MAINT: Review all print output generated by the GUI

cmp/bidsappmanager/gui.py

@@ -34,7 +34,7 @@
 from cmp.info import __version__
 
 from cmtklib.util import return_button_style_sheet, \
- print_blue, print_warning, print_error
+ BColors, print_blue, print_warning, print_error
 
 # Remove warnings visible whenever you import scipy (or another package) 
 # that was compiled against an older numpy than is installed.
@@ -910,6 +910,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  fmri_config : string
  Path to functional pipeline configuration file (Default: \'\')
  """
+ print('> Initialize window...')
  if multiprocessing.cpu_count() < 4:
  self.number_of_threads_max = multiprocessing.cpu_count()
 
@@ -920,7 +921,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  try:
  bids_layout = BIDSLayout(self.bids_root)
  except Exception:
- print_error("Exception : Raised at BIDSLayout")
+ print_error(" .. Exception : Raised at BIDSLayout")
  sys.exit(1)
 
  # Check if sMRI data is available in the dataset
@@ -934,7 +935,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  else:
  anat_inputs_checked = True
 
- print(f'T1w available: {anat_inputs_checked}')
+ print(f' .. T1w available: {anat_inputs_checked}')
 
  # Check if dMRI data is available in the dataset
  dmri_files = bids_layout.get(datatype='dwi',
@@ -949,7 +950,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  self.dmri_inputs_checked = True
  self.run_dmri_pipeline = True
 
- print(f'DWI available: {self.dmri_inputs_checked}')
+ print(f' .. DWI available: {self.dmri_inputs_checked}')
 
  # Check if fMRI data is available in the dataset
  fmri_files = bids_layout.get(task='rest',
@@ -964,7 +965,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  self.fmri_inputs_checked = True
  self.run_fmri_pipeline = True
 
- print(f'rsfMRI available: {self.fmri_inputs_checked}')
+ print(f' .. rsfMRI available: {self.fmri_inputs_checked}')
 
  # Initialize output directory to be /bids_dir/derivatives
  self.output_dir = os.path.join(bids_root, 'derivatives')
@@ -979,7 +980,7 @@ def __init__(self, project_info=None, bids_root='', subjects=None, list_of_subje
  self.fs_license = os.path.join(
  os.environ['FREESURFER_HOME'], 'license.txt')
  else:
- print_error('Environment variable $FREESURFER_HOME not found')
+ print_error(' .. ERROR: Environment variable $FREESURFER_HOME not found')
  self.fs_license = ''
  print_warning('Freesurfer license unset ({})'.format(self.fs_license))
 
@@ -1012,12 +1013,12 @@ def number_of_parallel_procs_updated(self, new):
  else:
  self.number_of_threads_max = number_of_threads_max
 
- print('Update number of threads max to : {}'.format(self.number_of_threads_max))
+ print(' .. INFO : Update number of threads max to : {}'.format(self.number_of_threads_max))
 
  def update_run_anat_pipeline(self, new):
  """Callback function when ``run_anat_pipeline`` is updated."""
  if new is False:
- print('At least anatomical pipeline should be run!')
+ print_warning(' .. WARNING: At least anatomical pipeline should be run!')
  self.run_anat_pipeline = True
 
  def update_run_dmri_pipeline(self, new):
@@ -1059,19 +1060,19 @@ def check_settings(self):
  self.settings_checked = True
 
  if os.path.isdir(self.bids_root):
- print(f'BIDS root directory : {self.bids_root}')
+ print(f'* BIDS root directory : {self.bids_root}')
  else:
  print_error("Error: BIDS root invalid!")
  self.settings_checked = False
 
  if os.path.exists(os.path.join(self.output_dir, 'cmp')):
- print(f'Output directory (existing) : {self.output_dir}')
+ print(f'* Output directory (existing) : {self.output_dir}')
  else:
  os.makedirs(os.path.join(self.output_dir, 'cmp'))
  print_warning(f'Output directory (created) : {self.output_dir}')
 
  if len(self.list_of_subjects_to_be_processed) > 0:
- print(f'Participant labels to be processed : {self.list_of_subjects_to_be_processed}')
+ print(f'* Participant labels to be processed : {self.list_of_subjects_to_be_processed}')
  else:
  print_error("Error: At least one participant label to be processed should selected!")
  self.settings_checked = False
@@ -1081,23 +1082,23 @@ def check_settings(self):
  # print("Warning: List of subjects empty!")
 
