def save_outputs(self):
# savestring_qt, ok = QInputDialog.getText(
# None,
# "Save",
# 'Save output data? Yes/No/All with input data (y/n/a):',
# text="a"
# )
# savestring = str(savestring_qt)
# if savestring in ['Y', 'y', 'a', 'A']:
odp = self.output_datapath
if not op.exists(odp):
os.makedirs(odp)
data = self.export()
data['version'] = self.version # qmisc.getVersionString()
data['experiment_caption'] = self.experiment_caption
data['lisa_operator_identifier'] = self.lisa_operator_identifier
# data['organ_interactivity_counter'] = self.organ_interactivity_counter
pth, filename = op.split(op.normpath(self.datapath))
filename += "-" + self.experiment_caption
# if savestring in ['a', 'A']:
# save renamed file too
filepath = 'org-' + filename + '.' + self.save_filetype
# rint filepath
# rint 'op ', op
filepath = op.join(odp, filepath)
filepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype=self.save_filetype)
filepath = 'organ_last.' + self.save_filetype
filepath = op.join(odp, filepath)
# ilepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype=self.save_filetype)
# save to mat
# iparams = self.get_iparams()
# filepath = 'organ_iparams.pklz'
# filepath = op.join(odp, filepath)
# misc.obj_to_file(iparams, filepath, filetype='pklz')
# f savestring in ['a', 'A']:
if False:
# save renamed file too
data['data3d'] = None
filepath = 'organ_small-' + filename + '.pklz'
filepath = op.join(odp, filepath)
filepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype='pklz')
def save_outputs_dcm_overlay(self):
# TODO add
logger.debug('save dcm')
from PyQt4.QtCore import pyqtRemoveInputHook
pyqtRemoveInputHook()
# mport ipdb; ipdb.set_trace() # BREAKPOINT
odp = self.output_datapath
pth, filename = op.split(op.normpath(self.datapath))
filename += "-" + self.experiment_caption
# f savestring in ['ad']:
# save to DICOM
filepath = 'dicom-' + filename
filepath = os.path.join(odp, filepath)
filepath = misc.suggest_filename(filepath)
output_dicom_dir = filepath
data = self.export()
# mport ipdb; ipdb.set_trace() # BREAKPOINT
overlays = {
3:
(data['segmentation'] == self.output_label).astype(np.int8)
}
if self.dcmfilelist is not None:
datawriter.saveOverlayToDicomCopy(
self.dcmfilelist,
output_dicom_dir, overlays,
data['crinfo'], data['orig_shape'])
def test_suggest_filename(self):
"""
Testing some files. Not testing recursion in filenames. It is situation
if there exist file0, file1, file2 and input file is file
"""
import misc
filename = "mujsoubor"
#import ipdb; ipdb.set_trace() # BREAKPOINT
new_filename = misc.suggest_filename(filename, exists=True)
self.assertTrue(new_filename == "mujsoubor2")
filename = "mujsoubor112"
new_filename = misc.suggest_filename(filename, exists=True)
self.assertTrue(new_filename == "mujsoubor113")
filename = "mujsoubor-2.txt"
new_filename = misc.suggest_filename(filename, exists=True)
self.assertTrue(new_filename == "mujsoubor-3.txt")
filename = "mujsoubor-a24.txt"
new_filename = misc.suggest_filename(filename, exists=False)
self.assertTrue(new_filename == "mujsoubor-a24.txt")
def get_standard_ouptut_filename(self, filetype=None, suffix=''):
"""
It can be settet filename, or filename end with suffix.
"""
if filetype is None:
filetype = self.save_filetype
output_dir = self.output_datapath
pth, filename = op.split(op.normpath(self.datapath))
filename += "-" + self.experiment_caption
# if savestring in ['a', 'A']:
# save renamed file too
filename = '' + filename + suffix + '.' + filetype
filepath = op.join(output_dir, filename)
filepath = misc.suggest_filename(filepath)
return filepath
def save_outputs(args, oseg, qt_app):
from PyQt4.QtGui import QInputDialog
savestring_qt, ok = QInputDialog.getText(
None,
"Save",
'Save output data? Yes/No/All+Dicom with input data (y/n/a/ad):',
text="a"
)
savestring = str(savestring_qt)
#import pdb; pdb.set_trace()
#savestring = raw_input(
# 'Save output data? Yes/No/All with input data (y/n/a): '
#)
if savestring in ['Y', 'y', 'a', 'A', 'ad']:
if not os.path.exists(args["output_datapath"]):
os.makedirs(args['output_datapath'])
op = args['output_datapath']
# rename
data = oseg.export()
data['version'] = qmisc.getVersionString()
data['experiment_caption'] = args['experiment_caption']
data['lisa_operator_identifier'] = args['lisa_operator_identifier']
#data['organ_segmentation_time'] = t1
iparams = oseg.get_iparams()
#import pdb; pdb.set_trace()
pth, filename = os.path.split(os.path.normpath(args['datapath']))
filename += "-" + args['experiment_caption']
if savestring in ['a', 'A', 'ad']:
# save renamed file too
filepath = 'ob-' + filename + '.pklz'
filepath = os.path.join(op, filepath)
filepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype='pklz')
filepath = 'organ.pklz'
filepath = os.path.join(op, filepath)
#filepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype='pklz')
filepath = 'organ_iparams.pklz'
filepath = os.path.join(op, filepath)
misc.obj_to_file(iparams, filepath, filetype='pklz')
data['data3d'] = None
filepath = 'organ_small-' + filename + '.pklz'
filepath = os.path.join(op, filepath)
filepath = misc.suggest_filename(filepath)
misc.obj_to_file(data, filepath, filetype='pklz')
#output = segmentation.vesselSegmentation(oseg.data3d,
# oseg.orig_segmentation)
# print "uf"
if savestring in ['ad']:
# save to DICOM
filepath = 'dicom-' + filename
filepath = os.path.join(op, filepath)
filepath = misc.suggest_filename(filepath)
output_dicom_dir = filepath
#import ipdb; ipdb.set_trace() # BREAKPOINT
overlays = {
3:
(data['segmentation'] == args['output_label']).astype(np.int8)
}
saveOverlayToDicomCopy(oseg.metadata['dcmfilelist'],
output_dicom_dir, overlays,
data['crinfo'], data['orig_shape'])