source: trunk/src/series/particle_detect.m @ 1107

Last change on this file since 1107 was 1107, checked in by g7moreau, 2 years ago

Update Copyright to 2022

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[1088]1%'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates
2%------------------------------------------------------------------------
3% function ParamOut=merge_proj(Param)
4%------------------------------------------------------------------------
5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
6%
7%OUTPUT
8% ParamOut: sets options in the GUI series.fig needed for the function
9%
10%INPUT:
11% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
12% In batch mode, Param is the name of the corresponding xml file containing the same information
13% when Param.Action.RUN=0 (as activated when the current Action is selected
14% in series), the function ouput paramOut set the activation of the needed GUI elements
15%
16% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
17% see the current structure Param)
18%    .InputTable: cell of input file names, (several lines for multiple input)
19%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
20%    .OutputSubDir: name of the subdirectory for data outputs
21%    .OutputDirExt: directory extension for data outputs
22%    .Action: .ActionName: name of the current activated function
23%             .ActionPath:   path of the current activated function
24%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
25%             .RUN =0 for GUI input, =1 for function activation
26%             .RunMode='local','background', 'cluster': type of function  use
27%             
28%    .IndexRange: set the file or frame indices on which the action must be performed
29%    .FieldTransform: .TransformName: name of the selected transform function
30%                     .TransformPath:   path  of the selected transform function
31%    .InputFields: sub structure describing the input fields withfields
32%              .FieldName: name(s) of the field
33%              .VelType: velocity type
34%              .FieldName_1: name of the second field in case of two input series
35%              .VelType_1: velocity type of the second field in case of two input series
36%              .Coord_y: name of y coordinate variable
37%              .Coord_x: name of x coordinate variable
38%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
39%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
40
41%=======================================================================
[1107]42% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[1088]43%   http://www.legi.grenoble-inp.fr
44%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
45%
46%     This file is part of the toolbox UVMAT.
47%
48%     UVMAT is free software; you can redistribute it and/or modify
49%     it under the terms of the GNU General Public License as published
50%     by the Free Software Foundation; either version 2 of the license,
51%     or (at your option) any later version.
52%
53%     UVMAT is distributed in the hope that it will be useful,
54%     but WITHOUT ANY WARRANTY; without even the implied warranty of
55%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
56%     GNU General Public License (see LICENSE.txt) for more details.
57%=======================================================================
58
59function ParamOut=particle_detect(Param)
60
61%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
62if isstruct(Param) && isequal(Param.Action.RUN,0)
63    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
64    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
65    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
66    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
67    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
68    ParamOut.FieldTransform = 'off';%can use a transform function
69    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
70    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
71    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputDirExt='.detect';%set the output dir extension
73    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
74      %check the input files
75    ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
76    first_j=[];
77    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
78    PairString='';
79    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
80    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
81    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
82        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
83    if ~exist(FirstFileName,'file')
84        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
85    end
86   
87    prompt = {'threshold(th)';...
