junifer 0.0.5__py3-none-any.whl → 0.0.5.dev11__py3-none-any.whl

junifer/datagrabber/aomic/piop1.py

@@ -16,9 +16,6 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
-__all__ = ["DataladAOMICPIOP1"]
-
-
 @register_datagrabber
 class DataladAOMICPIOP1(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP1.
@@ -29,8 +26,8 @@ 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", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
-           "FreeSurfer"} or 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", \
@@ -87,22 +84,23 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/func/"
-                        "{subject}_task-{task}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-                    ),
-                    "space": "MNI152NLin2009cAsym",
-                },
-                "confounds": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/func/"
-                        "{subject}_task-{task}_"
-                        "desc-confounds_regressors.tsv"
-                    ),
-                    "format": "fmriprep",
-                },
+                "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": (
@@ -111,14 +109,15 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "desc-preproc_T1w.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
-                        "desc-brain_mask.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": (
@@ -150,39 +149,6 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "{subject}_desc-preproc_dwi.nii.gz"
                 ),
             },
-            "FreeSurfer": {
-                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
-                "aseg": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
-                    )
-                },
-                "norm": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]"
-                    )
-                },
-                "lh_white": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]"
-                    )
-                },
-                "rh_white": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]"
-                    )
-                },
-                "lh_pial": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]"
-                    )
-                },
-                "rh_pial": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]"
-                    )
-                },
-            },
         }
         # Use native T1w assets
         self.native_t1w = False
@@ -196,13 +162,14 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                             "{subject}_desc-preproc_T1w.nii.gz"
                         ),
                         "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.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": (

junifer/datagrabber/aomic/piop2.py

@@ -16,9 +16,6 @@ from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
-__all__ = ["DataladAOMICPIOP2"]
-
-
 @register_datagrabber
 class DataladAOMICPIOP2(PatternDataladDataGrabber):
     """Concrete implementation for pattern-based data fetching of AOMIC PIOP2.
@@ -29,12 +26,12 @@ class DataladAOMICPIOP2(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", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
-           "FreeSurfer"} or 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", "stopsignal", "workingmemory"} or \
-            list of the options, optional
+    tasks : {"restingstate", "stopsignal", "workingmemory"} \
+            or list of the options, optional
         AOMIC PIOP2 task sessions. If None, all available task sessions are
         selected (default None).
     native_t1w : bool, optional
@@ -84,22 +81,23 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/func/"
-                        "{subject}_task-{task}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-                    ),
-                    "space": "MNI152NLin2009cAsym",
-                },
-                "confounds": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/func/"
-                        "{subject}_task-{task}_"
-                        "desc-confounds_regressors.tsv"
-                    ),
-                    "format": "fmriprep",
-                },
+                "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": (
@@ -108,14 +106,15 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "desc-preproc_T1w.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
-                        "desc-brain_mask.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": (
@@ -147,39 +146,6 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "{subject}_desc-preproc_dwi.nii.gz"
                 ),
             },
-            "FreeSurfer": {
-                "pattern": "derivatives/freesurfer/[!f]{subject}/mri/T1.mg[z]",
-                "aseg": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/mri/aseg.mg[z]"
-                    )
-                },
-                "norm": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/mri/norm.mg[z]"
-                    )
-                },
-                "lh_white": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/lh.whit[e]"
-                    )
-                },
-                "rh_white": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/rh.whit[e]"
-                    )
-                },
-                "lh_pial": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/lh.pia[l]"
-                    )
-                },
-                "rh_pial": {
-                    "pattern": (
-                        "derivatives/freesurfer/[!f]{subject}/surf/rh.pia[l]"
-                    )
-                },
-            },
         }
         # Use native T1w assets
         self.native_t1w = False
@@ -193,13 +159,14 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                             "{subject}_desc-preproc_T1w.nii.gz"
                         ),
                         "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.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": (

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import List, Union
 
 import pytest
 
@@ -17,70 +17,125 @@ from junifer.datagrabber.aomic.id1000 import DataladAOMICID1000
 URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 
 
