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fold_slice/tomo/+tomo/alignslice_filt_v2.m
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% [deltastack outputsinogram] = alignslice_filt(sinogramder,theta,deltastack,pixtol,disp,paramsalign)
% Function to align projections. It relies on having already aligned the
% vertical direction. The code aligns using the consistency before and
% after tomographic combination of projections. Currently it can only deal
% with one slice. It is recommended to use small values of tomographic
% filter for best results.
% WARNING. The code aligns the center of rotation in the ROI defined by
% limsx so that it is consistent (within the window) with the center
% expected by iradon: ceil(size(R,1)/2). Also note that it expects the
% derivative of the sinogram as input
%
%
% Inputs %
% sinogramder Sinogram derivative, the second index should be the angle
% deltastack Row array with initial estimates of positions (1,n)
% disp Display = 0 no images
% = 1 Final diagnostic images
% = 2 Diagnostic images per iteration (significant overhead)
% pixtol Tolerance for alignment, it is also used as a search step
%
% Extra parameters (in structure paramsalign)
% paramsalign.interpmeth = 'sinc' - Shift images with sinc interpolation (default)
% = 'linear' - Shift images with linear interpolation (default)
% paramsalign.usecircle Use a circular mask to eliminate corners of
% tomogram
% paramsalign.filtertomo Frequency cutoff for tomography filter
% paramsalign.cliplow Minimum value in tomogram
% paramsalign.cliphigh Maximum value in tomogram
% paramsalign.masklims Mask in sinograms to evaluate error metric
% paramsalign.binning Binning of sinograms to increase speed. I am
% not fully aware
%
% Outputs %
% deltastack Object positions
% outputsinogram Aligned sinogram derivatives (optional)
%
% Manuel Guizar 13 July 2011
% This code is provided as is and without guarantees on its performance
% The algorithm is not yet published. Do not distribute and contact
% (mguizar@gmail.com) prior to publication of results where this code plays
% a significant role, or to report a bug.
% Please acknowledge if used.
% v2 Manuel Guizar 2011 09 29
% Added clipping values to tomogram
% Manuel Guizar 2016 03 01 - Adding binning possiblity. Currenlty I suspect
% there may be an offset introduced between different binnings. Beware of
% this while using it and report any behavior that points in this direction.
function [deltastack outputsinogram] = alignslice_filt_v2(sinogramder,theta,deltastack,pixtol,disp,paramsalign)
import utils.*
import math.projectleg1D_2
%deltastack = round(deltastack);
maxit = 40;
display([' Registration of sinogram - Single pixel'])
if nargout>1,
outputsinogram = sinogramder;
end
if exist('paramsalign') == 0,
paramsalign = 0;
end
%%%%%%%
if isfield(paramsalign,'binning') == 0,
binning = 0;
else
binning = paramsalign.binning;
display(['Using binning = ' num2str(binning)])
end
if (binning ~=0)&&(binning ~=1)
display(['Using binning on sinogram = ' num2str(binning)]);
sinogramder_orig = sinogramder;
sinoaux = sinogramder(1:binning:end-binning+1,:);
for ii = 2:binning
sinoaux = sinoaux + sinogramder(ii:binning:end-binning+ii,:);
end
sinogramder = sinoaux/binning;
deltastack = deltastack/binning;
end
%%%%%%
if isfield(paramsalign,'masklims') == 0,
masklims = [1:size(sinogramder,1)];
else
display('Error computed using masked values of sinogram')
masklims = paramsalign.masklims;
end
if isfield(paramsalign,'interpmeth') == 0,
paramsalign.interpmeth = 'sinc';
interpmeth = paramsalign.interpmeth;
else
interpmeth = paramsalign.interpmeth;
if (strcmp(interpmeth,'sinc'))||(strcmp(interpmeth,'linear'))
else
error('Undefined interpolation method')
end
end
if isfield(paramsalign,'usecircle') == 0,
usecircle = true;
else
usecircle = paramsalign.usecircle;
end