88        'particle size (sz)' };
89    dlg_title = 'get processing parameters';
90    num_lines= 2;
91    def     = {'4000';'3'};
92    answer = inputdlg(prompt,dlg_title,num_lines,def);
93    if isempty(answer)
94        return
95    end
96    %check input consistency
97    ParamOut.ActionInput.th=str2num(answer{1});
98    ParamOut.ActionInput.sz=str2num(answer{2});
99    return
100end
101
102%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
103ParamOut=[]; %default output
104RUNHandle=[];
105WaitbarHandle=[];
106%% read input parameters from an xml file if input is a file name (batch mode)
107checkrun=1;
108if ischar(Param)
109    Param=xml2struct(Param);% read Param as input file (batch case)
110    checkrun=0;
111else
112    hseries=findobj(allchild(0),'Tag','series');
113    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
114    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
115end
116
117%% define the directory for result file (with path=RootPath{1})
118OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
119
120if ~isfield(Param,'InputFields')
121    Param.InputFields.FieldName='';
122end
123
124%% root input file(s) name, type and index series
125RootPath=Param.InputTable{1,1};
126RootFile=Param.InputTable{1,3};
127SubDir=Param.InputTable{1,2};
128NomType=Param.InputTable{1,4};
129FileExt=Param.InputTable{1,5};
130
131hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
132% gives the series of input file names and indices set by the input parameters:
133%[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
134% filecell{iview,fileindex}:
135%        iview: line in the table corresponding to a given file series
136%        fileindex: file index with i and j reshaped as a 1D array
137% 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
138% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
139if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
140
141
142%% determine the file type on each line from the first input file
143
144
145%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
146% EDIT FROM HERE
147
148RootFileOut=RootFile;
149
150
151%% MAIN LOOP ON FIELDS
152%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
153% for i_slice=1:NbSlice
154%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
155%     NbFiles=0;
156%     nbmissing=0;
157
158%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
159tstart=tic; %used to record the computing time
160CheckOverwrite=1;%default
161if isfield(Param,'CheckOverwrite')
162    CheckOverwrite=Param.CheckOverwrite;
163end
164%%%%%%   INPUT %%%%%%
165th=Param.ActionInput.th
166sz=Param.ActionInput.sz
167% th=4000;%threshold on image intensity
168% sz=3; %size of particles
169
170NbImage=Param.IndexRange.last_i-Param.IndexRange.first_i+1;
171incr_i=Param.IndexRange.incr_i;
172NbBlock=floor(NbImage/incr_i);
173
174%% MAIN LOOP
175for index1=1:NbBlock
176    OutputFile=fullfile_uvmat(RootPath,OutputDir,RootFileOut,'.mat','_1-2',(index1-1)*incr_i+1,index1*incr_i)
177    if ~CheckOverwrite && exist(OutputFile,'file')
178        disp(['existing output file ' OutputFile ' already exists, skip to next field'])
179    end
180    for index=(index1-1)*incr_i+1:index1*incr_i
181        index
182       
183        %% reading input file(s)
184        ImgName=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,index)
185        Im=imread(ImgName);
186        [Ny,Nx]=size(Im);
187        %
188        %
189        %         frame = kframe+idfile*framesperfiles;
190        %     disp(frame);
191        %     ImgName = sprintf(join(['%s/%s_cam%d_' format],''),folderin, ManipName, CamNum, frame);
192        %     fprintf("%s \n",ImgName);
193        %Im = (cast(imread(ImgName),'like',Background) - Background).*mask;
194        %% normalizeimage
195        Im = double(Im);
196       
197        %     Imfiltered=filter2(transfert_coef,Im);
198        %
199        %     Imfiltered(:,1:windowsize)=Imfiltered(:,windowsize)*ones(1,windowsize);
