load_image_with_visStim.m

function [image, newBasePoints] = load_image_with_visStim(varargin)
% load_image_with_visStim()
% load_image_with_visStim(basePoints)
% load_image_with_visStim(f, p)
% load_image_with_visStim(f, p, basePoints)

GCaMPch=1;
REDch=2;
PDch=3;
ballTRACKch=4;

if nargin == 0
    [f, p]  = uigetfile('*.tif','Select your 3 or 4 chan file');            % generalized to 4 channels Aug3 2013
elseif nargin == 1
    [f, p]  = uigetfile('*.tif','Select your 3 or 4 chan file');            % generalized to 4 channels Aug3 2013
    basePoints = varargin{1};
elseif nargin == 2
    f = varargin{1};
    p = varargin{2};
elseif nargin ==3
    f = varargin{1};
    p = varargin{2};
    basePoints = varargin{3};
end

%select .mat vis stim file with suggestion:
DirInfoImage=dir(f);
DirInfoVSF=dir('*.mat');

for i=1:size(DirInfoVSF,1)
    ad(i)=abs(diff([DirInfoImage.datenum DirInfoVSF(i).datenum]));
end
[~,indexMin]= min(ad); 
mfSuggest=DirInfoVSF(indexMin).name;
%[mf,mp]  = uigetfile(mfSuggest,'Select your .mat vis stim file');

image.f = f;
image.p = p;
image.mf = mfSuggest;
image.mp = p;

%read in header info of image file
hgeneric=imfinfo([p f]);
header=hgeneric(1).ImageDescription;
header=parseHeader(header);
%ScanImage specifc:
image.numFrames=header.acq.numberOfFrames;
image.pxPline=header.acq.pixelsPerLine;
image.linePfram=header.acq.linesPerFrame;
image.numChans=header.acq.numberOfChannelsAcquire;
image.zoomFactor=header.acq.zoomFactor;
image.frameRate=header.acq.frameRate;

CS = zeros(image.numFrames,256,256);  %CS- calcium signal channel
R = zeros(image.numFrames,256,256); %R- red channel
PD = zeros(256,256,image.numFrames);  % photodiode channel, feedback from vis stim monitor

for i=1:image.numFrames
    CS(i,:,:)=imread(f,'Index',GCaMPch+(i-1)*image.numChans);  %use 1+(i-1)*3 if first channel aquired is calcium signal and three channels were aquired
    R(i,:,:)=imread(f,'Index',REDch+(i-1)*image.numChans); %1+(i-1)*3 is becuase three channels were aquired
    PD(:,:,i) = imread(f,'Index',PDch+(i-1)*image.numChans);
end
image.PDm= squeeze(mean(mean(PD)));

CSm = squeeze(mean(CS,1));
image.CSm = (CSm-min(CSm(:)))/(max(CSm(:))-min(CSm(:)));
image.CSma = imadjust(image.CSm);

Rm = squeeze(mean(R,1));
image.Rm = (Rm-min(Rm(:)))/(max(Rm(:))-min(Rm(:)));
image.Rma = imadjust(image.Rm);

image.fuse=imfuse(image.CSma,image.Rma, 'falsecolor', 'colorchannels', [2,1,0]);

if exist('basePoints','var')
    newBasePoints = basePoints;
    image.basePoints = basePoints;
else
    %select cells for analysis across trials
    [~, ~,x] = cpselect_sk(image.fuse,image.CSma, 'Wait',true); %modified toolbox cpselect so outputs ALL cells, not just pairs
    % imcontrast(gca)  %possible to incorperate imcontrast to adjust image contrast
    newBasePoints = round(x.basePoints);
    image.basePoints = round(x.basePoints);
end

% generate mask from image
image.CSmsk = generate_CS_mask(image);

% now pull the signals out...
image.CSsig = generate_CS_signal_map(image, CS);