source: trunk/src/series/sub_background.m @ 661

Last change on this file since 661 was 642, checked in by sommeria, 11 years ago

civ_input improved and small bug corrections

File size: 20.9 KB
Line 
1%'sub_background': substract a sliding background to an image series
2%------------------------------------------------------------------------
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:
11    % The program is working on a series of images,
12    % In the mode 'volume', nbfield2=1 (1 image at each level)and NbSlice (=nbfield_j)
13    % Else nbfield2=nbfield_j =nbre of images in a burst (j index)
14   
15% function GUI_config=sub_background(Param)
16%
17%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
18%
19%OUTPUT
20% ParamOut: sets options in the GUI series.fig needed for the function
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% when Param.Action.RUN=0 (as activated when the current Action is selected
26% in series), the function ouput paramOut set the activation of the needed GUI elements
27%
28% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
29% see the current structure Param)
30%    .InputTable: cell of input file names, (several lines for multiple input)
31%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
32%    .OutputSubDir: name of the subdirectory for data outputs
33%    .OutputDirExt: directory extension for data outputs
34%    .Action: .ActionName: name of the current activated function
35%             .ActionPath:   path of the current activated function
36%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
37%             .RUN =0 for GUI input, =1 for function activation
38%             .RunMode='local','background', 'cluster': type of function  use
39%             
40%    .IndexRange: set the file or frame indices on which the action must be performed
41%    .FieldTransform: .TransformName: name of the selected transform function
42%                     .TransformPath:   path  of the selected transform function
43%    .InputFields: sub structure describing the input fields withfields
44%              .FieldName: name(s) of the field
45%              .VelType: velocity type
46%              .FieldName_1: name of the second field in case of two input series
47%              .VelType_1: velocity type of the second field in case of two input series
48%              .Coord_y: name of y coordinate variable
49%              .Coord_x: name of x coordinate variable
50%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
51%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
52   
53function ParamOut=sub_background (Param)
54
55%% input preparation mode (no RUN)
56if isstruct(Param) && isequal(Param.Action.RUN,0)
57    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
58    ParamOut.WholeIndexRange='on';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
59    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
60    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
61    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
62    ParamOut.FieldTransform = 'off';%can use a transform function
63    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
64    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
65    ParamOut.OutputDirExt='.sback';%set the output dir extension
66    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
67    filecell=get_file_series(Param);%check existence of the first input file
68    %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
69   
70    %% root input file(s) and type
71    [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
72    if ~exist(filecell{1,1},'file')
73        msgbox_uvmat('WARNING','the first input file does not exist')
74        return
75    end
76    %%%%%%%%%%%%
77    % The cell array filecell is the list of input file names, while
78    % filecell{iview,fileindex}:
79    %        iview: line in the table corresponding to a given file series
80    %        fileindex: file index within  the file series,
81    % 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
82    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
83    %%%%%%%%%%%%
84    NbSlice=1;%default
85    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
86        NbSlice=Param.IndexRange.NbSlice;
87    end
88    nbview=numel(i1_series);%number of input file series (lines in InputTable)
89    nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
90    nbfield_i=size(i1_series{1},2); %nb of fields for the i index
91    nbfield=nbfield_j*nbfield_i; %total number of fields
92    nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
93    nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
94   
95    %determine the file type on each line from the first input file
96
97   
98    %% calibration data and timing: read the ImaDoc files
99    %not relevant here
100   
101    %% check coincidence in time for several input file series
102    %not relevant here
103   
104    %% coordinate transform or other user defined transform
105    %not relevant here
106   
107    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
108    % EDIT FROM HERE
109   
110    %% check the validity of  input file types
111    ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
112    FileType=get_file_type(filecell{1,1});
113    CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images
114    if ~CheckImage
115        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not an image'])
116        return
117    end
118   
119    %% Set field names and velocity types
120    %not relevant here
121   
122    %% Initiate output fields
123    %not relevant here
124   
125    %%% SPECIFIC PART BEGINS HERE
126    NbSlice=1;
127    if isfield(Param.IndexRange,'NbSlice')
