def add_finaltractandlabels(connectome):
resolution = gconf.parcellation.keys()
for r in resolution:
log.info("Adding final fiber labels array (%s) to connectome..." % str(r))
cda = cf.CData(name="Final fiber labels (%s)" % str(r),
src=op.join(gconf.get_cmp_fibers(), 'final_fiberlabels_%s.npy' % str(r)),
fileformat='NumPy',
dtype='FiberLabels')
connectome.add_connectome_data(cda)
log.info("Adding final tractography for resolution %s" % str(r))
ctr = cf.CTrack(name='Final Tractography (%s)' % str(r),
src=op.join(gconf.get_cmp_fibers(), 'streamline_final_%s.trk' % str(r)),
fileformat='TrackVis', dtype='FinalFibers')
connectome.add_connectome_track(ctr)
log.info("Adding final fiber length array")
fiberlabels_fname = op.join(gconf.get_cmp_fibers(), 'final_fiberslength_%s.npy' % str(r))
cda = cf.CData(name="Final fiber lengths (%s)" % str(r),
src=fiberlabels_fname,
fileformat='NumPy',
dtype='FiberLength')
connectome.add_connectome_data(cda)
def add_fibersoriginal2connectome(connectome):
log.info("Adding original fibers to connectome...")
fibers_path = gconf.get_cmp_fibers()
ctr = cf.CTrack(name='Original Tractography',
src=op.join(fibers_path, 'streamline.trk'),
fileformat='TrackVis', dtype='OriginalFibers')
connectome.add_connectome_track(ctr)
def add_fibers2connectome(connectome):
log.info("Adding filtered fibers to connectome...")
fibers_path = gconf.get_cmp_fibers()
ctr = cf.CTrack(name='Filtered Tractography',
src=op.join(fibers_path, 'streamline_filtered.trk'),
fileformat='TrackVis',dtype='FilteredFibers')
# add filter settings as metadata
ctr.update_metadata({'spline_filtered' : str(gconf.apply_splinefilter),
'fiber_cutoff_lower': gconf.fiber_cutoff_lower,
'fiber_cutoff_upper': gconf.fiber_cutoff_upper})
connectome.add_connectome_track(ctr)
def _run_interface(self, runtime):
a = cf.connectome()
if isdefined(self.inputs.title):
a.connectome_meta.set_title(self.inputs.title)
else:
a.connectome_meta.set_title(self.inputs.out_file)
if isdefined(self.inputs.creator):
a.connectome_meta.set_creator(self.inputs.creator)
else:
#Probably only works on some OSes...
a.connectome_meta.set_creator(os.getenv('USER'))
if isdefined(self.inputs.email):
a.connectome_meta.set_email(self.inputs.email)
if isdefined(self.inputs.publisher):
a.connectome_meta.set_publisher(self.inputs.publisher)
if isdefined(self.inputs.license):
a.connectome_meta.set_license(self.inputs.license)
if isdefined(self.inputs.rights):
a.connectome_meta.set_rights(self.inputs.rights)
if isdefined(self.inputs.references):
a.connectome_meta.set_references(self.inputs.references)
if isdefined(self.inputs.relation):
a.connectome_meta.set_relation(self.inputs.relation)
if isdefined(self.inputs.species):
a.connectome_meta.set_species(self.inputs.species)
if isdefined(self.inputs.description):
a.connectome_meta.set_description(self.inputs.description)
a.connectome_meta.set_created(datetime.date.today())
count = 0
if isdefined(self.inputs.graphml_networks):
for ntwk in self.inputs.graphml_networks:
# There must be a better way to deal with the unique name problem
#(i.e. tracks and networks can't use the same name, and previously we were pulling them both from the input files)
ntwk_name = 'Network {cnt}'.format(cnt=count)
a.add_connectome_network_from_graphml(ntwk_name, ntwk)
count += 1
if isdefined(self.inputs.gpickled_networks):
unpickled = []
for ntwk in self.inputs.gpickled_networks:
_, ntwk_name, _ = split_filename(ntwk)
unpickled = nx.read_gpickle(ntwk)
cnet = cf.CNetwork(name = ntwk_name)
cnet.set_with_nxgraph(unpickled)
a.add_connectome_network(cnet)
count += 1
count = 0
if isdefined(self.inputs.tract_files):
for trk in self.inputs.tract_files:
_, trk_name, _ = split_filename(trk)
ctrack = cf.CTrack(trk_name, trk)
a.add_connectome_track(ctrack)
count += 1
count = 0
if isdefined(self.inputs.gifti_surfaces):
for surf in self.inputs.gifti_surfaces:
_, surf_name, _ = split_filename(surf)
csurf = cf.CSurface.create_from_gifti("Surface %d - %s" % (count,surf_name), surf)
csurf.fileformat='Gifti'
csurf.dtype='Surfaceset'
a.add_connectome_surface(csurf)
