Merge pull request #621 from FCP-INDI/101_to_master

101 to master

CPAC/GUI/interface/pages/settings.py

@@ -85,7 +85,7 @@ def __init__(self, parent, counter=0):
 
         self.page.add(label="Maximum Memory Per Participant (GB) ",
                       control=control.INT_CTRL,
-                      name='memoryAllocatedPerSubject',
+                      name='maximumMemoryPerParticipant',
                       type=dtype.NUM,
                       comment="The maximum amount of memory each " \
                               "participant's workflow can allocate. Use " \
@@ -104,7 +104,7 @@ def __init__(self, parent, counter=0):
 
         self.page.add(label="Maximum Number of Cores Per Participant ",
                       control=control.INT_CTRL,
-                      name='numCoresPerSubject',
+                      name='maxCoresPerParticipant',
                       type=dtype.NUM,
                       comment="The maximum amount of cores (on a single " \
                               "machine) or slots on a node (on a " \
@@ -125,7 +125,7 @@ def __init__(self, parent, counter=0):
 
         self.page.add(label="Number of Participants to Run Simultaneously ",
                       control=control.INT_CTRL,
-                      name='numSubjectsAtOnce',
+                      name='numParticipantsAtOnce',
                       type=dtype.NUM,
                       comment="The number of participant workflows to run " \
                               "at the same time. The maximum number of " \

CPAC/GUI/interface/windows/config_window.py

@@ -385,7 +385,6 @@ def test_sublist(self, sublist):
                                        wx.OK | wx.ICON_ERROR)
             errDlg4.ShowModal()
             errDlg4.Destroy()
-
             # Raise Exception
             raise Exception
 
@@ -399,20 +398,41 @@ def test_sublist(self, sublist):
                                        wx.OK | wx.ICON_ERROR)
             errDlg3.ShowModal()
             errDlg3.Destroy()
-
             # Raise Exception
             raise Exception
 
         # Iterate and test each subject's files
         for sub in sublist:
             anat_file = sub['anat']
-            func_files = sub['rest']
+            try:
+                func_files = sub['func']
+            except KeyError:
+                func_files = sub['rest']
+            checked_anat_s3 = False
+
+            if not anat_file:
+                err = "\n\n[!] Could not read in at least one of your anatom"\
+                      "ical input files. Please double-check the formatting "\
+                      "of your participant list YAML file.\n\n"
+                raise Exception(err)
+
+            if not func_files:
+                err = "\n\n[!] Could not read in at least one of your functi"\
+                      "onal input files. Please double-check the formatting "\
+                      "of your participant list YAML file.\n\n"
+                raise Exception(err)
+
             if anat_file.lower().startswith(s3_str):
-                if checked_s3:
-                    break
                 dl_dir = tempfile.mkdtemp()
-                creds_path = sub['creds_path']
+                try:
+                    creds_path = sub['creds_path']
+                except KeyError:
+                    # if no creds path is provided, it could be that the user
+                    # is downloading public data - leave it to downstream to
+                    # handle creds issues
+                    creds_path = None
                 anat_file = check_for_s3(anat_file, creds_path, dl_dir=dl_dir)
+                checked_anat_s3 = True
             # Check if anatomical file exists
             if os.path.exists(anat_file):
                 img = nb.load(anat_file)
@@ -429,11 +449,25 @@ def test_sublist(self, sublist):
                 not_found_flg = True
                 err_str_suffix = 'File not found: %s\n' % anat_file
                 err_str = err_str + err_str_suffix
+            # If we're just checking s3 files, remove the temporarily 
+            # downloaded
+            if checked_anat_s3:
+                try:
+                    os.remove(anat_file)
+                except:
+                    pass
             # For each functional file
             for func_file in func_files.values():
+                checked_s3 = False
                 if func_file.lower().startswith(s3_str):
                     dl_dir = tempfile.mkdtemp()
-                    creds_path = sub['creds_path']
+                    try:
+                        creds_path = sub['creds_path']
+                    except KeyError:
+                        # if no creds path is provided, it could be that the 
+                        # user is downloading public data - leave it to down-
+                        # stream to handle creds issues
+                        creds_path = None
                     func_file = check_for_s3(func_file, creds_path, dl_dir=dl_dir,img_type='func')
                     checked_s3 = True
                 # Check if functional file exists
@@ -452,14 +486,13 @@ def test_sublist(self, sublist):
                     not_found_flg = True
                     err_str_suffix = 'File not found: %s\n' % func_file
                     err_str = err_str + err_str_suffix
-                # If we're just checking s3 files, remove the temporarily downloaded
+                # If we're just checking s3 files, remove the temporarily 
+                # downloaded
                 if checked_s3:
                     try:
-                        os.remove(anat_file)
                         os.remove(func_file)
                     except:
                         pass
-                    break
             # Check flags for error message
             if not_found_flg:
                 err_msg = 'One or more of your input files are missing.\n'
@@ -754,15 +787,16 @@ def testFile(filepath, paramName, switch):
         except Exception as xxx:
 
