def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration"
button in the pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will
be using with the config they are building). Then it builds the
pipeline but does not run it. It then reports whether or not the
config will run or not depending on if the pipeline gets built
successfully.
'''
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline configuration.' \
' Click OK to provide a subject list you will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(
self, message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
# Load and test the subject list
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
sub_flg = self.test_sublist(sublist)
if not sub_flg:
raise Exception
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
for page in self.nb.get_page_list():
switch = page.page.get_switch()
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
if switch_val == 'on' or switch_val == 'true' or switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
# option_name will be the selection name as it is written
# as the dictionary key of the config.yml dictionary
option_name = ctrl.get_name()
#validating
if (switch == None or validate) and ctrl.get_validation() \
and (option_name != 'derivativeList') and (option_name != 'modelConfigs'):
win = ctrl.get_ctrl()
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win, "%s field is empty or the items are not checked!" % ctrl.get_name(), False)
return
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not isinstance(value, list):
if not os.path.exists(ctrl.get_selection()) and value != 'On/Off':
display(
win, "%s field contains incorrect path. Please update the path!" % ctrl.get_name())
return
config_list.append(ctrl)
# Get the user's CPAC output directory for use in this script
for config in config_list:
if config.get_name() == 'outputDirectory':
outDir = config.get_selection()
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
self.write(outDir + 'testConfig.yml', config_list)
c = Configuration(yaml.load(open(os.path.realpath(outDir + 'testConfig.yml'), 'r')))
os.remove(outDir + 'testConfig.yml')
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Corrections != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
testDlg1 = wx.MessageDialog(
self, 'Click OK to run the test. This should take only a few seconds.',
'Running Test',
wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
# Check file paths first
# Just getting proper names of config file parameters
try:
params_file = open(p.resource_filename('CPAC', 'GUI/resources/config_parameters.txt'), "r")
except:
print "Error: Could not open configuration parameter file.", "\n"
raise Exception
paramInfo = params_file.read().split('\n')
paramList = []
for param in paramInfo:
if param != '':
paramList.append(param.split(','))
# function for file path checking
def testFile(filepath, paramName, switch):
try:
if (1 in switch) and (filepath != None):
fileTest = open(filepath)
fileTest.close()
except:
testDlg1.Destroy()
for param in paramList:
if param[0] == paramName:
paramTitle = param[1]
paramGroup = param[2]
break
errDlgFileTest = wx.MessageDialog(
self, 'Error reading file - either it does not exist or you' \
' do not have read access. \n\n' \
'Parameter: %s \n' \
'In tab: %s \n\n' \
'Path: %s' % (paramTitle, paramGroup, filepath),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlgFileTest.ShowModal()
errDlgFileTest.Destroy()
testFile(c.template_brain_only_for_anat,'template_brain_only_for_anat',c.runRegistrationPreprocessing)
testFile(c.template_skull_for_anat,'template_skull_for_anat',c.runRegistrationPreprocessing)
testFile(c.PRIORS_WHITE,'PRIORS_WHITE',c.runSegmentationPreprocessing)
testFile(c.PRIORS_GRAY,'PRIORS_GRAY',c.runSegmentationPreprocessing)
testFile(c.PRIORS_CSF,'PRIORS_CSF',c.runSegmentationPreprocessing)
testFile(c.template_brain_only_for_func,'template_brain_only_for_func',c.runRegisterFuncToMNI)
testFile(c.template_skull_for_func,'template_skull_for_func',c.runRegisterFuncToMNI)
testFile(c.identityMatrix,'identityMatrix',c.runRegisterFuncToMNI)