count += 1
count = 0
if isdefined(self.inputs.gifti_labels):
for label in self.inputs.gifti_labels:
_, label_name, _ = split_filename(label)
csurf = cf.CSurface.create_from_gifti("Surface Label %d - %s" % (count,label_name), label)
csurf.fileformat='Gifti'
csurf.dtype='Labels'
a.add_connectome_surface(csurf)
count += 1
if isdefined(self.inputs.nifti_volumes):
for vol in self.inputs.nifti_volumes:
_, vol_name, _ = split_filename(vol)
cvol = cf.CVolume.create_from_nifti(vol_name,vol)
a.add_connectome_volume(cvol)
if isdefined(self.inputs.script_files):
for script in self.inputs.script_files:
_, script_name, _ = split_filename(script)
cscript = cf.CScript.create_from_file(script_name, script)
a.add_connectome_script(cscript)
if isdefined(self.inputs.data_files):
for data in self.inputs.data_files:
_, data_name, _ = split_filename(data)
cda = cf.CData(name=data_name, src=data, fileformat='NumPy')
if not string.find(data_name,'lengths') == -1:
cda.dtype = 'FinalFiberLengthArray'
if not string.find(data_name,'endpoints') == -1:
cda.dtype = 'FiberEndpoints'
if not string.find(data_name,'labels') == -1:
cda.dtype = 'FinalFiberLabels'
a.add_connectome_data(cda)
a.print_summary()
_, name, ext = split_filename(self.inputs.out_file)
if not ext == '.cff':
ext = '.cff'
cf.save_to_cff(a,op.abspath(name + ext))
return runtime
def perform(self, event, cfile=None):
""" Performs the action. """
logger.info('Performing open connectome file action')
# helper variable to use this function not only in the menubar
exec_as_funct = True
if cfile is None:
# get the instance of the current CFile
# with the help of the Service Registry
cfile = self.window.application.get_service(
'cviewer.plugins.cff2.cfile.CFile')
exec_as_funct = False
wildcard = "All files (*.*)|*.*|" \
"Nifti-1 (*.nii.gz)|*.nii.gz|" \
"Gifti (*.gii)|*.gii|" \
"TrackVis tracks (*.trk)|*.trk|" \
"Network Pickle (*.gpickle)|*.gpickle|" \
"Network GraphML (*.graphml)|*.graphml|" \
"Numpy Data (*.npy)|*.npy|" \
"Pickle Data (*.pkl)|*.pkl|" \
"Text Data (*.txt)|*.txt|" \
"CSV Data (*.csv)|*.csv|"
dlg = FileDialog(wildcard=wildcard,title="Choose a file",\
resizeable=False, \
default_directory=preference_manager.cviewerui.cffpath,)
if dlg.open() == OK:
if not os.path.isfile(dlg.path):
logger.error("File '%s' does not exist!" % dlg.path)
return
logger.info('Read file: %s' % dlg.path)
fname = os.path.split(dlg.paths[0])[-1]
if os.path.exists(dlg.paths[0]) and (fname.endswith('.nii.gz')
or fname.endswith('.nii')):
cvol = cfflib.CVolume.create_from_nifti(
name=fname, nii_filename=dlg.paths[0])
cfile.obj.add_connectome_volume(cvol)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.gii'):
csurf = cfflib.CSurface.create_from_gifti(
name=fname, gii_filename=dlg.paths[0])
cfile.obj.add_connectome_surface(csurf)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.trk'):
ctrk = cfflib.CTrack(name=fname, src=dlg.paths[0])
cfile.obj.add_connectome_track(ctrk)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.gpickle'):
ctrk = cfflib.CNetwork(name=fname,
src=dlg.paths[0],
fileformat="NXGPickle")
cfile.obj.add_connectome_network(ctrk)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.graphml'):
ctrk = cfflib.CNetwork.create_from_graphml(
name=fname, ml_filename=dlg.paths[0])
cfile.obj.add_connectome_network(ctrk)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.npy'):
cdat = cfflib.CData(name=fname,
src=dlg.paths[0],
fileformat='NumPy')
cfile.obj.add_connectome_data(cdat)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.csv'):
cdat = cfflib.CData(name=fname,
src=dlg.paths[0],
fileformat='CSV')
cfile.obj.add_connectome_data(cdat)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.txt'):
cdat = cfflib.CData(name=fname,
src=dlg.paths[0],
fileformat='TXT')
cfile.obj.add_connectome_data(cdat)
elif os.path.exists(dlg.paths[0]) and fname.endswith('.pkl'):
cdat = cfflib.CData(name=fname,
src=dlg.paths[0],
fileformat='Pickle')
cfile.obj.add_connectome_data(cdat)
else:
logger.info('Could not load file: ' + dlg.paths)
cfile.update_children()
