function EntropyTest_4Regions(SmallObjThres,RoundThresh,NhoodRad,Filter)
%EntropyTest_4Regions(SmallObjThres,RoundThresh,NhoodRad,Filter)
%This function process the entropy in the input *jpg images in the selected folder
%Processing parameters can be changed inside the function
%SmallObjThres defines the pixel count of an object which defines it as
%small, and make it deletable.
%Default Value = 8
%RoundThresh is a simmilarity coefficient with a perfect circle object.
%the closer to 1, the closer to a perfect circle an object is.
%Objects marked as circles are deleted by the preprocessing function
%Default Value = 0.95
%NhoodRad defines Neighborhood size for entropy calculation 7 pixels by default---means 13x13
%Default Value = 7
%Filter is a flag which defines whether preprocessing is small and round
%objects are deleted or not
%Typical Example of usage:
%        EntropyTest_4Regions(8,0.95,7,1);
% (c) Gustavo Liņan Cembrano
% IMSE-CNM-CSIC
% linan@imse-cnm.csic.es

%% Getting input dir

IM_PATH=uigetdir([],'Select Image Folder');

cd(IM_PATH)
DeletePrevious = questdlg('Delete previous results?','Delete','No');
if(strcmp(DeletePrevious,'Yes'))
    delete('*.tiff')
    delete('*.csv');
elseif(strcmp(DeletePrevious,'Cancel'))
    return;
else
    %Do nothing
end


%% Getting File name structure

FileName=dir('*.jpg');
NFiles=length(FileName);

msgstr=sprintf('%d Images Found in directory',NFiles);

h=msgbox(msgstr);
pause(1); delete(h)



clc;


%% Creating output variables


Region1AvgEntropy=zeros(1,NFiles);
Region2AvgEntropy=zeros(1,NFiles);
Region3AvgEntropy=zeros(1,NFiles);
Region4AvgEntropy=zeros(1,NFiles);

Region1StdEntropy=zeros(1,NFiles);
Region2StdEntropy=zeros(1,NFiles);
Region3StdEntropy=zeros(1,NFiles);
Region4StdEntropy=zeros(1,NFiles);

Region1Area=zeros(1,NFiles);
Region2Area=zeros(1,NFiles);
Region3Area=zeros(1,NFiles);
Region4Area=zeros(1,NFiles);

ProcTime=zeros(1,NFiles);

%Pixels count of an object which defines it as small, and make it deletable
% SmallObjThres=8;
%Simmilarity coefficient with a perfect circle object. 1-->Perfect Circle
% RoundThresh=0.95;
%Neighborhood for entropy calculation 7 pixels by default---means 13x13
%area
% NhoodRad=7;
STREL=strel('disk',NhoodRad);
NHOOD=getnhood(STREL);

%% Looping

for j=1:NFiles
    t1=tic;
    %% Accessing file
    CURRENT_FILE=FileName(j).name;
    fprintf('###################################################### \n');
    fprintf('      Accesing File %s\n', CURRENT_FILE);
    LocationsFile=strcat(CURRENT_FILE,'_Locations.mat');
    LocFileExist=exist(LocationsFile,'file');
    if(LocFileExist)
        load(LocationsFile)
        Nregions=length(whos('region*'));
        fprintf('Found location definition for %d regions\n',Nregions);
        DoIt=1;
    else
        MSG=sprintf('Locations file for %s does not exist skipping this file', CURRENT_FILE);
        h=msgbox(MSG);
        DoIt=0;
    end
    if(DoIt)
        
        
        INPUT_IM=imread(CURRENT_FILE);
        
        
        
        %% Increasing contrast
        INPUT_IM=imsharpen(INPUT_IM);
        
        %% Preprocessing regions before entropy calculation
        fprintf('Preprocessing regions and preparing images\n');
        if(Nregions>=1)
            [Region1Image,Region1BinaryImage,Region1X,Region1Y]=PreProcessRegion(region1,INPUT_IM,SmallObjThres,RoundThresh,Filter);
        end
        if(Nregions>=2)
            [Region2Image,Region2BinaryImage,Region2X,Region2Y]=PreProcessRegion(region2,INPUT_IM,SmallObjThres,RoundThresh,Filter);
        end
        if(Nregions>=3)
            [Region3Image,Region3BinaryImage,Region3X,Region3Y]=PreProcessRegion(region3,INPUT_IM,SmallObjThres,RoundThresh,Filter);
        end
        if(Nregions==4)
            [Region4Image,Region4BinaryImage,Region4X,Region4Y]=PreProcessRegion(region4,INPUT_IM,SmallObjThres,RoundThresh,Filter);
        end
        
        
        %% Entropy Calculation
        fprintf('      Processing Entropy for file %s\n', CURRENT_FILE);
        fprintf('######################################################\n');
        if(Nregions>=1)
            Region1EntropyImage=entropyfilt(Region1Image,NHOOD);
            Region1EntropyImage=Region1EntropyImage(:,:,1).*Region1EntropyImage(:,:,2).*Region1EntropyImage(:,:,3);
            Region1EntropyImage=Region1EntropyImage.*double(Region1BinaryImage);
            figure(1);
            imagesc(Region1EntropyImage);colormap jet; colorbar;
            print(gcf,'-dtiff',strcat(CURRENT_FILE,'_Region1EntropyImage.tiff'));
            Region1AvgEntropy(j)=mean(Region1EntropyImage(find(Region1BinaryImage==1)));
            Region1StdEntropy(j)=std(Region1EntropyImage(find(Region1BinaryImage==1)));
            Region1Area(j)=length(region1);
        end
        if(Nregions>=2)
            
