def check_configuration_version(config):
"""Check the version of CMP3 used to generate a configuration.
Parameters
----------
config : Dict
Dictionary of configuration parameters loaded from JSON file
Returns
-------
is_same : bool
`True` if the version used to generate the
configuration matches the version currently used
(`cmp.info.__version__`).
"""
is_same = False
if 'version' in config['Global'].keys():
if config['Global']['version'] == __version__:
print(BColors.OKGREEN +
' .. INFO: Generated with the same CMP3 version' +
BColors.ENDC)
is_same = True
else:
conf_version = config['Global']['version']
print_warning(' .. WARNING: CMP3 version used to generate the ' +
f'configuration files ({conf_version}) ' +
f' and version of CMP3 used ({__version__}) differ')
is_same = False
return is_same
def refresh_folder(derivatives_directory,
subject,
input_folders,
session=None):
"""Creates (if needed) the folder hierarchy.
Parameters
----------
derivatives_directory : string
subject : string
Subject label (``sub-XX``) for which we create the output folder hierarchy
session : string
Subject session label (``ses-YY``)
input_folders : list of string
List of folders to create in ``derivative_directory/sub-XX/(ses-YY)/`` folder
for the given ``subject``
"""
paths = []
if session is None or session == "":
paths.append(
os.path.join(derivatives_directory, __freesurfer_directory__,
subject))
paths.append(
os.path.join(derivatives_directory, __cmp_directory__, subject))
paths.append(
os.path.join(derivatives_directory, __nipype_directory__, subject))
for in_f in input_folders:
paths.append(
os.path.join(derivatives_directory, __cmp_directory__, subject,
in_f))
else:
paths.append(
os.path.join(derivatives_directory, __freesurfer_directory__,
"%s_%s" % (subject, session)))
paths.append(
os.path.join(derivatives_directory, __cmp_directory__, subject,
session))
paths.append(
os.path.join(derivatives_directory, __nipype_directory__, subject,
session))
for in_f in input_folders:
paths.append(
os.path.join(derivatives_directory, __cmp_directory__, subject,
session, in_f))
for full_p in paths:
if not os.path.exists(full_p):
try:
os.makedirs(full_p)
except os.error:
print_warning(" .. INFO: %s was already existing" % full_p)
finally:
print(" .. INFO: Created directory %s" % full_p)
def info():
"""Print version and copyright information."""
print("\nConnectome Mapper {} - BIDS App Manager ".format(__version__))
print_warning("------------------------------------------------------")
print_warning("""{}""".format(__copyright__))
print_warning("------------------------------------------------------")
print("------------------------------------------------------")
print(" .. INFO: Use {} for graphical backend".format(ETSConfig.toolkit))
print("------------------------------------------------------\n")
def clean_cache(bids_root):
"""Clean cache stored in /tmp.
Target issue related to that a dataset directory is mounted into /tmp and
used for caching by java/matlab/matplotlib/xvfb-run in the container image.
