""" + +# Authors: Federico Raimondo +# License: AGPL + +from junifer.testing.datagrabbers import OasisVBMTestingDatagrabber + + +def test_OasisVBMTestingDatagrabber() -> None: + """Test Oasis VBM datagrabber.""" + expected_elements = [ + "sub-01", + "sub-02", + "sub-03", + "sub-04", + "sub-05", + "sub-06", + "sub-07", + "sub-08", + "sub-09", + "sub-10", + ] + with OasisVBMTestingDatagrabber() as dg: + all_elements = dg.get_elements() + assert set(all_elements) == set(expected_elements) + out = dg["sub-01"] + assert "VBM_GM" in out + assert out["VBM_GM"]["path"].exists() + assert out["VBM_GM"]["path"].is_file() diff --git a/junifer/testing/tests/test_partlycloudytesting_datagrabber.py b/junifer/testing/tests/test_partlycloudytesting_datagrabber.py new file mode 100644 index 000000000..aceb93dad --- /dev/null +++ b/junifer/testing/tests/test_partlycloudytesting_datagrabber.py @@ -0,0 +1,40 @@ +"""Provide tests for PartlyCloudy datagrabber.""" + +# Authors: Federico Raimondo +# License: AGPL + +from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber + + +def test_PartlyCloudyTestingDataGrabber() -> None: + """Test PartlyCloudy datagrabber.""" + expected_elements = [ + "sub-01", + "sub-02", + "sub-03", + "sub-04", + "sub-05", + "sub-06", + "sub-07", + "sub-08", + "sub-09", + "sub-10", + ] + with PartlyCloudyTestingDataGrabber() as dg: + all_elements = dg.get_elements() + assert set(all_elements) == set(expected_elements) + out = dg["sub-01"] + assert "BOLD" in out + assert out["BOLD"]["path"].exists() + assert out["BOLD"]["path"].is_file() + + assert "BOLD_confounds" in out + assert out["BOLD_confounds"]["path"].exists() + assert out["BOLD_confounds"]["path"].is_file() + assert "format" in out["BOLD_confounds"] + assert "adhoc" == out["BOLD_confounds"]["format"] + + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + out = dg["sub-01"] + assert "format" in out["BOLD_confounds"] + assert "fmriprep" == out["BOLD_confounds"]["format"] -- 2.52.0 From da95bdaab6dc4fea7c12ee40be09acbe36281d2c Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 27 Oct 2022 12:12:22 +0300 Subject: [PATCH 121/142] Still WIP, but with more tests --- junifer/preprocess/confounds.py | 245 ++++++++++++++------- junifer/preprocess/tests/test_confounds.py | 186 ++++++++++++++++ 2 files changed, 352 insertions(+), 79 deletions(-) diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index fe121c386..b753590c7 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -21,6 +21,65 @@ if TYPE_CHECKING: from nibabel import MGHImage, Nifti1Image, Nifti2Image +FMRIPREP_BASICS = { + "motion": [ + "trans_x", + "trans_y", + "trans_z", + "rot_x", + "rot_y", + "rot_z", + ], + "wm_csf": ["csf", "white_matter"], + "global_signal": ["global_signal"], +} + +FMRIPREP_POWER2 = { + "motion": [ + "trans_x_power2", + "trans_y_power2", + "trans_z_power2", + "rot_x_power2", + "rot_y_power2", + "rot_z_power2", + ], + "wm_csf": ["csf_power2", "white_matter_power2"], + "global_signal": ["global_signal_power2"], +} + +FMRIPREP_DERIVATIVES = { + "motion": [ + "trans_x_derivative1", + "trans_y_derivative1", + "trans_z_derivative1", + "rot_x_derivative1", + "rot_y_derivative1", + "rot_z_derivative1", + ], + "wm_csf": ["csf_derivative1", "white_matter_derivative1"], + "global_signal": ["global_signal_derivative1"], +} + +FMRIPREP_DERIVATIVES_POWER2 = { + "motion": [ + "trans_x_derivative1_power2", + "trans_y_derivative1_power2", + "trans_z_derivative1_power2", + "rot_x_derivative1_power2", + "rot_y_derivative1_power2", + "rot_z_derivative1_power2", + ], + "wm_csf": ["csf_derivative1_power2", "white_matter_derivative1_power2"], + "global_signal": ["global_signal_derivative1_power2"], +} + +FMRIPREP_VALID_NAMES = [ + elem for x in [FMRIPREP_BASICS, FMRIPREP_POWER2, FMRIPREP_DERIVATIVES, + FMRIPREP_DERIVATIVES_POWER2] + for t_list in x.values() + for elem in t_list] + + class FMRIPrepConfoundRemover(PipelineStepMixin): """Class for confound removal. @@ -124,7 +183,7 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): if any(x not in self._valid_confounds for x in strategy.values()): raise_error( - msg=f"Invalid component names {list(strategy.values())}. " + msg=f"Invalid confound types {list(strategy.values())}. " f"Valid confound types are {self._valid_confounds}.\n" f"If any of them is a valid parameter in " "nilearn.interfaces.fmriprep.load_confounds we may " @@ -175,45 +234,33 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): # Does not add any new keys return input - def _pick_confounds(self, input: Dict[str, Any]) -> pd.DataFrame: - """Select relevant confounds from the specified file.""" + def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]): + """Map the adhoc format to the fmpriprep format spec. - confounds_format = input["format"] - if confounds_format == "adhoc": - self._map_adhoc_to_fmriprep(input) - elif confounds_format != "fmriprep": - raise ValueError(f"Invalid confounds format {confounds_format}") + Based on the spec, map the column names to match the fmriprep format. - processed_spec = self._process_fmriprep_spec(input) + It asumes that the data is valid, meaning that all the mapping + keys are in the confounds dataframe columns and all the mapped + values are valid fmriprep column names. - ( - to_select, - squares_to_compute, - derivatives_to_compute, - spike_name, - ) = processed_spec - # Copy the confounds - out_df = input["data"].copy() + This method modifies the dataframe in place. - # Add derivatives if needed - for t_dst, t_src in derivatives_to_compute.items(): - out_df[t_dst] = np.append(np.diff(out_df[t_src]), 0) + Parameters + ---------- + input : dict + Dictionary containing the following keys: + - data: the confounds file loaded in memory (dataframe) + - format: format of the confounds file (must be "adhoc") + - mappings: dictionary containing the mappings from the adhoc + format to the fmriprep format as a dictionary with key "fmriprep" - # Add squares (of base confounds and derivatives) if needed - for t_dst, t_src in squares_to_compute.items(): - out_df[t_dst] = out_df[t_src] ** 2 + """ - # add binary spike regressor if needed at given threshold - if self.spike is not None: - fd = out_df[spike_name].copy() - fd.loc[fd > self.spike] = 1 - fd.loc[fd != 1] = 0 - out_df["spike"] = fd - to_select.append("spike") + confounds_df = input["data"] + confounds_mapping = input["mappings"]["fmriprep"] - # Now pick all the relevant confounds - out_df = out_df[to_select] - return out_df + # Rename the columns + confounds_df.rename(columns=confounds_mapping, inplace=True) def _process_fmriprep_spec( self, input: Dict[str, Any] @@ -255,21 +302,8 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): squares_to_compute = {} # the dictionary of missing squares derivatives_to_compute = {} # the dictionary of missing derivatives - basics = { - "motion": [ - "trans_x", - "trans_y", - "trans_z", - "rot_x", - "rot_y", - "rot_z", - ], - "wm_csf": ["csf", "white_matter"], - "global_signal": ["global_signal"], - } - for t_kind, t_strategy in self.strategy.items(): - t_basics = basics[t_kind] + t_basics = FMRIPREP_BASICS[t_kind] if any(x not in available_vars for x in t_basics): missing = [x for x in t_basics if x not in available_vars] @@ -301,48 +335,54 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): if x_derivative_2 not in available_vars: squares_to_compute[x_derivative_2] = x_derivative spike_name = "framewise_displacement" - + if self.spike is not None: + if spike_name not in available_vars: + raise ValueError( + "Invalid confounds file. Missing framewise_displacement " + "(spike) confound. " + "Check if this file is really an fmriprep confounds file. " + "You can also deactivate spike (set spike = None)." + ) out = to_select, squares_to_compute, derivatives_to_compute, spike_name return out - def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]): - """Map the adhoc format to the fmpriprep format spec. + def _pick_confounds(self, input: Dict[str, Any]) -> pd.DataFrame: + """Select relevant confounds from the specified file.""" - Based on the spec, map the column names to match the fmriprep format. + confounds_format = input["format"] + if confounds_format == "adhoc": + self._map_adhoc_to_fmriprep(input) - This method modifies the dataframe in place. + processed_spec = self._process_fmriprep_spec(input) - Parameters - ---------- - input : dict - Dictionary containing the following keys: - - path: path to the confounds file - - data: the confounds file loaded in memory (dataframe) - - format: format of the confounds file (must be "adhoc") - """ + ( + to_select, + squares_to_compute, + derivatives_to_compute, + spike_name, + ) = processed_spec + # Copy the confounds + out_df = input["data"].copy() - confounds_df = input["data"] + # Add derivatives if needed + for t_dst, t_src in derivatives_to_compute.items(): + out_df[t_dst] = np.append(np.diff(out_df[t_src]), 0) - # This is an - confounds_mapping = input["mappings"] + # Add squares (of base confounds and derivatives) if needed + for t_dst, t_src in squares_to_compute.items(): + out_df[t_dst] = out_df[t_src] ** 2 - # Check that all the required columns are present - missing = [ - x - for x in confounds_mapping.keys() - if x not in confounds_df.columns - ] + # add binary spike regressor if needed at given threshold + if self.spike is not None: + fd = out_df[spike_name].copy() + fd.loc[fd > self.spike] = 1 + fd.loc[fd != 1] = 0 + out_df["spike"] = fd + to_select.append("spike") - if len(missing) is not None: - raise ValueError( - "Invalid confounds file. Missing columns: " - f"{missing}. " - "Check if this file matches the adhoc specification for " - "this dataset." - ) - - # Rename the columns - confounds_df.rename(columns=confounds_mapping, inplace=True) + # Now pick all the relevant confounds + out_df = out_df[to_select] + return out_df def _remove_confounds( self, bold_img: "Nifti1Image", confounds_df: pd.DataFrame @@ -414,6 +454,53 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): f"\tConfounds: {len(confound_df)}" ) + if "format" not in input["BOLD_confounds"]: + raise_error( + "Confounds format must be specified in " + "input[\"BOLD_confounds\"]" + ) + + t_format = input["BOLD_confounds"]["format"] + + if t_format == "adhoc": + if "mappings" not in input["BOLD_confounds"]: + raise_error( + "When using adhoc format, you must specify " + "the variables names mappings in " + "input[\"BOLD_confounds\"][\"mappings\"]" + ) + if "fmriprep" not in input["BOLD_confounds"]["mappings"]: + raise_error( + "When using adhoc format, you must specify " + "the variables names mappings to fmriprep format in " + "input[\"BOLD_confounds\"][\"mappings\"][\"fmriprep\"]" + ) + fmriprep_mappings = input["BOLD_confounds"]["mappings"]["fmriprep"] + wrong_names = [ + x for x in fmriprep_mappings.values() + if x not in FMRIPREP_VALID_NAMES] + if len(wrong_names) > 0: + raise_error( + "The following mapping values are not valid fmriprep " + f"names: {wrong_names}" + ) + # Check that all the required columns are present + missing = [ + x + for x in fmriprep_mappings.keys() + if x not in confound_df.columns + ] + + if len(missing) is not None: + raise ValueError( + "Invalid confounds file. Missing columns: " + f"{missing}. " + "Check if this file matches the adhoc specification for " + "this dataset." + ) + elif t_format != "fmriprep": + raise ValueError(f"Invalid confounds format {t_format}") + # Check the column names of the dataframe and the spec # spec must be a dictionary: # { diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 2dfe9a8f4..a6b9ec254 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -7,6 +7,9 @@ from numpy.testing import assert_array_equal, assert_raises +import pytest +import pandas as pd +import numpy as np from junifer.preprocess.confounds import FMRIPrepConfoundRemover from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber @@ -32,6 +35,189 @@ from junifer.datareader import DefaultDataReader # return img, mask +def test_FMRIPrepConfoundRemover_init() -> None: + """Test FMRIPrepConfoundRemover init.""" + + with pytest.raises(ValueError, match="keys must be strings"): + FMRIPrepConfoundRemover(strategy={1: "full"}) # type: ignore + + with pytest.raises(ValueError, match="values must be strings"): + FMRIPrepConfoundRemover(strategy={"motion": 1}) # type: ignore + + with pytest.raises(ValueError, match="component names"): + FMRIPrepConfoundRemover(strategy={"wrong": "full"}) + + with pytest.raises(ValueError, match="confound types"): + FMRIPrepConfoundRemover(strategy={"motion": "wrong"}) + + +def test_FMRIPrepConfoundRemover_validate_input() -> None: + """Test FMRIPrepConfoundRemover validate_input.""" + confound_remover = FMRIPrepConfoundRemover() + + # Input is valid when both BOLD and BOLD_confounds are present + + input = ["T1w"] + with pytest.raises(ValueError, match="not have the required data"): + confound_remover.validate_input(input) + + input = ["BOLD"] + with pytest.raises(ValueError, match="not have the required data"): + confound_remover.validate_input(input) + + input = ["BOLD", "T1w"] + with pytest.raises(ValueError, match="not have the required data"): + confound_remover.validate_input(input) + + input = ["BOLD", "T1w", "BOLD_confounds"] + confound_remover.validate_input(input) + + +def test_FMRIPrepConfoundRemover_get_output_kind() -> None: + """Test FMRIPrepConfoundRemover validate_input.""" + confound_remover = FMRIPrepConfoundRemover() + inputs = [ + ["BOLD", "T1w", "BOLD_confounds"], + ["BOLD", "VBM_GM", "BOLD_confounds"], + ["BOLD", "BOLD_confounds"], + ] + # Confound remover works in place + for input in inputs: + assert confound_remover.get_output_kind(input) == input + + +def test_FMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None: + """Test FMRIPrepConfoundRemover adhoc to fmriprep spec mapping.""" + confound_remover = FMRIPrepConfoundRemover() + # Use non fmriprep variable names + adhoc_names = [f"var{i}" for i in range(6)] + adhoc_df = pd.DataFrame(np.random.randn(10, 6), columns=adhoc_names) + + # map them to valid variable names + fmriprep_names = [ + "trans_x", + "trans_y", + "trans_z", + "rot_x", + "rot_y", + "rot_z", + ] + + # Build mappings dictionary + mappings = {x: y for x, y in zip(adhoc_names, fmriprep_names)} + input = { + "mappings": {"fmriprep": mappings}, + "data" : adhoc_df, + } + + confound_remover._map_adhoc_to_fmriprep(input) + # This should work in-place + assert adhoc_df.columns.tolist() == fmriprep_names + + +def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: + """Test FMRIPrepConfoundRemover fmriprep spec processing.""" + + # Test one strategy, full, no spike + confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) + + var_names = [ + "csf", "white_matter", "csf_power2", "white_matter_power2", + "csf_derivative1", "white_matter_derivative1", + "csf_derivative1_power2", "white_matter_derivative1_power2"] + + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names)), columns=var_names) + + out = confound_remover._process_fmriprep_spec({"data": confounds_df}) + to_select, sq_to_compute, der_to_compute, spike_name = out + assert set(to_select) == set(var_names) + assert len(sq_to_compute) == 0 + assert len(der_to_compute) == 0 + assert spike_name == "framewise_displacement" + + # Same strategy, but derivatives are not present + var_names = [ + "csf", "white_matter", "csf_power2", "white_matter_power2"] + missing_der_names = ["csf_derivative1", "white_matter_derivative1"] + missing_sq_names = [ + "csf_derivative1_power2", "white_matter_derivative1_power2"] + + all_names = var_names + missing_der_names + missing_sq_names + + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names)), columns=var_names) + out = confound_remover._process_fmriprep_spec({"data": confounds_df}) + to_select, sq_to_compute, der_to_compute, spike_name = out + assert set(to_select) == set(all_names) + assert set(sq_to_compute) == set(missing_sq_names) + assert set(der_to_compute) == set(missing_der_names) + assert spike_name == "framewise_displacement" + + # Same strategy, with spike, only basics are present + confound_remover = FMRIPrepConfoundRemover( + strategy={"wm_csf": "full"}, spike=0.2) + + var_names = ["csf", "white_matter"] + missing_der_names = ["csf_derivative1", "white_matter_derivative1"] + missing_sq_names = [ + "csf_power2", "white_matter_power2", + "csf_derivative1_power2", "white_matter_derivative1_power2"] + + all_names = var_names + missing_der_names + missing_sq_names + + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names) + 1), + columns=var_names + ["framewise_displacement"]) + out = confound_remover._process_fmriprep_spec({"data": confounds_df}) + to_select, sq_to_compute, der_to_compute, spike_name = out + assert set(to_select) == set(all_names) + assert set(sq_to_compute) == set(missing_sq_names) + assert set(der_to_compute) == set(missing_der_names) + assert spike_name == "framewise_displacement" + + # Two component strategy, mixed confounds, no spike + confound_remover = FMRIPrepConfoundRemover( + strategy={"wm_csf": "power2", "global_signal": "full"}) + + var_names = ["csf", "white_matter", "global_signal"] + missing_der_names = ["global_signal_derivative1"] + missing_sq_names = [ + "csf_power2", "white_matter_power2", "global_signal_power2", + "global_signal_derivative1_power2"] + + all_names = var_names + missing_der_names + missing_sq_names + + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names)), columns=var_names) + out = confound_remover._process_fmriprep_spec({"data": confounds_df}) + to_select, sq_to_compute, der_to_compute, spike_name = out + assert set(to_select) == set(all_names) + assert set(sq_to_compute) == set(missing_sq_names) + assert set(der_to_compute) == set(missing_der_names) + assert spike_name == "framewise_displacement" + + # Test for wrong columns/strategy pairs + + confound_remover = FMRIPrepConfoundRemover( + strategy={"wm_csf": "full"}, spike=0.2) + var_names = ["csf"] + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names)), columns=var_names) + + msg = r"Missing basic confounds: \['white_matter'\]" + with pytest.raises(ValueError, match=msg): + confound_remover._process_fmriprep_spec({"data": confounds_df}) + + var_names = ["csf", "white_matter"] + confounds_df = pd.DataFrame( + np.random.randn(7, len(var_names)), columns=var_names) + + msg = r"Missing framewise_displacement" + with pytest.raises(ValueError, match=msg): + confound_remover._process_fmriprep_spec({"data": confounds_df}) + + def test_FMRIPrepConfoundRemover_allpresent() -> None: """Test FMRIPrepConfoundRemover with all confounds present.""" -- 2.52.0 From a15f8fc9cedd2fba97f45bcdfe95b8a3e94a1197 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 27 Oct 2022 12:14:57 +0300 Subject: [PATCH 122/142] codespell --- junifer/preprocess/confounds.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index b753590c7..6ed35ae39 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -239,7 +239,7 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): Based on the spec, map the column names to match the fmriprep format. - It asumes that the data is valid, meaning that all the mapping + It assumes that the data is valid, meaning that all the mapping keys are in the confounds dataframe columns and all the mapped values are valid fmriprep column names. -- 2.52.0 From 4a833e27def48f3fda8eec1b359c43a9e28bf2c7 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 29 Oct 2022 20:39:47 +0300 Subject: [PATCH 123/142] Code ready, needs DOC --- junifer/preprocess/base.py | 182 ++++++ junifer/preprocess/confounds.py | 412 +++++--------- junifer/preprocess/tests/test_confounds.py | 623 ++++++++++----------- junifer/testing/datagrabbers.py | 5 +- 4 files changed, 616 insertions(+), 606 deletions(-) create mode 100644 junifer/preprocess/base.py diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py new file mode 100644 index 000000000..6e710dbe6 --- /dev/null +++ b/junifer/preprocess/base.py @@ -0,0 +1,182 @@ +"""Provide base class for preprocessor.""" + +# Authors: Federico Raimondo +# Synchon Mandal +# License: AGPL + +from abc import ABC, abstractmethod +from typing import Dict, List, Optional, Union, Tuple, Any + + +from ..pipeline import PipelineStepMixin +from ..utils import logger, raise_error + + +class BasePreprocessor(ABC, PipelineStepMixin): + """Abstract base class for all preprocessors. + + Parameters + ---------- + on : str or list of str + The kind of data to apply the preprocessor to. If None, + will work on all available data (default: None). + + """ + + def __init__( + self, + on: Optional[Union[List[str], str]] = None, + ) -> None: + """Initialize the class.""" + if on is None: + on = self.get_valid_inputs() + if not isinstance(on, list): + on = [on] + + if any(x not in self.get_valid_inputs() for x in on): + name = self.__class__.__name__ + wrong_on = [x for x in on if x not in self.get_valid_inputs()] + raise ValueError(f"{name} cannot be computed on {wrong_on}") + self._on = on + + def validate_input(self, input: List[str]) -> None: + """Validate input. + + Parameters + ---------- + input : list of str + The input to the pipeline step. The list must contain the + available Junifer Data dictionary keys. + + Raises + ------ + ValueError + If the input does not have the required data. + + """ + if not any(x in input for x in self._on): + raise_error( + "Input does not have the required data." + f"\t Input: {input}" + f"\t Required (any of): {self._on}" + ) + + @abstractmethod + def get_output_kind(self, input: List[str]) -> List[str]: + """Get output kind. + + Parameters + ---------- + input : list of str + The input to the marker. The list must contain the + available Junifer Data dictionary keys. + + Returns + ------- + list of str + The updated list of output kinds, as storage possibilities. + + """ + raise_error( + msg="Concrete classes need to implement get_output_kind().", + klass=NotImplementedError, + ) + + def get_valid_inputs(self) -> List[str]: + """Get valid data types for input. + + Returns + ------- + list of str + The list of data types that can be used as input for this marker + + """ + raise_error( + msg="Concrete classes need to implement get_valid_inputs().", + klass=NotImplementedError, + ) + + def get_meta(self, kind: str) -> Dict: + """Get metadata. + + Parameters + ---------- + kind : str + The kind of pipeline step. + + Returns + ------- + dict + The metadata as a dictionary with the only key 'marker'. + + """ + s_meta = super().get_meta() + # same marker can be "fit"ted into different kinds, so the name + # is created from the kind and the name of the marker + s_meta["kind"] = kind + return {"preprocess": s_meta} + + def fit_transform( + self, + input: Dict[str, Dict], + ) -> Dict: + """Fit and transform. + + Parameters + ---------- + input : dict + The Junifer Data object. + + Returns + ------- + dict + The processed output as a dictionary. + + """ + out = input + for kind in self._on: + if kind in input.keys(): + logger.info(f"Computing {kind}") + t_input = input[kind] + extra_input = input.copy() + extra_input.pop(kind) + t_meta = t_input.get("meta", {}) # input kind meta + t_meta.update(self.get_meta(kind)) + key, t_out = self.preprocess( + input=t_input, extra_input=extra_input) + t_out.update(meta=t_meta) + out[key] = t_out + return out + + @abstractmethod + def preprocess( + self, + input: Dict[str, Any], + extra_input: Optional[Dict[str, Any]] = None, + ) -> Tuple[str, Dict[str, Any]]: + """Preprocess. + + Parameters + ---------- + input : Dict[str, Dict] + A single input from the pipeline data object in which to compute + the marker. + extra_input : Dict, optional + The other fields in the pipeline data object. Useful for accessing + other data kind that needs to be used in the computation. For + example, the functional connectivity markers can make use of the + confounds if available (default None). + + Returns + ------- + key : str + The key to store the output in the Junifer Data object. + object : dict + The computed result as dictionary. This will be stored in the + Junifer Data object under the key 'key'. + + """ + raise_error( + msg="Concrete classes need to implement preprocess().", + klass=NotImplementedError, + ) diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index 6ed35ae39..8b9eb5fff 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -13,7 +13,7 @@ from nilearn._utils.niimg_conversions import check_niimg_4d from nilearn.image import clean_img from nilearn.masking import compute_brain_mask -from ..pipeline import PipelineStepMixin +from .base import BasePreprocessor from ..utils import logger, raise_error @@ -74,13 +74,19 @@ FMRIPREP_DERIVATIVES_POWER2 = { } FMRIPREP_VALID_NAMES = [ - elem for x in [FMRIPREP_BASICS, FMRIPREP_POWER2, FMRIPREP_DERIVATIVES, - FMRIPREP_DERIVATIVES_POWER2] + elem + for x in [ + FMRIPREP_BASICS, + FMRIPREP_POWER2, + FMRIPREP_DERIVATIVES, + FMRIPREP_DERIVATIVES_POWER2, + ] for t_list in x.values() - for elem in t_list] + for elem in t_list +] -class FMRIPrepConfoundRemover(PipelineStepMixin): +class FMRIPrepConfoundRemover(BasePreprocessor): """Class for confound removal. Read confound files and select columns according to @@ -129,12 +135,9 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): """ - # lower priority # TODO: implement more strategies from - # nilearn.interfaces.fmriprep.load_confounds for Felix's confound files, + # nilearn.interfaces.fmriprep.load_confounds, # in particular scrubbing - # TODO: Implement read_confounds for fmriprep data - def __init__( self, strategy: Optional[Dict[str, str]] = None, @@ -147,6 +150,7 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): mask_img: Optional["Nifti1Image"] = None, ) -> None: """Initialise the class.""" + super().__init__() if strategy is None: strategy = { "motion": "full", @@ -234,6 +238,17 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): # Does not add any new keys return input + def get_valid_inputs(self) -> List[str]: + """Get the valid inputs for the pipeline step. + + Returns + ------- + list of str + The valid inputs for the pipeline step. + + """ + return ["BOLD"] + def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]): """Map the adhoc format to the fmpriprep format spec. @@ -384,6 +399,88 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): out_df = out_df[to_select] return out_df + def _validate_data( + self, + input: Dict[str, Any], + extra_input: Optional[Dict[str, Any]] = None, + ) -> None: + """Validate input data.""" + + # Bold must be 4D niimg + check_niimg_4d(input["data"]) + + if extra_input is None: + raise_error("No extra input provided", ValueError) + if "BOLD_confounds" not in extra_input: + raise_error("No BOLD_confounds provided", ValueError) + if "data" not in extra_input["BOLD_confounds"]: + raise_error("No BOLD_confounds data provided", ValueError) + # Confounds must be a dataframe + if not isinstance(extra_input["BOLD_confounds"]["data"], pd.DataFrame): + raise_error( + "Confounds data must be a pandas dataframe", ValueError + ) + + confound_df = extra_input["BOLD_confounds"]["data"] + bold_img = input["data"] + if bold_img.get_fdata().shape[3] != len(confound_df): + raise_error( + "Image time series and confounds have different length!\n" + f"\tImage time series: { bold_img.get_fdata().shape[3]}\n" + f"\tConfounds: {len(confound_df)}" + ) + + if "format" not in extra_input["BOLD_confounds"]: + raise_error( + "Confounds format must be specified in " + 'input["BOLD_confounds"]' + ) + + t_format = extra_input["BOLD_confounds"]["format"] + + if t_format == "adhoc": + if "mappings" not in extra_input["BOLD_confounds"]: + raise_error( + "When using adhoc format, you must specify " + "the variables names mappings in " + 'input["BOLD_confounds"]["mappings"]' + ) + if "fmriprep" not in extra_input["BOLD_confounds"]["mappings"]: + raise_error( + "When using adhoc format, you must specify " + "the variables names mappings to fmriprep format in " + 'input["BOLD_confounds"]["mappings"]["fmriprep"]' + ) + fmriprep_mappings = extra_input["BOLD_confounds"]["mappings"][ + "fmriprep" + ] + wrong_names = [ + x + for x in fmriprep_mappings.values() + if x not in FMRIPREP_VALID_NAMES + ] + if len(wrong_names) > 0: + raise_error( + "The following mapping values are not valid fmriprep " + f"names: {wrong_names}" + ) + # Check that all the required columns are present + missing = [ + x + for x in fmriprep_mappings.keys() + if x not in confound_df.columns + ] + + if len(missing) is not None: + raise ValueError( + "Invalid confounds file. Missing columns: " + f"{missing}. " + "Check if this file matches the adhoc specification for " + "this dataset." + ) + elif t_format != "fmriprep": + raise ValueError(f"Invalid confounds format {t_format}") + def _remove_confounds( self, bold_img: "Nifti1Image", confounds_df: pd.DataFrame ) -> Union["Nifti1Image", "Nifti2Image", "MGHImage", List]: @@ -421,6 +518,11 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): logger.info("Computing brain mask from image") mask_img = compute_brain_mask(bold_img) + logger.info("Cleaning image") + logger.debug(f"\tdetrend: {self.detrend}") + logger.debug(f"\tstandardize: {self.standardize}") + logger.debug(f"\tlow_pass: {self.low_pass}") + logger.debug(f"\thigh_pass: {self.high_pass}") clean_bold = clean_img( imgs=bold_img, detrend=self.detrend, @@ -434,268 +536,36 @@ class FMRIPrepConfoundRemover(PipelineStepMixin): return clean_bold - def _validate_data(self, input: Dict[str, Any]): - """Validate input data.""" - # Bold must be 4D niimg - check_niimg_4d(input["BOLD"]["data"]) + def preprocess( + self, + input: Dict[str, Any], + extra_input: Optional[Dict[str, Any]] = None, + ) -> Tuple[str, Dict[str, Any]]: + """Preprocess. - # Confounds must be a dataframe - if not isinstance(input["BOLD_confounds"]["data"], pd.DataFrame): - raise_error( - "Confounds data must be a pandas dataframe", ValueError - ) + Parameters + ---------- + input : Dict[str, Dict] + A single input from the pipeline data object in which to compute + the marker. + extra_input : Dict, optional + The other fields in the pipeline data object. Useful for accessing + other data kind that needs to be used in the computation. For + example, the functional connectivity markers can make use of the + confounds if available (default None). - confound_df = input["BOLD_confounds"]["data"] - bold_img = input["BOLD"]["data"] - if bold_img.get_fdata().shape[3] != len(confound_df): - raise_error( - "Image time series and confounds have different length!