Merge pull request #491 from mgxd/enh/cifti-carpet

ENH: CIFTI carpetplot

Author: mgxd

niworkflows/interfaces/plotting.py

@@ -6,7 +6,7 @@
 
 from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (
-    File, BaseInterfaceInputSpec, TraitedSpec, SimpleInterface, traits
+    File, BaseInterfaceInputSpec, TraitedSpec, SimpleInterface, traits, isdefined
 )
 from ..viz.plots import (
     fMRIPlot, compcor_variance_plot, confounds_correlation_plot
@@ -15,8 +15,8 @@
 
 class _FMRISummaryInputSpec(BaseInterfaceInputSpec):
     in_func = File(exists=True, mandatory=True, desc='')
-    in_mask = File(exists=True, mandatory=True, desc='')
-    in_segm = File(exists=True, mandatory=True, desc='')
+    in_mask = File(exists=True, desc='')
+    in_segm = File(exists=True, desc='')
     in_spikes_bg = File(exists=True, mandatory=True, desc='')
     fd = File(exists=True, mandatory=True, desc='')
     fd_thres = traits.Float(0.2, usedefault=True, desc='')
@@ -56,8 +56,8 @@ def _run_interface(self, runtime):
 
         fig = fMRIPlot(
             self.inputs.in_func,
-            mask_file=self.inputs.in_mask,
-            seg_file=self.inputs.in_segm,
+            mask_file=self.inputs.in_mask if isdefined(self.inputs.in_mask) else None,
+            seg_file=self.inputs.in_segm if isdefined(self.inputs.seg_file) else None,
             spikes_files=[self.inputs.in_spikes_bg],
             tr=self.inputs.tr,
             data=dataframe[['outliers', 'DVARS', 'FD']],

niworkflows/tests/data/sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii

@@ -10,19 +10,32 @@
 
 def test_carpetplot():
     """Write a carpetplot"""
-    out_file = None
+    out_file_nifti = None
+    out_file_cifti = None
     save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
     if save_artifacts:
-        out_file = os.path.join(save_artifacts, 'carpetplot.svg')
+        out_file_nifti = os.path.join(save_artifacts, 'carpetplot_nifti.svg')
+        out_file_cifti = os.path.join(save_artifacts, 'carpetplot_cifti.svg')
+
+    # volumetric NIfTI
     viz.plot_carpet(
         os.path.join(datadir, 'sub-ds205s03_task-functionallocalizer_run-01_bold_volreg.nii.gz'),
-        np.asanyarray(nb.load(os.path.join(
+        atlaslabels=np.asanyarray(nb.load(os.path.join(
             datadir,
             'sub-ds205s03_task-functionallocalizer_run-01_bold_parc.nii.gz')).dataobj),
-        output_file=out_file,
+        output_file=out_file_nifti,
         legend=True
     )
 
+    # CIFTI
+    viz.plot_carpet(
+        os.path.join(
+            datadir,
+            'sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii'
+        ),
+        output_file=out_file_cifti,
+    )
+
 
 def test_plot_melodic_components(tmp_path):
     """Test plotting melodic components"""