[169] | 1 | %'sub_background': substract background to an image series, used with series.fig |
---|
| 2 | %------------------------------------------------------------------------ |
---|
[24] | 3 | % Method: |
---|
| 4 | %calculate the background image by sorting the luminosity of each point |
---|
| 5 | % over a sliding sub-sequence of 'nbaver_ima' images. |
---|
| 6 | % The luminosity value of rank 'rank' is selected as the |
---|
| 7 | % 'background'. rank=nbimages/2 gives the median value. Smaller values are appropriate |
---|
| 8 | % for a dense set of particles. The extrem value rank=1 gives the true minimum |
---|
| 9 | % luminosity, but it can be polluted by noise. |
---|
| 10 | % Organization of image indices: |
---|
[454] | 11 | % The program is working on a series of images, |
---|
| 12 | % The processing can be done over groups of nbfield2 consecutive files in slices (parameter NbSlice) |
---|
| 13 | % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j) |
---|
| 14 | % Else nbfield2=nbfield_j =nbre of images in a burst (j index) |
---|
[451] | 15 | |
---|
[454] | 16 | % function GUI_series_config=sub_background(Param) |
---|
[169] | 17 | % |
---|
[451] | 18 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 19 | %OUTPUT |
---|
[454] | 20 | % GUI_series_config=list of options in the GUI series.fig needed for the function |
---|
[451] | 21 | % |
---|
| 22 | %INPUT: |
---|
| 23 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
---|
| 24 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
---|
| 25 | % In the absence of input (as activated when the current Action is selected |
---|
[454] | 26 | % in series), the function ouput GUI_series_config set the activation of the needed GUI elements |
---|
[451] | 27 | % |
---|
| 28 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
---|
| 29 | % .InputTable: cell of input file names, (several lines for multiple input) |
---|
| 30 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
---|
| 31 | % .OutputSubDir: name of the subdirectory for data outputs |
---|
| 32 | % .OutputDir: directory for data outputs, including path |
---|
| 33 | % .Action: .ActionName: name of the current activated function |
---|
| 34 | % .ActionPath: path of the current activated function |
---|
| 35 | % .IndexRange: set the file or frame indices on which the action must be performed |
---|
| 36 | % .FieldTransform: .TransformName: name of the selected transform function |
---|
| 37 | % .TransformPath: path of the selected transform function |
---|
| 38 | % .TransformHandle: corresponding function handle |
---|
| 39 | % .InputFields: sub structure describing the input fields withfields |
---|
| 40 | % .FieldName: name of the field |
---|
| 41 | % .VelType: velocity type |
---|
| 42 | % .FieldName_1: name of the second field in case of two input series |
---|
| 43 | % .VelType_1: velocity type of the second field in case of two input series |
---|
| 44 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
---|
| 45 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
---|
| 46 | |
---|
| 47 | |
---|
[455] | 48 | function GUI_config=sub_background (Param) |
---|
[24] | 49 | |
---|
[451] | 50 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
---|
| 51 | if ~exist('Param','var') % case with no input parameter |
---|
[454] | 52 | GUI_config={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation) |
---|
[451] | 53 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
---|
[24] | 54 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
---|
[451] | 55 | 'VelType';'off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
---|
| 56 | 'FieldName';'off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
---|
| 57 | 'FieldTransform'; 'off';...%can use a transform function |
---|
| 58 | 'ProjObject';'off';...%can use projection object(option 'off'/'on', |
---|
| 59 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
---|
[454] | 60 | 'OutputDirExt';'.sback';...%set the output dir extension |
