7

I am using the python API of openslide packages to read some ndpi file.When I use the read_region function, sometimes it return a odd image. What problems could have happend?

I have tried to read the full image, and it will be worked well. Therefore, I think there is no problem with the original file.

from openslide import OpenSlide
import cv2
import numpy as np

slide = OpenSlide('/Users/xiaoying/django/ndpi-rest-api/slide/read/21814102D-PAS - 2018-05-28 17.18.24.ndpi')
image = slide.read_region((1, 0),6, (780, 960))
image.save('image1.png')

The output is strange output

kinomoto-sakura
  • 71
  • 1
  • 2

2 Answers2

3

As the read_region documentation says, the x and y parameters are always in the coordinate space of level 0. For the behavior you want, you'll need to multiply those parameters by the downsample of the level you're reading.

Toya Teramoto
  • 39
  • 2
0

This appears to be a version-realted bug, see also

https://github.com/openslide/openslide/issues/291#issuecomment-722935212

The problem seems to relate to libpixman verions 0.38.x . There is a Workaround section written by GunnarFarneback suggesting to load a different version first e.g.

export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libpixman-1.so.0.34.0

upadte easier solution is:

We are using Python 3.6.8+ and this did the trick for us: conda install pixman=0.36.0

André Aichert
  • 313
  • 2
  • 11