Merge pull request #91 from oesteban/fix/one-session-one-run

Fix/one session one run

mriqc/utils/mriqc_run.py

@@ -19,7 +19,7 @@
 from argparse import RawTextHelpFormatter
 from nipype import config as ncfg
 
-from mriqc.workflows import ms_anat, ms_func
+from mriqc.workflows import core as mwc
 from mriqc import __version__
 
 
@@ -107,15 +107,16 @@ def main():
             plugin_settings['plugin'] = 'MultiProc'
             plugin_settings['plugin_args'] = {'n_procs': settings['nthreads']}
 
-    if 'anat' in opts.data_type:
-        workflow = ms_anat(subject_id=opts.subject_id, session_id=opts.session_id,
-                           run_id=opts.run_id, settings=settings)
-        workflow.run(**plugin_settings)
-
-    if 'func' in opts.data_type:
+    for dtype in opts.data_type:
+        ms_func = getattr(mwc, 'ms_' + dtype)
         workflow = ms_func(subject_id=opts.subject_id, session_id=opts.session_id,
                            run_id=opts.run_id, settings=settings)
+        workflow.base_dir = settings['work_dir']
+        if settings.get('write_graph', False):
+            workflow.write_graph()
+
         workflow.run(**plugin_settings)
 
+
 if __name__ == '__main__':
     main()

mriqc/workflows/anatomical.py

@@ -36,7 +36,6 @@ def anat_qc_workflow(name='MRIQC_Anat', settings=None):
     workflow = pe.Workflow(name=name)
     deriv_dir = op.abspath('./derivatives')
     if 'work_dir' in settings.keys():
-        workflow.base_dir = settings['work_dir']
         deriv_dir = op.abspath(op.join(settings['work_dir'], 'derivatives'))
 
     if not op.exists(deriv_dir):

mriqc/workflows/core.py

@@ -51,8 +51,6 @@ def ms_anat(settings=None, subject_id=None, session_id=None, run_id=None):
                            ('out3', 'inputnode.run_id')])
     ])
 
-    if settings.get('write_graph', False):
-        workflow.write_graph()
     return workflow
 
 
@@ -92,6 +90,4 @@ def ms_func(settings=None, subject_id=None, session_id=None, run_id=None):
                            ('out3', 'inputnode.run_id')])
     ])
 
-    if settings.get('write_graph', False):
-        workflow.write_graph()
     return workflow

mriqc/workflows/functional.py

@@ -32,7 +32,6 @@ def fmri_qc_workflow(name='fMRIQC', settings=None):
     workflow = pe.Workflow(name=name)
     deriv_dir = op.abspath('./derivatives')
     if 'work_dir' in settings.keys():
-        workflow.base_dir = settings['work_dir']
         deriv_dir = op.abspath(op.join(settings['work_dir'], 'derivatives'))
 
     if not op.exists(deriv_dir):