junifer 0.0.3.dev188__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/datagrabber/aomic/piop2.py

@@ -26,14 +26,21 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         The directory where the datalad dataset will be cloned. If None,
         the datalad dataset will be cloned into a temporary directory
         (default None).
-    types: {"BOLD", "BOLD_confounds", "T1w", "probseg_CSF", "probseg_GM", \
-           "probseg_WM", "DWI"} or a list of the options, optional
+    types: {"BOLD", "BOLD_confounds", "T1w", "VBM_CSF", "VBM_GM", \
+           "VBM_WM", "DWI"} or a list of the options, optional
         AOMIC data types. If None, all available data types are selected.
         (default None).
     tasks : {"restingstate", "stopsignal", "workingmemory"} \
             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).
+
+    Raises
+    ------
+    ValueError
+        If invalid value is passed for ``tasks``.
 
     """
 
@@ -42,6 +49,7 @@ 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,
     ) -> None:
         # Declare all tasks
         all_tasks = [
@@ -66,51 +74,111 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         self.tasks = tasks
         # The patterns
         patterns = {
-            "BOLD": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
-            ),
-            "BOLD_confounds": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "desc-confounds_regressors.tsv"
-            ),
-            "BOLD_mask": (
-                "derivatives/fmriprep/sub-{subject}/func/"
-                "sub-{subject}_task-{task}_"
-                "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
-            ),
-            "T1w": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-preproc_T1w.nii.gz"
-            ),
-            "T1w_mask": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_"
-                "desc-brain_mask.nii.gz"
-            ),
-            "probseg_CSF": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "CSF_probseg.nii.gz"
-            ),
-            "probseg_GM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "GM_probseg.nii.gz"
-            ),
-            "probseg_WM": (
-                "derivatives/fmriprep/sub-{subject}/anat/"
-                "sub-{subject}_space-MNI152NLin2009cAsym_label-"
-                "WM_probseg.nii.gz"
-            ),
-            "DWI": (
-                "derivatives/dwipreproc/sub-{subject}/dwi/"
-                "sub-{subject}_desc-preproc_dwi.nii.gz"
-            ),
+            "BOLD": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "BOLD_mask",
+            },
+            "BOLD_confounds": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "desc-confounds_regressors.tsv"
+                ),
+                "format": "fmriprep",
+            },
+            "BOLD_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/func/"
+                    "{subject}_task-{task}_"
+                    "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "T1w": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-preproc_T1w.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+                "mask_item": "T1w_mask",
+            },
+            "T1w_mask": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_"
+                    "desc-brain_mask.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_CSF": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "CSF_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_GM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "GM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "VBM_WM": {
+                "pattern": (
+                    "derivatives/fmriprep/{subject}/anat/"
+                    "{subject}_space-MNI152NLin2009cAsym_label-"
+                    "WM_probseg.nii.gz"
+                ),
+                "space": "MNI152NLin2009cAsym",
+            },
+            "DWI": {
+                "pattern": (
+                    "derivatives/dwipreproc/{subject}/dwi/"
+                    "{subject}_desc-preproc_dwi.nii.gz"
+                ),
+            },
         }
+        # 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_item": "T1w_mask",
+                    },
+                    "T1w_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",
+                    },
+                }
+            )
         # Set default types
         if types is None:
             types = list(patterns.keys())
@@ -140,7 +208,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             imposing constraints based on specified tasks.
 
         """
-        subjects = [f"{x:04d}" for x in range(1, 227)]
+        subjects = [f"sub-{x:04d}" for x in range(1, 227)]
         elems = []
         for subject, task in product(subjects, self.tasks):
             elems.append((subject, task))
@@ -163,9 +231,4 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
             specified element.
 
         """
-        out = super().get_item(subject=subject, task=f"{task}_acq-seq")
-        if out.get("BOLD"):
-            out["BOLD"]["mask_item"] = "BOLD_mask"
-        if out.get("T1w"):
-            out["T1w"]["mask_item"] = "T1w_mask"
-        return out
+        return super().get_item(subject=subject, task=f"{task}_acq-seq")

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -34,7 +34,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["BOLD"]["path"].name
-            == f"sub-{test_element}_task-moviewatching_"
+            == f"{test_element}_task-moviewatching_"
             "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
         )
 
@@ -46,7 +46,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["BOLD_confounds"]["path"].name
-            == f"sub-{test_element}_task-moviewatching_"
+            == f"{test_element}_task-moviewatching_"
             "desc-confounds_regressors.tsv"
         )
 
