clear all;close all;clc;
[num,txt] = xlsread('Trial');
finish= size(txt);
for i=1:finish(1)
i
location= txt(i);
filename=location{1,1};
data=envelope(readeye_hdi(filename));
rows=size(data,1);
columns=size(data,2);


TRACES=readalltrc(filename);

tumor=TRACES(5);
tumor.x=round((rows/512)*tumor.x);
tumor.y=round((columns/512)*tumor.y);

BW_data= roipoly(data,tumor.y, tumor.x);

Fs= 20000000;
c= 1540;
pitch= 0.2;
t= (0:rows-1)*(1/Fs);
axial= c*(t/2)*1e3;
lateral= (0:columns-1)*pitch;

max_axial= max(axial);
max_lateral= max(lateral);

% lesion selection
[region_xcoords, region_ycoords] = ROI_segmenter_atten_trial(data, lateral, axial,BW_data);
% LL selection
[region_xcoords1, region_ycoords1] = ROI_segmenter_atten_trial(data, lateral, axial,BW_data);
% RL selection
[region_xcoords2, region_ycoords2] = ROI_segmenter_atten_trial(data, lateral, axial,BW_data);
axial= axial';
lateral= lateral';
% positions for tumor
 ROI_positions = generate_ROI_positions(lateral, axial, 2.2, 2.2, 0.8, 0.8, region_xcoords, region_ycoords);
% positions for LL
 ROI_positions1 = generate_ROI_positions(lateral, axial, 2.2, 2.2, 0.8, 0.8, region_xcoords1, region_ycoords1);
% positions for RL
 ROI_positions2 = generate_ROI_positions(lateral, axial, 2.2, 2.2, 0.8, 0.8, region_xcoords2, region_ycoords2);

 % scaling of ROI positions
ROI_positions.top= ((rows-1)/max_axial)*ROI_positions.top;
ROI_positions.bottom= ((rows-1)/max_axial)*ROI_positions.bottom;
ROI_positions.left= ((columns-1)/max_lateral)*ROI_positions.left;
ROI_positions.right= ((columns-1)/max_lateral)*ROI_positions.right;

ROI_positions1.top= ((rows-1)/max_axial)*ROI_positions1.top;
ROI_positions1.bottom= ((rows-1)/max_axial)*ROI_positions1.bottom;
ROI_positions1.left= ((columns-1)/max_lateral)*ROI_positions1.left;
ROI_positions1.right= ((columns-1)/max_lateral)*ROI_positions1.right;

ROI_positions2.top= ((rows-1)/max_axial)*ROI_positions2.top;
ROI_positions2.bottom= ((rows-1)/max_axial)*ROI_positions2.bottom;
ROI_positions2.left= ((columns-1)/max_lateral)*ROI_positions2.left;
ROI_positions2.right= ((columns-1)/max_lateral)*ROI_positions2.right;

coords=struct('x',cell(1,1),'y',cell(1,1));

% parameter calculation for tumor
for j= 1:length(ROI_positions.top)

    temp_data= zeros(rows,columns);
    coords.x(1)= ROI_positions.top(j);
    coords.x(2)= ROI_positions.bottom(j);
    coords.y(1)= ROI_positions.left(j);
    coords.y(2)= ROI_positions.right(j);
    temp_data(coords.x(1):coords.x(2),coords.y(1):coords.y(2))=1;
    temp_data=logical(temp_data);
    Nibo_data=data(temp_data);
    part= Nibo_data;
    pd=fitdist(part,'Nakagami');
    e(j,1)=pd.mu;
    f(j,1)=pd.omega;
end
m_tumor= mean(e);
omega_tumor= mean(f);

coords=struct('x1',cell(1,1),'y1',cell(1,1));

%parameter calculation for LL region

for j= 1:length(ROI_positions1.top)

    temp_data1= zeros(rows,columns);
    coords.x1(1)= ROI_positions1.top(j);
    coords.x1(2)= ROI_positions1.bottom(j);
    coords.y1(1)= ROI_positions1.left(j);
    coords.y1(2)= ROI_positions1.right(j);
    temp_data1(coords.x1(1):coords.x1(2),coords.y1(1):coords.y1(2))=1;
    temp_data1=logical(temp_data1);
    Nibo_data1=data(temp_data1);
    part1= Nibo_data1;
    pd1=fitdist(part1,'Nakagami');
    e1(j,1)=pd1.mu;
    f1(j,1)=pd1.omega;
end
m_LL= mean(e1);
omega_LL= mean(f1);

coords=struct('x2',cell(1,1),'y2',cell(1,1));

% parameter calculation for RL region

for j= 1:length(ROI_positions2.top)

    temp_data2= zeros(rows,columns);
    coords.x2(1)= ROI_positions2.top(j);
    coords.x2(2)= ROI_positions2.bottom(j);
    coords.y2(1)= ROI_positions2.left(j);
    coords.y2(2)= ROI_positions2.right(j);
    temp_data2(coords.x2(1):coords.x2(2),coords.y2(1):coords.y2(2))=1;
    temp_data2=logical(temp_data2);
    Nibo_data2=data(temp_data2);
    part2= Nibo_data2;
    pd2=fitdist(part2,'Nakagami');
    e2(j,1)=pd2.mu;
    f2(j,1)=pd2.omega;
end
m_RL= mean(e2);
omega_RL= mean(f2);

M_site=m_tumor;
M_away=(m_LL+m_RL)/2;
Omega_site=omega_tumor;
Omega_away=(omega_LL+omega_RL)/2;

Alpha_site=0.5*sqrt((Omega_site*((1-M_site)))/(2*M_site));
Alpha_away=0.5*sqrt((Omega_away*((1-M_away)))/(2*M_away));

M_norm=(M_away)/(M_site);
Alpha_norm=(Alpha_site)/(Alpha_away);


B9_Result_Nak(i,1) = M_site;
B9_Result_Nak(i,2) = M_away;
B9_Result_Nak(i,3) = Omega_site;
B9_Result_Nak(i,4) = Omega_away;
B9_Result_Nak(i,5) = Alpha_site;
B9_Result_Nak(i,6) = Alpha_away;
B9_Result_Nak(i,7) = M_norm;
B9_Result_Nak(i,8) = Alpha_norm;

end