junifer 0.0.4.dev576__tar.gz → 0.0.4.dev594__tar.gz

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev576
+Version: 0.0.4.dev594
 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>

junifer-0.0.4.dev594/docs/changes/newsfragments/249.feature

@@ -0,0 +1 @@
+Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_

junifer-0.0.4.dev594/docs/changes/newsfragments/302.enh

@@ -0,0 +1 @@
+Allow :class:`.BOLDWarper` to warp BOLD data to other MNI spaces by `Synchon Mandal`_

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/docs/using/queueing.rst

@@ -52,11 +52,13 @@ The following parameters are available for HTCondor:
   * ``kind``: This is the kind of virtual environment to use:
 
     * ``conda``
-    * ``virtualenv`` (not yet supported)
+    * ``venv``
     * ``local`` (no virtual environment)
 
   * ``name``: This is the name of the environment to use in case a virtual
-    environment is used.
+    environment is used. It should be the name when ``conda`` is used and
+    the absolute or relative path to the virtualenv when ``venv`` is used.
+    If relative path is used then it should be relative to the YAML.
 
 * ``mem``: Memory to be used by the job. It must be provided as a string with
   the units (e.g. ``2GB``).

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev576'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev576')
+__version__ = version = '0.0.4.dev594'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev594')

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer/api/functions.py

@@ -418,7 +418,10 @@ def _queue_condor(
         env_name = env["name"]
         executable = "run_venv.sh"
         arguments = f"{env_name} junifer"
-        # TODO: Copy run_venv.sh to jobdir
+        exec_path = jobdir / executable
+        logger.info(f"Copying {executable} to {exec_path.absolute()!s}")
+        shutil.copy(Path(__file__).parent / "res" / executable, exec_path)
+        make_executable(exec_path)
     elif env["kind"] == "local":
         executable = "junifer"
         arguments = ""

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer/api/parser.py

@@ -99,4 +99,17 @@ def parse_yaml(filepath: Union[str, Path]) -> Dict:
                 contents["storage"]["uri"] = str(
                     (filepath.parent / uri_path).resolve()
                 )
+
+    # Allow relative path if queue env kind is venv; same motivation as above
+    if "queue" in contents:
+        if "env" in contents["queue"]:
+            if "venv" == contents["queue"]["env"]["kind"]:
+                # Check if the env name is relative
+                venv_path = Path(contents["queue"]["env"]["name"])
+                if not venv_path.is_absolute():
+                    # Compute the absolute path
+                    contents["queue"]["env"]["name"] = str(
+                        (filepath.parent / venv_path).resolve()
+                    )
+
     return contents

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer/api/res/run_conda.sh

@@ -1,17 +1,17 @@
 #!/bin/bash
 
 if [ $# -lt 2 ]; then
-    echo "This script is meant to run a command within a python environment"
+    echo "This script is meant to run a command within a conda environment."
     echo "It needs at least 2 parameters."
     echo "The first one must be the environment name."
-    echo "The rest will be the command"
+    echo "The rest will be the command."
     exit 255
 fi
 
 eval "$(conda shell.bash hook)"
 env_name=$1
 echo "Activating ${env_name}"
-conda activate "$1"
+conda activate "${env_name}"
 shift 1
 
 if [ -f "pre_run.sh" ]; then
@@ -19,5 +19,5 @@ if [ -f "pre_run.sh" ]; then
     . ./pre_run.sh
 fi
 
-echo "Running ${*} in virtual environment"
+echo "Running ${*} in conda environment"
 "$@"

junifer-0.0.4.dev594/junifer/api/res/run_venv.sh

@@ -0,0 +1,22 @@
+#!/bin/bash
+
+if [ $# -lt 2 ]; then
+    echo "This script is meant to run a command within a Python virtual environment."
+    echo "It needs at least 2 parameters."
+    echo "The first one must be the virtualenv path."
+    echo "The rest will be the command."
+    exit 255
+fi
+
+env_path=$1
+echo "Activating ${env_path}"
+source "${env_path}"/bin/activate
+shift 1
+
+if [ -f "pre_run.sh" ]; then
+    echo "Sourcing pre_run.sh"
+    . ./pre_run.sh
+fi
+
+echo "Running ${*} in Python virtual environment"
+"$@"