@@ -61,7 +61,7 @@ def test_DataladAOMICID1000() -> None:
 
         assert (
             out["T1w"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_"
+            == f"{test_element}_space-MNI152NLin2009cAsym_"
             "desc-preproc_T1w.nii.gz"
         )
 
@@ -71,48 +71,48 @@ def test_DataladAOMICID1000() -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_CSF"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_GM"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
-            == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_WM"]["path"].name
+            == f"{test_element}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        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-{test_element}_desc-preproc_dwi.nii.gz"
+            == f"{test_element}_desc-preproc_dwi.nii.gz"
         )
 
         assert out["DWI"]["path"].exists()
@@ -132,13 +132,13 @@ def test_DataladAOMICID1000() -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -56,7 +56,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         acq = task_acqs[task]
         new_task = f"{task}_acq-{acq}"
         assert (
-            out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_"
+            out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
             "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
         )
 
@@ -67,7 +67,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         assert "BOLD_confounds" in out
 
         assert (
-            out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_"
+            out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
             "desc-confounds_regressors.tsv"
         )
 
@@ -81,7 +81,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         assert "T1w" in out
 
         assert (
-            out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_"
+            out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
             "desc-preproc_T1w.nii.gz"
         )
 
@@ -91,46 +91,46 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_CSF"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_GM"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_WM"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        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-{sub}_desc-preproc_dwi.nii.gz"
+        assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
 
         assert out["DWI"]["path"].exists()
         assert out["DWI"]["path"].is_file()
@@ -149,13 +149,13 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -50,7 +50,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
 
         new_task = f"{task}_acq-seq"
         assert (
-            out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_"
+            out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
             "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
         )
 
@@ -61,7 +61,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         assert "BOLD_confounds" in out
 
         assert (
-            out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_"
+            out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
             "desc-confounds_regressors.tsv"
         )
 
@@ -75,7 +75,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         assert "T1w" in out
 
         assert (
-            out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_"
+            out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
             "desc-preproc_T1w.nii.gz"
         )
 
@@ -85,46 +85,46 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         # asserts T1w_mask
         assert out["T1w_mask"]["path"].exists()
 
-        # asserts type "probseg_CSF"
-        assert "probseg_CSF" in out
+        # asserts type "VBM_CSF"
+        assert "VBM_CSF" in out
 
         assert (
-            out["probseg_CSF"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_CSF"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "CSF_probseg.nii.gz"
         )
 
-        assert out["probseg_CSF"]["path"].exists()
-        assert out["probseg_CSF"]["path"].is_file()
+        assert out["VBM_CSF"]["path"].exists()
+        assert out["VBM_CSF"]["path"].is_file()
 
-        # asserts type "probseg_GM"
-        assert "probseg_GM" in out
+        # asserts type "VBM_GM"
+        assert "VBM_GM" in out
 
         assert (
-            out["probseg_GM"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_GM"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "GM_probseg.nii.gz"
         )
 
-        assert out["probseg_GM"]["path"].exists()
-        assert out["probseg_GM"]["path"].is_file()
+        assert out["VBM_GM"]["path"].exists()
+        assert out["VBM_GM"]["path"].is_file()
 
-        # asserts type "probseg_WM"
-        assert "probseg_WM" in out
+        # asserts type "VBM_WM"
+        assert "VBM_WM" in out
 
         assert (
-            out["probseg_WM"]["path"].name
-            == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
+            out["VBM_WM"]["path"].name
+            == f"{sub}_space-MNI152NLin2009cAsym_label-"
             "WM_probseg.nii.gz"
         )
 
-        assert out["probseg_WM"]["path"].exists()
-        assert out["probseg_WM"]["path"].is_file()
+        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-{sub}_desc-preproc_dwi.nii.gz"
+        assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
 
         assert out["DWI"]["path"].exists()
         assert out["DWI"]["path"].is_file()
@@ -143,13 +143,13 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
         "BOLD",
         "BOLD_confounds",
         "T1w",
-        "probseg_CSF",
-        "probseg_GM",
-        "probseg_WM",
+        "VBM_CSF",
+        "VBM_GM",
+        "VBM_WM",
         "DWI",
         ["BOLD", "BOLD_confounds"],
-        ["T1w", "probseg_CSF"],
-        ["probseg_GM", "probseg_WM"],
+        ["T1w", "VBM_CSF"],
+        ["VBM_GM", "VBM_WM"],
         ["DWI", "BOLD"],
     ],
 )