junifer 0.0.5.dev242__py3-none-any.whl → 0.0.6__py3-none-any.whl

junifer/datagrabber/aomic/piop2.py

@@ -9,7 +9,7 @@
 
 from itertools import product
 from pathlib import Path
-from typing import Dict, List, Union
+from typing import Union
 
 from ...api.decorators import register_datagrabber
 from ...utils import raise_error
@@ -33,12 +33,12 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
            "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 \
+    tasks : {"restingstate", "stopsignal", "workingmemory", "emomatching"} or \
             list of the options, optional
         AOMIC PIOP2 task sessions. If None, all available task sessions are
         selected (default None).
-    native_t1w : bool, optional
-        Whether to use T1w in native space (default False).
+    space : {"native", "MNI152NLin2009cAsym"}, optional
+        The space to use for the data (default "MNI152NLin2009cAsym").
 
     Raises
     ------
@@ -50,15 +50,21 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
     def __init__(
         self,
         datadir: Union[str, Path, None] = None,
-        types: Union[str, List[str], None] = None,
-        tasks: Union[str, List[str], None] = None,
-        native_t1w: bool = False,
+        types: Union[str, list[str], None] = None,
+        tasks: Union[str, list[str], None] = None,
+        space: str = "MNI152NLin2009cAsym",
     ) -> None:
+        valid_spaces = ["native", "MNI152NLin2009cAsym"]
+        if space not in ["native", "MNI152NLin2009cAsym"]:
+            raise_error(
+                f"Invalid space {space}. Must be one of {valid_spaces}"
+            )
         # Declare all tasks
         all_tasks = [
             "restingstate",
             "stopsignal",
             "workingmemory",
+            "emomatching",
         ]
         # Set default tasks
         if tasks is None:
@@ -75,22 +81,32 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                         " dataset!"
                     )
         self.tasks = tasks
+        # Descriptor for space in `anat`
+        sp_anat_desc = (
+            "" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
+        # Descriptor for space in `func`
+        sp_func_desc = (
+            "space-T1w_" if space == "native" else "space-MNI152NLin2009cAsym_"
+        )
         # The patterns
         patterns = {
             "BOLD": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/func/"
                     "{subject}_task-{task}_"
-                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                    f"{sp_func_desc}"
+                    "desc-preproc_bold.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/func/"
                         "{subject}_task-{task}_"
-                        "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                        f"{sp_func_desc}"
+                        "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
                 "confounds": {
                     "pattern": (
@@ -100,46 +116,59 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     ),
                     "format": "fmriprep",
                 },
+                "reference": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/func/"
+                        "{subject}_task-{task}_"
+                        f"{sp_func_desc}"
+                        "boldref.nii.gz"
+                    ),
+                },
             },
             "T1w": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
                     "desc-preproc_T1w.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
                 "mask": {
                     "pattern": (
                         "derivatives/fmriprep/{subject}/anat/"
-                        "{subject}_space-MNI152NLin2009cAsym_"
+                        "{subject}_"
+                        f"{sp_anat_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
             },
             "VBM_CSF": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
-                    "CSF_probseg.nii.gz"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
+                    "label-CSF_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_GM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
-                    "GM_probseg.nii.gz"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
+                    "label-GM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "VBM_WM": {
                 "pattern": (
                     "derivatives/fmriprep/{subject}/anat/"
-                    "{subject}_space-MNI152NLin2009cAsym_label-"
-                    "WM_probseg.nii.gz"
+                    "{subject}_"
+                    f"{sp_anat_desc}"
+                    "label-WM_probseg.nii.gz"
                 ),
-                "space": "MNI152NLin2009cAsym",
+                "space": space,
             },
             "DWI": {
                 "pattern": (
@@ -180,38 +209,38 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                     )
                 },
             },
+            "Warp": [
+                {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/anat/"
+                        "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
+                        "mode-image_xfm.h5"
+                    ),
+                    "src": "MNI152NLin2009cAsym",
+                    "dst": "native",
+                    "warper": "ants",
+                },
+                {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/anat/"
+                        "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
+                        "mode-image_xfm.h5"
+                    ),
+                    "src": "native",
+                    "dst": "MNI152NLin2009cAsym",
+                    "warper": "ants",
+                },
+            ],
         }
+
+        if space == "native":
+            patterns["BOLD"]["prewarp_space"] = "MNI152NLin2009cAsym"
+        else:
+            patterns["BOLD"]["prewarp_space"] = "native"
+
         # Use native T1w assets
-        self.native_t1w = False
-        if native_t1w:
-            self.native_t1w = True
-            patterns.update(
-                {
-                    "T1w": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_desc-preproc_T1w.nii.gz"
-                        ),
-                        "space": "native",
-                        "mask": {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_desc-brain_mask.nii.gz"
-                            ),
-                            "space": "native",
-                        },
-                    },
-                    "Warp": {
-                        "pattern": (
-                            "derivatives/fmriprep/{subject}/anat/"
-                            "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
-                            "mode-image_xfm.h5"
-                        ),
-                        "src": "MNI152NLin2009cAsym",
-                        "dst": "native",
-                    },
-                }
-            )
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())
@@ -231,7 +260,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             confounds_format="fmriprep",
         )
 
-    def get_elements(self) -> List:
+    def get_elements(self) -> list:
         """Implement fetching list of elements in the dataset.
 
