Update utils.py

GANDLF/data/patch_miner/opm/utils.py

@@ -10,8 +10,9 @@
 from skimage.morphology import remove_small_holes
 from skimage.color.colorconv import rgb2hsv
 import cv2
-#from skimage.exposure import rescale_intensity
-#from skimage.color import rgb2hed
+
+# from skimage.exposure import rescale_intensity
+# from skimage.color import rgb2hed
 
 # import matplotlib.pyplot as plt
 import yaml
@@ -238,7 +239,8 @@ def alpha_rgb_2d_channel_check(img):
     else:
         return False
 
-#def pen_marking_check(img, intensity_thresh=225, intensity_thresh_saturation =50, intensity_thresh_b = 128):
+
+# def pen_marking_check(img, intensity_thresh=225, intensity_thresh_saturation =50, intensity_thresh_b = 128):
 #    """
 #    This function is used to curate patches from the input image. It is used to remove patches that have pen markings.
 #    Args:
@@ -259,7 +261,14 @@ def alpha_rgb_2d_channel_check(img):
 #    #Assume patch is valid
 #    return True
 
-def patch_artifact_check(img, intensity_thresh = 250, intensity_thresh_saturation = 5, intensity_thresh_b = 128, patch_size = (256,256)):
+
+def patch_artifact_check(
+    img,
+    intensity_thresh=250,
+    intensity_thresh_saturation=5,
+    intensity_thresh_b=128,
+    patch_size=(256, 256),
+):
     """
     This function is used to curate patches from the input image. It is used to remove patches that are mostly background.
     Args:
@@ -271,23 +280,36 @@ def patch_artifact_check(img, intensity_thresh = 250, intensity_thresh_saturatio
     Returns:
         bool: Whether the patch is valid (True) or not (False)
     """
-    #patch_size = config["patch_size"]
+    # patch_size = config["patch_size"]
     patch_hsv = cv2.cvtColor(img, cv2.COLOR_RGB2HSV)
     count_white_pixels = np.sum(np.logical_and.reduce(img > intensity_thresh, axis=2))
     percent_pixels = count_white_pixels / (patch_size[0] * patch_size[1])
     count_black_pixels = np.sum(np.logical_and.reduce(img < intensity_thresh_b, axis=2))
     percent_pixel_b = count_black_pixels / (patch_size[0] * patch_size[1])
-    percent_pixel_2 = np.sum(patch_hsv[...,1] < intensity_thresh_saturation) / (patch_size[0] * patch_size[1])
-    percent_pixel_3 = np.sum(patch_hsv[...,2] > intensity_thresh) / (patch_size[0] * patch_size[1])
+    percent_pixel_2 = np.sum(patch_hsv[..., 1] < intensity_thresh_saturation) / (
+        patch_size[0] * patch_size[1]
+    )
+    percent_pixel_3 = np.sum(patch_hsv[..., 2] > intensity_thresh) / (
+        patch_size[0] * patch_size[1]
+    )
 
-    if percent_pixel_2 > 0.99 or np.mean(patch_hsv[...,1]) < 5 or percent_pixel_3 > 0.99:
+    if (
+        percent_pixel_2 > 0.99
+        or np.mean(patch_hsv[..., 1]) < 5
+        or percent_pixel_3 > 0.99
+    ):
         if percent_pixel_2 < 0.1:
             return False
-    elif (percent_pixel_2 > 0.99 and percent_pixel_3 > 0.99) or percent_pixel_b > 0.99 or percent_pixels > 0.9:
+    elif (
+        (percent_pixel_2 > 0.99 and percent_pixel_3 > 0.99)
+        or percent_pixel_b > 0.99
+        or percent_pixels > 0.9
+    ):
         return False
     # assume that the patch is valid
     return True
 
+
 def parse_config(config_file):
     """
     Parse config file and return a dictionary of config values.
@@ -304,7 +326,7 @@ def parse_config(config_file):
     config["value_map"] = config.get("value_map", None)
     config["read_type"] = config.get("read_type", "random")
     config["overlap_factor"] = config.get("overlap_factor", 0.0)
-    config["patch_size"] = config.get("patch_size", [256,256])
+    config["patch_size"] = config.get("patch_size", [256, 256])
 
     return config