コード例 #1
0
    def run(self, workspace):
        image = workspace.image_set.get_image(self.image_name.value,
                                              must_be_grayscale=True)
        orig_pixels = image.pixel_data
        if image.has_mask:
            mask = image.mask
        else:
            mask = np.ones(orig_pixels.shape, bool)
        if self.method == M_SOBEL:
            if self.direction == E_ALL:
                output_pixels = sobel(orig_pixels, mask)
            elif self.direction == E_HORIZONTAL:
                output_pixels = hsobel(orig_pixels, mask)
            elif self.direction == E_VERTICAL:
                output_pixels = vsobel(orig_pixels, mask)
            else:
                raise NotImplementedError(
                    "Unimplemented direction for Sobel: %s",
                    self.direction.value)
        elif self.method == M_LOG:
            sigma = self.get_sigma()
            size = int(sigma * 4) + 1
            output_pixels = laplacian_of_gaussian(orig_pixels, mask, size,
                                                  sigma)
        elif self.method == M_PREWITT:
            if self.direction == E_ALL:
                output_pixels = prewitt(orig_pixels)
            elif self.direction == E_HORIZONTAL:
                output_pixels = hprewitt(orig_pixels, mask)
            elif self.direction == E_VERTICAL:
                output_pixels = vprewitt(orig_pixels, mask)
            else:
                raise NotImplementedError(
                    "Unimplemented direction for Prewitt: %s",
                    self.direction.value)
        elif self.method == M_CANNY:
            high_threshold = self.manual_threshold.value
            low_threshold = self.low_threshold.value
            if (self.wants_automatic_low_threshold.value
                    or self.wants_automatic_threshold.value):
                sobel_image = sobel(orig_pixels, mask)
                low, high = otsu3(sobel_image[mask])
                if self.wants_automatic_low_threshold.value:
                    low_threshold = low * self.threshold_adjustment_factor.value
                if self.wants_automatic_threshold.value:
                    high_threshold = high * self.threshold_adjustment_factor.value
            output_pixels = canny(orig_pixels, mask, self.get_sigma(),
                                  low_threshold, high_threshold)
        elif self.method == M_ROBERTS:
            output_pixels = roberts(orig_pixels, mask)
        else:
            raise NotImplementedError(
                "Unimplemented edge detection method: %s" % self.method.value)

        output_image = cpi.Image(output_pixels, parent_image=image)
        workspace.image_set.add(self.output_image_name.value, output_image)

        if self.show_window:
            workspace.display_data.orig_pixels = orig_pixels
            workspace.display_data.output_pixels = output_pixels
コード例 #2
0
ファイル: EnhanceEdgesPlus.py プロジェクト: tischi/scripts
    def run(self, workspace):
        image = workspace.image_set.get_image(self.image_name.value,
                                              must_be_grayscale = True)
        orig_pixels = image.pixel_data
        if image.has_mask:
            mask = image.mask
        else:
            mask = np.ones(orig_pixels.shape,bool)
        if self.method == M_SOBEL:
            if self.direction == E_ALL:
                output_pixels = sobel(orig_pixels, mask)
            elif self.direction == E_HORIZONTAL:
                output_pixels = hsobel(orig_pixels, mask)
            elif self.direction == E_VERTICAL:
                output_pixels = vsobel(orig_pixels, mask)
            else:
                raise NotImplementedError("Unimplemented direction for Sobel: %s",self.direction.value)
        elif self.method == M_LOG:
            sigma = self.get_sigma()
            size = int(sigma * 4)+1
            output_pixels = laplacian_of_gaussian(orig_pixels, mask, size, sigma)
        elif self.method == M_VARIANCE:
            sigma = self.get_sigma()
            size = int(sigma)+1
            output_pixels = variance_transform(orig_pixels, size, mask)
        elif self.method == M_PREWITT:
            if self.direction == E_ALL:
                output_pixels = prewitt(orig_pixels)
            elif self.direction == E_HORIZONTAL:
                output_pixels = hprewitt(orig_pixels, mask)
            elif self.direction == E_VERTICAL:
                output_pixels = vprewitt(orig_pixels, mask)
            else:
                raise NotImplementedError("Unimplemented direction for Prewitt: %s",self.direction.value)
        elif self.method == M_CANNY:
            high_threshold = self.manual_threshold.value
            low_threshold = self.low_threshold.value
            if (self.wants_automatic_low_threshold.value or
                self.wants_automatic_threshold.value):
                sobel_image = sobel(orig_pixels, mask)
                low, high = otsu3(sobel_image[mask])
                if self.wants_automatic_low_threshold.value:
