#16 partially working parameters completion

brainvisa · Feb 3, 2022 · c3a41b5 · c3a41b5
1 parent effd14b
commit c3a41b5
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/bv_use_cases/tiny_morphologist/__init__.py b/bv_use_cases/tiny_morphologist/__init__.py
@@ -97,22 +97,27 @@ def execute(self, context):
 class TinyMorphologist(Pipeline):
     def pipeline_definition(self):
         self.add_process('nobias', BiasCorrection)
+
         self.add_switch('normalization', ['none', 'spm', 'aims'], ['output'])
         self.add_process('spm_normalization', SPMNormalization)
         self.add_process('aims_normalization', AimsNormalization)
         self.add_process('split', SplitBrain)
         self.add_process('right_hemi', ProcessHemisphere)
         self.add_process('left_hemi', ProcessHemisphere)
 
+
         self.add_link('nobias.output->normalization.none_switch_output')
 
         self.add_link('nobias.output->spm_normalization.input')
         self.add_link('spm_normalization.output->normalization.spm_switch_output')
 
         self.add_link('nobias.output->aims_normalization.input')
         self.add_link('aims_normalization.output->normalization.aims_switch_output')
-
+
+        self.export_parameter('nobias', 'output', 'nobias')
+
         self.add_link('normalization.output->split.input')
+        self.export_parameter('normalization', 'output', 'normalized')
         self.add_link('split.right_output->right_hemi.input')
         self.export_parameter('right_hemi', 'output', 'right_hemisphere')
         self.add_link('split.left_output->left_hemi.input')

diff --git a/bv_use_cases/tiny_morphologist/__main__.py b/bv_use_cases/tiny_morphologist/__main__.py
@@ -131,13 +131,18 @@
         # Complete outputs following BraiVISA organization
         # Make the link between BIDS metadata and BrainVISA metadata 
         output_dataset.set_output_paths(tiny_morphologist,
+            center='whaterver',
             subject=t1_mri['sub'],
-            acquisition=t1_mri.get('acq', 'default'),
+            acquisition=t1_mri['ses'],
+            extension = 'nii'
         )
         # Add the current TinyMorhpologist pipeline to the main
         # pipeline that will be executed
         processing_pipeline.add_process(f'pipeline_{count}', tiny_morphologist)
         print('Created', f'pipeline_{count}')
+        for field in tiny_morphologist.fields():
+            value = getattr(tiny_morphologist, field.name, None)
+            print('   ', ('<-' if tiny_morphologist.is_output(field) else '->'), field.name, '=', value)
         count = count + 1
     # # Finally execute all the TinyMorphologist instances
     # capsul.run(processing_pipeline)