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🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata #568

Merged
merged 16 commits into from
Mar 27, 2023
Merged

🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata #568

merged 16 commits into from
Mar 27, 2023

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John-P
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@John-P John-P commented Mar 17, 2023 •
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To-Do

  • Handle missing version keys and null values.
  • Add test for missing value
  • Add test for non-numeric values e.g. "0.5-dev" see current spec doc
  • Warn if version < or > 0.4
  • Warn for inconsistent versions

@John-P John-P added the bug Something isn't working label Mar 17, 2023
@John-P John-P linked an issue Mar 17, 2023 that may be closed by this pull request
Minor issue: errors do not follow intended path due to int conversion fail on empty string #535
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@John-P John-P self-assigned this Mar 17, 2023
@John-P John-P changed the title 🐛 BUG: Fix Parsing Missing Omero Version NGFF Metadata 🩹 BUG: Fix Parsing Missing Omero Version NGFF Metadata Mar 17, 2023
@John-P John-P requested a review from shaneahmed March 17, 2023 13:23
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codecov bot commented Mar 17, 2023 •
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Codecov Report

Merging #568 (3cfc66b) into develop (09bd197) will increase coverage by 0.12%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #568      +/-   ##
===========================================
+ Coverage    99.51%   99.63%   +0.12%     
===========================================
  Files           62       62              
  Lines         6610     6626      +16     
  Branches      1078     1081       +3     
===========================================
+ Hits          6578     6602      +24     
+ Misses          20       15       -5     
+ Partials        12        9       -3
Impacted Files Coverage Δ
tiatoolbox/wsicore/wsireader.py 99.42% <100.00%> (+0.94%) ⬆️

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

@John-P John-P requested a review from shaneahmed March 24, 2023 12:47
shaneahmed
shaneahmed approved these changes Mar 24, 2023
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Just one comment. Otherwise I am happy to merge.

@shaneahmed shaneahmed merged commit 6ec1083 into develop Mar 27, 2023
@shaneahmed shaneahmed deleted the bug-535-omero-missing-version branch March 27, 2023 09:18
@shaneahmed shaneahmed added this to the Release v1.4.0 milestone Apr 10, 2023
This was referenced May 5, 2023
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shaneahmed added a commit that referenced this pull request May 5, 2023
@shaneahmed
🔖 Release 1.4.0 (#599)
5231f9d 
## 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
@shaneahmed
🔖 Release 1.4.0 (#600)
b879374 
## 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.
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Minor issue: errors do not follow intended path due to int conversion fail on empty string
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