---|
[24] | 61 | ''}; |
---|
[451] | 62 | return |
---|
[24] | 63 | end |
---|
| 64 | |
---|
[451] | 65 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
---|
| 66 | %% get input parameters, file names and indices |
---|
| 67 | % BATCH case: read the xml file for batch case |
---|
[455] | 68 | if ischar(Param) && ~isempty(find(regexp(Param,'.xml$'))) %batch mode |
---|
[454] | 69 | Param=xml2struct(Param); |
---|
| 70 | checkrun=0; |
---|
| 71 | % RUN case: parameters introduced as the input structure Param |
---|
| 72 | else |
---|
[374] | 73 | hseries=guidata(Param.hseries);%handles of the GUI series |
---|
[451] | 74 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
---|
| 75 | checkrun=1; % indicate the RUN option is used |
---|
[374] | 76 | end |
---|
[451] | 77 | % get the set of input file names (cell array filecell), and the lists of |
---|
| 78 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
---|
| 79 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
---|
| 80 | % filecell{iview,fileindex}: cell array representing the list of file names |
---|
| 81 | % iview: line in the table corresponding to a given file series |
---|
| 82 | % fileindex: file index within the file series, |
---|
| 83 | % i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j |
---|
| 84 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
---|
| 85 | % set of frame indices used for movie or multimage input |
---|
[394] | 86 | |
---|
[454] | 87 | |
---|
[451] | 88 | %% root input file(s) and type |
---|
| 89 | RootPath=Param.InputTable(:,1); |
---|
| 90 | RootFile=Param.InputTable(:,3); |
---|
| 91 | SubDir=Param.InputTable(:,2); |
---|
| 92 | NomType=Param.InputTable(:,4); |
---|
| 93 | FileExt=Param.InputTable(:,5); |
---|
[89] | 94 | |
---|
[451] | 95 | % numbers of slices and file indices |
---|
| 96 | NbSlice=1;%default |
---|
| 97 | if isfield(Param.IndexRange,'NbSlice') |
---|
| 98 | NbSlice=Param.IndexRange.NbSlice; |
---|
[54] | 99 | end |
---|
[454] | 100 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
---|
| 101 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
---|
| 102 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
---|
| 103 | nbfield=nbfield_j*nbfield_i; %total number of fields |
---|
| 104 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
---|
| 105 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
---|
[451] | 106 | |
---|
| 107 | %determine the file type on each line from the first input file |
---|
[454] | 108 | ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) |
---|
[451] | 109 | |
---|
[454] | 110 | [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); |
---|
| 111 | CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images |
---|
| 112 | if ~isempty(j1_series{1}) |
---|
| 113 | frame_index{1}=j1_series{1}; |
---|
| 114 | else |
---|
| 115 | frame_index{1}=i1_series{1}; |
---|
| 116 | end |
---|
[451] | 117 | |
---|
| 118 | %% calibration data and timing: read the ImaDoc files |
---|
| 119 | %not relevant here |
---|
| 120 | |
---|
| 121 | %% check coincidence in time for several input file series |
---|
| 122 | %not relevant here |
---|
| 123 | |
---|
| 124 | %% coordinate transform or other user defined transform |
---|
| 125 | %not relevant here |
---|
| 126 | |
---|
| 127 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
---|
| 128 | % EDIT FROM HERE |
---|
| 129 | |
---|
| 130 | %% check the validity of input file types |
---|
[454] | 131 | if CheckImage{1} |
---|
[451] | 132 | FileExtOut='.png'; % write result as .png images for image inputs |
---|
[454] | 133 | if strcmp(lower(NomType{1}(end)),'a') |
---|
| 134 | NomTypeOut=NomType{1};%case of letter appendix |
---|
| 135 | else |
---|
| 136 | NomTypeOut='_1_1';% caseof purely numerical indexing |
---|
| 137 | end |
---|
[451] | 138 | else |
---|
| 139 | msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image']) |
---|
[54] | 140 | return |
---|
