Scripts for handling the images

bg_to_rgb.py

@@ -2,7 +2,7 @@
 from imageio import imread, imwrite
 import glob
 import os
-import matplotlib.pyplot as plt
+# import matplotlib.pyplot as plt
 
 for ind, image_path in enumerate(glob.glob("data/MSD/Task09_Spleen_2D_512_Balanced/images/training/*.png")):
     image = imread(image_path)

check_images.py

@@ -0,0 +1,59 @@
+from imageio import imread, imwrite
+import numpy as np
+import glob
+import shutil as sh
+import os
+
+name = "Task06_Lungs_RGB_2D_512_Balanced"
+
+tr_root_img_folder = f"data/MSD/{name}/images/training"
+val_root_img_folder = f"data/MSD/{name}/images/validation"
+tr_root_annot_folder = f"data/MSD/{name}/annotations/training"
+val_root_annot_folder = f"data/MSD/{name}/annotations/validation"
+
+for ind, image_path in enumerate(glob.glob(f"{tr_root_img_folder}/*.png")):
+    image_bg = imread(image_path)
+    if not isinstance(image_bg, np.ndarray):
+        print("-----------------")
+        print(image_path)
+        print(type(image_bg))
+    else:
+        if image_bg.shape != (512, 512, 3):
+            print("-----------------")
+            print(image_path)
+            print(type(image_bg))
+for ind, image_path in enumerate(glob.glob(f"{val_root_img_folder}/*.png")):
+    image_bg = imread(image_path)
+    if not isinstance(image_bg, np.ndarray):
+        print("-----------------")
+        print(image_path)
+        print(type(image_bg))
+    else:
+        if image_bg.shape != (512, 512, 3):
+            print("-----------------")
+            print(image_path)
+            print(type(image_bg))
+
+for ind, image_path in enumerate(glob.glob(f"{tr_root_annot_folder}/*.png")):
+    image_bg = imread(image_path)
+    if not isinstance(image_bg, np.ndarray):
+        print("-----------------")
+        print(image_path)
+        print(type(image_bg))
+    else:
+        if image_bg.shape != (512, 512):
+            print("-----------------")
+            print(image_path)
+            print(type(image_bg))
+for ind, image_path in enumerate(glob.glob(f"{val_root_annot_folder}/*.png")):
+    image_bg = imread(image_path)
+    if not isinstance(image_bg, np.ndarray):
+        print("-----------------")
+        print(image_path)
+        print(type(image_bg))
+    else:
+        if image_bg.shape != (512, 512):
+            print("-----------------")
+            print(image_path)
+            print(type(image_bg))
+

rgb_to_bg.py

@@ -0,0 +1,25 @@
+from imageio import imread, imwrite
+import numpy as np
+import glob
+import shutil as sh
+import os
+
+name = "Task06_Lungs_RGB_2D_512_Balanced"
+
+tr_root_folder = f"data/MSD/{name}/annotations/training"
+val_root_folder = f"data/MSD/{name}/annotations/validation"
+
+if not os.path.exists(tr_root_folder + "_copy"):
+    sh.copytree(tr_root_folder, tr_root_folder + "_copy")
+if not os.path.exists(val_root_folder + "_copy"):
+    sh.copytree(val_root_folder, val_root_folder + "_copy")
+
+for ind, image_path in enumerate(glob.glob(f"{tr_root_folder}/*.png")):
+    image_rgb = imread(image_path)
+    image_bg = image_rgb[:, :, 0]
+    imwrite(image_path, image_bg)
+
+for ind, image_path in enumerate(glob.glob(f"{val_root_folder}/*.png")):
+    image_rgb = imread(image_path)
+    image_bg = image_rgb[:, :, 0]
+    imwrite(image_path, image_bg)