def prefilter(self, img_in, radius=None):
img_temp = img_in
if self.params['togglemappings']:
img_temp = ccore.toggle_mapping(img_in, self.params['tm_size'])
if radius is None:
radius = self.params['medianradius']
img_out = ccore.disc_median(img_temp, radius)
return img_out
def _run(self, meta_image, container):
image = meta_image.image
img_prefiltered = ccore.disc_median(image, self.params['presegmentation_median_radius'])
t = int(ccore.get_otsu_threshold(img_prefiltered) * self.params['presegmentation_alpha'])
img_bin = ccore.threshold_image(img_prefiltered, t)
img_labels = ccore.segmentation_propagate(img_prefiltered, img_bin,
container.img_labels,
self.params['lambda'],
self.params['delta_width'])
return ccore.ImageMaskContainer(image, img_labels, False, True, True)
def prefilter(self, img_in, radius=None):
if radius is None:
radius = self.params['medianradius']
img_out = ccore.disc_median(img_in, radius)
return img_out
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
def __call__(self, meta_image):
stopwatch_total = StopWatch()
stopwatch = StopWatch()
#print "moo123"
#image = meta_image.image
#print type(image), image.getMinmax()
#meta_image.setImageXY(convertImageMinMax(image))
image = meta_image.image
#print type(image), image.getMinmax()
width, height = meta_image.width, meta_image.height
#print width, height, self.strPathOutDebug
if self.bSpeedup:
imgTmp1 = ccore.Image(width, height)
ccore.binImage(image, imgTmp1, 2)
width /= 2
height /= 2
imgTmp2 = ccore.Image(width, height)
ccore.scaleImage(imgTmp1, imgTmp2, "no")
image = imgTmp2
# if self.bDebugMode:
# strPathOutDebug = self.strPathOutDebug
# ccore.writeImage(image,
# os.path.join(strPathOutDebug,
# meta_image.format("00raw.jpg", bC=True)),
# self.strImageOutCompression)
img_prefiltered = ccore.disc_median(image,
self.iMedianRadius)
self._logger.debug(" --- median ok, %s" %
stopwatch.current_interval())
stopwatch.reset()
#print self.bDebugMode, self.strPathOutDebug
# if self.bDebugMode:
# ccore.writeImage(img_prefiltered,
# os.path.join(strPathOutDebug,
# meta_image.format("00pre.jpg", bC=True)),
# self.strImageOutCompression)
imgBin = ccore.window_average_threshold(img_prefiltered,
self.iLatWindowSize,
self.iLatLimit)
self._logger.debug(" --- local threshold ok, %s" %
stopwatch.current_interval())
if self.hole_filling:
ccore.fill_holes(imgBin, False)
stopwatch.reset()
#self._logger.debug(" --- local threshold2 %s %s" % (self.iLatWindowSize2, )
if not self.iLatWindowSize2 is None and not self.iLatLimit2 is None:
imgBin2 = ccore.window_average_threshold(img_prefiltered,
self.iLatWindowSize2,
self.iLatLimit2)
imgBin = ccore.projectImage([imgBin, imgBin2], ccore.ProjectionType.MaxProjection)
self._logger.debug(" --- local threshold2 ok, %s" %
stopwatch.current_interval())
stopwatch.reset()
# if self.bDebugMode:
# strPathOutDebug = self.strPathOutDebug
# ccore.writeImage(imgBin,
# os.path.join(strPathOutDebug,
# meta_image.format("01bin.jpg", bC=True)),
# self.strImageOutCompression)
# else:
# strPathOutDebug = ""
if self.bDoShapeWatershed:
imgBin = ccore.segmentation_correction_shape(img_prefiltered,
imgBin,
self.iLatWindowSize,
self.iGaussSizeShape,
self.iMaximaSizeShape,
self.iMinMergeSize)
if self.bDoIntensityWatershed:
imgBin = ccore.segmentation_correction_intensity(img_prefiltered,
imgBin,
self.iLatWindowSize,
self.iGaussSizeIntensity,
self.iMaximaSizeIntensity,
self.iMinMergeSize)
self._logger.debug(" --- segmentation ok, %s" %
stopwatch.current_interval())
stopwatch.reset()
if self.bSpeedup:
width, height = meta_image.width, meta_image.height
imgTmpBin = ccore.Image(width, height)
ccore.scaleImage(imgBin, imgTmpBin, "no")
imgBin = imgTmpBin
image = meta_image.image
container = ccore.ImageMaskContainer(image,
imgBin,
self.bRemoveBorderObjects)
self._logger.debug(" --- container ok, %s" %
stopwatch.current_interval())
stopwatch.reset()
# post-processing
#print self.bPostProcessing, self.lstPostprocessingFeatureCategories
if self.bPostProcessing:
# extract features
for strFeature in self.lstPostprocessingFeatureCategories:
container.applyFeature(strFeature)
dctObjects = container.getObjects()
lstGoodObjectIds = []
lstRejectedObjectIds = []
for iObjectId in dctObjects.keys()[:]:
dctObjectFeatures = dctObjects[iObjectId].getFeatures()
if not eval(self.strPostprocessingConditions, dctObjectFeatures):
if self.bPostProcessDeleteObjects:
del dctObjects[iObjectId]
container.delObject(iObjectId)
lstRejectedObjectIds.append(iObjectId)
else:
lstGoodObjectIds.append(iObjectId)
self._logger.debug(" --- post-processing ok, %s" %
stopwatch.current_interval())
else:
lstGoodObjectIds = container.getObjects().keys()
lstRejectedObjectIds = []
container.lstGoodObjectIds = lstGoodObjectIds
container.lstRejectedObjectIds = lstRejectedObjectIds
# if self.bDebugMode:
# container.markObjects(ccore.RGBValue(0,255,0), False, False)
# #container.markObjects(lstGoodObjectIds, ccore.RGBValue(0,255,0), False, False)
# #container.markObjects(lstRejectedObjectIds, ccore.RGBValue(255,0,0), False, False)
# container.exportRGB(os.path.join(strPathOutDebug,
# meta_image.format("03Contour.jpg", bC=True)),
# self.strImageOutCompression)
#
# # reset the container RGB
# container.eraseRGB()
# container.combineExtraRGB([7],[1])
self._logger.debug(" total time: %s" %
stopwatch_total.current_interval())
return container
