fix: some minor changes

Author: akeshavan

bin/bips

@@ -12,21 +12,44 @@ import argparse
 
 """
 Examples
-bips -m fmri -t task -w preproc -c config.py
-bips -m fmri -t task -w qa -c config.py
-bips -m fmri -t resting -w qa -c config.py
 
-bips -m dmri -w preproc -c config.py
-bips -m dmri -w track -c config.py
-
-bips -m smri -w recon -c config.py
-bips -m smri -t volume -w normalize -c config.py
-bips -m smri -t volume -w template -c config.py
-bips -m smri -t surface -w template -c config.py
-
-alternatively
 bips -i -u uuid # display info about workflow
 bips -u uuid -c config.json # create config for running workflow
 bips -r config.json # run workflow
 
-"""
+"""
+
+def main(args):
+    print args.config,args.uuid, args.info
+    
+    
+    
+
+if __name__== "__main__":
+    parser = argparse.ArgumentParser(description="example: \
+                        bips -m fmri -t task -w preproc -c config.py")
+    parser.add_argument('-c','--config',
+                        dest='config',
+                        required=False,
+                        help='location of config file'
+                        )
+    parser.add_argument('-u','--uuid',
+                        dest = 'uuid',
+                        required=False,
+                        help='workflow to run')
+    parser.add_argument('-i','--info',
+                        dest = 'info',
+                        required=False,
+                        help='print detailed info of uuid')
+    parser.add_argument('-I',
+                        dest = 'all_info',
+                        required=False,
+                        help='print information on all bips workflows')
+    parser.add_argument('-r',
+                        dest = 'run',
+                        required=False,
+                        help='run the workflow')
+    
+    args = parser.parse_args()
+    main(args)
+    

bips/fmri/qa/QA_fmri.py

@@ -255,13 +255,13 @@ def QA_workflow(name='QA'):
     # Define Nodes
 
     plot_m = pe.MapNode(util.Function(input_names=['motion_parameters'],
-                                      output_names=['fname'],
+                                      output_names=['fname_t','fname_r'],
                                       function=plot_motion),
                         name="motion_plots",
                         iterfield=['motion_parameters'])
 
     workflow.connect(datagrabber,'motion_parameters',plot_m,'motion_parameters')
-    workflow.connect(plot_m, 'fname',inputspec,'motion_plots')
+    #workflow.connect(plot_m, 'fname',inputspec,'motion_plots')
 
     tsdiff = pe.MapNode(util.Function(input_names = ['img'], 
                                       output_names = ['out_file'], 
@@ -341,7 +341,8 @@ def QA_workflow(name='QA'):
                                                           'Art_Detect',
                                                           'Mean_Functional',
                                                           'Ribbon',
-                                                          'motion_plots',
+                                                          'motion_plot_translations',
+                                                          'motion_plot_rotations',
                                                           'tsdiffana',
                                                           'ADnorm',
                                                           'TSNR_Images',
@@ -367,7 +368,9 @@ def QA_workflow(name='QA'):
     workflow.connect(inputspec,'in_file',write_rep,'in_file')
     workflow.connect(inputspec,'art_file',art_info,'art_file')
     workflow.connect(art_info,('table',to1table), write_rep,'Art_Detect')
-    workflow.connect(inputspec,'motion_plots',write_rep,'motion_plots')
+    #workflow.connect(inputspec,'motion_plots',write_rep,'motion_plots')
+    workflow.connect(plot_m, 'fname_t',write_rep,'motion_plot_translations')
+    workflow.connect(plot_m, 'fname_r',write_rep,'motion_plot_rotations')
     workflow.connect(inputspec,'in_file',tsdiff,'img')
     workflow.connect(tsdiff,"out_file",write_rep,"tsdiffana")
     workflow.connect(inputspec,('config_params',totable), write_rep,'config_params')

bips/fmri/qa/QA_utils.py

@@ -300,7 +300,7 @@ def plot_motion(motion_parameters):
     plt.savefig(fname_r)
     plt.close()
     fname = [fname_t, fname_r]
-    return fname
+    return fname_t, fname_r
 
 def plot_ribbon(Brain):
     import os.path

bips/fmri/task/preproc.py

@@ -13,11 +13,11 @@
 # -------------------------------------------------------------
 
 
-def prep_workflow(subjects,fieldmap):
+def prep_workflow(c,fieldmap):
 
     infosource = pe.Node(util.IdentityInterface(fields=['subject_id']),
                          name='subject_names')
-    infosource.iterables = ('subject_id', subjects)
+    infosource.iterables = ('subject_id', c.subjects)
 
     modelflow = pe.Workflow(name='preproc')
 
@@ -108,21 +108,12 @@ def prep_workflow(subjects,fieldmap):
     modelflow.base_dir = os.path.join(c.working_dir,'work_dir')
     return modelflow
 
-if __name__ == "__main__":
-
-    parser = argparse.ArgumentParser(description="example: \
-                        run resting_preproc.py -c config.py")
-    parser.add_argument('-c','--config',
-                        dest='config',
-                        required=True,
-                        help='location of config file'
-                        )
-    args = parser.parse_args()
-    path, fname = os.path.split(os.path.realpath(args.config))
+def main(config):
+    
+    path, fname = os.path.split(os.path.realpath(config))
     sys.path.append(path)
     c = __import__(fname.split('.')[0])
-
-    preprocess = prep_workflow(c.subjects, c.use_fieldmap)
+    preprocess = prep_workflow(c, c.use_fieldmap)
     realign = preprocess.get_node('preproc.realign')
     realign.plugin_args = {'qsub_args': '-l nodes=1:ppn=3'}
     realign.inputs.loops = 2
@@ -134,4 +125,17 @@ def prep_workflow(subjects,fieldmap):
         preprocess.run(plugin=c.plugin,plugin_args = c.plugin_args)
     else:
         preprocess.run()
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="example: \
+                        run resting_preproc.py -c config.py")
+    parser.add_argument('-c','--config',
+                        dest='config',
+                        required=True,
+                        help='location of config file'
+                        )
+    args = parser.parse_args()
+    main(args.config)
+    
 

example_configs/sad_resting_config.py

@@ -113,12 +113,12 @@
         'SAD_POST46','SAD_POST47','SAD_POST50','SAD_POST51',
         'SAD_POST52','SAD_POST53','SAD_POST54','SAD_POST56',
         'SAD_POST58']
-subjects = patients+tp2s
+subjects = ['SAD_017']#patients+tp2s
 #['SAD_POST06','SAD2_036','SAD_POST07','SAD_POST46','SAD_023','SAD_018','SAD_POST52','SAD_P57',
 # 'SAD_POST50','SAD_P12','SAD2_022','SAD_POST54','SAD2_050','SAD_P43','SAD_024','SAD_POST10',
 # 'SAD_POST13','SAD_POST05','SAD_POST44','SAD2_044']  #These people had errors
 
-run_on_grid = True
+run_on_grid = False
 
 plugin = 'PBS'