\n" - f"\tImage time series: { bold_img.get_fdata().shape[3]}\n" - f"\tConfounds: {len(confound_df)}" - ) + Returns + ------- + key : str + The key to store the output in the Junifer Data object. + object : dict + The computed result as dictionary. This will be stored in the + Junifer Data object under the key 'key'. - if "format" not in input["BOLD_confounds"]: - raise_error( - "Confounds format must be specified in " - "input[\"BOLD_confounds\"]" - ) - - t_format = input["BOLD_confounds"]["format"] - - if t_format == "adhoc": - if "mappings" not in input["BOLD_confounds"]: - raise_error( - "When using adhoc format, you must specify " - "the variables names mappings in " - "input[\"BOLD_confounds\"][\"mappings\"]" - ) - if "fmriprep" not in input["BOLD_confounds"]["mappings"]: - raise_error( - "When using adhoc format, you must specify " - "the variables names mappings to fmriprep format in " - "input[\"BOLD_confounds\"][\"mappings\"][\"fmriprep\"]" - ) - fmriprep_mappings = input["BOLD_confounds"]["mappings"]["fmriprep"] - wrong_names = [ - x for x in fmriprep_mappings.values() - if x not in FMRIPREP_VALID_NAMES] - if len(wrong_names) > 0: - raise_error( - "The following mapping values are not valid fmriprep " - f"names: {wrong_names}" - ) - # Check that all the required columns are present - missing = [ - x - for x in fmriprep_mappings.keys() - if x not in confound_df.columns - ] - - if len(missing) is not None: - raise ValueError( - "Invalid confounds file. Missing columns: " - f"{missing}. " - "Check if this file matches the adhoc specification for " - "this dataset." - ) - elif t_format != "fmriprep": - raise ValueError(f"Invalid confounds format {t_format}") - - # Check the column names of the dataframe and the spec - # spec must be a dictionary: - # { - # 'motion': { - # 'basic': [(list of columns)] - # 'power2', [(list of columns)] - # 'derivatives', [(list of columns)] - # 'full', [(list of columns)]}, - # 'wm_csf': { - # 'basic': [(list of columns)] - # 'power2', [(list of columns)] - # 'derivatives', [(list of columns)] - # 'full', [(list of columns)]} - # 'global_signal': { - # 'basic': [(list of columns)] - # 'power2', [(list of columns)] - # 'derivatives', [(list of columns)] - # 'full', [(list of columns)]} - # } - - # # Check the columns in the dataframe - # conf_spec = input["confounds"]["names"]["spec"] - # if any(x not in conf_spec.keys() for x in self._valid_components): - # raise_error( - # "All of the component types must be in the confounds data " - # "object `spec`. Please check your datagrabber.", - # ValueError, - # ) - - # if any( - # x not in v.keys() - # for x in self._valid_confounds - # for v in conf_spec.values() - # ): - # raise_error( - # "All of the confound types must be in the confounds data " - # "object `spec`. Please check your datagrabber.", - # ValueError, - # ) - - # spike_name = input["confounds"]["names"]["spike"] - - # derivatives_to_compute = input["confounds"]["names"].get( - # "derivatives", {} - # ) - # if not (isinstance(derivatives_to_compute, dict)): - # raise_error( - # 'input["confounds"]["names"]["derivatives"] ' - # "must be a dictionary. Please check your datagrabber", - # ValueError, - # ) - - # if any( - # not (isinstance(k, str) or isinstance(v, str)) - # for k, v in derivatives_to_compute.items() - # ): - # raise_error( - # 'input["confounds"]["names"]["derivatives"] ' - # "must be a dictionary with string keys and values. " - # "Please check your datagrabber", - # ValueError, - # ) - - # missing_derivatives = [ - # x - # for x in derivatives_to_compute.values() - # if x not in confound_df.columns - # ] - # if len(missing_derivatives) > 0: - # raise_error( - # "Some of the derivatives to calculate are not in the " - # "confounds" - # f" dataframe: {missing_derivatives}." - # "Please check your data " - # f'({input["confounds"]["path"].as_posix()}) ' - # "and the datagrabber.", - # ValueError, - # ) - - # t_conf_spec = { - # k: input["confounds"]["names"]["spec"][k][v] - # for k, v in self.strategy.items() - # } - - # column_names = set([x for y in t_conf_spec.values() for x in y]) - # column_names.add(spike_name) - - # missing_columns = [ - # x - # for x in column_names - # if x not in confound_df.columns - # and x not in derivatives_to_compute.keys() - # ] - - # if len(missing_columns) > 0: - # raise_error( - # "Some of the columns in the confound spec are not in the " - # f"confounds dataframe: {missing_columns}. " - # "Please check your data " - # f'({input["confounds"]["path"].as_posix()}) ' - # "and the datagrabber.", - # ValueError, - # ) - - # TODO: complete type annotations - def fit_transform(self, input): - """Fit and transform.""" - self._validate_data(input) - bold_img = input["BOLD"]["data"] - confounds_df = self._pick_confounds(input["BOLD_confounds"]) - input["BOLD"]["data"] = self._remove_confounds(bold_img, confounds_df) - - # TODO: Update meta - return input - - -# class FelixConfoundRemover(BaseConfoundRemover): -# """ A class to read confounds from confound files generated by Felix's -# pipeline using CAT and some other custom scripts. It is meant to emulate -# the new nilearn.interfaces.fmriprep.load_confounds as closely as -# possible. - -# """ - -# def read_confounds(self, confound_dataframe): - -# confounds_to_select = [] -# # for some confounds we need to manually calculate derivatives using -# # numpy and add them to the output -# derivatives_to_compute = [] - -# for comp, param in self.strategy.items(): -# if comp == 'motion': -# confounds = [] -# # there should be six rigid body parameters -# for i in range(1, 7): -# # select basic -# confounds_to_select.append(f'RP.{i}') - -# # select squares -# if param in ['power2', 'full']: -# confounds_to_select.append(f'RP^2.{i}') - -# # select derivatives -# if param in ['derivatives', 'full']: -# confounds_to_select.append(f'DRP.{i}') - -# # if 'full' we should not forget the derivative -# # of the squares -# if param in ['full']: -# confounds_to_select.append(f'DRP^2.{i}') - -# elif comp == 'wm_csf': -# confounds = ['WM', 'CSF'] -# elif comp == 'global_signal': -# confounds = ['GS'] - -# for conf in confounds: - -# confounds_to_select.append(conf) - -# # select squares -# if param in ['power2', 'full']: -# confounds_to_select.append(f'{conf}^2') - -# # we have to calculate derivatives (not included in felix' -# # confound files) -# if param in ['derivatives', 'full']: -# derivatives_to_compute.append(conf) - -# if param in ['full']: -# derivatives_to_compute.append(f'{conf}^2') - -# confounds_to_remove = confound_dataframe[confounds_to_select] - -# # calc additional derivatives -# for conf in derivatives_to_compute: -# confounds_to_remove[f'D{conf}'] = np.append( -# np.diff(confound_dataframe[conf]), 0 -# ) - -# # add binary spike regressor if needed at given threshold -# if self.spike is not None: -# fd = confound_dataframe["FD"].copy() -# fd.loc[fd > self.spike] = 1 -# fd.loc[fd != 1] = 0 -# confounds_to_remove['spike'] = fd - -# return confounds_to_remove - - -# class FmriprepConfoundRemover(BaseConfoundRemover): -# """ A ConfoundRemover class for fmriprep output utilising -# nilearn's nilearn.interfaces.fmriprep.load_confounds -# """ - -# def read_confounds(self): -# raise NotImplementedError('read_confounds not implemented') + """ + self._validate_data(input, extra_input) + assert extra_input is not None + bold_img = input["data"] + confounds_df = self._pick_confounds(extra_input["BOLD_confounds"]) + input["data"] = self._remove_confounds(bold_img, confounds_df) + return "BOLD", input diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index a6b9ec254..e28826879 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -5,14 +5,21 @@ # Synchon Mandal # License: AGPL - +import typing from numpy.testing import assert_array_equal, assert_raises import pytest import pandas as pd +from pandas.testing import assert_frame_equal import numpy as np +import nibabel as nib +from nilearn._utils.exceptions import DimensionError + from junifer.preprocess.confounds import FMRIPrepConfoundRemover -from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber +from junifer.testing.datagrabbers import ( + OasisVBMTestingDatagrabber, + PartlyCloudyTestingDataGrabber, +) from junifer.datareader import DefaultDataReader # Set RNG seed for reproducibility @@ -107,7 +114,7 @@ def test_FMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None: mappings = {x: y for x, y in zip(adhoc_names, fmriprep_names)} input = { "mappings": {"fmriprep": mappings}, - "data" : adhoc_df, + "data": adhoc_df, } confound_remover._map_adhoc_to_fmriprep(input) @@ -122,12 +129,19 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) var_names = [ - "csf", "white_matter", "csf_power2", "white_matter_power2", - "csf_derivative1", "white_matter_derivative1", - "csf_derivative1_power2", "white_matter_derivative1_power2"] + "csf", + "white_matter", + "csf_power2", + "white_matter_power2", + "csf_derivative1", + "white_matter_derivative1", + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] confounds_df = pd.DataFrame( - np.random.randn(7, len(var_names)), columns=var_names) + np.random.randn(7, len(var_names)), columns=var_names + ) out = confound_remover._process_fmriprep_spec({"data": confounds_df}) to_select, sq_to_compute, der_to_compute, spike_name = out @@ -137,16 +151,18 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: assert spike_name == "framewise_displacement" # Same strategy, but derivatives are not present - var_names = [ - "csf", "white_matter", "csf_power2", "white_matter_power2"] + var_names = ["csf", "white_matter", "csf_power2", "white_matter_power2"] missing_der_names = ["csf_derivative1", "white_matter_derivative1"] missing_sq_names = [ - "csf_derivative1_power2", "white_matter_derivative1_power2"] + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] all_names = var_names + missing_der_names + missing_sq_names confounds_df = pd.DataFrame( - np.random.randn(7, len(var_names)), columns=var_names) + np.random.randn(7, len(var_names)), columns=var_names + ) out = confound_remover._process_fmriprep_spec({"data": confounds_df}) to_select, sq_to_compute, der_to_compute, spike_name = out assert set(to_select) == set(all_names) @@ -156,19 +172,24 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: # Same strategy, with spike, only basics are present confound_remover = FMRIPrepConfoundRemover( - strategy={"wm_csf": "full"}, spike=0.2) + strategy={"wm_csf": "full"}, spike=0.2 + ) var_names = ["csf", "white_matter"] missing_der_names = ["csf_derivative1", "white_matter_derivative1"] missing_sq_names = [ - "csf_power2", "white_matter_power2", - "csf_derivative1_power2", "white_matter_derivative1_power2"] + "csf_power2", + "white_matter_power2", + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] all_names = var_names + missing_der_names + missing_sq_names confounds_df = pd.DataFrame( np.random.randn(7, len(var_names) + 1), - columns=var_names + ["framewise_displacement"]) + columns=var_names + ["framewise_displacement"], + ) out = confound_remover._process_fmriprep_spec({"data": confounds_df}) to_select, sq_to_compute, der_to_compute, spike_name = out assert set(to_select) == set(all_names) @@ -178,18 +199,23 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: # Two component strategy, mixed confounds, no spike confound_remover = FMRIPrepConfoundRemover( - strategy={"wm_csf": "power2", "global_signal": "full"}) + strategy={"wm_csf": "power2", "global_signal": "full"} + ) var_names = ["csf", "white_matter", "global_signal"] missing_der_names = ["global_signal_derivative1"] missing_sq_names = [ - "csf_power2", "white_matter_power2", "global_signal_power2", - "global_signal_derivative1_power2"] + "csf_power2", + "white_matter_power2", + "global_signal_power2", + "global_signal_derivative1_power2", + ] all_names = var_names + missing_der_names + missing_sq_names confounds_df = pd.DataFrame( - np.random.randn(7, len(var_names)), columns=var_names) + np.random.randn(7, len(var_names)), columns=var_names + ) out = confound_remover._process_fmriprep_spec({"data": confounds_df}) to_select, sq_to_compute, der_to_compute, spike_name = out assert set(to_select) == set(all_names) @@ -200,10 +226,12 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: # Test for wrong columns/strategy pairs confound_remover = FMRIPrepConfoundRemover( - strategy={"wm_csf": "full"}, spike=0.2) + strategy={"wm_csf": "full"}, spike=0.2 + ) var_names = ["csf"] confounds_df = pd.DataFrame( - np.random.randn(7, len(var_names)), columns=var_names) + np.random.randn(7, len(var_names)), columns=var_names + ) msg = r"Missing basic confounds: \['white_matter'\]" with pytest.raises(ValueError, match=msg): @@ -211,14 +239,239 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: var_names = ["csf", "white_matter"] confounds_df = pd.DataFrame( - np.random.randn(7, len(var_names)), columns=var_names) + np.random.randn(7, len(var_names)), columns=var_names + ) msg = r"Missing framewise_displacement" with pytest.raises(ValueError, match=msg): confound_remover._process_fmriprep_spec({"data": confounds_df}) -def test_FMRIPrepConfoundRemover_allpresent() -> None: +def test_FMRIPrepConfoundRemover__pick_confounds_adhoc() -> None: + """Test FMRIPrepConfoundRemover pick confounds on adhoc confounds.""" + confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) + # Use non fmriprep variable names + adhoc_names = [f"var{i}" for i in range(2)] + adhoc_df = pd.DataFrame(np.random.randn(10, 2), columns=adhoc_names) + + # map them to valid variable names + fmriprep_names = ["csf", "white_matter"] + fmriprep_all_vars = [ + "csf", + "white_matter", + "csf_power2", + "white_matter_power2", + "csf_derivative1", + "white_matter_derivative1", + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] + + # Build mappings dictionary + mappings = {x: y for x, y in zip(adhoc_names, fmriprep_names)} + input = { + "mappings": {"fmriprep": mappings}, + "data": adhoc_df, + "format": "adhoc", + } + + out = confound_remover._pick_confounds(input) + assert set(out.columns) == set(fmriprep_all_vars) + + +def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None: + """Test FMRIPrepConfoundRemover pick confounds on fmriprep confounds.""" + confound_remover = FMRIPrepConfoundRemover( + strategy={"wm_csf": "full"}, spike=0.2 + ) + fmriprep_all_vars = [ + "csf", + "white_matter", + "csf_power2", + "white_matter_power2", + "csf_derivative1", + "white_matter_derivative1", + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] + + reader = DefaultDataReader() + out1, out2 = None, None + with PartlyCloudyTestingDataGrabber() as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + out1 = confound_remover._pick_confounds(input["BOLD_confounds"]) + assert set(out1.columns) == set(fmriprep_all_vars + ["spike"]) + + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + out2 = confound_remover._pick_confounds(input["BOLD_confounds"]) + assert set(out2.columns) == set(fmriprep_all_vars + ["spike"]) + + assert_frame_equal(out1, out2) + # TODO: Test if fmriprep returns the same derivatives/power2 as we compute + + +def test_FMRIPrepConfoundRemover__validate_data() -> None: + """Test FMRIPrepConfoundRemover validate data.""" + confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) + reader = DefaultDataReader() + with OasisVBMTestingDatagrabber() as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + new_input = input["VBM_GM"] + with pytest.raises( + DimensionError, match="incompatible dimensionality" + ): + confound_remover._validate_data(new_input, None) + + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + new_input = input["BOLD"] + + with pytest.raises(ValueError, match="No extra input"): + confound_remover._validate_data(new_input, None) + with pytest.raises(ValueError, match="No BOLD_confounds provided"): + confound_remover._validate_data(new_input, {}) + with pytest.raises( + ValueError, match="No BOLD_confounds data provided" + ): + confound_remover._validate_data(new_input, {"BOLD_confounds": {}}) + + extra_input = { + "BOLD_confounds": {"data": "wrong"}, + } + msg = "must be a pandas dataframe" + with pytest.raises(ValueError, match=msg): + confound_remover._validate_data(new_input, extra_input) + + extra_input = {"BOLD_confounds": {"data": pd.DataFrame()}} + with pytest.raises(ValueError, match="Image time series and"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": {"data": input["BOLD_confounds"]["data"]} + } + with pytest.raises(ValueError, match="format must be specified"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "wrong", + } + } + with pytest.raises(ValueError, match="Invalid confounds format wrong"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "adhoc", + } + } + with pytest.raises(ValueError, match="variables names mappings"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "adhoc", + "mappings": {}, + } + } + with pytest.raises(ValueError, match="mappings to fmriprep"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "adhoc", + "mappings": { + "fmriprep": { + "rot_x": "wrong", + "rot_y": "rot_z", + "rot_z": "rot_y", + } + }, + } + } + with pytest.raises(ValueError, match=r"names: \['wrong'\]"): + confound_remover._validate_data(new_input, extra_input) + + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "adhoc", + "mappings": { + "fmriprep": { + "wrong": "rot_x", + "rot_y": "rot_z", + "rot_z": "rot_y", + } + }, + } + } + with pytest.raises(ValueError, match=r"Missing columns: \['wrong'\]"): + confound_remover._validate_data(new_input, extra_input) + + +def test_FMRIPrepConfoundRemover__remove_confounds() -> None: + """Test FMRIPrepConfoundRemover remove confounds.""" + confound_remover = FMRIPrepConfoundRemover( + strategy={"wm_csf": "full"}, spike=0.2 + ) + reader = DefaultDataReader() + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + confounds = confound_remover._pick_confounds(input["BOLD_confounds"]) + raw_bold = input["BOLD"]["data"] + clean_bold = confound_remover._remove_confounds( + bold_img=raw_bold, confounds_df=confounds + ) + clean_bold = typing.cast(nib.Nifti1Image, clean_bold) + # TODO: Find a better way to test functionality here + assert ( + clean_bold.header.get_zooms() # type: ignore + == raw_bold.header.get_zooms() + ) + assert clean_bold.get_fdata().shape == raw_bold.get_fdata().shape + # TODO: Test confound remover with mask, needs #79 to be implemented + + +def test_FMRIPrepConfoundRemover_preprocess() -> None: + """Test FMRIPrepConfoundRemover with all confounds present.""" + + # need reader for the data + reader = DefaultDataReader() + # All strategies full, no spike + confound_remover = FMRIPrepConfoundRemover() + + with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: + input = dg["sub-01"] + input = reader.fit_transform(input) + orig_bold = input["BOLD"]["data"].get_fdata().copy() + pre_input = input["BOLD"] + pre_extra_input = {"BOLD_confounds": input["BOLD_confounds"]} + key, output = confound_remover.preprocess(pre_input, pre_extra_input) + trans_bold = output["data"].get_fdata() + # Transformation is in place + assert_array_equal(trans_bold, input["BOLD"]["data"].get_fdata()) + + # Data should have the same shape + assert orig_bold.shape == trans_bold.shape + + # but be different + assert_raises( + AssertionError, assert_array_equal, orig_bold, trans_bold + ) + assert key == "BOLD" + + +def test_FMRIPrepConfoundRemover_fit_transform() -> None: """Test FMRIPrepConfoundRemover with all confounds present.""" # need reader for the data @@ -237,315 +490,23 @@ def test_FMRIPrepConfoundRemover_allpresent() -> None: # Data should have the same shape assert orig_bold.shape == trans_bold.shape + + # but be different assert_raises( AssertionError, assert_array_equal, orig_bold, trans_bold ) - -# # TODO: split the tests -# def test_baseconfoundremover() -> None: -# """Test BaseConfoundRemover.""" -# # Generate a simulated BOLD img -# siimg, simsk = _simu_img() - -# # generate random confound dataframe with Felix's column naming - -# motion_basic = [f"RP.{i}" for i in range(1, 7)] -# motion_power2 = [f"RP^2.{i}" for i in range(1, 7)] -# motion_derivatives = [f"DRP.{i}" for i in range(1, 7)] -# motion_full = [f"DRP^2.{i}" for i in range(1, 7)] - -# wm_csf_basic = ["WM", "CSF"] -# wm_csf_power2 = ["WM^2", "CSF^2"] -# wm_csf_derivatives = ["DWM", "DCSF"] -# wm_csf_full = ["DWM^2", "DCSF^2"] - -# gs_basic = ["GS"] -# gs_power2 = ["GS^2"] -# gs_derivatives = ["DGS"] -# gs_full = ["DGS^2"] - -# confound_column_names = [] - -# confound_column_names.append("FD") # spike - -# confound_column_names.extend(motion_basic) -# confound_column_names.extend(motion_power2) -# confound_column_names.extend(motion_derivatives) -# confound_column_names.extend(motion_full) - -# confound_column_names.extend(wm_csf_basic) -# confound_column_names.extend(wm_csf_power2) -# confound_column_names.extend(wm_csf_derivatives) -# confound_column_names.extend(wm_csf_full) - -# confound_column_names.extend(gs_basic) -# confound_column_names.extend(gs_power2) -# confound_column_names.extend(gs_derivatives) -# confound_column_names.extend(gs_full) - -# # add some random irrelevant confounds -# for _ in range(10): -# confound_column_names.append(generate_conf_name()) - -# np.random.shuffle(confound_column_names) -# n_cols = len(confound_column_names) -# confounds_df = pd.DataFrame( -# np.random.randint(0, 100, size=(100, n_cols)), -# columns=confound_column_names, -# ) - -# # Generate spec from Felix's column naming -# spec = { -# "motion": { -# "basic": motion_basic, -# "power2": motion_basic + motion_power2, -# "derivatives": motion_basic + motion_derivatives, -# "full": motion_basic -# + motion_derivatives -# + motion_power2 -# + motion_full, -# }, -# "wm_csf": { -# "basic": wm_csf_basic, -# "power2": wm_csf_basic + wm_csf_power2, -# "derivatives": wm_csf_basic + wm_csf_derivatives, -# "full": wm_csf_basic -# + wm_csf_derivatives -# + wm_csf_power2 -# + wm_csf_full, -# }, -# "global_signal": { -# "basic": gs_basic, -# "power2": gs_basic + gs_power2, -# "derivatives": gs_basic + gs_derivatives, -# "full": gs_basic + gs_derivatives + gs_power2 + gs_full, -# }, -# } - -# # generate a junifer pipeline data object dictionary -# input_data_obj = {} -# input_data_obj["meta"] = {} -# input_data_obj["BOLD"] = {} -# input_data_obj["BOLD"]["data"] = siimg -# input_data_obj["confounds"] = {} -# input_data_obj["confounds"]["path"] = Path("/test.df") -# input_data_obj["confounds"]["data"] = confounds_df -# input_data_obj["confounds"]["names"] = {} -# input_data_obj["confounds"]["names"]["spec"] = spec -# input_data_obj["confounds"]["names"]["spike"] = "FD" - -# # generate confound removal strategies with varying numbers of parameters - -# # Test #1: 36 params, no derivatives to compute, no spike -# # 36 params -# strat1 = {"motion": "full", "wm_csf": "full", "global_signal": "full"} - -# cr = BaseConfoundRemover( -# strategy=strat1, spike=None, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 36 -# assert all(x in t_df.columns for x in motion_basic) -# assert all(x in t_df.columns for x in motion_power2) -# assert all(x in t_df.columns for x in motion_derivatives) -# assert all(x in t_df.columns for x in motion_full) -# assert all(x in t_df.columns for x in wm_csf_basic) -# assert all(x in t_df.columns for x in wm_csf_power2) -# assert all(x in t_df.columns for x in wm_csf_derivatives) -# assert all(x in t_df.columns for x in wm_csf_full) -# assert all(x in t_df.columns for x in gs_basic) -# assert all(x in t_df.columns for x in gs_power2) -# assert all(x in t_df.columns for x in gs_derivatives) -# assert all(x in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" not in t_df.columns - -# # Test #2: 24 params, no derivatives to compute, no spike -# # 24 params -# strat2 = { -# "motion": "full", -# } - -# cr = BaseConfoundRemover( -# strategy=strat2, spike=None, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 24 -# assert all(x in t_df.columns for x in motion_basic) -# assert all(x in t_df.columns for x in motion_power2) -# assert all(x in t_df.columns for x in motion_derivatives) -# assert all(x in t_df.columns for x in motion_full) -# assert all(x not in t_df.columns for x in wm_csf_basic) -# assert all(x not in t_df.columns for x in wm_csf_power2) -# assert all(x not in t_df.columns for x in wm_csf_derivatives) -# assert all(x not in t_df.columns for x in wm_csf_full) -# assert all(x not in t_df.columns for x in gs_basic) -# assert all(x not in t_df.columns for x in gs_power2) -# assert all(x not in t_df.columns for x in gs_derivatives) -# assert all(x not in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" not in t_df.columns - -# # Test #3: 9 params, no derivatives to compute, no spike -# strat3 = {"motion": "basic", "wm_csf": "basic", "global_signal": "basic"} - -# cr = BaseConfoundRemover( -# strategy=strat3, spike=None, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 9 -# assert all(x in t_df.columns for x in motion_basic) -# assert all(x not in t_df.columns for x in motion_power2) -# assert all(x not in t_df.columns for x in motion_derivatives) -# assert all(x not in t_df.columns for x in motion_full) -# assert all(x in t_df.columns for x in wm_csf_basic) -# assert all(x not in t_df.columns for x in wm_csf_power2) -# assert all(x not in t_df.columns for x in wm_csf_derivatives) -# assert all(x not in t_df.columns for x in wm_csf_full) -# assert all(x in t_df.columns for x in gs_basic) -# assert all(x not in t_df.columns for x in gs_power2) -# assert all(x not in t_df.columns for x in gs_derivatives) -# assert all(x not in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" not in t_df.columns - -# # Test #4: 6 params, no derivatives to compute, no spike -# strat4 = { -# "motion": "basic", -# } -# cr = BaseConfoundRemover( -# strategy=strat4, spike=None, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 6 -# assert all(x in t_df.columns for x in motion_basic) -# assert all(x not in t_df.columns for x in motion_power2) -# assert all(x not in t_df.columns for x in motion_derivatives) -# assert all(x not in t_df.columns for x in motion_full) -# assert all(x not in t_df.columns for x in wm_csf_basic) -# assert all(x not in t_df.columns for x in wm_csf_power2) -# assert all(x not in t_df.columns for x in wm_csf_derivatives) -# assert all(x not in t_df.columns for x in wm_csf_full) -# assert all(x not in t_df.columns for x in gs_basic) -# assert all(x not in t_df.columns for x in gs_power2) -# assert all(x not in t_df.columns for x in gs_derivatives) -# assert all(x not in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" not in t_df.columns - -# # Test #5: 2 params, no derivatives to compute, no spike -# strat5 = { -# "wm_csf": "basic", -# } -# cr = BaseConfoundRemover( -# strategy=strat5, spike=None, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 2 -# assert all(x not in t_df.columns for x in motion_basic) -# assert all(x not in t_df.columns for x in motion_power2) -# assert all(x not in t_df.columns for x in motion_derivatives) -# assert all(x not in t_df.columns for x in motion_full) -# assert all(x in t_df.columns for x in wm_csf_basic) -# assert all(x not in t_df.columns for x in wm_csf_power2) -# assert all(x not in t_df.columns for x in wm_csf_derivatives) -# assert all(x not in t_df.columns for x in wm_csf_full) -# assert all(x not in t_df.columns for x in gs_basic) -# assert all(x not in t_df.columns for x in gs_power2) -# assert all(x not in t_df.columns for x in gs_derivatives) -# assert all(x not in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" not in t_df.columns - -# out = cr.fit_transform(input_data_obj) -# check_niimg_4d(out["BOLD"]["data"]) -# # TODO: check meta - -# # Test #6: 12 params, derivatives to compute, spike -# to_select = [ -# x for x in confounds_df.columns if x not in motion_derivatives -# ] -# no_d_df = confounds_df[to_select] -# input_data_obj["confounds"]["data"] = no_d_df - -# derivatives = {f"D{x}": x for x in motion_basic} - -# input_data_obj["confounds"]["names"]["derivatives"] = derivatives - -# strat6 = { -# "motion": "derivatives", -# } -# cr = BaseConfoundRemover( -# strategy=strat6, spike=0.75, mask_img=simsk, t_r=0.75 -# ) -# cr.validate_input(list(input_data_obj.keys())) -# out_type = cr.get_output_kind(list(input_data_obj.keys())) - -# assert "BOLD" in out_type - -# # Check if the input data is valid -# cr._validate_data(input_data_obj) - -# # Check that the confounds are picked correctly: -# t_df = cr._pick_confounds(input_data_obj["confounds"]) -# assert len(t_df.columns) == 13 -# assert all(x in t_df.columns for x in motion_basic) -# assert all(x not in t_df.columns for x in motion_power2) -# assert all(x in t_df.columns for x in motion_derivatives) -# assert all(x not in t_df.columns for x in motion_full) -# assert all(x not in t_df.columns for x in wm_csf_basic) -# assert all(x not in t_df.columns for x in wm_csf_power2) -# assert all(x not in t_df.columns for x in wm_csf_derivatives) -# assert all(x not in t_df.columns for x in wm_csf_full) -# assert all(x not in t_df.columns for x in gs_basic) -# assert all(x not in t_df.columns for x in gs_power2) -# assert all(x not in t_df.columns for x in gs_derivatives) -# assert all(x not in t_df.columns for x in gs_full) -# assert "FD" not in t_df.columns -# assert "spike" in t_df.columns + assert output["meta"] == input["meta"] # general meta does not change + assert "meta" in output["BOLD"] + assert "preprocess" in output["BOLD"]["meta"] + t_meta = output["BOLD"]["meta"]["preprocess"] + assert t_meta["class"] == "FMRIPrepConfoundRemover" + # It should have all the default parameters + assert t_meta["strategy"] == confound_remover.strategy + assert t_meta["spike"] is None + assert t_meta["detrend"] is True + assert t_meta["standardize"] is True + assert t_meta["low_pass"] is None + assert t_meta["high_pass"] is None + assert t_meta["t_r"] is None + assert t_meta["mask_img"] is None diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index 0bff71f10..ceff77137 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -199,16 +199,13 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber): out = super().