[MAINT]: Release 0.0.4 #328
78 changed files with 225 additions and 78 deletions
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Introduce complexity markers: :class:`.HurstExponent`, :class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`, :class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy` by `Amir Omidvarnia`_
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Support element(s) to be specified via text file for ``--element`` option of ``junifer run`` by `Synchon Mandal`_
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Make copying of assets in ``with`` block of YAML, relative to YAML and not to current working directory by `Fede Raimondo`_ and `Synchon Mandal`_
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Adapt ``junifer queue`` to properly use HTCondor >=10.4.0 ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_
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Add ``junifer reset`` to reset storage and jobs directory by `Synchon Mandal`_
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Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_
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Add support for ``Power2013`` coordinates by `Synchon Mandal`_
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Add Zenodo badge in ``README`` and improve general documentation by `Synchon Mandal`_
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Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon Mandal`_
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Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_
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Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_
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Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_
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Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching of T1w data in subject-native space by `Synchon Mandal`_
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Add support for subject-native space by `Synchon Mandal`_ and `Fede Raimondo`_
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Update dependencies requirements by `Fede Raimondo`_
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Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage working and temporary directories across pipeline by `Synchon Mandal`_
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Support element-scoped directory and temporary directories for :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_
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Improve element directory cleanup via ``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon Mandal`_
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Improve :class:`.BasePreprocessor` for easy subclassing and adapt :class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_
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Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit`` config by `Synchon Mandal`_
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Add support for accessing FSL via Docker wrapper along with ``flirt``, ``applywarp`` and ``std2imgcoord`` commands by `Synchon Mandal`_
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Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and ``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to accept multiple preprocessors by `Synchon Mandal`_
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Introduce :func:`.get_parcellation` to fetch parcellation tailored for the data by `Synchon Mandal`_
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Introduce :func:`.get_coordinates` to fetch coordinates tailored for the data by `Synchon Mandal`_
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Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's ``applywarp`` by `Synchon Mandal`_
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Introduce :class:`.BOLDWarper` for warping BOLD data via FSL's ``applywarp`` by `Synchon Mandal`_
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Add ``space`` parameter to :func:`.register_coordinates`, :func:`.register_parcellation` and :func:`.register_mask` and return space from :func:`.load_coordinates`, :func:`.load_parcellation` and :func:`.load_mask` by `Synchon Mandal`_ and `Fede Raimondo`_
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Add ``space`` information to existing datagrabbers, masks, parcellations and coordinates by `Synchon Mandal`_ and `Fede Raimondo`_
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Improve documentation, packaging and code style by `Synchon Mandal`_
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Add support for Python 3.12 and make Python 3.11 the base for code coverage and CI checks by `Synchon Mandal`_
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Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset <https://openneuro.org/datasets/ds003452/versions/1.0.1>`_ by `Synchon Mandal`_
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Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by `Synchon Mandal`_
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Store native warped parcellations, coordinates and masks in element-scoped tempdirs for the pipeline to work by `Synchon Mandal`_
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Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_
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Change interpolation scheme for parcel and mask native space transformation to nearest neighbour by `Synchon Mandal`_
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Add support for accessing ANTs via Docker wrapper along with ``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon Mandal`_
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Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_
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Make the external tool wrappers output to stderr instead of stdout by `Synchon Mandal`_
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Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by `Synchon Mandal`_
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Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect for coordinates transformation to other template spaces.
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Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by `Synchon Mandal`_
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Propagate ReHo and fALFF maps, for aggregation to convert to other template spaces when required by `Synchon Mandal`_
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Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the ``workdir`` parameter by `Synchon Mandal`_
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Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and used by markers with ``mask="inherit"`` in subject-native template space by `Fede Raimondo`_ and `Synchon Mandal`_
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Pass down input path if input space is "native" for ``ReHoEstimator`` and ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and `Synchon Mandal`_
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Add ``mode`` as an aggregation function option in :func:`.get_aggfunc_by_name` by `Synchon Mandal`_
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Make :class:`.BOLDWarper` tool-agnostic by moving it from ``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_
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Fixed typo in code example for adding masks from "register_custom_mask" to "register_mask" by `Tobias Muganga`_
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Adapt :class:`.BOLDWarper` to use FSL or ANTs depending on warp file extension by `Synchon Mandal`_
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Introduce ``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper`` to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_
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Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by `Synchon Mandal`_
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Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon Mandal`_
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Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for running external commands from FSL, ANTs and others by `Synchon Mandal`_
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Introduce :func:`.get_xfm` to fetch transformation files for moving between template spaces by `Synchon Mandal`_
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Introduce :func:`.get_template` to fetch template space image tailored to a target data by `Synchon Mandal`_
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Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_
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Rewrite :func:`.compute_brain_mask` to allow variable template fetching via templateflow, according to target data by `Synchon Mandal`_
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Add support for on-the-fly template space transformation in :func:`.get_parcellation` and :func:`.get_mask` to allow parcellation and mask in different template spaces to work with a ``DataGrabber``'s data in a specified template space.
