# Changelog

All notable changes to PyFlowReg will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]

## [0.1.0a8]

### Fixed

- **TIFF**: Reader now clamps `frame_count` to available pages (respecting deinterleave) to avoid out-of-range access when metadata overreports SizeT/series length.

## [0.1.0a7]

### Added

- **Flow parameter overrides for sessions**: `SessionConfig` now exposes a `flow_options` field (inline dict or path to a saved `OF_options` JSON), so Stage 1 optical-flow parameters can be managed directly from TOML/YAML configs, the CLI, or job-array invocations without ad-hoc override code.

### Fixed

- **Dtype preservation**: `VideoReader` and `compensate_recording` pipeline now preserve the input file dtype. Averaging for binning changed dtypes to float in the readers.
- **BigTIFF**: tiff writers properly use the bigtiff property now.

## [0.1.0a6]

### Added

- **Multi-session processing module** with full MATLAB parity
  - Three-stage pipeline for aligning multiple recordings
  - `SessionConfig` with TOML/YAML support
  - Per-recording motion correction with valid mask persistence
  - Inter-sequence alignment via phase cross-correlation and optical flow
  - Session-wide valid mask computation
  - HPC array job support (SLURM, SGE, PBS)
  - Command-line interface: `pyflowreg-session`
  - Crash-safe atomic file writes
  - HDF5 completeness verification
- Refactored and extended warping utilities
- Example session configuration files (TOML and YAML)

### Fixed
- Batch size parameter confusion (removed unused parameter from RegistrationConfig)
- Thread oversubscription in multiprocessing executor (now sets thread limits)

## [0.1.0a5]

### Added

- **GPU Acceleration**: New `flowreg_cuda` and `flowreg_torch` backends with device-aware resize utilities, runtime detection, `pyflowreg[gpu]` optional extra, and `examples/jupiter_demo_arr_gpu.py` walkthrough
- **Napari-oriented APIs**: `BatchMotionCorrector.register_w_callback` / `register_registered_callback` matching `compensate_arr` parameters, plus `NullVideoWriter` and `OutputFormat.NULL` for headless pipelines
- **Documentation**: Complete MyST/Sphinx site with installation, quickstart, API reference, theory, workflows, and GPU setup guides, backed by ReadTheDocs config and executable quickstart/parallelization tests

### Fixed

- **Critical weight handling**: Multi-dimensional weight handling in `OFOptions` now correctly preserves numpy arrays, rejects invalid 4D arrays, and properly handles 2D `(H, W)` and 3D `(H, W, C)` spatial weight maps
- **Executor registration**: Restored side-effect imports for multiprocessing/threading executor registration that were removed by pre-commit hooks, preventing silent fallback to sequential mode
- **Dimensionality checks**: Fixed edge cases in `OF_options` weight and sigma parameter validation

### Changed

- **Backend registry**: Now restricts executor choices per backend, improves availability checks, and provides clearer logging so sequential fallback is visible
- **Testing**: Added regression tests for weights, callbacks, executors, and Null writer; GPU-aware test skips for platforms without CuPy
- **Tooling**: Applied FlowRegSuite pre-commit hooks and reorganized public exports without breaking external API

## [0.1.0a4]

Fixed batch normalization to use reference values.

## [0.1.0a3]

- Cross-correlation pre-alignment feature
- Backend architecture refactoring
- ScanImage TIFF format compatibility fix

## [0.1.0a2]

- CI/CD improvements and Python 3.13 support
- Demo download utilities
- Refactored CLI and paper benchmarks into separate repositories

## [0.1.0a1]

Initial alpha release with core variational optical flow engine, multi-channel 2D motion correction, and modular I/O system.

[Unreleased]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a7...HEAD
[0.1.0a7]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a6...v0.1.0a7
[0.1.0a6]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a5...v0.1.0a6
[0.1.0a5]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a4...v0.1.0a5
[0.1.0a4]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a3...v0.1.0a4
[0.1.0a3]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a2...v0.1.0a3
[0.1.0a2]: https://github.com/FlowRegSuite/pyflowreg/compare/v0.1.0a1...v0.1.0a2
[0.1.0a1]: https://github.com/FlowRegSuite/pyflowreg/releases/tag/v0.1.0a1