         Returns
@@ -247,7 +276,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             elems.append((subject, task))
         return elems
 
-    def get_item(self, subject: str, task: str) -> Dict:
+    def get_item(self, subject: str, task: str) -> dict:
         """Index one element in the dataset.
 
         Parameters

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 Optional, Union
 
 import pytest
 
@@ -18,20 +18,25 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomic1000"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types",
+    "type_, nested_types, space",
     [
-        ("BOLD", ["confounds", "mask"]),
-        ("T1w", ["mask"]),
-        ("VBM_CSF", None),
-        ("VBM_GM", None),
-        ("VBM_WM", None),
-        ("DWI", None),
-        ("FreeSurfer", None),
+        ("BOLD", ["confounds", "mask", "reference"], "MNI152NLin2009cAsym"),
+        ("BOLD", ["confounds", "mask", "reference"], "native"),
+        ("T1w", ["mask"], "MNI152NLin2009cAsym"),
+        ("T1w", ["mask"], "native"),
+        ("VBM_CSF", None, "MNI152NLin2009cAsym"),
+        ("VBM_CSF", None, "native"),
+        ("VBM_GM", None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, "native"),
+        ("VBM_WM", None, "MNI152NLin2009cAsym"),
+        ("DWI", None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICID1000(
     type_: str,
-    nested_types: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber.
 
@@ -41,9 +46,11 @@ def test_DataladAOMICID1000(
         The parametrized type.
     nested_types : list of str or None
         The parametrized nested types.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICID1000(types=type_)
+    dg = DataladAOMICID1000(types=type_, space=space)
     # Set URI to Gin
     dg.uri = URI
 
@@ -87,7 +94,7 @@ def test_DataladAOMICID1000(
     ],
 )
 def test_DataladAOMICID1000_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICID1000 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -18,30 +18,62 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop1"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types, tasks",
+    "type_, nested_types, tasks, space",
     [
-        ("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"],
+            ["confounds", "mask", "reference"],
+            None,
+            "MNI152NLin2009cAsym",
+        ),
+        ("BOLD", ["confounds", "mask", "reference"], None, "native"),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["anticipation"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["emomatching", "faces"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["restingstate"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory", "gstroop"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
             ["anticipation", "faces", "restingstate"],
+            "MNI152NLin2009cAsym",
         ),
-        ("T1w", ["mask"], None),
-        ("VBM_CSF", None, None),
-        ("VBM_GM", None, None),
-        ("VBM_WM", None, None),
-        ("DWI", None, None),
-        ("FreeSurfer", None, None),
+        ("T1w", ["mask"], None, "MNI152NLin2009cAsym"),
+        ("T1w", ["mask"], None, "native"),
+        ("VBM_CSF", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_CSF", None, None, "native"),
+        ("VBM_GM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, None, "native"),
+        ("VBM_WM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_WM", None, None, "native"),
+        ("DWI", None, None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICPIOP1(
     type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    tasks: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber.
 
@@ -53,9 +85,11 @@ def test_DataladAOMICPIOP1(
         The parametrized nested types.
     tasks : list of str or None
         The parametrized task values.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICPIOP1(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP1(types=type_, tasks=tasks, space=space)
     # Set URI to Gin
     dg.uri = URI
 
@@ -117,7 +151,7 @@ def test_DataladAOMICPIOP1(
     ],
 )
 def test_DataladAOMICPIOP1_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICPIOP1 DataGrabber partial data access.
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -7,7 +7,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Optional, Union
 
 import pytest
 
@@ -18,25 +18,56 @@ URI = "https://gin.g-node.org/juaml/datalad-example-aomicpiop2"
 
 
 @pytest.mark.parametrize(
-    "type_, nested_types, tasks",
+    "type_, nested_types, tasks, space",
     [
-        ("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),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            None,
+            "MNI152NLin2009cAsym",
+        ),
+        ("BOLD", ["confounds", "mask", "reference"], None, "native"),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["restingstate"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["restingstate", "stopsignal"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory", "stopsignal"],
+            "MNI152NLin2009cAsym",
+        ),
+        (
+            "BOLD",
+            ["confounds", "mask", "reference"],
+            ["workingmemory"],
+            "MNI152NLin2009cAsym",
+        ),
+        ("T1w", ["mask"], None, "MNI152NLin2009cAsym"),
+        ("T1w", ["mask"], None, "native"),
+        ("VBM_CSF", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_CSF", None, None, "native"),
+        ("VBM_GM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_GM", None, None, "native"),
+        ("VBM_WM", None, None, "MNI152NLin2009cAsym"),
+        ("VBM_WM", None, None, "native"),
+        ("DWI", None, None, "MNI152NLin2009cAsym"),
+        ("FreeSurfer", None, None, "MNI152NLin2009cAsym"),
     ],
 )
 def test_DataladAOMICPIOP2(
     type_: str,
-    nested_types: Optional[List[str]],
-    tasks: Optional[List[str]],
+    nested_types: Optional[list[str]],
+    tasks: Optional[list[str]],
+    space: str,
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber.
 