testFile(c.boundaryBasedRegistrationSchedule,'boundaryBasedRegistrationSchedule',c.runRegisterFuncToAnat)
testFile(c.lateral_ventricles_mask,'lateral_ventricles_mask',c.runNuisance)
testFile(c.seedSpecificationFile,'seedSpecificationFile',[1])
testFile(c.roiSpecificationFile,'roiSpecificationFile',c.runROITimeseries)
testFile(c.roiSpecificationFileForSCA,'roiSpecificationFileForSCA',c.runROITimeseries)
testFile(c.maskSpecificationFile,'maskSpecificationFile',c.runVoxelTimeseries)
testFile(c.maskSpecificationFileForSCA,'maskSpecificationFileForSCA',c.runVoxelTimeseries)
testFile(c.spatialPatternMaps,'spatialPatternMaps',c.runSpatialRegression)
testFile(c.template_symmetric_brain_only,'template_symmetric_brain_only',c.runVMHC)
testFile(c.template_symmetric_skull,'template_symmetric_skull',c.runVMHC)
testFile(c.dilated_symmetric_brain_mask,'dilated_symmetric_brain_mask',c.runVMHC)
testFile(c.configFileTwomm,'configFileTwomm',c.runVMHC)
testFile(c.templateSpecificationFile,'templateSpecificationFile',c.runNetworkCentrality)
testFile(c.bascAffinityThresholdFile,'bascAffinityThresholdFile',c.runBASC)
testFile(c.cwasROIFile,'cwasROIFile',c.runCWAS)
testFile(c.cwasRegressorFile,'cwasRegressorFile',c.runCWAS)
try:
# Run the pipeline building
prep_workflow(sublist[0], c, strategies, 0)
except Exception as xxx:
print xxx
print "an exception occured"
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,
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You can safely' \
' save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()
def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration"
button in the pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will
be using with the config they are building). Then it builds the
pipeline but does not run it. It then reports whether or not the
config will run or not depending on if the pipeline gets built
successfully.
'''
# Import packages
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline '\
'configuration. Click OK to provide a subject list you ' \
'will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(self,
message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
# Load and test the subject list
print 'Checking subject list: %s...' % subListPath
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
sub_flg = self.test_sublist(sublist)
if not sub_flg:
raise Exception
print 'Subject list looks good!'
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
for page in self.nb.get_page_list():
switch = page.page.get_switch()
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
if switch_val == 'on' or switch_val == 'true' or \
switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
# option_name will be the selection name as it is written
# as the dictionary key of the config.yml dictionary
option_name = ctrl.get_name()
#validating
if (switch == None or validate) and ctrl.get_validation() \
and (option_name != 'derivativeList') and \
(option_name != 'modelConfigs'):
win = ctrl.get_ctrl()
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win, "%s field is empty or the items are " \
"not checked!" % ctrl.get_name(), False)
return
elif (option_name == "tsa_roi_paths") or \
(option_name == "sca_roi_paths"):
# fires if the control is the checkbox grid for
# multiple paths assigned to multiple options
# (i.e. timeseries analysis)
config_list.append(ctrl)
continue
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not \
isinstance(value, list):
if not os.path.exists(ctrl.get_selection()) and \
value != 'On/Off':
display(
win, "%s field contains incorrect path. " \
"Please update the path!" % ctrl.get_name())
return
config_list.append(ctrl)
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
test_cfg_yml = '/tmp/test_config.yml'
self.write(test_cfg_yml, config_list)
c = Configuration(
yaml.load(open(os.path.realpath(test_cfg_yml), 'r')))
os.remove(test_cfg_yml)
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Regressors != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
testDlg1 = wx.MessageDialog(
self,
'Click OK to run the test. This should take only a few seconds.',
