From 29d9e30fc03cadb6a82f562cd252307712a9b785 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 5 Apr 2024 17:11:24 +0200 Subject: [PATCH] chore: update whats_new.rst for 0.0.4 --- docs/changes/newsfragments/145.feature | 1 - docs/changes/newsfragments/182.enh | 1 - docs/changes/newsfragments/224.bugfix | 1 - docs/changes/newsfragments/233.bugfix | 1 - docs/changes/newsfragments/240.feature | 1 - docs/changes/newsfragments/245.change | 1 - docs/changes/newsfragments/245.feature | 1 - docs/changes/newsfragments/247.doc | 1 - docs/changes/newsfragments/248.change | 1 - docs/changes/newsfragments/249.feature | 1 - docs/changes/newsfragments/250.feature | 1 - docs/changes/newsfragments/251.doc | 1 - docs/changes/newsfragments/252.change | 1 - docs/changes/newsfragments/252.feature | 1 - docs/changes/newsfragments/253.misc | 1 - docs/changes/newsfragments/254.feature | 1 - docs/changes/newsfragments/258.enh | 1 - docs/changes/newsfragments/259.enh | 1 - docs/changes/newsfragments/260.enh | 1 - docs/changes/newsfragments/261.misc | 1 - docs/changes/newsfragments/262.misc | 1 - docs/changes/newsfragments/263.change | 1 - docs/changes/newsfragments/264.feature | 1 - docs/changes/newsfragments/265.feature | 1 - docs/changes/newsfragments/266.feature | 1 - docs/changes/newsfragments/267.feature | 1 - docs/changes/newsfragments/268.change | 1 - docs/changes/newsfragments/268.enh | 1 - docs/changes/newsfragments/269.misc | 1 - docs/changes/newsfragments/270.misc | 1 - docs/changes/newsfragments/271.feature | 1 - docs/changes/newsfragments/272.bugfix | 1 - docs/changes/newsfragments/274.bugfix | 1 - docs/changes/newsfragments/275.feature | 1 - docs/changes/newsfragments/276.bugfix | 1 - docs/changes/newsfragments/277.misc | 1 - docs/changes/newsfragments/278.bugfix | 1 - docs/changes/newsfragments/279.misc | 1 - docs/changes/newsfragments/280.bugfix | 1 - docs/changes/newsfragments/281.bugfix | 1 - docs/changes/newsfragments/281.misc | 1 - docs/changes/newsfragments/282.bugfix | 1 - docs/changes/newsfragments/283.bugfix | 1 - docs/changes/newsfragments/284.bugfix | 1 - docs/changes/newsfragments/286.bugfix | 1 - docs/changes/newsfragments/287.enh | 1 - docs/changes/newsfragments/288.misc | 1 - docs/changes/newsfragments/291.doc | 1 - docs/changes/newsfragments/293.enh | 1 - docs/changes/newsfragments/293.feature | 1 - docs/changes/newsfragments/293.misc | 1 - docs/changes/newsfragments/294.misc | 1 - docs/changes/newsfragments/295.feature | 1 - docs/changes/newsfragments/297.feature | 1 - docs/changes/newsfragments/298.feature | 1 - docs/changes/newsfragments/299.change | 1 - docs/changes/newsfragments/299.enh | 1 - docs/changes/newsfragments/299.feature | 1 - docs/changes/newsfragments/300.doc | 1 - docs/changes/newsfragments/300.enh | 1 - docs/changes/newsfragments/300.misc | 1 - docs/changes/newsfragments/301.feature | 1 - docs/changes/newsfragments/301.removal | 1 - docs/changes/newsfragments/302.enh | 1 - docs/changes/newsfragments/306.enh | 1 - docs/changes/newsfragments/308.enh | 1 - docs/changes/newsfragments/309.feature | 1 - docs/changes/newsfragments/310.change | 1 - docs/changes/newsfragments/310.enh | 1 - docs/changes/newsfragments/311.change | 1 - docs/changes/newsfragments/311.enh | 1 - docs/changes/newsfragments/312.bugfix | 1 - docs/changes/newsfragments/314.bugfix | 1 - docs/changes/newsfragments/317.doc | 1 - docs/changes/newsfragments/320.change | 1 - docs/changes/newsfragments/322.bugfix | 1 - docs/changes/newsfragments/325.change | 1 - docs/whats_new.rst | 226 ++++++++++++++++++++++++- 78 files changed, 225 insertions(+), 78 deletions(-) delete mode 100644 docs/changes/newsfragments/145.feature delete mode 100644 docs/changes/newsfragments/182.enh delete mode 100644 docs/changes/newsfragments/224.bugfix delete mode 100644 docs/changes/newsfragments/233.bugfix delete mode 100644 docs/changes/newsfragments/240.feature delete mode 100644 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delete mode 100644 docs/changes/newsfragments/325.change diff --git a/docs/changes/newsfragments/145.feature b/docs/changes/newsfragments/145.feature deleted file mode 100644 index 2b6625951..000000000 --- a/docs/changes/newsfragments/145.