def _interactivity_end(self, igc):
"""
This is called after processing step. All data are rescaled to original
resolution.
"""
logger.debug('_interactivity_end()')
self.__resize_to_orig(igc.seeds)
self.organ_interactivity_counter = igc.interactivity_counter
logger.debug("org inter counter " +
str(self.organ_interactivity_counter))
logger.debug('nonzero segm ' + str(np.nonzero(self.segmentation)))
# if False:
if False:
# TODO dodělat postprocessing PV
import segmentation
outputSegmentation = segmentation.vesselSegmentation( # noqa
self.data3d,
self.segmentation,
threshold=-1,
inputSigma=0.15,
dilationIterations=10,
nObj=1,
biggestObjects=False,
seeds=(self.segmentation > 0).astype(np.int8),
useSeedsOfCompactObjects=True,
interactivity=True,
binaryClosingIterations=2,
binaryOpeningIterations=0)
self._segmentation_postprocessing()
# rint 'autocrop', self.autocrop
if self.autocrop is True:
# rint
# mport pdb; pdb.set_trace()
tmpcrinfo = qmisc.crinfo_from_specific_data(
self.segmentation,
self.autocrop_margin)
self.crop(tmpcrinfo)
if self.texture_analysis not in (None, False):
import texture_analysis
# doplnit nějaký kód, parametry atd
# elf.orig_scale_segmentation =
# texture_analysis.segmentation(self.data3d,
# self.orig_scale_segmentation, params = self.texture_analysis)
self.segmentation = texture_analysis.segmentation(
self.data3d,
self.segmentation,
self.voxelsize_mm
)
# set label number
# !! pomaly!!!
# @TODO make faster
self.segmentation[self.segmentation == 1] = self.output_label
#
logger.debug('self.slab')
logger.debug(str(self.slab))
self.processing_time = (
datetime.datetime.now() - self.time_start).total_seconds()
logger.debug('processing_time = ' + str(self.processing_time))
def _interactivity_end(self, igc):
logger.debug('_interactivity_end')
#print "sh3", self.data3d.shape
# import pdb; pdb.set_trace()
# scipy.ndimage.zoom(
# self.segmentation,
# 1.0 / self.zoom,
# output=segm_orig_scale,
# mode='nearest',
# order=0
# )
segm_orig_scale = scipy.ndimage.zoom(
self.segmentation,
1.0 / self.zoom,
mode='nearest',
order=0
).astype(np.int8)
seeds = scipy.ndimage.zoom(
igc.seeds,
1.0 / self.zoom,
mode='nearest',
order=0
)
#print np.sum(self.segmentation)*np.prod(self.voxelsize_mm)
# @TODO odstranit hack pro oříznutí na stejnou velikost
# v podstatě je to vyřešeno, ale nechalo by se to dělat elegantněji v zoom
# tam je bohužel patrně bug
shp = [
np.min([segm_orig_scale.shape[0], self.data3d.shape[0]]),
np.min([segm_orig_scale.shape[1], self.data3d.shape[1]]),
np.min([segm_orig_scale.shape[2], self.data3d.shape[2]]),
]
#self.data3d = self.data3d[0:shp[0], 0:shp[1], 0:shp[2]]
self.segmentation = np.zeros(self.data3d.shape, dtype=np.int8)
self.segmentation[
0:shp[0],
0:shp[1],
0:shp[2]] = segm_orig_scale[0:shp[0], 0:shp[1], 0:shp[2]]
del segm_orig_scale
self.iparams['seeds'] = np.zeros(self.data3d.shape, dtype=np.int8)
self.iparams['seeds'][
0:shp[0],
0:shp[1],
0:shp[2]] = seeds[0:shp[0], 0:shp[1], 0:shp[2]]
#
if self.segmentation_smoothing:
self.segm_smoothing(self.smoothing_mm)
#print 'crinfo: ', self.crinfo
#print 'autocrop', self.autocrop
if self.autocrop is True:
#print
#import pdb; pdb.set_trace()
tmpcrinfo = self._crinfo_from_specific_data(
self.segmentation,
self.autocrop_margin)
self.segmentation = self._crop(self.segmentation, tmpcrinfo)