'Running Test', wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
# Check file paths first
# Just getting proper names of config file parameters
try:
params_file = open(
p.resource_filename('CPAC',
'GUI/resources/config_parameters.txt'),
"r")
except:
print "Error: Could not open configuration parameter file.", "\n"
raise Exception
paramInfo = params_file.read().split('\n')
paramList = []
for param in paramInfo:
if param != '':
paramList.append(param.split(','))
# function for file path checking
def testFile(filepath, paramName, switch):
try:
if (1 in switch) and (filepath != None):
fileTest = open(filepath)
fileTest.close()
except:
testDlg1.Destroy()
for param in paramList:
if param[0] == paramName:
paramTitle = param[1]
paramGroup = param[2]
break
errDlgFileTest = wx.MessageDialog(
self, 'Error reading file - either it does not exist or '\
'you do not have read access. \n\n' \
'Parameter: %s \n' \
'In tab: %s \n\n' \
'Path: %s' % (paramTitle, paramGroup, filepath),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlgFileTest.ShowModal()
errDlgFileTest.Destroy()
# Check S3 output bucket access if writing to S3
output_dir = c.outputDirectory
s3_str = 's3://'
if output_dir.lower().startswith(s3_str):
output_dir_sp = output_dir.split('/')
output_dir_sp[0] = output_dir_sp[0].lower()
output_dir = '/'.join(output_dir_sp)
if type(output_dir) is str and output_dir.lower().startswith(s3_str):
from indi_aws import fetch_creds
creds_path = c.awsOutputBucketCredentials
bucket_name = output_dir.split(s3_str)[1].split('/')[0]
try:
bucket = fetch_creds.return_bucket(creds_path, bucket_name)
print 'Connection with output bucket "%s" successful!' % bucket_name
except Exception as exc:
err_msg = 'Unable to access output S3 bucket: "%s" with '\
'credentials in: "%s". Check bucket name '\
'and credentials file and try again'\
% (bucket_name, creds_path)
testDlg1.Destroy()
errDlg1 = wx.MessageDialog(self, err_msg, 'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
return
testFile(c.template_brain_only_for_anat, \
'template_brain_only_for_anat',[1])
testFile(c.template_skull_for_anat, 'template_skull_for_anat', [1])
testFile(c.PRIORS_WHITE, 'PRIORS_WHITE',
c.runSegmentationPreprocessing)
testFile(c.PRIORS_GRAY, 'PRIORS_GRAY', c.runSegmentationPreprocessing)
testFile(c.PRIORS_CSF, 'PRIORS_CSF', c.runSegmentationPreprocessing)
testFile(c.template_brain_only_for_func, \
'template_brain_only_for_func',c.runRegisterFuncToMNI)
testFile(c.template_skull_for_func,'template_skull_for_func', \
c.runRegisterFuncToMNI)
testFile(c.identityMatrix, 'identityMatrix', c.runRegisterFuncToMNI)
testFile(c.boundaryBasedRegistrationSchedule, \
'boundaryBasedRegistrationSchedule', \
c.runRegisterFuncToAnat)
testFile(c.lateral_ventricles_mask,'lateral_ventricles_mask', \
c.runNuisance)
testFile(c.template_symmetric_brain_only, \
'template_symmetric_brain_only',c.runVMHC)
testFile(c.template_symmetric_skull,'template_symmetric_skull', \
c.runVMHC)
testFile(c.dilated_symmetric_brain_mask, \
'dilated_symmetric_brain_mask',c.runVMHC)
testFile(c.configFileTwomm, 'configFileTwomm', c.runVMHC)
testFile(c.templateSpecificationFile,'templateSpecificationFile', \
c.runNetworkCentrality)
if c.tsa_roi_paths and type(c.tsa_roi_paths[0]) == dict:
for roi_path in c.tsa_roi_paths[0].keys():
testFile(roi_path, "tsa_roi_paths", c.runROITimeseries)
if c.sca_roi_paths and type(c.sca_roi_paths[0]) == dict:
for roi_path in c.sca_roi_paths[0].keys():
testFile(roi_path, "sca_roi_paths", c.runSCA)
try:
# Run the pipeline building
prep_workflow(sublist[0], c, strategies, 0)
except Exception as xxx:
print xxx
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' \
% str(xxx),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You '\
'can safely save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()
def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration"
button in the pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will
be using with the config they are building). Then it builds the
pipeline but does not run it. It then reports whether or not the
config will run or not depending on if the pipeline gets built
successfully.