  if os.path.isfile(self.anat_config):
- print(f'Anatomical configuration file : {self.anat_config}')
+ print(f'* Anatomical configuration file : {self.anat_config}')
  else:
  print_error("Error: Configuration file for anatomical pipeline not existing!")
  self.settings_checked = False
 
  if os.path.isfile(self.dmri_config):
- print(f'Diffusion configuration file : {self.dmri_config}')
+ print(f'* Diffusion configuration file : {self.dmri_config}')
  else:
  print_warning("Warning: Configuration file for diffusion pipeline not existing!")
 
  if os.path.isfile(self.fmri_config):
- print(f'fMRI configuration file : {self.fmri_config}')
+ print(f'* fMRI configuration file : {self.fmri_config}')
  else:
  print_warning("Warning: Configuration file for fMRI pipeline not existing!")
 
  if os.path.isfile(self.fs_license):
- print(f'Freesurfer license : {self.fs_license}')
+ print(f'* Freesurfer license : {self.fs_license}')
  else:
  print_error(f'Error: Invalid Freesurfer license ({self.fs_license})!')
  self.settings_checked = False
@@ -1205,13 +1206,6 @@ def start_bidsapp_participant_level_process(self, bidsapp_tag, participant_label
 
  print_blue('... BIDS App execution command: {}'.format(' '.join(cmd)))
 
- # log_filename = os.path.join(
- # self.bids_root, 'derivatives', 'cmp', 'main_log-cmpbidsapp.txt')
-
- # with open(log_filename, 'w+') as log:
- # proc = Popen(cmd, stdout=log, stderr=log)
- # #docker_process.communicate()
-
  proc = Popen(cmd)
  # proc = Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
 
@@ -1290,17 +1284,7 @@ def start_bidsapp_participant_level_process_with_datalad(self, bidsapp_tag, part
 
  print_blue('... Datalad cmd : {}'.format(' '.join(cmd)))
 
- # log_filename = os.path.join(self.bids_root,'derivatives','cmp','main-datalad_log-cmpbidsapp.txt')
-
- # if not os.path.exists(os.path.join(self.bids_root,'derivatives','cmp')):
- # os.makedirs(os.path.join(self.bids_root,'derivatives','cmp'))
-
- # with open(log_filename, 'a+') as log:
- # proc = Popen(cmd, stdout=log, stderr=log, cwd=os.path.join(self.bids_root))
- # #docker_process.communicate()
-
  proc = Popen(cmd, cwd=os.path.join(self.bids_root))
-
  # proc = Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, cwd=os.path.join(self.bids_root,'derivatives'))
 
  return proc
@@ -1357,15 +1341,18 @@ def run(self, command, env=None, cwd=os.getcwd()):
  if line == '' and process.poll() is not None:
  break
  if process.returncode != 0:
- raise Exception("Non zero return code: %d" % process.returncode)
+ raise Exception(
+ BColors.FAIL +
+ f'Non zero return code: {process.returncode}' +
+ BColors.ENDC)
 
  def start_bids_app(self):
  """Function executed when the Run BIDS App button is clicked.
 
  It implements all steps in the creation and execution of the BIDS App
  with or without datalad.
  """
- print_blue("Start BIDS App")
+ print_blue("[Run BIDS App]")
 
  # Copy freesurfer license into dataset/code directory at the location
  # the BIDS app expects to find it.
@@ -1782,6 +1769,7 @@ def __init__(self, project_info=None, anat_pipeline=None, dmri_pipeline=None, fm
  Boolean that indicates if functional pipeline inputs are available
  (Default: False)
  """
+ print('> Initialize window...')
  self.project_info = project_info
 
  self.anat_pipeline = anat_pipeline
@@ -1805,25 +1793,25 @@ def update_diffusion_imaging_model(self, new):
  self.dmri_pipeline.diffusion_imaging_model = new
 
  def _save_all_config_fired(self):
- print('Saving pipeline configuration files...')
+ print_blue('[Save all pipeline configuration files]')
 
  if self.anat_inputs_checked:
  anat_config_file = os.path.join(
  self.project_info.base_directory, 'code', 'ref_anatomical_config.json')
  project.anat_save_config(self.anat_pipeline, anat_config_file)
- print('Anatomical config saved as {}'.format(anat_config_file))
+ print(' * Anatomical config saved as {}'.format(anat_config_file))
 
