junifer 0.0.4.dev831__py3-none-any.whl → 0.0.5__py3-none-any.whl

junifer/datagrabber/aomic/piop1.py

@@ -16,6 +16,9 @@ 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.
@@ -26,8 +29,8 @@ 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", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
-           "VBM_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
+           "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "anticipation", "emomatching", "faces", \
@@ -84,23 +87,22 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "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",
+                "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",
+                },
             },
             "T1w": {
                 "pattern": (
@@ -109,15 +111,14 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                     "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",
+                "mask": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/anat/"
+                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "desc-brain_mask.nii.gz"
+                    ),
+                    "space": "MNI152NLin2009cAsym",
+                },
             },
             "VBM_CSF": {
                 "pattern": (
@@ -149,6 +150,39 @@ 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
@@ -162,14 +196,13 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                             "{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",
+                        "mask": {
+                            "pattern": (
+                                "derivatives/fmriprep/{subject}/anat/"
+                                "{subject}_desc-brain_mask.nii.gz"
+                            ),
+                            "space": "native",
+                        },
                     },
                     "Warp": {
                         "pattern": (

junifer/datagrabber/aomic/piop2.py

@@ -16,6 +16,9 @@ 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.
@@ -26,12 +29,12 @@ 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", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
-           "VBM_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
+           "FreeSurfer"} or 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
@@ -81,23 +84,22 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "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",
+                "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",
+                },
             },
             "T1w": {
                 "pattern": (
@@ -106,15 +108,14 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     "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",
+                "mask": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/anat/"
+                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "desc-brain_mask.nii.gz"
+                    ),
+                    "space": "MNI152NLin2009cAsym",
+                },
             },
             "VBM_CSF": {
                 "pattern": (
@@ -146,6 +147,39 @@ 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
@@ -159,14 +193,13 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                             "{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",
+                        "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, Union
+from typing import List, Optional, Union
 
 import pytest
 
@@ -17,126 +17,70 @@ from junifer.datagrabber.aomic.id1000 import DataladAOMICID1000
 URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 
 
-def test_DataladAOMICID1000() -> None:
-    """Test DataladAOMICID1000 DataGrabber."""
-    dg = DataladAOMICID1000()
+@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_)
     # 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]
-
-        # 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 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"]
         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", "BOLD_confounds"],
+        ["BOLD", "VBM_CSF"],
         ["T1w", "VBM_CSF"],
         ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],