| 141 | end |
---|
| 142 | |
---|
[451] | 143 | %% Set field names and velocity types |
---|
| 144 | %not relevant here |
---|
| 145 | |
---|
| 146 | %% Initiate output fields |
---|
| 147 | %not relevant here |
---|
| 148 | |
---|
| 149 | %%% SPECIFIC PART BEGINS HERE |
---|
| 150 | NbSlice=Param.IndexRange.NbSlice; %number of slices |
---|
[454] | 151 | %siz=size(i1_series); |
---|
[24] | 152 | nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts |
---|
[394] | 153 | j1=[];%default |
---|
[24] | 154 | |
---|
[214] | 155 | %% adjust the proposed number of images in the sliding average to include an integer number of bursts |
---|
[454] | 156 | if nbfield_i~=1 |
---|
| 157 | nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background, |
---|
[24] | 158 | if isequal(floor(nbaver/2),nbaver) |
---|
| 159 | nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined) |
---|
| 160 | end |
---|
[454] | 161 | nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts |
---|
[24] | 162 | end |
---|
| 163 | |
---|
[214] | 164 | %% set processing parameters |
---|
[455] | 165 | if ~isfield(Param,'Specific') |
---|
[454] | 166 | prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';... |
---|
| 167 | 'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'}; |
---|
| 168 | dlg_title = ['get (slice by slice) a sliding background and substract to each image, result in subdir ' Param.OutputDir]; |
---|
| 169 | num_lines= 3; |
---|
| 170 | def = { 'No';num2str(nbaver_init);'0.1'}; |
---|
| 171 | answer = inputdlg(prompt,dlg_title,num_lines,def); |
---|
| 172 | |
---|
| 173 | %check input consistency |
---|
| 174 | if strcmp(answer{1},'No') && ~isequal(NbSlice,1) |
---|
| 175 | check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']); |
---|
| 176 | if ~strcmp(check,'Yes') |
---|
| 177 | return |
---|
| 178 | end |
---|
| 179 | end |
---|
| 180 | if strcmp(answer{1},'Yes') |
---|
| 181 | step=1; |
---|
| 182 | else |
---|
| 183 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
---|
| 184 | end |
---|
| 185 | nbaver_ima=str2num(answer{2});%number of images for the sliding background |
---|
| 186 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
---|
| 187 | if isequal(floor(nbaver/2),nbaver) |
---|
| 188 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
---|
| 189 | end |
---|
| 190 | nbaver_ima=nbaver*step; |
---|
| 191 | if nbaver_ima > nbfield |
---|
| 192 | msgbox_uvmat('ERROR','number of images in a slice smaller than the proposed number of images for the sliding average') |
---|
| 193 | return |
---|
| 194 | end |
---|
| 195 | GUI_config.CheckVolume=strcmp(answer{1},'Yes'); |
---|
| 196 | GUI_config.SlidingSequenceSize=nbaver_ima; |
---|
| 197 | GUI_config.BrightnessRankThreshold=str2num(answer{3}); |
---|
| 198 | |
---|
| 199 | % apply the image rescaling function 'level' (avoid the blinking effects of bright particles) |
---|
| 200 | answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background'); |
---|
| 201 | GUI_config.CheckLevelTransform=strcmp(answer,'Yes'); |
---|
| 202 | |
---|
[455] | 203 | % % return to BATCH mode |
---|
| 204 | % if checkrun==-1 |
---|
[454] | 205 | return %transfer to BATCH mode |
---|
[455] | 206 | % end |
---|
[24] | 207 | else |
---|
[454] | 208 | GUI_config=Param.Specific; |
---|
| 209 | if isequal(GUI_config.CheckVolume,1) |
---|
| 210 | step=1; |
---|
[24] | 211 | else |
---|
[454] | 212 | step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst |
---|
[24] | 213 | end |
---|
[454] | 214 | nbaver_ima=GUI_config.SlidingSequenceSize;%number of images for the sliding background |
---|
| 215 | nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background |
---|
| 216 | if isequal(floor(nbaver/2),nbaver) |
---|
| 217 | nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined) |
---|
| 218 | end |
---|
| 219 | nbaver_ima=nbaver*step; |
---|
| 220 | if nbaver_ima > nbfield |
---|
