Feature/remote backends by jonasteuwen · Pull Request #221 · NKI-AI/dlup

jonasteuwen · 2024-03-26T12:53:40Z

Add remote backends

* New API for tiling, WholeSlideImage * Added basic tests, drafted new API * Use pre-commit fixes, adding pydantic to dev req * Added tox * Implemented CI with Github Actions (Closes #8) * New CLI interface for tiling (Closes #3) Co-authored-by: Leonardo Romor <leonardo.romor@gmail.com> Co-authored-by: Mensel123 <43986008+Mensel123@users.noreply.github.com> Co-authored-by: Francesco Dal Canton <francidalca@gmail.com>

- Bugfix to improper int casting which was sometimes breaking the read_region method. - Improved read_region() docstring. - Added related testcase.

Update Docker - Make resulting docker smaller - Install pixman and cairo from scratch - Compile pytorch and torchvision specifically for dlup

* Update documentation - Added warning to installation.rst that pixman 0.40 or higher is required. * Update documentation - Added line about virtual environment, move pixman warning up. * Update documentation - Added information about openslide versions.

* Improved SlideImage initialization exception messages. * Convert tiling tool to new Dataset class * Improve mypy and pylint parsing * Create Dataset class that reads from tiles * Updated docstrings * Few CI fixes * Removed previous glue code to ease development and introduce caching. (#29) * Removed TiledRegionView class, replaced with a leaner Lattice class that serves as interface to generate a lattice. * Added LRU cache on top of the dataset, to reduce memory requirements. * Bump version: 0.2.0-dev0 → 0.2.0-dev3 Co-authored-by: Leonardo Romor <leonardo.romor@gmail.com>

* Remove pytorch dependency (Closes #18) * Add possibility to check if pytorch is available

- Added support for an extra parameter during Grid() creation to specify a global offset for every coordinate. - Improved naming and docstring

Use multiprocessing for tile extraction

* Refactored dataset class * Added TiledROIsSlideDataset class to allow flexible tiling, at different mpps for different ROIs. * Added more parameters to returned dictionary to backtrack original grid of a tile. * Remove joblib * Added dataset example to documentation https://docs.aiforoncology.nl/dlup/dataset_examples.html Co-authored-by: Jonas Teuwen <j.teuwen@nki.nl>

…turn rgba pil in SlideImageDataset, return rgb pil for thumbnail (#43) Consistently output RGBA PIL Images for DLUP datasets (closes #43) * Return RGBA PIL Images for DLUP Datasets * Return RGBA PIL Images for SlideImage.thumbnail * Add TypedDicts to specify the returned objects of each dataset class * Generally improve typing and docstrings

Allow saving the masks in cli tool

* Added FileNotFoundError to from_file_path() * Raised FileNotFoundError while reading WSI.

* Add more flexibility for passing filepath to load WSI from in SlideImage * Import sequence from `collections.abc`, not from `collections`. This is soon deprecated. * Upgrade scikit-image version to version above 0.19

* Add example shell tool to tile entire directory of wsis * Update documentation

* Added experimental multiscale dataset * Add out-of-region reading and pad with zeros

* Add z_index to geojson properties when importing and exporting * Fix annotation crop for Polygons in read_region and test_annotations * Created new AnnotatedGeometry, adhere to shapely dunder and functions * Add helper function to utils and Enum for Darwin/ASAP annotation types * Add darwin_annotation_type to color look up and move Darwin util function to utils * Bugfix for WsiAnnotations.filter function

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BPdeRooij · 2024-09-06T12:09:57Z

PR overview

This PR implements three new backends. These new backends are an abstract class RemoteSlideBackend, DeepZoomSlide and SlideScoreSlide. DeepZoomSlide is mainly created to support the remote SlideScoreSlide backend, which uses API calls to a DeepZoom tile server provided by SlideScore.

To use the SlideScoreSlide backend:

Install the optional dependencies (slidescore_remote)
Export your slidescore API key (with the correct privileges) using dlup.backends.slidescore_backend.export_api_key
Use a SlideScore URL (from a study for which your API key has the correct privileges) as the input for filename (SlideScoreSlide), wsi_file_path (SlideImage.from_file_path), or path (TiledWsiDataset).
Use the initialized wsi object how you normally would.

Changes

Introduced new backends RemoteSlideBackend, DeepZoomSlide and SlideScoreSlide.
Added backend utility functions to parse deep zoom dzi and xml files.
Allow RemoteSlideBackend to use strings as wsi_file_path in dlup._image
Added optional dependecy slidescore_remote, which installs aiohttp for asynchronous requests to SlideScore's tile server.

Notes

The focus of this PR was mainly on the SlideScoreSlide backend. The DeepZoomSlide has been tested using several different conversion methods (libvips vs openslide, different overlaps, different tile sizes, etc.), but is not guaranteed to work in every scenario.
When creating deep zoom files with libvips, cmyk colourspace can be used. This will also output images, which use the same colourspace. Converting to rgb is possible, but this will create altered colours when this conversion is done with pyvips. RGB colours seem correct when the conversion is done with PILLOW. SlideScore API calls will output images with RGB colours. Do we always want to convert output images to RGB?
Using pyvips.arrayjoin in the read_region would probably be faster than inserting each tile into the blank canvas, but this is not possible due to edge tiles having different sizes.
A maximum of 6 simultaneous asynchronous requests are made to the Slidescore tile server. This limit was set after discussion with Jan Hudecek. Using a lot of simultaneous calls can cause the tile server to crash. Therefore, this backend is better suited for inference or without using multiprocessing.
ICC profiles are stripped when creating deep zoom tiles and slidescore does not (yet) support retrieval of the ICC profile. Thus, ICC profiles are not included. (Update: I am currently in contact with Jan to get ICC profiles supported for SlideScoreSlide)
No tests are written for the new backends.