200        %     Imfiltered(:,end-windowsize+1:end)=Imfiltered(:,end-windowsize+1)*ones(1,windowsize);
201        %     Imfiltered(1:windowsize,:)=ones(windowsize,1)*Imfiltered(windowsize,:);
202        %     Imfiltered(end-windowsize+1:end,:)=ones(windowsize,1)*Imfiltered(end-windowsize,:);
203        %     Im=Im./(2*Imfiltered);
204        %%
205       
206        out=pkfnd(Im,th,sz); % Provides intensity maxima positionsth,sz,Test,BackgroundType,format
207        npar = size(out,1);
208       
209        %% We keep only spots with a gaussian shape
210        cnt = 0;
211        x = [];
212        y = [];
213        for j = 1:npar
214            Nwidth = 1;
215            if (out(j,2)-Nwidth >0)&&(out(j,1)-Nwidth>0)&&(out(j,2)+Nwidth<Ny)&&(out(j,1)+Nwidth<Nx)
216                cnt = cnt+1;
217               
218                Ip = double(Im(out(j,2)-Nwidth:out(j,2)+Nwidth,out(j,1)-Nwidth:out(j,1)+Nwidth));
219               
220                x(end+1) = out(j, 1) + 0.5*log(Ip(2,3)/Ip(2,1))/(log((Ip(2,2)*Ip(2,2))/(Ip(2,1)*Ip(2,3))));
221                y(end+1) = out(j, 2) + 0.5*log(Ip(3,2)/Ip(1,2))/(log((Ip(2,2)*Ip(2,2))/(Ip(1,2)*Ip(3,2))));
222            end
223        end
224       
225        CC(index).X=x;
226        CC(index).Y=y;
227    end
228   
229    %% Centers saving into a .mat file
230    if Param.IndexRange.last_i>1
231        savefile=OutputFile;
232        save(savefile,"CC",'-v7.3')
233        m = matfile(savefile,'Writable',true);
234        m.nframes = incr_i;
235    else
236        figure("NumberTitle","Off","Name",['RAW picture,' SubDir])
237        imshow(imread(ImgName),[0,5000])
238        colormap gray
239        %     figure("NumberTitle","Off","Name",sprintf("%s, cam %d",BackgroundType,CamNum))
240        %     imshow(BackgroundMin,[0,5000])
241        %     colormap gray
242        %     figure("NumberTitle","Off","Name",sprintf("RAW picture - Background, cam %d, frame %d",CamNum,kframe))
243        %     imshow(Im,[0,th])
244        %     colormap gray
245        colorbar
246       
247        %% Tracé de l'histogramme des intensités pour définir le seuil
248        fig = figure('NumberTitle','Off','Name','Intensity histogram');
249        histogram(Im,1000)
250        xlabel("Intensity")
251        ylabel("Number")
252        set(gca, 'XScale', 'log')
253        set(gca, 'YScale', 'log')
254       
255        Nx = size(Im,2);
256        Ny = size(Im,1);
257       
258        out=pkfnd(Im,th,sz); % Provides intensity maxima positions
259        npar = size(out,1);
260       
261        %% We keep only spots with a gaussian shape
262        cnt = 0;
263        x = [];
264        y = [];
265        for j = 1:npar
266            Nwidth = 1;
267            if (out(j,2)-Nwidth >0)&&(out(j,1)-Nwidth>0)&&(out(j,2)+Nwidth<Ny)&&(out(j,1)+Nwidth<Nx)
268                cnt = cnt+1;
269               
270                Ip = double(Im(out(j,2)-Nwidth:out(j,2)+Nwidth,out(j,1)-Nwidth:out(j,1)+Nwidth));
271               
272                x(end+1) = out(j, 1) + 0.5*log(Ip(2,3)/Ip(2,1))/(log((Ip(2,2)*Ip(2,2))/(Ip(2,1)*Ip(2,3))));
273                y(end+1) = out(j, 2) + 0.5*log(Ip(3,2)/Ip(1,2))/(log((Ip(2,2)*Ip(2,2))/(Ip(1,2)*Ip(3,2))));
274            end
275        end
276        CC(1).X=x;
277        CC(1).Y=y;
278       
279        fprintf("%d treated \n",1)
280       
281        %% Let's plot picture and detected points on a graph !!! Be careful the vertical axis is reversed compared to reality !!!
282        figure('NumberTitle','Off','Name',sprintf("frame %d, %d detected points",1,numel(x)))
283        imshow(Im,[0,th])
284        colormap gray
285       
286        hold on
287        plot(flip(x),flip(y),'r+')
288    end
289end
290
291%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
292    function CC = CenterFinding2D(session,ManipName,CamNum,firstFrame,nframes,th,sz,Test,BackgroundType,format,withmask)
293%%% Detect particles position in picture and provides their positions in
294%%% px.