128        NbSlice=Param.IndexRange.NbSlice; %number of slices
129    end
130    %siz=size(i1_series);
131    nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts
132    j1=[];%default
133   
134    %% adjust the proposed number of images in the sliding average to include an integer number of bursts
135    if nbfield_i~=1
136        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
137        if isequal(floor(nbaver/2),nbaver)
138            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
139        end
140        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
141    end
142   
143    %% input of specific parameters
144    %if checkrun %get specific parameters interactively
145    if isequal(Param.Action.RUN,0)
146        prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
147            'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'};
148        dlg_title = 'get (slice by slice) a sliding background and substract to each image';
149        num_lines= 3;
150        def     = { 'No';num2str(nbaver_init);'0.1'};
151        answer = inputdlg(prompt,dlg_title,num_lines,def);
152       
153        %check input consistency
154        if strcmp(answer{1},'No') && ~isequal(NbSlice,1)
155            check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']);
156            if ~strcmp(check,'Yes')
157                return
158            end
159        end
160        if strcmp(answer{1},'Yes')
161            step=1;
162        else
163            step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
164        end
165        nbaver_ima=str2num(answer{2});%number of images for the sliding background
166        nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
167        if isequal(floor(nbaver/2),nbaver)
168            nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
169        end
170        nbaver_ima=nbaver*step;
171    end
172    ParamOut.ActionInput.CheckVolume=strcmp(answer{1},'Yes');
173    ParamOut.ActionInput.SlidingSequenceLength=nbaver_ima;
174    ParamOut.ActionInput.BrightnessRankThreshold=str2num(answer{3});
175   
176    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
177    answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
178    ParamOut.ActionInput.CheckLevelTransform=strcmp(answer,'Yes');
179    return
180end
181%%%%%%%%%%%%%%%%%%%%%%  STOP HERE FOR PAMETER INPUT MODE  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
182
183%% read input parameters from an xml file if input is a file name (batch mode)
184checkrun=1;
185if ischar(Param)
186    Param=xml2struct(Param);% read Param as input file (batch case)
187    checkrun=0;
188end
189hseries=findobj(allchild(0),'Tag','series');
190RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
191WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
192%% Input preparation
193nbaver_ima=Param.ActionInput.SlidingSequenceLength;
194NbSlice=Param.IndexRange.NbSlice;
195if ~isequal(NbSlice,1)
196    display(['multi-level splitting into ' num2str(NbSlice) ' slices']);
197end
198RootPath=Param.InputTable(:,1);
199RootFile=Param.InputTable(:,3);
200SubDir=Param.InputTable(:,2);
201NomType=Param.InputTable(:,4);
202FileExt=Param.InputTable(:,5);
203[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
204[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
205    if ~isempty(j1_series{1})
206        frame_index{1}=j1_series{1};
207    else
208        frame_index{1}=i1_series{1};
209    end
210nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
211nbfield_i=size(i1_series{1},2); %nb of fields for the i index
212nbfield=nbfield_j*nbfield_i; %total number of fields
213nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
214nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
215
216%% Output
217FileExtOut='.png'; % write result as .png images for image inputs
218if strcmp(lower(NomType{1}(end)),'a')
219    NomTypeOut=NomType{1};%case of letter appendix
220elseif isempty(j1_series)
221    NomTypeOut='_1';
222else
223    NomTypeOut='_1_1';% caseof purely numerical indexing
224end
225
226OutputDir=[Param.OutputSubDir Param.OutputDirExt];
227
228if isequal(Param.ActionInput.CheckVolume,1)
229    step=1;
230else
231    step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
232end
233nbaver_ima=Param.ActionInput.SlidingSequenceLength;%number of images for the sliding background
234nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
235if isequal(floor(nbaver/2),nbaver)
236    nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
237end
238nbaver_ima=nbaver*step;
239if nbaver_ima > nbfield
240    display('number of images in a slice smaller than the proposed number of images for the sliding average')
241    return
242end
243
244% calculate absolute brightness rank
245rank=floor(Param.ActionInput.BrightnessRankThreshold*nbaver_ima);
246if rank==0
247    rank=1;%rank selected in the sorted image series
248end
249
250%% prealocate memory for the sliding background
251try
252    Afirst=read_image(filecell{1,1},FileType{1},MovieObject{1},frame_index{1}(1));
253    [npy,npx]=size(Afirst);
254    if strcmp(class(Afirst),'uint8') % case of 8bit images
255        Ak=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
256        Asort=zeros(npy,npx,nbaver_ima,'uint8'); %prealocate memory
257    else
258        Ak=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
259        Asort=zeros(npy,npx,nbaver_ima,'uint16'); %prealocate memory
260    end
261catch ME
262    msgbox_uvmat('ERROR',['sub_background/read_image/' ME.message])
263    return
264end
265
266%% update the xml file
267% SubDirBase=regexprep(Param.InputTable{1,2},'\..*','');%take the root part of SubDir, before the first dot '.'
