Closed Himanshunitrr closed 2 months ago
jacksonjacobs1
commented
2 months ago Hi @Himanshunitrr , Can you try using openslide.OpenSlide() instead of open_slide()?
Also, it looks like your jupyter notebook was run outside of your HistoQC docker container. Try opening the image from within the docker container to ensure the environment is exactly the same.
Himanshunitrr
commented
2 months ago I looked in the code in __main__.py,
files = [] with open("tcga_path_histoqc.tsv", 'rt') as f: for line in f: if line[0] == "#": continue fn = line.strip().split("\t")[0] print(fn)
it gave the entire list as a single file name, the tsv file was corrupted. I made the changes (ensured that the tabs delimiter are there) and its now running
I am trying to run histoqc on selected files in a dataset (TCGA Breast) using
python -m histoqc -c /workspace/histoqc_config.ini -n 3 /workspace/tcga_path_histoqc.tsv
where tcga_path_histoqc.tsv looks is a tsv file containing list of all files of interest as mentioned in docs
... .more files . /data/TCGA-XX-A89A-01Z-00-DX1.671E2AD6-4D1A-4579-88C1-5B0B15818126.svs, /data/TCGA-Z7-A8R6-01Z-00-DX1.CE4ED818-D762-4324-9DEA-2ACB38B9B0B9.svs,] The error which I am getting is : 2024-08-26 22:00:16,886 - ERROR - /data/TCGA-XX-A89A-01Z-00-DX1.671E2AD6-4D1A-4579-88C1-5B0B15818126.svs, - Error analyzing file (skipping): <class 'openslide.lowlevel.OpenSlideUnsupportedFormatError'> OpenSlide does not support the requested file. Import this from openslide rather than from openslide.lowlevel. Unsupported or missing image file But I can open the file using openslide:
The path is also correct (i think so) root@3241fa9fceee:/opt/HistoQC# ls /data | grep TCGA-XX-A89A-01Z-00-DX1.671E2AD6-4D1A-4579-88C1-5B0B15818126 TCGA-XX-A89A-01Z-00-DX1.671E2AD6-4D1A-4579-88C1-5B0B15818126.svs So, wanted to know if this is a bug or if I am using something wrongly.