             print xxx
-            print "an exception occured"
+            print "an exception occurred"
 
             testDlg1.Destroy()
 
             errDlg1 = wx.MessageDialog(
                 self, 'There are issues with the current configuration ' \
                       'which need to be resolved - please check to make ' \
                       'sure the options you are running have the proper ' \
-                      'pre-requisites selected.\n\nIssue Info:\n%s' % xxx,
+                      'pre-requisites selected.\n\nIssue Info:\n%s' \
+                      % str(xxx),
                 'Pipeline Not Ready',
                 wx.OK | wx.ICON_ERROR)
             errDlg1.ShowModal()
@@ -990,11 +1024,15 @@ def update_listbox(self, value):
     def write(self, path, config_list):
 
         import ast
+        import CPAC
 
         try:
 
             f = open(path, 'w')
 
+            print >>f, "# CPAC Pipeline Configuration YAML file"
+            print >>f, "# version %s\n" % str(CPAC.__version__)
+
             for item in config_list:
 
                 label = item.get_name()

CPAC/GUI/interface/windows/dataconfig_window.py

@@ -261,9 +261,9 @@ def run(self, config):
                 CPAC.utils.extract_data.generate_supplementary_files(sublist_outdir, sublist_name)
 
             # Prompt user with naming subject list for main GUI
+            dlg2 = wx.TextEntryDialog(self, 'Please enter a name for the Subject List',
+                                             'Sublist Name', '%s' % sublist_name)
             while True:
-                dlg2 = wx.TextEntryDialog(self, 'Please enter a name for the Subject List',
-                                                 'Sublist Name', '%s' % sublist_name)
                 if dlg2.ShowModal() == wx.ID_OK:
                     if len(dlg2.GetValue()) >0:
                         parent = self.Parent
@@ -272,14 +272,19 @@ def run(self, config):
                             map[dlg2.GetValue()]= out_location
                             parent.listbox2.Append(dlg2.GetValue())
                             dlg2.Destroy()
+                            ret = 1
                             break
                         else:
                             dlg3 = wx.MessageDialog(self, 'Subject List with this name already exist','Error!',
                                                     wx.OK | wx.ICON_ERROR)
                             dlg3.ShowModal()
                             dlg3.Destroy()
+                elif dlg2.ShowModal() == wx.ID_CANCEL:
+                    dlg2.Destroy()
+                    ret = -1
+                    break
             # Return value
-            return 1
+            return ret
 
         # Import error if CPAC not available
         except ImportError as exc:
@@ -304,6 +309,7 @@ def run(self, config):
     def save(self, event, flag):
 
         config_list =[]
+        config_dict = {}
         def display(win, msg):
             wx.MessageBox(msg, "Error")
             win.SetBackgroundColour("pink")
@@ -338,6 +344,67 @@ def display(win, msg):
                         display(win,"%s field contains incorrect path. Please update the path!"%ctrl.get_name())
 
                 config_list.append((name, value, dtype))
+                config_dict[name] = (value, dtype)
+
+            # some final checks
+            if "BIDS" in config_dict["dataFormat"][0]:
+                if len(config_dict["anatomicalTemplate"][0]) > 0 or \
+                    len(config_dict["functionalTemplate"][0]) > 0:
+                    err = wx.MessageDialog(self, "Custom filepath template " \
+                                                 "provided, but data format "\
+                                                 "is set to BIDS instead of "\
+                                                 "Custom.",
+                                                 'Error!',
+                                                 wx.OK | wx.ICON_ERROR)
+                    err.ShowModal()
+                    err.Destroy()
+                    return
+
+                elif not os.path.exists(config_dict["bidsBaseDir"][0]):
+                    err = wx.MessageDialog(self, "Data format is set to " \
+                                                 "BIDS, but no BIDS base " \
+                                                 "directory is set, or the " \
+                                                 "BIDS directory does not " \
+                                                 "exist.",
+                                                 'Error!',
+                                                 wx.OK | wx.ICON_ERROR)
+                    err.ShowModal()
+                    err.Destroy()
+                    return
+
+            elif "Custom" in config_dict["dataFormat"][0]:
+                if len(config_dict["bidsBaseDir"][0]) > 0:
+                    err = wx.MessageDialog(self, "BIDS base directory " \
+                                                 "provided, but data format "\
+                                                 "is set to Custom instead " \
+                                                 "of BIDS.",
+                                                 'Error!',
+                                                 wx.OK | wx.ICON_ERROR)
+                    err.ShowModal()
+                    err.Destroy()
+                    return
+
+                if len(config_dict["anatomicalTemplate"][0]) == 0:
+                    err = wx.MessageDialog(self, "Custom data format " \
+                                                 "selected, but no custom " \
+                                                 "anatomical filepath " \
+                                                 "template provided.",
+                                                 'Error!',
+                                                 wx.OK | wx.ICON_ERROR)
+                    err.ShowModal()
+                    err.Destroy()
+                    return
+
+                if len(config_dict["functionalTemplate"][0]) == 0:
+                    err = wx.MessageDialog(self, "Custom data format " \
+                                                 "selected, but no custom " \
+                                                 "functional filepath " \
+                                                 "template provided.",
+                                                 'Error!',
+                                                 wx.OK | wx.ICON_ERROR)
+                    err.ShowModal()
+                    err.Destroy()
+                    return
 
         except Exception, e:
 