% if isfield(paramsalign,'expshift') == 0,
% expshift = false;
% else
% expshift = paramsalign.expshift;
% end
if isfield(paramsalign,'filtertomo') == 0,
filtertomo = 1;
display('Using default filter cutoff = 1')
else
filtertomo = paramsalign.filtertomo;
display(['Using filtertomo = ' num2str(filtertomo)])
end
if isfield(paramsalign,'cliplow') == 0,
cliplow = [];
else
cliplow = paramsalign.cliplow;
display(['Low limit for tomo values = ' num2str(cliplow)])
end
if isfield(paramsalign,'cliphigh') == 0,
cliphigh = [];
else
cliphigh = paramsalign.cliphigh;
display(['High limit for tomo values = ' num2str(cliphigh)])
warning('Code will use a background "cliphigh", assumes tomogram will go negative from there')
end
if exist('pixtol') == 0,
pixtol = 1;
end
if exist('deltastack') == 0,
deltastack = zeros(1,size(sinogramder,2));
end
% Pad sinogram derivatives
padval = 2*round(1/filtertomo);
sinogramder = padarray(sinogramder,[padval 0]);
%%%%%%%%%%%%% Single pixel precision %%%%%%%%%%%%%%
% loop here
clear auxinit; % Before main loop
domain = 1;
count = 0;
N = size(sinogramder,1);
center = floor((N+1)/2);
xt = [-N/2:N/2-1];
[Xt Yt] = meshgrid(xt,xt);
circulo = 1-radtap(Xt,Yt,10,N/2-10);
filteraux = 1-fract_hanning_pad(N,N,round(N*(1-filtertomo)));
filteraux = repmat(fftshift(filteraux(:,1)),[1 length(theta)]);
sinogramderorig_nofilt = sinogramder;
sinogramderorig = real(ifft(fft(sinogramder).*filteraux));
erroryreg = inf;
while domain == 1,
count = count+1;
deltaprev = deltastack;
erroryregprev = erroryreg;
for ii = 1:size(sinogramder,2)
if strcmp(interpmeth,'sinc')
sinogramder(:,ii) = real(shiftpp2(sinogramderorig(:,ii),deltastack(1,ii),0));
elseif strcmp(interpmeth,'linear')
sinogramder(:,ii) = shiftwrapbilinear(sinogramderorig(:,ii),deltastack(1,ii),0);
end
if disp>1,
if strcmp(interpmeth,'sinc')
sinogramder_nofilt(:,ii) = real(shiftpp2(sinogramderorig_nofilt(:,ii),deltastack(1,ii),0));
elseif strcmp(interpmeth,'linear')
sinogramder_nofilt(:,ii) = shiftwrapbilinear(sinogramderorig_nofilt(:,ii),deltastack(1,ii),0);
end
end
end
%%%%%% Sinogram alignment single pixel precision
% Compute tomogram with current sinogramder
% recons = iradonfast_v3(double(sinogramder),...
% theta,'linear','derivative','Han',size(sinogramder,1),filtertomo);
recons = tomo.iradonfast_v3(double(sinogramder),...
theta,'linear','derivative','Ram-Lak',size(sinogramder,1),1);
if ~isempty(cliplow)
recons = recons.*(recons>=cliplow) + cliplow*(recons<cliplow);
end
if ~isempty(cliphigh)
recons = recons.*(recons<=cliphigh) + cliphigh*(recons>cliphigh);
recons = recons-cliphigh;
end
if usecircle
recons = recons.*circulo;
end
figure(203)
imagesc(recons);
axis xy equal tight
colorbar
% Computed sinogram
sinogramcomp = radon(recons,theta);
Nbig = size(sinogramcomp,1);
centerbig = floor((Nbig+1)/2);
if strcmp(interpmeth,'sinc')
sinogramcompder = real(shiftpp2(sinogramcomp,0.5,0)-shiftpp2(sinogramcomp,-0.5,0));
elseif strcmp(interpmeth,'linear')
sinogramcompder = real(shiftwrapbilinear(sinogramcomp,0.5,0)-shiftwrapbilinear(sinogramcomp,-0.5,0));
end
sinogramcompder = sinogramcompder([1:N]+centerbig-center,:);
% Compare sinogramder with sinogramcompder
for ii = 1:size(sinogramder,2)
%ii,
errorinit(ii) = sum(abs(sinogramder(padval+masklims,ii)-sinogramcompder(padval+masklims,ii)).^2);
end
display(['Initial error metric, E = ' num2str(sum(errorinit))])
%%% Search for shifts with respect to sinthetic
for ii = 1:size(sinogramder,2);
shift = 0;
%%% Looking bothways
% compute current shift error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-shift,0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-shift,0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
currenterror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
% compute shift forward error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift+1),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift+1),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
