Adding the visualisation module for producing the mosaic of the align…

…ed images.
parichit · Jul 11, 2018 · 5e6ca3585fccd4bac44e0943dd1ace2e7d03cd43 · 5e6ca35
1 parent 56dbb2e
commit 5e6ca3585fccd4bac44e0943dd1ace2e7d03cd43
Unified Split

Showing with 100 additions and 1 deletion.

+100 −1 dipy/workflows/align.py
diff --git a/dipy/workflows/align.py b/dipy/workflows/align.py
@@ -15,6 +15,8 @@
 from dipy.viz.regtools import overlay_images
 from dipy.segment.mask import median_otsu
+  
+from dipy.viz import window, actor, ui
+  
+
 class ResliceFlow(Workflow):
@@ -85,6 +87,101 @@ class ImageRegistrationFlow(Workflow):
    This can be controlled by using the progressive flag (True by default).
    """
+  
+    def test_visual(self, static_img, static_grid2world, moved_img,
+  
+                               moving_grid2world):
+  
+
+  
+        # Normalize the input images to [0,255]
+  
+        static_img = 255 * ((static_img - static_img.min()) / (static_img.max() - static_img.min()))
+  
+        moved_img = 255 * ((moved_img - moved_img.min()) / (moved_img.max() - moved_img.min()))
+  
+
+  
+        # Create the color images
+  
+        overlay = np.zeros(shape=(static_img.shape) + (3,), dtype=np.uint8)
+  
+
+  
+        # Copy the normalized intensities into the appropriate channels of the
+  
+        # color images
+  
+        overlay[..., 0] = static_img
+  
+        overlay[..., 1] = moved_img
+  
+
+  
+        data = overlay
+  
+        affine = moving_grid2world
+  
+
+  
+        renderer = window.Renderer()
+  
+        renderer.background((0.5, 0.5, 0.5))
+  
+
+  
+        mean, std = data[data > 0].mean(), data[data > 0].std()
+  
+        value_range = (mean - 0.5 * std, mean + 1.5 * std)
+  
+
+  
+        lut = actor.colormap_lookup_table(scale_range=(0, 255),
+  
+                                          hue_range=(0.4, 1.),
+  
+                                          saturation_range=(1, 1.),
+  
+                                          value_range=(0., 1.))
+  
+
+  
+        slice_actor = actor.slicer(data, affine, value_range, lookup_colormap=lut)
+  
+        renderer.projection('parallel')
+  
+
+  
+        result_position = ui.TextBlock2D(text='')
+  
+        result_value = ui.TextBlock2D(text='')
+  
+
+  
+        result_position.message = ''
+  
+        result_value.message = ''
+  
+
+  
+        show_m_mosaic = window.ShowManager(renderer, size=(1200, 900))
+  
+        show_m_mosaic.initialize()
+  
+
+  
+        def left_click_callback_mosaic(obj, ev):
+  
+            """Get the value of the clicked voxel and show it in the panel."""
+  
+            event_pos = show_m_mosaic.iren.GetEventPosition()
+  
+
+  
+            obj.picker.Pick(event_pos[0],
+  
+                            event_pos[1],
+  
+                            0,
+  
+                            show_m_mosaic.ren)
+  
+
+  
+            i, j, k = obj.picker.GetPointIJK()
+  
+            result_position.message = '({}, {}, {})'.format(str(i), str(j), str(k))
+  
+            result_value.message = '%.8f' % data[i, j, k]
+  
+
+  
+        cnt = 0
+  
+        print('hello')
+  
+        print(slice_actor.shape)
+  
+        X, Y, Z = slice_actor.shape
+  
+
+  
+        rows = 10
+  
+        cols = 15
+  
+        border = 10
+  
+        # panel_picking = ui.Panel2D(center=(200, 120),
+  
+        #                            size=(250, 125),
+  
+        #                            color=(0, 0, 0),
+  
+        #                            opacity=0.75,
+  
+        #                            align="left")
+  
+
+  
+        for j in range(rows):
+  
+            for i in range(cols):
+  
+                slice_mosaic = slice_actor.copy()
+  
+                slice_mosaic.display(None, None, cnt)
+  
+                slice_mosaic.SetPosition((X + border) * i,
+  
+                                         0.5 * cols * (Y + border) - (Y + border) * j,
+  
+                                         0)
+  
+                slice_mosaic.SetInterpolate(False)
+  
+                slice_mosaic.AddObserver('LeftButtonPressEvent',
+  
+                                         left_click_callback_mosaic,
+  
+                                         1.0)
+  
+                renderer.add(slice_mosaic)
+  
+                cnt += 1
+  
+                if cnt > Z:
+  
+                    break
+  
+            if cnt > Z:
+  
+                break
+  
+
+  
+        renderer.reset_camera()
+  
+        renderer.zoom(1.6)
+  
+
+  
+        #show_m_mosaic.ren.add(panel_picking)
+  
+        #show_m_mosaic.start()
+  
+
+  
+        window.record(renderer, out_path='mosaic.png', size=(900, 600),
+  
+                      reset_camera=False)
+  
+
    def create_overlaid_images(self, static_img, static_grid2world, moved_img,
                               moving_grid2world):
@@ -473,6 +570,8 @@ def run(self, static_img_file, moving_img_file, transform='affine',
                                                          static_grid2world,
                                                          moving,
                                                          moving_grid2world)
+  
+                self.test_visual(static, static_grid2world,
+  
+                                 moved_image, moving_grid2world)
            else:
                params0 = None
@@ -526,7 +625,7 @@ def run(self, static_img_file, moving_img_file, transform='affine',
                Saving the moved image file and the affine matrix.
                """
-  
-                self.create_overlaid_images(static, static_grid2world,
+  
+                self.test_visual(static, static_grid2world,
                                            moved_image, moving_grid2world)
                logging.info("Similarity metric:"+str(xopt))
                logging.info("Distance measure:"+str(fopt))