-@pytest.mark.parametrize(
-    "type_, nested_types",
-    [
-        ("BOLD", ["confounds", "mask"]),
-        ("T1w", ["mask"]),
-        ("VBM_CSF", None),
-        ("VBM_GM", None),
-        ("VBM_WM", None),
-        ("DWI", None),
-        ("FreeSurfer", None),
-    ],
-)
-def test_DataladAOMICID1000(
-    type_: str,
-    nested_types: Optional[List[str]],
-) -> None:
-    """Test DataladAOMICID1000 DataGrabber.
-
-    Parameters
-    ----------
-    type_ : str
-        The parametrized type.
-    nested_types : list of str or None
-        The parametrized nested types.
-
-    """
-    dg = DataladAOMICID1000(types=type_)
+def test_DataladAOMICID1000() -> None:
+    """Test DataladAOMICID1000 DataGrabber."""
+    dg = DataladAOMICID1000()
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
-        # Get all elements
         all_elements = dg.get_elements()
-        # Get test element
         test_element = all_elements[0]
-        # Get test element data
+
         out = dg[test_element]
-        # Assert data type
-        assert type_ in out
-        assert out[type_]["path"].exists()
-        assert out[type_]["path"].is_file()
-        # Asserts data type metadata
-        assert "meta" in out[type_]
-        meta = out[type_]["meta"]
+
+        # asserts type "BOLD"
+        assert "BOLD" in out
+
+        assert (
+            out["BOLD"]["path"].name == f"{test_element}_task-moviewatching_"
+            "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+        )
+
+        assert out["BOLD"]["path"].exists()
+        assert out["BOLD"]["path"].is_file()
+
+        # asserts type "BOLD_confounds"
+        assert "BOLD_confounds" in out
+
+        assert (
+            out["BOLD_confounds"]["path"].name
+            == f"{test_element}_task-moviewatching_"
+            "desc-confounds_regressors.tsv"
+        )
+
+        assert out["BOLD_confounds"]["path"].exists()
+        assert out["BOLD_confounds"]["path"].is_file()
+
+        # assert BOLD_mask
+        assert out["BOLD_mask"]["path"].exists()
+
+        # asserts type "T1w"
+        assert "T1w" in out
+
+        assert (
+            out["T1w"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_"
+            "desc-preproc_T1w.nii.gz"
+        )
+
+        assert out["T1w"]["path"].exists()
+        assert out["T1w"]["path"].is_file()
+
+        # asserts T1w_mask
+        assert out["T1w_mask"]["path"].exists()
+
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
+
+        assert (
+            out["VBM_CSF"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
+            "CSF_probseg.nii.gz"
+        )
+
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
+
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
+
+        assert (
+            out["VBM_GM"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
+            "GM_probseg.nii.gz"
+        )
+
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
+
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
+
+        assert (
+            out["VBM_WM"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
+            "WM_probseg.nii.gz"
+        )
+
+        assert out["VBM_WM"]["path"].exists()
+        assert out["VBM_WM"]["path"].is_file()
+
+        # asserts type "DWI"
+        assert "DWI" in out
+
+        assert (
+            out["DWI"]["path"].name
+            == f"{test_element}_desc-preproc_dwi.nii.gz"
+        )
+
+        assert out["DWI"]["path"].exists()
+        assert out["DWI"]["path"].is_file()
+
+        # asserts meta
+        assert "meta" in out["BOLD"]
+        meta = out["BOLD"]["meta"]
         assert "element" in meta
         assert "subject" in meta["element"]
         assert test_element == meta["element"]["subject"]
-        # Assert nested data type if not None
-        if nested_types is not None:
-            for nested_type in nested_types:
-                assert out[type_][nested_type]["path"].exists()
-                assert out[type_][nested_type]["path"].is_file()
 
 
 @pytest.mark.parametrize(
     "types",
     [
         "BOLD",
+        "BOLD_confounds",
         "T1w",
         "VBM_CSF",
         "VBM_GM",
         "VBM_WM",
         "DWI",
-        ["BOLD", "VBM_CSF"],
+        ["BOLD", "BOLD_confounds"],
         ["T1w", "VBM_CSF"],
         ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],