Parameters
----------
bids_root : string
BIDS root dataset directory
"""
print_warning("> Clean generated docker image cache")
for d in glob.glob(os.path.join(bids_root, " hsperfdata_cmp")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for f in glob.glob(os.path.join(bids_root, "._java*")):
print_warning("... DEL: {}".format(f))
os.remove(f)
for f in glob.glob(os.path.join(bids_root, "mri_segstats.tmp*")):
print_warning("... DEL: {}".format(f))
os.remove(f)
for d in glob.glob(os.path.join(bids_root, "MCR_*")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for d in glob.glob(os.path.join(bids_root, "matplotlib*")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for d in glob.glob(os.path.join(bids_root, "xvfb-run.*")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for d in glob.glob(os.path.join(bids_root, ".X11*")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for d in glob.glob(os.path.join(bids_root, ".X11-unix")):
print_warning("... DEL: {}".format(d))
shutil.rmtree(d)
for f in glob.glob(os.path.join(bids_root, ".X99*")):
print_warning("... DEL: {}".format(f))
os.remove(d)
def init_dmri_project(project_info, bids_layout, is_new_project, gui=True):
"""Create and initialize a :class:`DiffusionPipelineUI` instance
Parameters
----------
project_info : ProjectInfoUI
Instance of :class:`ProjectInfoUI` class
bids_layout : bids.BIDSLayout
PyBIDS BIDS Layout object describing the BIDS dataset
is_new_project : bool
If True, this is a new project which has been never processed
gui : bool
If True, display messages in GUI
"""
dmri_pipeline = diffusion_pipeline.DiffusionPipelineUI(project_info)
derivatives_directory = os.path.join(project_info.base_directory,
"derivatives")
if (project_info.subject_session != "") and (project_info.subject_session
is not None):
refresh_folder(
derivatives_directory,
project_info.subject,
dmri_pipeline.input_folders,
session=project_info.subject_session,
)
else:
refresh_folder(derivatives_directory, project_info.subject,
dmri_pipeline.input_folders)
dmri_inputs_checked = dmri_pipeline.check_input(layout=bids_layout,
gui=gui)
if dmri_inputs_checked:
if is_new_project and dmri_pipeline is not None:
print("> Initialize dMRI project")
if not os.path.exists(derivatives_directory):
try:
os.makedirs(derivatives_directory)
except os.error:
print_warning(" .. INFO: %s was already existing" %
derivatives_directory)
finally:
print(" .. INFO: Created directory %s" %
derivatives_directory)
if (project_info.subject_session !=
"") and (project_info.subject_session is not None):
project_info.dmri_config_file = os.path.join(
derivatives_directory,
"%s_%s_diffusion_config.json" %
(project_info.subject, project_info.subject_session),
)
else:
project_info.dmri_config_file = os.path.join(
derivatives_directory,
"%s_diffusion_config.json" % project_info.subject,
)
if os.path.exists(project_info.dmri_config_file):
warn_res = project_info.configure_traits(
view="dmri_warning_view")
if warn_res:
print(" .. INFO: Read diffusion config file (%s)" %
project_info.dmri_config_file)
dmri_save_config(dmri_pipeline,
project_info.dmri_config_file)
else:
return None
else:
print(" .. INFO: Create diffusion config file (%s)" %
project_info.dmri_config_file)
dmri_save_config(dmri_pipeline, project_info.dmri_config_file)
else:
print("> Load dMRI project")
dmri_conf_loaded = dmri_load_config_json(
dmri_pipeline, project_info.dmri_config_file)
if not dmri_conf_loaded:
return None
dmri_pipeline.config_file = project_info.dmri_config_file
else:
print_error(" .. ERROR: Missing diffusion inputs")
return dmri_inputs_checked, dmri_pipeline
def info():
"""Print version of copyright."""
print_blue(f"\nConnectome Mapper {__version__}")
print_warning(f"{__copyright__}\n")
def save_configparser_as_json(config,
config_json_path,
ini_mode=False,
debug=False):
"""Save a ConfigParser to JSON file.
