-
Notifications
You must be signed in to change notification settings - Fork 89
/
apply_shifts.m
306 lines (281 loc) · 12.9 KB
/
apply_shifts.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
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