'''
# Import packages
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline '
'configuration. Click OK to provide a subject list you '
'will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(
self, message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
# Load and test the subject list
print 'Checking subject list: %s...' % subListPath
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
sub_flg = self.test_sublist(sublist)
if not sub_flg:
raise Exception
print 'Subject list looks good!'
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
for page in self.nb.get_page_list():
switch = page.page.get_switch()
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
if switch_val == 'on' or switch_val == 'true' or \
switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
# option_name will be the selection name as it is written
# as the dictionary key of the config.yml dictionary
option_name = ctrl.get_name()
#validating
if (switch == None or validate) and ctrl.get_validation() \
and (option_name != 'derivativeList') and \
(option_name != 'modelConfigs'):
win = ctrl.get_ctrl()
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win, "%s field is empty or the items are " \
"not checked!" % ctrl.get_name(), False)
return
elif (option_name == "tsa_roi_paths") or \
(option_name == "sca_roi_paths"):
# fires if the control is the checkbox grid for
# multiple paths assigned to multiple options
# (i.e. timeseries analysis)
config_list.append(ctrl)
continue
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not \
isinstance(value, list):
if not os.path.exists(ctrl.get_selection()) and \
value != 'On/Off':
display(
win, "%s field contains incorrect path. " \
"Please update the path!" % ctrl.get_name())
return
config_list.append(ctrl)
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
test_cfg_yml = '/tmp/test_config.yml'
self.write(test_cfg_yml, config_list)
c = Configuration(yaml.load(open(os.path.realpath(test_cfg_yml), 'r')))
os.remove(test_cfg_yml)
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Regressors != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
testDlg1 = wx.MessageDialog(
self, 'Click OK to run the test. This should take only a few seconds.',
'Running Test',
wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
# Check file paths first
# Just getting proper names of config file parameters
try:
params_file = open(p.resource_filename('CPAC', 'GUI/resources/config_parameters.txt'), "r")
except:
print "Error: Could not open configuration parameter file.", "\n"
raise Exception
paramInfo = params_file.read().split('\n')
paramList = []
for param in paramInfo:
if param != '':
paramList.append(param.split(','))
# function for file path checking
def testFile(filepath, paramName, switch):
try:
if (1 in switch) and (filepath != None):
fileTest = open(filepath)
fileTest.close()
except:
testDlg1.Destroy()
for param in paramList:
if param[0] == paramName:
paramTitle = param[1]
paramGroup = param[2]
break
errDlgFileTest = wx.MessageDialog(
self, 'Error reading file - either it does not exist or '\
'you do not have read access. \n\n' \
'Parameter: %s \n' \
'In tab: %s \n\n' \
'Path: %s' % (paramTitle, paramGroup, filepath),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlgFileTest.ShowModal()
errDlgFileTest.Destroy()
# Check S3 output bucket access if writing to S3
output_dir = c.outputDirectory
s3_str = 's3://'
if output_dir.lower().startswith(s3_str):
output_dir_sp = output_dir.split('/')
output_dir_sp[0] = output_dir_sp[0].lower()
output_dir = '/'.join(output_dir_sp)
if type(output_dir) is str and output_dir.lower().startswith(s3_str):
from indi_aws import fetch_creds
creds_path = c.awsOutputBucketCredentials
bucket_name = output_dir.split(s3_str)[1].split('/')[0]
try:
bucket = fetch_creds.return_bucket(creds_path, bucket_name)
print 'Connection with output bucket "%s" successful!' % bucket_name
except Exception as exc:
err_msg = 'Unable to access output S3 bucket: "%s" with '\
'credentials in: "%s". Check bucket name '\
'and credentials file and try again'\
% (bucket_name, creds_path)
testDlg1.Destroy()
errDlg1 = wx.MessageDialog(self, err_msg, 'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
return
