junifer 0.0.5.dev98__py3-none-any.whl → 0.0.5.dev131__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev98'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev98')
+__version__ = version = '0.0.5.dev131'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev131')

junifer/api/tests/test_api_utils.py

@@ -45,6 +45,7 @@ def test_get_dependency_information_short() -> None:
         "httpx",
         "tqdm",
         "templateflow",
+        "lapy",
         "looseversion",
     ]
 
@@ -74,6 +75,7 @@ def test_get_dependency_information_long() -> None:
         "httpx",
         "tqdm",
         "templateflow",
+        "lapy",
     ]
     for key in dependency_list:
         assert key in dependency_information_keys

junifer/data/tests/test_masks.py

@@ -350,7 +350,7 @@ def test_get_mask_errors() -> None:
         with pytest.raises(ValueError, match=r"callable params"):
             get_mask(masks={"GM_prob0.2": {"param": 1}}, target_data=vbm_gm)
 
-        # Pass only parametesr to the intersection function
+        # Pass only parameters to the intersection function
         with pytest.raises(
             ValueError, match=r" At least one mask is required."
         ):

junifer/datagrabber/aomic/id1000.py

@@ -24,8 +24,8 @@ 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", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI"} or \
-           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).
     native_t1w : bool, optional
@@ -112,6 +112,39 @@ class DataladAOMICID1000(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

junifer/datagrabber/aomic/piop1.py

@@ -26,8 +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"} or \
-           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", \
@@ -147,6 +147,39 @@ 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

junifer/datagrabber/aomic/piop2.py

@@ -26,8 +26,8 @@ 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"} or \
-           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 \
@@ -144,6 +144,39 @@ 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

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
 
@@ -17,112 +17,58 @@ 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 "confounds" in out["BOLD"]
-
-        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(

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -18,129 +18,87 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 
 
 @pytest.mark.parametrize(
-    "tasks",
-    [None, "restingstate"],
+    "type_, nested_types, tasks",
+    [
+        ("BOLD", ["confounds", "mask"], None),
+        ("BOLD", ["confounds", "mask"], ["anticipation"]),
+        ("BOLD", ["confounds", "mask"], ["emomatching", "faces"]),
+        ("BOLD", ["confounds", "mask"], ["restingstate"]),
+        ("BOLD", ["confounds", "mask"], ["workingmemory", "gstroop"]),
+        (
+            "BOLD",
+            ["confounds", "mask"],
+            ["anticipation", "faces", "restingstate"],
+        ),
+        ("T1w", ["mask"], None),
+        ("VBM_CSF", None, None),
+        ("VBM_GM", None, None),
+        ("VBM_WM", None, None),
+        ("DWI", None, None),
+        ("FreeSurfer", None, None),
+    ],
 )
-def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
+def test_DataladAOMICPIOP1(
+    type_: str,
+    nested_types: Optional[List[str]],
+    tasks: Optional[List[str]],
+) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
     Parameters
     ----------
-    tasks : str or None
+    type_ : str
+        The parametrized type.
+    nested_types : list of str or None
+        The parametrized nested types.
+    tasks : list of str or None
         The parametrized task values.
 
     """
-    dg = DataladAOMICPIOP1(tasks=tasks)
+    dg = DataladAOMICPIOP1(types=type_, tasks=tasks)
     # 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]
-        sub, task = test_element
-
+        # Get test element data
         out = dg[test_element]
-
-        # asserts type "BOLD"
-        assert "BOLD" in out
-
-        # depending on task 'acquisition is different'
-        task_acqs = {
-            "anticipation": "seq",
-            "emomatching": "seq",
-            "faces": "mb3",
-            "gstroop": "seq",
-            "restingstate": "mb3",
-            "workingmemory": "seq",
-        }
-        acq = task_acqs[task]
-        new_task = f"{task}_acq-{acq}"
-        assert (
-            out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
-            "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
-        )
-
-        assert out["BOLD"]["path"].exists()
-        assert out["BOLD"]["path"].is_file()
-
-        # asserts type BOLD.confounds
-        assert "confounds" in out["BOLD"]
-
-        assert (
-            out["BOLD"]["confounds"]["path"].name == f"{sub}_task-{new_task}_"
-            "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"{sub}_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"{sub}_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"{sub}_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"{sub}_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"{sub}_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"]
+        # 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
+        # Check task name if BOLD
+        if type_ == "BOLD" and tasks is not None:
+            # Depending on task 'acquisition is different'
+            task_acqs = {
+                "anticipation": "seq",
+                "emomatching": "seq",
+                "faces": "mb3",
+                "gstroop": "seq",
+                "restingstate": "mb3",
+                "workingmemory": "seq",
+            }
+            assert task_acqs[test_element[1]] in out[type_]["path"].name
+        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 sub == meta["element"]["subject"]
+        assert test_element[0] == 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(