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce complexity markers: :class:`.HurstExponent`, :class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`, :class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy` by `Amir Omidvarnia`_ diff --git a/docs/changes/newsfragments/182.enh b/docs/changes/newsfragments/182.enh deleted file mode 100644 index 615c16ade..000000000 --- a/docs/changes/newsfragments/182.enh +++ /dev/null @@ -1 +0,0 @@ -Support element(s) to be specified via text file for ``--element`` option of ``junifer run`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/224.bugfix b/docs/changes/newsfragments/224.bugfix deleted file mode 100644 index ec0b01b64..000000000 --- a/docs/changes/newsfragments/224.bugfix +++ /dev/null @@ -1 +0,0 @@ -Make copying of assets in ``with`` block of YAML, relative to YAML and not to current working directory by `Fede Raimondo`_ and `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/233.bugfix b/docs/changes/newsfragments/233.bugfix deleted file mode 100644 index 167b774fc..000000000 --- a/docs/changes/newsfragments/233.bugfix +++ /dev/null @@ -1 +0,0 @@ -Adapt ``junifer queue`` to properly use HTCondor >=10.4.0 ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/240.feature b/docs/changes/newsfragments/240.feature deleted file mode 100644 index b7fc67ea0..000000000 --- a/docs/changes/newsfragments/240.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``junifer reset`` to reset storage and jobs directory by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/245.change b/docs/changes/newsfragments/245.change deleted file mode 100644 index 8a6ce9d23..000000000 --- a/docs/changes/newsfragments/245.change +++ /dev/null @@ -1 +0,0 @@ -Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/245.feature b/docs/changes/newsfragments/245.feature deleted file mode 100644 index 8d1a6de32..000000000 --- a/docs/changes/newsfragments/245.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for ``Power2013`` coordinates by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/247.doc b/docs/changes/newsfragments/247.doc deleted file mode 100644 index bd85a54f9..000000000 --- a/docs/changes/newsfragments/247.doc +++ /dev/null @@ -1 +0,0 @@ -Add Zenodo badge in ``README`` and improve general documentation by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/248.change b/docs/changes/newsfragments/248.change deleted file mode 100644 index 55162a23f..000000000 --- a/docs/changes/newsfragments/248.change +++ /dev/null @@ -1 +0,0 @@ -Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/249.feature b/docs/changes/newsfragments/249.feature deleted file mode 100644 index 1d36037e1..000000000 --- a/docs/changes/newsfragments/249.feature +++ /dev/null @@ -1 +0,0 @@ -Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/250.feature b/docs/changes/newsfragments/250.feature deleted file mode 100644 index b24159465..000000000 --- a/docs/changes/newsfragments/250.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/251.doc b/docs/changes/newsfragments/251.doc deleted file mode 100644 index 4ee20dc01..000000000 --- a/docs/changes/newsfragments/251.doc +++ /dev/null @@ -1 +0,0 @@ -Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/252.change b/docs/changes/newsfragments/252.change deleted file mode 100644 index 70bf6bd8d..000000000 --- a/docs/changes/newsfragments/252.change +++ /dev/null @@ -1 +0,0 @@ -Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching of T1w data in subject-native space by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/252.feature b/docs/changes/newsfragments/252.feature deleted file mode 100644 index 57f767c22..000000000 --- a/docs/changes/newsfragments/252.feature +++ /dev/null @@ -1 +0,0 @@ -Add support for subject-native space by `Synchon Mandal`_ and `Fede Raimondo`_ diff --git a/docs/changes/newsfragments/253.misc b/docs/changes/newsfragments/253.misc deleted file mode 100644 index 43f38ef69..000000000 --- a/docs/changes/newsfragments/253.misc +++ /dev/null @@ -1 +0,0 @@ -Update dependencies requirements by `Fede Raimondo`_ diff --git a/docs/changes/newsfragments/254.feature b/docs/changes/newsfragments/254.feature deleted file mode 100644 index cdc461cb6..000000000 --- a/docs/changes/newsfragments/254.