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Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by `Synchon Mandal`_
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Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon Mandal`_
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Update dependency listing in ``pyproject.toml``, add ``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and ``FSL`` installation in CI and improve general code style by `Synchon Mandal`_
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Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_
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Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_
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Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon Mandal`_
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Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_
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Improve :class:`.PatternDataGrabber` and :class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``, ``format``, ``mask_item`` and other metadata description handling via YAML by `Synchon Mandal`_
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Introduce :class:`.QueueContextAdapter` as an abstract base class for job queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by `Synchon Mandal`_
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Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed target data and "helper" data types as a dictionary by `Synchon Mandal`_
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Improve :class:`.BasePreprocessor` by revamping :meth:`.BasePreprocessor.preprocess` and ``BasePreprocessor._fit_transform`` to handle "helper" data types better and make the pipeline explicit where data is being altered by `Synchon Mandal`_
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Add a positional argument ``using`` for Markers and Preprocessors having implementation-based variations, in particular :class:`.ReHoParcels`, :class:`.ReHoSpheres`, :class:`.ALFFParcels`, :class:`.ALFFSpheres` and :class:`.BOLDWarper` by `Synchon Mandal`_
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Improve external dependency handling for :class:`.PipelineStepMixin`-derived objects having implementation-based variations by `Synchon Mandal`_
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Fix :class:`.HTCondorAdapter`'s script generation to use double quotes instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_
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Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon Mandal`_
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Improve documentation by adding information about space transformation and writing custom Preprocessors by `Synchon Mandal`_
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Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_
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Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_
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Change the subject and session patterns for :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` so that they are consistent with their own ``"participants.tsv"`` file by `Fede Raimondo`_
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@ -8,8 +8,232 @@ What's new
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.. towncrier release notes start
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.. towncrier release notes start
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Junifer 0.0.4 (2024-04-05)
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--------------------------
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Bugfixes
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^^^^^^^^
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- Make copying of assets in ``with`` block of YAML, relative to YAML and not to
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current working directory by `Fede Raimondo`_ and `Synchon Mandal`_
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(:gh:`224`)
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- Adapt ``junifer queue`` to properly use HTCondor >=10.4.0
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``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`233`)
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- Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by
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`Synchon Mandal`_ (:gh:`272`)
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- Store native warped parcellations, coordinates and masks in element-scoped
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tempdirs for the pipeline to work by `Synchon Mandal`_ (:gh:`274`)
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- Change interpolation scheme for parcel and mask native space transformation
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to nearest neighbour by `Synchon Mandal`_ (:gh:`276`)
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- Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for
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coordinates transformation by `Synchon Mandal`_ (:gh:`278`)
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- Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by
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`Synchon Mandal`_ (:gh:`280`)
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- Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect
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for coordinates transformation to other template spaces. (:gh:`281`)
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- Propagate ReHo and fALFF maps, for aggregation to convert to other template
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spaces when required by `Synchon Mandal`_ (:gh:`282`)
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- Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the
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``workdir`` parameter by `Synchon Mandal`_ (:gh:`283`)
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- Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and
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used by markers with ``mask="inherit"`` in subject-native template space by
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`Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`284`)
