junifer 0.0.5__py3-none-any.whl → 0.0.5.dev24__py3-none-any.whl

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -18,99 +18,142 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 
 
 @pytest.mark.parametrize(
-    "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),
-    ],
+    "tasks",
+    [None, "restingstate"],
 )
-def test_DataladAOMICPIOP1(
-    type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
-) -> None:
+def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
     Parameters
     ----------
-    type_ : str
-        The parametrized type.
-    nested_types : list of str or None
-        The parametrized nested types.
-    tasks : list of str or None
+    tasks : str or None
         The parametrized task values.
 
     """
-    dg = DataladAOMICPIOP1(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP1(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]
-        # Get test element data
-        out = dg[test_element]
-        # Get all elements
         all_elements = dg.get_elements()
-        # Get test element
         test_element = all_elements[0]
-        # Get test element data
+        sub, task = test_element
+
         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"]
+
+        # 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 "BOLD_confounds" in out
+
+        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"]
         assert "element" in meta
         assert "subject" in meta["element"]
-        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()
+        assert sub == meta["element"]["subject"]
 
 
 @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"],

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -18,79 +18,136 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types, tasks",
-    [
-        ("BOLD", ["confounds", "mask"], None),
-        ("BOLD", ["confounds", "mask"], ["restingstate"]),
-        ("BOLD", ["confounds", "mask"], ["restingstate", "stopsignal"]),
-        ("BOLD", ["confounds", "mask"], ["workingmemory", "stopsignal"]),
-        ("BOLD", ["confounds", "mask"], ["workingmemory"]),
-        ("T1w", ["mask"], None),
-        ("VBM_CSF", None, None),
-        ("VBM_GM", None, None),
-        ("VBM_WM", None, None),
-        ("DWI", None, None),
-        ("FreeSurfer", None, None),
-    ],
+    "tasks",
+    [None, "restingstate"],
 )
-def test_DataladAOMICPIOP2(
-    type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
-) -> None:
+def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
 
     Parameters
     ----------
-    type_ : str
-        The parametrized type.
-    nested_types : list of str or None
-        The parametrized nested types.
-    tasks : list of str or None
+    tasks : str or None
         The parametrized task values.
 
     """
-    dg = DataladAOMICPIOP2(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP2(tasks=tasks)
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
-        # Get all elements
         all_elements = dg.get_elements()
-        # Get test element
+
+        if tasks == "restingstate":
+            for el in all_elements:
+                assert el[1] == "restingstate"
+
         test_element = all_elements[0]
-        # Get test element data
+        sub, task = test_element
         out = dg[test_element]
-        # Assert data type
-        assert type_ in out
-        # Check task name if BOLD
-        if type_ == "BOLD" and tasks is not None:
-            assert 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"]
+
+        # asserts type "BOLD"
+        assert "BOLD" in out
+
+        new_task = f"{task}_acq-seq"
+        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 "BOLD_confounds" in out
+
+        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"]
         assert "element" in meta
         assert "subject" in meta["element"]
-        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()
+        assert sub == meta["element"]["subject"]
 
 
 @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"],

junifer/datagrabber/base.py

@@ -11,9 +11,7 @@ from typing import Dict, Iterator, List, Tuple, Union
 
 from ..pipeline import UpdateMetaMixin
 from ..utils import logger, raise_error
-
-
-__all__ = ["BaseDataGrabber"]
+from .utils import validate_types
 
 
 class BaseDataGrabber(ABC, UpdateMetaMixin):
@@ -29,21 +27,16 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
     datadir : str or pathlib.Path
         The directory where the data is / will be stored.
 
-    Raises
-    ------
-    TypeError
-        If ``types`` is not a list or if the values are not string.
+    Attributes
+    ----------
+    datadir : pathlib.Path
+        The directory where the data is / will be stored.
 
     """
 
     def __init__(self, types: List[str], datadir: Union[str, Path]) -> None:
         # Validate types
-        if not isinstance(types, list):
-            raise_error(msg="`types` must be a list", klass=TypeError)
-        if any(not isinstance(x, str) for x in types):
-            raise_error(
-                msg="`types` must be a list of strings", klass=TypeError
-            )
+        validate_types(types)
         self.types = types
 
         # Convert str to Path

junifer/datagrabber/datalad_base.py

@@ -21,9 +21,6 @@ from ..utils import logger, raise_error, warn_with_log
 from .base import BaseDataGrabber
 
 
-__all__ = ["DataladDataGrabber"]
-
-
 class DataladDataGrabber(BaseDataGrabber):
     """Abstract base class for datalad-based data fetching.
 
@@ -179,16 +176,7 @@ class DataladDataGrabber(BaseDataGrabber):
             The unmodified input dictionary.
 