  if self.dmri_inputs_checked:
  dmri_config_file = os.path.join(
  self.project_info.base_directory, 'code', 'ref_diffusion_config.json')
  project.dmri_save_config(self.dmri_pipeline, dmri_config_file)
- print('Diffusion config saved as {}'.format(dmri_config_file))
+ print(' * Diffusion config saved as {}'.format(dmri_config_file))
 
  if self.fmri_inputs_checked:
  fmri_config_file = os.path.join(
  self.project_info.base_directory, 'code', 'ref_fMRI_config.json')
  project.fmri_save_config(self.fmri_pipeline, fmri_config_file)
- print('fMRI config saved as {}'.format(fmri_config_file))
+ print(' * fMRI config saved as {}'.format(fmri_config_file))
 
 
 # Window class of the ConnectomeMapper_Pipeline Quality Inspector
@@ -1952,6 +1940,7 @@ def __init__(self, project_info=None, anat_inputs_checked=False, dmri_inputs_che
  Boolean that indicates if functional pipeline inputs are available
  (Default: False)
  """
+ print('> Initialize window...')
  self.project_info = project_info
 
  self.anat_inputs_checked = anat_inputs_checked
@@ -1962,11 +1951,14 @@ def __init__(self, project_info=None, anat_inputs_checked=False, dmri_inputs_che
 
  if aborded:
  raise Exception(
- 'ABORDED: The quality control window will not be displayed.'
- 'Selection of subject/session was cancelled at initialization.')
+ BColors.FAIL +
+ ' .. ABORDED: The quality control window will not be displayed.' +
+ 'Selection of subject/session was cancelled at initialization.' +
+ BColors.ENDC)
 
  def select_subject(self):
  """Function to select the subject and session for which to inspect outputs."""
+ print('> Selection of subject (and session) for which to inspect outputs')
  valid_selected_subject = False
  select = True
  aborded = False
@@ -1980,7 +1972,7 @@ def select_subject(self):
  aborded = True
  break
 
- print("Selected subject: {}".format(self.project_info.subject))
+ print(" .. INFO: Selected subject: {}".format(self.project_info.subject))
 
  # Select session if any
  bids_layout = BIDSLayout(self.project_info.base_directory)
@@ -1990,7 +1982,7 @@ def select_subject(self):
  target='session', return_type='id', subject=subject)
 
  if len(sessions) > 0:
- print("Detected sessions")
+ print(" .. INFO: Input dataset has sessions")
  print(sessions)
 
  self.project_info.subject_sessions = []
@@ -2067,14 +2059,14 @@ def select_subject(self):
  # if self.fmri_pipeline is not None:
  # self.fmri_pipeline.global_conf.subject_session = self.project_info.subject_session
 
- print("Selected session %s" %
+ print(" .. INFO: Selected session %s" %
  self.project_info.subject_session)
  if self.anat_pipeline is not None:
  self.anat_pipeline.stages['Segmentation'].config.freesurfer_subject_id = os.path.join(
  self.project_info.base_directory, 'derivatives', 'freesurfer',
  '{}_{}'.format(self.project_info.subject, self.project_info.subject_session))
  else:
- print("No session detected")
+ print(" .. INFO: No session detected")
  self.project_info.anat_config_file = os.path.join(self.project_info.base_directory, 'derivatives',
  'cmp', '{}'.format(
  self.project_info.subject),
@@ -2152,16 +2144,17 @@ def select_subject(self):
  if (len(stage.inspect_outputs) > 0) and (stage.inspect_outputs[0] != 'Outputs not available'):
  self.output_fmri_available = True
 
