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apply_shifts.m
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apply_shifts.m
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function M_final = apply_shifts(Y,shifts,options,td1,td2,td3,col_shift)
% apply shifts using fft/cubic or linear interpolation
% INPUTS
% Y: Input data, can be already loaded in memory as a 3D
% tensor, a memory mapped file, or a pointer to a tiff stack
% shifts: calculated shifts
% options: options structure for motion correction
% td1,td2,td3: extend patches on the boundaries by that much
% OUTPUTS
% I: registered data
if nargin < 6 || isempty(td3); td3 = 0; end
if nargin < 5 || isempty(td2); td2 = 0; end
if nargin < 4 || isempty(td1); td1 = 0; end
if isa(Y,'char')
[~,~,ext] = fileparts(Y);
ext = ext(2:end);
if strcmpi(ext,'tif') || strcmpi(ext,'tiff')
tiffInfo = imfinfo(Y);
sizY = [tiffInfo(1).Height,tiffInfo(1).Width,length(tiffInfo)];
filetype = 'tif';
data_type = class(imread(Y,'Index',1,'Info',tiffInfo));
elseif strcmpi(ext,'mat')
filetype = 'mem';
Y = matfile(Y,'Writable',true);
sizY = size(Y,'Y');
details = whos(Y,'Y');
data_type = details.class;
elseif strcmpi(ext,'hdf5') || strcmpi(ext,'h5')
filetype = 'hdf5';
fileinfo = hdf5info(Y);
data_name = fileinfo.GroupHierarchy.Datasets.Name;
sizY = fileinfo.GroupHierarchy.Datasets.Dims;
data_type = class(read_file(Y,1,1));
elseif strcmpi(ext,'raw')
filetype = 'raw';
fid = fopen(Y);
FOV = [options.d1,options.d2];
bitsize = options.bitsize;
imsize = FOV(1)*FOV(2)*bitsize; % Bit size of single frame
current_seek = ftell(fid);
fseek(fid, 0, 1);
file_length = ftell(fid);
fseek(fid, current_seek, -1);
T = file_length/imsize;
sizY = [FOV,T];
fclose(fid);
data_type = 'single';
elseif strcmpi(ext,'avi')
filetype = 'avi';
v = VideoReader(Y);
T = v.Duration*v.FrameRate;
sizY = [v.Height,v.Width,T];
data_type = class(readFrame(v));
end
elseif isobject(Y)
filetype = 'mem';
sizY = size(Y,'Y');
details = whos(Y,'Y');
data_type = details.class;
else % array loaded in memory
filetype = 'mat';
data_type = class(Y);
Y = single(Y);
sizY = size(Y);
end
if strcmpi(options.boundary,'nan')
fill_value = NaN;
else
fill_value = options.add_value;
end
T = length(shifts);
if sizY(end) == T && T > 1
flag_constant = false;
nd = length(sizY)-1;
sizY = sizY(1:end-1);
else
flag_constant = true;
nd = length(sizY);
end
d1 = sizY(1); d2 = sizY(2);
if nd == 2; d3 = 1; else d3 = sizY(3); end
if ~isfield(options, 'print_msg') || isempty(options.print_msg)
print_msg = true;
else
print_msg = options.print_msg;
end
if strcmpi(options.shifts_method,'fft')
% precompute some quantities that are used repetitively for template matching and applying shifts
