junifer 0.0.2.dev139__py3-none-any.whl → 0.0.2.dev140__py3-none-any.whl

junifer/_version.py

@@ -1,4 +1,4 @@
 # file generated by setuptools_scm
 # don't change, don't track in version control
-__version__ = version = '0.0.2.dev139'
-__version_tuple__ = version_tuple = (0, 0, 2, 'dev139')
+__version__ = version = '0.0.2.dev140'
+__version_tuple__ = version_tuple = (0, 0, 2, 'dev140')

junifer/datagrabber/aomic/id1000.py

@@ -7,7 +7,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import Union
+from typing import Union, Dict
 
 from junifer.datagrabber import PatternDataladDataGrabber
 
@@ -34,7 +34,9 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
         types = [
             "BOLD",
             "BOLD_confounds",
+            "BOLD_mask",
             "T1w",
+            "T1w_mask",
             "probseg_CSF",
             "probseg_GM",
             "probseg_WM",
@@ -52,11 +54,22 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
                 "sub-{subject}_task-moviewatching_"
                 "desc-confounds_regressors.tsv"
             ),
+            "BOLD_mask": (
+                "derivatives/fmriprep/sub-{subject}/func/"
+                "sub-{subject}_task-moviewatching_"
+                "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-"
@@ -88,3 +101,22 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
             replacements=replacements,
             confounds_format="fmriprep",
         )
+
+    def get_item(self, subject: str) -> Dict:
+        """Index one element in the dataset.
+
+        Parameters
+        ----------
+        subject : str
+            The subject ID.
+
+        Returns
+        -------
+        out : dict
+            Dictionary of paths for each type of data required for the
+            specified element.
+        """
+        out = super().get_item(subject=subject)
+        out["BOLD"]["mask_item"] = "BOLD_mask"
+        out["T1w"]["mask_item"] = "T1w_mask"
+        return out

junifer/datagrabber/aomic/piop1.py

@@ -41,7 +41,9 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         types = [
             "BOLD",
             "BOLD_confounds",
+            "BOLD_mask",
             "T1w",
+            "T1w_mask",
             "probseg_CSF",
             "probseg_GM",
             "probseg_WM",
@@ -83,11 +85,21 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
                 "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-"
@@ -149,6 +161,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
         new_task = f"{task}_acq-{acq}"
 
         out = super().get_item(subject=subject, task=new_task)
+        out["BOLD"]["mask_item"] = "BOLD_mask"
+        out["T1w"]["mask_item"] = "T1w_mask"
         return out
 
     def get_elements(self) -> List:

junifer/datagrabber/aomic/piop2.py

@@ -7,7 +7,7 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List, Union
+from typing import List, Union, Dict
 
 from junifer.datagrabber import PatternDataladDataGrabber
 
@@ -40,7 +40,9 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         types = [
             "BOLD",
             "BOLD_confounds",
+            "BOLD_mask",
             "T1w",
+            "T1w_mask",
             "probseg_CSF",
             "probseg_GM",
             "probseg_WM",
@@ -80,11 +82,21 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
                 "sub-{subject}_task-{task}_acq-seq_"
                 "desc-confounds_regressors.tsv"
             ),
+            "BOLD_mask": (
+                "derivatives/fmriprep/sub-{subject}/func/"
+                "sub-{subject}_task-{task}_acq-seq_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-"
@@ -127,3 +139,25 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
         """
         all_elements = super().get_elements()
         return [x for x in all_elements if x[1] in self.tasks]
+
+    def get_item(self, subject: str, task: str) -> Dict:
+        """Index one element in the dataset.
+
+        Parameters
+        ----------
+        subject : str
+            The subject ID.
+        task : str
+            The task to get. Possible values are:
+            {"restingstate", "stopsignal", "emomatching", "workingmemory"}
+
+        Returns
+        -------
+        out : dict
+            Dictionary of paths for each type of data required for the
+            specified element.
+        """
+        out = super().get_item(subject=subject, task=task)
+        out["BOLD"]["mask_item"] = "BOLD_mask"
+        out["T1w"]["mask_item"] = "T1w_mask"
+        return out

junifer/datagrabber/aomic/tests/test_id1000.py

@@ -51,6 +51,9 @@ def test_aomic1000_datagrabber() -> None:
         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
 