@@ -48,9 +79,11 @@ def test_DataladAOMICPIOP2(
         The parametrized nested types.
     tasks : list of str or None
         The parametrized task values.
+    space: str
+        The parametrized space.
 
     """
-    dg = DataladAOMICPIOP2(types=type_, tasks=tasks)
+    dg = DataladAOMICPIOP2(types=type_, tasks=tasks, space=space)
     # Set URI to Gin
     dg.uri = URI
 
@@ -97,7 +130,7 @@ def test_DataladAOMICPIOP2(
     ],
 )
 def test_DataladAOMICPIOP2_partial_data_access(
-    types: Union[str, List[str]],
+    types: Union[str, list[str]],
 ) -> None:
     """Test DataladAOMICPIOP2 DataGrabber partial data access.
 

junifer/datagrabber/base.py

@@ -6,10 +6,12 @@
 # License: AGPL
 
 from abc import ABC, abstractmethod
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Dict, Iterator, List, Tuple, Union
+from typing import Union
 
 from ..pipeline import UpdateMetaMixin
+from ..typing import Element, Elements
 from ..utils import logger, raise_error
 
 
@@ -36,7 +38,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
     """
 
-    def __init__(self, types: List[str], datadir: Union[str, Path]) -> None:
+    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)
@@ -66,9 +68,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         """
         yield from self.get_elements()
 
-    def __getitem__(
-        self, element: Union[str, Tuple[str, ...]]
-    ) -> Dict[str, Dict]:
+    def __getitem__(self, element: Element) -> dict[str, dict]:
         """Enable indexing support.
 
         Parameters
@@ -89,14 +89,19 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
             element = (element,)
         # Zip through element keys and actual values to construct element
         # access dictionary
-        named_element: Dict = dict(zip(self.get_element_keys(), element))
+        named_element: dict = dict(zip(self.get_element_keys(), element))
         logger.debug(f"Named element: {named_element}")
         # Fetch element
         out = self.get_item(**named_element)
         # Update metadata
         for _, t_val in out.items():
             self.update_meta(t_val, "datagrabber")
-            t_val["meta"]["element"] = named_element
+            # Conditional for list dtype vals like Warp
+            if isinstance(t_val, list):
+                for entry in t_val:
+                    entry["meta"]["element"] = named_element
+            else:
+                t_val["meta"]["element"] = named_element
 
         return out
 
@@ -108,7 +113,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         """Context exit."""
         return None
 
-    def get_types(self) -> List[str]:
+    def get_types(self) -> list[str]:
         """Get types.
 
         Returns
@@ -131,13 +136,13 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         """
         return self._datadir
 
-    def filter(self, selection: List[Union[str, Tuple[str]]]) -> Iterator:
+    def filter(self, selection: Elements) -> Iterator:
         """Filter elements to be grabbed.
 
         Parameters
         ----------
-        selection : list of str or tuple
-            The list of partial element key values to filter using.
+        selection : list
+            The list of partial or complete element selectors to filter using.
 
         Yields
         ------
@@ -146,7 +151,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
 
         """
 
-        def filter_func(element: Union[str, Tuple[str]]) -> bool:
+        def filter_func(element: Element) -> bool:
             """Filter element based on selection.
 
             Parameters
@@ -177,7 +182,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         yield from filter(filter_func, self.get_elements())
 
     @abstractmethod
-    def get_element_keys(self) -> List[str]:
+    def get_element_keys(self) -> list[str]:
         """Get element keys.
 
         For each item in the ``element`` tuple passed to ``__getitem__()``,
@@ -195,15 +200,14 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         )  # pragma: no cover
 
     @abstractmethod
-    def get_elements(self) -> List[Union[str, Tuple[str]]]:
+    def get_elements(self) -> Elements:
         """Get elements.
 
         Returns
         -------
         list
-            List of elements that can be grabbed. The elements can be strings,
-            tuples or any object that will be then used as a key to index the
-            DataGrabber.
+            List of elements that can be grabbed. The elements can be strings
+            or tuples of strings to index the DataGrabber.
 
         """
         raise_error(
@@ -212,7 +216,7 @@ class BaseDataGrabber(ABC, UpdateMetaMixin):
         )  # pragma: no cover
 
     @abstractmethod
-    def get_item(self, **element: Dict) -> Dict[str, Dict]:
+    def get_item(self, **element: dict) -> dict[str, dict]:
         """Get the specified item from the dataset.
 
         Parameters