junifer-0.0.4.dev594/junifer/preprocess/bold_warper.py

@@ -0,0 +1,244 @@
+"""Provide class for warping BOLD to other template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+import nibabel as nib
+from templateflow import api as tflow
+
+from ..api.decorators import register_preprocessor
+from ..data import get_template, get_xfm
+from ..pipeline import WorkDirManager
+from ..utils import logger, raise_error, run_ext_cmd
+from .ants.ants_apply_transforms_warper import _AntsApplyTransformsWarper
+from .base import BasePreprocessor
+from .fsl.apply_warper import _ApplyWarper
+
+
+@register_preprocessor
+class BOLDWarper(BasePreprocessor):
+    """Class for warping BOLD NIfTI images.
+
+    Parameters
+    ----------
+    reference : str
+        The data type to use as reference for warping, can be either a data
+        type like "T1w" or a template space like "MNI152NLin2009cAsym".
+
+    Raises
+    ------
+    ValueError
+        If ``reference`` is invalid.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[
+        List[Dict[str, Union[str, bool, List[str]]]]
+    ] = [
+        {
+            "name": "fsl",
+            "optional": True,
+            "commands": ["flirt", "applywarp"],
+        },
+        {
+            "name": "ants",
+            "optional": True,
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    def __init__(self, reference: str) -> None:
+        """Initialize the class."""
+        self.ref = reference
+        # Initialize superclass based on reference
+        if self.ref == "T1w":
+            super().__init__(
+                on="BOLD", required_data_types=["BOLD", self.ref, "Warp"]
+            )
+        elif self.ref in tflow.templates():
+            super().__init__(on="BOLD", required_data_types=["BOLD"])
+        else:
+            raise_error(f"Unknown reference: {self.ref}")
+
+    def get_valid_inputs(self) -> List[str]:
+        """Get valid data types for input.
+
+        Returns
+        -------
+        list of str
+            The list of data types that can be used as input for this
+            preprocessor.
+
+        """
+        return ["BOLD"]
+
+    def get_output_type(self, input: List[str]) -> List[str]:
+        """Get output type.
+
+        Parameters
+        ----------
+        input : list of str
+            The input to the preprocessor. The list must contain the
+            available Junifer Data dictionary keys.
+
+        Returns
+        -------
+        list of str
+            The updated list of available Junifer Data object keys after
+            the pipeline step.
+
+        """
+        # Does not add any new keys
+        return input
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> Tuple[str, Dict[str, Any]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            The BOLD input from the Junifer Data object.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object. Must include the
+            ``Warp`` and ``ref`` value's keys if native space transformation is
+            needed.
+
+        Returns
+        -------
+        str
+            The key to store the output in the Junifer Data object.
+        dict
+            The computed result as dictionary. This will be stored in the
+            Junifer Data object under the key ``data`` of the data type.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None when transforming to native space
+            i.e., using "T1w" as reference.
+        RuntimeError
+            If warp / transformation file extension is not ".mat" or ".h5"
+            when transforming to native space or
+            if the BOLD data is in the correct space and does not require
+            warping.
+
+        """
+        logger.info(f"Warping BOLD to {self.ref} space using BOLDWarper")
+        # Transform to native space
+        if self.ref == "T1w":
+            # Check for extra inputs
+            if extra_input is None:
+                raise_error(
+                    "No extra input provided, requires `Warp` and "
+                    f"`{self.ref}` data types in particular."
+                )
+            # Check for warp file type to use correct tool
+            warp_file_ext = extra_input["Warp"]["path"].suffix
+            if warp_file_ext == ".mat":
+                logger.debug("Using FSL with BOLDWarper")
+                # Initialize ApplyWarper for computation
+                apply_warper = _ApplyWarper(reference=self.ref, on="BOLD")
+                # Replace original BOLD data with warped BOLD data
+                _, input = apply_warper.preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            elif warp_file_ext == ".h5":
+                logger.debug("Using ANTs with BOLDWarper")
+                # Initialize AntsApplyTransformsWarper for computation
+                ants_apply_transforms_warper = _AntsApplyTransformsWarper(
+                    reference=self.ref, on="BOLD"
+                )
+                # Replace original BOLD data with warped BOLD data
+                _, input = ants_apply_transforms_warper.preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            else:
+                raise_error(
+                    msg=(
+                        "Unknown warp / transformation file extension: "
+                        f"{warp_file_ext}"
+                    ),
+                    klass=RuntimeError,
+                )
+        # Transform to template space
+        else:
+            # Check pre-requirements for space manipulation
+            if self.ref == input["space"]:
+                raise_error(
+                    (
+                        f"Skipped warping as the BOLD data is in {self.ref} "
+                        "space which would mean that you can remove the "
+                        "BOLDWarper from the preprocess step."
+                    ),
+                    klass=RuntimeError,
+                )
+            else:
+                # Get xfm file
+                xfm_file_path = get_xfm(src=input["space"], dst=self.ref)
+                # Get template space image
+                template_space_img = get_template(
+                    space=self.ref,
+                    target_data=input,
+                    extra_input=None,
+                )
+
+                # Create component-scoped tempdir
+                tempdir = WorkDirManager().get_tempdir(prefix="boldwarper")
+                # Create element-scoped tempdir so that warped BOLD is
+                # available later as nibabel stores file path reference for
+                # loading on computation
+                element_tempdir = WorkDirManager().get_element_tempdir(
+                    prefix="boldwarper"
+                )
+
+                # Save template
+                template_space_img_path = tempdir / f"{self.ref}_T1w.nii.gz"
+                nib.save(template_space_img, template_space_img_path)
+
+                # Create a tempfile for warped output
+                warped_bold_path = (
+                    element_tempdir
+                    / f"bold_warped_from_{input['space']}_to_{self.ref}.nii.gz"
+                )
+
+                logger.debug(
+                    f"Using ANTs to warp BOLD "
+                    f"from {input['space']} to {self.ref}"
+                )
+                # 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_bold_path.resolve()}",
+                ]
+                # Call antsApplyTransforms
+                run_ext_cmd(
+                    name="antsApplyTransforms", cmd=apply_transforms_cmd
+                )
+
+                # Modify target data
+                input["data"] = nib.load(warped_bold_path)
+                input["space"] = self.ref
+
+        return "BOLD", input

