process 2 channels

matlabcode/FCS/dyeFcsmodel.m

@@ -55,13 +55,26 @@ classdef dyeFcsmodel < absFcsmodel
         end
 
         function vol = computeVolume(MO, par, dyetype)
-            % COMPUTEVOLUME Compute focal volume return value in picoliter
+            % COMPUTEVOLUME Compute focal volume return value in femtoliter
             %   par  - vector or struct of parameters
             if isstruct(par)
-                vol = pi^(3/2).*((2*sqrt(MO.diffCoeff(dyetype)*par.tauD1)/1000).^3).*par.kappa;
-                
+                vol = pi^(3/2).*MO.computeRadius(par, dyetype).^3.*par.kappa;
+            else
+                vol = pi^(3/2).*MO.computeRadius(par, dyetype).^3.*par(:,9);
+            end
+        end
+        
+        function vol = computeConcentration(MO, par, dyetype)
+            % COMPUTECONCENTRATION Compute concentration and returns value
+            % in nM
+            %   par  - vector or struct of parameters
+            % Na = 0.6022140 (=
+            % 6.022140*10^23*10^-15(femtoliter)*10^-9(to get nM))
+            Na = 0.6022140;
+            if isstruct(par)
+                vol = par.N./MO.computeVolume(par, dyetype)/Na; 
             else
-                vol = pi^(3/2).*((2*sqrt(MO.diffCoeff(dyetype)*par(:,5))/1000).^3).*par(:,9);
+                vol = par(:,1)./MO.computeVolume(par, dyetype)/Na;
             end
         end
         
@@ -110,11 +123,12 @@ classdef dyeFcsmodel < absFcsmodel
             norm(1,1) = normT(pos);
         end
         
-        function [thetaT, tauT] = fitThetaTtauTArray(MO, dataC, kappa)
+        function [thetaT, tauT] = fitThetaTtauTArray(MO, dataC, kappa, iC)
             % FITTHETATTAUTARRAY find optimal thetaT and tauT for several data simultaneously with fixed kappa
             %   INPUT:
-            %       dataC  - a cell array containing [tau, corr] arrays
+            %       dataC  - a cell array containing [tau corrCh1 corrCh1_e corrCh2 corrCh2_e Xcorr Xcorr_e] arrays
             %       kappa  - fixed kappa value
+            %       iC     - index of channel to be used 1 - Ch1, 2 - Ch2, 3 - XCorr 
             %   OUTPUT:
             %       thetaT - mean optimal thetaT for several measurements
             %       tauT   - mean optimal tauT for several measurements
@@ -126,7 +140,7 @@ classdef dyeFcsmodel < absFcsmodel
             outParCorr = [];
             outParCorr_thetaT = [];
             for idata = 1:length(dataC)
-                data = dataC{idata}(:,[1 2 3]);
+                data = dataC{idata}(:,[1 iC*2 iC*2+1]);
                 [thetTfit(idata,:), normCorr_thetaT(:,idata)] = MO.fitThetaTtauT(data, kappa);
             end
             tauT = mean(thetTfit(:,3));