testFile(c.template_brain_only_for_anat, \
'template_brain_only_for_anat',[1])
testFile(c.template_skull_for_anat,'template_skull_for_anat',[1])
testFile(c.PRIORS_WHITE,'PRIORS_WHITE',c.runSegmentationPreprocessing)
testFile(c.PRIORS_GRAY,'PRIORS_GRAY',c.runSegmentationPreprocessing)
testFile(c.PRIORS_CSF,'PRIORS_CSF',c.runSegmentationPreprocessing)
testFile(c.template_brain_only_for_func, \
'template_brain_only_for_func',c.runRegisterFuncToMNI)
testFile(c.template_skull_for_func,'template_skull_for_func', \
c.runRegisterFuncToMNI)
testFile(c.identityMatrix,'identityMatrix',c.runRegisterFuncToMNI)
testFile(c.boundaryBasedRegistrationSchedule, \
'boundaryBasedRegistrationSchedule', \
c.runRegisterFuncToAnat)
testFile(c.lateral_ventricles_mask,'lateral_ventricles_mask', \
c.runNuisance)
testFile(c.template_symmetric_brain_only, \
'template_symmetric_brain_only',c.runVMHC)
testFile(c.template_symmetric_skull,'template_symmetric_skull', \
c.runVMHC)
testFile(c.dilated_symmetric_brain_mask, \
'dilated_symmetric_brain_mask',c.runVMHC)
testFile(c.configFileTwomm,'configFileTwomm',c.runVMHC)
testFile(c.templateSpecificationFile,'templateSpecificationFile', \
c.runNetworkCentrality)
if c.tsa_roi_paths and type(c.tsa_roi_paths[0]) == dict:
for roi_path in c.tsa_roi_paths[0].keys():
testFile(roi_path, "tsa_roi_paths", c.runROITimeseries)
if c.sca_roi_paths and type(c.sca_roi_paths[0]) == dict:
for roi_path in c.sca_roi_paths[0].keys():
testFile(roi_path, "sca_roi_paths", c.runSCA)
try:
# Run the pipeline building
prep_workflow(sublist[0], c, strategies, 0)
except Exception as xxx:
print xxx
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' \
% str(xxx),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You '\
'can safely save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()
def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration" button in the
pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will be using
with the config they are building). Then it builds the pipeline but does not
run it. It then reports whether or not the config will run or not depending
on if the pipeline gets built successfully.
'''
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline configuration.' \
' Click OK to provide a subject list you will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(self,
message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
# Check to ensure the user is providing an actual subject
# list and not some other kind of file
try:
subInfo = sublist[0]
except:
errDlg4 = wx.MessageDialog(
self, 'ERROR: Subject list file not in proper format - check if you' \
' loaded the correct file? \n\n' \
'Error name: config_window_0001',
'Subject List Error',
wx.OK | wx.ICON_ERROR)
errDlg4.ShowModal()
errDlg4.Destroy()
raise Exception
# Another check to ensure the actual subject list was generated
# properly and that it will work
if 'subject_id' not in subInfo:
errDlg3 = wx.MessageDialog(
self, 'ERROR: Subject list file not in proper format - check if you' \
' loaded the correct file? \n\n' \
'Error name: config_window_0002',
'Subject List Error',
wx.OK | wx.ICON_ERROR)
errDlg3.ShowModal()
errDlg3.Destroy()
raise Exception
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
#print "self.nb.get_page_list()", self.nb.get_page_list()
for page in self.nb.get_page_list():
#print "page ----> ", page
switch = page.page.get_switch()
#print "switch ---->", switch
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
#print "switch_val ---->", switch_val
if switch_val == 'on' or switch_val == 'true' or switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
#validating
if (switch == None or validate) and ctrl.get_validation():
win = ctrl.get_ctrl()
#print "validating ctrl-->", ctrl.get_name()
#print "ctrl.get_selection()", ctrl.get_selection()
#print "type(ctrl.get_selection())", type(ctrl.get_selection())
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win,
"%s field is empty or the items are not checked!"
% ctrl.get_name(), False)
return
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not isinstance(
value, list):
if not os.path.exists(ctrl.get_selection()):
display(
win,
"%s field contains incorrect path. Please update the path!"