295%--------------------------------------------------------------------------------
296%%% Parameters :
297%%%     session                    : Path to the achitecture root (2 fields: session.input_path
298% and session.output_path)
299%%%     ManipName                  : Name of the folder experiment
300%%%     NumCam                     : number of the camera studied
301%%%     nframes                    : total number of pictures
302%%%     th                         : threshold
303%%%     sz                         : typical size of the particles
304%%%     Test                       : true-> test mode, false-> classic mode (optional)
305%%%     BackgroundType (optional)  : determine which background is substracted to pictures. By defaut is equal to BackgroundMean,
306%%%     format (optional)          : picture names. By defaut it is '%05d.tif'.
307%%%     The beginning of picture names has to be %ManipName_cam%CamNum_%format
308%--------------------------------------------------------------------------------
309%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
310close all
311
312framesperfiles = 1000;
313
314%% Test if Test exist or not
315if ~exist('Test','var')
316    Test=false;
317end
318
319%% Test if BackgroundType exist or not
320if ~exist('BackgroundType','var')
321    BackgroundType="BackgroundMean";
322end
323
324% By defaut format='%05d.tif'
325if ~exist('format','var')
326    format='%05d.tif';
327end
328
329if ~exist('withmask','var')
330    withmask=false;
331end
332
333
334
335%% Definition of folders
336fprintf(ManipName);
337folderin = sprintf("%sDATA/%s/cam%d",session.input_path,ManipName,CamNum)
338folderout = sprintf("%sProcessed_DATA/%s",session.output_path,ManipName)
339BackgroundFile = sprintf("%s/Background_cam%d.mat",folderout,CamNum);
340
341%% Find centers
342if exist(folderout,'dir')==0
343    mkdir(char(folderout));
344end
345
346% if exist(strcat(folderout,'/Parallel/Matching'),'dir')==0
347%     mkdir(char(strcat(folderout,'/Parallel/Matching')));
348% end
349
350load(BackgroundFile,'BackgroundMin','BackgroundMax','BackgroundMean')
351%% Choice of background type
352if BackgroundType=="BackgroundMean"
353    Background=BackgroundMean;
354elseif BackgroundType=="BackgroundMax"
355    Background=BackgroundMax;
356elseif BackgroundType=="BackgroundMin"
357    Background=BackgroundMin;
358end
359Nx = size(Background,2);
360Ny = size(Background,1);
361
362if withmask
363    ImgName = sprintf(join(['%s/%s_cam%d_' format],''),folderin, ManipName, CamNum, 1);
364    Im = imread(ImgName);
365    imshow(Im,[0,10000])
366    BW = roipoly;
367    mask = cast(BW,'like',Background);
368else
369    mask = cast(ones(Ny,Nx),'like',Background);
370end
371
372%% param for normailze image
373windowsize=round(min(Ny,Nx)/20);
374transfert_coef = ones(windowsize)/windowsize^2;
375%%
376
377close all
378if ~Test
379    idfirstfile = fix(firstFrame/framesperfiles);
380    idlastfile = fix((nframes-1)/framesperfiles);
381    for idfile = idfirstfile:idlastfile
382        firstFrame = rem(firstFrame,framesperfiles);
383        lastframe = min(framesperfiles,nframes-idfile*framesperfiles);
384        for kframe=firstFrame:lastframe
