CIAtah 4.0

[bahanonu]

Main features and changes

• All CIAtah functions have been moved to +ciapkg folder so they are part of the ciapkg package or sub-packages. The ciapkg folder has been removed.
• Major version incremented due to large change in organization of many CIAtah/ciapkg functions and thus the underlying API.
  • All relevant CIAtah functions can now be called via ciapkg.api.FUNCTION_NAME, which allows for a central location to call all functions as well as allowing importing of relevant CIAtah functions into a function if want to reduce visual clutter. Full function can be found in respective +ciapkg sub-packages.
• Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package and ciatah class.
• Current support is MATLAB 2019b or later due to function of nested packages.
  • See https://www.mathworks.com/help/matlab/matlab_prog/upgrade-code-for-r2019b-changes-to-function-precedence-order.html#mw_8a31cdce-6dc1-4ae0-ae4a-ca0fbae7d1ff.
• Updates to certain functions for speed, UI, and other improvements.
• Move all NWB functions to ciapkg.nwb sub-package.
• Re-organized several File Exchange functions and removed unused ones.

Example of movie slider and cell-extraction in the main GUI.

Updated @ciatah functions

• ciatahMainGui - Added support for file list when selecting a specific folder. Font scaling support.
• modelPreprocessMovieFunction - Fix to handle folders with no files.
• modelExtractSignalsFromMovie - Added nwbpkg support. Updated EXTRACT support.

Updated +ciapkg functions

• Move Turboreg to _external_programs
• loadBatchFxns - Improved handling of external programs both in adding and removing from path. Additional support for removing specific packages that are not always needed.
• cropMatrix - Updated to allow specifying the size of the rectangle.
• getFileList - Added support to exclude adding the input directory to each file path.
• getMovieFileType - Added HDF5 capitalized file extension.
• getOptions - Ensure no warnings are shown. Added fix to handle users calling API version of getOptions with getOptions variable input arguments.
• loadDependencies - Added Turboreg (moved from within ciapkg) to make explicit that this is an external program. Update Schnitzer NWB package to new URL (https://github.com/schnitzer-lab/nwbpkg). Default to download GRAMmar.
• loadMovieList - Added HDF5 capitalized file extension. Ensure that loadMovieList has all output arguments set no matter return conditions.
• computeManualMotionCorrection - Added acceleration based on rapid user clicks or holding down direction keys. Add support for 90 degree quick rotation, fix passing of flip dims. Change number of pixels to translate per click and UI improvements. Improved pre-allocation.
• turboregMovie - Additional matlab disk normalizeType options. Additional display of information.
• normalizeVector - Added percentile name-value options for soft zero to one.
• playMovie - Update to avoid caxis with rgb movies, making them hard to view.
• setupNwb - Update to include check for each of the NWB dependencies, moved from saveNeurodataWithoutBorders. Added nwbpkg support.
• cmdLinePipeline - Updated to handle CIAtah v4.0 switch to all functions inside ciapkg package.
• saveNeurodataWithoutBorders - Added nwbpkg support.

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This discussion was created from the release CIAtah 4.0.