% ctrl.get_name())
return
config_list.append(ctrl)
# Get the user's CPAC output directory for use in this script
for config in config_list:
#print config.get_name(), " ", config.get_selection()
if config.get_name() == 'outputDirectory':
outDir = config.get_selection()
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
self.write(outDir + 'testConfig.yml', config_list)
c = Configuration(
yaml.load(
open(os.path.realpath(outDir + 'testConfig.yml'), 'r')))
os.remove(outDir + 'testConfig.yml')
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Corrections != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
try:
testDlg1 = wx.MessageDialog(
self,
'Click OK to run the test. This should take only a few seconds.',
'Running Test', wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
prep_workflow(sublist[0], c, strategies, 0)
except:
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.',
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You can safely' \
' save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()
def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration"
button in the pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will
be using with the config they are building). Then it builds the
pipeline but does not run it. It then reports whether or not the
config will run or not depending on if the pipeline gets built
successfully.
'''
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline configuration.' \
' Click OK to provide a subject list you will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(self,
message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
# Load and test the subject list
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
sub_flg = self.test_sublist(sublist)
if not sub_flg:
raise Exception
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
for page in self.nb.get_page_list():
switch = page.page.get_switch()
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
if switch_val == 'on' or switch_val == 'true' or switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
# option_name will be the selection name as it is written
# as the dictionary key of the config.yml dictionary
option_name = ctrl.get_name()
#validating
if (switch == None or validate) and ctrl.get_validation() \
and (option_name != 'derivativeList') and (option_name != 'modelConfigs'):
win = ctrl.get_ctrl()
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win,
"%s field is empty or the items are not checked!"
% ctrl.get_name(), False)
return
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not isinstance(
value, list):
if not os.path.exists(
ctrl.get_selection()) and value != 'On/Off':
display(
win,
"%s field contains incorrect path. Please update the path!"
% ctrl.get_name())
return
config_list.append(ctrl)
# Get the user's CPAC output directory for use in this script
for config in config_list:
if config.get_name() == 'outputDirectory':
outDir = config.get_selection()
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
self.write(outDir + 'testConfig.yml', config_list)
c = Configuration(
yaml.load(
open(os.path.realpath(outDir + 'testConfig.yml'), 'r')))
os.remove(outDir + 'testConfig.yml')
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Corrections != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
testDlg1 = wx.MessageDialog(
self,
'Click OK to run the test. This should take only a few seconds.',
'Running Test', wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
# Check file paths first
# Just getting proper names of config file parameters
try:
params_file = open(
p.resource_filename('CPAC',
'GUI/resources/config_parameters.txt'),
"r")
except:
print "Error: Could not open configuration parameter file.", "\n"
raise Exception
paramInfo = params_file.read().split('\n')
paramList = []
for param in paramInfo:
if param != '':
paramList.append(param.split(','))
# function for file path checking
def testFile(filepath, paramName, switch):
try:
if (1 in switch) and (filepath != None):
fileTest = open(filepath)
