def ImportMedicalImages(self, directory, gui=True):
patients_groups = dcm.GetDicomGroups(directory)
name = directory.rpartition('\\')[-1].split('.')
print("patients: ", patients_groups)
if len(patients_groups):
# OPTION 1: DICOM
group = dcm.SelectLargerDicomGroup(patients_groups)
matrix, matrix_filename, dicom = self.OpenDicomGroup(group,
0, [0, 0],
gui=gui)
self.CreateDicomProject(dicom, matrix, matrix_filename)
else:
# OPTION 2: NIfTI, Analyze or PAR/REC
if name[-1] == 'gz':
name[1] = 'nii.gz'
suptype = ('hdr', 'nii', 'nii.gz', 'par')
filetype = name[1].lower()
if filetype in suptype:
group = oth.ReadOthers(directory)
else:
utils.debug("No medical images found on given directory")
return
matrix, matrix_filename = self.OpenOtherFiles(group)
self.CreateOtherProject(str(name[0]), matrix, matrix_filename)
# OPTION 4: Nothing...
self.LoadProject()
Publisher.sendMessage("Enable state project", state=True)
def use_cmd_optargs(options, args):
# If debug argument...
if options.debug:
Publisher.subscribe(print_events, Publisher.ALL_TOPICS)
session = ses.Session()
session.debug = 1
# If import DICOM argument...
if options.dicom_dir:
import_dir = options.dicom_dir
Publisher.sendMessage('Import directory', {
'directory': import_dir,
'gui': not options.no_gui
})
if options.save:
Publisher.sendMessage('Save project',
os.path.abspath(options.save))
exit(0)
check_for_export(options)
return True
elif options.import_all:
import invesalius.reader.dicom_reader as dcm
for patient in dcm.GetDicomGroups(options.import_all):
for group in patient.GetGroups():
Publisher.sendMessage('Import group', {
'group': group,
'gui': not options.no_gui
})
check_for_export(options,
suffix=group.title,
remove_surfaces=False)
Publisher.sendMessage('Remove masks', [0])
return True
# Check if there is a file path somewhere in what the user wrote
# In case there is, try opening as it was a inv3
else:
for arg in reversed(args):
file = utils.decode(arg, FS_ENCODE)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', path)
check_for_export(options)
return True
file = utils.decode(arg, sys.stdin.encoding)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', path)
check_for_export(options)
return True
return False
def use_cmd_optargs(options, args):
# If import DICOM argument...
if options.dicom_dir:
import_dir = options.dicom_dir
Publisher.sendMessage('Import directory',
directory=import_dir,
use_gui=not options.no_gui)
if options.save:
Publisher.sendMessage('Save project',
filepath=os.path.abspath(options.save))
exit(0)
check_for_export(options)
return True
elif options.import_folder:
Publisher.sendMessage('Import folder', folder=options.import_folder)
if options.save:
Publisher.sendMessage('Save project',
filepath=os.path.abspath(options.save))
exit(0)
check_for_export(options)
elif options.import_all:
import invesalius.reader.dicom_reader as dcm
for patient in dcm.GetDicomGroups(options.import_all):
for group in patient.GetGroups():
Publisher.sendMessage('Import group',
group=group,
use_gui=not options.no_gui)
check_for_export(options,
suffix=group.title,
remove_surfaces=False)
Publisher.sendMessage('Remove masks', mask_indexes=(0, ))
return True
# Check if there is a file path somewhere in what the user wrote
# In case there is, try opening as it was a inv3
else:
for arg in reversed(args):
file = utils.decode(arg, FS_ENCODE)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
file = utils.decode(arg, sys.stdin.encoding)
if os.path.isfile(file):
path = os.path.abspath(file)
Publisher.sendMessage('Open project', filepath=path)
check_for_export(options)
return True
return False
def ImportMedicalImages(self, directory):
# OPTION 1: DICOM?
patients_groups = dcm.GetDicomGroups(directory)
if len(patients_groups):
group = dcm.SelectLargerDicomGroup(patients_groups)
matrix, matrix_filename, dicom = self.OpenDicomGroup(group,
0, [0, 0],
gui=True)
self.CreateDicomProject(dicom, matrix, matrix_filename)
# OPTION 2: ANALYZE?
else:
imagedata = analyze.ReadDirectory(directory)
if imagedata:
self.CreateAnalyzeProject(imagedata)
# OPTION 3: Nothing...
else:
utils.debug("No medical images found on given directory")
return
self.LoadProject()
Publisher.sendMessage("Enable state project", True)
