NCRF: slide/mask mismatch

If I follow the instructions for testing as given in readme. I get the following error

Traceback (most recent call last):
  File "wsi/bin/probs_map.py", line 163, in <module>
    main()
  File "wsi/bin/probs_map.py", line 159, in main
    run(args)
  File "wsi/bin/probs_map.py", line 115, in run
    args, cfg, flip='NONE', rotate='NONE')
  File "wsi/bin/probs_map.py", line 87, in make_dataloader
    flip=flip, rotate=rotate),
  File "/media/udion/a2c5c487-f939-4b82-a348-86b3d1bdb024/udion_home/Projects/NCRF/wsi/bin/../../wsi/data/wsi_producer.py", line 42, in __init__
    self._preprocess()
  File "/media/udion/a2c5c487-f939-4b82-a348-86b3d1bdb024/udion_home/Projects/NCRF/wsi/bin/../../wsi/data/wsi_producer.py", line 55, in _preprocess
    .format(X_slide, X_mask, Y_slide, Y_mask))
Exception: Slide/Mask dimension does not match , X_slide / X_mask : 98304 / 1536, Y_slide / Y_mask : 103936 / 2048

what’s the issue?

About this issue

Original URL
State: closed
Created 6 years ago
Comments: 30

Most upvoted comments

@yil8 @udion

I upgraded my OpenSlide binary to 3.4.1 and the slides have the same dimension as mentioned by @yil8:

In [1]: import openslide

In [2]: slide = openslide.OpenSlide('./test_026.tif')

In [3]: slide.level_dimensions
Out[3]: 
((98304, 103936),
 (49152, 51968),
 (24576, 25984),
 (12288, 12992),
 (6144, 6496),
 (3072, 3248),
 (1536, 1624),
 (768, 812),
 (384, 406))

meetps on Jul 5, 2018

@meetshah1995 my binary version:

openslide-show-properties --version
openslide-show-properties 3.4.1, using OpenSlide 3.4.1
Copyright (C) 2007-2015 Carnegie Mellon University and others

OpenSlide is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License, version 2.1.
<http://gnu.org/licenses/lgpl-2.1.html>

OpenSlide comes with NO WARRANTY, to the extent permitted by law.  See the
GNU Lesser General Public License for more details.

yil8 on Jul 5, 2018

@yil8 The slide does not keep a consistent ratio occurs in Training dataset(almost all ). Tumor026: (97280, 220672) (48640, 110592) (24576, 55296) (12288, 27648) (6144, 13824) (3072, 7168) (1536, 3584) (1024, 2048) (512, 1024) (512, 512) Here is my solution in tisuue_mask.py:

    slide = openslide.OpenSlide(args.wsi_path)
    dims_tuple =  (int(slide.level_dimensions[0][0]/(2**args.level)), int(slide.level_dimensions[0][1]/(2**args.level)))
    #print(dims_tuple)
    # note the shape of img_RGB is the transpose of slide.level_dimensions
    img_RGB = np.transpose(np.array(slide.read_region((0, 0),
                           args.level,
                           slide.level_dimensions[args.level]).convert('RGB')),
                           axes=[1, 0, 2])
    #print((img_RGB.shape))
    img_RGB = cv2.resize(img_RGB,(dims_tuple[1],dims_tuple[0]))

sketchplanet on Jun 29, 2018

@meetshah1995 Thanks so much for spotting this potential issue! I’ll add this into README.

yil8 on Jul 5, 2018

I’m splitting the file using tiffsplit which created one tif file for each level:

tiffsplit <input_multilevel_tiff>

meetps on Jul 2, 2018

@udion I was using the data from Google drive. BTW, there seems to be a application free download link from GigaDB, and I just downloaded test_026.tif, which gave me the correct level_dimensions:

In [1]: import openslide

In [2]: slide = openslide.OpenSlide('./test_026.tif')

In [3]: slide.level_dimensions
Out[3]: 
((98304, 103936),
 (49152, 51968),
 (24576, 25984),
 (12288, 12992),
 (6144, 6496),
 (3072, 3248),
 (1536, 1624),
 (768, 812),
 (384, 406))

yil8 on Jun 29, 2018