fileTest.close()
except:
testDlg1.Destroy()
for param in paramList:
if param[0] == paramName:
paramTitle = param[1]
paramGroup = param[2]
break
errDlgFileTest = wx.MessageDialog(
self, 'Error reading file - either it does not exist or you' \
' do not have read access. \n\n' \
'Parameter: %s \n' \
'In tab: %s \n\n' \
'Path: %s' % (paramTitle, paramGroup, filepath),
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlgFileTest.ShowModal()
errDlgFileTest.Destroy()
testFile(c.template_brain_only_for_anat,
'template_brain_only_for_anat',
c.runRegistrationPreprocessing)
testFile(c.template_skull_for_anat, 'template_skull_for_anat',
c.runRegistrationPreprocessing)
testFile(c.PRIORS_WHITE, 'PRIORS_WHITE',
c.runSegmentationPreprocessing)
testFile(c.PRIORS_GRAY, 'PRIORS_GRAY', c.runSegmentationPreprocessing)
testFile(c.PRIORS_CSF, 'PRIORS_CSF', c.runSegmentationPreprocessing)
testFile(c.template_brain_only_for_func,
'template_brain_only_for_func', c.runRegisterFuncToMNI)
testFile(c.template_skull_for_func, 'template_skull_for_func',
c.runRegisterFuncToMNI)
testFile(c.identityMatrix, 'identityMatrix', c.runRegisterFuncToMNI)
testFile(c.boundaryBasedRegistrationSchedule,
'boundaryBasedRegistrationSchedule', c.runRegisterFuncToAnat)
testFile(c.lateral_ventricles_mask, 'lateral_ventricles_mask',
c.runNuisance)
testFile(c.seedSpecificationFile, 'seedSpecificationFile', [1])
testFile(c.roiSpecificationFile, 'roiSpecificationFile',
c.runROITimeseries)
testFile(c.roiSpecificationFileForSCA, 'roiSpecificationFileForSCA',
c.runROITimeseries)
testFile(c.maskSpecificationFile, 'maskSpecificationFile',
c.runVoxelTimeseries)
testFile(c.maskSpecificationFileForSCA, 'maskSpecificationFileForSCA',
c.runVoxelTimeseries)
testFile(c.spatialPatternMaps, 'spatialPatternMaps',
c.runSpatialRegression)
testFile(c.template_symmetric_brain_only,
'template_symmetric_brain_only', c.runVMHC)
testFile(c.template_symmetric_skull, 'template_symmetric_skull',
c.runVMHC)
testFile(c.dilated_symmetric_brain_mask,
'dilated_symmetric_brain_mask', c.runVMHC)
testFile(c.configFileTwomm, 'configFileTwomm', c.runVMHC)
testFile(c.templateSpecificationFile, 'templateSpecificationFile',
c.runNetworkCentrality)
testFile(c.bascAffinityThresholdFile, 'bascAffinityThresholdFile',
c.runBASC)
testFile(c.cwasROIFile, 'cwasROIFile', c.runCWAS)
testFile(c.cwasRegressorFile, 'cwasRegressorFile', c.runCWAS)
try:
# Run the pipeline building
prep_workflow(sublist[0], c, strategies, 0)
except Exception as xxx:
print xxx
print "an exception occured"
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,
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You can safely' \
' save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()
def testConfig(self, event):
'''
This function runs when the user clicks the "Test Configuration" button in the
pipeline configuration window.
It prompts the user for a sample subject list (i.e. one that they will be using
with the config they are building). Then it builds the pipeline but does not
run it. It then reports whether or not the config will run or not depending
on if the pipeline gets built successfully.
'''
import os
import yaml
from CPAC.utils import Configuration
from CPAC.pipeline.cpac_pipeline import prep_workflow
from CPAC.pipeline.cpac_runner import build_strategies
def display(win, msg, changeBg=True):
wx.MessageBox(msg, "Error")
if changeBg:
win.SetBackgroundColour("pink")
win.SetFocus()
win.Refresh()
# Collect a sample subject list and parse it in
testDlg0 = wx.MessageDialog(
self, 'This tool will run a quick check on the current pipeline configuration.' \
' Click OK to provide a subject list you will be using with this setup.',
'Subject List',
wx.OK | wx.ICON_INFORMATION)
testDlg0.ShowModal()
testDlg0.Destroy()
dlg = wx.FileDialog(
self, message="Choose the CPAC Subject list file",
defaultDir=os.getcwd(),
defaultFile="CPAC_subject_list.yml",
wildcard="YAML files(*.yaml, *.yml)|*.yaml;*.yml",
style=wx.OPEN | wx.CHANGE_DIR)
if dlg.ShowModal() == wx.ID_OK:
