Version 1.3.0

New features:

• Added functions that plot violin plots (FlowCal.plot.violin() and FlowCal.plot.violin_dose_response()). [PR335]
• Added a new way to save and reuse density gates (FlowCal.gate.density2d() now accepts and returns a bin_mask array). [PR337]
• Added channel_labels() method to FCSData objects, which returns $PnS keyword values (i.e., long channel names). [PR323]

API changes:

• FlowCal.gate.density2d() now accepts and returns a bin_mask array. [PR337]
• All outputs returned by FlowCal.excel_ui.process_beads_table() and FlowCal.excel_ui.process_samples_table() are now OrderedDicts. [PR334]

Other changes:

• Migrated Excel engine to openpyxl. [PR325, PR329, 8bcb607, 9714791]
• Removed dependency on palettable. [PR328]
• Modified macOS install and run scripts to work with both bash and zsh. [f4f055f, 067a1ec]
• Refactored FlowCal.plot.hist1d() to permit weights kwarg. [PR333]
• FlowCal.mef.get_transform_fxn() now accepts None in mef_channels list. [PR331]

Version 1.2.2

• Compatibility fixes with matplotlib 3.1.0.
• Installation and usage improvements for macOS.
• FCSData can be used with the pickle module.

Version 1.2.1

Fixed small incompatibility bug with Python 3.7.

Version 1.2.0

• Added compatibility with Python 3.6.
• Added a command line entrypoint: The Excel UI can be called from the command line by entering flowcal.
• Resolved several issues with more recent versions of prerequisite packages.

Version 1.1.4

• Added compatibility with pandas 0.20.1.
• Improved documentation on installing Anaconda.

Version 1.1.3

• Restored default black edges in histograms when using matplotlib 2.0.0.
• Made histogram sheet from the Excel UI optional.
• Improved error detection of nonsensical error fractions (e.g. 1.5).

Version 1.1.2

Fixed incompatibility with matplotlib 2.0.0.

Version 1.1.1

This version fixes minor bugs and improves compatibility with respect to version 1.1.0.

Bug fixes

• FCSData now loads fcs files successfully when the file contains information on $PnG and $PnV other than numbers.
• Linear gain in specific files generated by FlowJo Collectors Edition is now properly extracted.
• FlowCal.gate.start_end() now behaves as expected when num_end=0.
• plot.scatter3d() now works with matplitlib 1.5.1.

Code improvements

• FlowCal.excel_ui.process_beads_table() and FlowCal.excel_ui.process_samples_table now plot to the standard output when plot_dir is not specified.
• excel_ui.process_beads_table() now contains an additional argument to directly control mef.get_transform_fxn().

Version 1.1.0

High-level changes

• Improved compatibility with different FCS files.
• Improved ability to handle high-resolution FCS data and floating-point data, and transform this data to MEF.
• Logicle scale implemented. This is the new default for plotting.

Important code changes

Gating and plotting

• gate.density2d and all simple plotting functions now include arguments xscale, yscale, and zscale as appropriate, to define the scale of each axis. Valid options are 'linear', 'log', and 'logicle'. All these functions default to logicle.
• Arguments log, xlog, ylog, and zlog in plotting functions are deprecated.

I/O

• FCSData property domain has been deprecated. New function range returns, for each specified channel, the lower and upper bounds as specified by the FCS file.
• FCSData property hist_bin_edges has been deprecated. New function hist_bins allows for dynamic generation of histogram bins using either linear, logarithmic, or logicle scaling.

MEF

• The transformation function returned by get_transform_fxn is now meant to be used with data previously transformed to RFI using transform.to_rfi().
• Functions clustering_gmm and selection_std now allow for rescaling of the data before performing their operations. The default scaling is logicle.
• fit_beads_autofluorescence now uses a model that transforms data from RFI to MEF. Previously, the model was meant to be used to transform data in raw channel numbers to MEF, when using a logarithmic amplifier. The new approach allows for transformation of data taken with linear amplifiers as well.

Version 1.0.0

Changes in Excel UI:

• Statistics for beads files, including bead model parameter, detector gain, and others.
• User-friendly error reporting for files with low event counts, non-existing files, and acquisition settings of corresponding beads and samples not identical.
• Command-line parameters for the Excel UI, which allows the user to batch-process several files, and turn on or off the generation of plots.

Changes in code:

• transform.exponentiate() deprecated in favor of transform.to_rfi(), which automatically decides whether to exponentiate the data based on acquisition settings.

Other changes:

• Bug when loading files that do not contain a valid $DATE keyword.