junifer 0.0.3.dev186__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/data/tests/test_template_spaces.py

@@ -0,0 +1,104 @@
+"""Provide tests for template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import socket
+from pathlib import Path
+
+import nibabel as nib
+import pytest
+
+from junifer.data import get_template, get_xfm
+from junifer.datareader import DefaultDataReader
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
+)
+
+
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_get_xfm(tmp_path: Path) -> None:
+    """Test warp file fetching.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    xfm_path = get_xfm(
+        src="MNI152NLin6Asym", dst="MNI152NLin2009cAsym", xfms_dir=tmp_path
+    )
+    assert isinstance(xfm_path, Path)
+
+
+@pytest.mark.parametrize(
+    "template_type",
+    [
+        "T1w",
+        "brain",
+        "gm",
+        "wm",
+        "csf",
+    ],
+)
+def test_get_template(template_type: str) -> None:
+    """Test tailored template image fetch.
+
+    Parameters
+    ----------
+    template_type : str
+        The parametrized template type.
+
+    """
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        bold = element_data["BOLD"]
+        # Get tailored parcellation
+        tailored_template = get_template(
+            space=bold["space"], target_data=bold, template_type=template_type
+        )
+        assert isinstance(tailored_template, nib.Nifti1Image)
+
+
+def test_get_template_invalid_space() -> None:
+    """Test invalid space check for template fetch."""
+    with OasisVBMTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        vbm_gm = element_data["VBM_GM"]
+        # Get tailored parcellation
+        with pytest.raises(ValueError, match="Unknown template space:"):
+            get_template(space="andromeda", target_data=vbm_gm)
+
+
+def test_get_template_invalid_template_type() -> None:
+    """Test invalid template type check for template fetch."""
+    with OasisVBMTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        vbm_gm = element_data["VBM_GM"]
+        # Get tailored parcellation
+        with pytest.raises(ValueError, match="Unknown template type:"):
+            get_template(
+                space=vbm_gm["space"],
+                target_data=vbm_gm,
+                template_type="xenon",
+            )
+
+
+def test_get_template_closest_resolution() -> None:
+    """Test closest resolution check for template fetch."""
+    with OasisVBMTestingDataGrabber() as dg:
+        element = dg["sub-01"]
+        element_data = DefaultDataReader().fit_transform(element)
+        vbm_gm = element_data["VBM_GM"]
+        # Change header resolution to fetch closest resolution
+        element_data["VBM_GM"]["data"].header.set_zooms((3, 3, 3))
+        template = get_template(space=vbm_gm["space"], target_data=vbm_gm)
+        assert isinstance(template, nib.Nifti1Image)

junifer/data/utils.py

@@ -1,4 +1,5 @@
 """Provide utilities for data module."""
+
 from typing import List, Optional, Union
 
 import numpy as np
@@ -7,14 +8,14 @@ from ..utils.logging import logger
 
 
 def closest_resolution(
-    resolution: Optional[float],
+    resolution: Optional[Union[float, int]],
     valid_resolution: Union[List[float], List[int], np.ndarray],
 ) -> Union[float, int]:
     """Find the closest resolution.
 
     Parameters
     ----------
-    resolution : float, optional
+    resolution : float or int, optional
         The given resolution. If None, will return the highest resolution
         (default None).
     valid_resolution : list of float or int, or np.ndarray
@@ -24,6 +25,7 @@ def closest_resolution(
     -------
     float or int
         The closest valid resolution.
+
     """
     # Convert list of int to numpy.ndarray
     if not isinstance(valid_resolution, np.ndarray):

junifer/datagrabber/__init__.py

@@ -15,3 +15,4 @@ from .pattern_datalad import PatternDataladDataGrabber
 from .aomic import DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2
 from .hcp1200 import HCP1200, DataladHCP1200
 from .multiple import MultipleDataGrabber
+from .dmcc13_benchmark import DMCC13Benchmark

junifer/datagrabber/aomic/id1000.py

@@ -8,7 +8,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import List, Union
 
 from ...api.decorators import register_datagrabber
 from ..pattern_datalad import PatternDataladDataGrabber
@@ -24,10 +24,12 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
+    native_t1w : bool, optional
+        Whether to use T1w in native space (default False).
 
     """
 
