Optimap

✨ What's Changed

* [Added support for URLs and DOIs in `om.download_example_data()`](https://github.com/cardiacvision/optimap/commit/82ea3e58428d12c7eacf3cc4c26182c4a794a929)
* Added Dense Inverse Search (DIS) optical flow algorithm
* Fixed C++ bindings when using non-contiguous input arrays
* Updated documentation

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.3.0...v0.3.1

✨ What's Changed

🎉 **PyPI Project Name Change**: optimap can now be installed with `pip install optimap`!

Previously, optimap had to be installed with `pip install opticalmapping`. Thanks to a successful name transfer, we are now using the name `optimap` on [PyPi](https://pypi.org/project/optimap/). The old `opticalmapping` package has been deprecated, to migrate from an existing `opticalmapping` installation follow the upgrade instructions:

Upgrade Instructions
1. Uninstall the old `opticalmapping` package:

pip uninstall opticalmapping

2. Install the new `optimap` package:

pip install optimap


The new `optimap` package includes all recommended dependencies (including OpenCV and PySide6), which was previously only installed when using `pip install opticalmapping[all]`. See the [documentation](https://cardiacvision.github.io/optimap/main/chapters/getting_started/#installation-using-pip-macos-windows-linux) if you want to install a version with minimal dependencies.


Other Changes
* [Fix image segmentation incompatibility with matplotlib>3.10](https://github.com/cardiacvision/optimap/commit/dc6df397073c63c579ae4ad65de69154d3375b7d)
* [Image Segmenter: Add invert mask keyboard shortcut: 'i'](https://github.com/cardiacvision/optimap/commit/b5df67a8820a028db7f734e900e74950a0bd856d)
* [Add optimap.video.collage](https://github.com/cardiacvision/optimap/commit/023006383cbc10e1e81168f349c4ad829ce52172)

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.2.4...v0.3.0

What's Changed
* Support numpy>2.0 in https://github.com/cardiacvision/optimap/pull/4
* Fix MATLAB video reader to work with files from other labs
* load_metadata: Include number of frames/image size for MultiRecorder imports
* Interactive segmentation: Add largest connected component filter, update icons
* The monochrome PyPi package was renamed to monochrome from monochrome-viewer
* Fix video looping in documentation
* Update documentation

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.2.3...v0.2.4

What's Changed

* Migrated docs from readthedocs to GitHub pages (due to memory limits). Automatic docs builds are now much faster!
* Updated and improved docs and tutorials
* Added support for python 3.13
* Added video importer for .mp4/.avi/.mov/...
* Added `export_image()` function in addition to `save_image()`. `export_image()` will always convert to uint8 for best compatibility with image viewers.
* `save_image()`: added compat parameter to convert image to 8bit
* Renamed `export_video_collage()` to `export_videos()`, now included in main namespace
* Fixed issue with numpy>=2.0, require numpy<2.0 as some dependencies rely on it for now
* Fixed videoplayer out of bounds
* Fixed `export_videos()` cmap and alpha clipping
* Fixed animation reset after saving to mp4 bug
* Fixed `compare_traces()` for videos with different lengths
* Removed WIP `adp` module to feature branch
* Fixed documentation builds for sphinx >= 7.4.6

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.2.2...v0.2.3

What's Changed

* Renamed video.play* functions to start with show_video, old functions are deprecated
* Renamed `retrieve_example_data()` to `download_example_data()`, added to top-level import. Old function name is deprecated.
* Renamed example data file names, added dual channel example. Old file names are deprecated.
* Changed order of arguments for video.save_image_sequence, path is now first arg. Old convention is deprecated.
* Change order of arguments for show_positions, positions are now first argument
* `video.normalize`: adedd dtype argument, infer maximum for integer output dtypes, support complex numbers
* Temporal difference filter: added `fill_value` and `center` arguments
* Contrast enhancement: support mask of valid values
* Added kwargs to `load_video()` for plugins
* `InteractivePlayer.save()`: added hide_slider/buttons/framecounter params
* Fixed `export_video()` for odd-sized videos
* Fixed `print_properties()` for videos with NaNs

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.2.0...v0.2.2

What's Changed

Interactive masking editor and more:

https://github.com/cardiacvision/optimap/assets/423552/2f574b82-bb77-4fa4-b50a-f42f96ab22d3


Breaking changes:

* `om.video.resize`: parameters are now `shape` or `scale`, instead of `newx`, `newy`
* All `save` and `export` functions now expect the filename first, e.g. `save(filename, value, ...)` instead of `save(value, filename, ...)`. The deprecated `save(value, filename, ...)` order will raise a warning but still work.
* `om.load_video`: Raises `FileNotFoundError` instead of `ValueError` if file not found
* MacOS 12+ is now required

New functionality & other changes

Python 3.12 is now supported.

**`optimap.image`**:
* Added `interactive_mask()`: Create a mask interactively by drawing on an image.
* Added `load_mask()` function
* `show_mask()`: only show True values in overlay. If no image passed show a black border around mask. Added `alpha`, `color`, `cmap` parameters
* Fixed `load_mask()`
* Added `collage()` function to arrange list of images in a grid
* Added `resize()`, `rotate_left()`, `rotate_right()`, `flip_left_right()`, `flip_up_down()`, `crop()`, `pad()` functions analogous to the `om.video` equivalents
* Fixed `smooth_gaussian()` for RGB(A) images

**`optimap.video`**:
* Added `om.video.export_video_collage()` to arrange a list of videos in a grid and save to a media file
* `om.video.load_image_folder()` function is now public API in addition to the `load_video()` wrapper
* `om.video.InteractivePlayer` class is now public API
* `om.video.MultiRecorderImporter`: added `get_frametimes()` function to load the frametimings (if supported by MultiRecorder camera plugin)
* `export_video()`, `export_video_with_overlay()`: add `progress_bar` parameter
* `resize`: add `interpolation` parameter for the different OpenCV interpolation methods

**`optimap.trace`**:
* `show_positions()`: add size, cmap, vmin, vmax and kwargs parameters
* Fixed `random_positions()`
* Add `collage_positions()` as equivalent to `image.collage()` or `video.export_video_collage()`

**Full Changelog**: https://github.com/cardiacvision/optimap/compare/v0.1.4...v0.2.0