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- Pass down input path if input space is "native" for ``ReHoEstimator`` and
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``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and
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`Synchon Mandal`_ (:gh:`286`)
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- Fix :class:`.HTCondorAdapter`'s script generation to use double quotes
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instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_
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(:gh:`312`)
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- Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon
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Mandal`_ (:gh:`314`)
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- Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_
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(:gh:`322`)
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API Changes
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^^^^^^^^^^^
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- Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_
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(:gh:`245`)
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- Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon
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Mandal`_ (:gh:`248`)
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- Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`,
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:class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching
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of T1w data in subject-native space by `Synchon Mandal`_ (:gh:`252`)
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- Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and
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``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to
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accept multiple preprocessors by `Synchon Mandal`_ (:gh:`263`)
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- Add ``space`` parameter to :func:`.register_coordinates`,
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:func:`.register_parcellation` and :func:`.register_mask` and return space
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from :func:`.load_coordinates`, :func:`.load_parcellation` and
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:func:`.load_mask` by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
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- Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_
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(:gh:`299`)
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- Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed
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target data and "helper" data types as a dictionary by `Synchon Mandal`_
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(:gh:`310`)
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- Add a positional argument ``using`` for Markers and Preprocessors having
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implementation-based variations, in particular :class:`.ReHoParcels`,
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:class:`.ReHoSpheres`, :class:`.ALFFParcels`, :class:`.ALFFSpheres` and
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:class:`.BOLDWarper` by `Synchon Mandal`_ (:gh:`311`)
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- Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_
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(:gh:`320`)
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- Change the subject and session patterns for :class:`.DataladAOMICID1000`,
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:class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and
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:class:`.DMCC13Benchmark` so that they are consistent with their own
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``"participants.tsv"`` file by `Fede Raimondo`_ (:gh:`325`)
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Improved Documentation
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^^^^^^^^^^^^^^^^^^^^^^
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- Add Zenodo badge in ``README`` and improve general documentation by `Synchon
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Mandal`_ (:gh:`247`)
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||||||
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- Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix
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listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_
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||||||
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(:gh:`251`)
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||||||
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- Fixed typo in code example for adding masks from "register_custom_mask" to
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||||||
|
"register_mask" by `Tobias Muganga`_ (:gh:`291`)
|
||||||
|
- Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by
|
||||||
|
`Synchon Mandal`_ (:gh:`300`)
|
||||||
|
- Improve documentation by adding information about space transformation and
|
||||||
|
writing custom Preprocessors by `Synchon Mandal`_ (:gh:`317`)
|
||||||
|
|
||||||
|
|
||||||
|
Enhancements
|
||||||
|
^^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Support element(s) to be specified via text file for ``--element`` option of
|
||||||
|
``junifer run`` by `Synchon Mandal`_ (:gh:`182`)
|
||||||
|
- Support element-scoped directory and temporary directories for
|
||||||
|
:class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_ (:gh:`258`)
|
||||||
|
- Improve element directory cleanup via
|
||||||
|
``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon
|
||||||
|
Mandal`_ (:gh:`259`)
|
||||||
|
- Improve :class:`.BasePreprocessor` for easy subclassing and adapt
|
||||||
|
:class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_ (:gh:`260`)
|
||||||
|
- Add ``space`` information to existing datagrabbers, masks, parcellations and
|
||||||
|
coordinates by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
|
||||||
|
- Add ``mode`` as an aggregation function option in
|
||||||
|
:func:`.get_aggfunc_by_name` by `Synchon Mandal`_ (:gh:`287`)
|
||||||
|