385            frame = kframe+idfile*framesperfiles;
386            disp(frame);
387            ImgName = sprintf(join(['%s/%s_cam%d_' format],''),folderin, ManipName, CamNum, frame);
388            fprintf("%s \n",ImgName);
389            Im = (cast(imread(ImgName),'like',Background) - Background).*mask;
390            %% normalizeimage
391            Im = double(Im);
392
393            Imfiltered=filter2(transfert_coef,Im);
394
395            Imfiltered(:,1:windowsize)=Imfiltered(:,windowsize)*ones(1,windowsize);
396            Imfiltered(:,end-windowsize+1:end)=Imfiltered(:,end-windowsize+1)*ones(1,windowsize);
397            Imfiltered(1:windowsize,:)=ones(windowsize,1)*Imfiltered(windowsize,:);
398            Imfiltered(end-windowsize+1:end,:)=ones(windowsize,1)*Imfiltered(end-windowsize,:);
399            Im=Im./(2*Imfiltered);
400            %%
401           
402           
403            out=pkfnd(Im,th,sz); % Provides intensity maxima positions
404            npar = size(out,1);
405
406            %% We keep only spots with a gaussian shape
407            cnt = 0;
408            x = [];
409            y = [];
410            for j = 1:npar
411                Nwidth = 1;
412                if (out(j,2)-Nwidth >0)&&(out(j,1)-Nwidth>0)&&(out(j,2)+Nwidth<Ny)&&(out(j,1)+Nwidth<Nx)
413                    cnt = cnt+1;
414
415                    Ip = double(Im(out(j,2)-Nwidth:out(j,2)+Nwidth,out(j,1)-Nwidth:out(j,1)+Nwidth));
416
417                    x(end+1) = out(j, 1) + 0.5*log(Ip(2,3)/Ip(2,1))/(log((Ip(2,2)*Ip(2,2))/(Ip(2,1)*Ip(2,3))));
418                    y(end+1) = out(j, 2) + 0.5*log(Ip(3,2)/Ip(1,2))/(log((Ip(2,2)*Ip(2,2))/(Ip(1,2)*Ip(3,2))));
419                end
420            end
421
422            CC(kframe).X=x;
423            CC(kframe).Y=y;
424        end
425        %% Centers saving into a .mat file
426        firstFramefile = framesperfiles*idfile+1;
427        lastFramefile = framesperfiles*(idfile+1);
428        savefile = sprintf(['%s/Parallel/Matching/centers_cam%d_',format(1:end-4),'-',format(1:end-4),'.mat'],folderout,CamNum,firstFramefile,lastFramefile);
429        if exist(savefile,'file')
430            m = matfile(savefile,'Writable',true);
431            m.CC(1,firstFrame:lastframe) = CC(firstFrame:lastframe);
432            m.nframes = framesperfiles;
433        else
434            save(savefile,"CC","nframes",'-v7.3')
435            m = matfile(savefile,'Writable',true);
436            m.nframes = framesperfiles;
437        end
438        firstFrame = 1;
439    end
440else
441    kframe=1
442    ImgName = sprintf(join(['%s/%s_cam%d_' format],''),folderin, ManipName, CamNum, kframe);
443    fprintf("%s \n",ImgName);
444    Im = (cast(imread(ImgName),'like',Background) - Background).*mask;
445    %% normalizeimage
446    Im = double(Im);
447
448    Imfiltered=filter2(transfert_coef,Im);
449
450    Imfiltered(:,1:windowsize)=Imfiltered(:,windowsize)*ones(1,windowsize);
451    Imfiltered(:,end-windowsize+1:end)=Imfiltered(:,end-windowsize+1)*ones(1,windowsize);
452    Imfiltered(1:windowsize,:)=ones(windowsize,1)*Imfiltered(windowsize,:);
453    Imfiltered(end-windowsize+1:end,:)=ones(windowsize,1)*Imfiltered(end-windowsize,:);