forwarderror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
% compute shift backward error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift-1),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift-1),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
backwarderror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
mini = min([currenterror backwarderror forwarderror]);
switch mini
case currenterror
deltastack(1,ii) = deltastack(1,ii) - shift;
auxtempreg(:,ii) = auxshift; %temporary for debugging
erroryreg(ii) = currenterror;
dir = 0;
continue;
case backwarderror % Looking backward
dir = -1;
case forwarderror % Looking forward
dir = 1;
end
if dir~=0,
shift = shift+dir;
currenterror = mini;
do = 1;
end
while do==1,
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift+dir),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift+dir),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
nexterror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
%shift,
if nexterror<=currenterror
shift = shift+dir;
currenterror = nexterror;
else
do = 0;
deltastack(1,ii) = deltastack(1,ii) - shift;
auxtempreg(:,ii) = auxshift;
erroryreg(ii) = currenterror;
end
end
end
%end
%deltastack(1,:) = deltastack(1,:) - round(mean(deltastack(1,:)));
display(['Final error mectric, E = ' num2str(sum(erroryreg))])
changey = abs(deltaprev(1,:) - deltastack(1,:));
display(['Max correction = ' num2str(max(abs(changey)))])
if (max(abs(changey))<max(pixtol,1)),
domain = 0;
end
if count >= maxit,
domain = 0;
warning('Maximum number of iterations exceeded, increase maxit')
end
if sum(erroryregprev)<sum(erroryreg)
warning('Last iteration made error worse, keeping previous to last positions')
deltastack = deltaprev;
domain = 0;
end
if disp>1,
figure(200);
subplot(2,1,1)
imagesc(sinogramderorig_nofilt);
axis xy tight
%colorbar
title('Initial Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
subplot(2,1,2),
imagesc(sinogramder_nofilt);
axis xy tight
%colorbar
title('Current Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
figure(201);
imagesc(sinogramcompder);
axis xy tight
%colorbar
title('Synthetic Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
figure(2),
plot(deltastack')
drawnow,
title('Object position')
% figure(205);
% plot(erroryinit)
% hold on,
% plot(erroryreg,'r')
% hold off
% legend('Initial error per projection','Current error per projection')
end
end
% if pixtol >= 1,
% % Compute the shifted images
% if nargout == 2,
% display('Computing aligned images')
% for ii = 1:size(regstack,3),
% switch interpmeth
% case 'sinc'
% regstack(:,:,ii) = real(shiftpp2(regstack(:,:,ii),deltastack(1,ii),deltastack(2,ii)));
% case 'linear'
% regstack(:,:,ii) = shiftwrapbilinear(regstack(:,:,ii),deltastack(1,ii),deltastack(2,ii));
% end
% if mod(ii,20) == 0,
% display(['Image ' num2str(ii) ' of ' num2str(size(regstack,3))]),
% end
% end
% end
% end
%%
if pixtol<1,
display(' Subpixel refinement')
clear auxinit; % Before main loop
domain = 1;
count = 0;
while domain == 1,
count = count+1;
deltaprev = deltastack;
erroryregprev = erroryreg;
for ii = 1:size(sinogramder,2)
if strcmp(interpmeth,'sinc')
sinogramder(:,ii) = real(shiftpp2(sinogramderorig(:,ii),deltastack(1,ii),0));
elseif strcmp(interpmeth,'linear')
sinogramder(:,ii) = shiftwrapbilinear(sinogramderorig(:,ii),deltastack(1,ii),0);
end
if disp>1,
if strcmp(interpmeth,'sinc')
sinogramder_nofilt(:,ii) = real(shiftpp2(sinogramderorig_nofilt(:,ii),deltastack(1,ii),0));
elseif strcmp(interpmeth,'linear')
sinogramder_nofilt(:,ii) = shiftwrapbilinear(sinogramderorig_nofilt(:,ii),deltastack(1,ii),0);
end
end
end
%%%%%% Sinogram alignment subpixel precision
% Compute tomogram with current sinogramder
% recons = iradonfast_v3(double(sinogramder),...