- Adapt :class:`.BOLDWarper` to use FSL or ANTs depending on warp file
|
||||||
|
extension by `Synchon Mandal`_ (:gh:`293`)
|
||||||
|
- Rewrite :func:`.compute_brain_mask` to allow variable template fetching via
|
||||||
|
templateflow, according to target data by `Synchon Mandal`_ (:gh:`299`)
|
||||||
|
- Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon
|
||||||
|
Mandal`_ (:gh:`300`)
|
||||||
|
- Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon
|
||||||
|
Mandal`_ (:gh:`302`)
|
||||||
|
- Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_
|
||||||
|
(:gh:`306`)
|
||||||
|
- Improve :class:`.PatternDataGrabber` and
|
||||||
|
:class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``,
|
||||||
|
``format``, ``mask_item`` and other metadata description handling via YAML by
|
||||||
|
`Synchon Mandal`_ (:gh:`308`)
|
||||||
|
- Improve :class:`.BasePreprocessor` by revamping
|
||||||
|
:meth:`.BasePreprocessor.preprocess` and ``BasePreprocessor._fit_transform``
|
||||||
|
to handle "helper" data types better and make the pipeline explicit where
|
||||||
|
data is being altered by `Synchon Mandal`_ (:gh:`310`)
|
||||||
|
- Improve external dependency handling for :class:`.PipelineStepMixin`-derived
|
||||||
|
objects having implementation-based variations by `Synchon Mandal`_
|
||||||
|
(:gh:`311`)
|
||||||
|
|
||||||
|
|
||||||
|
Features
|
||||||
|
^^^^^^^^
|
||||||
|
|
||||||
|
- Introduce complexity markers: :class:`.HurstExponent`,
|
||||||
|
:class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`,
|
||||||
|
:class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy`
|
||||||
|
by `Amir Omidvarnia`_ (:gh:`145`)
|
||||||
|
- Add ``junifer reset`` to reset storage and jobs directory by `Synchon
|
||||||
|
Mandal`_ (:gh:`240`)
|
||||||
|
- Add support for ``Power2013`` coordinates by `Synchon Mandal`_ (:gh:`245`)
|
||||||
|
- Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_
|
||||||
|
(:gh:`249`)
|
||||||
|
- Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_
|
||||||
|
(:gh:`250`)
|
||||||
|
- Add support for subject-native space by `Synchon Mandal`_ and `Fede
|
||||||
|
Raimondo`_ (:gh:`252`)
|
||||||
|
- Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage
|
||||||
|
working and temporary directories across pipeline by `Synchon Mandal`_
|
||||||
|
(:gh:`254`)
|
||||||
|
- Introduce :func:`.get_parcellation` to fetch parcellation tailored for the
|
||||||
|
data by `Synchon Mandal`_ (:gh:`264`)
|
||||||
|
- Introduce :func:`.get_coordinates` to fetch coordinates tailored for the data
|
||||||
|
by `Synchon Mandal`_ (:gh:`265`)
|
||||||
|
- Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's
|
||||||
|
``applywarp`` by `Synchon Mandal`_ (:gh:`266`)
|
||||||
|
- Introduce :class:`.BOLDWarper` for warping BOLD data via FSL's ``applywarp``
|
||||||
|
by `Synchon Mandal`_ (:gh:`267`)
|
||||||
|
- Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset
|
||||||
|
<https://openneuro.org/datasets/ds003452/versions/1.0.1>`_ by `Synchon
|
||||||
|
Mandal`_ (:gh:`271`)
|
||||||
|
- Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_
|
||||||
|
(:gh:`275`)
|
||||||
|
- Introduce
|
||||||
|
``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper``
|
||||||
|
to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_ (:gh:`293`)
|
||||||
|
- Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for
|
||||||
|
running external commands from FSL, ANTs and others by `Synchon Mandal`_
|
||||||
|
(:gh:`295`)
|
||||||
|
- Introduce :func:`.get_xfm` to fetch transformation files for moving between
|
||||||
|
template spaces by `Synchon Mandal`_ (:gh:`297`)
|
||||||
|
- Introduce :func:`.get_template` to fetch template space image tailored to a
|
||||||
|
target data by `Synchon Mandal`_ (:gh:`298`)
|
||||||
|
- Add support for on-the-fly template space transformation in
|
||||||
|
:func:`.get_parcellation` and :func:`.get_mask` to allow parcellation and
|
||||||
|
mask in different template spaces to work with a ``DataGrabber``'s data in a
|
||||||
|
specified template space. (:gh:`299`)
|
||||||
|
- Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``,
|
||||||
|
``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon
|
||||||
|
Mandal`_ (:gh:`301`)
|
||||||
|
- Introduce :class:`.QueueContextAdapter` as an abstract base class for job
|
||||||
|
queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by
|
||||||
|
`Synchon Mandal`_ (:gh:`309`)
|
||||||
|
|
||||||
|
|
||||||
|
Miscellaneous
|
||||||
|
^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Update dependencies requirements by `Fede Raimondo`_ (:gh:`253`)
|
||||||
|
- Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit``
|
||||||
|
config by `Synchon Mandal`_ (:gh:`261`)
|
||||||
|
- Add support for accessing FSL via Docker wrapper along with ``flirt``,
|
||||||
|
``applywarp`` and ``std2imgcoord`` commands by `Synchon Mandal`_ (:gh:`262`)
|
||||||
|
- Improve documentation, packaging and code style by `Synchon Mandal`_
|
||||||
|
(:gh:`269`)
|
||||||
|
- Add support for Python 3.12 and make Python 3.11 the base for code coverage
|
||||||
|
and CI checks by `Synchon Mandal`_ (:gh:`270`)
|
||||||
|
- Add support for accessing ANTs via Docker wrapper along with
|
||||||
|
``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon
|
||||||
|
Mandal`_ (:gh:`277`)
|
||||||
|
- Make the external tool wrappers output to stderr instead of stdout by
|
||||||
|
`Synchon Mandal`_ (:gh:`279`)
|
||||||
|
- Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by
|
||||||
|
`Synchon Mandal`_ (:gh:`281`)
|
||||||
|
- Make :class:`.BOLDWarper` tool-agnostic by moving it from
|
||||||
|
``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_
|
||||||
|
(:gh:`288`)
|
||||||
|
- Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by
|
||||||
|
`Synchon Mandal`_ (:gh:`293`)
|
||||||
|
- Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon
|
||||||
|
Mandal`_ (:gh:`294`)
|
||||||
|
- Update dependency listing in ``pyproject.toml``, add
|
||||||
|
``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and
|
||||||
|
``FSL`` installation in CI and improve general code style by `Synchon
|
||||||
|
Mandal`_ (:gh:`300`)
|
||||||
|
|
||||||
|
|
||||||
|
Deprecations and Removals
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon
|
||||||
|
Mandal`_ (:gh:`301`)
|
||||||
|
|
||||||
|
|
||||||
Junifer 0.0.3 (2023-07-21)
|
Junifer 0.0.3 (2023-07-21)
|
||||||
---------------------------------
|
--------------------------
|
||||||
|
|
||||||
Bugfixes
|
Bugfixes
|
||||||
^^^^^^^^
|
^^^^^^^^
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue