From 38bf5cb2ae80945caf40ed47ca2c6b079734f2c3 Mon Sep 17 00:00:00 2001
From: drkostas <georgiou.kostas94@gmail.com>
Date: Tue, 17 May 2022 13:29:47 -0400
Subject: [PATCH] Scripts for handling the images

---
 bg_to_rgb.py    |  2 +-
 check_images.py | 59 +++++++++++++++++++++++++++++++++++++++++++++++++
 rgb_to_bg.py    | 25 +++++++++++++++++++++
 3 files changed, 85 insertions(+), 1 deletion(-)
 create mode 100644 check_images.py
 create mode 100644 rgb_to_bg.py

diff --git a/bg_to_rgb.py b/bg_to_rgb.py
index 98d616b..07ff915 100644
--- a/bg_to_rgb.py
+++ b/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)
diff --git a/check_images.py b/check_images.py
new file mode 100644
index 0000000..66075ad
--- /dev/null
+++ b/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))
+
diff --git a/rgb_to_bg.py b/rgb_to_bg.py
new file mode 100644
index 0000000..263e522
--- /dev/null
+++ b/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)