workflow fit fye

matlabcode/FCS/master_workflow_fit_dye.m

+function master_workflow_fit_dye
+% MASTER_WORKFLOW_FIT_DYE call workflow_fit_dye for several directorie
+% specified in the script
+% 
+% Antonio Politi, EMBL, January 2017
+
+wd = 'Z:\AntonioP_elltier1\CelllinesImaging\MitoSysPipelines';
+cd(wd);
+if ~exist(fullfile(wd, 'ProcessingHelpFiles'));
+    mkdir(fullfile(wd, 'ProcessingHelpFiles'));
+end
+    
+if ~exist(fullfile(wd, 'ProcessingHelpFiles', 'alexaDirectories.mat'))
+    [indirCell] = getAllFolders(wd, 'Alexa');
+    save(fullfile(wd, 'ProcessingHelpFiles', 'alexaDirectories.mat'), 'indirCell');
+else
+    load(fullfile(wd, 'ProcessingHelpFiles', 'alexaDirectories.mat'));
+end
+% output subdiretoy to store results
+outputdir = 'optimisedFit';
+
+% range to fit kappa
+kappaVal = [2:0.1:7]';
+
+for idir = 1:length(indirCell)
+    indir = indirCell{idir};
+    display(['master_workflow_fit_dye processing directory ' num2str(idir) ' ' indir])
+    workflow_fit_dye(indir, kappaVal, outputdir, '1c');
+end
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