Added support for dwi

Author: TheChymera

samri/pipelines/reposit.py

@@ -25,6 +25,7 @@
 
 N_PROCS=max(N_PROCS-4, 2)
 
+@argh.arg('-d','--diffusion-match', type=json.loads)
 @argh.arg('-f','--functional-match', type=json.loads)
 @argh.arg('-s','--structural-match', type=json.loads)
 @argh.arg('-m','--measurements', nargs='*', type=str)
@@ -113,6 +114,14 @@ def bru2bids(measurements_base,
 			)
 		functional_scan_types = list(f_data_selection['scan_type'].unique())
 		data_selection = pd.concat([data_selection,f_data_selection])
+	if diffusion_match:
+		d_data_selection = get_data_selection(measurements_base,
+			match=diffusion_match,
+			exclude=exclude,
+			measurements=measurements,
+			)
+		diffusion_scan_types = list(d_data_selection['scan_type'].unique())
+		data_selection = pd.concat([data_selection,d_data_selection])
 
 	# we start to define nipype workflow elements (nodes, connections, meta)
 	subjects_sessions = data_selection[["subject","session"]].drop_duplicates().values.tolist()
@@ -221,6 +230,76 @@ def bru2bids(measurements_base,
 			except (FileNotFoundError, OSError):
 				pass
 
+	if diffusion_scan_types:
+		get_d_scan = pe.Node(name='get_d_scan', interface=util.Function(function=get_scan, input_names=inspect.getargspec(get_scan)[0], output_names=['scan_path','scan_type','task']))
+		get_d_scan.inputs.ignore_exception = True
+		get_d_scan.inputs.data_selection = data_selection
+		get_d_scan.inputs.measurements_base = measurements_base
+		get_d_scan.iterables = ("scan_type", diffusion_scan_types)
+
+		d_bru2nii = pe.Node(interface=bru2nii.Bru2(), name="d_bru2nii")
+		d_bru2nii.inputs.force_conversion=True
+		d_bru2nii.inputs.actual_size = not inflated_size
+
+		d_filename = pe.Node(name='d_filename', interface=util.Function(function=bids_naming,input_names=inspect.getargspec(bids_naming)[0], output_names=['filename']))
+		d_filename.inputs.metadata = data_selection
+		d_filename.inputs.extension=''
+
+		d_metadata_filename = pe.Node(name='d_metadata_filename', interface=util.Function(function=bids_naming,input_names=inspect.getargspec(bids_naming)[0], output_names=['filename']))
+		d_metadata_filename.inputs.extension = ".json"
+		d_metadata_filename.inputs.metadata = data_selection
+
+		d_metadata_file = pe.Node(name='d_metadata_file', interface=util.Function(function=write_bids_metadata_file,input_names=inspect.getargspec(write_bids_metadata_file)[0], output_names=['out_file']))
+		d_metadata_file.inputs.extraction_dicts = BIDS_METADATA_EXTRACTION_DICTS
+
+		workflow_connections = [
+			(infosource, datasink, [(('subject_session',ss_to_path), 'container')]),
+			(infosource, get_d_scan, [('subject_session', 'selector')]),
+			(infosource, d_filename, [('subject_session', 'subject_session')]),
+			(infosource, d_metadata_filename, [('subject_session', 'subject_session')]),
+			(get_d_scan, d_bru2nii, [('scan_path','input_dir')]),
+			(get_d_scan, d_filename, [('scan_type', 'scan_type')]),
+			(get_d_scan, d_metadata_filename, [('scan_type', 'scan_type')]),
+			(get_d_scan, d_metadata_file, [('scan_path', 'scan_dir')]),
+			(d_filename, d_bru2nii, [('filename','output_filename')]),
+			(d_metadata_filename, d_metadata_file, [('filename', 'out_file')]),
+			(d_bru2nii, datasink, [('nii_file', 'dwi')]),
+			(d_metadata_file, datasink, [('out_file', 'dwi.@metadata')]),
+			]
+		crashdump_dir = path.join(out_base,'bids_crashdump')
+		workflow_config = {'execution': {'crashdump_dir': crashdump_dir}}
+		if debug:
+			workflow_config['logging'] = {
+				'workflow_level':'DEBUG',
+				'utils_level':'DEBUG',
+				'interface_level':'DEBUG',
+				'filemanip_level':'DEBUG',
+				'log_to_file':'true',
+				}
+
+		workdir_name = 'bids_work'
+		workflow = pe.Workflow(name=workdir_name)
+		workflow.connect(workflow_connections)
+		workflow.base_dir = path.join(out_base)
+		workflow.config = workflow_config
+		workflow.write_graph(dotfilename=path.join(workflow.base_dir,workdir_name,"graph_diffusion.dot"), graph2use="hierarchical", format="png")
+
+		#Execute the workflow
+		if not keep_work or not keep_crashdump:
+			try:
+				workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
+			except RuntimeError:
+				pass
+		else:
+			workflow.run(plugin="MultiProc", plugin_args={'n_procs' : n_procs})
+		if not keep_work:
+			shutil.rmtree(path.join(workflow.base_dir,workdir_name))
+		if not keep_crashdump:
+			try:
+				shutil.rmtree(crashdump_dir)
+			except (FileNotFoundError, OSError):
+				pass
+
 	if structural_scan_types:
 		get_s_scan = pe.Node(name='get_s_scan', interface=util.Function(function=get_scan, input_names=inspect.getargspec(get_scan)[0], output_names=['scan_path','scan_type','task']))
 		get_s_scan.inputs.ignore_exception = True