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standalone_background_correction.m
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standalone_background_correction.m
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function standalone_background_correction(varargin)
% function standalone_background_correction
%
% Usage: standalone_background_correction(base_dir)
% standalone_background_correction(base_dir, 'fitonly')
% standalone_background_correction(base_dir, 'fitonly', maskFile, fitorder)
% standalone_background_correction(base_dir, 'writeonly')
%
% standalone_background_correction
% corrects PCVIPR 4D Flow Data for background phase offsets
%
% Written by Kevin Johnson
% Updated by Phil Corrado June 2018 to be faster by correcting all slices
% at once
if nargin>0 && exist(varargin{1}, 'dir')
base_dir = varargin{1};
else
base_dir = uigetdir();
end
data = readPCVIPR(base_dir);
vx_name =fullfile(base_dir,'comp_vd_1.dat');
vy_name =fullfile(base_dir,'comp_vd_2.dat');
vz_name =fullfile(base_dir,'comp_vd_3.dat');
mag_name = fullfile(base_dir,'MAG.dat');
VELX = memmapfile(vx_name,'Format',{'int16',[data.xSize data.ySize data.zSize],'vals'});
VELY = memmapfile(vy_name,'Format',{'int16',[data.xSize data.ySize data.zSize],'vals'});
VELZ = memmapfile(vz_name,'Format',{'int16',[data.xSize data.ySize data.zSize],'vals'});
MAG = memmapfile(mag_name,'Format',{'int16',[data.xSize data.ySize data.zSize],'vals'});
if nargin < 2 || ~ischar(varargin{2}) || ~strcmp(varargin{2},'writeonly')
if nargin < 4 || ~exist(varargin{3}, 'file') || ~isnumeric(varargin{4})
[poly_fitx,poly_fity, poly_fitz] = background_phase_correction(MAG,VELX,VELY,VELZ);
else
mask = niftiread(varargin{3});
fit_order = varargin{4};
% Plot Mask
slice = round(size(VELX.Data.vals,3)/2);
vx_slice = single(VELX.Data.vals(:,:,slice) );
vy_slice = single(VELY.Data.vals(:,:,slice) );
vz_slice = single(VELZ.Data.vals(:,:,slice) );
mag_slice= single(MAG.Data.vals(:,:,slice) );
idx = find( mask(:,:,slice) > 0);
mag_slice = 200 * mag_slice/max(mag_slice(:));
mag_slice(idx) = 257; %#ok<FNDSB>
map =[ gray(200); jet(10)];
figure();
imagesc(mag_slice,[0,200+10]);
colormap(map);
set(gca,'XTickLabel','')
set(gca,'YTickLabel','')
daspect([1 1 1]);
% Fit background phase
[px,py,pz]=meshgrid(0:fit_order,0:fit_order,0:fit_order);
idx2 = find( (px+py+pz) <= fit_order);
px = px(idx2);
py = py(idx2);
pz = pz(idx2);
A = [px(:) py(:) pz(:)];
N = size(A,1);
AhA = zeros(N,N);
AhBx = zeros(N,1);
AhBy = zeros(N,1);
AhBz = zeros(N,1);
xrange = single( linspace(-1,1,size(VELX.Data.vals,1)) );
yrange = single( linspace(-1,1,size(VELY.Data.vals,2)) );
zrange = single( linspace(-1,1,size(VELZ.Data.vals,3)) );
[y,x,z] = meshgrid( yrange,xrange,zrange );
idx = find( mask > 0);
x = x(idx);
y = y(idx);
z = z(idx);
for i = 1:N
for j = 1:N
AhA(i,j) = AhA(i,j) + sum( ( x.^px(i).*y.^py(i).*z.^pz(i)).*( ( x.^px(j).*y.^py(j).*z.^pz(j))));
end
end
for i = 1:N
AhBx(i) = AhBx(i) + sum( single(VELX.Data.vals(idx)).* ( x.^px(i).*y.^py(i).*z.^pz(i)));
AhBy(i) = AhBy(i) + sum( single(VELY.Data.vals(idx)).* ( x.^px(i).*y.^py(i).*z.^pz(i)));
AhBz(i) = AhBz(i) + sum( single(VELZ.Data.vals(idx)).* ( x.^px(i).*y.^py(i).*z.^pz(i)));
end
poly_fitx.vals = linsolve(AhA,AhBx);
poly_fitx.px = px;
poly_fitx.py = py;
poly_fitx.pz = pz;
poly_fity.vals = linsolve(AhA,AhBy);
poly_fity.px = px;
poly_fity.py = py;
poly_fity.pz = pz;
poly_fitz.vals = linsolve(AhA,AhBz);
poly_fitz.px = px;
poly_fitz.py = py;
poly_fitz.pz = pz;
end
else
data = readPCVIPR(base_dir);
a = load(fullfile(base_dir,'bgPhaseFitCoefficients.mat'));
poly_fitx = a.poly_fitx;
poly_fity = a.poly_fity;
poly_fitz = a.poly_fitz;
end
if nargin <2 || ~ischar(varargin{2}) || ~strcmp(varargin{2},'fitonly')
xrange = single( linspace(-1,1,data.xSize) );
yrange = single( linspace(-1,1,data.ySize) );
zrange = single( linspace(-1,1,data.zSize) );
[y,x,z] = ndgrid(yrange,xrange,zrange);
new_dir = fullfile(base_dir,'CORRECTED');
mkdir(new_dir);
fid = fopen(fullfile(new_dir,'comp_vd_1.dat'),'w');
fwrite(fid,double(VELX.Data.vals) - evaluate_poly(x,y,z,poly_fitx),'int16');
fclose(fid);
fid = fopen(fullfile(new_dir,'comp_vd_2.dat'),'w');
fwrite(fid,double(VELY.Data.vals) - evaluate_poly(x,y,z,poly_fity),'int16');
fclose(fid);
fid = fopen(fullfile(new_dir,'comp_vd_3.dat'),'w');
fwrite(fid,double(VELZ.Data.vals) - evaluate_poly(x,y,z,poly_fitz),'int16');
fclose(fid);
copyfile(fullfile(base_dir,'pcvipr_header.txt'),fullfile(new_dir,'pcvipr_header.txt'));
for ii = 1:data.nT
copyfile(fullfile(base_dir,sprintf('ph_%.3d_mag.dat',ii-1)),fullfile(new_dir,sprintf('ph_%.3d_mag.dat',ii-1)));
copyfile(fullfile(base_dir,sprintf('ph_%.3d_cd.dat',ii-1)),fullfile(new_dir,sprintf('ph_%.3d_cd.dat',ii-1)));
fid = fopen(fullfile(new_dir,sprintf('ph_%.3d_vd_1.dat',ii-1)),'w');
fwrite(fid,double(data.velX(:,:,:,ii)) - evaluate_poly(x,y,z,poly_fitx),'int16');
fclose(fid);
fid = fopen(fullfile(new_dir,sprintf('ph_%.3d_vd_2.dat',ii-1)),'w');
fwrite(fid,double(data.velY(:,:,:,ii)) - evaluate_poly(x,y,z,poly_fity),'int16');
fclose(fid);
fid = fopen(fullfile(new_dir,sprintf('ph_%.3d_vd_3.dat',ii-1)),'w');
fwrite(fid,double(data.velZ(:,:,:,ii)) - evaluate_poly(x,y,z,poly_fitz),'int16');
fclose(fid);
end
else
save(fullfile(base_dir,'bgPhaseFitCoefficients.mat'),'poly_fitx','poly_fity','poly_fitz');
end
end