Parameters
----------
config : Instance(configparser.ConfigParser)
Instance of ConfigParser
config_json_path : string
Output path of JSON configuration file
ini_mode : bool
If `True`, handles all content stored in strings
debug : bool
If `True`, show additional prints
"""
config_json = {}
# In the case of diffusion pipeline
if 'diffusion_stage' in config.sections():
recon_processing_tool = config['diffusion_stage'].get(
'recon_processing_tool')
tracking_processing_tool = config['diffusion_stage'].get(
'tracking_processing_tool')
for section in config.sections():
config_json[section] = {}
for name, value in config.items(section):
# Keep only parameters that are used by the diffusion stage
# of the diffusion pipeline. This simplifies the reading of
# its configuration file
if 'diffusion_stage' in section:
# Skip adding diffusion reconstruction parameters
if recon_processing_tool == 'Dipy':
if 'mrtrix_recon_config' in name:
continue
elif recon_processing_tool == 'MRtrix':
if 'dipy_recon_config' in name:
continue
# Skip adding tracking parameters
if tracking_processing_tool == 'Dipy':
if 'mrtrix_tracking_config' in name:
continue
elif tracking_processing_tool == 'MRtrix':
if 'dipy_tracking_config' in name:
continue
if '_editor' in name:
if debug:
print_warning(
f' .. DEBUG: Skip parameter {section} / {name}')
continue
if 'log_visualization' in name:
if debug:
print_warning(
f' .. DEBUG: Skip parameter {section} / {name}')
continue
if 'circular_layout' in name:
if debug:
print_warning(
f' .. DEBUG: Skip parameter {section} / {name}')
continue
is_iterable = False
if ini_mode:
try:
if not (section == 'parcellation_stage'
and name == 'ants_precision_type'):
value = eval(value)
if debug:
print_warning(
f' .. DEBUG: String {value} evaluated')
else:
if debug:
print_warning(
f' .. DEBUG: String {value} not evaluated')
except Exception:
if debug:
print_error(
f' .. EXCEPTION: String {value} COULD NOT BE evaluated'
)
pass
if isinstance(value, dict):
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as dict'
)
config_json[section][name] = value
is_iterable = True
elif isinstance(value, list):
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as list'
)
config_json[section][name] = value
is_iterable = True
elif isinstance(value, Iterable) and not isinstance(value, str):
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as iterable'
)
config_json[section][name] = [x for x in value if x]
is_iterable = True
elif isinstance(value, bool):
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as boolean'
)
config_json[section][name] = [value]
elif value and not isinstance(value, str):
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as not a string'
)
config_json[section][name] = [value]
elif value and isinstance(value, str):
value = value.strip()
if value.isnumeric():
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as number'
)
value = float(value)
if value.is_integer():
value = int(value)
config_json[section][name] = [value]
else:
if debug:
print_warning(
f' .. DEBUG: Processing {section} / {name} / {value} as string'
)
config_json[section][name] = [value]
else:
if debug:
print_warning(
f' .. DEBUG : Type: {type(value)} / value : {value}')
config_json[section][name] = ''
if not is_iterable:
if len(config_json[section][name]) == 1:
config_json[section][name] = config_json[section][name][0]
elif len(config_json[section][name]) == 0:
config_json[section][name] = ''
if config_json[section][name] == '':
del config_json[section][name]
config_json['Global']['version'] = __version__
if debug:
print_blue(f' .. DEBUG: {config_json}')
with open(config_json_path, 'w') as outfile:
json.dump(config_json, outfile, indent=4)
def set_pipeline_attributes_from_config(pipeline, config, debug=False):
"""Set the pipeline stage attributes given a configuration.
Parameters
----------
pipeline : Instance(Pipeline)
Instance of pipeline
config : Dict
Dictionary of configuration parameter loaded
from the JSON configuration file
debug : bool
If `True`, show additional prints
"""
global_keys = [
prop for prop in list(pipeline.global_conf.traits().keys())
if 'trait' not in prop
] # possibly dangerous..?
for key in global_keys:
if key != "subject" and \
key != "subjects" and \
key != "subject_session" and \
key != "subject_sessions":
if key in config['Global'].keys():
conf_value = config['Global'][key]
setattr(pipeline.global_conf, key, conf_value)
for stage in list(pipeline.stages.values()):
stage_keys = [
prop for prop in list(stage.config.traits().keys())
if 'trait' not in prop
] # possibly dangerous..?
