source: trunk/src/series/sub_background.m @ 592

Last change on this file since 592 was 592, checked in by sommeria, 8 years ago

commit the series fcts with the new form

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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    % 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)
15   
16% function GUI_config=sub_background(Param)
17%
18%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
19%
20% This function is used in four modes by the GUI series:
21%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
22%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
23%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
24%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
25%
26%OUTPUT
27% GUI_series_config=list of options in the GUI series.fig needed for the function
28%
29%INPUT:
30% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
31% In batch mode, Param is the name of the corresponding xml file containing the same information
32% In the absence of input (as activated when the current Action is selected
33% in series), the function ouput GUI_series_config set the activation of the needed GUI elements
34%
35% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
36%    .InputTable: cell of input file names, (several lines for multiple input)
37%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
38%    .OutputSubDir: name of the subdirectory for data outputs
39%    .OutputDirExt: extension for the directory for data outputs
40%    .Action: .ActionName: name of the current activated function
41%             .ActionPath:   path of the current activated function
42%    .IndexRange: set the file or frame indices on which the action must be performed
43%    .FieldTransform: .TransformName: name of the selected transform function
44%                     .TransformPath:   path  of the selected transform function
45%                     .TransformHandle: corresponding function handle
46%    .InputFields: sub structure describing the input fields withfields
47%              .FieldName: name of the field
48%              .VelType: velocity type
49%              .FieldName_1: name of the second field in case of two input series
50%              .VelType_1: velocity type of the second field in case of two input series
51%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
52%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
53
54   
55function ParamOut=sub_background (Param)
56
57%% input preparation mode (no RUN)
58if isstruct(Param) && isequal(Param.Action.RUN,0)
59    ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
60    ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
61    ParamOut.NbSlice='on'; ...%nbre of slices ('off' by default)
62    ParamOut.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
63    ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
64    ParamOut.FieldTransform = 'off';...%can use a transform function
65    ParamOut.ProjObject='off';...%can use projection object(option 'off'/'on',
66    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
67    ParamOut.OutputDirExt='.sback';%set the output dir extension
68   
69    %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
70   
71    %% root input file(s) and type
72%     RootPath=Param.InputTable(:,1);
73%     RootFile=Param.InputTable(:,3);
74%     SubDir=Param.InputTable(:,2);
75%     NomType=Param.InputTable(:,4);
76%     FileExt=Param.InputTable(:,5);
77    [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
78    %%%%%%%%%%%%
79    % The cell array filecell is the list of input file names, while
80    % filecell{iview,fileindex}:
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    %%%%%%%%%%%%
86    NbSlice=1;%default
87    if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
88        NbSlice=Param.IndexRange.NbSlice;
89    end
90    nbview=numel(i1_series);%number of input file series (lines in InputTable)
91    nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
92    nbfield_i=size(i1_series{1},2); %nb of fields for the i index
93    nbfield=nbfield_j*nbfield_i; %total number of fields
94    nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
95    nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
96   
97    %determine the file type on each line from the first input file
98
99   
100    %% calibration data and timing: read the ImaDoc files
101    %not relevant here
102   
103    %% check coincidence in time for several input file series
104    %not relevant here
105   
106    %% coordinate transform or other user defined transform
107    %not relevant here
108   
109    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
110    % EDIT FROM HERE
111   
112    %% check the validity of  input file types
113    ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
114    FileType=get_file_type(filecell{1,1});
115    CheckImage=~isempty(find(strcmp(FileType,ImageTypeOptions), 1));% =1 for images
116    if ~CheckImage
117        msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
118        return
119    end
120   
121    %% Set field names and velocity types
122    %not relevant here
123   
124    %% Initiate output fields
125    %not relevant here
126   
127    %%% SPECIFIC PART BEGINS HERE
128    NbSlice=1;
129    if isfield(Param.IndexRange,'NbSlice')
130        NbSlice=Param.IndexRange.NbSlice; %number of slices
131    end
132    %siz=size(i1_series);
133    nbaver_init=23;%approximate number of images used for the sliding background: to be adjusted later to include an integer number of bursts
134    j1=[];%default
135   
136    %% adjust the proposed number of images in the sliding average to include an integer number of bursts
137    if nbfield_i~=1
138        nbaver=floor(nbaver_init/nbfield_j); % number of bursts used for the sliding background,
139        if isequal(floor(nbaver/2),nbaver)
140            nbaver=nbaver+1;%put the number of burst to an odd number (so the middle burst is defined)
141        end
142        nbaver_init=nbaver*nbfield_j;%propose by default an integer number of bursts
143    end
144   
145    %% input of specific parameters
146    %if checkrun %get specific parameters interactively
147    if isequal(Param.Action.RUN,0)
148        prompt = {'volume scan mode (Yes/No)';'Number of images for the sliding background (MUST FIT IN COMPUTER MEMORY)';...