- print_blue("Anatomical output(s) available : %s" %
+ print_blue(" .. Anatomical output(s) available : %s" %
  self.output_anat_available)
- print_blue("Diffusion output(s) available : %s" %
+ print_blue(" .. Diffusion output(s) available : %s" %
  self.output_dmri_available)
- print_blue("fMRI output(s) available : %s" % self.output_fmri_available)
+ print_blue(" .. fMRI output(s) available : %s" % self.output_fmri_available)
 
  if self.output_anat_available or self.output_dmri_available or self.output_fmri_available:
  valid_selected_subject = True
  else:
- self.error_msg = "No output available! Please select another subject (and session if any)!"
+ self.error_msg = " .. ERROR: No output available! " +\
+ "Please select another subject (and session if any)!"
  print_error(self.error_msg)
  select = error(message=self.error_msg,
  title='Error', buttons=['OK', 'Cancel'])
@@ -2240,11 +2233,6 @@ class CMP_MainWindow(HasTraits):
  spring,
  HGroup(
  Item('configurator', style='custom', width=200, height=200, resizable=False, label='', show_label=False,
- # editor_args={
- # 'image': get_icon(pkg_resources.resource_filename('cmp',
- # os.path.join('bidsappmanager/images',
- # 'configurator_200x200.png'))),
- # 'label': "", 'label_value': ""},
  style_sheet=return_button_style_sheet(
  ImageResource(
  pkg_resources.resource_filename('cmp',
@@ -2298,6 +2286,7 @@ class CMP_MainWindow(HasTraits):
 
  def _bidsapp_fired(self):
  """ Callback of the "bidsapp" button. This displays the BIDS App Interface window."""
+ print_blue("[Open BIDS App Window]")
  bids_layout = BIDSLayout(self.project_info.base_directory)
  subjects = bids_layout.get_subjects()
 
@@ -2323,19 +2312,20 @@ def _bidsapp_fired(self):
 
  def _configurator_fired(self):
  """Callback of the "configurator" button. This displays the Configurator Window."""
+ print_blue("[Open Pipeline Configurator Window]")
  if self.project_info.t1_available:
  if os.path.isfile(self.project_info.anat_config_file):
- print("Anatomical config file : %s" %
+ print(" .. Anatomical config file : %s" %
  self.project_info.anat_config_file)
 
  if self.project_info.dmri_available:
  if os.path.isfile(self.project_info.dmri_config_file):
- print("Diffusion config file : %s" %
+ print(" .. Diffusion config file : %s" %
  self.project_info.dmri_config_file)
 
  if self.project_info.fmri_available:
  if os.path.isfile(self.project_info.fmri_config_file):
- print("fMRI config file : %s" %
+ print(" .. fMRI config file : %s" %
  self.project_info.fmri_config_file)
 
  self.configurator_ui = CMP_ConfiguratorWindow(project_info=self.project_info,
@@ -2351,19 +2341,20 @@ def _configurator_fired(self):
 
  def _quality_control_fired(self):
  """Callback of the "Inspector" button. This displays the Quality Control (Inspector) Window."""
+ print_blue("[Open Quality Inspector Window]")
  if self.project_info.t1_available:
  if os.path.isfile(self.project_info.anat_config_file):
- print("Anatomical config file : %s" %
+ print(" .. Anatomical config file : %s" %
  self.project_info.anat_config_file)
 
  if self.project_info.dmri_available:
  if os.path.isfile(self.project_info.dmri_config_file):
- print("Diffusion config file : %s" %
+ print(" .. Diffusion config file : %s" %
  self.project_info.dmri_config_file)
 
  if self.project_info.fmri_available:
  if os.path.isfile(self.project_info.fmri_config_file):
- print("fMRI config file : %s" %
+ print(" .. fMRI config file : %s" %
  self.project_info.fmri_config_file)
 
  try:
@@ -2375,24 +2366,3 @@ def _quality_control_fired(self):
  self.quality_control_ui.configure_traits()
  except Exception as e:
  print(e)
-
- def show_bidsapp_interface(self):
- """Callback of the "BIDS App" button. This displays the BIDS App Interface Window."""
- bids_layout = BIDSLayout(self.project_info.base_directory)
- subjects = bids_layout.get_subjects()
-
- anat_config = os.path.join(
- self.project_info.base_directory, 'code/', 'ref_anatomical_config.json')
- dmri_config = os.path.join(
- self.project_info.base_directory, 'code/', 'ref_diffusion_config.json')
- fmri_config = os.path.join(
- self.project_info.base_directory, 'code/', 'ref_fMRI_config.json')
-
- self.bidsapp = CMP_BIDSAppWindow(project_info=self.project_info,
- bids_root=self.project_info.base_directory,
- subjects=subjects,
- list_of_subjects_to_be_processed=subjects,
- anat_config=anat_config,
- dmri_config=dmri_config,
- fmri_config=fmri_config
- )