[xx_s,xx_f,yy_s,yy_f,zz_s,zz_f,xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf] = construct_grid(options.grid_size,options.mot_uf,options.d1,options.d2,options.d3,options.min_patch_size);
xx_us = xx_us + td1; xx_us(1) = 1;
yy_us = yy_us + td2; yy_us(1) = 1;
zz_us = zz_us + td3; zz_us(1) = 1;
xx_uf = xx_uf + td1; xx_uf(end) = d1;
yy_uf = yy_uf + td2; yy_uf(end) = d2;
zz_uf = zz_uf + td3; zz_uf(end) = d3;
temp_cell = mat2cell_ov(zeros(d1,d2,d3,'single'),xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf,options.overlap_post,[d1,d2,d3]);
Nr = cell(size(temp_cell));
Nc = cell(size(temp_cell));
Np = cell(size(temp_cell));
Bs = cell(size(temp_cell));
for i = 1:length(xx_us)
for j = 1:length(yy_us)
for k = 1:length(zz_us)
[nr,nc,np] = size(temp_cell{i,j,k});
nr = ifftshift(-fix(nr/2):ceil(nr/2)-1);
nc = ifftshift(-fix(nc/2):ceil(nc/2)-1);
np = ifftshift(-fix(np/2):ceil(np/2)-1);
[Nc{i,j,k},Nr{i,j,k},Np{i,j,k}] = meshgrid(nc,nr,np);
extended_grid = [max(xx_us(i)-options.overlap_post(1),1),min(xx_uf(i)+options.overlap_post(1),d1),max(yy_us(j)-options.overlap_post(2),1),min(yy_uf(j)+options.overlap_post(2),d2),max(zz_us(k)-options.overlap_post(3),1),min(zz_uf(k)+options.overlap_post(3),d3)];
Bs{i,j,k} = permute(construct_weights([xx_us(i),xx_uf(i),yy_us(j),yy_uf(j),zz_us(k),zz_uf(k)],extended_grid),[2,1,3]);
end
end
end
if nd == 2; Np = cellfun(@(x) 0,Nr,'un',0); end
shift_fun = @(yfft,shfts,ph,nr,nc,np) shift_reconstruct(yfft,shfts,ph,options.us_fac,nr,nc,np,options.boundary,0);
Xq = []; Yq = []; Zq = [];
else
if nd == 3
dim = [d1,d2,d3];
ds = size(shifts(1).shifts);
do = [d1,d2,d3,1]./size(shifts(1).shifts);
%tform = affine3d(diag([do([2,1,3])';1]));
[Xq,Yq,Zq] = meshgrid(linspace((1+1/do(2))/2,ds(2)+(1-1/do(2))/2,dim(2)),linspace((1+1/do(1))/2,ds(1)+(1-1/do(1))/2,dim(1)),linspace((1+1/do(3))/2,ds(3)+(1-1/do(3))/2,dim(3)));
else
Xq = []; Yq = []; Zq = [];
end
end
switch lower(options.output_type)
case 'mat'
M_final = zeros([sizY(1:nd),T],data_type);
case 'memmap'
M_final = matfile(options.mem_filename,'Writable',true);
if nd == 2; M_final.Y(d1,d2,T) = zeros(1,data_type); end
if nd == 3; M_final.Y(d1,d2,d3,T) = zeros(1,data_type); end
M_final.Yr(d1*d2*d3,T) = zeros(1,data_type);
case {'hdf5','h5'}
if exist(options.h5_filename,'file')
[pathstr,fname,ext] = fileparts(options.h5_filename);
new_filename = fullfile(pathstr,[fname,'_',datestr(now,30),ext]);
warning_msg = ['File ',options.h5_filename,'already exists. Saving motion corrected file as',new_filename];
warning('%s',warning_msg);
options.h5_filename = new_filename;
end
M_final = options.h5_filename;
if nd == 2
h5create(options.h5_filename,['/',options.h5_groupname],[d1,d2,Inf],'Chunksize',[d1,d2,options.mem_batch_size],'Datatype',data_type);
