#16

bv_use_cases/simplest/__main__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from pprint import pprint
 
 from capsul.api import Capsul

bv_use_cases/tiny_morphologist/__init__.py

@@ -1,4 +1,8 @@
+# -*- coding: utf-8 -*-
+from pathlib import Path
+
 from soma.controller import field, file
+
 from capsul.api import Process, Pipeline
 
 
@@ -7,22 +11,40 @@ class BiasCorrection(Process):
     strength: float = 0.8
     output: field(type_=file(), output=True)
 
-    def execute(self):
+    def execute(self, context):
         with open(self.input) as f:
             content = self.read()
         content = f'{content}\nBias correction with strength={self.strength}'
         with open(self.output, 'w') as f:
             f.write(content)
 
+    path_layout = dict(
+        bids={'output': {'part': 'nobias'}},
+        brainvisa={'output': {'prefix': 'nobias'}}
+    )
+
 class SPMNormalization(Process):
     input: field(type_=file())
     template: field(type_=file())
     output: field(type_=file(), output=True)
-
-    def execute(self):
+
+    requirements = {
+        'fakespm': {
+            'version': '12'
+        }
+    }
+
+    path_layout = dict(
+        bids={'output': {'part': 'normalized'}},
+        brainvisa={'output': {'prefix': 'normalized'}}
+    )
+
+    def execute(self, context):
+        spmdir = Path(context.spm.directory)
+        real_version = (spmdir / 'spm').read_text().strip()
         with open(self.input) as f:
             content = self.read()
-        content = f'{content}\nSPM normalization with template "{self.template}"'
+        content = f'{content}\nNormalization with fakespm {real_version} installed in {spmdir} using template "{self.template}"'
         with open(self.output, 'w') as f:
             f.write(content)
 
@@ -31,10 +53,15 @@ class AimsNormalization(Process):
     origin: field(type_=list[float], default_factory=lambda: [1.2, 3.4, 5.6])
     output: field(type_=file(), output=True)
 
-    def execute(self):
+    path_layout = dict(
+        bids={'output': {'part': 'normalized'}},
+        brainvisa={'output': {'prefix': 'normalized'}}
+    )
+
+    def execute(self, context):
         with open(self.input) as f:
             content = self.read()
-        content = f'{content}\nSPM normalization with origin={self.origin}'
+        content = f'{content}\nNormalization with Aims, origin={self.origin}'
         with open(self.output, 'w') as f:
             f.write(content)
 
@@ -43,7 +70,12 @@ class SplitBrain(Process):
     right_output: field(type_=file(), output=True)
     left_output: field(type_=file(), output=True)
 
-    def execute(self):
+    path_layout = dict(
+        bids={'output': {'part': 'split'}},
+        brainvisa={'output': {'prefix': 'split'}}
+    )
+
+    def execute(self, context):
         with open(self.input) as f:
             content = self.read()
         content = f'{content}\nBias correction with strength={self.strength}'
@@ -55,7 +87,7 @@ class ProcessHemisphere(Process):
     input: field(type_=file())
     output: field(type_=file(), output=True)
 
-    def execute(self):
+    def execute(self, context):
         with open(self.input) as f:
             content = self.read()
         content = f'{content}\nProcess hemisphere'
@@ -86,4 +118,15 @@ def pipeline_definition(self):
         self.add_link('split.left_output->left_hemi.input')
         self.export_parameter('left_hemi', 'output', 'left_hemisphere')
 
+    path_layout = dict(
+        bids={
+            '*': {'pipeline': 'tinymorphologist'},
+            'right_hemi': {'part': 'right_hemi'}
+        },
+        brainvisa={
+            '*': {'process': 'tinymorphologist'},
+            'left_hemi': {'prefix': 'left_hemi'}
+        }
+    )
+
 

bv_use_cases/tiny_morphologist/__main__.py

@@ -1,6 +1,10 @@
+# -*- coding: utf-8 -*-
+import json
 import os
+from pathlib import Path
 import shutil
 import tempfile
+
 from bv_use_cases import tiny_morphologist
 
 from capsul.api import Capsul
@@ -39,38 +43,73 @@
 )
 