| 221 | msgbox_uvmat('ERROR','number of images in a slice smaller than the proposed number of images for the sliding average') |
---|
[24] | 222 | return |
---|
| 223 | end |
---|
| 224 | end |
---|
[454] | 225 | |
---|
| 226 | % calculate absolute brightness rank |
---|
| 227 | rank=floor(GUI_config.BrightnessRankThreshold*nbaver_ima); |
---|
[24] | 228 | if rank==0 |
---|
| 229 | rank=1;%rank selected in the sorted image series |
---|
| 230 | end |
---|
| 231 | |
---|
[239] | 232 | %% prealocate memory for the sliding background |
---|
[394] | 233 | try |
---|
[454] | 234 | Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1)); |
---|
| 235 | [npy,npx]=size(Afirst); |
---|
| 236 | if strcmp(class(Afirst),'uint8') % case of 8bit images |
---|
| 237 | Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
---|
| 238 | Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory |
---|
| 239 | else |
---|
| 240 | Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
---|
| 241 | Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory |
---|
| 242 | end |
---|
[239] | 243 | catch ME |
---|
| 244 | msgbox_uvmat('ERROR',ME.message) |
---|
| 245 | return |
---|
| 246 | end |
---|
| 247 | |
---|
[442] | 248 | %% update the xml file |
---|
[454] | 249 | % SubDirBase=regexprep(Param.InputTable{1,2},'\..*','');%take the root part of SubDir, before the first dot '.' |
---|
| 250 | % filexml=fullfile(RootPath{1},[SubDirBase '.xml']); |
---|
| 251 | % if ~exist(filexml,'file') && exist([fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml'],'file')% xml inside the image directory |
---|
| 252 | % copyfile([filebase '.xml'],filexml);% copy the .xml file |
---|
| 253 | % end |
---|
| 254 | % if exist(filexml,'file') |
---|
| 255 | % t=xmltree(filexml); |
---|
| 256 | % %update information on the first image name in the series |
---|
| 257 | % uid_Heading=find(t,'ImaDoc/Heading'); |
---|
| 258 | % if isempty(uid_Heading) |
---|
| 259 | % [t,uid_Heading]=add(t,1,'element','Heading'); |
---|
| 260 | % end |
---|
| 261 | % uid_ImageName=find(t,'ImaDoc/Heading/ImageName'); |
---|
| 262 | % if ~isempty(j1_series{1}) |
---|
| 263 | % j1=j1_series{1}(1); |
---|
| 264 | % end |
---|
| 265 | % ImageName=fullfile_uvmat([dir_images term],'',RootFile{1},'.png',NomType,i1_series(1,1),[],j1); |
---|
| 266 | % [pth,ImageName]=fileparts(ImageName); |
---|
| 267 | % ImageName=[ImageName '.png']; |
---|
| 268 | % if isempty(uid_ImageName) |
---|
| 269 | % [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName'); |
---|
| 270 | % end |
---|
| 271 | % uid_value=children(t,uid_ImageName); |
---|
| 272 | % if isempty(uid_value) |
---|
| 273 | % t=add(t,uid_ImageName,'chardata',ImageName);%indicate name of the first image, with ;png extension |
---|
| 274 | % else |
---|
| 275 | % t=set(t,uid_value(1),'value',ImageName);%indicate name of the first image, with ;png extension |
---|
| 276 | % end |
---|
| 277 | % |
---|
| 278 | % %add information about image transform |
---|
| 279 | % [t,new_uid]=add(t,1,'element','ImageTransform'); |
---|
| 280 | % [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
---|
| 281 | % [t]=add(t,NameFunction_uid,'chardata','sub_background'); |
---|
| 282 | % if GUI_config.CheckLevel |
---|
| 283 | % [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction'); |
---|
| 284 | % [t]=add(t,NameFunction_uid,'chardata','levels'); |
---|
| 285 | % end |
---|
| 286 | % [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice'); |
---|
| 287 | % [t]=add(t,new_uid,'chardata',num2str(NbSlice)); |
---|
| 288 | % [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages'); |
---|
| 289 | % [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver)); |
---|
| 290 | % [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground'); |
---|
| 291 | % [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images |
---|
| 292 | % save(t,filexml) |
---|
| 293 | % end |
---|
[24] | 294 | %copy the mask |
---|
[442] | 295 | % if exist([filebase '_1mask_1'],'file') |
---|