         """
-        to_get = []
-        for type_val in out.values():
-            # Iterate to check for nested "types" like mask
-            for k, v in type_val.items():
-                # Add base data type path
-                if k == "path":
-                    to_get.append(v)
-                # Add nested data type path
-                if isinstance(v, dict) and "path" in v:
-                    to_get.append(v["path"])
+        to_get = [v["path"] for v in out.values() if "path" in v]
 
         if len(to_get) > 0:
             logger.debug(f"Getting {len(to_get)} files using datalad:")

junifer/datagrabber/dmcc13_benchmark.py

@@ -25,16 +25,16 @@ class DMCC13Benchmark(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"} or \
-           list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM"} or a list of the options, optional
         DMCC data types. If None, all available data types are selected.
         (default None).
-    sessions: {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"} or \
-              list of the options, optional
+    sessions: {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"} or list of \
+            the options, optional
         DMCC sessions. If None, all available sessions are selected
         (default None).
     tasks: {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} or \
-           list of the options, optional
+            list of the options, optional
         DMCC task sessions. If None, all available task sessions are selected
         (default None).
     phase_encodings : {"AP", "PA"} or list of the options, optional
@@ -147,23 +147,24 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                     "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep-1.3.2/{subject}/{session}/"
-                        "/func/{subject}_{session}_task-{task}_acq-mb4"
-                        "{phase_encoding}_run-{run}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-                    ),
-                    "space": "MNI152NLin2009cAsym",
-                },
-                "confounds": {
-                    "pattern": (
-                        "derivatives/fmriprep-1.3.2/{subject}/{session}/"
-                        "func/{subject}_{session}_task-{task}_acq-mb4"
-                        "{phase_encoding}_run-{run}_desc-confounds_regressors.tsv"
-                    ),
-                    "format": "fmriprep",
-                },
+                "mask_item": "BOLD_mask",
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "derivatives/fmriprep-1.3.2/{subject}/{session}/"
+                    "func/{subject}_{session}_task-{task}_acq-mb4"
+                    "{phase_encoding}_run-{run}_desc-confounds_regressors.tsv"
+                ),
+                "format": "fmriprep",
+            },
+            "BOLD_mask": {
+                "pattern": (
+                    "derivatives/fmriprep-1.3.2/{subject}/{session}/"
+                    "/func/{subject}_{session}_task-{task}_acq-mb4"
+                    "{phase_encoding}_run-{run}_"
+                    "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
             },
             "T1w": {
                 "pattern": (
@@ -171,13 +172,14 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                     "{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "mask": {
-                    "pattern": (
-                        "derivatives/fmriprep-1.3.2/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-                    ),
-                    "space": "MNI152NLin2009cAsym",
-                },
+                "mask_item": "T1w_mask",
+            },
+            "T1w_mask": {
+                "pattern": (
+                    "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
             },
             "VBM_CSF": {
                 "pattern": (
@@ -213,13 +215,14 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                             "{subject}_desc-preproc_T1w.nii.gz"
                         ),
                         "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep-1.3.2/{subject}/anat/"
-                                "{subject}_desc-brain_mask.nii.gz"
-                            ),
-                            "space": "native",
-                        },
+                        "mask_item": "T1w_mask",
+                    },
+                    "T1w_mask": {
+                        "pattern": (
+                            "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                            "{subject}_desc-brain_mask.nii.gz"
+                        ),
+                        "space": "native",
                     },
                     "Warp": {
                         "pattern": (
@@ -294,6 +297,20 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
             phase_encoding=phase_encoding,
             run=run,
         )
+        if out.get("BOLD"):
+            out["BOLD"]["mask_item"] = "BOLD_mask"
+            # Add space information
+            out["BOLD"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("T1w"):
+            out["T1w"]["mask_item"] = "T1w_mask"
+            # Add space information
+            if self.native_t1w:
+                out["T1w"].update({"space": "native"})
+            else:
+                out["T1w"].update({"space": "MNI152NLin2009cAsym"})
+        if out.get("Warp"):
+            # Add source space information
+            out["Warp"].update({"src": "MNI152NLin2009cAsym"})
         return out
 
     def get_elements(self) -> List:

junifer/datagrabber/hcp1200/__init__.py

@@ -5,6 +5,3 @@
 
 from .hcp1200 import HCP1200
 from .datalad_hcp1200 import DataladHCP1200
-
-
-__all__ = ["HCP1200", "DataladHCP1200"]

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -14,9 +14,6 @@ from ...api.decorators import register_datagrabber
 from .hcp1200 import HCP1200
 
 
-__all__ = ["DataladHCP1200"]
-
-
 @register_datagrabber
 class DataladHCP1200(DataladDataGrabber, HCP1200):
     """Concrete implementation for datalad-based data fetching of HCP1200.

junifer/datagrabber/hcp1200/hcp1200.py

@@ -10,11 +10,8 @@ from pathlib import Path
 from typing import Dict, List, Union
 
 from ...api.decorators import register_datagrabber
-from ...utils import raise_error
 from ..pattern import PatternDataGrabber
-
-
-__all__ = ["HCP1200"]
+from ..utils import raise_error
 
 
 @register_datagrabber