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage working and temporary directories across pipeline by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/258.enh b/docs/changes/newsfragments/258.enh deleted file mode 100644 index f19542dfc..000000000 --- a/docs/changes/newsfragments/258.enh +++ /dev/null @@ -1 +0,0 @@ -Support element-scoped directory and temporary directories for :class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/259.enh b/docs/changes/newsfragments/259.enh deleted file mode 100644 index 84347bc7b..000000000 --- a/docs/changes/newsfragments/259.enh +++ /dev/null @@ -1 +0,0 @@ -Improve element directory cleanup via ``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/260.enh b/docs/changes/newsfragments/260.enh deleted file mode 100644 index fa0920093..000000000 --- a/docs/changes/newsfragments/260.enh +++ /dev/null @@ -1 +0,0 @@ -Improve :class:`.BasePreprocessor` for easy subclassing and adapt :class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/261.misc b/docs/changes/newsfragments/261.misc deleted file mode 100644 index 51ec52be2..000000000 --- a/docs/changes/newsfragments/261.misc +++ /dev/null @@ -1 +0,0 @@ -Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit`` config by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/262.misc b/docs/changes/newsfragments/262.misc deleted file mode 100644 index 809ebc2a4..000000000 --- a/docs/changes/newsfragments/262.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for accessing FSL via Docker wrapper along with ``flirt``, ``applywarp`` and ``std2imgcoord`` commands by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/263.change b/docs/changes/newsfragments/263.change deleted file mode 100644 index 9b585d90b..000000000 --- a/docs/changes/newsfragments/263.change +++ /dev/null @@ -1 +0,0 @@ -Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and ``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to accept multiple preprocessors by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/264.feature b/docs/changes/newsfragments/264.feature deleted file mode 100644 index dc3b111de..000000000 --- a/docs/changes/newsfragments/264.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :func:`.get_parcellation` to fetch parcellation tailored for the data by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/265.feature b/docs/changes/newsfragments/265.feature deleted file mode 100644 index eb3416c85..000000000 --- a/docs/changes/newsfragments/265.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :func:`.get_coordinates` to fetch coordinates tailored for the data by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/266.feature b/docs/changes/newsfragments/266.feature deleted file mode 100644 index a207b8a9d..000000000 --- a/docs/changes/newsfragments/266.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's ``applywarp`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/267.feature b/docs/changes/newsfragments/267.feature deleted file mode 100644 index 73b7626e5..000000000 --- a/docs/changes/newsfragments/267.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.BOLDWarper` for warping BOLD data via FSL's ``applywarp`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/268.change b/docs/changes/newsfragments/268.change deleted file mode 100644 index 78a2f2030..000000000 --- a/docs/changes/newsfragments/268.change +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/268.enh b/docs/changes/newsfragments/268.enh deleted file mode 100644 index f45544395..000000000 --- a/docs/changes/newsfragments/268.enh +++ /dev/null @@ -1 +0,0 @@ -Add ``space`` information to existing datagrabbers, masks, parcellations and coordinates by `Synchon Mandal`_ and `Fede Raimondo`_ diff --git a/docs/changes/newsfragments/269.misc b/docs/changes/newsfragments/269.misc deleted file mode 100644 index 7a88e10b0..000000000 --- a/docs/changes/newsfragments/269.misc +++ /dev/null @@ -1 +0,0 @@ -Improve documentation, packaging and code style by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/270.misc b/docs/changes/newsfragments/270.misc deleted file mode 100644 index 738f5d6bc..000000000 --- a/docs/changes/newsfragments/270.