454    Im=Im./(2*Imfiltered);
455    %%
456    figure("NumberTitle","Off","Name",sprintf("RAW picture, cam %d, frame %d",CamNum,kframe))
457    imshow(imread(ImgName),[0,5000])
458    colormap gray
459    figure("NumberTitle","Off","Name",sprintf("%s, cam %d",BackgroundType,CamNum))
460    imshow(BackgroundMin,[0,5000])
461    colormap gray
462    figure("NumberTitle","Off","Name",sprintf("RAW picture - Background, cam %d, frame %d",CamNum,kframe))
463    imshow(Im,[0,th])
464    colormap gray
465    colorbar
466   
467%     if exist('Erosion','var')
468%         se = strel('disk',1);
469%         Imerode = imerode(Im,se);
470%         Imdilate = imdilate(Imerode,se);
471%         figure()
472%         imagesc(Imdilate)
473%         axis image
474%         colormap gray
475%
476%         Image = Im;
477%         Im = Imdilate;
478%     end
479
480    %% Tracé de l'histogramme des intensités pour définir le seuil
481    fig = figure('NumberTitle','Off','Name','Intensity histogram');
482    histogram(Im,1000)
483    xlabel("Intensity")
484    ylabel("Number")
485    set(gca, 'XScale', 'log')
486    set(gca, 'YScale', 'log')
487   
488    Nx = size(Im,2);
489    Ny = size(Im,1);
490
491    out=pkfnd(Im,th,sz); % Provides intensity maxima positions
492    npar = size(out,1);
493       
494    %% We keep only spots with a gaussian shape
495    cnt = 0;
496    x = [];
497    y = [];
498    for j = 1:npar
499        Nwidth = 1;
500        if (out(j,2)-Nwidth >0)&&(out(j,1)-Nwidth>0)&&(out(j,2)+Nwidth<Ny)&&(out(j,1)+Nwidth<Nx)
501            cnt = cnt+1;
502
503            Ip = double(Im(out(j,2)-Nwidth:out(j,2)+Nwidth,out(j,1)-Nwidth:out(j,1)+Nwidth));
504
505            x(end+1) = out(j, 1) + 0.5*log(Ip(2,3)/Ip(2,1))/(log((Ip(2,2)*Ip(2,2))/(Ip(2,1)*Ip(2,3))));
506            y(end+1) = out(j, 2) + 0.5*log(Ip(3,2)/Ip(1,2))/(log((Ip(2,2)*Ip(2,2))/(Ip(1,2)*Ip(3,2))));
507        end
508    end
509    CC(kframe).X=x;
510    CC(kframe).Y=y;
511
512    fprintf("%d treated \n",kframe)
513
514    %% Let's plot picture and detected points on a graph !!! Be careful the vertical axis is reversed compared to reality !!!
515    figure('NumberTitle','Off','Name',sprintf("frame %d, %d detected points",kframe,numel(x)))
516    imshow(Im,[0,th])
517    colormap gray
518   
519    hold on
520    plot(flip(x),flip(y),'r+')
521end
522
523%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
524function out=pkfnd(im,th,sz)
525% finds local maxima in an image to pixel level accuracy. 
526%  this provides a rough guess of particle
527%  centers to be used by cntrd.m.  Inspired by the lmx subroutine of Grier
528%  and Crocker's feature.pro
529%--------------------------------------------------------------------------------
530% INPUTS:
531%   im  : image to process, particle should be bright spots on dark background with little noise
532%       ofen an bandpass filtered brightfield image (fbps.m, fflt.m or bpass.m) or a nice
533%       fluorescent image
534%   th  : the minimum brightness of a pixel that might be local maxima.
535%       (NOTE: Make it big and the code runs faster
536%       but you might miss some particles.  Make it small and you'll get
537%       everything and it'll be slow.)
