def _run(self, meta_image, container):
image = meta_image.image
if self.params['expansion_size'] > 0 or self.params['shrinking_size'] > 0:
nr_objects = container.img_labels.getMinmax()[1] + 1
if self.params['shrinking_size'] > 0:
img_labelsA = ccore.seeded_region_shrinking(image,
container.img_labels,
nr_objects,
self.params['shrinking_size'])
else:
img_labelsA = container.img_labels
if self.params['expansion_size'] > 0:
img_labelsB = ccore.seeded_region_expansion(image,
container.img_labels,
ccore.SrgType.KeepContours,
nr_objects,
0,
self.params['expansion_size'],
0)
else:
img_labelsB = container.img_labels
img_labels = ccore.substractImages(img_labelsB, img_labelsA)
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
else:
raise ValueError("Parameters are not valid. Requirements: 'expansion_size' > 0 and/or "
"'shrinking_size' > 0")
def seededExpandedRegion(self,
image,
label_image,
srg_type,
label_number,
region_statistics_array=0,
expansion_size=1,
sep_expansion_size=0,
norm_min=0,
norm_max=255):
if label_number is None:
label_number = label_image.max() + 1
image = self.normalize(image, norm_min, norm_max)
image = ccore.numpy_to_image(image, copy=True)
limage = ccore.numpy_to_image(label_image, copy=True)
img_labels = ccore.seeded_region_expansion(image, limage, srg_type,
label_number,
region_statistics_array,
expansion_size,
sep_expansion_size)
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
def _run(self, meta_image, container):
image = meta_image.image
if self.params['expansion_size'] > 0:
nr_objects = container.img_labels.getMinmax()[1] + 1
img_labels = ccore.seeded_region_expansion(
image, container.img_labels, ccore.SrgType.KeepContours,
nr_objects, 0, self.params['expansion_size'], 0)
else:
img_labels = container.img_labels
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
def _run(self, meta_image, container):
image = meta_image.image
if self.params['expansion_size'] > 0:
nr_objects = container.img_labels.getMinmax()[1] + 1
img_labels = ccore.seeded_region_expansion(image,
container.img_labels,
ccore.SrgType.KeepContours,
nr_objects,
0,
self.params['expansion_size'],
0)
else:
img_labels = container.img_labels
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
def _run(self, meta_image, container):
image = meta_image.image
if self.params['expansion_size'] > 0 and self.params['expansion_size'] > self.params['separation_size']:
nr_objects = container.img_labels.getMinmax()[1] + 1
img_labels = ccore.seeded_region_expansion(image,
container.img_labels,
ccore.SrgType.KeepContours,
nr_objects,
0,
self.params['expansion_size'],
self.params['separation_size'])
img_labels = ccore.substractImages(img_labels, container.img_labels)
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
else:
raise ValueError("Parameters are not valid. Requirements: 'expansion_size' > 0 and "
"'expansion_size' > 'separation_size'")
def seededExpandedRegion(self, image, label_image, srg_type, label_number,
region_statistics_array=0,
expansion_size=1,
sep_expansion_size=0,
norm_min=0, norm_max=255):
if label_number is None:
label_number = label_image.max() + 1
image = self.normalize(image, norm_min, norm_max)
image = ccore.numpy_to_image(image, copy=True)
limage = ccore.numpy_to_image(label_image, copy=True)
img_labels = ccore.seeded_region_expansion(image, limage,
srg_type,
label_number,
region_statistics_array,
expansion_size,
sep_expansion_size)
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
def __call__(self, meta_image, container):
stopwatch_total = StopWatch()
stopwatch = StopWatch()
image, width, height = meta_image.image, meta_image.width, meta_image.height
containers = {}
iLabelNumber = container.img_labels.getMinmax()[1]+1
img_prefiltered = image
