def normalize_image(self, plate_id=None): img_in = self.meta_image.image if self.bFlatfieldCorrection: self.logger.debug("* using flat field correction with image from %s" % self.strBackgroundImagePath) imgBackground = self._load_flatfield_correction_image(plate_id) crop_coordinated = MetaImage.get_crop_coordinates() if crop_coordinated is not None: self.logger.debug("* applying cropping to background image") imgBackground = ccore.subImage(imgBackground, ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]), ccore.Diff2D(crop_coordinated[2], crop_coordinated[3])) img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True) img_out = ccore.linearTransform2(img_in, self.fNormalizeMin, self.fNormalizeMax, 0, 255, 0, 255) else: self.logger.debug("* not using flat field correction") if type(img_in) == ccore.UInt16Image: img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) elif type(img_in) == ccore.Image: img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) else: img_out = img_in self.meta_image.set_image(img_out)
def normalize_image(self, plate_id=None): try: import pydevd pydevd.connected = True pydevd.settrace(suspend=False) print 'Thread enabled interactive eclipse debuging...' except: pass img_in = self.meta_image.image if self.bFlatfieldCorrection: self.logger.debug( "* using flat field correction with image from %s" % self.strBackgroundImagePath) imgBackground = self._load_flatfield_correction_image(plate_id) crop_coordinated = MetaImage.get_crop_coordinates() if crop_coordinated is not None: self.logger.debug("* applying cropping to background image") imgBackground = ccore.subImage( imgBackground, ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]), ccore.Diff2D(crop_coordinated[2], crop_coordinated[3])) img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True) img_out = ccore.linearTransform2(img_in, self.fNormalizeMin, self.fNormalizeMax, 0, 255, 0, 255) else: self.logger.debug("* not using flat field correction") if type(img_in) == ccore.UInt16Image: img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) elif type(img_in) == ccore.Image: img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) else: img_out = img_in self.meta_image.set_image(img_out)
def normalize_image(self, plate_id=None): try: import pydevd pydevd.connected = True pydevd.settrace(suspend=False) print 'Thread enabled interactive eclipse debuging...' except: pass img_in = self.meta_image.image if self.bFlatfieldCorrection: self.logger.debug("* using flat field correction with image from %s" % self.strBackgroundImagePath) imgBackground = self._load_flatfield_correction_image(plate_id) crop_coordinated = MetaImage.get_crop_coordinates() if crop_coordinated is not None: self.logger.debug("* applying cropping to background image") imgBackground = ccore.subImage(imgBackground, ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]), ccore.Diff2D(crop_coordinated[2], crop_coordinated[3])) img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True) img_out = ccore.linearTransform2(img_in, self.fNormalizeMin, self.fNormalizeMax, 0, 255, 0, 255) else: self.logger.debug("* not using flat field correction") if type(img_in) == ccore.UInt16Image: img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) elif type(img_in) == ccore.Image: img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) else: img_out = img_in self.meta_image.set_image(img_out)
def normalize_image(self, plate_id=None): img_in = self.meta_image.image if self.bFlatfieldCorrection: self.logger.debug( "* using flat field correction with image from %s" % self.strBackgroundImagePath) imgBackground = self._load_flatfield_correction_image(plate_id) crop_coordinated = MetaImage.get_crop_coordinates() if crop_coordinated is not None: self.logger.debug("* applying cropping to background image") imgBackground = ccore.subImage( imgBackground, ccore.Diff2D(crop_coordinated[0], crop_coordinated[1]), ccore.Diff2D(crop_coordinated[2], crop_coordinated[3])) img_in = ccore.flatfieldCorrection(img_in, imgBackground, 0.0, True) img_out = ccore.linearTransform2(img_in, self.fNormalizeMin, self.fNormalizeMax, 0, 255, 0, 255) else: self.logger.debug("* not using flat field correction") if type(img_in) == ccore.UInt16Image: img_out = ccore.linearTransform3(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) elif type(img_in) == ccore.Image: img_out = ccore.linearTransform2(img_in, int(self.fNormalizeMin), int(self.fNormalizeMax), 0, 255, 0, 255) else: img_out = img_in self.meta_image.set_image(img_out)