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for Python 3.12 and make Python 3.11 the base for code coverage and CI checks by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/271.feature b/docs/changes/newsfragments/271.feature deleted file mode 100644 index 48c8aa888..000000000 --- a/docs/changes/newsfragments/271.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset `_ by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/272.bugfix b/docs/changes/newsfragments/272.bugfix deleted file mode 100644 index 52c5dac6d..000000000 --- a/docs/changes/newsfragments/272.bugfix +++ /dev/null @@ -1 +0,0 @@ -Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/274.bugfix b/docs/changes/newsfragments/274.bugfix deleted file mode 100644 index 1ae09259f..000000000 --- a/docs/changes/newsfragments/274.bugfix +++ /dev/null @@ -1 +0,0 @@ -Store native warped parcellations, coordinates and masks in element-scoped tempdirs for the pipeline to work by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/275.feature b/docs/changes/newsfragments/275.feature deleted file mode 100644 index 38faed47c..000000000 --- a/docs/changes/newsfragments/275.feature +++ /dev/null @@ -1 +0,0 @@ -Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/276.bugfix b/docs/changes/newsfragments/276.bugfix deleted file mode 100644 index 54bc1a62c..000000000 --- a/docs/changes/newsfragments/276.bugfix +++ /dev/null @@ -1 +0,0 @@ -Change interpolation scheme for parcel and mask native space transformation to nearest neighbour by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/277.misc b/docs/changes/newsfragments/277.misc deleted file mode 100644 index 1dd1eb639..000000000 --- a/docs/changes/newsfragments/277.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for accessing ANTs via Docker wrapper along with ``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/278.bugfix b/docs/changes/newsfragments/278.bugfix deleted file mode 100644 index a1318c46b..000000000 --- a/docs/changes/newsfragments/278.bugfix +++ /dev/null @@ -1 +0,0 @@ -Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for coordinates transformation by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/279.misc b/docs/changes/newsfragments/279.misc deleted file mode 100644 index 03f589c58..000000000 --- a/docs/changes/newsfragments/279.misc +++ /dev/null @@ -1 +0,0 @@ -Make the external tool wrappers output to stderr instead of stdout by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/280.bugfix b/docs/changes/newsfragments/280.bugfix deleted file mode 100644 index 0f2b91563..000000000 --- a/docs/changes/newsfragments/280.bugfix +++ /dev/null @@ -1 +0,0 @@ -Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/281.bugfix b/docs/changes/newsfragments/281.bugfix deleted file mode 100644 index 5f80b93b8..000000000 --- a/docs/changes/newsfragments/281.bugfix +++ /dev/null @@ -1 +0,0 @@ -Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect for coordinates transformation to other template spaces. diff --git a/docs/changes/newsfragments/281.misc b/docs/changes/newsfragments/281.misc deleted file mode 100644 index 5b38e2974..000000000 --- a/docs/changes/newsfragments/281.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/282.bugfix b/docs/changes/newsfragments/282.bugfix deleted file mode 100644 index 76f531d1e..000000000 --- a/docs/changes/newsfragments/282.bugfix +++ /dev/null @@ -1 +0,0 @@ -Propagate ReHo and fALFF maps, for aggregation to convert to other template spaces when required by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/283.bugfix b/docs/changes/newsfragments/283.bugfix deleted file mode 100644 index f069765c0..000000000 --- a/docs/changes/newsfragments/283.bugfix +++ /dev/null @@ -1 +0,0 @@ -Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the ``workdir`` parameter by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/284.bugfix b/docs/changes/newsfragments/284.bugfix deleted file mode 100644 index dd780eb32..000000000 --- a/docs/changes/newsfragments/284.bugfix +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/286.bugfix b/docs/changes/newsfragments/286.bugfix deleted file mode 100644 index 302c07dfc..000000000 --- a/docs/changes/newsfragments/286.bugfix +++ /dev/null @@ -1 +0,0 @@ -Pass down input path if input space is "native" for ``ReHoEstimator`` and ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/287.enh b/docs/changes/newsfragments/287.enh deleted file mode 100644 index e389e2a99..000000000 --- a/docs/changes/newsfragments/287.enh +++ /dev/null @@ -1 +0,0 @@ -Add ``mode`` as an aggregation function option in :func:`.get_aggfunc_by_name` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/288.misc b/docs/changes/newsfragments/288.misc deleted file mode 100644 index 454bbe3d6..000000000 --- a/docs/changes/newsfragments/288.misc +++ /dev/null @@ -1 +0,0 @@ -Make :class:`.BOLDWarper` tool-agnostic by moving it from ``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/291.doc b/docs/changes/newsfragments/291.doc deleted file mode 100644 index 815e34b20..000000000 --- a/docs/changes/newsfragments/291.doc +++ /dev/null @@ -1 +0,0 @@ -Fixed typo in code example for adding masks from "register_custom_mask" to "register_mask" by `Tobias Muganga`_ diff --git a/docs/changes/newsfragments/293.enh b/docs/changes/newsfragments/293.enh deleted file mode 100644 index a9084c0cf..000000000 --- a/docs/changes/newsfragments/293.enh +++ /dev/null @@ -1 +0,0 @@ -Adapt :class:`.BOLDWarper` to use FSL or ANTs depending on warp file extension by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/293.feature b/docs/changes/newsfragments/293.feature deleted file mode 100644 index 7d6f01a28..000000000 --- a/docs/changes/newsfragments/293.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce ``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper`` to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/293.misc b/docs/changes/newsfragments/293.misc deleted file mode 100644 index 5196cadcf..000000000 --- a/docs/changes/newsfragments/293.misc +++ /dev/null @@ -1 +0,0 @@ -Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/294.misc b/docs/changes/newsfragments/294.misc deleted file mode 100644 index 5230b082e..000000000 --- a/docs/changes/newsfragments/294.misc +++ /dev/null @@ -1 +0,0 @@ -Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/295.feature b/docs/changes/newsfragments/295.feature deleted file mode 100644 index e14508e21..000000000 --- a/docs/changes/newsfragments/295.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for running external commands from FSL, ANTs and others by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/297.feature b/docs/changes/newsfragments/297.feature deleted file mode 100644 index 4a23bd147..000000000 --- a/docs/changes/newsfragments/297.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :func:`.get_xfm` to fetch transformation files for moving between template spaces by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/298.feature b/docs/changes/newsfragments/298.feature deleted file mode 100644 index 1b62ae002..000000000 --- a/docs/changes/newsfragments/298.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :func:`.get_template` to fetch template space image tailored to a target data by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/299.change b/docs/changes/newsfragments/299.change deleted file mode 100644 index c42f194f3..000000000 --- a/docs/changes/newsfragments/299.change +++ /dev/null @@ -1 +0,0 @@ -Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/299.enh b/docs/changes/newsfragments/299.enh deleted file mode 100644 index eadf2622a..000000000 --- a/docs/changes/newsfragments/299.enh +++ /dev/null @@ -1 +0,0 @@ -Rewrite :func:`.compute_brain_mask` to allow variable template fetching via templateflow, according to target data by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/299.feature b/docs/changes/newsfragments/299.feature deleted file mode 100644 index 13219b002..000000000 --- a/docs/changes/newsfragments/299.feature +++ /dev/null @@ -1 +0,0 @@ -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. diff --git a/docs/changes/newsfragments/300.doc b/docs/changes/newsfragments/300.doc deleted file mode 100644 index 71875158d..000000000 --- a/docs/changes/newsfragments/300.doc +++ /dev/null @@ -1 +0,0 @@ -Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/300.enh b/docs/changes/newsfragments/300.enh deleted file mode 100644 index 9aa210e63..000000000 --- a/docs/changes/newsfragments/300.enh +++ /dev/null @@ -1 +0,0 @@ -Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/300.misc b/docs/changes/newsfragments/300.misc deleted file mode 100644 index a9605b8fb..000000000 --- a/docs/changes/newsfragments/300.misc +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/301.feature b/docs/changes/newsfragments/301.feature deleted file mode 100644 index 5ad08b386..000000000 --- a/docs/changes/newsfragments/301.