__getitem__(element) i_sub = int(element.split("-")[1]) - 1 out["BOLD"] = {"path": Path(self._dataset["func"][i_sub])} - conf_format = "adhoc" if self.reduce_confounds else "fmriprep" + conf_format = "fmriprep" out["BOLD_confounds"] = { "path": Path(self._dataset["confounds"][i_sub]), "format": conf_format, } - # if self.reduce_confounds: - # spec = { - # } # Set the element accordingly out["meta"]["element"] = {"subject": element} return out -- 2.52.0 From 00172fee4ff2db8d9a6fedaa9c1bdbd5fda97533 Mon Sep 17 00:00:00 2001 From: Fede Date: Sat, 29 Oct 2022 22:38:43 +0300 Subject: [PATCH 124/142] damn test --- junifer/testing/tests/test_partlycloudytesting_datagrabber.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/testing/tests/test_partlycloudytesting_datagrabber.py b/junifer/testing/tests/test_partlycloudytesting_datagrabber.py index aceb93dad..e45f1e373 100644 --- a/junifer/testing/tests/test_partlycloudytesting_datagrabber.py +++ b/junifer/testing/tests/test_partlycloudytesting_datagrabber.py @@ -32,7 +32,7 @@ def test_PartlyCloudyTestingDataGrabber() -> None: assert out["BOLD_confounds"]["path"].exists() assert out["BOLD_confounds"]["path"].is_file() assert "format" in out["BOLD_confounds"] - assert "adhoc" == out["BOLD_confounds"]["format"] + assert "fmriprep" == out["BOLD_confounds"]["format"] with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: out = dg["sub-01"] -- 2.52.0 From 42f25c2c3fc7d0199dc5786f32da235806b105f7 Mon Sep 17 00:00:00 2001 From: Fede Date: Sun, 30 Oct 2022 11:51:20 +0200 Subject: [PATCH 125/142] One more test --- .../preprocess/tests/test_preprocess_base.py | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 junifer/preprocess/tests/test_preprocess_base.py diff --git a/junifer/preprocess/tests/test_preprocess_base.py b/junifer/preprocess/tests/test_preprocess_base.py new file mode 100644 index 000000000..aaf5e5882 --- /dev/null +++ b/junifer/preprocess/tests/test_preprocess_base.py @@ -0,0 +1,52 @@ +"""Provide tests for base marker.""" + +# Authors: Federico Raimondo +# Synchon Mandal +# License: AGPL + +import pytest + +from junifer.preprocess.base import BasePreprocessor + + +def test_base_preprocessor_abstractness() -> None: + """Test BasePreprocessor is abstract base class.""" + with pytest.raises(TypeError, match=r"abstract"): + BasePreprocessor(on=["BOLD"]) # type: ignore + + +def test_base_preprocessor_subclassing() -> None: + """Test proper subclassing of BasePreprocessor.""" + # Create concrete class + class MyBasePreprocessor(BasePreprocessor): + def get_valid_inputs(self): + return ["BOLD", "T1w"] + + def get_output_kind(self, input): + return ["timeseries"] + + def preprocess(self, input, extra_input): + return "BOLD", input + + with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"): + MyBasePreprocessor(on=["BOLD", "T2w"]) + + # Create input for marker + input_ = { + "meta": {"datagrabber": "dg", "element": "elem", "datareader": "dr"}, + "BOLD": { + "path": ".", + "data": "data", + }, + } + prep = MyBasePreprocessor(on=["BOLD"]) + + with pytest.raises(ValueError, match="not have the required data"): + prep.validate_input(["T1w"]) + + output = prep.fit_transform(input=input_) # process + # Check output + assert "BOLD" in output + assert "data" in output["BOLD"] + assert "path" in output["BOLD"] + assert "meta" in output["BOLD"] -- 2.52.0 From 796778123e8203e60894daa392f9ef774aecb9c7 Mon Sep 17 00:00:00 2001 From: Fede Date: Sun, 30 Oct 2022 14:01:54 +0200 Subject: [PATCH 126/142] One more --- junifer/preprocess/tests/test_preprocess_base.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/junifer/preprocess/tests/test_preprocess_base.py b/junifer/preprocess/tests/test_preprocess_base.py index aaf5e5882..11a3e1b46 100644 --- a/junifer/preprocess/tests/test_preprocess_base.py +++ b/junifer/preprocess/tests/test_preprocess_base.py @@ -31,6 +31,9 @@ def test_base_preprocessor_subclassing() -> None: with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"): MyBasePreprocessor(on=["BOLD", "T2w"]) + with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"): + MyBasePreprocessor(on="T2w") + # Create input for marker input_ = { "meta": {"datagrabber": "dg", "element": "elem", "datareader": "dr"}, -- 2.52.0 From c7a3cc3ed4ec0ab00c964570a16fcc872aa1086d Mon Sep 17 00:00:00 2001 From: Fede Date: Sun, 30 Oct 2022 14:08:34 +0200 Subject: [PATCH 127/142] test modify only what is expected --- junifer/preprocess/tests/test_preprocess_base.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/junifer/preprocess/tests/test_preprocess_base.py b/junifer/preprocess/tests/test_preprocess_base.py index 11a3e1b46..cb4687772 100644 --- a/junifer/preprocess/tests/test_preprocess_base.py +++ b/junifer/preprocess/tests/test_preprocess_base.py @@ -26,6 +26,7 @@ def test_base_preprocessor_subclassing() -> None: return ["timeseries"] def preprocess(self, input, extra_input): + input["data"] = f"mofidied_{input['data']}" return "BOLD", input with pytest.raises(ValueError, match=r"cannot be computed on \['T2w'\]"): @@ -41,6 +42,10 @@ def test_base_preprocessor_subclassing() -> None: "path": ".", "data": "data", }, + "T1w": { + "path": ".", + "data": "data", + }, } prep = MyBasePreprocessor(on=["BOLD"]) @@ -51,5 +56,10 @@ def test_base_preprocessor_subclassing() -> None: # Check output assert "BOLD" in output assert "data" in output["BOLD"] + assert output["BOLD"]["data"] == "mofidied_data" assert "path" in output["BOLD"] assert "meta" in output["BOLD"] + + assert "T1w" in output + assert "data" in output["T1w"] + assert output["T1w"]["data"] == "data" -- 2.52.0 From db026a3f62e5e50bc2f0c36a6db4a26142f800ef Mon Sep 17 00:00:00 2001 From: Fede Date: Mon, 31 Oct 2022 08:23:40 +0200 Subject: [PATCH 128/142] Test for derivative only --- junifer/preprocess/tests/test_confounds.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index e28826879..9c2cedddb 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -199,7 +199,7 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: # Two component strategy, mixed confounds, no spike confound_remover = FMRIPrepConfoundRemover( - strategy={"wm_csf": "power2", "global_signal": "full"} + strategy={"wm_csf": "power2", "global_signal": "derivatives"} ) var_names = ["csf", "white_matter", "global_signal"] @@ -207,8 +207,6 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: missing_sq_names = [ "csf_power2", "white_matter_power2", - "global_signal_power2", - "global_signal_derivative1_power2", ] all_names = var_names + missing_der_names + missing_sq_names -- 2.52.0 From e8b8abc1f826840fe0b5e09d5614e0231d6a5a2e Mon Sep 17 00:00:00 2001 From: Fede Date: Mon, 31 Oct 2022 08:37:58 +0200 Subject: [PATCH 129/142] Fix bug --- junifer/preprocess/confounds.py | 2 +- junifer/preprocess/tests/test_confounds.py | 15 +++++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index 8b9eb5fff..0a38fd96c 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -471,7 +471,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): if x not in confound_df.columns ] - if len(missing) is not None: + if len(missing) > 0: raise ValueError( "Invalid confounds file. Missing columns: " f"{missing}. " diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 9c2cedddb..8bdaa1835 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -415,6 +415,21 @@ def test_FMRIPrepConfoundRemover__validate_data() -> None: with pytest.raises(ValueError, match=r"Missing columns: \['wrong'\]"): confound_remover._validate_data(new_input, extra_input) + extra_input = { + "BOLD_confounds": { + "data": input["BOLD_confounds"]["data"], + "format": "adhoc", + "mappings": { + "fmriprep": { + "rot_x": "rot_x", + "rot_y": "rot_z", + "rot_z": "rot_y", + } + }, + } + } + confound_remover._validate_data(new_input, extra_input) + def test_FMRIPrepConfoundRemover__remove_confounds() -> None: """Test FMRIPrepConfoundRemover remove confounds.""" -- 2.52.0 From 3fc9287d0c3213f4ace69e9354ad9abb679ca62f Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 14:10:00 +0200 Subject: [PATCH 130/142] Addressing review + decorator --- junifer/api/decorators.py | 24 +++++ junifer/preprocess/__init__.py | 3 +- junifer/preprocess/base.py | 18 ++-- junifer/preprocess/confounds.py | 63 +++++++---- junifer/preprocess/tests/test_confounds.py | 101 +++++++----------- .../preprocess/tests/test_preprocess_base.py | 2 +- junifer/testing/datagrabbers.py | 11 +- .../tests/test_oasisvmbtesting_datagrabber.py | 4 +- 8 files changed, 127 insertions(+), 99 deletions(-) diff --git a/junifer/api/decorators.py b/junifer/api/decorators.py index a5252486a..3b9d832f9 100644 --- a/junifer/api/decorators.py +++ b/junifer/api/decorators.py @@ -32,6 +32,30 @@ def register_datagrabber(klass: type) -> type: return klass +def register_preprocessor(klass: type) -> type: + """Preprocessor registration decorator. + + Registers the preprocessor so it can be used by name. + + Parameters + ---------- + klass: class + The class of the preprocessor to register. + + Returns + ------- + klass: class + The unmodified input class. + + """ + register( + step="preprocessing", + name=klass.__name__, + klass=klass, + ) + return klass + + def register_marker(klass: type) -> type: """Marker registration decorator. diff --git a/junifer/preprocess/__init__.py b/junifer/preprocess/__init__.py index 532763ce5..20959dfd4 100644 --- a/junifer/preprocess/__init__.py +++ b/junifer/preprocess/__init__.py @@ -4,4 +4,5 @@ # Leonard Sasse # License: AGPL -from .confounds import FMRIPrepConfoundRemover +from .confounds import fMRIPrepConfoundRemover +from .base import BasePreprocessor \ No newline at end of file diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py index 6e710dbe6..13b00b5ba 100644 --- a/junifer/preprocess/base.py +++ b/junifer/preprocess/base.py @@ -13,13 +13,13 @@ from ..utils import logger, raise_error class BasePreprocessor(ABC, PipelineStepMixin): - """Abstract base class for all preprocessors. + """Provide abstract base class for all preprocessors. Parameters ---------- - on : str or list of str + on : str or list of str, optional The kind of data to apply the preprocessor to. If None, - will work on all available data (default: None). + will work on all available data (default None). """ @@ -88,7 +88,8 @@ class BasePreprocessor(ABC, PipelineStepMixin): Returns ------- list of str - The list of data types that can be used as input for this marker + The list of data types that can be used as input for this + preprocessor """ raise_error( @@ -107,13 +108,10 @@ class BasePreprocessor(ABC, PipelineStepMixin): Returns ------- dict - The metadata as a dictionary with the only key 'marker'. + The metadata as a dictionary with the only key 'preprocess'. """ s_meta = super().get_meta() - # same marker can be "fit"ted into different kinds, so the name - # is created from the kind and the name of the marker - s_meta["kind"] = kind return {"preprocess": s_meta} def fit_transform( @@ -158,10 +156,10 @@ class BasePreprocessor(ABC, PipelineStepMixin): Parameters ---------- - input : Dict[str, Dict] + input : dict[str, dict] A single input from the pipeline data object in which to compute the marker. - extra_input : Dict, optional + extra_input : dict, optional The other fields in the pipeline data object. Useful for accessing other data kind that needs to be used in the computation. For example, the functional connectivity markers can make use of the diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index 0a38fd96c..72a441b91 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -1,4 +1,4 @@ -"""Provide base class for confound removal.""" +"""Provide class for confound removal using FMRIPrep format.""" # Authors: Federico Raimondo # Leonard Sasse @@ -14,6 +14,7 @@ from nilearn.image import clean_img from nilearn.masking import compute_brain_mask from .base import BasePreprocessor +from ..api.decorators import register_preprocessor from ..utils import logger, raise_error @@ -86,8 +87,9 @@ FMRIPREP_VALID_NAMES = [ ] -class FMRIPrepConfoundRemover(BasePreprocessor): - """Class for confound removal. +@register_preprocessor +class fMRIPrepConfoundRemover(BasePreprocessor): + """Class for confound removal using fMRIPrep confounds format. Read confound files and select columns according to a pre-defined strategy. @@ -113,7 +115,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): If None, no spike regressor is added. If spike is a float, it will add a spike regressor for every point at which framewise displacement exceeds the specified float (default None). - detrend : bool, Optional + detrend : bool, optional If True, detrending will be applied on timeseries (before confound removal) (default True). standardize : bool, optional @@ -150,7 +152,6 @@ class FMRIPrepConfoundRemover(BasePreprocessor): mask_img: Optional["Nifti1Image"] = None, ) -> None: """Initialise the class.""" - super().__init__() if strategy is None: strategy = { "motion": "full", @@ -194,6 +195,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): "include it in the future", klass=ValueError, ) + super().