feat: add "mask support" for reading & composition

[ptahmose]

[x] I followed the How to structure your PR.
[ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version.
[ ] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version.
[x] In case of API changes, I updated API.md.

This PR is updating libCZI to latest version, which includes support for "mask" (c.f. ZEISS/libczi#153).
The new functionality of "mask-aware tile-composition" is made available to pylibczirw by introducing a ReaderOptions object which optionally can be passed to open_czi. Mask-aware composition is therefore an opt-in function at this point (motivation is to limit risk and ensure backwards compatibility).

[codecov]

Codecov Report

❌ Patch coverage is 82.35294% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.56%. Comparing base (0dabe3a) to head (461126d).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #96      +/-   ##
==========================================
- Coverage   97.25%   96.56%   -0.69%     
==========================================
  Files           1        1              
  Lines         364      379      +15     
  Branches       50       51       +1     
==========================================
+ Hits          354      366      +12     
- Misses          5        7       +2     
- Partials        5        6       +1     

Components	Coverage Δ
pylibczirw_python	96.56% <82.35%> (-0.69%)	⬇️
pylibczirw_c	∅ <ø> (∅)

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[Copilot]

Pull Request Overview

This PR adds "mask support" functionality to pylibczirw by updating to the latest version of libCZI. The primary purpose is to enable mask-aware tile composition as an opt-in feature while maintaining backwards compatibility.

Key changes:

• Introduction of a ReaderOptions dataclass to configure mask awareness and visibility check optimization
• Updated libCZI submodule to support mask functionality
• Modified the open_czi function and CziReader class to accept and utilize reader options

Reviewed Changes

Copilot reviewed 11 out of 11 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pylibCZIrw/czi.py	Adds ReaderOptions dataclass and integrates it into CziReader constructor and open_czi function
libs/libCZIrw	Updates libCZI submodule to version with mask support
_pylibCZIrw/src/pylibCZIrw_Config.h	Adds new configuration header file
_pylibCZIrw/src/bindings/PbHelper.h	Adds atomic lock counting for bitmap wrapper
_pylibCZIrw/src/bindings/CZIrw.cpp	Exposes ReaderOptions class and new constructor to Python bindings
_pylibCZIrw/src/api/ReaderOptions.h	Defines C++ ReaderOptions structure
_pylibCZIrw/src/api/CZIreadAPI.h	Adds new constructor overload accepting ReaderOptions
_pylibCZIrw/src/api/CZIreadAPI.cpp	Implements ReaderOptions support in API
_pylibCZIrw/src/api/CMakeLists.txt	Adds ReaderOptions.h to build
API.md	Documents the new ReaderOptions functionality
.gitmodules	Updates submodule configuration

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[Copilot]

Pull Request Overview

Copilot reviewed 11 out of 11 changed files in this pull request and generated 4 comments.

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