junifer 0.0.6.dev302__py3-none-any.whl → 0.0.6.dev311__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev302'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev302')
+__version__ = version = '0.0.6.dev311'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev311')

junifer/datagrabber/aomic/id1000.py

@@ -11,6 +11,7 @@ from pathlib import Path
 from typing import Union
 
 from ...api.decorators import register_datagrabber
+from ...utils import raise_error
 from ..pattern_datalad import PatternDataladDataGrabber
 
 
@@ -31,8 +32,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
            "FreeSurfer"} or list of the options, optional
         AOMIC data types. If None, all available data types 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").
 
     """
 
@@ -40,25 +41,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         self,
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        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}"
+            )
+
+        # 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-moviewatching_"
-                    "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-moviewatching_"
-                        "space-MNI152NLin2009cAsym_"
+                        f"{sp_func_desc}"
                         "desc-brain_mask.nii.gz"
                     ),
-                    "space": "MNI152NLin2009cAsym",
+                    "space": space,
                 },
                 "confounds": {
                     "pattern": (
@@ -68,46 +84,59 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                     ),
                     "format": "fmriprep",
                 },
+                "reference": {
+                    "pattern": (
+                        "derivatives/fmriprep/{subject}/func/"
+                        "{subject}_task-moviewatching_"
+                        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": (
@@ -148,51 +177,38 @@ class DataladAOMICID1000(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",
-                            "warper": "ants",
-                        },
-                        {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
-                                "mode-image_xfm.h5"
-                            ),
-                            "src": "native",
-                            "dst": "MNI152NLin2009cAsym",
-                            "warper": "ants",
-                        },
-                    ],
-                }
-            )
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/piop1.py

@@ -37,8 +37,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
             "gstroop", "workingmemory"} or list of the options, optional
         AOMIC PIOP1 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
     ------
@@ -52,8 +52,13 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
         tasks: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        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",
@@ -78,22 +83,32 @@ class DataladAOMICPIOP1(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": (
@@ -103,46 +118,59 @@ class DataladAOMICPIOP1(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": (
@@ -183,51 +211,38 @@ class DataladAOMICPIOP1(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",
-                            "warper": "ants",
-                        },
-                        {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
-                                "mode-image_xfm.h5"
-                            ),
-                            "src": "native",
-                            "dst": "MNI152NLin2009cAsym",
-                            "warper": "ants",
-                        },
-                    ],
-                }
-            )
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/piop2.py

@@ -37,8 +37,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             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
     ------
@@ -52,8 +52,13 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         datadir: Union[str, Path, None] = None,
         types: Union[str, list[str], None] = None,
         tasks: Union[str, list[str], None] = None,
-        native_t1w: bool = False,
+        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",
@@ -76,22 +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": (
@@ -101,46 +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": (
@@ -181,51 +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",
-                            "warper": "ants",
-                        },
-                        {
-                            "pattern": (
-                                "derivatives/fmriprep/{subject}/anat/"
-                                "{subject}_from-T1w_to-MNI152NLin2009cAsym_"
-                                "mode-image_xfm.h5"
-                            ),
-                            "src": "native",
-                            "dst": "MNI152NLin2009cAsym",
-                            "warper": "ants",
-                        },
-                    ],
-                }
-            )
+        self.space = space
+
         # Set default types
         if types is None:
             types = list(patterns.keys())

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -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]],
+    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
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -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]],
+    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
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -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]],
+    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
 

junifer/pipeline/utils.py

@@ -237,7 +237,7 @@ def _check_ants(commands: Optional[list[str]] = None) -> bool:
                 shell=True,  # is unsafe but kept for resolution via PATH
                 check=False,
             )
-            command_found = command_process.returncode == 0
+            command_found = command_process.returncode == 1
             commands_found_results[command] = (
                 "found" if command_found else "not found"
             )