Please let me know what you think of these new features and any potential changes you would like to see!

moerlemans · 2024-09-11T15:09:48Z

dlup/backends/remote_backends.py

+from dlup.backends.common import AbstractSlideBackend
+
+
+class RemoteSlideBackend(AbstractSlideBackend):


I have no idea what this is haha. Maybe some docs could help :)

- Add DLUP XML output - Rewrite setup to use meson-py --------- Co-authored-by: Bart de Rooij <33282665+BPdeRooij@users.noreply.github.com> Co-authored-by: Jonas Teuwen <j.teuwen@.nki.nl> Co-authored-by: JorenB <jorenb@gmail.com>

- Use dynamic loading for annotation reading and writing

…in workflows

jonasteuwen and others added 30 commits June 7, 2021 18:48

Close request when not downloading slide

0b4511c

RST fix

39fb3f3

Bugfix in casting which could break the read_region method. (Closes #19)

6ad870d

- Bugfix to improper int casting which was sometimes breaking the read_region method. - Improved read_region() docstring. - Added related testcase.

Update CLI (#25)

29412a5

Docker patch (#22)

647ccdf

Update Docker - Make resulting docker smaller - Install pixman and cairo from scratch - Compile pytorch and torchvision specifically for dlup

Update documentation (#24)

44470db

* Update documentation - Added warning to installation.rst that pixman 0.40 or higher is required. * Update documentation - Added line about virtual environment, move pixman warning up. * Update documentation - Added information about openslide versions.

rollback openslide-python

9e36e11

Remove pytorch (#30)

ad60148

* Remove pytorch dependency (Closes #18) * Add possibility to check if pytorch is available

Update __init__.py

251ea77

Disable import errors in pylint, mypy

f78342d

Update ignore lines

1716796

Fix CI disables

179ee65

Bump version: 0.2.0-dev3 → 0.2.0

84d107f

Fix docker warning

0d6b4c4

Extra flexibility to the Grid class (#35)

8a4e385

- Added support for an extra parameter during Grid() creation to specify a global offset for every coordinate. - Improved naming and docstring

Multiprocessing for tile extraction (#32)

fb7a8ad

Use multiprocessing for tile extraction

Remove SlideScore API (Closes #31). (#38)

0dfa2e4

Add saving masks to cli (#49)

234a0ce

Allow saving the masks in cli tool

Added FileNotFoundError (#52)

0bdeca8

* Added FileNotFoundError to from_file_path() * Raised FileNotFoundError while reading WSI.

Set the anisotropy relative tolerance limit to 1.e-2. (#54, Closes #53)

d69208c

Update README.md

57f1aae

Create codecov.yml

8fc3e5f

Allow string in slide imagefromfilepath (#60, Closes #59)

5353b00

* Add more flexibility for passing filepath to load WSI from in SlideImage * Import sequence from `collections.abc`, not from `collections`. This is soon deprecated. * Upgrade scikit-image version to version above 0.19

add shell tool to tile entire directory of wsis (#51)

a34b883

* Add example shell tool to tile entire directory of wsis * Update documentation

update numpy to 1.21 to allow use of numpy.typing.NDArray (#62)

09f95a6

Multiscale dataset (#69)

accce6a

* Added experimental multiscale dataset * Add out-of-region reading and pad with zeros

BPdeRooij and others added 3 commits August 14, 2024 00:16

Merge branch 'main' into feature/remote-backends

0ddfd79

Remove v7 remote backend

6220985

BPdeRooij added 3 commits August 29, 2024 18:05

Output pyvips Image for DeepZoomSlide.read_region

65222b5

Move helper functions to utils/backends

0628a56

Insert images to fix bug with pyvips.arrayjoin & remove cmyk2rgb conv…

94925fb

…ersion

BPdeRooij marked this pull request as ready for review September 6, 2024 11:24

BPdeRooij requested review from AjeyPaiK, EricMarcus-ai, VanessaBotha, YoniSchirris and moerlemans September 6, 2024 12:11

Add optional dependencies for slidescore_remote to pylint

5b0beae

moerlemans reviewed Sep 11, 2024

View reviewed changes

jonasteuwen and others added 3 commits September 26, 2024 10:56

Implement WsiAnnotations in C++ (#252)

b6260de

- Add DLUP XML output - Rewrite setup to use meson-py --------- Co-authored-by: Bart de Rooij <33282665+BPdeRooij@users.noreply.github.com> Co-authored-by: Jonas Teuwen <j.teuwen@.nki.nl> Co-authored-by: JorenB <jorenb@gmail.com>

Use dynamic loading for annotations (#255)

92ebd51

- Use dynamic loading for annotation reading and writing

Update README.md

626740e

github-actions bot added the Stale label Nov 26, 2024

BPdeRooij added 8 commits January 9, 2025 09:44

Move ImageBackend to init to prevent circular imports

c3532b2

Split deepzoom backend, simplify remote backend, small edge case fix

09f08a5

Add testing for deepzoom and remote backends

361d119

Merge main into feature/remote-backends

9a475c9

Replace with and for compatibility with ubuntu-latest (ubuntu-24.04) …

34234a6

…in workflows

Fix mypy errors

aa14eb2

Add slidescore tsv importer / exporter and add boxes to SlideAnnotations

88e77d2

Improve error handling and reuse clientsession

1b75cdc

jonasteuwen closed this Jan 31, 2026

jonasteuwen force-pushed the main branch from 626740e to 6ea6688 Compare January 31, 2026 14:24

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Feature/remote backends#221

Feature/remote backends#221
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		from dlup.backends.common import AbstractSlideBackend


		class RemoteSlideBackend(AbstractSlideBackend):

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