s3seg fails on single-channel images #16
Description
- Download
exemplar-001:
curl -f -o test.ome.tif https://mcmicro.s3.amazonaws.com/ci/exemplar-001-cycle6.ome.tif
- Cut the image down to the first channel (
recyzeuses 0-based channel indexing):
nextflow run labsyspharm/mcmicro/roadie.nf --do recyze --in test.ome.tif --channels 0
- Verify image dimensionality:
$ python -c "import tifffile; print(tifffile.TiffFile('test.ome.tif').series[0].shape)"
(4, 3139, 2511)
$ python -c "import tifffile; print(tifffile.TiffFile('test_crop.ome.tif').series[0].shape)"
(3139, 2511)
- UnMicst runs fine on the single-channel image:
docker run --rm -v "$PWD":/data labsyspharm/unmicst:2.7.4 python /app/unmicstWrapper.py /data/test_crop.ome.tif --stackOutput --outputPath /data --channel 1
- However, s3seg fails:
docker run --rm -v "$PWD":/data labsyspharm/s3segmenter:1.3.18 python /app/S3segmenter.py --imagePath /data/test_crop.ome.tif --stackProbPath /data/test_crop_Probabilities_1.tif --probMapChan 1 --outputPath /data
with an out-of-bounds errors:
Traceback (most recent call last):
File "/app/S3segmenter.py", line 484, in <module>
tissueCrop =tifffile.imread(imagePath,key=iChan)
File "/usr/local/lib/python3.8/site-packages/tifffile/tifffile.py", line 800, in imread
return tif.asarray(**kwargs)
File "/usr/local/lib/python3.8/site-packages/tifffile/tifffile.py", line 3128, in asarray
pages = self.pages._getlist(key)
File "/usr/local/lib/python3.8/site-packages/tifffile/tifffile.py", line 5311, in _getlist
return [getitem(key)]
File "/usr/local/lib/python3.8/site-packages/tifffile/tifffile.py", line 5360, in _getitem
self._seek(key)
File "/usr/local/lib/python3.8/site-packages/tifffile/tifffile.py", line 5281, in _seek
raise IndexError('index out of range')
IndexError: index out of range