@@ -63,6 +66,9 @@ def test_aomic1000_datagrabber() -> None:
         assert out["T1w"]["path"].exists()
         assert out["T1w"]["path"].is_file()
 
+        # asserts T1w_mask
+        assert out["T1w_mask"]["path"].exists()
+
         # asserts type "probseg_CSF"
         assert "probseg_CSF" in out
 

junifer/datagrabber/aomic/tests/test_piop1.py

@@ -66,6 +66,9 @@ def test_aomic_piop1_datagrabber() -> None:
             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
 
@@ -78,6 +81,9 @@ def test_aomic_piop1_datagrabber() -> None:
             assert out["T1w"]["path"].exists()
             assert out["T1w"]["path"].is_file()
 
+            # asserts T1w_mask
+            assert out["T1w_mask"]["path"].exists()
+
             # asserts type "probseg_CSF"
             assert "probseg_CSF" in out
 

junifer/datagrabber/aomic/tests/test_piop2.py

@@ -35,7 +35,6 @@ def test_aomic_piop2_datagrabber() -> None:
 
             test_element = all_elements[0]
             sub, task = test_element
-
             out = dg[test_element]
 
             # asserts type "BOLD"
@@ -62,6 +61,9 @@ def test_aomic_piop2_datagrabber() -> None:
             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
 
@@ -74,6 +76,9 @@ def test_aomic_piop2_datagrabber() -> None:
             assert out["T1w"]["path"].exists()
             assert out["T1w"]["path"].is_file()
 
+            # asserts T1w_mask
+            assert out["T1w_mask"]["path"].exists()
+
             # asserts type "probseg_CSF"
             assert "probseg_CSF" in out
 