                    low_threshold = low * self.threshold_adjustment_factor.value
                if self.wants_automatic_threshold.value:
                    high_threshold = high * self.threshold_adjustment_factor.value
            output_pixels = canny(orig_pixels,mask, self.get_sigma(),
                                  low_threshold,
                                  high_threshold)
        elif self.method == M_ROBERTS:
            output_pixels = roberts(orig_pixels, mask)
        else:
            raise NotImplementedError("Unimplemented edge detection method: %s"%
                                      self.method.value)

        output_image = cpi.Image(output_pixels, parent_image = image)
        workspace.image_set.add(self.output_image_name.value, output_image)

        if self.show_window:
            workspace.display_data.orig_pixels = orig_pixels
            workspace.display_data.output_pixels = output_pixels
コード例 #3
0
 def test_03_02_prewitt_vertical(self):
     '''Test the prewitt vertical transform'''
     np.random.seed(0)
     image = np.random.uniform(size=(20,20)).astype(np.float32)
     workspace, module = self.make_workspace(image)
     module.method.value = F.M_PREWITT
     module.direction.value = F.E_VERTICAL
     module.run(workspace)
     output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
     self.assertTrue(np.all(output.pixel_data == FIL.vprewitt(image)))
コード例 #4
0
 def test_03_02_prewitt_vertical(self):
     '''Test the prewitt vertical transform'''
     np.random.seed(0)
     image = np.random.uniform(size=(20,20)).astype(np.float32)
     workspace, module = self.make_workspace(image)
     module.method.value = F.M_PREWITT
     module.direction.value = F.E_VERTICAL
     module.run(workspace)
     output = workspace.image_set.get_image(OUTPUT_IMAGE_NAME)
     self.assertTrue(np.all(output.pixel_data == FIL.vprewitt(image)))
コード例 #5
0
ファイル: enhanceedges.py プロジェクト: braniti/CellProfiler
 def run(self, workspace):
     image = workspace.image_set.get_image(self.image_name.value,
                                           must_be_grayscale = True)
     orig_pixels = image.pixel_data
     if image.has_mask:
         mask = image.mask
     else:
         mask = np.ones(orig_pixels.shape,bool)
     if self.method == M_SOBEL:
         if self.direction == E_ALL:
             output_pixels = sobel(orig_pixels, mask)
         elif self.direction == E_HORIZONTAL:
             output_pixels = hsobel(orig_pixels, mask)
         elif self.direction == E_VERTICAL:
             output_pixels = vsobel(orig_pixels, mask)
         else:
             raise NotImplementedError("Unimplemented direction for Sobel: %s",self.direction.value)
     elif self.method == M_LOG:
         sigma = self.get_sigma()
         size = int(sigma * 4)+1
         output_pixels = laplacian_of_gaussian(orig_pixels, mask, size, sigma)
     elif self.method == M_PREWITT:
         if self.direction == E_ALL:
             output_pixels = prewitt(orig_pixels)
         elif self.direction == E_HORIZONTAL:
             output_pixels = hprewitt(orig_pixels, mask)
         elif self.direction == E_VERTICAL:
             output_pixels = vprewitt(orig_pixels, mask)
         else:
             raise NotImplementedError("Unimplemented direction for Prewitt: %s",self.direction.value)
     elif self.method == M_CANNY:
         high_threshold = self.manual_threshold.value
         low_threshold = self.low_threshold.value
         if (self.wants_automatic_low_threshold.value or
             self.wants_automatic_threshold.value):
             sobel_image = sobel(orig_pixels, mask)
             low, high = otsu3(sobel_image[mask])
             if self.wants_automatic_low_threshold.value:
                 low_threshold = low * self.threshold_adjustment_factor.value
             if self.wants_automatic_threshold.value:
                 high_threshold = high * self.threshold_adjustment_factor.value
         output_pixels = canny(orig_pixels,mask, self.get_sigma(),
                               low_threshold,
                               high_threshold)
     elif self.method == M_ROBERTS:
         output_pixels = roberts(orig_pixels, mask)
     else:
         raise NotImplementedError("Unimplemented edge detection method: %s"%
                                   self.method.value)
     if not workspace.frame is None:
         figure = workspace.create_or_find_figure(title="EnhanceEdges, image cycle #%d"%(
             workspace.measurements.image_set_number),subplots=(2,2))
         figure.subplot_imshow_grayscale(0,0, orig_pixels,
                                         "Original: %s"%
                                         self.image_name.value)
         if self.method == M_CANNY:
             # Canny is binary
             figure.subplot_imshow_bw(0,1, output_pixels,
                                      self.output_image_name.value,
                                      sharex = figure.subplot(0,0),
                                      sharey = figure.subplot(0,0))
         else:
             figure.subplot_imshow_grayscale(0,1,output_pixels,
                                             self.output_image_name.value,
                                             sharex = figure.subplot(0,0),
                                             sharey = figure.subplot(0,0))
         color_image = np.zeros((output_pixels.shape[0],
                                 output_pixels.shape[1],3))
         color_image[:,:,0] = stretch(orig_pixels)
         color_image[:,:,1] = stretch(output_pixels)
         figure.subplot_imshow(1,0, color_image,"Composite image",
                               sharex = figure.subplot(0,0),
                               sharey = figure.subplot(0,0))
     output_image = cpi.Image(output_pixels, parent_image = image)
     workspace.image_set.add(self.output_image_name.value, output_image)   
コード例 #6
0
 def run(self, workspace):
     image = workspace.image_set.get_image(self.image_name.value,
                                           must_be_grayscale=True)
     orig_pixels = image.pixel_data
     if image.has_mask:
         mask = image.mask
     else:
         mask = np.ones(orig_pixels.shape, bool)
     if self.method == M_SOBEL:
         if self.direction == E_ALL:
             output_pixels = sobel(orig_pixels, mask)
         elif self.direction == E_HORIZONTAL:
             output_pixels = hsobel(orig_pixels, mask)
         elif self.direction == E_VERTICAL:
             output_pixels = vsobel(orig_pixels, mask)
         else:
             raise NotImplementedError(
                 "Unimplemented direction for Sobel: %s",
                 self.direction.value)
     elif self.method == M_LOG:
         sigma = self.get_sigma()
         size = int(sigma * 4) + 1
         output_pixels = laplacian_of_gaussian(orig_pixels, mask, size,
                                               sigma)
     elif self.method == M_PREWITT:
         if self.direction == E_ALL:
             output_pixels = prewitt(orig_pixels)
         elif self.direction == E_HORIZONTAL:
             output_pixels = hprewitt(orig_pixels, mask)
         elif self.direction == E_VERTICAL:
             output_pixels = vprewitt(orig_pixels, mask)
         else:
             raise NotImplementedError(
                 "Unimplemented direction for Prewitt: %s",
                 self.direction.value)
     elif self.method == M_CANNY:
         high_threshold = self.manual_threshold.value
         low_threshold = self.low_threshold.value
         if (self.wants_automatic_low_threshold.value
                 or self.wants_automatic_threshold.value):
             sobel_image = sobel(orig_pixels, mask)
             low, high = otsu3(sobel_image[mask])
             if self.wants_automatic_low_threshold.value:
                 low_threshold = low * self.threshold_adjustment_factor.value
             if self.wants_automatic_threshold.value:
                 high_threshold = high * self.threshold_adjustment_factor.value
         output_pixels = canny(orig_pixels, mask, self.get_sigma(),
                               low_threshold, high_threshold)
     elif self.method == M_ROBERTS:
         output_pixels = roberts(orig_pixels, mask)
     else:
         raise NotImplementedError(
             "Unimplemented edge detection method: %s" % self.method.value)
     if not workspace.frame is None:
         figure = workspace.create_or_find_figure(
             title="EnhanceEdges, image cycle #%d" %
             (workspace.measurements.image_set_number),
             subplots=(2, 2))
         figure.subplot_imshow_grayscale(
             0, 0, orig_pixels, "Original: %s" % self.image_name.value)
         if self.method == M_CANNY:
             # Canny is binary
             figure.subplot_imshow_bw(0,
                                      1,
                                      output_pixels,
                                      self.output_image_name.value,
                                      sharex=figure.subplot(0, 0),
                                      sharey=figure.subplot(0, 0))
         else:
             figure.subplot_imshow_grayscale(0,
                                             1,
                                             output_pixels,
                                             self.output_image_name.value,
                                             sharex=figure.subplot(0, 0),
                                             sharey=figure.subplot(0, 0))
         color_image = np.zeros(
             (output_pixels.shape[0], output_pixels.shape[1], 3))
         color_image[:, :, 0] = stretch(orig_pixels)
         color_image[:, :, 1] = stretch(output_pixels)
         figure.subplot_imshow(1,
                               0,
                               color_image,
                               "Composite image",
                               sharex=figure.subplot(0, 0),
                               sharey=figure.subplot(0, 0))
     output_image = cpi.Image(output_pixels, parent_image=image)
     workspace.image_set.add(self.output_image_name.value, output_image)