junifer 0.0.4.dev653__tar.gz → 0.0.4.dev691__tar.gz

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/.github/workflows/ci-docs.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
     steps:
       - run: 'echo "No build required"'
       - name: Create mock coverage.xml file
@@ -40,7 +40,7 @@ jobs:
           echo '</package>' >> coverage.xml
           echo '</packages>' >> coverage.xml
           echo '</coverage>' >> coverage.xml
-        if: matrix.python-version == 3.10
+        if: matrix.python-version == 3.11
       - name: Upload mock coverage to Codecov
         uses: codecov/codecov-action@v4
         with:
@@ -48,4 +48,4 @@ jobs:
           # Allow coverage upload failure
           fail_ci_if_error: false
           flags: docs
-        if: success() && matrix.python-version == 3.10
+        if: success() && matrix.python-version == 3.11

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
     - name: Set up system
@@ -65,11 +65,11 @@ jobs:
         curl -O https://afni.nimh.nih.gov/pub/dist/bin/misc/@update.afni.binaries
         sudo tcsh @update.afni.binaries -package linux_ubuntu_16_64 -bindir /afni
         echo "/afni" >> $GITHUB_PATH
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Check AFNI
       run: |
         echo "Using AFNI : $(afni --version)"
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Install ANTs
       run: |
         sudo apt-get install -y -qq unzip
@@ -78,11 +78,11 @@ jobs:
         mv /opt/ants-2.5.1/bin/* /opt/ants-2.5.1
         rm ants.zip
         echo "/opt/ants-2.5.1" >> $GITHUB_PATH
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Check ANTs
       run: |
         echo "Using ANTs : $(antsRegistration --version)"
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
     - name: Install FSL
       run: |
         sudo apt-get install -y -qq python3
@@ -96,13 +96,13 @@ jobs:
         FSLREMOTECALL=""
         FSLGECUDAQ="cuda.q"
         echo "/opt/fsl-6.0.6.4" >> $GITHUB_PATH
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true
     - name: Check FSL
       run: |
         echo "Using FSL : $(flirt -version)"
-      if: matrix.python-version == 3.10
+      if: matrix.python-version == 3.11
       # Bypass FSL installation failure
       continue-on-error: true
     - name: Test with tox
@@ -114,4 +114,4 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
         flags: junifer
-      if: success() && matrix.python-version == 3.10
+      if: success() && matrix.python-version == 3.11

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/.github/workflows/docs-preview.yml

@@ -24,10 +24,10 @@ jobs:
       with:
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Check for sudo
       shell: bash
       run: |

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/.github/workflows/docs.yml

@@ -19,10 +19,10 @@ jobs:
         # require all of history to see all tagged versions' docs
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Check for sudo
       shell: bash
       run: |

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/.github/workflows/pypi.yml

@@ -15,21 +15,16 @@ jobs:
       with:
         fetch-depth: 0
         submodules: true
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install build
       run:
         pip install build
     - name: Build a binary wheel and a source tarball
       run:
         python -m build --sdist --wheel --outdir dist/ .
-    # - name: Publish distribution 📦 to Test PyPI
-    #   uses: pypa/gh-action-pypi-publish@master
-    #   with:
-    #     password: ${{ secrets.testpypi_token }}
-    #     repository_url: https://test.pypi.org/legacy/
     - name: Publish distribution 📦 to PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev653
+Version: 0.0.4.dev691
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -23,6 +23,7 @@ Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
@@ -36,11 +37,12 @@ Requires-Dist: nibabel<5.11,>=3.2.0
 Requires-Dist: nilearn<=0.10.2,>=0.9.0
 Requires-Dist: sqlalchemy<=2.1.0,>=1.4.27
 Requires-Dist: ruamel.yaml<0.18,>=0.17
-Requires-Dist: importlib_metadata; python_version < "3.10"
-Requires-Dist: h5py<3.10,>=3.8.0
+Requires-Dist: h5py>=3.10
 Requires-Dist: httpx[http2]==0.26.0
 Requires-Dist: tqdm==4.66.1
 Requires-Dist: templateflow>=23.0.0
+Requires-Dist: importlib_metadata; python_version < "3.10"
+Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
 Requires-Dist: neurokit2>=0.1.7; extra == "all"

