junifer 0.0.4.dev576__py3-none-any.whl → 0.0.4.dev594__py3-none-any.whl

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/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/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/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/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/preprocess/bold_warper.py

@@ -13,8 +13,13 @@ from typing import (
     Union,
 )
 
+import nibabel as nib
+from templateflow import api as tflow
+
 from ..api.decorators import register_preprocessor
-from ..utils import logger, raise_error
+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
@@ -27,7 +32,13 @@ class BOLDWarper(BasePreprocessor):
     Parameters
     ----------
     reference : str
-        The data type to use as reference for warping.
+        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.
 
     """
 
@@ -49,9 +60,15 @@ class BOLDWarper(BasePreprocessor):
     def __init__(self, reference: str) -> None:
         """Initialize the class."""
         self.ref = reference
-        super().__init__(
-            on="BOLD", required_data_types=["BOLD", self.ref, "Warp"]
-        )
+        # 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.
@@ -97,7 +114,8 @@ class BOLDWarper(BasePreprocessor):
             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.
+            ``Warp`` and ``ref`` value's keys if native space transformation is
+            needed.
 
         Returns
         -------
@@ -110,46 +128,117 @@ class BOLDWarper(BasePreprocessor):
         Raises
         ------
         ValueError
-            If ``extra_input`` is None.
+            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".
+            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.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,
-            )
+        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:
-            raise_error(
-                msg=(
-                    "Unknown warp / transformation file extension: "
-                    f"{warp_file_ext}"
-                ),
-                klass=RuntimeError,
-            )
+            # 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/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.dist-info → junifer-0.0.4.dev594.dist-info}/METADATA

@@ -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.dist-info → junifer-0.0.4.dev594.dist-info}/RECORD

@@ -1,13 +1,14 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=Edi-6wTxm5peiCW_YzRz7zYTCQLJv7NFz4LzFJ1rBWE,428
+junifer/_version.py,sha256=Ji34482-PAWG6zwQO7I8NdFGpe6EM1-bfdOTbh3Sv4k,428
 junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=T6FTW3vDRlsdkSYerbQD7Q05uA9bV6f8oHvK1jxGUa8,12882
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
-junifer/api/functions.py,sha256=XSliwA2Q9NaplfYFcK9vy6G-B-EZz894ec9LsV2RA-s,23058
-junifer/api/parser.py,sha256=a0IBvH3KN1PJaEpF3cnSv8g7VCVpDY1VsCvc8b8FFmE,3849
+junifer/api/functions.py,sha256=ZNB9g7TRy6-r9U087sncKKD8ZGdQAgyplH4RHcZFRdU,23238
+junifer/api/parser.py,sha256=a3SSC2xO-PF1pqXZXFq8Sh9aVd-dmHolJbCkGyOUTAM,4416
 junifer/api/utils.py,sha256=dyjTdPMwX9qeCrn8SQT2Pjshfnu-y1FEyujV7lCzvm0,3333
-junifer/api/res/run_conda.sh,sha256=GerhBGReDw-_fp6RPnaorMHT9IHrp3LRgHJY4mgK4_Y,501
+junifer/api/res/run_conda.sh,sha256=eskIn-fotITOlh--IUQKXh-SBOZkDkK8QvDcdQsyJ0M,509
+junifer/api/res/run_venv.sh,sha256=OF-LOdOdpjCU0JX6Dz1boG4ErPutTiVVD_N7j520Fvk,499
 junifer/api/res/afni/3dAFNItoNIFTI,sha256=Fsy5S5rwIBb1MepLfl_5FQhE7gv6NDwNyAR_k036NmM,51
 junifer/api/res/afni/3dRSFC,sha256=MkPtS_nKEoJOHDAT3ZP9IA-SvMdhyzZDiyxObV_XI3g,44
 junifer/api/res/afni/3dReHo,sha256=Jb5B97iPPPQ14zAz7tK5BVG4jPZyOe9c6kgM6ixKaY8,44
@@ -193,7 +194,7 @@ junifer/pipeline/tests/test_update_meta_mixin.py,sha256=UeWwpUi-Q5WVd36Fgfn_utXp
 junifer/pipeline/tests/test_workdir_manager.py,sha256=E1WY4C-GDsx2c49sePqr1WR_Y3nZ1kiRn4Veu506uTs,2801
 junifer/preprocess/__init__.py,sha256=-3exohZnw-gJ-MjVM63WcXzBW1mbSetEVozcDfs5etc,342
 junifer/preprocess/base.py,sha256=syiNqI8pUjoGyShZSjs_RTsd5VHhwoqzIfPfFstr4f4,6230
-junifer/preprocess/bold_warper.py,sha256=KOYCPCTJE92yI1juXK-3yl7VUxUhbzqqQxJrCYgk-0E,4572
+junifer/preprocess/bold_warper.py,sha256=d99ZraDBXXd0UXxJJ3s-FTy76GY_AIhzBbNCzNN0QEY,8314
 junifer/preprocess/ants/__init__.py,sha256=Uobmbhh6_gOowkF2hQNSQOh3AYeaXzarBXEcLJzhERE,112
 junifer/preprocess/ants/ants_apply_transforms_warper.py,sha256=V3y9EIGdIeJhJpnEVi123fHTK3R0sv_-OmWY7R_DC1M,6627
 junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py,sha256=ibLLISss0o0wg3lqpLhL1oO7MfU_bZF5PBqY3OOd9sg,3737
@@ -203,7 +204,7 @@ junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=OKAC
 junifer/preprocess/fsl/__init__.py,sha256=DerGFQ-dIuX5PT9a_BH6QkIXkJZVymjYy-woXF7tYGc,111
 junifer/preprocess/fsl/apply_warper.py,sha256=_HU1-63A32cSQw9eNdgpKN52BFivn6cZaDa0_at-4UY,6215
 junifer/preprocess/fsl/tests/test_apply_warper.py,sha256=b--MMPlaJw284gJWw-QV8rz6Rb2zmcBjYaY-cb6-uNU,3024
-junifer/preprocess/tests/test_bold_warper.py,sha256=X4rs-IBu_Oe9wF81Xlh6ih9BCu8SUyDm64lXKk-l9Q8,2831
+junifer/preprocess/tests/test_bold_warper.py,sha256=oQooJt4yC09LzXJuFDL7ytlYMuhcf4SeCAWKGdVLJdQ,4890
 junifer/preprocess/tests/test_preprocess_base.py,sha256=UHuH_YOK7AU3AfApWqgB6YLG-J669BgztuxNSWCtmtI,2560
 junifer/storage/__init__.py,sha256=QlzBw9UrRhmg_f7zQVas9h313u3sfZIBicA3_0Skm4M,337
 junifer/storage/base.py,sha256=UxDvj81gSmqqHspbSs1X_i9HvW5wXysDippI7HWM7aM,9654
@@ -234,10 +235,10 @@ junifer/utils/logging.py,sha256=T0HgiCI6cS2tp9nbI4cM3nVzMMjiVzgoxuyo5Y1rCyY,9124
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev576.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev576.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev576.dist-info/METADATA,sha256=qUaRguN0cYYG_C8L_ZnNdk0D-6w0EOdEICc6-Gvivl0,8128
-junifer-0.0.4.dev576.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev576.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev576.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev576.dist-info/RECORD,,
+junifer-0.0.4.dev594.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev594.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev594.dist-info/METADATA,sha256=ARdjzo_GyiF8LMNkJZ3lnDrF2czE2b44g4ChzZhqjGk,8128
+junifer-0.0.4.dev594.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev594.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev594.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev594.dist-info/RECORD,,