subListPath = dlg.GetPath()
sublist = yaml.load(open(os.path.realpath(subListPath), 'r'))
# Check to ensure the user is providing an actual subject
# list and not some other kind of file
try:
subInfo = sublist[0]
except:
errDlg4 = wx.MessageDialog(
self, 'ERROR: Subject list file not in proper format - check if you' \
' loaded the correct file? \n\n' \
'Error name: config_window_0001',
'Subject List Error',
wx.OK | wx.ICON_ERROR)
errDlg4.ShowModal()
errDlg4.Destroy()
raise Exception
# Another check to ensure the actual subject list was generated
# properly and that it will work
if 'subject_id' not in subInfo:
errDlg3 = wx.MessageDialog(
self, 'ERROR: Subject list file not in proper format - check if you' \
' loaded the correct file? \n\n' \
'Error name: config_window_0002',
'Subject List Error',
wx.OK | wx.ICON_ERROR)
errDlg3.ShowModal()
errDlg3.Destroy()
raise Exception
# Following code reads in the parameters and selections from the
# pipeline configuration window and populate the config_list
config_list = []
wf_counter = []
#print "self.nb.get_page_list()", self.nb.get_page_list()
for page in self.nb.get_page_list():
#print "page ----> ", page
switch = page.page.get_switch()
#print "switch ---->", switch
ctrl_list = page.page.get_ctrl_list()
validate = False
if switch:
switch_val = str(switch.get_selection()).lower()
#print "switch_val ---->", switch_val
if switch_val == 'on' or switch_val == 'true' or switch_val == '1':
validate = True
wf_counter.append(page.get_counter())
for ctrl in ctrl_list:
#validating
if (switch == None or validate) and ctrl.get_validation():
win = ctrl.get_ctrl()
#print "validating ctrl-->", ctrl.get_name()
#print "ctrl.get_selection()", ctrl.get_selection()
#print "type(ctrl.get_selection())", type(ctrl.get_selection())
if isinstance(ctrl.get_selection(), list):
value = ctrl.get_selection()
if not value:
display(
win, "%s field is empty or the items are not checked!" % ctrl.get_name(), False)
return
else:
value = str(ctrl.get_selection())
if len(value) == 0:
display(win, "%s field is empty!" % ctrl.get_name())
return
if '/' in value and '$' not in value and not isinstance(value, list):
if not os.path.exists(ctrl.get_selection()):
display(
win, "%s field contains incorrect path. Please update the path!" % ctrl.get_name())
return
config_list.append(ctrl)
# Get the user's CPAC output directory for use in this script
for config in config_list:
#print config.get_name(), " ", config.get_selection()
if config.get_name() == 'outputDirectory':
outDir = config.get_selection()
# Write out a pipeline_config file, read it in and then delete it
# (Will revise the data structure of the config files later so this
# can just pass the data structure instead of doing it this way)
try:
self.write(outDir + 'testConfig.yml', config_list)
c = Configuration(yaml.load(open(os.path.realpath(outDir + 'testConfig.yml'), 'r')))
os.remove(outDir + 'testConfig.yml')
except:
errDlg2 = wx.MessageDialog(
self, 'A problem occurred with preparing the pipeline test run. \n\n' \
'Please ensure you have rights access to the directories you' \
' have chosen for the CPAC working, crash, and output folders.',
'Test Configuration Error',
wx.OK | wx.ICON_ERROR)
errDlg2.ShowModal()
errDlg2.Destroy()
if (1 in c.runNuisance) or (c.Corrections != None):
strategies = sorted(build_strategies(c))
else:
strategies = None
# Run the actual pipeline building prep and see if it works or not
try:
testDlg1 = wx.MessageDialog(
self, 'Click OK to run the test. This should take only a few seconds.',
'Running Test',
wx.OK | wx.ICON_INFORMATION)
testDlg1.ShowModal()
prep_workflow(sublist[0], c, strategies, 0)
except:
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.',
'Pipeline Not Ready',
wx.OK | wx.ICON_ERROR)
errDlg1.ShowModal()
errDlg1.Destroy()
else:
testDlg1.Destroy()
okDlg1 = wx.MessageDialog(
self, 'The current configuration will run successfully. You can safely' \
' save and run this setup!',
'Pipeline Ready',
wx.OK | wx.ICON_INFORMATION)
okDlg1.ShowModal()
okDlg1.Destroy()