clear all ; close all
% Load dicom


name = 'Ronald' ; 

if strcmp(name, 'Ronald')
    path_all = [
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/FH/DICOM/IM_0001',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/AP/DICOM/IM_0001',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/RL/DICOM/IM_0001'
        ] ; 
end

if strcmp(name, 'Jeremias')
    path_all = [
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/FH/DICOM/IM_0001',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/AP/DICOM/IM_0001',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/RL/DICOM/IM_0001'
        ] ; 
end

if strcmp(name, 'Hugo')
    path_all = [
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0013',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0009',
        '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0005'
        ] ; 
end

for i=1:3

    if i==1
        %path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0013'
        disp('Reading the FH component from ...')
        path = path_all(1,:)
    end
    
    if i==2
        %path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0009' ;
        disp('Reading the AP component from ...')
        path = path_all(2,:)
    end
    
    if i==3
        %path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0005' ;
        disp('Reading the RL component from ...')
        path = path_all(3,:)
    end
 

I_info = dicominfo(path);
I = double(dicomread(path));
VENC = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.MRVelocityEncodingSequence.Item_1.VelocityEncodingMaximumValue']) ;
heart_rate = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.Private_2005_140f.Item_1.HeartRate']);


MAG = zeros(size(I,1),size(I,2),I_info.Private_2001_1018,I_info.Private_2001_1017);
PHASE = zeros(size(I,1),size(I,2),I_info.Private_2001_1018,I_info.Private_2001_1017);

for n=1:size(I,4)
    
    RI = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.RescaleIntercept']); % intercept
    RS = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.RescaleSlope']); % slope
    cp = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2001_1008']); %cp
    slc = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2001_100a']); %scl
    id = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2005_106e']); % PCA o FFE
    
    if strcmp(id,'FFE')==1
        MAG(:,:,slc,cp) = I(:,:,1,n)*RS + RI;
    else
        PHASE(:,:,slc,cp) = I(:,:,1,n)*RS + RI;
    end 
    
end


MASK = double(abs((PHASE==PHASE(1,1,1,1))-1));
PHASE = PHASE.*MASK;


if i==1
    MR_FFE_FH = MAG;
    MR_PCA_FH = VENC*PHASE/pi/100;
end

if i==2
    MR_FFE_AP = MAG;
    MR_PCA_AP = VENC*PHASE/pi/100;
end
if i==3
    MR_FFE_RL = MAG;
    MR_PCA_RL = VENC*PHASE/pi/100;
end


end


disp('Saving the data ...')

spaceslices = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.SpacingBetweenSlices']);
pixelspacing = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.PixelSpacing']);

disp('voxel-size recognized:')
voxel_MR = [pixelspacing(1),pixelspacing(1),spaceslices]


data = [];
data.MR_FFE_AP = MR_FFE_AP;
data.MR_FFE_RL = MR_FFE_RL;
data.MR_FFE_FH = MR_FFE_FH;
data.MR_PCA_AP = MR_PCA_AP;
data.MR_PCA_RL = MR_PCA_RL;
data.MR_PCA_FH = MR_PCA_FH;
data.type = 'DAT';
data.VENC = VENC ;
data.voxel_MR = voxel_MR;
data.heart_rate = heart_rate;

save('/home/yeye/Desktop/data.mat','data','-v7.3');
disp('data saved')