%------------------------------------------------------------------------------------------
%
% Title:    Calcium Signals in Small Structures
% Filename: CaSignal_SVREndoCalmodTraces.m
% Author:   Ronald van Elburg
% 
% Associated Paper:
% Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007) 
% High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: 
% Consequences for Spine Calcium Kinetics and Buffer Capacity. 
% PLoS ONE 2(10): e1073 doi:10.1371/journal.pone.0001073
%------------------------------------------------------------------------------------------
% clear all;
close all;
addpath(genpath('..'))
myTraceNumbers={'_25_25','_1000_25','_25_1000','_1000_1000'};
for myIndex=1:4
    TraceNumbers=myTraceNumbers{myIndex};
    run CaSignal_ExpSVREndoZeroDyeTracesLoadData

    TotalEndogenousBuffer=45;
    DyeTotal = 100;            % muM
    Nshells = 6;               % number of shells in the output (NOT IN THE SIMULATION, THERE THE GRIDSIZE DEFINES THE COMPARTMENTS)
    R=1;
    dR=R/Nshells;


    Path='..\Output\';
    NameExperiment='SVREndo0DTraces';

    imageformat='fig';

    run CaSignal_Exp3Sub1
    run CaSignal_Exp3Sub2
    run CaSignal_Exp3Sub4

    axes_handles=zeros(3,2);

    figure(3112)
        axes_handles(1,1)=gca;
        figure(3000)
        axeshandle1=subplot(2,3,1);
        swapfigures(axeshandle1,axes_handles(1,1))

        axes(axes_handles(1,1))
        axis 'manual'
        axis([5,25,0,1])


    figure(3111)
        axes_handles(1,2)=gca;
        figure(3000)
        axeshandle1=subplot(2,3,4);
        swapfigures(axeshandle1,axes_handles(1,2))

        axes(axes_handles(1,2))
        axis 'manual'
        axis([5,25,0,1])


    figure(3212)
        axes_handles(2,1)=gca;
        figure(3000)
        axeshandle1=subplot(2,3,2);
        swapfigures(axeshandle1,axes_handles(2,1))

        axes(axes_handles(2,1))
        axis 'manual'
        axis([5,25,30,60])

    figure(3211)
        axes_handles(2,2)=gca;
        figure(3000)
        axeshandle1=subplot(2,3,5);
        swapfigures(axeshandle1,axes_handles(2,2))

        axes(axes_handles(2,2))
        axis 'manual'
        axis([5,25,30,60])

    figure(343)
        axes_handles(3,1)=subplot(2,2,3);
        axes_handles(3,2)=subplot(2,2,1);
        figure(3000)
        axeshandle1=subplot(2,3,3);
        swapfigures(axeshandle1,axes_handles(3,1))
        axeshandle1=subplot(2,3,6);
        swapfigures(axeshandle1,axes_handles(3,2))

        axes(axes_handles(3,2))
        axis auto
%         axis 'manual'
%         axis([0,7,0,6])

        axes(axes_handles(3,1))
        axis auto
%         axis 'manual'
%         axis([0,7,0,6])

    % orient landscape
    set(axes_handles,'FontSize',9)
    set(gcf,'PaperType','A4')
    figfilename=['..\Output\FreeAndDye',NameExperiment,TraceNumbers];
    saveas(gcf, figfilename,'pdf')
    saveas(gcf, figfilename,'png')
    saveas(gcf, figfilename,'fig')
end