def threshold(self, image, median_radius, window_size, min_contrast,
remove_borderobjects, fill_holes, norm_min=0, norm_max=255,
use_watershed=True, seeding_size=5, outline_smoothing=1,
*args, **kw):
image = self.normalize(image, norm_min, norm_max)
image = ccore.numpy_to_image(image, copy=True)
image_smoothed = ccore.gaussianFilter(image, median_radius)
label_image = ccore.window_average_threshold(
image_smoothed, window_size, min_contrast)
if fill_holes:
ccore.fill_holes(label_image)
if outline_smoothing >= 1:
label_image = outlineSmoothing(label_image.toArray(),
outline_smoothing)
label_image = ccore.numpy_to_image(label_image, copy=True)
if use_watershed:
label_image = label_image.toArray().copy()
label_image = watershed(label_image, seeding_size=seeding_size)
label_image = ccore.numpy_to_image(
label_image.astype(np.int16), copy=True)
return ccore.ImageMaskContainer(image, label_image,
remove_borderobjects, True, True)
else:
# a static type system sucks!
return ccore.ImageMaskContainer(image, label_image,
remove_borderobjects)
def getBackgroundROI(self, primary_name):
imgIn = ccore.readImageUInt16(primary_name)
imgConv = ccore.conversionTo8Bit(imgIn, 2**15, 2**15 + 4096, 0, 255)
imgSeg = ccore.window_average_threshold(imgConv, 50, 3)
imgDil = ccore.dilate(imgSeg, 20, 8)
imgMask = ccore.threshold(imgDil, 1, 255, 255, 0)
return imgMask
def threshold(self,
image,
median_radius,
window_size,
min_contrast,
remove_borderobjects,
fill_holes,
norm_min=0,
norm_max=255,
use_watershed=True,
seeding_size=5,
outline_smoothing=1,
*args,
**kw):
image = self.normalize(image, norm_min, norm_max)
image = ccore.numpy_to_image(image, copy=True)
image_smoothed = ccore.gaussianFilter(image, median_radius)
label_image = ccore.window_average_threshold(image_smoothed,
window_size, min_contrast)
if fill_holes:
ccore.fill_holes(label_image)
if outline_smoothing >= 1:
label_image = outlineSmoothing(label_image.toArray(),
outline_smoothing)
label_image = ccore.numpy_to_image(label_image, copy=True)
if use_watershed:
label_image = label_image.toArray().copy()
label_image = watershed(label_image, seeding_size=seeding_size)
label_image = ccore.numpy_to_image(label_image.astype(np.int16),
copy=True)
return ccore.ImageMaskContainer(image, label_image,
remove_borderobjects, True, True)
else:
# a static type system sucks!
return ccore.ImageMaskContainer(image, label_image,
remove_borderobjects)
def threshold(self, img_in, size, limit):
img_out = ccore.window_average_threshold(img_in, size, limit)
return img_out
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
