Code

Implement WsiAnnotations in C++#252

Code

Merged

jonasteuwen merged 98 commits intomainNKI-AI/dlup:mainfrom feature/geometryNKI-AI/dlup:feature/geometryCopy head branch name to clipboardSep 26, 2024

Commits

Commits on Aug 7, 2024

• Updated workflows

  jonasteuwen

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Commits on Aug 9, 2024

• Adding C++ TIFF writer

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Commits on Aug 10, 2024

• Add ZSTD compression, reformat some files

  jonasteuwen

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• First commit with geometries

  jonasteuwen

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• First writing of Polygon

  jonasteuwen

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Commits on Aug 11, 2024

• Some additional changes to cast the Polygon.

  jonasteuwen

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• Commiting to not lose work

  jonasteuwen

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• Updated for initial version of WsiAnnotations

  jonasteuwen

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Commits on Aug 12, 2024

• updates

  jonasteuwen

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• Some updates during development

  jonasteuwen

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• merge

  jonasteuwen

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  a784f79

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• Fix scaling issues

  jonasteuwen

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Commits on Aug 13, 2024

• Added functionality to remove polygons and points and to rebuild the RTree

  jonasteuwen

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• Implement complete initial version of geometry module

  jonasteuwen

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• We actually need to iterate over all layers, not just polys

  jonasteuwen

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  f7a3e1c

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• Implement scaling and offset functions

  jonasteuwen

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• Adding functionality to reindex polygons

  jonasteuwen

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• Created output container for results

  jonasteuwen

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• Sensible updates

  jonasteuwen

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• Add masking utility to AnnotationRegion

  jonasteuwen

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• Memory optimizations

  jonasteuwen

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• Adding sorting capabilities

  jonasteuwen

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• Add bounding box

  jonasteuwen

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• Added color LUT

  jonasteuwen

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Commits on Aug 14, 2024

• Refactor

  jonasteuwen

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Commits on Aug 17, 2024

• Extend dunder methods and code simplification for annotations (#251)

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  BPdeRooij

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  jonasteuwen

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  2be4b87

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• Merge branch 'main' into feature/geometry

  jonasteuwen

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  87c361d

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• Fixing the scaling, mypy and adding tests

  jonasteuwen

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  7f0db0e

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• minor changes in annotations

  jonasteuwen

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• Merge branch 'feature/geometry' of github.com:NKI-AI/dlup into feature/geometry

  jonasteuwen

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Commits on Aug 18, 2024

• Updating geometry module, and its tests.

  jonasteuwen

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• Rename modules, improve CI/CD

  jonasteuwen

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• Almost done with the geometry module

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  jonasteuwen

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• Disable a few tests, squash pylint errors

  jonasteuwen

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  efcfdc6

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• Fixing some bugs when trees get invalidated

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  jonasteuwen

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• Do an allclose rather than equal

  jonasteuwen

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• Weirdly enough different values on github

  jonasteuwen

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• Maybe a sudo install won't hurt

  jonasteuwen

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  35858e9

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• Remove assert

  jonasteuwen

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  a0377eb

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• Restructure C++ code

  jonasteuwen

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• Restructure C++ code

  jonasteuwen

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Commits on Aug 19, 2024

• Refactored code.

  jonasteuwen

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• Refactoring

  jonasteuwen

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• Refactor code

  jonasteuwen

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  d8ddb80

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• Rename functions, remove functions

  jonasteuwen

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  549f54a

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• Adhere to google C++ style guide

  jonasteuwen

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• Maybe include stdexcept so that github understandS?

  jonasteuwen

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  92b6145

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• Reducing a few compiler warnings

  jonasteuwen

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  84e53a9

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• Make sure mypy runs.

  jonasteuwen

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• Convenient helper function

  jonasteuwen

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• Implement XML export

  jonasteuwen

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• Add xsdata to requirements

  jonasteuwen

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• XML Schema reading now works

  jonasteuwen

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• Order can be 0...

  jonasteuwen

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Commits on Aug 20, 2024

• Several changes to support HaloXML

  jonasteuwen

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Commits on Aug 21, 2024

• Improve test coverage

  jonasteuwen

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• Improve test coverage to 90%

  jonasteuwen

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  5f6efe9

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• Streamlining

  jonasteuwen

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• Trying to get better CI/CD coverage

  jonasteuwen

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Commits on Aug 22, 2024

• Fix bug in annotations_experimental.py

  jonasteuwen

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• Add more tests, and fix bug in process

  jonasteuwen

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Commits on Aug 23, 2024

• Updating tests, updating schema, add box

  jonasteuwen

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  d75a072

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• Add more boxes functionality.

  jonasteuwen

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Commits on Aug 24, 2024

• Refactor factory methods to factory.h

  jonasteuwen

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  5236a52

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• Refactor

  jonasteuwen

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• Code simplifications

  jonasteuwen

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• Some final memory improvements

  jonasteuwen

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Commits on Aug 25, 2024

• Adding boxes to the geometry module

  jonasteuwen

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• Improve CI/CD

  jonasteuwen

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• Adding deprecation warnings

  jonasteuwen

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• Streamline meson

  jonasteuwen

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  3a3e66e

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• Attempt lazy initialization of the geometry collection in the region class

  jonasteuwen

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  fa862d1

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• Update tests for lazy evaluation

  jonasteuwen

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Commits on Aug 26, 2024

• Fixing memory error in region.h. Fix tox

  jonasteuwen

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Commits on Aug 27, 2024

• Improve workflows

  jonasteuwen

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  4f5ed1c

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• Improve workflows

  jonasteuwen

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• Handle tox merge

  jonasteuwen

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• Update tox.ini

  jonasteuwen

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• Remove line that doesn't work on github (?!)

  jonasteuwen

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  1ff5552

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• Cleanup code

  jonasteuwen

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• Try to run tests non-parallel

  jonasteuwen

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• Squash errors for now

  jonasteuwen

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Commits on Aug 28, 2024

• Fixes for ubuntu

  

  Jonas Teuwen

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Commits on Aug 31, 2024

• Improving annotations to mask conversion

  jonasteuwen

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  d1e4dcc

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• Merge branches 'feature/geometry' and 'feature/geometry' of github.com:NKI-AI/dlup into feature/geometry

  jonasteuwen

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• Reformat

  jonasteuwen

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Commits on Sep 1, 2024

• Add Lazy Array

  jonasteuwen

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• Added some extra functionality to lazy array

  jonasteuwen

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Commits on Sep 2, 2024

• Added lazy evaluation for PolygonCollection

  jonasteuwen

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• Added lazy evaluation for PolygonCollection

  jonasteuwen

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  e3fc083

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• Merge branch 'feature/geometry' of github.com:NKI-AI/dlup into feature/geometry

  jonasteuwen

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  bb8ba91

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• Make precommit run

  jonasteuwen

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  85f90f9

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• Updates to CI

  jonasteuwen

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• Fix mypy

  jonasteuwen

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Commits on Sep 3, 2024

• Add ROI to the GeometryCollection

  jonasteuwen

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• Added ROIs to DLUP XML

  jonasteuwen

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Commits on Sep 4, 2024

• Added ROIs to output xml and parsing

  jonasteuwen

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Commits on Sep 6, 2024

• move declarations to headers

  JorenB

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