junifer-0.0.4.dev691/docs/changes/newsfragments/270.misc

@@ -0,0 +1 @@
+Add support for Python 3.12 and make Python 3.11 the base for code coverage and CI checks by `Synchon Mandal`_

junifer-0.0.4.dev691/docs/changes/newsfragments/301.feature

@@ -0,0 +1 @@
+Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_

junifer-0.0.4.dev691/docs/changes/newsfragments/301.removal

@@ -0,0 +1 @@
+Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_

junifer-0.0.4.dev691/docs/changes/newsfragments/312.bugfix

@@ -0,0 +1 @@
+Fix :class:`.HTCondorAdapter`'s script generation to use double quotes instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev653'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev653')
+__version__ = version = '0.0.4.dev691'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev691')

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/api/queue_context/htcondor_adapter.py

@@ -274,8 +274,8 @@ class HTCondorAdapter(QueueContextAdapter):
             )
             fixed += (
                 f"JOB run{idx} {self._submit_run_path}\n"
-                f"VARS run{idx} element='{str_element}' "
-                f"log_element='{log_element}'\n\n"
+                f'VARS run{idx} element="{str_element}" '  # needs to be
+                f'log_element="{log_element}"\n\n'  # double quoted
             )
         var = ""
         if self._collect == "yes":

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -139,13 +139,13 @@ def test_HTCondorAdapter_run_collect(
         (
             [("sub01", "ses01")],
             "yes",
-            "element='sub01,ses01' log_element='sub01-ses01'",
+            'element="sub01,ses01" log_element="sub01-ses01"',
         ),
         (["sub01"], "on_success_only", "JOB collect"),
         (
             [("sub01", "ses01")],
             "on_success_only",
-            "element='sub01,ses01' log_element='sub01-ses01'",
+            'element="sub01,ses01" log_element="sub01-ses01"',
         ),
     ],
 )

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/api/tests/test_api_utils.py

@@ -45,9 +45,13 @@ def test_get_dependency_information_short() -> None:
         "httpx",
         "tqdm",
         "templateflow",
+        "looseversion",
     ]
-    if int(pl.python_version_tuple()[1]) < 10:
+
+    python_minor_version = int(pl.python_version_tuple()[1])
+    if python_minor_version < 10:
         dependency_list.append("importlib_metadata")
+
     assert frozenset(dependency_information.keys()) == frozenset(
         dependency_list
     )

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/preprocess/__init__.py

@@ -8,3 +8,4 @@
 from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
 from .bold_warper import BOLDWarper
+from .warping import SpaceWarper

{junifer-0.0.4.dev653 → junifer-0.0.4.dev691}/junifer/preprocess/bold_warper.py

@@ -30,6 +30,10 @@ from .fsl.apply_warper import _ApplyWarper
 class BOLDWarper(BasePreprocessor):
     """Class for warping BOLD NIfTI images.
 
+    .. deprecated:: 0.0.3
+              `BOLDWarper` will be removed in v0.0.4, it is replaced by
+              `SpaceWarper` because the latter works also with T1w data.
+
     Parameters
     ----------
     using : {"fsl", "ants"}

junifer-0.0.4.dev691/junifer/preprocess/warping/__init__.py

@@ -0,0 +1,6 @@
+"""Provide imports for warping sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .space_warper import SpaceWarper