# expanded - in case expansion size == 0 original regions are taken
if 'expanded' in self.lstAreaSelection:
stopwatch.reset()
if self.iExpansionSizeExpanded > 0:
imgLabelsOut = ccore.seeded_region_expansion(img_prefiltered,
container.img_labels,
ccore.SrgType.KeepContours,
iLabelNumber,
self.fExpansionCostThreshold,
self.iExpansionSizeExpanded,
0
)
else:
imgLabelsOut = container.img_labels
containers['expanded'] =\
ccore.ImageMaskContainer(image, imgLabelsOut, False, True, True)
self._logger.debug(" --- expanded region ok, %s" %
stopwatch.current_interval())
# inside - in case shrinking size == 0 original regions are taken
if 'inside' in self.lstAreaSelection:
stopwatch.reset()
if self.iShrinkingSizeInside > 0:
imgLabelsOut = ccore.seeded_region_shrinking(img_prefiltered,
container.img_labels,
iLabelNumber,
self.iShrinkingSizeInside
)
else:
imgLabelsOut = container.img_labels
containers['inside'] =\
ccore.ImageMaskContainer(image, imgLabelsOut, False, True, True)
self._logger.debug(" --- inside region ok, %s" %
stopwatch.current_interval())
# outside - expansion size > 0 AND expansion > separation size needed,
# otherwise area is 0
if ('outside' in self.lstAreaSelection
and self.iExpansionSizeOutside > 0
and self.iExpansionSizeOutside > self.iExpansionSeparationSizeOutside):
stopwatch.reset()
imgLabelsOut = ccore.seeded_region_expansion(img_prefiltered,
container.img_labels,
ccore.SrgType.KeepContours,
iLabelNumber,
self.fExpansionCostThreshold,
self.iExpansionSizeOutside,
self.iExpansionSeparationSizeOutside,
)
imgLabelsOut = ccore.substractImages(imgLabelsOut, container.img_labels)
containers['outside'] =\
ccore.ImageMaskContainer(image, imgLabelsOut, False, True, True)
self._logger.debug(" --- outside region ok, %s" %
stopwatch.current_interval())
# rim - one value > 0 needed, otherwise area is 0
if ('rim' in self.lstAreaSelection and
(self.iExpansionSizeRim > 0 or self.iShrinkingSizeRim > 0)):
stopwatch.reset()
if self.iShrinkingSizeRim > 0:
imgLabelsOutA = ccore.seeded_region_shrinking(img_prefiltered,
container.img_labels,
iLabelNumber,
self.iShrinkingSizeRim
)
else:
imgLabelsOutA = container.img_labels
if self.iExpansionSizeRim > 0:
imgLabelsOutB = ccore.seeded_region_expansion(img_prefiltered,
container.img_labels,
ccore.SrgType.KeepContours,
iLabelNumber,
self.fExpansionCostThreshold,
self.iExpansionSizeRim,
0
)
else:
imgLabelsOutB = container.img_labels
imgLabelsOut = ccore.substractImages(imgLabelsOutB, imgLabelsOutA)
containers['rim'] =\
ccore.ImageMaskContainer(image, imgLabelsOut, False, True, True)
self._logger.debug(" --- rim region ok, %s" %
stopwatch.current_interval())
if ('propagate' in self.lstAreaSelection):
stopwatch.reset()
if self.iPresegmentationMedianRadius > 0:
img_prefiltered = ccore.disc_median(image,
self.iPresegmentationMedianRadius)
t = int(ccore.get_otsu_threshold(img_prefiltered) *
self.fPresegmentationAlpha)
img_binary = ccore.threshold_image(img_prefiltered, t)
#self._logger.debug(" --- pre-segmentation ok, %s" %
# stopwatch.current_interval())
labels_out = ccore.segmentation_propagate(img_prefiltered, img_binary,
container.img_labels,
self.fPropagateLambda,
self.iPropagateDeltaWidth)
containers['propagate'] =\
ccore.ImageMaskContainer(image, labels_out, False, True, True)
self._logger.debug(" --- propagate region ok, %s" %
stopwatch.current_interval())
if ('constrained_watershed' in self.lstAreaSelection):
labels_out = self.constrainedWatershedApproach(image, container.img_labels,
iGaussFilterSize=self.iConstrainedWatershedGaussFilterSize)
containers['constrained_watershed'] =\
ccore.ImageMaskContainer(image, labels_out, False, True, True)
self._logger.debug(" --- constrained_watershed region ok, %s",
stopwatch.current_interval())
self._logger.debug(" total time: %s" %
stopwatch_total.current_interval())
return containers
