% Formerly CBT.Hca.Settings.set_fast_sets
%
%
%
timeFramesNr = 0; % 0 - take all timeframes
alignMethod = 1; % 1 - nralign, 2 - ssdalign, 3 - ssg
genConsensus = 1; % generate consensus

saveinfoscores = 0;
adddefaulttheorysets = 0;
  
skipEdgeDetection = 0; % skip edge detection
edgeSettings = 1;
skipDoubleTanhAdjustment = 1;
comparisonMethod = 'mass_pcc'; % method for comparison of exp vs theory, alt 'unmasked_pcc_corr', 'mass_pcc'

displayResults = 0; % display result figure
plotallmatches = 0; % plot matches to all barcodes as txt files

skipPrechoice = 1;
prestretchMethod = 0; % 0 - do not prestretch % 1 - prestretch to common length
theories = 'theories_2020-04-20_13_39_51_.txt'; % theories either as mat or directly txts
dtwscriptpath = '/Development/hca/tests/features/6_dtw/Tests';
[filterSettings]
filter = 0; % filter
% filter settings. For one timeframe, refer to P.Torche paper for best
filterMethod = 0; % 0 - filter after stretching, 1 - before
filterSize = 2.3;
  
[kymosets]
askforkymos = 0; % sould we ask for kymos  
% sample filename, comment out for the release version
kymoFile = 'kymos_2020-04-20_13_41_38_.txt'; % if file with kymograph txt's was generated before, this is the name of the folder
% all the different setting choices
askforsets = 0; % should we ask for settings
[random]
generate = 0; % generate random
noOfCutouts = 2; % number of random cutouts from the input set
cutoutSize = 200; % size of region to be cut out (units: pixels)

% bitmask settings
[bitmasking]
prestretchPixelWidth_nm = 130; % camera nm/px
psfSigmaWidth_nm = 300; % psf in nanometers
deltaCut = 3; % how many delta's should we take
numPixels = 10;
%untrustedPx = sets.bitmasking.deltaCut*sets.bitmasking.psfSigmaWidth_nm/sets.bitmasking.prestretchPixelWidth_nm;

[consensus]
barcodeNormalization = 'bgmean';
promptForBarcodeClusterLimit = 0;
threshold = 0.75;

% import OptMap.MoleculeDetection.EdgeDetection.get_default_edge_detection_settings;
%  sets.edgeDetectionSettings = get_default_edge_detection_settings(sets.skipDoubleTanhAdjustment);

[export]
savetxt = 1;

[theory]
askfortheory = 0;
precision = 5;  %default is 5;
askfornmbp = 0;
nmbp = 0.25;
skipStretch = 1;
stretchFactors = [0.95 0.96 0.9700    0.9800    0.9900    1.0000    1.0100    1.0200    1.0300 1.04 1.05];

[pvalue];    
file = ''; 
promtforparams = 0;
len2 = 5000000;
pixelWidth_nm = 130;
lenMin = 100;
lenMax = 1000;
numRnd = 1000;
psfSigmaWidth_nm = 300;
    
[output]
matDirpath = 'output/'
askforoutputdir = 0;