@@ -35,55 +37,116 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         self,
         datadir: Union[str, Path, None] = None,
         types: Union[str, List[str], None] = None,
+        native_t1w: bool = False,
     ) -> None:
         # The patterns
         patterns = {
-            "BOLD": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-moviewatching_"
-                "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
-            ),
-            "BOLD_confounds": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-moviewatching_"
-                "desc-confounds_regressors.tsv"
-            ),
-            "BOLD_mask": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-moviewatching_"
-                "space-MNI152NLin2009cAsym_"
-                "desc-brain_mask.nii.gz"
-            ),
-            "T1w": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-preproc_T1w.nii.gz"
-            ),
-            "T1w_mask": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-brain_mask.nii.gz"
-            ),
-            "probseg_CSF": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "CSF_probseg.nii.gz"
-            ),
-            "probseg_GM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "GM_probseg.nii.gz"
-            ),
-            "probseg_WM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "WM_probseg.nii.gz"
-            ),
-            "DWI": (
-                "derivatives/dwipreproc/sub-{subject}/dwi/"
-                "sub-{subject}_desc-preproc_dwi.nii.gz"
-            ),
+            "BOLD": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-moviewatching_"
+                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "BOLD_mask",
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-moviewatching_"
+                    "desc-confounds_regressors.tsv"
+                ),
+                "format": "fmriprep",
+            },
+            "BOLD_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-moviewatching_"
+                    "space-MNI152NLin2009cAsym_"
+                    "desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "T1w": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-preproc_T1w.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "T1w_mask",
+            },
+            "T1w_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_CSF": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "CSF_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_GM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "GM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_WM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "WM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "DWI": {
+                "pattern": (
+                    "derivatives/dwipreproc/{subject}/dwi/"
+                    "{subject}_desc-preproc_dwi.nii.gz"
+                ),
+            },
         }
+        # Use native T1w assets
+        self.native_t1w = False
+        if native_t1w:
+            self.native_t1w = True
+            patterns.update(
+                {
+                    "T1w": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_desc-preproc_T1w.nii.gz"
+                        ),
+                        "space": "native",
+                        "mask_item": "T1w_mask",
+                    },
+                    "T1w_mask": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_desc-brain_mask.nii.gz"
+                        ),
+                        "space": "native",
+                    },
+                    "Warp": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                            "mode-image_xfm.h5"
+                        ),
+                        "src": "MNI152NLin2009cAsym",
+                        "dst": "native",
+                    },
+                }
+            )
         # Set default types
         if types is None:
             types = list(patterns.keys())
@@ -102,25 +165,3 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
             replacements=replacements,
             confounds_format="fmriprep",
         )
-
-    def get_item(self, subject: str) -> Dict:
-        """Index one element in the dataset.
-
-        Parameters
-        ----------
-        subject : str
-            The subject ID.
-
-        Returns
-        -------
-        out : dict
-            Dictionary of paths for each type of data required for the
-            specified element.
-
-        """
-        out = super().get_item(subject=subject)
-        if out.get("BOLD"):
-            out["BOLD"]["mask_item"] = "BOLD_mask"
-        if out.get("T1w"):
-            out["T1w"]["mask_item"] = "T1w_mask"
-        return out

junifer/datagrabber/aomic/piop1.py

@@ -26,14 +26,21 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "anticipation", "emomatching", "faces", \
             "gstroop", "workingmemory"} or list of the options, optional
         AOMIC PIOP1 task sessions. If None, all available task sessions are
         selected (default None).
+    native_t1w : bool, optional
+        Whether to use T1w in native space (default False).
+
+    Raises
+    ------
+    ValueError
+        If invalid value is passed for ``tasks``.
 
     """
 
@@ -42,6 +49,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         datadir: Union[str, Path, None] = None,
         types: Union[str, List[str], None] = None,
         tasks: Union[str, List[str], None] = None,
+        native_t1w: bool = False,
     ) -> None:
         # Declare all tasks
         all_tasks = [
@@ -69,51 +77,111 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         self.tasks = tasks
         # The patterns
         patterns = {
-            "BOLD": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
-            ),
-            "BOLD_confounds": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "desc-confounds_regressors.tsv"
-            ),
-            "BOLD_mask": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-            ),
-            "T1w": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-preproc_T1w.nii.gz"
-            ),
-            "T1w_mask": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-brain_mask.nii.gz"
-            ),
-            "probseg_CSF": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "CSF_probseg.nii.gz"
-            ),
-            "probseg_GM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "GM_probseg.nii.gz"
-            ),
-            "probseg_WM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "WM_probseg.nii.gz"
-            ),
-            "DWI": (
-                "derivatives/dwipreproc/sub-{subject}/dwi/"
-                "sub-{subject}_desc-preproc_dwi.nii.gz"
-            ),
+            "BOLD": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "BOLD_mask",
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "desc-confounds_regressors.tsv"
+                ),
+                "format": "fmriprep",
+            },
+            "BOLD_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "T1w": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-preproc_T1w.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "T1w_mask",
+            },
+            "T1w_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_CSF": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "CSF_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_GM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "GM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_WM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "WM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "DWI": {
+                "pattern": (
+                    "derivatives/dwipreproc/{subject}/dwi/"
+                    "{subject}_desc-preproc_dwi.nii.gz"
+                ),
+            },
         }
+        # Use native T1w assets
+        self.native_t1w = False
+        if native_t1w:
+            self.native_t1w = True
+            patterns.update(
+                {
+                    "T1w": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_desc-preproc_T1w.nii.gz"
+                        ),
+                        "space": "native",
+                        "mask_item": "T1w_mask",
+                    },
+                    "T1w_mask": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_desc-brain_mask.nii.gz"
+                        ),
+                        "space": "native",
+                    },
+                    "Warp": {
+                        "pattern": (
+                            "derivatives/fmriprep/{subject}/anat/"
+                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                            "mode-image_xfm.h5"
+                        ),
+                        "src": "MNI152NLin2009cAsym",
+                        "dst": "native",
+                    },
+                }
+            )
         # Set default types
         if types is None:
             types = list(patterns.keys())
@@ -163,12 +231,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         acq = task_acqs[task]
         new_task = f"{task}_acq-{acq}"
 
-        out = super().get_item(subject=subject, task=new_task)
-        if out.get("BOLD"):
-            out["BOLD"]["mask_item"] = "BOLD_mask"
-        if out.get("T1w"):
-            out["T1w"]["mask_item"] = "T1w_mask"
-        return out
+        return super().get_item(subject=subject, task=new_task)
 
     def get_elements(self) -> List:
         """Implement fetching list of subjects in the dataset.
@@ -179,7 +242,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             The list of subjects in the dataset.
 
         """
-        subjects = [f"{x:04d}" for x in range(1, 217)]
+        subjects = [f"sub-{x:04d}" for x in range(1, 217)]
         elems = []
         for subject, task in product(subjects, self.tasks):
             elems.append((subject, task))