elseif nd == 3
h5create(options.h5_filename,['/',options.h5_groupname],[d1,d2,d3,Inf],'Chunksize',[d1,d2,d3,options.mem_batch_size],'Datatype',data_type);
end
case {'tif','tiff'}
M_final = options.tiff_filename;
opts_tiff.append = true;
opts_tiff.big = true;
if nd == 3
error('Saving volumetric tiff stacks is currently not supported. Use a different filetype');
end
otherwise
error('This filetype is currently not supported')
end
if exist('col_shift','var'); options.col_shift = col_shift; end
if ~isempty(options.col_shift)
col_shift = options.col_shift;
options.correct_bidir = false;
elseif ~options.correct_bidir
col_shift = 0;
end
if options.correct_bidir
col_shift = correct_bidirectional_offset(Y,options.nFrames,options.bidir_us);
end
if col_shift
if strcmpi(options.shifts_method,'fft')
options.shifts_method = 'cubic';
if print_msg; fprintf('Offset %1.1f pixels due to bidirectional scanning detected. Cubic shifts will be applied. \n',col_shift); end
end
end
if print_msg; prevstr = []; end
bin_width = min([options.mem_batch_size,T,ceil((512^2*3000)/(d1*d2*d3))]);
for t = 1:bin_width:T
switch filetype
case 'tif'
Ytm = single(read_file(Y, t, min(t+bin_width-1,T)-t+1, [], tiffInfo));
% Ytm = zeros(sizY(1),sizY(2),min(t+bin_width-1,T)-t+1,'single');
% for tt = 1:min(t+bin_width-1,T)-t+1
% Ytm(:,:,tt) = single(imread(Y,'Index',t+tt-1,'Info',tiffInfo));
% end
case 'hdf5'
Ytm = single(h5read(Y,data_name,[ones(1,length(sizY)-1),t],[sizY(1:end-1),min(t+bin_width-1,T)-t+1]));
case 'mem'
if nd == 2; Ytm = single(Y.Y(:,:,t:min(t+bin_width-1,T))); end
if nd == 3; Ytm = single(Y.Y(:,:,:,t:min(t+bin_width-1,T))); end
case 'mat'
if nd == 2; Ytm = single(Y(:,:,t:min(t+bin_width-1,T))); end
if nd == 3; Ytm = single(Y(:,:,:,t:min(t+bin_width-1,T))); end
case 'raw'
Ytm = read_raw_file(Y,t,min(t+bin_width-1,T)-t+1,FOV,bitsize);
case 'avi'
Ytm = read_file(Y,t,min(t+bin_width-1,T)-t+1);
end
% if ~flag_constant
if nd == 2; Ytc = mat2cell(Ytm,d1,d2,ones(1,size(Ytm,3))); end
if nd == 3; Ytc = mat2cell(Ytm,d1,d2,d3,ones(1,size(Ytm,4))); end
Mf = cell(size(Ytc));
lY = length(Ytc);
shifts_temp = shifts(t:t+lY-1);
switch lower(options.shifts_method)
case 'fft'
parfor ii = 1:lY
Yc = mat2cell_ov(Ytc{ii},xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf,options.overlap_post,[d1,d2,d3]);
Yfft = cellfun(@(x) fftn(x),Yc,'un',0);
minY = min(Ytc{ii}(:));
maxY = max(Ytc{ii}(:));
if all([length(xx_s),length(yy_s),length(zz_s)] == 1)
M_fin = shift_reconstruct(Yfft{1},shifts_temp(ii).shifts,shifts_temp(ii).diff,options.us_fac,Nr{1},Nc{1},Np{1},options.boundary,0);
Mf{ii} = M_fin;
else
shifts_up = shifts_temp(ii).shifts_up;
shifts_cell = mat2cell(shifts_up,ones(length(xx_uf),1),ones(length(yy_uf),1),ones(length(zz_uf),1),nd);