self.data3d = self._crop(self.data3d, tmpcrinfo)
self.crinfo = qmisc.combinecrinfo(self.crinfo, tmpcrinfo)
if self.texture_analysis not in (None, False):
import texture_analysis
# doplnit nějaký kód, parametry atd
#self.orig_scale_segmentation =
# texture_analysis.segmentation(self.data3d,
# self.orig_scale_segmentation, params = self.texture_analysis)
self.segmentation = texture_analysis.segmentation(
self.data3d,
self.segmentation,
self.voxelsize_mm
)
# set label number
self.segmentation[self.segmentation == 1] = self.output_label
#
self.processing_time = time.time() - self.time_start
def _interactivity_end(self, igc):
logger.debug('_interactivity_end()')
# @TODO remove old code in except part
try:
# rint 'pred vyjimkou'
# aise Exception ('test without skimage')
# rint 'za vyjimkou'
import skimage
import skimage.transform
# Now we need reshape seeds and segmentation to original size
segm_orig_scale = skimage.transform.resize(
self.segmentation, self.data3d.shape, order=0)
seeds = skimage.transform.resize(
igc.seeds, self.data3d.shape, order=0)
self.segmentation = segm_orig_scale
self.seeds = seeds
except:
segm_orig_scale = scipy.ndimage.zoom(
self.segmentation,
1.0 / self.zoom,
mode='nearest',
order=0
).astype(np.int8)
seeds = scipy.ndimage.zoom(
igc.seeds,
1.0 / self.zoom,
mode='nearest',
order=0
)
self.organ_interactivity_counter = igc.interactivity_counter
logger.debug("org inter counter " +
str(self.organ_interactivity_counter))
# @TODO odstranit hack pro oříznutí na stejnou velikost
# v podstatě je to vyřešeno, ale nechalo by se to dělat elegantněji v zoom
# tam je bohužel patrně bug
# rint 'd3d ', self.data3d.shape
# rint 's orig scale shape ', segm_orig_scale.shape
shp = [
np.min([segm_orig_scale.shape[0], self.data3d.shape[0]]),
np.min([segm_orig_scale.shape[1], self.data3d.shape[1]]),
np.min([segm_orig_scale.shape[2], self.data3d.shape[2]]),
]
# elf.data3d = self.data3d[0:shp[0], 0:shp[1], 0:shp[2]]
# mport ipdb; ipdb.set_trace() # BREAKPOINT
self.segmentation = np.zeros(self.data3d.shape, dtype=np.int8)
self.segmentation[
0:shp[0],
0:shp[1],
0:shp[2]] = segm_orig_scale[0:shp[0], 0:shp[1], 0:shp[2]]
del segm_orig_scale
self.seeds[
0:shp[0],
0:shp[1],
0:shp[2]] = seeds[0:shp[0], 0:shp[1], 0:shp[2]]
if self.segmentation_smoothing:
self.segm_smoothing(self.smoothing_mm)
# rint 'autocrop', self.autocrop
if self.autocrop is True:
# rint
# mport pdb; pdb.set_trace()
tmpcrinfo = qmisc.crinfo_from_specific_data(
self.segmentation,
self.autocrop_margin)
self.crop(tmpcrinfo)
# seg = self
# rint 'ms d3d ', oseg.data3d.shape
# rint 'ms seg ', oseg.segmentation.shape
# rint 'crinfo ', oseg.crinfo
# elf.segmentation = qmisc.crop(self.segmentation, tmpcrinfo)
# elf.data3d = qmisc.crop(self.data3d, tmpcrinfo)
# elf.crinfo = qmisc.combinecrinfo(self.crinfo, tmpcrinfo)
if self.texture_analysis not in (None, False):
import texture_analysis
# doplnit nějaký kód, parametry atd
# elf.orig_scale_segmentation =
# texture_analysis.segmentation(self.data3d,
# self.orig_scale_segmentation, params = self.texture_analysis)
self.segmentation = texture_analysis.segmentation(
self.data3d,
self.segmentation,
self.voxelsize_mm
)
# set label number
# !! pomaly!!!
# @TODO make faster
self.segmentation[self.segmentation == 1] = self.output_label
#
self.processing_time = time.time() - self.time_start