for key in stage_keys:
if 'config' in key: # subconfig
sub_config = getattr(stage.config, key)
stage_sub_keys = [
prop for prop in list(sub_config.traits().keys())
if 'trait' not in prop
]
for sub_key in stage_sub_keys:
if stage.name in config.keys():
tmp_key = key + '.' + sub_key
if tmp_key in config[stage.name].keys():
conf_value = config[stage.name][tmp_key]
try:
# Convert parameter to proper expected type
if isinstance(getattr(sub_config, sub_key),
tuple):
conf_value = tuple(conf_value)
elif isinstance(getattr(sub_config, sub_key),
bool):
conf_value = bool(conf_value)
elif isinstance(getattr(sub_config, sub_key),
list):
conf_value = list(conf_value)
elif isinstance(getattr(sub_config, sub_key),
dict):
conf_value = dict(conf_value)
elif isinstance(getattr(sub_config, sub_key),
int):
conf_value = int(float(conf_value))
elif isinstance(getattr(sub_config, sub_key),
float):
conf_value = float(conf_value)
setattr(sub_config, sub_key, conf_value)
if debug:
print(
f' .. DEBUG: Set {sub_config}.{sub_key} to {conf_value}'
)
except Exception as e:
if debug:
print_warning(
' .. EXCEPTION raised while setting '
+
f'{sub_config}.{sub_key} to {conf_value}'
)
print_error(f' {e}')
pass
else:
if stage.name in config.keys():
if key in config[stage.name].keys():
conf_value = config[stage.name][key]
try:
# Convert parameter to proper expected type
if isinstance(getattr(stage.config, key), tuple):
conf_value = tuple(conf_value)
elif isinstance(getattr(stage.config, key), bool):
conf_value = bool(conf_value)
elif isinstance(getattr(stage.config, key), list):
conf_value = list(conf_value)
elif isinstance(getattr(stage.config, key), dict):
conf_value = dict(conf_value)
elif isinstance(getattr(stage.config, key), int):
conf_value = int(float(conf_value))
elif isinstance(getattr(stage.config, key), float):
conf_value = float(conf_value)
setattr(stage.config, key, conf_value)
if debug:
print(
f' .. DEBUG: Set {stage.config}.{key} to {conf_value}'
)
except Exception as e:
if debug:
print_warning(
' .. EXCEPTION raised while setting ' +
f'{stage.config}.{key} to {conf_value}')
print_error(f' {e}')
pass
setattr(pipeline, 'number_of_cores',
int(config['Multi-processing']['number_of_cores']))
def create_subject_configuration_from_ref(project,
ref_conf_file,
pipeline_type,
multiproc_number_of_cores=1):
"""Create the pipeline configuration file for an individual subject from a reference given as input.
Parameters
----------
project : cmp.project.CMP_Project_Info
Instance of `cmp.project.CMP_Project_Info`
ref_conf_file : string
Reference configuration file
pipeline_type : 'anatomical', 'diffusion', 'fMRI'
Type of pipeline
multiproc_number_of_cores : int
Number of threads used by Nipype
Returns
-------
subject_conf_file : string
Configuration file of the individual subject
"""
subject_derivatives_dir = os.path.join(project.output_directory)
# print('project.subject_session: {}'.format(project.subject_session))
if project.subject_session != '': # Session structure
# print('With session : {}'.format(project.subject_session))
subject_conf_file = os.path.join(
subject_derivatives_dir, 'cmp', project.subject,
project.subject_session,
"{}_{}_{}_config.json".format(project.subject,
project.subject_session,
pipeline_type))
else:
# print('With NO session ')
subject_conf_file = os.path.join(
subject_derivatives_dir, 'cmp', project.subject,
"{}_{}_config.json".format(project.subject, pipeline_type))
if os.path.isfile(subject_conf_file):
print_warning(
" .. WARNING: rewriting config file {}".format(subject_conf_file))
os.remove(subject_conf_file)
# Change relative path to absolute path if needed (required when using singularity)
if not os.path.isabs(ref_conf_file):
ref_conf_file = os.path.abspath(ref_conf_file)
with open(ref_conf_file, 'r') as f:
config = json.load(f)
config['Global']['subject'] = project.subject
config['Global']['subjects'] = project.subjects
if 'subject_sessions' in config['Global'].keys():
config['Global']['subject_sessions'] = project.subject_sessions
if 'subject_session' in config['Global'].keys():
config['Global']['subject_session'] = project.subject_session
config['Multi-processing']['number_of_cores'] = multiproc_number_of_cores
with open(subject_conf_file, 'w') as outfile:
json.dump(config, outfile, indent=4)
return subject_conf_file