268% filexml=fullfile(RootPath{1},[SubDirBase '.xml']);
269% if ~exist(filexml,'file') && exist([fullfile(RootPath{1},SubDir{1},RootFile{1}) '.xml'],'file')% xml inside the image directory
270%     copyfile([filebase '.xml'],filexml);% copy the .xml file
271% end
272% if exist(filexml,'file')
273%     t=xmltree(filexml); 
274%     %update information on the first image name in the series
275%     uid_Heading=find(t,'ImaDoc/Heading');
276%     if isempty(uid_Heading)
277%         [t,uid_Heading]=add(t,1,'element','Heading');
278%     end
279%     uid_ImageName=find(t,'ImaDoc/Heading/ImageName');
280%     if ~isempty(j1_series{1})
281%         j1=j1_series{1}(1);
282%     end
283%     ImageName=fullfile_uvmat([dir_images term],'',RootFile{1},'.png',NomType,i1_series(1,1),[],j1);
284%     [pth,ImageName]=fileparts(ImageName);
285%     ImageName=[ImageName '.png'];
286%     if isempty(uid_ImageName)
287%         [t,uid_ImageName]=add(t,uid_Heading,'element','ImageName');
288%     end
289%     uid_value=children(t,uid_ImageName);
290%     if isempty(uid_value)
291%         t=add(t,uid_ImageName,'chardata',ImageName);%indicate  name of the first image, with ;png extension
292%     else
293%         t=set(t,uid_value(1),'value',ImageName);%indicate  name of the first image, with ;png extension
294%     end
295%     
296%     %add information about image transform
297%     [t,new_uid]=add(t,1,'element','ImageTransform');
298%     [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction');
299%     [t]=add(t,NameFunction_uid,'chardata','sub_background');
300%     if GUI_config.CheckLevel
301%         [t,NameFunction_uid]=add(t,new_uid,'element','NameFunction');
302%         [t]=add(t,NameFunction_uid,'chardata','levels');
303%     end
304%     [t,NbSlice_uid]=add(t,new_uid,'element','NbSlice');
305%     [t]=add(t,new_uid,'chardata',num2str(NbSlice));
306%     [t,NbSlidingImages_uid]=add(t,new_uid,'element','NbSlidingImages');
307%     [t]=add(t,NbSlidingImages_uid,'chardata',num2str(nbaver));
308%     [t,LuminosityRank_uid]=add(t,new_uid,'element','RankBackground');
309%     [t]=add(t,LuminosityRank_uid,'chardata',num2str(rank));% luminosity rank almong the nbaver sliding images
310%     save(t,filexml)
311% end
312%copy the mask
313% if exist([filebase '_1mask_1'],'file')
314%     copyfile([filebase '_1mask_1'],[filebase_b '_1mask_1']);% copy the mask file
315% end
316
317%MAIN LOOP ON SLICES
318% for islice=1:NbSlice
319%% select the series of image indices
320indselect=1:step:nbfield;% select file indices of the slice
321for ifield=1:step-1
322    indselect=[indselect;indselect(end,:)+1];
323end
324
325%% read the first series of nbaver_ima images and sort by luminosity at each pixel
326for ifield = 1:nbaver_ima
327    ifile=indselect(ifield);
328    filename=filecell{1,ifile};
329    Aread=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
330    if ndims(Aread)==3;%color images
331        Aread=sum(double(Aread),3);% take the sum of color components
332    end
333    Ak(:,:,ifield)=Aread;
334end
335Asort=sort(Ak,3);%sort the luminosity of images at each point
336B=Asort(:,:,rank);%background image
337display( 'first background image will be substracted')
338nbfirst=(ceil(nbaver/2))*step;
339for ifield=1:nbfirst
340    Acor=double(Ak(:,:,ifield))-double(B);%substract background to the current image
341    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
342    ifile=indselect(ifield);
343    if ~isempty(j1_series{1})
344        j1=j1_series{1}(ifile);
345    end
346    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
347   
348    %write result file
349    if Param.ActionInput.CheckLevelTransform
350        C=levels(Acor);
351        imwrite(C,newname,'BitDepth',8); % save the new image
352    else
353        if isequal(FileInfo{1}.BitDepth,16)
354            C=uint16(Acor);
355            imwrite(C,newname,'BitDepth',16); % save the new image
356        else
357            C=uint8(Acor);
358            imwrite(C,newname,'BitDepth',8); % save the new image
359        end
360    end
361    display([newname ' written'])
362end
363
364%% repeat the operation on a sliding series of images
365display('sliding background image will be substracted')
366if nbfield_i > nbaver_ima
367    for ifield = step*ceil(nbaver/2)+1:step:nbfield_i-step*floor(nbaver/2)
368                update_waitbar(WaitbarHandle,ifield/nbfield_i)
