Add ProtocolSerializer API for streaming

[naegelejd]

No description provided.

[Copilot]

Pull Request Overview

This PR adds a new ProtocolSerializer API for streaming ISMRMRD objects, enabling serialization and deserialization of acquisitions, images, waveforms, headers, ndarrays, and text data to/from binary streams. The implementation includes comprehensive testing and example usage for streaming-based MRI data processing.

Key changes:

• New ProtocolSerializer and ProtocolDeserializer classes for binary streaming
• Comprehensive test suite covering all supported object types and interleaved serialization
• Stream copy utility and end-to-end reconstruction example
• Refactored common test utilities and removed deprecated warning behavior

Reviewed Changes

Copilot reviewed 13 out of 13 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
ismrmrd/serialization.py	Core implementation of protocol serialization classes
utilities/ismrmrd_copy_stream.py	Simple utility for copying ISMRMRD streams
tests/test_serialization.py	Comprehensive test suite for serialization functionality
examples/stream_recon.py	Full streaming reconstruction example with FFT processing
tests/end-to-end/validate_results.py	End-to-end test validation script
tests/end-to-end/test-reconstruction.sh	Bash script for comprehensive end-to-end testing
tests/test_common.py	Common test utilities moved from test_file.py
tests/test_file.py	Updated to use common utilities
ismrmrd/image.py	Converted deprecated warning to documentation comment
ismrmrd/init.py	Added serialization classes to public API
examples/demo.py	Removed old demo file
README.md	Updated with proper ISMRMRD link
.github/workflows/python-publish.yml	Added end-to-end test execution

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[hansenms]

Nice one. Thanks @naegelejd.

[hansenms]

Are we no longer emitting this warning? I know we should stop threatening to remove this behavior, but what is the thinking about removing the warning? Just noisy?

[naegelejd]

Yes, it's very noisy. I decided that this API is stable and solid and therefore nothing will change in a future version, contrary to the warning message. It's better to just document the API discrepancy.