            Region2EntropyImage=entropyfilt(Region2Image,NHOOD);
            Region2EntropyImage=Region2EntropyImage(:,:,1).*Region2EntropyImage(:,:,2).*Region2EntropyImage(:,:,3);
            Region2EntropyImage=Region2EntropyImage.*double(Region2BinaryImage);
            figure(2);
            imagesc(Region2EntropyImage);colormap jet; colorbar;
            print(gcf,'-dtiff',strcat(CURRENT_FILE,'_Region2EntropyImage.tiff'));
            Region2AvgEntropy(j)=mean(Region2EntropyImage(find(Region2BinaryImage==1)));
            Region2StdEntropy(j)=std(Region2EntropyImage(find(Region2BinaryImage==1)));
            Region2Area(j)=length(region2);
            
        end
        if(Nregions>=3)
            
            Region3EntropyImage=entropyfilt(Region3Image,NHOOD);
            Region3EntropyImage=Region3EntropyImage(:,:,1).*Region3EntropyImage(:,:,2).*Region3EntropyImage(:,:,3);
            Region3EntropyImage=Region3EntropyImage.*double(Region3BinaryImage);
            figure(3);
            imagesc(Region3EntropyImage);colormap jet; colorbar;
            print(gcf,'-dtiff',strcat(CURRENT_FILE,'_Region3EntropyImage.tiff'));
            Region3AvgEntropy(j)=mean(Region3EntropyImage(find(Region3BinaryImage==1)));
            Region3StdEntropy(j)=std(Region3EntropyImage(find(Region3BinaryImage==1)));
            Region3Area(j)=length(region3);
            
        end
        if(Nregions==4)
            
            Region4EntropyImage=entropyfilt(Region4Image,NHOOD);
            Region4EntropyImage=Region4EntropyImage(:,:,1).*Region4EntropyImage(:,:,2).*Region4EntropyImage(:,:,3);
            Region4EntropyImage=Region4EntropyImage.*double(Region4BinaryImage);
            figure(4);
            imagesc(Region4EntropyImage);colormap jet; colorbar;
            print(gcf,'-dtiff',strcat(CURRENT_FILE,'_Region4EntropyImage.tiff'));
            Region4AvgEntropy(j)=mean(Region4EntropyImage(find(Region4BinaryImage==1)));
            Region4StdEntropy(j)=std(Region4EntropyImage(find(Region4BinaryImage==1)));
            Region4Area(j)=length(region4);
            
        end
        
        
        
        
        
        %% Displaying resulting images
        
        
        pause(1); close all;
        
        %% Calculating mean  std  and area for entropy regions
        
        figure(1)
        
        imshow(INPUT_IM);
        if(Nregions>=1)
            text(Region1X,Region1Y,strcat('+ Region1Entropy=',num2str(Region1AvgEntropy(j))),'color',[0.6 0 0]);
        end
        if(Nregions>=2)
            text(Region2X,Region2Y,strcat('+ Region2Entropy=',num2str(Region2AvgEntropy(j))),'color',[0.6 0 0]);
        end
        if(Nregions>=3)
            text(Region3X,Region3Y,strcat('+ Region3Entropy=',num2str(Region3AvgEntropy(j))),'color',[0.6 0 0]);
        end
        if(Nregions==4)
            
            text(Region4X,Region4Y,strcat('+ Region4Entropy=',num2str(Region4AvgEntropy(j))),'color',[0.6 0 0]);
        end
        
        print(gcf, '-dtiff', strcat(CURRENT_FILE,'_ENTROPY_RESULTS.tiff'));
        
        ProcTime(j)=toc(t1);
        
        fprintf('Processing time = %1.3fs\n',ProcTime(j));
        
        
    end
end

OutFile='Results.csv';
fid=fopen(OutFile,'w+');
fprintf(fid,'FileName,');
fprintf(fid,'Reg1AvgEntropy,Reg1StdEntropy,Reg1Area,');
fprintf(fid,'Reg2AvgEntropy,Reg2StdEntropy,Reg2Area,');
fprintf(fid,'Reg3AvgEntropy,Reg3StdEntropy,Reg3Area,');
fprintf(fid,'Reg4AvgEntropy,Reg4StdEntropy,Reg4Area');
fprintf(fid,'ProcTime(s)\n');



for j=1:NFiles
    fprintf(fid,'%s,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f,%2.3f\n',FileName(j).name,...
        Region1AvgEntropy(j),Region1StdEntropy(j),Region1Area(j),...
        Region2AvgEntropy(j),Region2StdEntropy(j),Region2Area(j),...
        Region3AvgEntropy(j),Region3StdEntropy(j),Region3Area(j),...
        Region4AvgEntropy(j),Region4StdEntropy(j),Region4Area(j),...
        ProcTime(j));
    
end


fclose(fid);





end