junifer-0.0.4.dev691/junifer/preprocess/warping/_ants_warper.py

@@ -0,0 +1,167 @@
+"""Provide class for space warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...data import get_template, get_xfm
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class ANTsWarper:
+    """Class for space warping via ANTs antsApplyTransforms.
+
+    This class uses ANTs' ``ResampleImage`` for resampling (if required) and
+    ``antsApplyTransforms`` for transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+        reference: str,
+    ) -> Dict[str, Any]:
+        """Preprocess using ANTs.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+        reference : str
+            The data type or template space to use as reference for warping.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="ants_warper"
+        )
+
+        # Native space warping
+        if reference == "T1w":
+            logger.debug("Using ANTs for space warping")
+
+            # Get the min of the voxel sizes from input and use it as the
+            # resolution
+            resolution = np.min(input["data"].header.get_zooms()[:3])
+
+            # Create a tempfile for resampled reference output
+            resample_image_out_path = (
+                element_tempdir / "resampled_reference.nii.gz"
+            )
+            # Set ResampleImage command
+            resample_image_cmd = [
+                "ResampleImage",
+                "3",  # image dimension
+                f"{extra_input['T1w']['path'].resolve()}",
+                f"{resample_image_out_path.resolve()}",
+                f"{resolution}x{resolution}x{resolution}",
+                "0",  # option for spacing and not size
+                "3 3",  # Lanczos windowed sinc
+            ]
+            # Call ResampleImage
+            run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
+
+            # Create a tempfile for warped output
+            apply_transforms_out_path = element_tempdir / "output.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {input['path'].resolve()}",
+                # use resampled reference
+                f"-r {resample_image_out_path.resolve()}",
+                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-o {apply_transforms_out_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Load nifti
+            input["data"] = nib.load(apply_transforms_out_path)
+            # Save resampled reference path
+            input["reference_path"] = resample_image_out_path
+            # Use reference input's space as warped input's space
+            input["space"] = extra_input["T1w"]["space"]
+
+        # Template space warping
+        else:
+            logger.debug(
+                f"Using ANTs to warp data from {input['space']} to {reference}"
+            )
+
+            # Get xfm file
+            xfm_file_path = get_xfm(src=input["space"], dst=reference)
+            # Get template space image
+            template_space_img = get_template(
+                space=reference,
+                target_data=input,
+                extra_input=None,
+            )
+
+            # Create component-scoped tempdir
+            tempdir = WorkDirManager().get_tempdir(prefix="ants_warper")
+            # Save template
+            template_space_img_path = tempdir / f"{reference}_T1w.nii.gz"
+            nib.save(template_space_img, template_space_img_path)
+
+            # Create a tempfile for warped output
+            warped_output_path = element_tempdir / (
+                f"data_warped_from_{input['space']}_to_" f"{reference}.nii.gz"
+            )
+
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {input['path'].resolve()}",
+                f"-r {template_space_img_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_output_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Delete tempdir
+            WorkDirManager().delete_tempdir(tempdir)
+
+            # Modify target data
+            input["data"] = nib.load(warped_output_path)
+            input["space"] = reference
+
+        return input

junifer-0.0.4.dev691/junifer/preprocess/warping/_fsl_warper.py

@@ -0,0 +1,109 @@
+"""Provide class for space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class FSLWarper:
+    """Class for space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``flirt`` for resampling and ``applywarp`` for
+    transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "fsl",
+            "commands": ["flirt", "applywarp"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+    ) -> Dict[str, Any]:
+        """Preprocess using FSL.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        logger.debug("Using FSL for space warping")
+
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="fsl_warper"
+        )
+
+        # Create a tempfile for resampled reference output
+        flirt_out_path = element_tempdir / "resampled_reference.nii.gz"
+        # Set flirt command
+        flirt_cmd = [
+            "flirt",
+            "-interp spline",
+            f"-in {extra_input['T1w']['path'].resolve()}",
+            f"-ref {extra_input['T1w']['path'].resolve()}",
+            f"-applyisoxfm {resolution}",
+            f"-out {flirt_out_path.resolve()}",
+        ]
+        # Call flirt
+        run_ext_cmd(name="flirt", cmd=flirt_cmd)
+
+        # Create a tempfile for warped output
+        applywarp_out_path = element_tempdir / "output.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {input['path'].resolve()}",
+            f"-r {flirt_out_path.resolve()}",  # use resampled reference
+            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-o {applywarp_out_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        input["data"] = nib.load(applywarp_out_path)
+        # Save resampled reference path
+        input["reference_path"] = flirt_out_path
+
+        # Use reference input's space as warped input's space
+        input["space"] = extra_input["T1w"]["space"]
+
+        return input