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer/preprocess/tests/test_bold_warper.py

@@ -7,6 +7,7 @@ import socket
 from typing import TYPE_CHECKING, List, Tuple
 
 import pytest
+from numpy.testing import assert_array_equal, assert_raises
 
 from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
 from junifer.datareader import DefaultDataReader
@@ -83,7 +84,7 @@ def test_BOLDWarper_get_output_type(input_: List[str]) -> None:
     socket.gethostname() != "juseless",
     reason="only for juseless",
 )
-def test_BOLDWarper_preprocess(
+def test_BOLDWarper_preprocess_to_native(
     datagrabber: "BaseDataGrabber", element: Tuple[str, ...]
 ) -> None:
     """Test BOLDWarper preprocess.
@@ -106,3 +107,70 @@ def test_BOLDWarper_preprocess(
         )
         assert data_type == "BOLD"
         assert isinstance(data, dict)
+
+
+@pytest.mark.parametrize(
+    "datagrabber, element, space",
+    [
+        [
+            DMCC13Benchmark(
+                types=["BOLD"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=False,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+            "MNI152NLin2009aAsym",
+        ],
+        [
+            DMCC13Benchmark(
+                types=["BOLD"],
+                sessions=["wave1bas"],
+                tasks=["Rest"],
+                phase_encodings=["AP"],
+                runs=["1"],
+                native_t1w=False,
+            ),
+            ("f9057kp", "wave1bas", "Rest", "AP", "1"),
+            "MNI152NLin6Asym",
+        ],
+    ],
+)
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_BOLDWarper_preprocess_to_multi_mni(
+    datagrabber: "BaseDataGrabber", element: Tuple[str, ...], space: str
+) -> None:
+    """Test BOLDWarper preprocess.
+
+    Parameters
+    ----------
+    datagrabber : DataGrabber-like object
+        The parametrized DataGrabber objects.
+    element : tuple of str
+        The parametrized elements.
+    space : str
+        The parametrized template space to transform to.
+
+    """
+    with datagrabber as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(dg[element])
+        pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
+        # Preprocess data
+        data_type, data = BOLDWarper(reference=space).preprocess(
+            input=element_data["BOLD"],
+            extra_input=element_data,
+        )
+        assert data_type == "BOLD"
+        assert isinstance(data, dict)
+        assert data["space"] == space
+        with assert_raises(AssertionError):
+            assert_array_equal(pre_xfm_data, data["data"])

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev576
+Version: 0.0.4.dev594
 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>