@@ -352,7 +419,7 @@ def display(win, msg):
             return
 
         else:
-        
+
             dlg = wx.FileDialog(
                 self, message="Save file as ...", 
                 defaultDir=os.getcwd(), 
@@ -364,15 +431,17 @@ def display(win, msg):
                 path = dlg.GetPath()
                 dlg.Destroy()
                 f = open(path, 'w')
-                for ctrl in config_list:
+                for ctrl_name in config_dict.keys():
 
-                    if "/" in ctrl[1] or "%s" in ctrl[1] \
-                       or 'None' in ctrl[1] or ctrl[0] =='subjectListName': 
-                        value = ctrl[1]
+                    val = config_dict[ctrl_name][0]
+
+                    if "/" in val or "%s" in val or 'None' in val or \
+                        ctrl_name =='subjectListName': 
+                        value = val
                     else:
-                        value =[val.strip() for val in ctrl[1].split(',')]
+                        value =[item.strip() for item in val.split(',')]
 
-                    print >>f, ctrl[0], " : ", value, "\n"
+                    print >>f, ctrl_name, " : ", value, "\n"
 
                 f.close()
                 print "saving %s"%path

CPAC/GUI/interface/windows/main_window.py

@@ -231,8 +231,8 @@ def runAnalysis1(self,pipeline, sublist, p):
             from CPAC.utils import Configuration
             from nipype.pipeline.plugins.callback_log import log_nodes_cb
             c = Configuration(yaml.load(open(os.path.realpath(pipeline), 'r')))
-            plugin_args = {'n_procs': c.numCoresPerSubject,
-                           'memory_gb': c.memoryAllocatedPerSubject,
+            plugin_args = {'n_procs': c.maxCoresPerParticipant,
+                           'memory_gb': c.maximumMemoryPerParticipant,
                            'callback_log' : log_nodes_cb}
 
             CPAC.pipeline.cpac_runner.run(pipeline, sublist, p,
@@ -676,12 +676,22 @@ def AddConfig(self, event):
                     try:
                         c = Configuration(f_cfg)
                     except Exception as e:
-                        print '\n\nERROR: Configuration file could not be '\
-                              'loaded properly - the file might be '\
-                              'access-protected or you might have chosen the '\
-                              'wrong file.\n'
-                        print 'Error name: main_window_0001\n\n'
-                        print 'Exception: %s' % e
+                        if "object has no attribute" in e:
+                            err = "%s\n\nIs this attribute linked (using " \
+                                  "'${}') in any of your configuration " \
+                                  "parameters? (Standard template paths, " \
+                                  "for example). If this is a pipeline " \
+                                  "configuration file from an older version "\
+                                  "of CPAC, this parameter may be obsolete. "\
+                                  "Double-check your selections.\n\n" % e
+                            print err
+                        else:
+                            print '\n\nERROR: Configuration file could not ' \
+                                  'be loaded properly - the file might be '\
+                                  'access-protected or you might have ' \
+                                  'chosen the wrong file.\n'
+                            print 'Error name: main_window_0001\n\n'
+                            print 'Exception: %s' % e
                     # Valid pipeline name
                     if c.pipelineName != None:
                             if self.pipeline_map.get(c.pipelineName) == None:

CPAC/GUI/resources/config_parameters.txt

@@ -3,10 +3,10 @@ FSLDIR,FSL Path,Computer Settings
 resourceManager,Job Scheduler / Resource Manager,Computer Settings
 parallelEnvironment,SGE Parallel Environment,Computer Settings
 queue,SGE Queue,Computer Settings
-numCoresPerSubject,Maximum Number of Cores Per Participant,Computer Settings
-numSubjectsAtOnce,Number of Participants to Run Simultaneously,Computer Settings
+maxCoresPerParticipant,Maximum Number of Cores Per Participant,Computer Settings
+numParticipantsAtOnce,Number of Participants to Run Simultaneously,Computer Settings
 num_ants_threads,Number of Cores for Anatomical Registration (ANTS only),Computer Settings
-memoryAllocatedPerSubject,Maximum Memory Per Participant (GB),Computer Settings
+maximumMemoryPerParticipant,Maximum Memory Per Participant (GB),Computer Settings
 pipelineName,Pipeline Name,Output Settings
 workingDirectory,Working Directory,Output Settings
 crashLogDirectory,Crash Log Directory,Output Settings

CPAC/__init__.py

@@ -49,7 +49,7 @@ def test(self, label='fast', verbose=1, extra_argv=['--exe'], doctests = False,
 #__version__ = '0.1-git'
 
 try:
-    version = '1.0.0'
+    version = '1.0.1'
 
 
 #    gitproc = Popen(['git', 'log', '--oneline'], stdout = PIPE)