Openslide will not read slide image files that don't adhere to assumptions about mpp properties

[Tkootstra]

I have found at least 3 slides which will not load with the new experimental backends. To reproduce: select one of these slides from TCGA-BRCA-DX:

'1c55f0d8-b0af-4a1e-84ef-f30aab5d749b/TCGA-OL-A5RY-01Z-00-DX1.AE4E9D74-FC1C-4C1E-AE6D-5DF38899BBA6.svs'

'69254fba-c85c-4bbb-8a4c-b2e14c8e5a2a/TCGA-OL-A5RZ-01Z-00-DX1.6394C05E-1C34-4F4B-8859-F5E961E7EFF9.svs'

'6eca5a11-0405-4619-88dd-04a12780e2bb/TCGA-OL-A5RX-01Z-00-DX1.15A0D4F4-2744-4D44-8883-27FF83D9C824.svs'

Full stacktrace:

Traceback (most recent call last): File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/init.py", line 97, in _try_pyvips slide = PyVipsSlide(filename) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/_pyvips.py", line 51, in init self._read_as_openslide(filename) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/_pyvips.py", line 111, in _read_as_openslide mpp_x = float(self._images[0].get("openslide.mpp-x")) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/pyvips/vimage.py", line 1062, in get raise Error('unable to get {0}'.format(name)) pyvips.error.Error: unable to get openslide.mpp-x vips_image_get: field "openslide.mpp-x" not found

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/init.py", line 58, in autodetect_backend return _try_pyvips(filename) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/init.py", line 102, in _try_pyvips raise UnsupportedSlideError(f"Cannot read {filename} with pyvips.") dlup._exceptions.UnsupportedSlideError: (UnsupportedSlideError(...), 'Cannot read /data/datasets/TCGA/data/slides/6eca5a11-0405-4619-88dd-04a12780e2bb/TCGA-OL-A5RX-01Z-00-DX1.15A0D4F4-2744-4D44-8883-27FF83D9C824.svs with pyvips.')

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/_image.py", line 119, in from_file_path wsi = backend(filename=wsi_file_path) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/experimental_backends/init.py", line 60, in autodetect_backend raise UnsupportedSlideError(f"Cannot read {filename} with pyvips or openslide.") dlup._exceptions.UnsupportedSlideError: (UnsupportedSlideError(...), 'Cannot read /data/datasets/TCGA/data/slides/6eca5a11-0405-4619-88dd-04a12780e2bb/TCGA-OL-A5RX-01Z-00-DX1.15A0D4F4-2744-4D44-8883-27FF83D9C824.svs with pyvips or openslide.')

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/tmp/pycharm_project_960/debug.py", line 26, in slide = SlideImage.from_file_path(files[2], backend=ImageBackends.AUTODETECT) File "/home/tkootstra/miniconda3/envs/dlup_test2/lib/python3.9/site-packages/dlup/_image.py", line 121, in from_file_path raise UnsupportedSlideError(f"Unsupported file: {wsi_file_path}") dlup._exceptions.UnsupportedSlideError: (UnsupportedSlideError(...), 'Unsupported file: /data/datasets/TCGA/data/slides/6eca5a11-0405-4619-88dd-04a12780e2bb/TCGA-OL-A5RX-01Z-00-DX1.15A0D4F4-2744-4D44-8883-27FF83D9C824.svs')

Process finished with exit code 1

Env is clean python 3.9, with dlup install via git with commit hash for the PR, as such: pip install git+https://github.com/NKI-AI/dlup.git@ff879a58ce8745ef6e9aa28d52f379c550dfdff4

Environment:

Name Version Build Channel _libgcc_mutex 0.1 main _openmp_mutex 5.1 1_gnu ca-certificates 2022.4.26 h06a4308_0 certifi 2022.6.15 py39h06a4308_0 cffi 1.15.1 pypi_0 pypi charset-normalizer 2.1.0 pypi_0 pypi cycler 0.11.0 pypi_0 pypi dlup 0.3.0.dev0 pypi_0 pypi fonttools 4.34.2 pypi_0 pypi idna 3.3 pypi_0 pypi imageio 2.19.3 pypi_0 pypi kiwisolver 1.4.3 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1 libffi 3.3 he6710b0_2 libgcc-ng 11.2.0 h1234567_1 libgomp 11.2.0 h1234567_1 libstdcxx-ng 11.2.0 h1234567_1 matplotlib 3.5.2 pypi_0 pypi ncurses 6.3 h5eee18b_3 networkx 2.8.4 pypi_0 pypi numpy 1.23.0 pypi_0 pypi openslide-python 1.2.0 pypi_0 pypi openssl 1.1.1p h5eee18b_0 packaging 21.3 pypi_0 pypi pillow 9.2.0 pypi_0 pypi pip 21.2.4 py39h06a4308_0 pkgconfig 1.5.5 pypi_0 pypi pycparser 2.21 pypi_0 pypi pyparsing 3.0.9 pypi_0 pypi python 3.9.12 h12debd9_1 python-dateutil 2.8.2 pypi_0 pypi pyvips 2.2.1 pypi_0 pypi pywavelets 1.3.0 pypi_0 pypi readline 8.1.2 h7f8727e_1 requests 2.28.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scipy 1.8.1 pypi_0 pypi setuptools 61.2.0 py39h06a4308_0 shapely 2.0.0.dev0+66.ga277741 pypi_0 pypi six 1.16.0 pypi_0 pypi sqlite 3.38.5 hc218d9a_0 tifffile 2022.5.4 pypi_0 pypi tifftools 1.3.4 pypi_0 pypi tk 8.6.12 h1ccaba5_0 tqdm 4.64.0 pypi_0 pypi tzdata 2022a hda174b7_0 urllib3 1.26.9 pypi_0 pypi wheel 0.37.1 pyhd3eb1b0_0 xz 5.2.5 h7f8727e_1 zlib 1.2.12 h7f8727e_2

Environment dlup version: How installed: Python version: Operating System:

Additional context This can likely be fixed by patching OpenSlide, according to Jonas (not tested by me)

[github-actions[bot]]

This issue is stale because it has been open 60 days with no activity. Remove stale label or comment or this will be closed in 15 days

[AjeyPaiK]

Hey @Tkootstra, do you still have this problem with the experimental backends?

[Tkootstra]

No, this issue can be closed. It has been working fine since many commits ago