diff_cell = num2cell(shifts_temp(ii).diff);
M_fin = cellfun(shift_fun,Yfft,shifts_cell,diff_cell,Nr,Nc,Np,'un',0);
gx = max(abs(reshape(diff(shifts_up,[],1),[],1)));
gy = max(abs(reshape(diff(shifts_up,[],2),[],1)));
gz = max(abs(reshape(diff(shifts_up,[],3),[],1)));
flag_interp = max([gx;gy;gz;0])<0.5; % detect possible smearing
if flag_interp
Mf{ii} = cell2mat_ov_sum(M_fin,xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf,options.overlap_post,sizY,Bs);
else
Mf{ii} = cell2mat_ov(M_fin,xx_us,xx_uf,yy_us,yy_uf,zz_us,zz_uf,options.overlap_post,sizY);
end
end
Mf{ii}(Mf{ii}<minY) = minY;
Mf{ii}(Mf{ii}>maxY) = maxY;
end
otherwise
parfor ii = 1:lY
minY = min(Ytc{ii}(:));
maxY = max(Ytc{ii}(:));
shifts_temp(ii).shifts_up = shifts_temp(ii).shifts;
if nd == 3
shifts_up = zeros([d1,d2,d3,3]);
if numel(shifts_temp(ii).shifts) > 3
%tform = affine3d(diag([options.mot_uf(:);1]));
%tform = affine3d(diag([do([2,1,3])';1]));
%for dm = 1:3; shifts_up(:,:,:,dm) = imwarp(shifts_temp(ii).shifts(:,:,:,dm),tform,'OutputView',imref3d([d1,d2,d3]),'SmoothEdges',true); end
for dm = 1:3; shifts_up(:,:,:,dm) = interp3(shifts_temp(ii).shifts(:,:,:,dm),Xq,Yq,Zq,'makima'); end
else
for dm = 1:3; shifts_up(:,:,:,dm) = shifts_temp(ii).shifts(:,:,:,dm); end
end
shifts_up(2:2:end,:,:,2) = shifts_up(2:2:end,:,:,2) + col_shift;
Mf{ii} = imwarp(Ytc{ii},-cat(4,shifts_up(:,:,:,2),shifts_up(:,:,:,1),shifts_up(:,:,:,3)),options.shifts_method,'FillValues',fill_value);
else
shifts_up = imresize(shifts_temp(ii).shifts,[options.d1,options.d2]);
shifts_up(2:2:end,:,2) = shifts_up(2:2:end,:,2) + col_shift;
Mf{ii} = imwarp(Ytc{ii},-cat(3,shifts_up(:,:,2),shifts_up(:,:,1)),options.shifts_method,'FillValues',fill_value);
end
Mf{ii}(Mf{ii}<minY) = minY;
Mf{ii}(Mf{ii}>maxY) = maxY;
end
end
Mf = cast(cell2mat(Mf),data_type);
switch lower(options.output_type)
case 'mat'
if nd == 2; M_final(:,:,t:min(t+bin_width-1,T)) = Mf; end
if nd == 3; M_final(:,:,:,t:min(t+bin_width-1,T)) = Mf; end
case 'memmap'
if nd == 2; M_final.Y(:,:,t:min(t+bin_width-1,T)) = Mf; end
if nd == 3; M_final.Y(:,:,:,t:min(t+bin_width-1,T)) = Mf; end
M_final.Yr(:,t:min(t+bin_width-1,T)) = reshape(Mf,d1*d2*d3,[]);
case {'hdf5','h5'}
rem_mem = min(bin_width,T-t+1);
if nd == 2; h5write(options.h5_filename,['/',options.h5_groupname],Mf,[ones(1,nd),t],[sizY(1:nd),rem_mem]); end
if nd == 3; h5write(options.h5_filename,['/',options.h5_groupname],Mf,[ones(1,nd),t],[sizY(1:nd),rem_mem]); end
case {'tif','tiff'}
saveastiff(cast(Mf,data_type),options.tiff_filename,opts_tiff);
end
if print_msg
str = sprintf('%i out of %i frames registered \n',t+lY-1,T);
refreshdisp(str, prevstr, t);
prevstr=str;
end
end
if print_msg; fprintf('\n'); end