plots

Author: kaftanski

keypoint_plots.py

@@ -17,11 +17,12 @@
 result_folder = 'results/plots/keypoints'
 
 
-def plot_keypoints(image, mode, patid, slice_num, slice_dim=1, spacing=1.5):
+def plot_keypoints(image, mode, patid, slice_num, slice_dim=1, spacing=1.5, crop_indices=None):
     pts, _, _, _ = load_points(os.path.join(POINT_DIR_TS, mode), patid)
     pts = (pts.T + 1)/2 * np.flip(np.array(image.shape))[None]
 
-    crop_indices = crop_to_lung_indices(image)
+    if crop_indices is None:
+        crop_indices = crop_to_lung_indices(image)
     slice_num_cropped = slice_num - crop_indices[slice_dim].start
     image = image[crop_indices]
     index = [slice(None)] * slice_dim + [slice(slice_num_cropped, slice_num_cropped + 1)]
@@ -37,7 +38,7 @@ def plot_keypoints(image, mode, patid, slice_num, slice_dim=1, spacing=1.5):
     ax.set_axis_off()
     ax.imshow(img_slice, cmap='gray')
     ax.scatter(pts_slice[:, pts_index[0]], pts_slice[:, pts_index[1]], marker='+', s=150, c='orangered', linewidths=2)
-    save_fig(fig, result_folder, f'{mode}_keypoints_s0070_slice{slice_num}', pdf=False)
+    save_fig(fig, result_folder, f'{mode}_keypoints_{patid}_slice{slice_num}', pdf=False)
 
 
 def plot_all(patid='s0070'):
@@ -50,6 +51,31 @@ def plot_all(patid='s0070'):
         plot_keypoints(img_window, mode, slice_num=118, patid=patid, slice_dim=1)
 
 
+def plot_bad_example_enhancement():
+    patid = 's1024'
+    slice_num = 287# 316
+    ds = ImageDataset(IMG_DIR_TS)
+    img_index = ds.get_index(patid, 'fixed')
+    enhanced = ds.get_enhanced_fissures(img_index)
+    enhanced = sitk.GetArrayFromImage(enhanced)
+    mask = resample_equal_spacing(ds.get_lung_mask(img_index), use_nearest_neighbor=True)
+    mask = sitk.GetArrayFromImage(mask)
+    enhanced[mask == 0], _ = slice_image(enhanced, slice_num=slice_num, slice_dim=1).max()
+    crop_indices = (slice(15, 200), slice(0, enhanced.shape[1]), slice(130, 400))
+    plot_keypoints(enhanced, 'enhancement', slice_num=slice_num, patid=patid, slice_dim=1, crop_indices=crop_indices)
+
+    img = ds.get_image(img_index)
+    img = resample_equal_spacing(img)
+    img_window = fissure_window_level_and_mask(sitk.GetArrayFromImage(img), mask, high=0)
+    img_crop = img_window[crop_indices]
+    img_slice, _ = slice_image(img_crop, slice_num=slice_num, slice_dim=1)
+    fig = create_image_figure(img_window)
+    ax = fig.gca()
+    ax.set_axis_off()
+    ax.imshow(img_slice, cmap='gray')
+    save_fig(fig, result_folder, f'{patid}_slice{slice_num}', pdf=False)
+
+
 def plot_enhancement(patid='s0070'):
     ds = ImageDataset(IMG_DIR_TS)
     img_index = ds.get_index(patid, 'fixed')
@@ -77,21 +103,21 @@ def plot_enhancement(patid='s0070'):
     slice_num = 118
     slice_num_cropped = slice_num - crop_indices[slice_dim].start
 
-    enhanced = slice_image(enhanced, slice_num_cropped, slice_dim)
+    enhanced, _ = slice_image(enhanced, slice_num_cropped, slice_dim)
     fig = create_image_figure(enhanced)
     ax = fig.gca()
     ax.set_axis_off()
     ax.imshow(enhanced)
     save_fig(fig, result_folder, 'enhancement_result', pdf=False)
 
-    planeness = slice_image(planeness, slice_num_cropped, slice_dim)
+    planeness, _ = slice_image(planeness, slice_num_cropped, slice_dim)
     fig = create_image_figure(planeness)
     ax = fig.gca()
     ax.set_axis_off()
     ax.imshow(planeness)
     save_fig(fig, result_folder, 'enhancement_planeness', pdf=False)
 
-    hu_weights = slice_image(hu_weights, slice_num_cropped, slice_dim)
+    hu_weights, _ = slice_image(hu_weights, slice_num_cropped, slice_dim)
     fig = create_image_figure(hu_weights)
     ax = fig.gca()
     ax.set_axis_off()
@@ -102,4 +128,5 @@ def plot_enhancement(patid='s0070'):
 if __name__ == '__main__':
     KP_MODES.remove('noisy')
     # plot_all()
-    plot_enhancement()
+    # plot_enhancement()
+    plot_bad_example_enhancement()

qualitative.py

@@ -22,12 +22,11 @@ def create_image_figure(img):
 
 def slice_image(img_3d, slice_num, slice_dim):
     index = [slice(None)] * slice_dim + [slice(slice_num, slice_num + 1)]
-    return img_3d[index].squeeze()
+    return img_3d[index].squeeze(), index
 
 
-def fissure_window_level_and_mask(img: np.ndarray, mask: np.ndarray):
+def fissure_window_level_and_mask(img: np.ndarray, mask: np.ndarray, high=-600):
     low = -1024
-    high = -600
     img[img < low] = low
     img[img > high] = high
     img[mask == 0] = high + 1
@@ -126,12 +125,12 @@ def kp_comparison_figure(patid='s0070', ae=False):
     img_windowed, fold = get_image_and_fold(patid)
     result_folders = {model: os.path.join(folder, f'fold{fold}', 'test_predictions', 'labelmaps') for model, folder in model_folders.items()}
 
-    target = sitk.ReadImage(os.path.join(result_folders['cnn'], f'{patid}_fissures_targ_fixed.nii.gz'))
+    target = sitk.ReadImage(os.path.join(result_folders['cnn'].replace(model, 'DGCNN_seg'), f'{patid}_fissures_targ_fixed.nii.gz'))
     label_maps = {model: sitk.ReadImage(os.path.join(path, f'{patid}_fissures_pred_fixed.nii.gz')) for model, path in result_folders.items()}
     label_maps['ground-truth'] = target
 
     for kp in label_maps.keys():
-        model_name = f'DGCNN_seg_{kp}_image' if kp != 'ground-truth' else 'ground-truth'
+        model_name = f'{model}_{kp}_image' if kp != 'ground-truth' else 'ground-truth'
         multi_class_overlay(img_windowed, label_maps[kp], slice_dim=2, model_name=model_name, patid=patid)
 
 
@@ -161,4 +160,4 @@ def comparative_figures(patid='s0070'):
 
 if __name__ == '__main__':
     # comparative_figures()
-    kp_comparison_figure()
+    kp_comparison_figure(ae=True)