def _load_parcellation_check(self):
pcw = self.parcellation_chooser_window
if not pcw.finished: return
if pcw.ctl.new_dataset:
if pcw.ctl.new_dataset_name == '':
self.error_dialog('Must specify a dataset name!')
return
elif pcw.ctl.new_dataset_name in self.controller.ds_instances:
self.error_dialog('Dataset name is not unique')
return
else:
ds_name = pcw.ctl.new_dataset_name
import preprocessing
parc_struct = preprocessing.process_parc(pcw.ctl, self)
if parc_struct is None: return #preprocessing errored out
lab_pos, labnam, srf, labv, subject_name, parc_name = parc_struct
display_metadata = DisplayMetadata(subject_name=subject_name,
parc_name=parc_name,
adj_filename='')
ds = Dataset(ds_name, lab_pos, labnam, srf, labv, gui=self)
self.controller.add_dataset(ds, display_metadata)
else:
import preprocessing
parc_struct = preprocessing.process_parc(pcw.ctl, self)
if parc_struct is None: return
lab_pos, labnam, srf, labv, subject_name, parc_name = parc_struct
pcw.ctl.ds_ref._load_parc(lab_pos, labnam, srf, labv)
self.controller.update_display_metadata(pcw.ctl.ds_ref.name,
subject_name=subject_name,
parc_name=parc_name)
#find the viewports that were previously holding this scene
#find_dataset_views returns a DatasetViewportInterface object
#with references to the viewports (source in viewport.py)
ds_interface = self.controller.find_dataset_views(pcw.ctl.ds_ref)
ds_interface.mayavi_port = Viewport(pcw.ctl.ds_ref)
ds_interface.matrix_port = Viewport(pcw.ctl.ds_ref)
ds_interface.circle_port = Viewport(pcw.ctl.ds_ref)
def _load_parcellation_check(self):
pcw=self.parcellation_chooser_window
if not pcw.finished: return
if pcw.ctl.new_dataset:
if pcw.ctl.new_dataset_name=='':
self.error_dialog('Must specify a dataset name!'); return
elif pcw.ctl.new_dataset_name in self.controller.ds_instances:
self.error_dialog('Dataset name is not unique'); return
else:
ds_name = pcw.ctl.new_dataset_name
import preprocessing
parc_struct=preprocessing.process_parc(pcw.ctl,self)
if parc_struct is None: return #preprocessing errored out
lab_pos,labnam,srf,labv,subject_name,parc_name=parc_struct
display_metadata=DisplayMetadata(subject_name=subject_name,
parc_name=parc_name,adj_filename='')
ds=Dataset(ds_name,lab_pos,labnam,srf,labv,gui=self)
self.controller.add_dataset(ds,display_metadata)
else:
import preprocessing
parc_struct=preprocessing.process_parc(pcw.ctl,self)
if parc_struct is None: return
lab_pos,labnam,srf,labv,subject_name,parc_name=parc_struct
pcw.ctl.ds_ref.load_parc(lab_pos,labnam,srf,labv)
self.controller.update_display_metadata(pcw.ctl.ds_ref.name,
subject_name=subject_name, parc_name=parc_name)
#find the viewports that were previously holding this scene
#find_dataset_views returns a DatasetViewportInterface object
#with references to the viewports (source in viewport.py)
ds_interface=self.controller.find_dataset_views(pcw.ctl.ds_ref)
ds_interface.mayavi_port = Viewport(pcw.ctl.ds_ref)
ds_interface.matrix_port = Viewport(pcw.ctl.ds_ref)
ds_interface.circle_port = Viewport(pcw.ctl.ds_ref)
def load_parc(parcellation, ordering, new_dataset=False, dataset_name = None,
dataset=None,
subjects_dir='.', subject='fsavg5', surface_type='pial'):
'''
Loads a parcellation, either onto a dataset or creating a new dataset.
This function is a scripting helper. In other words,
instead of clicking on the GUI or simulating button presses, this
function is provided for scripting purposes to just simulate the
process of loading a parcellation.
Parameters
----------
parcellation : str
The parcellation name. For instance, if your parcellation's annotation
files are called lh.aparc.annot, the parcellation name is 'aparc'.
Similarly if the annotation file is called lh.aparc.gii, enter 'aparc'.
ordering : str | list(str)
The name of a text file containing the parcellation ordering.
Alternately, a list of label names.
new_dataset : bool
If True, spawns a new dataset instead of placing the parcellation on
an existing dataset. Default value is False.
dataset_name : str | None
Required if and only if new_dataset is True.
If new_dataset is True, specifies the name of the new dataset.
Otherwise, has no effect.
dataset : instance(cvu.dataset.Dataset) | None
Required if and only if new_dataset is False.
If new_dataset is False, specifies the dataset onto which to load this
parcellation. If new_dataset is True, has no effect.
subjects_dir : str
The superordinate directory used to load the annotation, surface,
and segmentation files at $SUBJECTS_DIR/$SUBJECT/{surf|label|mri}/* .
The default value is '.', the current working directory. Under
normal circumstances this is the working directory relative to cvu's
main.py file, which is /path/to/cvu/cvu.
subject : str
The subject name used to load the annotation, surface, and segmentation
files at $SUBJECTS_DIR/$SUBJECT/{surf|label|mri}/*
The default value is 'fsavg5'. Some files for fsavg5 are provided in
the cvu installation.
surface_type
The surface to load. The default value is 'pial'.
Returns
-------
dataset : instance(cvu.dataset.Dataset)
The instance of the dataset now holding this parcellation. Helpful
if new_dataset is True.
'''
gui = globals()['self'] #explicitly allow dynamic scope
err_handler = ErrorHandler(quiet=True)
from preprocessing import process_parc
from options_struct import ParcellationChooserParameters
from utils import DisplayMetadata
from dataset import Dataset
if new_dataset and dataset_name is None:
print "Must specify a dataset name!"
return
elif new_dataset and dataset_name in gui.controller.ds_instances:
print "Dataset name is not unique"
return
elif not new_dataset and not isinstance(dataset, Dataset):
print "Must either supply an existing dataset or create a new one"
return
parc_params = ParcellationChooserParameters( ds_ref = dataset,
new_dataset = new_dataset,
new_dataset_name = dataset_name if dataset_name is not None else '',
subjects_dir = subjects_dir,
subject = subject, surface_type = surface_type,
labelnames_file = ordering, parcellation_name = parcellation)
parc_struct = process_parc(parc_params, err_handler)
if parc_struct is None: return #preprocessing errored out
lab_pos, labnam, srf, labv, _, _ = parc_struct
if new_dataset:
display_metadata = DisplayMetadata(subject_name = subject,
parc_name = parcellation, adj_filename='')
dataset = Dataset(dataset_name, lab_pos, labnam, srf, labv, gui=gui)
gui.controller.add_dataset(dataset, display_metadata)
else:
from viewport import Viewport
dataset._load_parc(lab_pos, labnam, srf, labv)
gui.controller.update_display_metadata(dataset.name,
subject_name = subject, parc_name = parcellation)
#update the viewports associated with this dataset
ds_interface = gui.controller.find_dataset_views(dataset)
ds_interface.mayavi_port = Viewport(dataset)
ds_interface.matrix_port = Viewport(dataset)
ds_interface.circle_port = Viewport(dataset)
return dataset
