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

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -18,142 +18,99 @@ 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 "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"]
+        # 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(
     "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"],

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -18,136 +18,79 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 
 
 @pytest.mark.parametrize(
-    "tasks",
-    [None, "restingstate"],
+    "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),
+    ],
 )
-def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
+def test_DataladAOMICPIOP2(
+    type_: str,
+    nested_types: Optional[List[str]],
+    tasks: Optional[List[str]],
+) -> None:
     """Test DataladAOMICPIOP2 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 = DataladAOMICPIOP2(tasks=tasks)
+    dg = DataladAOMICPIOP2(types=type_, tasks=tasks)
     # Set URI to Gin
     dg.uri = URI
 
     with dg:
+        # Get all elements
         all_elements = dg.get_elements()
-
-        if tasks == "restingstate":
-            for el in all_elements:
-                assert el[1] == "restingstate"
-
+        # 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
-
-        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 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"]
         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(
     "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"],

junifer/datagrabber/base.py

@@ -11,7 +11,9 @@ from typing import Dict, Iterator, List, Tuple, Union
 
 from ..pipeline import UpdateMetaMixin
 from ..utils import logger, raise_error
-from .utils import validate_types
+
+
+__all__ = ["BaseDataGrabber"]
 
 
 class BaseDataGrabber(ABC, UpdateMetaMixin):
@@ -27,16 +29,21 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
     datadir : str or pathlib.Path
         The directory where the data is / will be stored.
 
-    Attributes
-    ----------
-    datadir : 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.
 
     """
 
     def __init__(self, types: List[str], datadir: Union[str, Path]) -> None:
         # Validate types
-        validate_types(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
+            )
         self.types = types
 
         # Convert str to Path

junifer/datagrabber/datalad_base.py

@@ -21,6 +21,9 @@ 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.
 
@@ -176,7 +179,16 @@ class DataladDataGrabber(BaseDataGrabber):
             The unmodified input dictionary.
 
         """
-        to_get = [v["path"] for v in out.values() if "path" in v]
+        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"])
 
         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", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
-           "VBM_WM"} or a list of the options, optional
+    types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM"} or \
+           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
@@ -147,24 +147,23 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                     "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
                 ),
                 "space": "MNI152NLin2009cAsym",
-                "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",
+                "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",
+                },
             },
             "T1w": {
                 "pattern": (
@@ -172,14 +171,13 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                     "{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.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",
+                "mask": {
+                    "pattern": (
+                        "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                        "{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                    ),
+                    "space": "MNI152NLin2009cAsym",
+                },
             },
             "VBM_CSF": {
                 "pattern": (
@@ -215,14 +213,13 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
                             "{subject}_desc-preproc_T1w.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",
+                        "mask": {
+                            "pattern": (
+                                "derivatives/fmriprep-1.3.2/{subject}/anat/"
+                                "{subject}_desc-brain_mask.nii.gz"
+                            ),
+                            "space": "native",
+                        },
                     },
                     "Warp": {
                         "pattern": (
@@ -297,20 +294,6 @@ 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

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

junifer/datagrabber/hcp1200/datalad_hcp1200.py

@@ -14,6 +14,9 @@ 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

@@ -10,8 +10,11 @@ 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
-from ..utils import raise_error
+
+
+__all__ = ["HCP1200"]
 
 
 @register_datagrabber