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/301.removal b/docs/changes/newsfragments/301.removal deleted file mode 100644 index 9b2c343ed..000000000 --- a/docs/changes/newsfragments/301.removal +++ /dev/null @@ -1 +0,0 @@ -Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/302.enh b/docs/changes/newsfragments/302.enh deleted file mode 100644 index 79bb91b30..000000000 --- a/docs/changes/newsfragments/302.enh +++ /dev/null @@ -1 +0,0 @@ -Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/306.enh b/docs/changes/newsfragments/306.enh deleted file mode 100644 index d14b06138..000000000 --- a/docs/changes/newsfragments/306.enh +++ /dev/null @@ -1 +0,0 @@ -Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/308.enh b/docs/changes/newsfragments/308.enh deleted file mode 100644 index 9625ee278..000000000 --- a/docs/changes/newsfragments/308.enh +++ /dev/null @@ -1 +0,0 @@ -Improve :class:`.PatternDataGrabber` and :class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``, ``format``, ``mask_item`` and other metadata description handling via YAML by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/309.feature b/docs/changes/newsfragments/309.feature deleted file mode 100644 index fd9336834..000000000 --- a/docs/changes/newsfragments/309.feature +++ /dev/null @@ -1 +0,0 @@ -Introduce :class:`.QueueContextAdapter` as an abstract base class for job queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/310.change b/docs/changes/newsfragments/310.change deleted file mode 100644 index 1dddd7b93..000000000 --- a/docs/changes/newsfragments/310.change +++ /dev/null @@ -1 +0,0 @@ -Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed target data and "helper" data types as a dictionary by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/310.enh b/docs/changes/newsfragments/310.enh deleted file mode 100644 index 1cb4b4a7b..000000000 --- a/docs/changes/newsfragments/310.enh +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/311.change b/docs/changes/newsfragments/311.change deleted file mode 100644 index cf6117d92..000000000 --- a/docs/changes/newsfragments/311.change +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/changes/newsfragments/311.enh b/docs/changes/newsfragments/311.enh deleted file mode 100644 index 9cfb9e82f..000000000 --- a/docs/changes/newsfragments/311.enh +++ /dev/null @@ -1 +0,0 @@ -Improve external dependency handling for :class:`.PipelineStepMixin`-derived objects having implementation-based variations by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/312.bugfix b/docs/changes/newsfragments/312.bugfix deleted file mode 100644 index a43ff95a1..000000000 --- a/docs/changes/newsfragments/312.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix :class:`.HTCondorAdapter`'s script generation to use double quotes instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/314.bugfix b/docs/changes/newsfragments/314.bugfix deleted file mode 100644 index d5cb0b731..000000000 --- a/docs/changes/newsfragments/314.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/317.doc b/docs/changes/newsfragments/317.doc deleted file mode 100644 index 6739cffd7..000000000 --- a/docs/changes/newsfragments/317.doc +++ /dev/null @@ -1 +0,0 @@ -Improve documentation by adding information about space transformation and writing custom Preprocessors by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/320.change b/docs/changes/newsfragments/320.change deleted file mode 100644 index 75659ba92..000000000 --- a/docs/changes/newsfragments/320.change +++ /dev/null @@ -1 +0,0 @@ -Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_ diff --git a/docs/changes/newsfragments/322.bugfix