369    if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
370        disp('program stopped by user')
371        return
372    end
373%         if isequal(stopstate,'queue')% enable STOP command
374            Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
375            %incorporate next burst in the current image series
376            for iburst=1:step
377                ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1);
378                filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile));
379                Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile));
380                if ndims(Aread)==3;%color images
381                    Aread=sum(double(Aread),3);% take the sum of color components
382                end
383                Ak(:,:,nbaver_ima-step+iburst)=Aread;
384            end
385            Asort=sort(Ak,3);%sort the new current image series by luminosity
386            B=Asort(:,:,rank);%current background image
387            for iburst=1:step
388                index=step*floor(nbaver/2)+iburst;
389                Acor=double(Ak(:,:,index))-double(B);
390                Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
391                ifile=indselect(ifield+iburst-1);
392                if ~isempty(j1_series{1})
393                    j1=j1_series{1}(ifile);
394                end
395                newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
396                %write result file
397                if Param.ActionInput.CheckLevelTransform
398                    C=levels(Acor);
399                    imwrite(C,newname,'BitDepth',8); % save the new image
400                else
401                    if isequal(FileInfo{1}.BitDepth,16)
402                        C=uint16(Acor);
403                        imwrite(C,newname,'BitDepth',16); % save the new image
404                    else
405                        C=uint8(Acor);
406                        imwrite(C,newname,'BitDepth',8); % save the new image
407                    end
408                end
409                display([newname ' written'])
410               
411            end
412%         else
413%             return
414%         end
415    end
416end
417
418%% substract the background from the last images
419display('last background image will be substracted')
420ifield=nbfield_i-(step*ceil(nbaver/2))+1:nbfield_i;
421for ifield=nbfield_i-(step*floor(nbaver/2))+1:nbfield_i
422    index=ifield-nbfield_i+step*(2*floor(nbaver/2)+1);
423    Acor=double(Ak(:,:,index))-double(B);
424    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
425    ifile=indselect(ifield);
426    if ~isempty(j1_series{1})
427        j1=j1_series{1}(ifile);
428    end
429    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
430   
431    %write result file
432    if Param.ActionInput.CheckLevelTransform
433        C=levels(Acor);
434        imwrite(C,newname,'BitDepth',8); % save the new image
435    else
436        if isequal(FileInfo{1}.BitDepth,16)
437            C=uint16(Acor);
438            imwrite(C,newname,'BitDepth',16); % save the new image
439        else
440            C=uint8(Acor);
441            imwrite(C,newname,'BitDepth',8); % save the new image
442        end
443    end
444    display([newname ' written'])
445end
446
447
448
449function C=levels(A)
450%whos A;
451B=double(A(:,:,1));
452windowsize=round(min(size(B,1),size(B,2))/20);
453windowsize=floor(windowsize/2)*2+1;
454ix=1/2-windowsize/2:-1/2+windowsize/2;%
455%del=np/3;
456%fct=exp(-(ix/del).^2);
457fct2=cos(ix/(windowsize-1)/2*pi/2);
458%Mfiltre=(ones(5,5)/5^2);
459%Mfiltre=fct2';
460Mfiltre=fct2'*fct2;
461Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
462
463C=filter2(Mfiltre,B);
464C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
465C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
466C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
467C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
468C=tanh(B./(2*C));
469[n,c]=hist(reshape(C,1,[]),100);
470% figure;plot(c,n);
471
472[m,i]=max(n);
473c_max=c(i);
474[dummy,index]=sort(abs(c-c(i)));
475n=n(index);
476c=c(index);
477i_select = find(cumsum(n)<0.95*sum(n));
478if isempty(i_select)
479    i_select = 1:length(c);
480end
481c_select=c(i_select);
482n_select=n(i_select);
483cmin=min(c_select);
484cmax=max(c_select);
485C=(C-cmin)/(cmax-cmin)*256;
486C=uint8(C);
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