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Recent Releases of optimap

optimap - v0.3.1

✨ What's Changed

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

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Published by sitic about 1 year ago

optimap - v0.3.0

✨ 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. 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 if you want to install a version with minimal dependencies.

Other Changes

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

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Published by sitic over 1 year ago

optimap - v0.2.4

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

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Published by sitic over 1 year ago

optimap - v0.2.3

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

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Published by sitic over 1 year ago

optimap - v0.2.2

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.saveimagesequence, 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

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Published by sitic about 2 years ago

optimap - v0.2.0: Interactive masking and more

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

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Published by sitic over 2 years ago

optimap - v0.1.4

What's Changed

Breaking Changes

  • compute_activation_map: returns time in milliseconds instead of seconds for computed activation times when fps parameter is specified

New Functionality

  • Added smooth_gaussian, erode_mask, dilate_mask, binary_closing, binary_opening functions to image module
  • image.show_image: added show_colorbar and colorbar_title parameters
  • image.show_mask added title parameter
  • compute_activation_map: added show (for plotting, True by default), inverted, and set_nan_for_inactive parameters

Other Changes

  • Ignore NaNs for play_video() and other functions
  • Added support for Python 3.12
  • Improved error handling for MultiRecorderImporter

Full Changelog: https://github.com/cardiacvision/optimap/compare/v0.1.3...v0.1.4

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Published by sitic over 2 years ago

optimap - v0.1.3

  • Add minmal GUI to om.play_video video.play/play2/playn
  • Fix om.load_video() when using a combination of step and frames parameters
  • Add vmin1, vmax1, vmin2, vmax2 arguments to video.play2
  • video.normalize: add vmin and vmax paramters
  • Fix overlay video code when overlay contains NaNs

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Published by sitic over 2 years ago

optimap - v0.1.2

  • Switch from QtCairo to QtAgg for the default interactive matplotlib backend. Simplifies installation as we don't depend on cairo anymore.
  • fix select_traces()
  • fix load_tiff_folder()
  • fix error handling when OpenCV is not installed
  • fix saveimagesequence for tiff files
  • add fps and x parameter to select_traces() and compare_traces()
  • added WIP ratiometry tutorial example

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Published by sitic over 2 years ago

optimap - v0.1.1

Fixes issue with example file download.

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Published by sitic almost 3 years ago

optimap - v0.1.0

Initial release of optimap.

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Published by sitic almost 3 years ago