% theta,'linear','derivative','Han',size(sinogramder,1),filtertomo);
recons = tomo.iradonfast_v3(double(sinogramder),...
theta,'linear','derivative','Ram-Lak',size(sinogramder,1),1);
if ~isempty(cliplow)
recons = recons.*(recons>=cliplow) + cliplow*(recons<cliplow);
end
if ~isempty(cliphigh)
recons = recons.*(recons<=cliphigh) + cliphigh*(recons>cliphigh);
recons = recons-cliphigh;
end
if usecircle
recons = recons.*circulo;
end
figure(203)
imagesc(recons);
axis xy equal tight
colorbar
% Computed sinogram
sinogramcomp = radon(recons,theta);
Nbig = size(sinogramcomp,1);
centerbig = floor((Nbig+1)/2);
if strcmp(interpmeth,'sinc')
sinogramcompder = real(shiftpp2(sinogramcomp,0.5,0)-shiftpp2(sinogramcomp,-0.5,0));
elseif strcmp(interpmeth,'linear')
sinogramcompder = real(shiftwrapbilinear(sinogramcomp,0.5,0)-shiftwrapbilinear(sinogramcomp,-0.5,0));
end
sinogramcompder = sinogramcompder([1:N]+centerbig-center,:);
% Compare sinogramder with sinogramcompder
for ii = 1:size(sinogramder,2)
%ii,
errorinit(ii) = sum(abs(sinogramder(padval+masklims,ii)-sinogramcompder(padval+masklims,ii)).^2);
end
display(['Initial error metric, E = ' num2str(sum(errorinit))])
%%% Search for shifts with respect to sinthetic
for ii = 1:size(sinogramder,2);
shift = 0;
%%% Looking bothways
% compute current shift error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-shift,0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-shift,0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
currenterror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
% compute shift forward error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift+pixtol),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift+pixtol),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
forwarderror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
% compute shift backward error
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift-pixtol),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift-pixtol),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
backwarderror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
mini = min([currenterror backwarderror forwarderror]);
switch mini
case currenterror
deltastack(1,ii) = deltastack(1,ii) - shift;
auxtempreg(:,ii) = auxshift; %temporary for debugging
erroryreg(ii) = currenterror;
dir = 0;
continue;
case backwarderror % Looking backward
dir = -pixtol;
case forwarderror % Looking forward
dir = pixtol;
end
if dir~=0,
shift = shift+dir;
currenterror = mini;
do = 1;
end
while do==1,
if strcmp(interpmeth,'sinc')
auxshift = real(shiftpp2(sinogramder(:,ii),-(shift+dir),0));
elseif strcmp(interpmeth,'linear')
auxshift = real(shiftwrapbilinear(sinogramder(:,ii),-(shift+dir),0));
end
% if rembias,
% [coeffs auxshift] = projectleg1D_2(auxshift,maxorder,Yp(:,1),1);
% end
nexterror = sum(abs(auxshift(padval+masklims)-sinogramcompder(padval+masklims,ii)).^2);
%shift,
if nexterror<=currenterror
shift = shift+dir;
currenterror = nexterror;
else
do = 0;
deltastack(1,ii) = deltastack(1,ii) - shift;
auxtempreg(:,ii) = auxshift;
erroryreg(ii) = currenterror;
end
end
end
%deltastack(1,:) = deltastack(1,:) - round(mean(deltastack(1,:)));
display(['Final error mectric, E = ' num2str(sum(erroryreg))])
changey = abs(deltaprev(1,:) - deltastack(1,:));
display(['Max correction = ' num2str(max(abs(changey)))])
if (max(abs(changey))<pixtol),
domain = 0;
end
if count >= maxit,
domain = 0;
warning('Maximum number of iterations exceeded, increase maxit')
end
if sum(erroryregprev)<sum(erroryreg)
warning('Last iteration made error worse, keeping previous to last positions')
deltastack = deltaprev;
domain = 0;
end
if disp>1,
figure(200);
subplot(2,1,1)
imagesc(sinogramderorig_nofilt);
axis xy tight
%colorbar
title('Initial Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
subplot(2,1,2),
imagesc(sinogramder_nofilt);
axis xy tight
%colorbar
title('Current Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
figure(201);
imagesc(sinogramcompder);
axis xy tight
%colorbar
title('Synthetic Sinogram')
ylabel('x [pixels]')
xlabel('Projection')
figure(2),
plot(deltastack')
drawnow,
title('Object position')
end
end
end
%%%%%
if (binning ~=0)&&(binning ~=1)
deltastack = deltastack*binning;
sinogramder = sinogramder_orig;
end
%%% Create ouput aligned sinogram sinogramdernopad outputsinogram
if nargout>1,
for ii = 1:size(sinogramder,2),
if strcmp(interpmeth,'sinc')
outputsinogram(:,ii) = real(shiftpp2(outputsinogram(:,ii),deltastack(1,ii),0));
elseif strcmp(interpmeth,'linear')
outputsinogram(:,ii) = shiftwrapbilinear(outputsinogram(:,ii),deltastack(1,ii),0);
end
end
end
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