Difference behaviour between WsiDicomFileSource and WsiDicomWebSource

[ChristianMarzahl]

Hi,

First of all, thank you very much for providing this great library.

I noticed a difference in the handling of the same DICOM file provided by WsiDicomFileSource and WsiDicomWebSource through a DICOMWeb interface.

The WsiDicomFileSource filters the DICOM levels for matching tile_size and UIDs:

wsidicom/wsidicom/file/wsidicom_file_source.py

Line 274 in b0d097c

filtered_files = cls._filter_files(files, series_uids, series_tile_size)

This filtering is not done in WsiDicomWebSource:

wsidicom/wsidicom/web/wsidicom_web_source.py

Line 58 in b0d097c

class WsiDicomWebSource(Source):

This discrepancy can lead to DICOMs that can be opened via file but not via the web interface. I wanted to ask if this was intended.

Regarding the same topic of opening images via file or DCMWeb:

wsidicom/wsidicom/web/wsidicom_web_source.py

Line 102 in b0d097c

transfer_syntax = self._determine_transfer_syntax(

If the DICOMWeb server does not support JPEG2000, for example, as a transfer syntax and throws an exception (requests.exceptions.HTTPError: 400 Client Error: BAD REQUEST for url: Google DICOM Archive), the code only catches 406 exceptions.

wsidicom/wsidicom/web/wsidicom_web_client.py

Line 218 in b0d097c

except HTTPError as exception:

With kind regards,
Christian Marzahl

[erikogabrielsson]

Hi @ChristianMarzahl
Thanks for the feedback and sorry for the late response.

Limiting WsiDicom to only handle pyramid levels of same tile size was an early design decision. I'm not sure if it is still needed, if it with some effort the restriction could be removed, or how common it is with DICOM WSI-files with non-uniform tile size. Handling WSIs with non-uniform tile size differently when opened by DICOM Web was not intended.

I can try to create some test files with non-uniform tile size, but it would also be helpful to know where the library fails when you open your example as DICOM Web.

For the second issue, my interpretation of the standard is that the server should respond with 406 (Not Acceptable) when the requested transfer syntax is not accepted. Does the more generic 400 (Bad Request) response from Google DICOM Archive give a clear status reason that can be used to check if the error is due to the requested transfer syntax?

[erikogabrielsson]

I played around a bit with disabling the tile size check together with a slide with levels with tile sizes of 200, 300, and 400 pixels. read_region() works as expected but it gets a bit weird when using get_tile() as (of coarse) the tiles will be of different size.

In the images that you have encountered, what levels are of different tile size? Is relaxation to allow different tile sizes a wanted feature or is it better to drop them (and implement the same checks for the DICOM web source)?

[erikogabrielsson]

@ChristianMarzahl
I have started working on this in this branch.

• Config strict_tile_size_check can be set to False to allow opening wsis with different tile size. The default is True
• Change to WsiDicomWebSource so that level instances are filtered by tile size if strict_tile_size_check is True.

Please try this on your problematic WSI.

Also please provide the HTTP error message for Google DICOM archive on unsupported transfer syntax.

[ChristianMarzahl]

Dear @erikogabrielsson,

Thank you very much for looking into it.
I hope to spend some time on it this week to answer your questions.

Best,
Christian