def run(self, args, extra_args):
meta_info = mdt.get_models_meta_info()
models = mdt.get_models_list()
max_model_name = max(map(len, models))
for model in models:
if args.long:
print(('%-' + str(max_model_name + 2) + 's%-s') %
(model, meta_info[model]['description']))
else:
print(model)
def run(self, args):
mdt.init_user_settings(pass_if_exists=True)
meta_info = mdt.get_models_meta_info()
models = mdt.get_models_list()
max_model_name = max(map(len, models))
for model in models:
if args.long:
print(('%-' + str(max_model_name + 2) + 's%-s') %
(model, meta_info[model]['description']))
else:
print(model)
def setupUi(self, tab_content):
super().setupUi(tab_content)
self._tab_content = tab_content
self.selectDWI.clicked.connect(lambda: self._select_dwi())
self.selectMask.clicked.connect(lambda: self._select_mask())
self.selectProtocol.clicked.connect(lambda: self._select_protocol())
self.selectOutputFolder.clicked.connect(lambda: self._select_output())
self.selectedDWI.textChanged.connect(self._check_enable_action_buttons)
self.selectedMask.textChanged.connect(
self._check_enable_action_buttons)
self.selectedProtocol.textChanged.connect(
self._check_enable_action_buttons)
self.selectedOutputFolder.textChanged.connect(
self._check_enable_action_buttons)
self.modelSelection.currentIndexChanged.connect(
self._check_enable_action_buttons)
self.runButton.clicked.connect(lambda: self._run_model())
self.viewResultsButton.clicked.connect(
lambda: self._start_maps_visualizer())
self.optimizationOptionsButton.clicked.connect(
self._run_optimization_options_dialog)
self.additionalDataButton.clicked.connect(self._extra_data_dialog)
self.modelSelection.addItems(mdt.get_models_list())
initial_model = 'BallStick_r1'
self.modelSelection.setCurrentText(initial_model)
if self._input_data_info.dwi:
self.selectedDWI.setText(self._input_data_info.dwi)
if self._input_data_info.mask:
self.selectedMask.setText(self._input_data_info.mask)
if self._input_data_info.protocol:
self.selectedProtocol.setText(self._input_data_info.protocol)
self.update_output_folder_text()
self._check_enable_action_buttons()
def setupUi(self, tab_content):
super(FitModelTab, self).setupUi(tab_content)
self._tab_content = tab_content
self.selectDWI.clicked.connect(lambda: self._select_dwi())
self.selectMask.clicked.connect(lambda: self._select_mask())
self.selectProtocol.clicked.connect(lambda: self._select_protocol())
self.selectOutputFolder.clicked.connect(lambda: self._select_output())
self.selectedDWI.textChanged.connect(self._check_enable_action_buttons)
self.selectedMask.textChanged.connect(
self._check_enable_action_buttons)
self.selectedProtocol.textChanged.connect(
self._check_enable_action_buttons)
self.runButton.clicked.connect(lambda: self.run_model())
self.optimizationOptionsButton.clicked.connect(
self._run_optimization_options_dialog)
self.modelSelection.addItems(list(sorted(mdt.get_models_list())))
self.modelSelection.setCurrentText('BallStick_r1 (Cascade)')
self._check_enable_action_buttons()
def _get_arg_parser(self, doc_parser=False):
description = textwrap.dedent(__doc__)
examples = textwrap.dedent('''
mdt-model-fit "BallStick_r1 (Cascade)" data.nii.gz data.prtcl roi_mask_0_50.nii.gz
mdt-model-fit "BallStick_r1 (Cascade)" data.nii.gz data.prtcl data_mask.nii.gz --no-recalculate
mdt-model-fit ... --cl-device-ind 1
mdt-model-fit ... --cl-device-ind {0, 1}
mdt-model-fit ... --protocol-maps T1=T1_map.nii.gz T2=T2_map.nii.gz
''')
epilog = self._format_examples(doc_parser, examples)
parser = argparse.ArgumentParser(
description=description,
epilog=epilog,
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('model',
metavar='model',
choices=mdt.get_models_list(),
help='model name, see mdt-list-models')
parser.add_argument(
'dwi',
action=mdt.shell_utils.get_argparse_extension_checker(
['.nii', '.nii.gz', '.hdr', '.img']),
help='the diffusion weighted image').completer = FilesCompleter(
['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'protocol',
action=mdt.shell_utils.get_argparse_extension_checker(['.prtcl']),
help='the protocol file, see mdt-generate-protocol'
).completer = FilesCompleter(['prtcl'], directories=False)
parser.add_argument(
'mask',
action=mdt.shell_utils.get_argparse_extension_checker(
['.nii', '.nii.gz', '.hdr', '.img']),
help='the (brain) mask to use').completer = FilesCompleter(
['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'-o',
'--output_folder',
help=
'the directory for the output, defaults to "output/<mask_name>" '
'in the same directory as the dwi volume'
).completer = FilesCompleter()
parser.add_argument(
'-n',
'--noise-std',
default=None,
help=
'the noise std, defaults to None for automatic noise estimation.'