b/docs/changes/newsfragments/322.bugfix deleted file mode 100644 index 462166332..000000000 --- a/docs/changes/newsfragments/322.bugfix +++ /dev/null @@ -1 +0,0 @@ -Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_ diff --git a/docs/changes/newsfragments/325.change b/docs/changes/newsfragments/325.change deleted file mode 100644 index 2d7f7facc..000000000 --- a/docs/changes/newsfragments/325.change +++ /dev/null @@ -1 +0,0 @@ -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`_ diff --git a/docs/whats_new.rst b/docs/whats_new.rst index e3816452a..ba5968ecf 100644 --- a/docs/whats_new.rst +++ b/docs/whats_new.rst @@ -8,8 +8,232 @@ What's new .. towncrier release notes start +Junifer 0.0.4 (2024-04-05) +-------------------------- + +Bugfixes +^^^^^^^^ + +- Make copying of assets in ``with`` block of YAML, relative to YAML and not to + current working directory by `Fede Raimondo`_ and `Synchon Mandal`_ + (:gh:`224`) +- Adapt ``junifer queue`` to properly use HTCondor >=10.4.0 + ``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`233`) +- Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by + `Synchon Mandal`_ (:gh:`272`) +- Store native warped parcellations, coordinates and masks in element-scoped + tempdirs for the pipeline to work by `Synchon Mandal`_ (:gh:`274`) +- Change interpolation scheme for parcel and mask native space transformation + to nearest neighbour by `Synchon Mandal`_ (:gh:`276`) +- Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for + coordinates transformation by `Synchon Mandal`_ (:gh:`278`) +- Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by + `Synchon Mandal`_ (:gh:`280`) +- Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect + for coordinates transformation to other template spaces. (:gh:`281`) +- Propagate ReHo and fALFF maps, for aggregation to convert to other template + spaces when required by `Synchon Mandal`_ (:gh:`282`) +- Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the + ``workdir`` parameter by `Synchon Mandal`_ (:gh:`283`) +- 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`_ (:gh:`284`) +- Pass down input path if input space is "native" for ``ReHoEstimator`` and + ``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and + `Synchon Mandal`_ (:gh:`286`) +- Fix :class:`.HTCondorAdapter`'s script generation to use double quotes + instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_ + (:gh:`312`) +- Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon + Mandal`_ (:gh:`314`) +- Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_ + (:gh:`322`) + + +API Changes +^^^^^^^^^^^ + +- Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_ + (:gh:`245`) +- Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon + Mandal`_ (:gh:`248`) +- Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`, + :class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching + of T1w data in subject-native space by `Synchon Mandal`_ (:gh:`252`) +- Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and + ``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to + accept multiple preprocessors by `Synchon Mandal`_ (:gh:`263`) +- 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`_ (:gh:`268`) +- Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_ + (:gh:`299`) +- Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed + target data and "helper" data types as a dictionary by `Synchon Mandal`_ + (:gh:`310`) +- 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`_ (:gh:`311`) +- Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_ + (:gh:`320`) +- 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`_ (:gh:`325`) + + +Improved Documentation +^^^^^^^^^^^^^^^^^^^^^^ + +- Add Zenodo badge in ``README`` and improve general documentation by `Synchon + Mandal`_ (:gh:`247`) +- Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix + listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_ + (:gh:`251`) +- Fixed typo in code example for adding masks from "register_custom_mask" to + "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 + `_ 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) ---------------------------------- +-------------------------- Bugfixes ^^^^^^^^ -- 2.52.0