538%   sz  :  if your data's noisy, (e.g. a single particle has multiple local
539%       maxima), then set this optional keyword to a value slightly larger than the diameter of your blob.  if
540%       multiple peaks are found withing a radius of sz/2 then the code will keep
541%       only the brightest.  Also gets rid of all peaks within sz of boundary
542% OUTPUT:  a N x 2 array containing, [row,column] coordinates of local maxima
543%          out(:,1) are the x-coordinates of the maxima
544%          out(:,2) are the y-coordinates of the maxima
545%--------------------------------------------------------------------------------
546%CREATED: Eric R. Dufresne, Yale University, Feb 4 2005
547%MODIFIED: ERD, 5/2005, got rid of ind2rc.m to reduce overhead on tip by
548%  Dan Blair;  added sz keyword
549% ERD, 6/2005: modified to work with one and zero peaks, removed automatic
550%  normalization of image
551% ERD, 6/2005: due to popular demand, altered output to give x and y
552%  instead of row and column
553% ERD, 8/24/2005: pkfnd now exits politely if there's nothing above
554%  threshold instead of crashing rudely
555% ERD, 6/14/2006: now exits politely if no maxima found
556% ERD, 10/5/2006:  fixed bug that threw away particles with maxima
557%  consisting of more than two adjacent points
558
559
560
561%find all the pixels above threshold
562%im=im./max(max(im));
563[nr,nc] = size(im);
564[i,j,ind]=find(im > th);
565n=length(ind);
566
567if n==0
568    out=[];[i,j,ind]=find(im > th);
569    fprintf('nothing above threshold');
570    return;
571end
572mx=[];
573%convert index from find to row and column
574rc=[i,j]; % j corresponds to x axis and i to y axis
575% rc=[j,i]; % j corresponds to x axis and i to y axis
576for ii=1:n
577    r=rc(ii,1);
578    c=rc(ii,2);
579    %check each pixel above threshold to see if it's brighter than it's neighbors
580    %  THERE'S GOT TO BE A FASTER WAY OF DOING THIS.  I'M CHECKING SOME MULTIPLE TIMES,
581    %  BUT THIS DOESN'T SEEM THAT SLOW COMPARED TO THE OTHER ROUTINES, ANYWAY.
582    if r>1 && r<nr && c>1 && c<nc
583        if im(r,c)>=im(r-1,c-1) && im(r,c)>=im(r,c-1) && im(r,c)>=im(r+1,c-1) && ...
584         im(r,c)>=im(r-1,c)  && im(r,c)>=im(r+1,c) &&   ...
585         im(r,c)>=im(r-1,c+1) && im(r,c)>=im(r,c+1) && im(r,c)>=im(r+1,c+1)
586         mx=[mx,[r,c]'];  %#ok<AGROW>
587         %tst(ind(i))=im(ind(i));
588        end
589    end
590end
591%out=tst;
592mx=mx';
593
594[npks,crap]=size(mx);
595
596%if size is specified, then get ride of pks within size of boundary
597if nargin==3 && npks>0
598   %throw out all pks within sz of boundary;
599    ind=find(mx(:,1)>sz & mx(:,1)<(nr-sz) & mx(:,2)>sz & mx(:,2)<(nc-sz));
600    mx=mx(ind,:);
601end
602
603%prevent from finding peaks within size of each other
604[npks,crap]=size(mx);
605if npks > 1
606    %CREATE AN IMAGE WITH ONLY PEAKS
607    nmx=npks;
608    tmp=0.*im;
609    for i=1:nmx
610        tmp(mx(i,1),mx(i,2))=im(mx(i,1),mx(i,2));
611    end
612    %LOOK IN NEIGHBORHOOD AROUND EACH PEAK, PICK THE BRIGHTEST
613    for i=1:nmx
614        roi=tmp( (mx(i,1)-floor(sz/2)):(mx(i,1)+(floor(sz/2)+1)),(mx(i,2)-floor(sz/2)):(mx(i,2)+(floor(sz/2)+1))) ;
615        [mv,indi]=max(roi);
616        [mv,indj]=max(mv);
617        tmp( (mx(i,1)-floor(sz/2)):(mx(i,1)+(floor(sz/2)+1)),(mx(i,2)-floor(sz/2)):(mx(i,2)+(floor(sz/2)+1)))=0;
618        tmp(mx(i,1)-floor(sz/2)+indi(indj)-1,mx(i,2)-floor(sz/2)+indj-1)=mv;
619    end
620    ind=find(tmp>0);
621    mx=[mod(ind,nr),floor(ind/nr)+1];
622end
623
624if size(mx)==[0,0]
625    out=[];
626else
627    out(:,2)=mx(:,1);
628    out(:,1)=mx(:,2);
629end
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