✨ Feature Engine for Multi-Task Segmenter #424
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## develop #424 +/- ##
=========================================
Coverage 99.74% 99.74%
=========================================
Files 62 63 +1
Lines 6616 6744 +128
Branches 1073 1107 +34
=========================================
+ Hits 6599 6727 +128
Misses 8 8
Partials 9 9
📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more |
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
…com/TissueImageAnalytics/tiatoolbox into feature-engine-multi-task-segmentor
shaneahmed
requested review from
shaneahmed
and removed request for
simongraham
shaneahmed
reviewed
Mar 31, 2023
- Add tests for the engine
- Fix failing tests
- Fix failing tests
- Fix failing tests
- Fix failing test
- Fix failing test
- Pin Pandas version
shaneahmed
changed the title
shaneahmed
approved these changes
Apr 11, 2023
Member
shaneahmed
left a comment
shaneahmed
left a comment
There was a problem hiding this comment.
Thanks @adamshephard Looks OK to me.
shaneahmed
added a commit
that referenced
this pull request
May 5, 2023
## 1.4.0 (2023-04-24) ### Major Updates and Feature Improvements - Adds Python 3.11 support \[experimental\] #500 - Python 3.11 is not fully supported by `pytorch` pytorch/pytorch#86566 and `openslide` openslide/openslide-python#188 - Removes Python 3.7 support - This allows upgrading all the dependencies which were dependent on an older version of Python. - Adds Neighbourhood Querying Support To AnnotationStore #540 - This enables easy and efficient querying of annotations within a neighbourhood of other annotations. - Adds `MultiTaskSegmentor` engine #424 - Fixes an issue with stain augmentation to apply augmentation to only tissue regions. - #546 contributed by @navidstuv - Filters logger output to stdout instead of stderr. - Fixes #255 - Allows import of some modules at higher level for improved usability - `WSIReader` can now be imported as `from tiatoolbox.wsicore import WSIReader` - `WSIMeta` can now be imported as `from tiatoolbox.wsicore import WSIMeta` - `HoVerNet`, `HoVerNetPlus`, `IDaRS`, `MapDe`, `MicroNet`, `NuClick`, `SCCNN` can now be imported as \`from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN - Improves `PatchExtractor` performance. Updates `WSIPatchDataset` to be consistent. #571 - Updates documentation for `License` for clarity on source code and model weights license. ### Changes to API - Updates SCCNN architecture to make it consistent with other models. #544 ### Bug Fixes and Other Changes - Fixes Parsing Missing Omero Version NGFF Metadata #568 - Fixes #535 raised by @benkamphaus - Fixes reading of DICOM WSIs at the correct level #564 - Fixes #529 - Fixes `scipy`, `matplotlib`, `scikit-image` deprecated code - Fixes breaking changes in `DICOMWSIReader` to make it compatible with latest `wsidicom` version. #539, #580 - Updates `shapely` dependency to version >=2.0.0 and fixes any breaking changes. - Fixes bug with `DictionaryStore.bquery` and `geometry=None`, i.e. only a where predicate given. - Partly Fixes #532 raised by @blaginin - Fixes local tests for Windows/Linux - Fixes `flake8`, `deepsource` errors. - Uses `logger` instead of `warnings` and `print` statements to properly log runs. ### Development related changes - Upgrades dependencies which are dependent on Python 3.7 - Moves `requirements*.txt` files to `requirements` folder - Removes `tox` - Uses `pyproject.toml` for `bdist_wheel`, `pytest` and `isort` - Adds `joblib` and `numba` as dependencies.
shaneahmed
added a commit
that referenced
this pull request
May 5, 2023
## 1.4.0 (2023-04-24) ### Major Updates and Feature Improvements - Adds Python 3.11 support \[experimental\] #500 - Python 3.11 is not fully supported by `pytorch` pytorch/pytorch#86566 and `openslide` openslide/openslide-python#188 - Removes Python 3.7 support - This allows upgrading all the dependencies which were dependent on an older version of Python. - Adds Neighbourhood Querying Support To AnnotationStore #540 - This enables easy and efficient querying of annotations within a neighbourhood of other annotations. - Adds `MultiTaskSegmentor` engine #424 - Fixes an issue with stain augmentation to apply augmentation to only tissue regions. - #546 contributed by @navidstuv - Filters logger output to stdout instead of stderr. - Fixes #255 - Allows import of some modules at higher level for improved usability - `WSIReader` can now be imported as `from tiatoolbox.wsicore import WSIReader` - `WSIMeta` can now be imported as `from tiatoolbox.wsicore import WSIMeta` - `HoVerNet`, `HoVerNetPlus`, `IDaRS`, `MapDe`, `MicroNet`, `NuClick`, `SCCNN` can now be imported as \`from tiatoolbox.models import HoVerNet, HoVerNetPlus, IDaRS, MapDe, MicroNet, NuClick, SCCNN - Improves `PatchExtractor` performance. Updates `WSIPatchDataset` to be consistent. #571 - Updates documentation for `License` for clarity on source code and model weights license. ### Changes to API - Updates SCCNN architecture to make it consistent with other models. #544 ### Bug Fixes and Other Changes - Fixes Parsing Missing Omero Version NGFF Metadata #568 - Fixes #535 raised by @benkamphaus - Fixes reading of DICOM WSIs at the correct level #564 - Fixes #529 - Fixes `scipy`, `matplotlib`, `scikit-image` deprecated code - Fixes breaking changes in `DICOMWSIReader` to make it compatible with latest `wsidicom` version. #539, #580 - Updates `shapely` dependency to version >=2.0.0 and fixes any breaking changes. - Fixes bug with `DictionaryStore.bquery` and `geometry=None`, i.e. only a where predicate given. - Partly Fixes #532 raised by @blaginin - Fixes local tests for Windows/Linux - Fixes `flake8`, `deepsource` errors. - Uses `logger` instead of `warnings` and `print` statements to properly log runs. ### Development related changes - Upgrades dependencies which are dependent on Python 3.7 - Moves `requirements*.txt` files to `requirements` folder - Removes `tox` - Uses `pyproject.toml` for `bdist_wheel`, `pytest` and `isort` - Adds `joblib` and `numba` as dependencies.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Add engine for the multi-task segmentor to allow simultaneous instance segmentation of nuclei and the semantic segmentation of regions. This replaces commit #216 due to history error in old PR.
TODO