{junifer-0.0.2.dev139.dist-info → junifer-0.0.2.dev140.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.2.dev139
+Version: 0.0.2.dev140
 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-0.0.2.dev139.dist-info → junifer-0.0.2.dev140.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=rJgTGeR-SOntQoLSGo36zKDTE8IMRBn2-YwC0JSNUpU,377
-junifer/_version.py,sha256=mb2dd3_Wfgu1XIw8_0VXeBHQMwJZNvnGFWNo3FtbY8w,177
+junifer/_version.py,sha256=HvZxramN6g_D--rQIkn39dXpmFhOcuXTkrv5rcfxKgs,177
 junifer/stats.py,sha256=3Yt9xD51S0S922T8R6hElO7itvf-Sz41P_SwPzR9KIg,3523
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=WiMF7c3SJuRi_rxxBaaTb7YCQOpfebvhAOh-cKDV8sM,8993
@@ -71,12 +71,12 @@ junifer/datagrabber/pattern.py,sha256=OjPqz6VM22bVTeWra1DEzDBe0jL1NMTqu8jHTWGCWy
 junifer/datagrabber/pattern_datalad.py,sha256=9_HDjChlqb4RLxaC3zrB5EO5fdKT43iroEDvDIk0xVI,1628
 junifer/datagrabber/utils.py,sha256=x2NG076T_jTiDLpl6lXy7-_RUVuPwSmygf3FZcOdK6k,2769
 junifer/datagrabber/aomic/__init__.py,sha256=e2PiVk95yR99Wzy6MBnNmUCAyuQcg9jzbfrA3Frm5fQ,295
-junifer/datagrabber/aomic/id1000.py,sha256=PuR2yRw4EVkfkUkq-V5c0X4CatC35pw_T_8PTX8MC8I,2944
-junifer/datagrabber/aomic/piop1.py,sha256=EeXsXIn-rNxJKHWivt9RkCL7LSlDp3Lylkj9lcv7gSE,5144
-junifer/datagrabber/aomic/piop2.py,sha256=NQP61YcWe5W5jDx1zcX5st2sbwvXAmWkA_DcEC_V3IY,4155
-junifer/datagrabber/aomic/tests/test_id1000.py,sha256=Nq8ENtXkDe8cz45w2hGcYsZysJ0It8NT60GidOGxmqk,3370
-junifer/datagrabber/aomic/tests/test_piop1.py,sha256=No_tq-q-mjErIcYnOZZZCuGRE6AOwp-avjC1ViDyeWk,4407
-junifer/datagrabber/aomic/tests/test_piop2.py,sha256=6BO8QrxIaNuj153CpIYan-Z7YEZvlKdbXEovmxQhykY,4183
+junifer/datagrabber/aomic/id1000.py,sha256=X_hs8Y0qP1CO7YXQM3g0KIGJiFQjFfexuGN0acypYLM,3944
+junifer/datagrabber/aomic/piop1.py,sha256=wd8-WlDG7KJRCUmZ7ORABxc8iFLMMedSfc6wYBAn9CI,5698
+junifer/datagrabber/aomic/piop2.py,sha256=hBOVvBsBSyeS9dPp7xSIhQFIqFl69y7wifjfkz5cypM,5303
+junifer/datagrabber/aomic/tests/test_id1000.py,sha256=-QCMDylQgGM0Re_EYHilnT4NrOVtyQ2AASPCpMXy0vk,3523
+junifer/datagrabber/aomic/tests/test_piop1.py,sha256=Aw9oRs_H-hnUyr6-w5CPf85yOVneAAx_T_XcAIVCy9I,4576
+junifer/datagrabber/aomic/tests/test_piop2.py,sha256=sCJXdc3-HG5rTkurdNJfTRgEzjnX8dlW1b7DrMnVryg,4351
 junifer/datagrabber/tests/test_base.py,sha256=gzyVbat1e9BE82zbcxEp22eR1yD7rFabQVO_0M2hELg,1994
 junifer/datagrabber/tests/test_datagrabber_utils.py,sha256=Y7g08B8neHiB4HMHDhBxMXDNOmXsQ4fTMalhoA0iLFA,2745
 junifer/datagrabber/tests/test_datalad_base.py,sha256=HeWVdXybfvsVfzQfZxC7wYD6gWTXz2dNCAbZ5thl01E,14683
@@ -172,10 +172,10 @@ junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=F2C6y5cNAb3OCVmBdiD8YW_tAknc8EeX_SgKewxcCEA,8852
 junifer/utils/tests/test_fs.py,sha256=o7XTk6OpafppxE4Kx_pDaUfYRt_bU_e1M86FTl5TPVk,862
 junifer/utils/tests/test_logging.py,sha256=uTzlwwlOv7bh_7DngitVFxCDbH_OWsqfeXEcNyKvF24,7748
-junifer-0.0.2.dev139.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.2.dev139.dist-info/LICENSE.md,sha256=z5aMVBrc-9kk0pxaOdOAkI62S5YhYMiF6ADsMtZmOZg,34353
-junifer-0.0.2.dev139.dist-info/METADATA,sha256=Ufo8ayR5QamXRp1En7NHH9FoWdlRd0XxLfmvK9FeFRA,5656
-junifer-0.0.2.dev139.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
-junifer-0.0.2.dev139.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.2.dev139.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.2.dev139.dist-info/RECORD,,
+junifer-0.0.2.dev140.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.2.dev140.dist-info/LICENSE.md,sha256=z5aMVBrc-9kk0pxaOdOAkI62S5YhYMiF6ADsMtZmOZg,34353
+junifer-0.0.2.dev140.dist-info/METADATA,sha256=fmFDkC4Bep5p-M_2Om4eDnyOmYbfuw9bW8S9KwjFFPo,5656
+junifer-0.0.2.dev140.dist-info/WHEEL,sha256=2wepM1nk4DS4eFpYrW1TTqPcoGNfHhhO_i5m4cOimbo,92
+junifer-0.0.2.dev140.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.2.dev140.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.2.dev140.dist-info/RECORD,,