getCardiacData.m

function [] = getCardiacData ()

%% REMEMBER TO SET CORRECT FS!!!
%User input variables
Fs = 200   ; %sampling rate (in Hz or fps)

tic

%%Hopefully this wrapper script will allow for user to select folders
%%containing tiff stacks of CM data to analyze, then run through specific
%%cAP data scripts to analyzed APD, risetime, etc.

%Author: Steven Boggess (sboggess@berkeley.edu)
%%Thanks to Julia and Ben for their guidance and support~

%%Input variables to change:
%% Find FS to set the aqc frequency. All tiff stacks must be of the same frequency to work with this current configuration

%Get all tif filenames from a selected folder
folder_name = uigetdir('C:\Users\Steven Boggess\Documents\Miller Lab\Data\', 'Select Folder Containing Tiff Stacks to Analyze');
% f = dir ([folder_name,'\*.tif']); %cell array containing info of all tif files in directory
f = rdir ([folder_name,'\**\*.tif']);% Will search all subfolders as well.
filenames = {f.name}; %tif filenames collected

disp(folder_name);

tifStacks = cell(numel(filenames),1);
for i=1:numel(filenames)
    if strfind(filenames{i} , 'vm')
        tiffname = fullfile(filenames{i});
        [pathstr,name,ext] = fileparts(filenames{i});
        filename = name;
%         disp (tiffname); %Show the file you are working with
        tifStacks = apdCalc(tiffname,Fs,filename,folder_name);
    else if strfind(filenames{i} , 'Vm')
            tiffname = fullfile(filenames{i});
            [pathstr,name,ext] = fileparts(filenames{i});
            filename = name;
%             disp (tiffname); %Show the file you are working with
            tifStacks = apdCalc(tiffname,Fs,filename,folder_name);
        else
            disp ('not a vm trace');
        end
    end
  
end
    fprintf(['While it is always best to believe in one’s self, \n' ...
         ' a little help from others can be a great blessing. --Iroh  \n' ...
         '   ']);
     
toc 
end