| 296 | % copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file |
---|
| 297 | % end |
---|
[24] | 298 | |
---|
| 299 | %MAIN LOOP ON SLICES |
---|
[451] | 300 | for islice=1:NbSlice |
---|
[214] | 301 | %% select the series of image indices at the level islice |
---|
[454] | 302 | indselect=islice:NbSlice*step:nbfield;% select file indices of the slice |
---|
| 303 | for ifield=1:step-1 |
---|
| 304 | indselect=[indselect;indselect(end,:)+1]; |
---|
[394] | 305 | end |
---|
[214] | 306 | |
---|
| 307 | %% read the first series of nbaver_ima images and sort by luminosity at each pixel |
---|
[24] | 308 | for ifield = 1:nbaver_ima |
---|
[54] | 309 | ifile=indselect(ifield); |
---|
[394] | 310 | filename=filecell{1,ifile}; |
---|
[454] | 311 | Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile)); |
---|
| 312 | if ndims(Aread)==3;%color images |
---|
| 313 | Aread=sum(double(Aread),3);% take the sum of color components |
---|
| 314 | end |
---|
[394] | 315 | Ak(:,:,ifield)=Aread; |
---|
[24] | 316 | end |
---|
| 317 | Asort=sort(Ak,3);%sort the luminosity of images at each point |
---|
| 318 | B=Asort(:,:,rank);%background image |
---|
[394] | 319 | display( 'first background image will be substracted') |
---|
[454] | 320 | nbfirst=(ceil(nbaver/2))*step; |
---|
[24] | 321 | for ifield=1:nbfirst |
---|
[394] | 322 | Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image |
---|
| 323 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
---|
| 324 | ifile=indselect(ifield); |
---|
| 325 | if ~isempty(j1_series{1}) |
---|
| 326 | j1=j1_series{1}(ifile); |
---|
| 327 | end |
---|
[454] | 328 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
---|
| 329 | |
---|
| 330 | %write result file |
---|
| 331 | if GUI_config.CheckLevelTransform |
---|
| 332 | C=levels(Acor); |
---|
[394] | 333 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 334 | else |
---|
[454] | 335 | if isequal(FileInfo{1}.BitDepth,16) |
---|
| 336 | C=uint16(Acor); |
---|
| 337 | imwrite(C,newname,'BitDepth',16); % save the new image |
---|
| 338 | else |
---|
| 339 | C=uint8(Acor); |
---|
| 340 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 341 | end |
---|
[394] | 342 | end |
---|
[454] | 343 | display([newname ' written']) |
---|
[24] | 344 | end |
---|
[214] | 345 | |
---|
[454] | 346 | %% repeat the operation on a sliding series of images |
---|
[214] | 347 | display('sliding background image will be substracted') |
---|
[454] | 348 | if nbfield_i > nbaver_ima |
---|
| 349 | for ifield = step*ceil(nbaver/2)+1:step:nbfield_i-step*floor(nbaver/2) |
---|
[442] | 350 | if checkrun |
---|
| 351 | stopstate=get(hseries.RUN,'BusyAction'); |
---|
[454] | 352 | update_waitbar(hseries.waitbar_frame,WaitbarPos,(ifield+(islice-1)*nbfield_i)/(nbfield_i*NbSlice)) |
---|
[442] | 353 | else |
---|
| 354 | stopstate='queue'; |
---|
| 355 | end |
---|
| 356 | if isequal(stopstate,'queue')% enable STOP command |
---|
[240] | 357 | Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step) |
---|
[24] | 358 | %incorporate next burst in the current image series |
---|
| 359 | for iburst=1:step |
---|
| 360 | ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1); |
---|
[454] | 361 | filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile)); |
---|
| 362 | Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile)); |
---|
| 363 | if ndims(Aread)==3;%color images |
---|
| 364 | Aread=sum(double(Aread),3);% take the sum of color components |
---|
| 365 | end |
---|
[24] | 366 | Ak(:,:,nbaver_ima-step+iburst)=Aread; |
---|
| 367 | end |
---|
| 368 | Asort=sort(Ak,3);%sort the new current image series by luminosity |
---|
| 369 | B=Asort(:,:,rank);%current background image |
---|
| 370 | for iburst=1:step |
---|
| 371 | index=step*floor(nbaver/2)+iburst; |
---|
| 372 | Acor=double(Ak(:,:,index))-double(B); |
---|
| 373 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
---|
| 374 | ifile=indselect(ifield+iburst-1); |
---|
