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postProcessCNMF.m
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postProcessCNMF.m
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% The code extracts results from CNMF algorithm.
% Author: Weijian Yang and Darcy S. Peterka
% toolbox:
% plotROIContour: plot the ROI contour ()
% signalExtraction: extract the raw, filtered, and inferred signal (dfof, F, df)
% plotActivityTrace: plot the signal
addpath(genpath('utilities'));
%% plot ROI contour
% [ CC, info ] = plotROIContour( A, d1, d2, plotControl )
% input parameters
% A: spatial component from CNMF
% d1, d2: dimension of the data
% plotControl.Cn: background image
% plotControl.displayLabel: if it is 1, the ROI number will be labelled on the plot
% plotControl.ROIID: id of ROIs to be plotted
% plotControl.option: 1: The contour is drawn around the value above which a specified fraction of energy is explained (default 99%)
% 2: The contour is drawn around the exterior boundary
% plotControl.thr: energy fraction included in the drawn contour in option 1
% plotControl.cmap: colormap of the background image
% plotControl.lineColor: line color of the drawn contour
% output parameters
% CC: outline of the contour
% info: contour information, contains ROI id, weighted contour map, boundary box, and centroid
% Author: Eftychios A. Pnevmatikakis, Weijian Yang and Darcy S. Peterka
plotControl.Cn=Cn;
plotControl.thr=0.95;
plotControl.option=1;
d1=options.d1;
d2=options.d2;
[coor, contourInfo] = plotROIContour( A2, d1, d2, plotControl );
%% extract the signal
% [ inferred, filtered, raw ] = signalExtraction(Y,A,C,b,f,d1,d2,extractControl)
% inputs: Y raw data (d X T matrix, d # number of pixels, T # of timesteps)
% A matrix of spatial components (d x K matrix, K # of components)
% C matrix of temporal components (K x T matrix)
% S matrix of deconvolved activity ((K-1) x T matrix) (optional)
% b matrix of background spatial components (d x options.nb, options.nb # of components)
% f matrix of background temporal components (options.nb x T matrix, options.nb # of components)
% extractControl.baselineRatio: residue baseline of signals from CNMF (default:0.25); set to 0 to ignore this residue baseline
% extractControl.thr: energy fraction included in the raw signal contour (default:0.99)
% inferred: spatial weighting on the ROI pixels, unmixing, background substraction, and denoising
% filtered: spatial weighting on the ROI pixels, unmixing, background substraction
% raw: uniform spatial weighting on the ROI pixels (with threshold to remove the very low energy pixels), background substraction
% inferred, filtered, raw contains structure fields: df, F, dfof, with definition below
% df: df signal
% F: baseline
% dfof: dfof
% in addition, raw contains a structure field named "CR", with definition below
% CR: information of the cell contour used in raw signal calculation
% Author: Eftychios A. Pnevmatikakis, and Weijian Yang
extractControl.baselineRatio = 0.25;
extractControl.thr = 0.95;
[inferred, filtered, raw] = signalExtraction(Yr,A2,C2,b2,f2,d1,d2,extractControl);
%% plot the signals
% plotActivityTrace( inferred, filtered, raw, plotControl)
% inputs: inferred, filtered, raw (from the output of "signalExtraction.m")
% plotControl.frameRate: frame rate in fps
% plotControl.normalization: normalize the amplitude of the temporal trace for plotting purpose
% plotControl.sep: vertical (amplitude) offset between adjacent temporal traces
% plotControl.displayLabel: whether to display ROI ID for the temporal traces
% plotControl.plotInferred: whether the inferred signal is plotted
% plotControl.plotFiltered: whether the filtered signal is plotted
% plotControl.plotRaw: whether the raw signal is plotted
% plotControl.rollingView: whether the display is set such that only 20 temporal traces are displayed at a time, followed by any key to move onto the next 20 traces, and etc.
% Author: Weijian Yang
plotControl2.frameRate=6.7468;
plotControl2.normalization=1; plotControl2.sep=1.2; plotControl2.displayLabel=1; plotControl2.rollingView=1;
plotControl2.plotInferred=1; plotControl2.plotFiltered=1; plotControl2.plotRaw=0;
plotActivityTrace( inferred.dfof, filtered.dfof, raw.dfof, plotControl2 );