149            'the luminosity rank chosen to define the background (0.1=for dense particle seeding, 0.5 (median) for sparse particles'};
150        dlg_title = 'get (slice by slice) a sliding background and substract to each image';
151        num_lines= 3;
152        def     = { 'No';num2str(nbaver_init);'0.1'};
153        answer = inputdlg(prompt,dlg_title,num_lines,def);
154       
155        %check input consistency
156        if strcmp(answer{1},'No') && ~isequal(NbSlice,1)
157            check=msgbox_uvmat('INPUT_Y-N',['confirm the multi-level splitting into ' num2str(NbSlice) ' slices']);
158            if ~strcmp(check,'Yes')
159                return
160            end
161        end
162        if strcmp(answer{1},'Yes')
163            step=1;
164        else
165            step=nbfield_j;%case of bursts: the sliding background is shifted by the length of one burst
166        end
167        nbaver_ima=str2num(answer{2});%number of images for the sliding background
168        nbaver=ceil(nbaver_ima/step);%number of bursts for the sliding background
169        if isequal(floor(nbaver/2),nbaver)
170            nbaver=nbaver+1;%set the number of bursts to an odd number (so the middle burst is defined)
171        end
172        nbaver_ima=nbaver*step;
173    end
174    ParamOut.InputGUI.CheckVolume=strcmp(answer{1},'Yes');
175    ParamOut.InputGUI.SlidingSequenceLength=nbaver_ima;
176    ParamOut.InputGUI.BrightnessRankThreshold=str2num(answer{3});
177   
178    % apply the image rescaling function 'level' (avoid the blinking effects of bright particles)
179    answer=msgbox_uvmat('INPUT_Y-N','apply image rescaling function levels.m after sub_background');
180    ParamOut.InputGUI.CheckLevelTransform=strcmp(answer,'Yes');
181    return
182end
183%%%%%%%%%%%%%%%%%%%%%%  STOP HERE FOR PAMETER INPUT MODE  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
184
185%% read input parameters from an xml file if input is a file name (batch mode)
186checkrun=1;
187if ischar(Param)
188    Param=xml2struct(Param);% read Param as input file (batch case)
189    checkrun=0;
190end
191
192%% Input preparation
193nbaver_ima=Param.InputGUI.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.InputGUI.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.InputGUI.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.InputGUI.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
318for islice=1:NbSlice
319    %% select the series of image indices at the level islice
320    indselect=islice:NbSlice*step:nbfield;% select file indices of the slice
321    for ifield=1:step-1
322        indselect=[indselect;indselect(end,:)+1];
323    end
324   
325    %% read the first series of nbaver_ima images and sort by luminosity at each pixel
326    for 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;
334    end
335    Asort=sort(Ak,3);%sort the luminosity of images at each point
336    B=Asort(:,:,rank);%background image
337    display( 'first background image will be substracted')
338    nbfirst=(ceil(nbaver/2))*step;
339    for 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.InputGUI.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'])
362    end
363   
364    %% repeat the operation on a sliding series of images
365    display('sliding background image will be substracted')
366    if nbfield_i > nbaver_ima
367        for ifield = step*ceil(nbaver/2)+1:step:nbfield_i-step*floor(nbaver/2)
368            if checkrun
369                stopstate=get(Param.RUNHandle,'BusyAction');
370                update_waitbar(Param.WaitbarHandle,(ifield+(islice-1)*nbfield_i)/(nbfield_i*NbSlice))
371            else
372                stopstate='queue';
373            end
374            if isequal(stopstate,'queue')% enable STOP command
375                Ak(:,:,1:nbaver_ima-step)=Ak(:,:,1+step:nbaver_ima);% shift the current image series by one burst (step)
376                %incorporate next burst in the current image series
377                for iburst=1:step
378                    ifile=indselect(ifield+step*floor(nbaver/2)+iburst-1);
379                    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1_series{1}(ifile));