'Either set this to a value, or to a filename.')
parser.add_argument('--gradient-deviations',
action=mdt.shell_utils.get_argparse_extension_checker(['.nii', '.nii.gz', '.hdr', '.img']),
help="The volume with the gradient deviations to use, in HCP WUMINN format.").\
completer = FilesCompleter(['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'--cl-device-ind',
type=int,
nargs='*',
choices=self.available_devices,
help=
"The index of the device we would like to use. This follows the indices "
"in mdt-list-devices and defaults to the first GPU.")
parser.add_argument(
'--recalculate',
dest='recalculate',
action='store_true',
help="Recalculate the model(s) if the output exists. (default)")
parser.add_argument(
'--no-recalculate',
dest='recalculate',
action='store_false',
help="Do not recalculate the model(s) if the output exists.")
parser.set_defaults(recalculate=True)
parser.add_argument(
'--only-recalculate-last',
dest='only_recalculate_last',
action='store_true',
help="Only recalculate the last model in a cascade. (default)")
parser.add_argument('--recalculate-all',
dest='only_recalculate_last',
action='store_false',
help="Recalculate all models in a cascade.")
parser.set_defaults(only_recalculate_last=True)
parser.add_argument('--double',
dest='double_precision',
action='store_true',
help="Calculate in double precision.")
parser.add_argument('--float',
dest='double_precision',
action='store_false',
help="Calculate in single precision. (default)")
parser.set_defaults(double_precision=False)
parser.add_argument(
'--use-cascade-subdir',
dest='cascade_subdir',
action='store_true',
help=
"Set if you want to create a subdirectory for the given cascade model"
", default is False.")
parser.set_defaults(cascade_subdir=False)
parser.add_argument(
'--tmp-results-dir',
dest='tmp_results_dir',
default='True',
type=str,
help=
'The directory for the temporary results. The default ("True") uses the config file '
'setting. Set to the literal "None" to disable.'
).completer = FilesCompleter()
parser.add_argument(
'--config-context',
dest='config_context',
type=str,
help='The configuration context to use during fitting the model. '
'Same syntax as config files')
parser.add_argument(
'--protocol-maps',
dest='protocol_maps',
type=str,
nargs='+',
help='The protocol maps, provide as <key>=<value> pairs')
return parser
def _get_arg_parser(self, doc_parser=False):
description = textwrap.dedent(__doc__)
examples = textwrap.dedent('''
mdt-model-fit BallStick_r1 data.nii.gz data.prtcl roi_mask_0_50.nii.gz
mdt-model-fit ... --cl-device-ind 1
mdt-model-fit ... --cl-device-ind {0, 1}
mdt-model-fit ... --extra-protocol T1=T1_map.nii.gz T2=10
''')
epilog = self._format_examples(doc_parser, examples)
parser = argparse.ArgumentParser(
description=description,
epilog=epilog,
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('model',
metavar='model',
choices=mdt.get_models_list(),
help='model name, see mdt-list-models')
parser.add_argument(
'dwi',
action=mdt.lib.shell_utils.get_argparse_extension_checker(
['.nii', '.nii.gz', '.hdr', '.img']),
help='the diffusion weighted image').completer = FilesCompleter(
['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'protocol',
action=mdt.lib.shell_utils.get_argparse_extension_checker(
['.prtcl']),
help='the protocol file, see mdt-create-protocol'
).completer = FilesCompleter(['prtcl'], directories=False)
parser.add_argument(
'mask',
action=mdt.lib.shell_utils.get_argparse_extension_checker(
['.nii', '.nii.gz', '.hdr', '.img']),
help='the (brain) mask to use').completer = FilesCompleter(
['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'-o',
'--output_folder',
help=
'the directory for the output, defaults to "output/<mask_name>" '
'in the same directory as the dwi volume'
).completer = FilesCompleter()
parser.add_argument(
'-n',
'--noise-std',
default=None,
help=
'the noise std, defaults to None for automatic noise estimation.'
'Either set this to a value, or to a filename.')
parser.add_argument('--gradient-deviations',
action=mdt.lib.shell_utils.get_argparse_extension_checker(['.nii', '.nii.gz', '.hdr', '.img']),
help="The volume with the gradient deviations to use, in HCP WUMINN format.").\
completer = FilesCompleter(['nii', 'gz', 'hdr', 'img'], directories=False)
parser.add_argument(
'--cl-device-ind',
type=int,
nargs='*',
choices=self.available_devices,
help=
"The index of the device we would like to use. This follows the indices "
"in mdt-list-devices and defaults to the first GPU.")
parser.add_argument(
'--recalculate',
dest='recalculate',
action='store_true',
help="Recalculate the model(s) if the output exists. (default)")
parser.add_argument(
'--no-recalculate',
dest='recalculate',
action='store_false',
help="Do not recalculate the model(s) if the output exists.")
parser.set_defaults(recalculate=True)
parser.add_argument(
'--dont-use-cascaded-inits',
dest='use_cascaded_inits',
action='store_false',
help="Do not initialize the model with a better starting point.")
parser.add_argument(
'--use-cascaded-inits',
dest='use_cascaded_inits',
action='store_true',
help="Initialize the model with a better starting point (default). "
"Only works for default MDT models.")
parser.set_defaults(use_cascaded_inits=True)
parser.add_argument(
'--method',
default='Powell',
choices=[
'Powell', 'Nelder-Mead', 'Levenberg-Marquardt', 'Subplex'
],
help='The optimization method to use, defaults to Powell.')
parser.add_argument('--patience',
type=int,
default=None,
help='The patience for the optimization routine')
parser.add_argument('--double',
dest='double_precision',
action='store_true',
help="Calculate in double precision.")
parser.add_argument('--float',
dest='double_precision',
action='store_false',
help="Calculate in single precision. (default)")
parser.set_defaults(double_precision=False)
parser.add_argument(
'--tmp-results-dir',
dest='tmp_results_dir',
default='True',
type=str,
help=
'The directory for the temporary results. The default ("True") uses the config file '
'setting. Set to the literal "None" to disable.'
).completer = FilesCompleter()
parser.add_argument(
'--config-context',
dest='config_context',
type=str,
help='The configuration context to use during fitting the model. '
'Same syntax as config files')
parser.add_argument(
'--extra-protocol',
dest='extra_protocol',
type=str,
nargs='+',
help='Additional protocol values, provide as <key>=<value> pairs')
return parser