{junifer-0.0.6.dev302.dist-info → junifer-0.0.6.dev311.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev302
+Version: 0.0.6.dev311
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev302.dist-info → junifer-0.0.6.dev311.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=6ivRaEJnq1nwi7sNAqQwwarVpyzKReHtuarvntATZ2E,428
+junifer/_version.py,sha256=Um0qpMM5T1_-HjlNcQSFRjfl7t4PTi-Tmwj5GjnZBzM,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -132,13 +132,13 @@ junifer/datagrabber/pattern_validation_mixin.py,sha256=6IlL5EMbr-XEtiiXs_buD3DJk
 junifer/datagrabber/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/datagrabber/aomic/__init__.py,sha256=ATxzXq9NBPmWowTMuL77zqrmIbbnk0Wd1iXtXCP3XDg,266
 junifer/datagrabber/aomic/__init__.pyi,sha256=Rp6C075fZDdKY8VIq508_g4NhVj8bWzR6zb9yln761Q,189
-junifer/datagrabber/aomic/id1000.py,sha256=9jjsb6SRSgxbuMFLJRQBlXaoP9JptyBpveEyWKmsjCA,7814
-junifer/datagrabber/aomic/piop1.py,sha256=AvqtvdL2iUfvXQTWt7BydYKVZ_sS3rp__2M6DbG8_r0,10226
-junifer/datagrabber/aomic/piop2.py,sha256=FyibCxPnaM-w1v3M5FrKHDMXTp-lpBnnuHL7ta-9Xqk,9887
+junifer/datagrabber/aomic/id1000.py,sha256=GNURDZUBqystS2fn9COtIJkDfUVkwsS2uBuVcZQArqc,7931
+junifer/datagrabber/aomic/piop1.py,sha256=johUxDm4rS0QOH9JwotxzVYOWeTrVAdfXuHnkE-o7TI,10329
+junifer/datagrabber/aomic/piop2.py,sha256=JxZqX6i_Jrj3evcxnblSdmWqS2bV5XxoIGhAUoSs8o4,9990
 junifer/datagrabber/aomic/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/datagrabber/aomic/tests/test_id1000.py,sha256=wie7Sc6MIpMyIbDMouXJ7r2_BRbdQv27rTsviwE19LE,3277
-junifer/datagrabber/aomic/tests/test_piop1.py,sha256=_NargKRI13PPtznpNhknOqlKLHlVgVWWVU7GFBeV3X8,4814
-junifer/datagrabber/aomic/tests/test_piop2.py,sha256=7ySdDKI7lioXAN6QVkefScNDNPrUM3lTL7IhGMJatVA,4160
+junifer/datagrabber/aomic/tests/test_id1000.py,sha256=N8jnL5bERP1N_DqNsbH_QeO-aQy8kBym1LihBrAYCsA,3708
+junifer/datagrabber/aomic/tests/test_piop1.py,sha256=8-vdcx2X4QraJV8PAaVwHsoul3kMu1QpLKR9naPMwiQ,5798
+junifer/datagrabber/aomic/tests/test_piop2.py,sha256=vGd43XzcqNXRy_usAJF803S_P-MwcyLHpOz7WA04EN0,5096
 junifer/datagrabber/hcp1200/__init__.py,sha256=2CUYsdWu3RbOdHWME_peYNHEqKUkiq_W3Aw-aczbFdY,214
 junifer/datagrabber/hcp1200/__init__.pyi,sha256=2ttZanYSzCsB195_xfXUyztPsVIF02ARM-sjlNK3Wdg,114
 junifer/datagrabber/hcp1200/datalad_hcp1200.py,sha256=49kWPrjLnmUKzJNYPbV9SD0g5KkkCLXlVVpkYRxwkow,2457
@@ -267,7 +267,7 @@ junifer/pipeline/pipeline_component_registry.py,sha256=TdLXjQcUZstEF9n6IszBYAwLs
 junifer/pipeline/pipeline_step_mixin.py,sha256=oXfJh27yifHs1V3V_tMPCanRiHX1ggOVIbHTvMzq3cY,7853
 junifer/pipeline/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/pipeline/update_meta_mixin.py,sha256=yzGCx8AUbc9mMnWKRu4qaIXTBBSIxtNlGH5zIQIUvzM,1812
-junifer/pipeline/utils.py,sha256=27KYbUS6t1kb3vP_C5BoRBFfKPzfUKQK8Ut-aBERshk,10285
+junifer/pipeline/utils.py,sha256=qS0Xg_43ri-xtLeMJR838Axj9FkQ6s2H4r8CmSD58X8,10285
 junifer/pipeline/workdir_manager.py,sha256=r5hhizktLat2bN_A-ZGeeBVWmpRUkUCiZeIDxG-9umM,8624
 junifer/pipeline/tests/test_marker_collection.py,sha256=edBHfmwMTXG_q0ZagApbAbkFNoegi3hVEQiNcBtZOKc,6959
 junifer/pipeline/tests/test_pipeline_component_registry.py,sha256=mrbz285K_TzSILRn9X-AyzcNXuPRHGBZY6dQiq5_9So,5776
@@ -341,10 +341,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev302.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev302.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev302.dist-info/METADATA,sha256=-xzY1LfIMeHg8ism1hOUBXsfcyjaW58Mu1VuATPtKXY,8429
-junifer-0.0.6.dev302.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev302.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev302.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev302.dist-info/RECORD,,
+junifer-0.0.6.dev311.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev311.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev311.dist-info/METADATA,sha256=A3vcsrgSmtY_rzNE4oPkyed8tfX0qw2Iy93uo03avn0,8429
+junifer-0.0.6.dev311.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev311.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev311.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev311.dist-info/RECORD,,