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fix inverse masking issue with transparent background #292

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fix inverse masking issue with transparent background #292

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33 changes: 28 additions & 5 deletions misc/wsi_handler.py
100755 → 100644
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from skimage import color
import re
import subprocess
from PIL import Image

import openslide

Expand All @@ -21,7 +22,24 @@ def __init__(self):
("mpp ", None),
("base_shape", None),
}
pass
self.image_ptr = None
self.read_lv = None

@staticmethod
def pil_to_rgb_array(pil_img):
"""Convert PIL image to RGB numpy array, properly handling transparency.

Args:
pil_img: PIL image object (can be RGBA or any other mode)

Returns:
numpy array with RGB values
"""
if pil_img.mode == 'RGBA':
background = Image.new('RGBA', pil_img.size, (255, 255, 255, 255))
return np.array(Image.alpha_composite(background, pil_img).convert('RGB'))
else:
return np.array(pil_img.convert('RGB'))

def __load_metadata(self):
raise NotImplementedError
Expand Down Expand Up @@ -157,12 +175,15 @@ def read_region(self, coords, size):
new_coord = [0, 0]
new_coord[0] = int(coords[0] * up_sample)
new_coord[1] = int(coords[1] * up_sample)
region = self.file_ptr.read_region(new_coord, self.read_lv, size)

# Read the region and handle transparency
region_pil = self.file_ptr.read_region(new_coord, self.read_lv, size)
return self.pil_to_rgb_array(region_pil)
else:
region = self.image_ptr[
coords[1] : coords[1] + size[1], coords[0] : coords[0] + size[0]
]
return np.array(region)[..., :3]
return np.array(region)[..., :3]

def get_full_img(self, read_mag=None, read_mpp=None):
"""Only use `read_mag` or `read_mpp`, not both, prioritize `read_mpp`.
Expand All @@ -176,8 +197,10 @@ def get_full_img(self, read_mag=None, read_mpp=None):

read_size = self.file_ptr.level_dimensions[read_lv]

wsi_img = self.file_ptr.read_region((0, 0), read_lv, read_size)
wsi_img = np.array(wsi_img)[..., :3] # remove alpha channel
# Read the WSI and handle transparency
wsi_pil = self.file_ptr.read_region((0, 0), read_lv, read_size)
wsi_img = self.pil_to_rgb_array(wsi_pil)

if scale_factor is not None:
# now rescale then return
if scale_factor > 1.0:
Expand Down