[394] | 375 | if ~isempty(j1_series{1}) |
---|
| 376 | j1=j1_series{1}(ifile); |
---|
| 377 | end |
---|
[454] | 378 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
---|
| 379 | %write result file |
---|
| 380 | if GUI_config.CheckLevelTransform |
---|
| 381 | C=levels(Acor); |
---|
[214] | 382 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 383 | else |
---|
[454] | 384 | if isequal(FileInfo{1}.BitDepth,16) |
---|
| 385 | C=uint16(Acor); |
---|
| 386 | imwrite(C,newname,'BitDepth',16); % save the new image |
---|
| 387 | else |
---|
| 388 | C=uint8(Acor); |
---|
| 389 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 390 | end |
---|
[214] | 391 | end |
---|
[454] | 392 | display([newname ' written']) |
---|
| 393 | |
---|
[214] | 394 | end |
---|
[24] | 395 | else |
---|
| 396 | return |
---|
| 397 | end |
---|
| 398 | end |
---|
| 399 | end |
---|
[394] | 400 | |
---|
| 401 | %% substract the background from the last images |
---|
[214] | 402 | display('last background image will be substracted') |
---|
[454] | 403 | ifield=nbfield_i-(step*ceil(nbaver/2))+1:nbfield_i; |
---|
| 404 | for ifield=nbfield_i-(step*floor(nbaver/2))+1:nbfield_i |
---|
| 405 | index=ifield-nbfield_i+step*(2*floor(nbaver/2)+1); |
---|
[394] | 406 | Acor=double(Ak(:,:,index))-double(B); |
---|
| 407 | Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor |
---|
| 408 | ifile=indselect(ifield); |
---|
| 409 | if ~isempty(j1_series{1}) |
---|
| 410 | j1=j1_series{1}(ifile); |
---|
| 411 | end |
---|
[454] | 412 | newname=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1); |
---|
| 413 | |
---|
| 414 | %write result file |
---|
| 415 | if GUI_config.CheckLevelTransform |
---|
| 416 | C=levels(Acor); |
---|
[394] | 417 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 418 | else |
---|
[454] | 419 | if isequal(FileInfo{1}.BitDepth,16) |
---|
| 420 | C=uint16(Acor); |
---|
| 421 | imwrite(C,newname,'BitDepth',16); % save the new image |
---|
| 422 | else |
---|
| 423 | C=uint8(Acor); |
---|
| 424 | imwrite(C,newname,'BitDepth',8); % save the new image |
---|
| 425 | end |
---|
[394] | 426 | end |
---|
[454] | 427 | display([newname ' written']) |
---|
[394] | 428 | end |
---|
[24] | 429 | end |
---|
| 430 | |
---|
| 431 | %finish the waitbar |
---|
[442] | 432 | if checkrun |
---|
| 433 | update_waitbar(hseries.waitbar,WaitbarPos,1) |
---|
| 434 | end |
---|
[24] | 435 | |
---|
[214] | 436 | |
---|
| 437 | function C=levels(A) |
---|
| 438 | %whos A; |
---|
| 439 | B=double(A(:,:,1)); |
---|
| 440 | windowsize=round(min(size(B,1),size(B,2))/20); |
---|
| 441 | windowsize=floor(windowsize/2)*2+1; |
---|
[239] | 442 | ix=1/2-windowsize/2:-1/2+windowsize/2;% |
---|
[214] | 443 | %del=np/3; |
---|
| 444 | %fct=exp(-(ix/del).^2); |
---|
| 445 | fct2=cos(ix/(windowsize-1)/2*pi/2); |
---|
| 446 | %Mfiltre=(ones(5,5)/5^2); |
---|
| 447 | %Mfiltre=fct2'; |
---|
| 448 | Mfiltre=fct2'*fct2; |
---|
| 449 | Mfiltre=Mfiltre/(sum(sum(Mfiltre))); |
---|
| 450 | |
---|
| 451 | C=filter2(Mfiltre,B); |
---|
| 452 | C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize); |
---|
| 453 | C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize); |
---|
| 454 | C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:); |
---|
| 455 | C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:); |
---|
| 456 | C=tanh(B./(2*C)); |
---|
| 457 | [n,c]=hist(reshape(C,1,[]),100); |
---|
| 458 | % figure;plot(c,n); |
---|
| 459 | |
---|
| 460 | [m,i]=max(n); |
---|
| 461 | c_max=c(i); |
---|
| 462 | [dummy,index]=sort(abs(c-c(i))); |
---|
| 463 | n=n(index); |
---|
| 464 | c=c(index); |
---|
| 465 | i_select = find(cumsum(n)<0.95*sum(n)); |
---|
| 466 | if isempty(i_select) |
---|
| 467 | i_select = 1:length(c); |
---|
| 468 | end |
---|
| 469 | c_select=c(i_select); |
---|
| 470 | n_select=n(i_select); |
---|
| 471 | cmin=min(c_select); |
---|
| 472 | cmax=max(c_select); |
---|
| 473 | C=(C-cmin)/(cmax-cmin)*256; |
---|
| 474 | C=uint8(C); |
---|