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CHANGELOG.md

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Changelog

  • v2.0.5
    • 2024-01-19
      • Moved Boris.TSV.load to Boris.Aggregated.load
      • Moved Boris.CSV.load to Boris.Tabulated.load
      • Created Boris.load which calls Aggregated or Tabulated automatically.
      • Modified Doric.load to provide more information during errors.
    • 2024-01-18
      • Added Doric.getLocations(filename)
      • Added datasets to the defaults in Doric.load(filename, [datasets])
      • Moved Boris.load to Boris.TSV.load
      • Added Boris.CSV.load
  • v2.0.4
    • 2023-12-07
      • Fixed bug when the user attempts to resample to frequencies higher than the sampling rate.
  • v2.0.3
    • 2023-12-07
      • Modified Doric.Load to handle more data storage choices.
  • v2.0.2
    • 2023-11-30
      • Made frequency a public property.
    • 2023-11-15
      • Changed defaults:
        • getF from @(fpa) fpa.signalCorrected - fpa.referenceFitted to @(fpa) fpa.signalStandardized - fpa.referenceFitted;
        • referenceFitted from referenceCorrected to referenceStandardized
        • f from signalCorrected to signalStandardized
      • Replaced default fitReferenceToSignal function to calculate non-negative, bisquare, linear regression from fit to lsqnonneg.
      • Changed legend from Baseline to Photobleaching
      • Moved signal in front of reference in plotTrace figures.
      • Added version number as a static field of FPA.
      • Removed exportAUC and added this and additional data to exportStatistics
  • v2.0.1
    • 2023-11-14
      • Rename release names
      • Removed unused tags
    • 2023-11-10
      • Changed version from 1.0.0 to 2.0.1 in the citation file.
      • Changed plotTraces to plotTrace in the documentation.
    • 2023-11-09
      • New changes saved to a new branch.
      • Packaged data loaders.
      • Renamed data properties to match the name of the corresponding function that generates it.
      • Analysis steps are part of the configuration.
      • Outcomes of the analysis are read-only.
      • Added standardization step in the analysis and plots.
      • Added 95% confidence interval to PowerSpectrumPlot and uses the Welch's method.
      • Added helper functions to customize analysis steps.
      • Window size and event times moved from the configuration to an argument of the plotting or exporting functions.
      • Exporting data may now occur in rows or columns.
      • Examples are described in the online documentation.
      • Removed deprecated data and example files.
  • v1.0.0
    • 2023-10-12
      • Configuration is now reflected as members of the FPA object.
      • Changed the signature of multiple parameters to provide flexibility with the analysis steps.
        • The following parameters are affected: configuration.threshold, configuration.signalCorrection and configuration.referenceCorrection. Now these functions expect dff as argument, configuration.threshold expect a single number as an output argument, whereas signal and referenceCorrection expect an array of the same size of fpa.dff as output.
      • User provided epochs are now used as is without consideration of edgeId or artifactFreeId.
      • Removed thresholdEpochs as the user may incorporate this information in the aformetioned function.
      • Added signalArtifactFree and referenceArtifactFree to fpa's properties.
    • 2023-04-12
      • Added option to modify the default baseline correction operation (signal bleaching is subtracted from signal and reference bleaching is subtracted from reference).
      • Changed the threshold function signature; arguments to calling function are now fpa and data.
    • 2023-04-05
      • Added option to provide separate baseline epochs for signal and reference.
    • 2023-02-03
      • Added h5 loader, which works for Doric lock-in datasets by default.
      • Fix an out of bounds bug that could happen for peaks at the beginning or end of a trace.
      • Removing time points later than the original time series.
    • 2022-12-16
      • Added option for detecting peaks using prominence or height (default). When prominence is selected, threshold is not plotted.
      • Changed the way thresholds are provided; using a raw value or a function that operates on input data.
      • Changed default peak separation from 2.0 to 0.5.
      • Removed rendering of negative peaks.
      • Removed examples. Will re-add on a request basis.
      • Event and peak windows can be defined as a range or as a vector.
      • Added option to plot event trigger average.
      • Added option normalize event data prior to plotting (undocumented).
      • Added a reader for Deep Lab Cut generated files (undocumented).
      • Added normalization options for peaks.
      • Event and peak are normalized to values left of the peak by default.
    • 2022-08-31
      • Updated exampleRA.m to show how to normalize.
      • Documented code and readme.md
    • 2022-06-30
      • Added setup.
      • Added exponential decay fit to trigger plots.
      • Removed smooth dff plots and object fields.
      • Thresholding value is calculated on both artifact and edge free data.
      • Removed peaksLowpassFrequency:
        • Peak detection is done directly in dff with minimum distance given by peakSeparation (convert with 1.0 / peaksLowpassFrequency).
      • Filtering includes data edges.
      • Fitting reference to signal uses all data.
      • Added event window for event triggers.
      • Added normalization options for events.
      • Refactored triggered window to peak window which can now be a range.
      • Removed start and stop triggers; using events instead.
      • Fixed epoch bands not drawing epochs with Inf values.
    • 2022-06-08
      • Added custom event triggers (similar to start, stop, and peak triggers).
      • Added custom epochs to calculate peak threshold.
      • All triggered data exported includes the column ConditionName.
    • 2022-05-10
      • Export f.
      • Added batch processing scripts to traverse project folders.
    • 2021-11-17
      • Patched loadData.m to remove columns with all NaN values and rows with any NaN values.
      • Added column normalizedArea (redundantly) to exported AUC file.
    • 2021-11-01
      • Process a project folder as an example.
      • First release.
    • 2021-03-25
      • Added baseline plot of reference for figure 1.1.
      • Figure 1.1 shows resampled raw data (before was corrected data).
    • 2021-03-15
      • Added heatmaps of raw triggers.
      • Plots are now methods.
    • 2021-03-02
      • Added thresholding options.
      • Default thresholding changed from k * mad(x) + mean(x) to k * mad(x) + median(x).
    • 2021-03-01
      • FPA changed from function to object.
      • Added export method.
      • Added epoch-start and epoch-stop to trigger averages.
      • Added BORIS reader.
    • 2021-02-25
      • Area under the curve is normalized and calculated with trapz.
      • Default normalization changed to "modified z-score".
      • Significant changes to normalization API.
    • 2021-01-15
      • Reference is fitted to signal.
      • Band-pass replaced by low-pass.
      • GUI example supports artifact removal.
    • 2019-08-22
      • Library and example code.
      • Added loaders for multiple data acquisition systems.
    • 2019-02-20
      • Initial release.

License

© 2018 Leonardo Molina

This project is licensed under the GNU GPLv3 License.