New load/save cell-extraction outputs, EXTRACT support, and misc. updates #66
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…ates ## New - Added support for the new cell-extraction method EXTRACT (https://github.com/schnitzer-lab/EXTRACT-public) to CIAtah. - `ciapkg.io.saveSignalExtraction` - universal function to save NWB or CIAtah-style cell-extraction outputs - `ciapkg.io.loadSignalExtraction` - function to load either NWB or CIAtah-style cell-extraction outputs. - `ciapkg.pkgName` - Outputs the package name, e.g. CIAtah. ## Updated: - `calciumImagingAnalysisMainGui` changed to `ciatahMainGui`. - `computeManualSortSignals` - If user hasn't called modelVarsFromFiles, computeManualSortSignals called the function. However, this lead to a mismatch between computeManualSortSignals fileNum and obj.fileNum, leading to mismatch between xcoords, etc. and input signals/images. - `loadDependencies` - Added EXTRACT support to list of functions to download. - `ciapkg.pkgName` - Option on whether to update package (only 0 for now). Also alert user if behind a version. - `modelExtractSignalsFromMovie` - Update `saveRunTimes` to handle case in which user selects multiple movies for cell extraction. Convert ndSparse outputs to single from cell-extraction algorithms (e.g. for CELLMax/EXTRACT) when saving as NWB. Updated EXTRACT support to include additional options. - `signalSorter` - User can now input just NWB path without a blank variable for inputSignals. Also added support for CIAtah mat files. - `saveNeurodataWithoutBorders` - Update to checking if only a single signal input. - `computeCnmfeSignalExtraction_batch` - extractedSignalsType, extractedSignalsEstType struct update. - `changeFont` - Add font name support. - Updated docs.
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Tested Matlab EXTRACT
Cross-session alignment for example movies. CNMF-E
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New
ciapkg.io.saveSignalExtraction- universal function to save NWB or CIAtah-style cell-extraction outputsciapkg.io.loadSignalExtraction- function to load either NWB or CIAtah-style cell-extraction outputs.ciapkg.pkgName- Outputs the package name, e.g. CIAtah.Updated:
calciumImagingAnalysisMainGuichanged tociatahMainGui.computeManualSortSignals- If user hasn't called modelVarsFromFiles, computeManualSortSignals called the function. However, this lead to a mismatch between computeManualSortSignals fileNum and obj.fileNum, leading to mismatch between xcoords, etc. and input signals/images.loadDependencies- Added EXTRACT support to list of functions to download.ciapkg.pkgName- Option on whether to update package (only 0 for now). Also alert user if behind a version.modelExtractSignalsFromMovie- UpdatesaveRunTimesto handle case in which user selects multiple movies for cell extraction. Convert ndSparse outputs to single from cell-extraction algorithms (e.g. for CELLMax/EXTRACT) when saving as NWB. Updated EXTRACT support to include additional options.signalSorter- User can now input just NWB path without a blank variable for inputSignals. Also added support for CIAtah mat files.saveNeurodataWithoutBorders- Update to checking if only a single signal input.computeCnmfeSignalExtraction_batch- extractedSignalsType, extractedSignalsEstType struct update.changeFont- Add font name support.