__init__() def validate_input(self, input: List[str]) -> None: """Validate the input to the pipeline step. @@ -202,7 +204,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): ---------- input : list of str The input to the pipeline step. The list must contain the - available Junifer Data dictionary keys. + available Junifer Data object keys. Raises ------ @@ -226,12 +228,12 @@ class FMRIPrepConfoundRemover(BasePreprocessor): ---------- input : list of str The input to the pipeline step. The list must contain the - available Junifer Data dictionary keys. + available Junifer Data object keys. Returns ------- list of str - The updated list of available Junifer Data dictionary keys after + The updated list of available Junifer Data object keys after the pipeline step. """ @@ -249,7 +251,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): """ return ["BOLD"] - def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]): + def _map_adhoc_to_fmriprep(self, input: Dict[str, Any]) -> None: """Map the adhoc format to the fmpriprep format spec. Based on the spec, map the column names to match the fmriprep format. @@ -279,7 +281,7 @@ class FMRIPrepConfoundRemover(BasePreprocessor): def _process_fmriprep_spec( self, input: Dict[str, Any] - ) -> Tuple[List, Dict, Dict, str]: + ) -> Tuple[List[str], Dict[str, str], Dict[str, str], str]: """Process the fmpriprep format spec from the specified file. Based on the strategy, find the relevant column names in the dataframe, @@ -298,10 +300,10 @@ class FMRIPrepConfoundRemover(BasePreprocessor): to_select : list of str List of confounds to select from the confounds file, based on the strategy - squares_to_compute : dict[str, str] + squares_to_compute : dict Dictionary containing the missing power2 confounds to compute (keys) and the corresponding confounds to square (values) - derivatives_to_compute : dict[str, str] + derivatives_to_compute : dict Dictionary containing the missing derivatives confounds to compute (keys) and the corresponding confounds to compute the derivative from (values) @@ -362,7 +364,20 @@ class FMRIPrepConfoundRemover(BasePreprocessor): return out def _pick_confounds(self, input: Dict[str, Any]) -> pd.DataFrame: - """Select relevant confounds from the specified file.""" + """Select relevant confounds from the specified file. + + Parameters + ---------- + input : dict + Dictionary containing the "BOLD_confounds" value from the + Junifer Data object. + + Returns + ------- + confounds_df : pandas.DataFrame + Dataframe containing the relevant confounds. + + """ confounds_format = input["format"] if confounds_format == "adhoc": @@ -404,7 +419,18 @@ class FMRIPrepConfoundRemover(BasePreprocessor): input: Dict[str, Any], extra_input: Optional[Dict[str, Any]] = None, ) -> None: - """Validate input data.""" + """Validate input data. + + Parameters + ---------- + input : dict + Dictionary containing the "BOLD" value from the + Junifer Data object. + extra_input : dict, optional + Dictionary containing the rest of the Junifer Data object. Must + include the "BOLD_confounds" key. + + """ # Bold must be 4D niimg check_niimg_4d(input["data"]) @@ -546,13 +572,10 @@ class FMRIPrepConfoundRemover(BasePreprocessor): Parameters ---------- input : Dict[str, Dict] - A single input from the pipeline data object in which to compute - the marker. + A single input from the Junifer Data object in which to preprocess. extra_input : Dict, optional - The other fields in the pipeline data object. Useful for accessing - other data kind that needs to be used in the computation. For - example, the functional connectivity markers can make use of the - confounds if available (default None). + The other fields in the Junifer Data object. Must include the + "BOLD_confounds" key. Returns ------- diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 8bdaa1835..2d7d21950 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -1,4 +1,4 @@ -"""Provide tests for confound removal.""" +"""Provide tests for fMRIPrepConfoundRemover.""" # Authors: Federico Raimondo # Leonard Sasse @@ -15,52 +15,33 @@ import numpy as np import nibabel as nib from nilearn._utils.exceptions import DimensionError -from junifer.preprocess.confounds import FMRIPrepConfoundRemover +from junifer.preprocess.confounds import fMRIPrepConfoundRemover from junifer.testing.datagrabbers import ( OasisVBMTestingDatagrabber, PartlyCloudyTestingDataGrabber, ) from junifer.datareader import DefaultDataReader -# Set RNG seed for reproducibility -# np.random.seed(1234567) - -# def generate_conf_name( -# size: int = 6, chars: str = string.ascii_uppercase + string.digits -# ) -> str: -# """Generate configuration name.""" -# return "".join(random.choice(chars) for _ in range(size)) - - -# def _simu_img() -> Tuple[Nifti1Image, Nifti1Image]: -# # Random 4D volume with 100 time points -# vol = 100 + 10 * np.random.randn(5, 5, 2, 100) -# img = Nifti1Image(vol, np.eye(4)) -# # Create an nifti image with the data, and corresponding mask -# mask = Nifti1Image(np.ones([5, 5, 2]), np.eye(4)) -# return img, mask - - -def test_FMRIPrepConfoundRemover_init() -> None: - """Test FMRIPrepConfoundRemover init.""" +def test_fMRIPrepConfoundRemover_init() -> None: + """Test fMRIPrepConfoundRemover init.""" with pytest.raises(ValueError, match="keys must be strings"): - FMRIPrepConfoundRemover(strategy={1: "full"}) # type: ignore + fMRIPrepConfoundRemover(strategy={1: "full"}) # type: ignore with pytest.raises(ValueError, match="values must be strings"): - FMRIPrepConfoundRemover(strategy={"motion": 1}) # type: ignore + fMRIPrepConfoundRemover(strategy={"motion": 1}) # type: ignore with pytest.raises(ValueError, match="component names"): - FMRIPrepConfoundRemover(strategy={"wrong": "full"}) + fMRIPrepConfoundRemover(strategy={"wrong": "full"}) with pytest.raises(ValueError, match="confound types"): - FMRIPrepConfoundRemover(strategy={"motion": "wrong"}) + fMRIPrepConfoundRemover(strategy={"motion": "wrong"}) -def test_FMRIPrepConfoundRemover_validate_input() -> None: - """Test FMRIPrepConfoundRemover validate_input.""" - confound_remover = FMRIPrepConfoundRemover() +def test_fMRIPrepConfoundRemover_validate_input() -> None: + """Test fMRIPrepConfoundRemover validate_input.""" + confound_remover = fMRIPrepConfoundRemover() # Input is valid when both BOLD and BOLD_confounds are present @@ -80,9 +61,9 @@ def test_FMRIPrepConfoundRemover_validate_input() -> None: confound_remover.validate_input(input) -def test_FMRIPrepConfoundRemover_get_output_kind() -> None: - """Test FMRIPrepConfoundRemover validate_input.""" - confound_remover = FMRIPrepConfoundRemover() +def test_fMRIPrepConfoundRemover_get_output_kind() -> None: + """Test fMRIPrepConfoundRemover validate_input.""" + confound_remover = fMRIPrepConfoundRemover() inputs = [ ["BOLD", "T1w", "BOLD_confounds"], ["BOLD", "VBM_GM", "BOLD_confounds"], @@ -93,9 +74,9 @@ def test_FMRIPrepConfoundRemover_get_output_kind() -> None: assert confound_remover.get_output_kind(input) == input -def test_FMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None: - """Test FMRIPrepConfoundRemover adhoc to fmriprep spec mapping.""" - confound_remover = FMRIPrepConfoundRemover() +def test_fMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None: + """Test fMRIPrepConfoundRemover adhoc to fmriprep spec mapping.""" + confound_remover = fMRIPrepConfoundRemover() # Use non fmriprep variable names adhoc_names = [f"var{i}" for i in range(6)] adhoc_df = pd.DataFrame(np.random.randn(10, 6), columns=adhoc_names) @@ -122,11 +103,11 @@ def test_FMRIPrepConfoundRemover__map_adhoc_to_fmriprep() -> None: assert adhoc_df.columns.tolist() == fmriprep_names -def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: - """Test FMRIPrepConfoundRemover fmriprep spec processing.""" +def test_fMRIPrepConfoundRemover__process_fmriprep_spec() -> None: + """Test fMRIPrepConfoundRemover fmriprep spec processing.""" # Test one strategy, full, no spike - confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) + confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) var_names = [ "csf", @@ -171,7 +152,7 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: assert spike_name == "framewise_displacement" # Same strategy, with spike, only basics are present - confound_remover = FMRIPrepConfoundRemover( + confound_remover = fMRIPrepConfoundRemover( strategy={"wm_csf": "full"}, spike=0.2 ) @@ -198,7 +179,7 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: assert spike_name == "framewise_displacement" # Two component strategy, mixed confounds, no spike - confound_remover = FMRIPrepConfoundRemover( + confound_remover = fMRIPrepConfoundRemover( strategy={"wm_csf": "power2", "global_signal": "derivatives"} ) @@ -223,7 +204,7 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: # Test for wrong columns/strategy pairs - confound_remover = FMRIPrepConfoundRemover( + confound_remover = fMRIPrepConfoundRemover( strategy={"wm_csf": "full"}, spike=0.2 ) var_names = ["csf"] @@ -245,9 +226,9 @@ def test_FMRIPrepConfoundRemover__process_fmriprep_spec() -> None: confound_remover._process_fmriprep_spec({"data": confounds_df}) -def test_FMRIPrepConfoundRemover__pick_confounds_adhoc() -> None: - """Test FMRIPrepConfoundRemover pick confounds on adhoc confounds.""" - confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) +def test_fMRIPrepConfoundRemover__pick_confounds_adhoc() -> None: + """Test fMRIPrepConfoundRemover pick confounds on adhoc confounds.""" + confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) # Use non fmriprep variable names adhoc_names = [f"var{i}" for i in range(2)] adhoc_df = pd.DataFrame(np.random.randn(10, 2), columns=adhoc_names) @@ -278,8 +259,8 @@ def test_FMRIPrepConfoundRemover__pick_confounds_adhoc() -> None: def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None: - """Test FMRIPrepConfoundRemover pick confounds on fmriprep confounds.""" - confound_remover = FMRIPrepConfoundRemover( + """Test fMRIPrepConfoundRemover pick confounds on fmriprep confounds.""" + confound_remover = fMRIPrepConfoundRemover( strategy={"wm_csf": "full"}, spike=0.2 ) fmriprep_all_vars = [ @@ -311,9 +292,9 @@ def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None: # TODO: Test if fmriprep returns the same derivatives/power2 as we compute -def test_FMRIPrepConfoundRemover__validate_data() -> None: - """Test FMRIPrepConfoundRemover validate data.""" - confound_remover = FMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) +def test_fMRIPrepConfoundRemover__validate_data() -> None: + """Test fMRIPrepConfoundRemover validate data.""" + confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) reader = DefaultDataReader() with OasisVBMTestingDatagrabber() as dg: input = dg["sub-01"] @@ -431,9 +412,9 @@ def test_FMRIPrepConfoundRemover__validate_data() -> None: confound_remover._validate_data(new_input, extra_input) -def test_FMRIPrepConfoundRemover__remove_confounds() -> None: - """Test FMRIPrepConfoundRemover remove confounds.""" - confound_remover = FMRIPrepConfoundRemover( +def test_fMRIPrepConfoundRemover__remove_confounds() -> None: + """Test fMRIPrepConfoundRemover remove confounds.""" + confound_remover = fMRIPrepConfoundRemover( strategy={"wm_csf": "full"}, spike=0.2 ) reader = DefaultDataReader() @@ -455,13 +436,13 @@ def test_FMRIPrepConfoundRemover__remove_confounds() -> None: # TODO: Test confound remover with mask, needs #79 to be implemented -def test_FMRIPrepConfoundRemover_preprocess() -> None: - """Test FMRIPrepConfoundRemover with all confounds present.""" +def test_fMRIPrepConfoundRemover_preprocess() -> None: + """Test fMRIPrepConfoundRemover with all confounds present.""" # need reader for the data reader = DefaultDataReader() # All strategies full, no spike - confound_remover = FMRIPrepConfoundRemover() + confound_remover = fMRIPrepConfoundRemover() with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: input = dg["sub-01"] @@ -484,13 +465,13 @@ def test_FMRIPrepConfoundRemover_preprocess() -> None: assert key == "BOLD" -def test_FMRIPrepConfoundRemover_fit_transform() -> None: - """Test FMRIPrepConfoundRemover with all confounds present.""" +def test_fMRIPrepConfoundRemover_fit_transform() -> None: + """Test fMRIPrepConfoundRemover with all confounds present.""" # need reader for the data reader = DefaultDataReader() # All strategies full, no spike - confound_remover = FMRIPrepConfoundRemover() + confound_remover = fMRIPrepConfoundRemover() with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg: input = dg["sub-01"] @@ -513,7 +494,7 @@ def test_FMRIPrepConfoundRemover_fit_transform() -> None: assert "meta" in output["BOLD"] assert "preprocess" in output["BOLD"]["meta"] t_meta = output["BOLD"]["meta"]["preprocess"] - assert t_meta["class"] == "FMRIPrepConfoundRemover" + assert t_meta["class"] == "fMRIPrepConfoundRemover" # It should have all the default parameters assert t_meta["strategy"] == confound_remover.strategy assert t_meta["spike"] is None diff --git a/junifer/preprocess/tests/test_preprocess_base.py b/junifer/preprocess/tests/test_preprocess_base.py index cb4687772..90d3c89ef 100644 --- a/junifer/preprocess/tests/test_preprocess_base.py +++ b/junifer/preprocess/tests/test_preprocess_base.py @@ -1,4 +1,4 @@ -"""Provide tests for base marker.""" +"""Provide tests for BasePreprocessor.""" # Authors: Federico Raimondo # Synchon Mandal diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index ceff77137..7bd4c7d2a 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -137,17 +137,18 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber): 6 anatomical compcor parameters. This selection only serves the purpose of having realistic examples. Depending on your research question, other confounds might be more appropriate. - If False, returns all :term:`fMRIPrep` confounds. - Default=True. + If False, returns all :term:`fMRIPrep` confounds (default True). - age_group : str, optional - Default='both'. Which age group to fetch + age_group : {"adults", "child", "both"}, optional + Which age group to fetch (default "both"). - 'adults' = fetch adults only (n=33, ages 18-39) - 'child' = fetch children only (n=122, ages 3-12) - 'both' = fetch full sample (n=155) """ - def __init__(self, reduce_confounds=True, age_group="both") -> None: + def __init__( + self, reduce_confounds: bool = True, age_group: str = "both" + ) -> None: """Initialize the class.""" datadir = tempfile.mkdtemp() # Define types diff --git a/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py index 9129b93c0..283be2716 100644 --- a/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +++ b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py @@ -1,4 +1,4 @@ -"""Provide tests for SPM Auditory datagrabber.""" +"""Provide tests for Oasis VBM Testing datagrabber.""" # Authors: Federico Raimondo # License: AGPL @@ -7,7 +7,7 @@ from junifer.testing.datagrabbers import OasisVBMTestingDatagrabber def test_OasisVBMTestingDatagrabber() -> None: - """Test Oasis VBM datagrabber.""" + """Test Oasis VBM Testing datagrabber.""" expected_elements = [ "sub-01", "sub-02", -- 2.52.0 From c32935374a7f3b63aa65f15fcc72ed8724d80516 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 14:13:15 +0200 Subject: [PATCH 131/142] done with review --- junifer/preprocess/base.py | 2 +- junifer/preprocess/confounds.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py index 13b00b5ba..35c547fd3 100644 --- a/junifer/preprocess/base.py +++ b/junifer/preprocess/base.py @@ -1,4 +1,4 @@ -"""Provide base class for preprocessor.""" +"""Provide abstract base class for preprocessor.""" # Authors: Federico Raimondo # Synchon Mandal diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index 72a441b91..37e864c91 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -571,9 +571,9 @@ class fMRIPrepConfoundRemover(BasePreprocessor): Parameters ---------- - input : Dict[str, Dict] + input : dict A single input from the Junifer Data object in which to preprocess. - extra_input : Dict, optional + extra_input : dict, optional The other fields in the Junifer Data object. Must include the "BOLD_confounds" key. -- 2.52.0 From 67556a003173ca96a983406c5178012ab33b8876 Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 14:17:59 +0200 Subject: [PATCH 132/142] more comments --- junifer/preprocess/base.py | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py index 35c547fd3..c6fc3a277 100644 --- a/junifer/preprocess/base.py +++ b/junifer/preprocess/base.py @@ -68,7 +68,7 @@ class BasePreprocessor(ABC, PipelineStepMixin): Parameters ---------- input : list of str - The input to the marker. The list must contain the + The input to the preprocessor. The list must contain the available Junifer Data dictionary keys. Returns @@ -89,7 +89,7 @@ class BasePreprocessor(ABC, PipelineStepMixin): ------- list of str The list of data types that can be used as input for this - preprocessor + preprocessor. """ raise_error( @@ -157,12 +157,11 @@ class BasePreprocessor(ABC, PipelineStepMixin): Parameters ---------- input : dict[str, dict] - A single input from the pipeline data object in which to compute - the marker. + A single input from the Junifer Data object to preprocess. extra_input : dict, optional - The other fields in the pipeline data object. Useful for accessing + The other fields in the Junifer Data object. Useful for accessing other data kind that needs to be used in the computation. For - example, the functional connectivity markers can make use of the + example, the confound removers can make use of the confounds if available (default None). Returns -- 2.52.0 From f5725e9a53f3ccab5cf4b2c13abad85fac98c15f Mon Sep 17 00:00:00 2001 From: Fede Date: Wed, 2 Nov 2022 22:02:17 +0200 Subject: [PATCH 133/142] more docs --- docs/understanding/preprocess.rst | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index 420de2bb7..429bea9e0 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -13,3 +13,12 @@ depending on the use-case. For example, you might want to perform confound remov feature extraction. This step is still under development and is an optional one for the pipeline to work. + +.. _preprocess_confounds: + +Confound Removal +^^^^^^^^^^^^^^^^ + +The *Confound Removal* step is meant to remove *confounds* from the ``BOLD`` data. The confounds are +extracted from the ``BOLD_confounds`` data (must be provided by the :ref:`DataGrabber `). +The confounds are then regressed out from the ``BOLD`` data using :func:`nilearn.image.clean_img`. \ No newline at end of file -- 2.52.0 From a977ab690fe15c791c971584aa267c2a5760d249 Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 13:38:54 +0200 Subject: [PATCH 134/142] Fix linting --- junifer/preprocess/base.py | 5 ---- junifer/preprocess/confounds.py | 45 ++++++++++++++++++--------------- 2 files changed, 24 insertions(+), 26 deletions(-) diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py index c6fc3a277..84d3e9d67 100644 --- a/junifer/preprocess/base.py +++ b/junifer/preprocess/base.py @@ -20,14 +20,12 @@ class BasePreprocessor(ABC, PipelineStepMixin): on : str or list of str, optional The kind of data to apply the preprocessor to. If None, will work on all available data (default None). - """ def __init__( self, on: Optional[Union[List[str], str]] = None, ) -> None: - """Initialize the class.""" if on is None: on = self.get_valid_inputs() if not isinstance(on, list): @@ -52,7 +50,6 @@ class BasePreprocessor(ABC, PipelineStepMixin): ------ ValueError If the input does not have the required data. - """ if not any(x in input for x in self._on): raise_error( @@ -90,7 +87,6 @@ class BasePreprocessor(ABC, PipelineStepMixin): list of str The list of data types that can be used as input for this preprocessor. - """ raise_error( msg="Concrete classes need to implement get_valid_inputs().", @@ -109,7 +105,6 @@ class BasePreprocessor(ABC, PipelineStepMixin): ------- dict The metadata as a dictionary with the only key 'preprocess'. - """ s_meta = super().get_meta() return {"preprocess": s_meta} diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index 37e864c91..f236cbd06 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -99,25 +99,30 @@ class fMRIPrepConfoundRemover(BasePreprocessor): Parameters ---------- strategy : dict, optional + The strategy to use for each component. If None, will use the *full* + strategy for all components (default None). The keys of the dictionary should correspond to names of noise components to include: - - 'motion' - - 'wm_csf' - - 'global_signal' + + * 'motion' + * 'wm_csf' + * 'global_signal' + The values of dictionary should correspond to types of confounds extracted from each signal: - - 'basic': only the confounding time series - - 'power2': signal + quadratic term - - 'derivatives': signal + derivatives - - 'full': signal + deriv. + quadratic terms + power2 deriv. - (default None). + + * 'basic': only the confounding time series + * 'power2': signal + quadratic term + * 'derivatives': signal + derivatives + * 'full': signal + deriv. + quadratic terms + power2 deriv. + spike : float, optional If None, no spike regressor is added. If spike is a float, it will add a spike regressor for every point at which framewise displacement exceeds the specified float (default None). detrend : bool, optional - If True, detrending will be applied on timeseries - (before confound removal) (default True). + If True, detrending will be applied on timeseries, before confound + removal (default True). standardize : bool, optional If True, returned signals are set to unit variance (default True). low_pass : float, optional @@ -133,13 +138,10 @@ class fMRIPrepConfoundRemover(BasePreprocessor): If provided, signal is only cleaned from voxels inside the mask. If mask is provided, it should have same shape and affine as imgs. If not provided, a mask is computed using - `nilearn.masking.compute_brain_mask` (default None). + :func:`nilearn.masking.compute_brain_mask` (default None). """ - # TODO: implement more strategies from - # nilearn.interfaces.fmriprep.load_confounds, - # in particular scrubbing def __init__( self, strategy: Optional[Dict[str, str]] = None, @@ -291,9 +293,10 @@ class fMRIPrepConfoundRemover(BasePreprocessor): ---------- input : dict Dictionary containing the following keys: - - path: path to the confounds file - - data: the confounds file loaded in memory (dataframe) - - format: format of the confounds file (must be "fmriprep") + + * path: path to the confounds file + * data: the confounds file loaded in memory (dataframe) + * format: format of the confounds file (must be "fmriprep") Returns ------- @@ -371,12 +374,12 @@ class fMRIPrepConfoundRemover(BasePreprocessor): input : dict Dictionary containing the "BOLD_confounds" value from the Junifer Data object. - + Returns ------- confounds_df : pandas.DataFrame Dataframe containing the relevant confounds. - + """ confounds_format = input["format"] @@ -420,7 +423,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor): extra_input: Optional[Dict[str, Any]] = None, ) -> None: """Validate input data. - + Parameters ---------- input : dict @@ -429,7 +432,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor): extra_input : dict, optional Dictionary containing the rest of the Junifer Data object. Must include the "BOLD_confounds" key. - + """ # Bold must be 4D niimg -- 2.52.0 From e1e9099b6296f8057edfe986189bbf80299fba5d Mon Sep 17 00:00:00 2001 From: Fede Date: Thu, 3 Nov 2022 16:23:14 +0200 Subject: [PATCH 135/142] Update doc --- docs/changes/latest.inc | 2 + docs/links.inc | 2 + docs/understanding/preprocess.rst | 96 ++++++++++++++++++++++++++++++- 3 files changed, 98 insertions(+), 2 deletions(-) diff --git a/docs/changes/latest.inc b/docs/changes/latest.inc index 112e44300..ea0b0d175 100644 --- a/docs/changes/latest.inc +++ b/docs/changes/latest.inc @@ -75,6 +75,8 @@ Enhancements - Change documentation template to furo. Fix references and standardize documentation (:gh:`114` by `Fede Raimondo`_). +- Add :class:`junifer.preprocess.fMRIPrepConfoundRemover` (:gh:`111` by `Fede Raimondo`_ and `Leonard Sasse`_). + Bugs ~~~~ diff --git a/docs/links.inc b/docs/links.inc index 6f8d31de1..27f6489c8 100644 --- a/docs/links.inc +++ b/docs/links.inc @@ -19,6 +19,8 @@ .. _`Python`: https://python.org .. _`seaborn`: https://seaborn.pydata.org .. _`matplotlib`: https://matplotlib.org +.. _`fMRIPrep`: https://fmriprep.org +.. _`nilearn`: https://nilearn.github.io .. _`venv`: https://docs.python.org/3/tutorial/venv.html .. _`conda env`: https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index 429bea9e0..e23cdb529 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -17,8 +17,100 @@ This step is still under development and is an optional one for the pipeline to .. _preprocess_confounds: Confound Removal -^^^^^^^^^^^^^^^^ +---------------- The *Confound Removal* step is meant to remove *confounds* from the ``BOLD`` data. The confounds are extracted from the ``BOLD_confounds`` data (must be provided by the :ref:`DataGrabber `). -The confounds are then regressed out from the ``BOLD`` data using :func:`nilearn.image.clean_img`. \ No newline at end of file +The confounds are then regressed out from the ``BOLD`` data using :func:`nilearn.image.clean_img`. + +Currently, junifer supports only one confound removal class: +:class:`junifer.preprocess.fMRIPrepConfoundRemover`. This class is meant to remove confounds as described +before, using the output of `fMRIPrep`_ as reference. + +Strategy +~~~~~~~~ + +This confound remover uses the `nilearn`_ API from :func:`nilearn.interfaces.fmriprep.load_confounds`. That is, +define a *strategy* to extract the confounds from the ``BOLD_confounds`` data. The *strategy* is defined +by choosing the *noise components* to be used and the *confounds* to be extracted from each noise components. +The *noise components* currently supported are: + +* ``motion`` +* ``wm_csf`` +* ``global_signal`` + +The confounds options for each *noise component* are: + +* ``basic``: the basic confounds for each *noise component*. For example, for ``motion``, the basic confounds + are the 6 motion parameters (3 translations and 3 rotations) and their derivatives. For ``wm_csf``, the basic + confounds are the mean signal of the white matter and CSF regions. For ``global_signal``, the basic confound + is the mean signal of the whole brain. +* ``power2``: the basic confounds plus the square of each basic confound. +* ``derivatives``: the basic confounds plus the derivative of each basic confound. +* ``full``: the basic confounds, the derivative of each basic confound, the square of each basic confound and the + square of each derivative of each basic confound. + +The *strategy* is defined as a dictionary, with the *noise components* as keys and the *confounds* as values. + +Example in python format: + +.. code-block:: + + strategy = { + "motion": "basic", + "wm_csf": "full", + "global_signal": "derivatives" + } + +or in YAML format: + +.. code-block:: + + strategy: + motion: basic + wm_csf: full + global_signal: derivatives + +The default value is to use all the *noise components* with the ``full`` *confounds*:abbr: + +.. code-block:: + + strategy = { + "motion": "full", + "wm_csf": "full", + "global_signal": "full" + } + +Other parameters +~~~~~~~~~~~~~~~~ + +Additionaly, the :class:`junifer.preprocess.fMRIPrepConfoundRemover` supports the following parameters: + +.. list-table:: + :widths: 10, 30, 5 + :header-rows: 1 + + * - Parameter + - Description + - Default + * - ``spike`` + - Add a spike regressor in the timepoints when the framewise displacement exceeds this threshold. + - deactivated + * - ``detrend`` + - Apply detrending on timeseries, before confound removal. + - activated + * - ``standardize`` + - Scale signals to unit variance. + - activated + * - ``low_pass`` + - Low cutoff frequencies, in Hertz. + - deactivated + * - ``high_pass`` + - High cutoff frequencies, in Hertz. + - deactivated + * - ``t_r`` + - Repetition time, in second (sampling period). + - from nifti header + * - ``mask`` + - If provided, signal is only cleaned from voxels inside the mask. If not, a mask is computed using :func:`nilearn.masking.compute_brain_mask`. + - compute \ No newline at end of file -- 2.52.0 From 62fb4998d4ccd21cbd99b312d27b204a78ad7d61 Mon Sep 17 00:00:00 2001 From: Fede Date: Fri, 4 Nov 2022 09:00:14 +0200 Subject: [PATCH 136/142] Test nilearn vs fmriprep --- docs/understanding/preprocess.rst | 4 +- junifer/preprocess/confounds.py | 9 +- junifer/preprocess/tests/test_confounds.py | 36 +++- junifer/testing/__init__.py | 1 + ...tion_acq-seq_desc-confounds_regressors.tsv | 201 ++++++++++++++++++ junifer/testing/datagrabbers.py | 9 +- junifer/testing/utils.py | 13 ++ 7 files changed, 265 insertions(+), 8 deletions(-) create mode 100644 junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv create mode 100644 junifer/testing/utils.py diff --git a/docs/understanding/preprocess.rst b/docs/understanding/preprocess.rst index e23cdb529..e3241ee9c 100644 --- a/docs/understanding/preprocess.rst +++ b/docs/understanding/preprocess.rst @@ -42,7 +42,7 @@ The *noise components* currently supported are: The confounds options for each *noise component* are: * ``basic``: the basic confounds for each *noise component*. For example, for ``motion``, the basic confounds - are the 6 motion parameters (3 translations and 3 rotations) and their derivatives. For ``wm_csf``, the basic + are the 6 motion parameters (3 translations and 3 rotations). For ``wm_csf``, the basic confounds are the mean signal of the white matter and CSF regions. For ``global_signal``, the basic confound is the mean signal of the whole brain. * ``power2``: the basic confounds plus the square of each basic confound. @@ -71,7 +71,7 @@ or in YAML format: wm_csf: full global_signal: derivatives -The default value is to use all the *noise components* with the ``full`` *confounds*:abbr: +The default value is to use all the *noise components* with the ``full`` *confounds*: .. code-block:: diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds.py index f236cbd06..575de40e7 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds.py @@ -399,7 +399,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor): # Add derivatives if needed for t_dst, t_src in derivatives_to_compute.items(): - out_df[t_dst] = np.append(np.diff(out_df[t_src]), 0) + out_df[t_dst] = np.insert(np.diff(out_df[t_src]), 0, np.nan) # Add squares (of base confounds and derivatives) if needed for t_dst, t_src in squares_to_compute.items(): @@ -415,6 +415,13 @@ class fMRIPrepConfoundRemover(BasePreprocessor): # Now pick all the relevant confounds out_df = out_df[to_select] + + # Derivatives have NaN on the first row + # Replace them by estimates at second time point, + # otherwise nilearn will crash. + mask_nan = np.isnan(out_df.values[0, :]) + out_df.iloc[0, mask_nan] = out_df.iloc[1, mask_nan] + return out_df def _validate_data( diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 2d7d21950..9ca8cee7e 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -13,6 +13,7 @@ from pandas.testing import assert_frame_equal import numpy as np import nibabel as nib +from nilearn.interfaces import fmriprep from nilearn._utils.exceptions import DimensionError from junifer.preprocess.confounds import fMRIPrepConfoundRemover @@ -20,6 +21,7 @@ from junifer.testing.datagrabbers import ( OasisVBMTestingDatagrabber, PartlyCloudyTestingDataGrabber, ) +from junifer.testing import get_testing_data from junifer.datareader import DefaultDataReader @@ -289,7 +291,39 @@ def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep() -> None: assert set(out2.columns) == set(fmriprep_all_vars + ["spike"]) assert_frame_equal(out1, out2) - # TODO: Test if fmriprep returns the same derivatives/power2 as we compute + + +def test_FMRIPRepConfoundRemover__pick_confounds_fmriprep_compute() -> None: + """Test if fmriprep returns the same derivatives/power2 as we compute.""" + + confound_remover = fMRIPrepConfoundRemover( + strategy={"wm_csf": "full"} + ) + fmriprep_all_vars = [ + "csf", + "white_matter", + "csf_power2", + "white_matter_power2", + "csf_derivative1", + "white_matter_derivative1", + "csf_derivative1_power2", + "white_matter_derivative1_power2", + ] + + t_fname = get_testing_data( + "sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv" + ) + t_full_confounds = pd.read_csv(t_fname, sep="\t")[fmriprep_all_vars] + t_basic_confounds = t_full_confounds[["csf", "white_matter"]] + + input_basic = {"data": t_basic_confounds, "format": "fmriprep"} + out_junifer = confound_remover._pick_confounds(input_basic) + + input_full = {"data": t_full_confounds, "format": "fmriprep"} + out_fmriprep = confound_remover._pick_confounds(input_full) + + assert np.all(out_fmriprep.values != np.nan) + assert_frame_equal(out_junifer, out_fmriprep) def test_fMRIPrepConfoundRemover__validate_data() -> None: diff --git a/junifer/testing/__init__.py b/junifer/testing/__init__.py index a1e573655..6a4cdba70 100644 --- a/junifer/testing/__init__.py +++ b/junifer/testing/__init__.py @@ -5,3 +5,4 @@ # License: AGPL from . import datagrabbers +from .utils import get_testing_data diff --git a/junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv b/junifer/testing/data/sub-0001_task-anticipation_acq-seq_desc-confounds_regressors.tsv new file mode 100644 index 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a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -140,10 +140,11 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber): If False, returns all :term:`fMRIPrep` confounds (default True). age_group : {"adults", "child", "both"}, optional - Which age group to fetch (default "both"). - - 'adults' = fetch adults only (n=33, ages 18-39) - - 'child' = fetch children only (n=122, ages 3-12) - - 'both' = fetch full sample (n=155) + Which age group to fetch (default "both"): + + * 'adults' = fetch adults only (n=33, ages 18-39) + * 'child' = fetch children only (n=122, ages 3-12) + * 'both' = fetch full sample (n=155) """ def __init__( diff --git a/junifer/testing/utils.py b/junifer/testing/utils.py new file mode 100644 index 000000000..8bb676647 --- /dev/null +++ b/junifer/testing/utils.py @@ -0,0 +1,13 @@ +"""Testing utils""" + +# Authors: Federico Raimondo +# License: AGPL + +from pathlib import Path + +def get_testing_data(fname): + """Get the path to a testing data file.""" + t_path = Path(__file__).parent / 'data' / fname + if not t_path.exists(): + raise FileNotFoundError(f"File {fname} not found in testing data") + return t_path \ No newline at end of file -- 2.52.0 From 109b2142f079001648939322a7f20bde0defa0e9 Mon Sep 17 00:00:00 2001 From: Fede Date: Fri, 4 Nov 2022 09:04:19 +0200 Subject: [PATCH 137/142] lint --- junifer/testing/utils.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/junifer/testing/utils.py b/junifer/testing/utils.py index 8bb676647..ac77b5258 100644 --- a/junifer/testing/utils.py +++ b/junifer/testing/utils.py @@ -5,9 +5,10 @@ from pathlib import Path + def get_testing_data(fname): """Get the path to a testing data file.""" - t_path = Path(__file__).parent / 'data' / fname + t_path = Path(__file__).parent / "data" / fname if not t_path.exists(): raise FileNotFoundError(f"File {fname} not found in testing data") - return t_path \ No newline at end of file + return t_path -- 2.52.0 From 321c7cc2a87cac14cce88a562ac03909a8b933f3 Mon Sep 17 00:00:00 2001 From: Fede Date: Fri, 4 Nov 2022 09:04:39 +0200 Subject: [PATCH 138/142] more lint --- junifer/preprocess/tests/test_confounds.py | 1 - junifer/testing/utils.py | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/tests/test_confounds.py index 9ca8cee7e..a842bafb4 100644 --- a/junifer/preprocess/tests/test_confounds.py +++ b/junifer/preprocess/tests/test_confounds.py @@ -13,7 +13,6 @@ from pandas.testing import assert_frame_equal import numpy as np import nibabel as nib -from nilearn.interfaces import fmriprep from nilearn._utils.exceptions import DimensionError from junifer.preprocess.confounds import fMRIPrepConfoundRemover diff --git a/junifer/testing/utils.py b/junifer/testing/utils.py index ac77b5258..7f6d22e41 100644 --- a/junifer/testing/utils.py +++ b/junifer/testing/utils.py @@ -1,4 +1,4 @@ -"""Testing utils""" +"""Testing utils.""" # Authors: Federico Raimondo # License: AGPL -- 2.52.0 From e7bd2ab2a9b19ec2a9c05f6603d616880e5df3d6 Mon Sep 17 00:00:00 2001 From: Fede Date: Fri, 4 Nov 2022 11:02:03 +0200 Subject: [PATCH 139/142] @synchon: comments addressed --- junifer/preprocess/base.py | 3 ++- junifer/preprocess/confounds/__init__.py | 7 +++++++ .../fmriprep_confound_remover.py} | 8 ++++---- .../tests/test_fmriprep_confound_remover.py} | 0 junifer/testing/utils.py | 17 ++++++++++++++--- 5 files changed, 27 insertions(+), 8 deletions(-) create mode 100644 junifer/preprocess/confounds/__init__.py rename junifer/preprocess/{confounds.py => confounds/fmriprep_confound_remover.py} (99%) rename junifer/preprocess/{tests/test_confounds.py => confounds/tests/test_fmriprep_confound_remover.py} (100%) diff --git a/junifer/preprocess/base.py b/junifer/preprocess/base.py index 84d3e9d67..792c31311 100644 --- a/junifer/preprocess/base.py +++ b/junifer/preprocess/base.py @@ -71,7 +71,8 @@ class BasePreprocessor(ABC, PipelineStepMixin): Returns ------- list of str - The updated list of output kinds, as storage possibilities. + The updated list of available Junifer Data object keys after + the pipeline step. """ raise_error( diff --git a/junifer/preprocess/confounds/__init__.py b/junifer/preprocess/confounds/__init__.py new file mode 100644 index 000000000..bd0189b10 --- /dev/null +++ b/junifer/preprocess/confounds/__init__.py @@ -0,0 +1,7 @@ +"""Provide imports for confounds sub-package.""" + +# Authors: Federico Raimondo +# Leonard Sasse +# License: AGPL + +from .fmriprep_confound_remover import fMRIPrepConfoundRemover diff --git a/junifer/preprocess/confounds.py b/junifer/preprocess/confounds/fmriprep_confound_remover.py similarity index 99% rename from junifer/preprocess/confounds.py rename to junifer/preprocess/confounds/fmriprep_confound_remover.py index 575de40e7..56ef80a6e 100644 --- a/junifer/preprocess/confounds.py +++ b/junifer/preprocess/confounds/fmriprep_confound_remover.py @@ -1,4 +1,4 @@ -"""Provide class for confound removal using FMRIPrep format.""" +"""Provide class for confound removal using fMRIPrep format.""" # Authors: Federico Raimondo # Leonard Sasse @@ -13,9 +13,9 @@ from nilearn._utils.niimg_conversions import check_niimg_4d from nilearn.image import clean_img from nilearn.masking import compute_brain_mask -from .base import BasePreprocessor -from ..api.decorators import register_preprocessor -from ..utils import logger, raise_error +from ..base import BasePreprocessor +from ...api.decorators import register_preprocessor +from ...utils import logger, raise_error if TYPE_CHECKING: diff --git a/junifer/preprocess/tests/test_confounds.py b/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py similarity index 100% rename from junifer/preprocess/tests/test_confounds.py rename to junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py diff --git a/junifer/testing/utils.py b/junifer/testing/utils.py index 7f6d22e41..391243c34 100644 --- a/junifer/testing/utils.py +++ b/junifer/testing/utils.py @@ -6,9 +6,20 @@ from pathlib import Path -def get_testing_data(fname): - """Get the path to a testing data file.""" +def get_testing_data(fname : str) -> Path: + """Get the path to a testing data file. + + Parameters + ---------- + fname : str + The name of the file. + + Returns + ------- + pathlib.Path + The absolute path to the file. + """ t_path = Path(__file__).parent / "data" / fname if not t_path.exists(): raise FileNotFoundError(f"File {fname} not found in testing data") - return t_path + return t_path.resolve() -- 2.52.0 From 9fd7bfcd80e3119616c43caaaa0f418481655d74 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 4 Nov 2022 13:09:59 +0100 Subject: [PATCH 140/142] docs: disable sqlalchemy mapping --- docs/conf.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index 8df7856aa..ed1670def 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -65,6 +65,7 @@ nitpick_ignore_regex = [ ("py:obj", "subclass"), # python 3.11 error ("py:class", "typing.Any"), # python 3.11 error # ('py:class', 'numpy.typing.ArrayLike') + ("py:obj", "sqlalchemy.engine.Engine"), # ignore sqlalchemy ] # numpydoc_validation_checks = { @@ -145,7 +146,7 @@ intersphinx_mapping = { "numpy": ("https://numpy.org/doc/stable/", None), "numpy": ("https://numpy.org/doc/stable/", None), "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None), - "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None), + # "sqlalchemy": ("https://docs.sqlalchemy.org/en/20/", None), "scipy": ("https://docs.scipy.org/doc/scipy/", None), } -- 2.52.0 From 69419e8199934bea73b3ac8a4a8f6609b251016c Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 4 Nov 2022 13:10:17 +0100 Subject: [PATCH 141/142] docs: reorganize and run black on conf.py --- docs/conf.py | 128 ++++++++++++++++++++++++++++----------------------- 1 file changed, 71 insertions(+), 57 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index ed1670def..f738b1e68 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -29,10 +29,8 @@ project = "junifer" copyright = "2022, Authors of junifer" author = "Fede Raimondo" - # -- General configuration --------------------------------------------------- - # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. @@ -49,12 +47,18 @@ extensions = [ ] # Add any paths that contain templates here, relative to this directory. -templates_path = ["_templates"] +templates_path = [ + "_templates", +] # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] +exclude_patterns = [ + "_build", + "Thumbs.db", + ".DS_Store", +] nitpicky = True @@ -68,46 +72,30 @@ nitpick_ignore_regex = [ ("py:obj", "sqlalchemy.engine.Engine"), # ignore sqlalchemy ] -# numpydoc_validation_checks = { -# "all", -# "GL01", -# "GL02", -# "GL03", -# "ES01", -# "SA01", -# "EX01", -# } -numpydoc_xref_param_type = True -numpydoc_xref_aliases = { - "Path": "pathlib.Path", - "Nifti1Image": "nibabel.nifti1.Nifti1Image", - "Nifti2Image": "nibabel.nifti2.Nifti2Image", - "Engine": "sqlalchemy.engine.Engine", -} -numpydoc_xref_ignore = { - "of", - "shape", - "optional", - "or", - "the", - "options", - "function", - "object", - "class", - "objects" -} - -autoclass_content = "class" -autodoc_typehints = "description" -autodoc_typehints_description_target = "documented" - # -- Options for HTML output ------------------------------------------------- -# The theme to use for HTML and HTML Help pages. See the documentation for +# The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = "furo" +html_logo = "./images/junifer_logo.png" + +# These paths are either relative to html_static_path +# or fully qualified paths (eg. https://...) +html_css_files = [ + "css/custom.css", +] + +html_js_files = [ + "js/custom.js", +] + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + html_sidebars = { "**": [ "sidebar/scroll-start.html", @@ -119,24 +107,19 @@ html_sidebars = { "sidebar/scroll-end.html", ] } -html_logo = "./images/junifer_logo.png" -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] +# -- sphinx.ext.autodoc configuration ---------------------------------------- -# These paths are either relative to html_static_path -# or fully qualified paths (eg. https://...) -html_css_files = [ - 'css/custom.css', -] +autoclass_content = "both" +autodoc_typehints = "description" +autodoc_typehints_description_target = "documented" -html_js_files = [ - 'js/custom.js', -] +# -- sphinx.ext.autosummary configuration ------------------------------------ + +autosummary_generate = True + +# -- sphinx.ext.intersphinx configuration ------------------------------------ -# Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { "python": ("https://docs.python.org/3/", None), "sklearn": ("https://scikit-learn.org/stable", None), @@ -150,6 +133,41 @@ intersphinx_mapping = { "scipy": ("https://docs.scipy.org/doc/scipy/", None), } +# -- numpydoc configuration -------------------------------------------------- + +numpydoc_show_class_members = False +numpydoc_xref_param_type = True +numpydoc_xref_aliases = { + "Path": "pathlib.Path", + "Nifti1Image": "nibabel.nifti1.Nifti1Image", + "Nifti2Image": "nibabel.nifti2.Nifti2Image", + # "Engine": "sqlalchemy.engine.Engine", +} +numpydoc_xref_ignore = { + "of", + "shape", + "optional", + "or", + "the", + "options", + "function", + "object", + "class", + "objects", + "Engine", +} +# numpydoc_validation_checks = { +# "all", +# "GL01", +# "GL02", +# "GL03", +# "ES01", +# "SA01", +# "EX01", +# } + +# -- Sphinx-Gallery configuration -------------------------------------------- + sphinx_gallery_conf = { "examples_dirs": ["../examples"], "gallery_dirs": ["auto_examples"], @@ -157,12 +175,8 @@ sphinx_gallery_conf = { "backreferences_dir": "generated", } +# -- sphinx-multiversion configuration --------------------------------------- -autosummary_generate = True -numpydoc_show_class_members = False -autoclass_content = "both" - -# sphinx-multiversion options smv_rebuild_tags = False smv_tag_whitelist = r"^v\d+\.\d+.\d+$" smv_branch_whitelist = r"main" -- 2.52.0 From 6f7e8e46e7dfdf73eb88826b6c02068911d42b5a Mon Sep 17 00:00:00 2001 From: Fede Date: Fri, 4 Nov 2022 23:44:55 +0200 Subject: [PATCH 142/142] fix this one --- docs/extending/datagrabber.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/extending/datagrabber.rst b/docs/extending/datagrabber.rst index 3ee2bc871..51e50fc03 100644 --- a/docs/extending/datagrabber.rst +++ b/docs/extending/datagrabber.rst @@ -14,7 +14,7 @@ the structure of a dataset and provide two specific functionalities: In this section, we will see how to create a datagrabber for a dataset. Basic aspects of datagrabbers are covedered in the -:ref:`Understanding DataGrabbers ` section. +:ref:`Understanding DataGrabbers ` section. .. _extending_datagrabbers_think: -- 2.52.0