{junifer-0.0.4.dev576 → junifer-0.0.4.dev594}/junifer.egg-info/SOURCES.txt

@@ -65,6 +65,7 @@ docs/changes/newsfragments/245.change
 docs/changes/newsfragments/245.feature
 docs/changes/newsfragments/247.doc
 docs/changes/newsfragments/248.change
+docs/changes/newsfragments/249.feature
 docs/changes/newsfragments/251.doc
 docs/changes/newsfragments/252.change
 docs/changes/newsfragments/252.feature
@@ -110,6 +111,7 @@ docs/changes/newsfragments/298.feature
 docs/changes/newsfragments/300.doc
 docs/changes/newsfragments/300.enh
 docs/changes/newsfragments/300.misc
+docs/changes/newsfragments/302.enh
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/extension.rst
@@ -159,6 +161,7 @@ junifer/api/functions.py
 junifer/api/parser.py
 junifer/api/utils.py
 junifer/api/res/run_conda.sh
+junifer/api/res/run_venv.sh
 junifer/api/res/afni/3dAFNItoNIFTI
 junifer/api/res/afni/3dRSFC
 junifer/api/res/afni/3dReHo

junifer-0.0.4.dev576/junifer/preprocess/bold_warper.py

@@ -1,155 +0,0 @@
-"""Provide class for warping BOLD to other template spaces."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-from typing import (
-    Any,
-    ClassVar,
-    Dict,
-    List,
-    Optional,
-    Tuple,
-    Union,
-)
-
-from ..api.decorators import register_preprocessor
-from ..utils import logger, raise_error
-from .ants.ants_apply_transforms_warper import _AntsApplyTransformsWarper
-from .base import BasePreprocessor
-from .fsl.apply_warper import _ApplyWarper
-
-
-@register_preprocessor
-class BOLDWarper(BasePreprocessor):
-    """Class for warping BOLD NIfTI images.
-
-    Parameters
-    ----------
-    reference : str
-        The data type to use as reference for warping.
-
-    """
-
-    _EXT_DEPENDENCIES: ClassVar[
-        List[Dict[str, Union[str, bool, List[str]]]]
-    ] = [
-        {
-            "name": "fsl",
-            "optional": True,
-            "commands": ["flirt", "applywarp"],
-        },
-        {
-            "name": "ants",
-            "optional": True,
-            "commands": ["ResampleImage", "antsApplyTransforms"],
-        },
-    ]
-
-    def __init__(self, reference: str) -> None:
-        """Initialize the class."""
-        self.ref = reference
-        super().__init__(
-            on="BOLD", required_data_types=["BOLD", self.ref, "Warp"]
-        )
-
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this
-            preprocessor.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input: List[str]) -> List[str]:
-        """Get output type.
-
-        Parameters
-        ----------
-        input : list of str
-            The input to the preprocessor. The list must contain the
-            available Junifer Data dictionary keys.
-
-        Returns
-        -------
-        list of str
-            The updated list of available Junifer Data object keys after
-            the pipeline step.
-
-        """
-        # Does not add any new keys
-        return input
-
-    def preprocess(
-        self,
-        input: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
-    ) -> Tuple[str, Dict[str, Any]]:
-        """Preprocess.
-
-        Parameters
-        ----------
-        input : dict
-            The BOLD input from the Junifer Data object.
-        extra_input : dict, optional
-            The other fields in the Junifer Data object. Must include the
-            ``Warp`` and ``ref`` value's keys.
-
-        Returns
-        -------
-        str
-            The key to store the output in the Junifer Data object.
-        dict
-            The computed result as dictionary. This will be stored in the
-            Junifer Data object under the key ``data`` of the data type.
-
-        Raises
-        ------
-        ValueError
-            If ``extra_input`` is None.
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
-
-        """
-        logger.debug("Warping BOLD using BOLDWarper")
-        # Check for extra inputs
-        if extra_input is None:
-            raise_error(
-                f"No extra input provided, requires `Warp` and `{self.ref}` "
-                "data types in particular."
-            )
-        # Check for warp file type to use correct tool
-        warp_file_ext = extra_input["Warp"]["path"].suffix
-        if warp_file_ext == ".mat":
-            logger.debug("Using FSL with BOLDWarper")
-            # Initialize ApplyWarper for computation
-            apply_warper = _ApplyWarper(reference=self.ref, on="BOLD")
-            # Replace original BOLD data with warped BOLD data
-            _, input = apply_warper.preprocess(
-                input=input,
-                extra_input=extra_input,
-            )
-        elif warp_file_ext == ".h5":
-            logger.debug("Using ANTs with BOLDWarper")
-            # Initialize AntsApplyTransformsWarper for computation
-            ants_apply_transforms_warper = _AntsApplyTransformsWarper(
-                reference=self.ref, on="BOLD"
-            )
-            # Replace original BOLD data with warped BOLD data
-            _, input = ants_apply_transforms_warper.preprocess(
-                input=input,
-                extra_input=extra_input,
-            )
-        else:
-            raise_error(
-                msg=(
-                    "Unknown warp / transformation file extension: "
-                    f"{warp_file_ext}"
-                ),
-                klass=RuntimeError,
-            )
-        return "BOLD", input