ENH: Specify in SRTV json if masks were manual/automatic

Medical-Image-Analysis-Laboratory · Nov 24, 2020 · d1f9ebc · d1f9ebc
1 parent 3d4bb07
commit d1f9ebc
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Showing 2 changed files with 4 additions and 0 deletions.
diff --git a/pymialsrtk/interfaces/reconstruction.py b/pymialsrtk/interfaces/reconstruction.py
@@ -277,6 +277,7 @@ class MialsrtkTVSuperResolutionInputSpec(BaseInterfaceInputSpec):
     input_rad_dilatation = traits.Float(1.0, usedefault=True)
 
     sub_ses = traits.Str("x", usedefault=True)
+    use_manual_masks = traits.Bool(False, usedefault=True)
 
 
 class MialsrtkTVSuperResolutionOutputSpec(TraitedSpec):
@@ -379,10 +380,12 @@ def _run_interface(self, runtime):
         self.m_output_dict["Input sources run order"] = self.inputs.stacks_order
         self.m_output_dict["CustomMetaData"] = {}
         self.m_output_dict["CustomMetaData"]["Number of scans used"] = str(len(self.inputs.stacks_order))
+        self.m_output_dict["CustomMetaData"]["Masks used"] = 'Manual' if self.inputs.use_manual_masks else 'Automatic'
         self.m_output_dict["CustomMetaData"]["TV regularization weight lambda"] = self.inputs.in_lambda
         self.m_output_dict["CustomMetaData"]["Optimization time step"] = self.inputs.in_deltat
         self.m_output_dict["CustomMetaData"]["Primal/dual loops"] = self.inputs.in_loop
 
+
         output_json_path = ''.join([self.m_out_files, '.json'])
         with open(output_json_path, 'w') as outfile:
             json.dump(self.m_output_dict, outfile)

diff --git a/pymialsrtk/pipelines/anatomical/srr.py b/pymialsrtk/pipelines/anatomical/srr.py
@@ -318,6 +318,7 @@ def create_workflow(self):
         srtkTVSuperResolution.inputs.in_loop = self.primal_dual_loops
         srtkTVSuperResolution.inputs.in_deltat = self.deltatTV
         srtkTVSuperResolution.inputs.in_lambda = self.lambdaTV
+        srtkTVSuperResolution.inputs.use_manual_masks = self.use_manual_masks
 
         srTVdictSink = Node(JSONFileSink(),name='srtv_json_sinker')