#16 fakespm module

brainvisa · Mar 10, 2022 · c1d4d9c · c1d4d9c
1 parent fef879a
commit c1d4d9c
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Showing 2 changed files with 10 additions and 15 deletions.
diff --git a/bv_use_cases/tiny_morphologist/__init__.py b/bv_use_cases/tiny_morphologist/__init__.py
@@ -26,12 +26,12 @@ def execute(self, context):
 
 class FakeSPMNormalization(Process):
     input: field(type_=File, extensions=('.nii',))
-    template: field(type_=File, extensions=('.nii',))
+    template: field(type_=File, extensions=('.nii',)) = '!{fakespm.directory}/template'
     output: field(type_=File, write=True, extensions=('.nii',))
 
     requirements = {
         'fakespm': {
-            'version': '12'
+            'version': '8'
         }
     }
 
@@ -45,7 +45,9 @@ def execute(self, context):
         real_version = (fakespmdir / 'fakespm').read_text().strip()
         with open(self.input) as f:
             content = f.read()
-        content = f'{content}Normalization with fakespm {real_version} installed in {fakespmdir} using template "{self.template}"\n'
+        with open(self.template) as f:
+            template = f.read().strip()
+        content = f'{content}Normalization with fakespm {real_version} installed in {fakespmdir} using template "{template}"\n'
         with open(self.output, 'w') as f:
             f.write(content)
 

diff --git a/bv_use_cases/tiny_morphologist/__main__.py b/bv_use_cases/tiny_morphologist/__main__.py
@@ -53,14 +53,6 @@
     'katrina',
     'lyda',
     'melite',
-    'mina',
-    'odalric',
-    'rainbow',
-    'rashn',
-    'shufen',
-    'simona',
-    'svanhildur',
-    'thilini',
     'til',
     'vanessza',
     'victoria'
@@ -106,9 +98,6 @@
     config = {
         'default': {
             'label': 'Local computer',
-            'modules': {}
-        },
-        'remote': {
             'label': 'triscotte',
             'type': 'ssh',
             'host': 'triscotte.cea.fr',
@@ -122,6 +111,8 @@
         # Write a file containing only the version string that will be used
         # by fakespm module to check installation.
         (fakespm / 'fakespm').write_text(version)
+        # Write a fake template file
+        (fakespm / 'template').write_text(f'template of fakespm {version}')
         fakespm_config = {
             'directory': str(fakespm),
             'version': version,
@@ -166,7 +157,7 @@
     for t1_mri in input_dataset.find(suffix='T1w'):
         # Create a TinyMorphologist pipeline
         tiny_morphologist = capsul.executable('bv_use_cases.tiny_morphologist.TinyMorphologist',
-                                              normalization='aims')
+                                              normalization='fakespm')
         # Set the input data
         tiny_morphologist.input = t1_mri['path']
         # Complete outputs following BraiVISA organization
@@ -211,6 +202,8 @@
     #             value = getattr(node, field.name, None)
     #             print('       ', ('<-' if field.is_output() else '->'), field.name, '=', value)
 
+    from pprint import pprint
+    pprint(processing_pipeline.json())
     try:
         with capsul.engine() as ce:
             # Finally execute all the TinyMorphologist instances