380                    Aread=read_image(filename,FileType{1},MovieObject{1},i1_series{1}(ifile));
381                    if ndims(Aread)==3;%color images
382                        Aread=sum(double(Aread),3);% take the sum of color components
383                    end
384                    Ak(:,:,nbaver_ima-step+iburst)=Aread;
385                end
386                Asort=sort(Ak,3);%sort the new current image series by luminosity
387                B=Asort(:,:,rank);%current background image
388                for iburst=1:step
389                    index=step*floor(nbaver/2)+iburst;
390                    Acor=double(Ak(:,:,index))-double(B);
391                    Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
392                    ifile=indselect(ifield+iburst-1);
393                    if ~isempty(j1_series{1})
394                        j1=j1_series{1}(ifile);
395                    end
396                    newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
397                    %write result file
398                    if Param.InputGUI.CheckLevelTransform
399                        C=levels(Acor);
400                        imwrite(C,newname,'BitDepth',8); % save the new image
401                    else
402                        if isequal(FileInfo{1}.BitDepth,16)
403                            C=uint16(Acor);
404                            imwrite(C,newname,'BitDepth',16); % save the new image
405                        else
406                            C=uint8(Acor);
407                            imwrite(C,newname,'BitDepth',8); % save the new image
408                        end
409                    end
410                    display([newname ' written'])
411                   
412                end
413            else
414                return
415            end
416        end
417    end
418   
419    %% substract the background from the last images
420    display('last background image will be substracted')
421    ifield=nbfield_i-(step*ceil(nbaver/2))+1:nbfield_i;
422    for ifield=nbfield_i-(step*floor(nbaver/2))+1:nbfield_i
423        index=ifield-nbfield_i+step*(2*floor(nbaver/2)+1);
424        Acor=double(Ak(:,:,index))-double(B);
425        Acor=(Acor>0).*Acor; % put to 0 the negative elements in Acor
426        ifile=indselect(ifield);
427        if ~isempty(j1_series{1})
428            j1=j1_series{1}(ifile);
429        end
430        newname=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
431       
432        %write result file
433        if Param.InputGUI.CheckLevelTransform
434            C=levels(Acor);
435            imwrite(C,newname,'BitDepth',8); % save the new image
436        else
437            if isequal(FileInfo{1}.BitDepth,16)
438                C=uint16(Acor);
439                imwrite(C,newname,'BitDepth',16); % save the new image
440            else
441                C=uint8(Acor);
442                imwrite(C,newname,'BitDepth',8); % save the new image
443            end
444        end
445        display([newname ' written'])
446    end
447end
448
449
450function C=levels(A)
451%whos A;
452B=double(A(:,:,1));
453windowsize=round(min(size(B,1),size(B,2))/20);
454windowsize=floor(windowsize/2)*2+1;
455ix=1/2-windowsize/2:-1/2+windowsize/2;%
456%del=np/3;
457%fct=exp(-(ix/del).^2);
458fct2=cos(ix/(windowsize-1)/2*pi/2);
459%Mfiltre=(ones(5,5)/5^2);
460%Mfiltre=fct2';
461Mfiltre=fct2'*fct2;
462Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
463
464C=filter2(Mfiltre,B);
465C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
466C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
467C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
468C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
469C=tanh(B./(2*C));
470[n,c]=hist(reshape(C,1,[]),100);
471% figure;plot(c,n);
472
473[m,i]=max(n);
474c_max=c(i);
475[dummy,index]=sort(abs(c-c(i)));
476n=n(index);
477c=c(index);
478i_select = find(cumsum(n)<0.95*sum(n));
479if isempty(i_select)
480    i_select = 1:length(c);
481end
482c_select=c(i_select);
483n_select=n(i_select);
484cmin=min(c_select);
485cmax=max(c_select);
486C=(C-cmin)/(cmax-cmin)*256;
487C=uint8(C);
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