About the execution of the "example.py"

[tiffanychang0101]

Hi, I have some problem about running the "example.py".

• running on terminal
• using conda virtual environment, and following README to install the environment

When I run the code using CMU-1.svs,
the process will hanging at pp.calculate_filters("slides_mpp_otsu.csv", "", "tiles_filters.csv") without errors.
This phenomenon also happened when I using my own data.

In the other hand,
if I run the code below first, then run pp.calculate_filters("slides_mpp_otsu.csv", "", "tiles_filters.csv"),
(that is, run calculate_filters funtion separately)
it will success.

What happened to this phenomenon?
Is it related to ProcessPoolExecutor?

import wsi_preprocessing as pp

# if, for instance, CMU-1.svs is in your current directory:
slides = pp.list_slides(".")

pp.save_slides_mpp_otsu(slides, "slides_mpp_otsu.csv")

# this may take some minutes, depending on your local machine
pp.run_tiling("slides_mpp_otsu.csv", "tiles.csv")

Thank you so much!!

[shanibenamitay]

Anyone encountered the following error when executing pp.save_slides_mpp_otsu(slides, "slides_mpp_otsu.csv") working on CMU-1.svs

File "", line 1, in
File "D:\Users\user\anaconda3\lib\site-packages\wsi_preprocessing\slides.py", line 37, in save_slides_mpp_otsu
vi = utils.read_image(file, access="sequential", level=2)
File "D:\Users\user\anaconda3\lib\site-packages\wsi_tile_cleanup\utils\pyvips.py", line 5, in read_image
vips_image = vips.Image.new_from_file(f"{image_path}", **kwargs)
File "D:\Users\user\anaconda3\lib\site-packages\pyvips\vimage.py", line 231, in new_from_file
return pyvips.Operation.call(name, filename,
File "D:\Users\user\anaconda3\lib\site-packages\pyvips\voperation.py", line 288, in call
raise Error('{0} does not support optional argument {1}'
pyvips.error.Error: VipsForeignLoadTiffFile does not support optional argument level

[ADE-17]

@lucasrla Can I work on this issue?

[LiuJin629]

@shanibenamitay I have the same question, and I don't know how to solve this question. Did you solve the question?

[LiuJin629]

What is the magnification of WSI after processing?