 # Create temporary directory for the use case
-tmp = tempfile.mkdtemp()
+tmp_name = tempfile.mkdtemp()
 try:
+    #-------------------#
+    # Environment setup #
+    #-------------------#
+
+    tmp = Path(tmp_name) 
     # Create BIDS directory
-    bids = f'{tmp}/bids'
+    bids = tmp / 'bids'
     # Write Capsul specific information
-    os.mkdir(bids)
-    with open(f'{bids}/capsul.json', 'w') as f:
+    bids.mkdir()
+    with (bids / 'capsul.json').open('w') as f:
         json.dump({
-            'paths_layout': 'bids-1.6'
+            'path_layout': 'bids-1.6'
         }, f)
 
     # Create BrainVISA directory
-    brainvisa = f'{tmp}/brainvisa'
-    os.mkdir(brainvisa)
+    brainvisa = tmp / 'brainvisa'
+    brainvisa.mkdir()
     # Write Capsul specific information
-    with open(f'{brainvisa}/capsul.json', 'w') as f:
+    with (brainvisa / 'capsul.json').open('w') as f:
         json.dump({
-            'paths_layout': 'brainvisa-6.0'
+            'path_layout': 'brainvisa-6.0'
         }, f)
 
     # Generate fake T1 and T2 data in bids directory
     for subject in subjects:
         for session in ('m0', 'm12', 'm24'):
             for data_type in ('T1w', 'T2w'):
-                file = f'{bids}/rawdata/sub-{subject}/ses-{session}/anat/sub-{subject}_ses-{session}_{data_type}.nii'
-                d = os.path.dirname(file)
-                if not os.path.exists(d):
-                    os.makedirs(d)
-                with open(file, 'w') as f:
+                file = (bids/ f'rawdata' / f'sub-{subject}' / f'ses-{session}' / 'anat' /
+                        f'sub-{subject}_ses-{session}_{data_type}.nii')
+                file.parent.mkdir(parents=True, exist_ok=True)
+                with file.open('w') as f:
                     print(f'{data_type} acquisition for subject {subject} acquired in session {session}', file=f)
 
-    capsul = Capsul()
+    # Configuration base dictionary
+    config = {
+        'default': {
+            'label': 'Local computer',
+            'modules': {}
+        }
+    }
+    # Create fake SPM directories
+    for version in ('8', '12'):
+        spm = tmp / 'software' / f'fakespm-{version}'
+        spm.mkdir(parents=True, exist_ok=True)
+        # Write a file containing only the version string that will be used
+        # by fakespm module to check installation.
+        (spm / 'spm').write_text(version)
+        fakespm_config = {
+            'directory': str(spm),
+            'version': version,
+        }
+        config['default']['modules'].setdefault('fakespm', []).append(fakespm_config)
+
+
+    # Create a configuration file
+    config_json = tmp / 'capsul_config.json'
+    with config_json.open('w') as f:
+        json.dump(config, f)
+
+
+    #---------------------#
+    # Pipelines execution #
+    #---------------------#
+
+    capsul = Capsul(config_file=config_json)
     # Input dataset is declared as following BIDS organization in capsul.json
     # therefore a BIDS specific object is returned
     input_dataset = capsul.dataset(bids)
@@ -83,21 +122,23 @@
     # Parse the dataset with BIDS-specific query (here "suffix" is part
     #  of BIDS specification). The object returned contains info for main
     # BIDS fields (sub, ses, acq, etc.)
-    for t1_mri in dataset.find(suffix='T1w'):
+    count = 0
+    for t1_mri in input_dataset.find(suffix='T1w'):
         # Create a TinyMorphologist pipeline
         tiny_morphologist = capsul.executable('bv_use_cases.tiny_morphologist.TinyMorphologist')
         # Set the input data
-        tiny_morphologist.input = t1_mri.path
+        tiny_morphologist.input = t1_mri['path']
         # Complete outputs following BraiVISA organization
         # Make the link between BIDS metadata and BrainVISA metadata 
         output_dataset.set_output_paths(tiny_morphologist,
-            subject=t1_mri.sub,
-            acquisition=t1_mri.acq,
+            subject=t1_mri['sub'],
+            acquisition=t1_mri.get('acq', 'default'),
         )
         # Add the current TinyMorhpologist pipeline to the main
         # pipeline that will be executed
-        custom_pipeline.add_executable(tiny_morphologist)
-    # Finally execute all the TinyMorphologist instances
-    capsul.run(processing_pipeline)
+        processing_pipeline.add_process(f'pipeline_{count}', tiny_morphologist)
+        count = count + 1
+    # # Finally execute all the TinyMorphologist instances
+    # capsul.run(processing_pipeline)
 finally:
     shutil.rmtree(tmp)