:sparkles: Define `SemanticSegmentor` with the New `EngineABC` by shaneahmed · Pull Request #866 · TissueImageAnalytics/tiatoolbox

shaneahmed · 2024-09-20T13:56:43Z

Summary of Changes

Major Additions

Dask Integration:
- Added dask as a dependency and integrated Dask arrays and lazy computation throughout the engine and patch predictor code.
- Added Dask-based merging, chunking, and memory-aware processing for large images and WSIs.
Zarr Output Support:
- Added support for saving model predictions and intermediate results directly to Zarr format.
- New CLI options and internal logic for Zarr output, including memory thresholding and chunked writes.
SemanticSegmentor Engine:
- Added a new SemanticSegmentor engine with Dask/Zarr support and new test coverage (test_semantic_segmentor.py).
- Added CLI entrypoint for semantic_segmentor and removed the old semantic_segment CLI.
Enhanced CLI and Config:
- Added CLI options for memory threshold, unified worker options, and improved mask handling.
- Updated YAML configs and sample data for new models and test images.
Utilities and Validation:
- Added utility functions for minimal dtype casting, patch/stride validation, and improved error handling (e.g., DimensionMismatchError).
- Improved annotation store conversion for Dask arrays and Zarr-backed outputs.
Changes to kwarg
- Add memory-threshold
- Unified num-loader-workers and num-postproc-workers into num-workers
- Removed cache_mode as cache mode is automatically handled.

Major Removals/Refactors

Removed Old CLI and Redundant Code:
- Deleted the old semantic_segment.py CLI and replaced it with semantic_segmentor.py.
- Removed legacy cache mode and patch prediction Zarr store tests.
Refactored Model and Dataset APIs:
- Unified and simplified model inference APIs to always return arrays (not dicts) for batch outputs.
- Refactored dataset classes to enforce patch shape validation and remove legacy “mode” logic.
Test Cleanup:
- Removed or updated tests that relied on old APIs or cache mode.
- Refactored test assertions for new output types and Dask array handling.
API Consistency:
- Standardized function and argument names across engines, CLI, and utility modules.
- Updated docstrings and type hints for clarity and consistency.

Notable File Changes

New:
- tiatoolbox/cli/semantic_segmentor.py
- tests/engines/test_semantic_segmentor.py
Removed:
- tiatoolbox/cli/semantic_segment.py
- Old cache mode and patch Zarr store tests
Heavily Modified:
- engine_abc.py, patch_predictor.py, semantic_segmentor.py
- CLI modules and test suites
- Dataset and utility modules for Dask/Zarr compatibility

Impact

Enables scalable, parallel, and memory-efficient inference and output saving for large images.
Simplifies downstream analysis by supporting Zarr as a native output format.
Lays the groundwork for further Dask-based optimizations in TIAToolbox.

codecov · 2024-09-20T14:10:14Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.72%. Comparing base (31b7995) to head (19b404b).
⚠️ Report is 28 commits behind head on dev-define-engines-abc.

Additional details and impacted files

@@                    Coverage Diff                     @@
##           dev-define-engines-abc     #866      +/-   ##
==========================================================
+ Coverage                   91.33%   94.72%   +3.38%     
==========================================================
  Files                          73       73              
  Lines                        9375     9235     -140     
  Branches                     1229     1208      -21     
==========================================================
+ Hits                         8563     8748     +185     
+ Misses                        776      452     -324     
+ Partials                       36       35       -1

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

for more information, see https://pre-commit.ci

review-notebook-app · 2025-01-03T11:31:41Z

Check out this pull request on

See visual diffs & provide feedback on Jupyter Notebooks.

Powered by ReviewNB

- Use `input_resolutions` instead of resolution to make engines outputs compatible with ioconfig. - Uses input resolution as a list of dictionaries on units and resolution.

…mentor # Conflicts: # tests/engines/test_engine_abc.py # tests/engines/test_patch_predictor.py # tiatoolbox/models/engine/engine_abc.py # tiatoolbox/models/engine/io_config.py # tiatoolbox/models/engine/patch_predictor.py

measty

I've done an initial review, looks nice overall but I found a few issues that need addressing before it could be merged.

# Conflicts: # tests/models/test_dataset.py

…entor # Conflicts: # tiatoolbox/models/engine/semantic_segmentor.py

for more information, see https://pre-commit.ci

…c.Callable` into a type-checking block

# Conflicts: # tests/test_utils.py

…nto dev-define-semantic-segmentor

✨ Define SemanticSegmentor with the New EngineABC

193c587

shaneahmed self-assigned this Sep 20, 2024

shaneahmed added the enhancement New feature or request label Sep 20, 2024

shaneahmed added this to the Release v2.0.0 milestone Sep 20, 2024

shaneahmed and others added 6 commits November 20, 2024 15:54

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

113fb6b

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

44e4b8c

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

7e8d78b

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

1ea6c80

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

d0b86a5

[pre-commit.ci] auto fixes from pre-commit.com hooks

399827a

for more information, see https://pre-commit.ci

shaneahmed added 3 commits January 24, 2025 11:01

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

333264a

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

c84099b

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

16a632f

shaneahmed marked this pull request as draft February 5, 2025 16:27

shaneahmed added 14 commits February 21, 2025 11:24

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

e03db92

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

13cc94a

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

dd83117

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

967dba1

🔨 Add run method to SemanticSegmentor

40e79a1

📝 Update docstring

85922ff

♻️ Refactor resolution to input_resolutions.

