Update GANDLF/data/patch_miner/opm/utils.py

GANDLF/data/patch_miner/opm/utils.py

@@ -262,33 +262,33 @@ def pen_marking_check(img, intensity_thresh=225, intensity_thresh_saturation =50
 """
 
 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:
- img (np.ndarray): Input Patch Array to check the artifact/background.
- intensity_thresh (int, optional): Threshold to check whiteness in the patch. Defaults to 225.
- intensity_thresh_saturation (int, optional): Threshold to check saturation in the patch. Defaults to 50.
- intensity_thresh_b (int, optional) : Threshold to check blackness in the patch
- patch_size (int, optional): Tiling Size of the WSI/patch size. Defaults to 256. patch_size=config["patch_size"]
- Returns:
- bool: Whether the patch is valid (True) or not (False)
- """
- #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])
-
- 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:
+ """
+ This function is used to curate patches from the input image. It is used to remove patches that are mostly background.
+ Args:
+ img (np.ndarray): Input Patch Array to check the artifact/background.
+ intensity_thresh (int, optional): Threshold to check whiteness in the patch. Defaults to 225.
+ intensity_thresh_saturation (int, optional): Threshold to check saturation in the patch. Defaults to 50.
+ intensity_thresh_b (int, optional) : Threshold to check blackness in the patch
+ patch_size (int, optional): Tiling Size of the WSI/patch size. Defaults to 256. patch_size=config["patch_size"]
+ Returns:
+ bool: Whether the patch is valid (True) or not (False)
+ """
+ #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])
+
+ 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
- # assume that the patch is valid
- return True
+ 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):
  """