bda0581

♻️ Use input_resolutions instead of resolution

a643ea6

- Use `input_resolutions` instead of resolution to make engines outputs compatible with ioconfig. - Uses input resolution as a list of dictionaries on units and resolution.

♻️ Use input_resolutions instead of resolution

7eed649

- Use `input_resolutions` instead of resolution to make engines outputs compatible with ioconfig. - Uses input resolution as a list of dictionaries on units and resolution.

✅ Add test to cli.

3dff881

✅ Add SemanticSegmentor patch_mode test.

03e07e6

🐛 Fix unet architecture

a37e71d

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

94a747f

shaneahmed added 8 commits August 29, 2025 10:36

💡 Address @Copilot comments

6c6bceb

🔥 Remove unnecessary tests

2130d90

📝 Update docstring

6eeb8a2

🐛 Fix missing support for WSIReader.

ee2d339

🐛 Fix deepsource error - simplify if statement

7e26b78

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

7d363e8

🥅 Raise an error if return_labels is True and patch_mode is False.

24eeff1

🎨 Use a variable instead of multiple calculations

610d355

adamshephard self-requested a review September 12, 2025 09:39

adamshephard reviewed Sep 12, 2025

View reviewed changes

Comment thread tiatoolbox/models/architecture/unet.py Outdated

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

5125146

measty requested changes Sep 19, 2025

View reviewed changes

Comment thread tiatoolbox/models/engine/semantic_segmentor.py

Comment thread tiatoolbox/models/engine/engine_abc.py

Comment thread tiatoolbox/models/engine/semantic_segmentor.py

Comment thread tests/engines/test_engine_abc.py

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

9106517

shaneahmed linked an issue Oct 3, 2025 that may be closed by this pull request

Shifted patches when merging patch predictions! #634

Closed

shaneahmed added 3 commits October 10, 2025 11:07

📝 Update output docstring

de816fc

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

585bf9a

# Conflicts: # tests/models/test_dataset.py

🔥 Remove unnecessary code

3a47fe1

shaneahmed force-pushed the dev-define-semantic-segmentor branch from fe21c69 to 3a47fe1 Compare October 16, 2025 16:12

shaneahmed and others added 10 commits October 16, 2025 17:47

🔀 Merge branch 'dev-define-engines-abc' into dev-define-semantic-segm…

5331e2a

…entor # Conflicts: # tiatoolbox/models/engine/semantic_segmentor.py

[pre-commit.ci] auto fixes from pre-commit.com hooks

5de542f

for more information, see https://pre-commit.ci

🐛 Fix ruff check TC003 Move standard library import `collections.ab…

82a9876

…c.Callable` into a type-checking block

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

6e1e585

# Conflicts: # tests/test_utils.py

✅ Update tests to use track_tmp_path for clean up

eea0dba

🐛 Fix reading of str input

1d2ca5f

🐛 Fix reading of str input

9e30164

Merge branch 'dev-define-engines-abc' into dev-define-semantic-segmentor

6947182

📌 Fix dask version

3396a3b

Merge remote-tracking branch 'origin/dev-define-semantic-segmentor' i…

19b404b

…nto dev-define-semantic-segmentor

shaneahmed merged commit b542c9a into dev-define-engines-abc Oct 20, 2025
39 checks passed

shaneahmed deleted the dev-define-semantic-segmentor branch October 20, 2025 12:08

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

✨ Define `SemanticSegmentor` with the New `EngineABC`#866

✨ Define `SemanticSegmentor` with the New `EngineABC`#866
shaneahmed merged 235 commits into
dev-define-engines-abcfrom
dev-define-semantic-segmentor

shaneahmed commented Sep 20, 2024 •

edited

Loading

Uh oh!

codecov Bot commented Sep 20, 2024 •

edited

Loading

Uh oh!

review-notebook-app Bot commented Jan 3, 2025

Uh oh!

Uh oh!

measty left a comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

shaneahmed commented Sep 20, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Summary of Changes

Major Additions

Major Removals/Refactors

Notable File Changes

Impact

Uh oh!

codecov Bot commented Sep 20, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

review-notebook-app Bot commented Jan 3, 2025

Uh oh!

Uh oh!

measty left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

shaneahmed commented Sep 20, 2024 •

edited

Loading

codecov Bot commented Sep 20, 2024 •

edited

Loading