source: trunk/src/series/ima_threshold.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
File size: 10.1 KB
Line 
1% function ParamOut=particle_tracking(Param)
2%
3% Method:
4   
5% Organization of image indices:
6   
7%INPUT:
8% num_i1: matrix of image indices i
9% num_j1: matrix of image indices j, must be the same size as num_i1
10% num_i2 and num_j2: not used for a function acting on images
11% Series: matlab structure containing parameters, as defined by the interface UVMAT/series
12%       Series.RootPath{1}: path to the image series
13%       Series.RootFile{1}: root file name
14%       Series.FileExt{1}: image file extension
15%       Series.NomType{1}: nomenclature type for file in
16%
17% Method:
18%       Series.NbSlice: %number of slices defined on the interface
19% global A rangx0 rangy0 minA maxA; % make current image A accessible in workspace
20% global hfig1 hfig2 scalar
21% global Abackg nbpart lum diam
22%%%%%%%%%%%%%%ᅵ
23%
24%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
25%
26%OUTPUT
27% ParamOut: sets 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% when Param.Action.RUN=0 (as activated when the current Action is selected
33% in series), the function ouput paramOut 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
36% see the current structure Param)
37%    .InputTable: cell of input file names, (several lines for multiple input)
38%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
39%    .OutputSubDir: name of the subdirectory for data outputs
40%    .OutputDirExt: directory extension for data outputs
41%    .Action: .ActionName: name of the current activated function
42%             .ActionPath:   path of the current activated function
43%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
44%             .RUN =0 for GUI input, =1 for function activation
45%             .RunMode='local','background', 'cluster': type of function  use
46%             
47%    .IndexRange: set the file or frame indices on which the action must be performed
48%    .FieldTransform: .TransformName: name of the selected transform function
49%                     .TransformPath:   path  of the selected transform function
50%    .InputFields: sub structure describing the input fields withfields
51%              .FieldName: name(s) of the field
52%              .VelType: velocity type
53%              .FieldName_1: name of the second field in case of two input series
54%              .VelType_1: velocity type of the second field in case of two input series
55%              .Coord_y: name of y coordinate variable
56%              .Coord_x: name of x coordinate variable
57%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
58%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
59
60%=======================================================================
61% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
62%   http://www.legi.grenoble-inp.fr
63%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
64%
65%     This file is part of the toolbox UVMAT.
66%
67%     UVMAT is free software; you can redistribute it and/or modify
68%     it under the terms of the GNU General Public License as published
69%     by the Free Software Foundation; either version 2 of the license,
70%     or (at your option) any later version.
71%
72%     UVMAT is distributed in the hope that it will be useful,
73%     but WITHOUT ANY WARRANTY; without even the implied warranty of
74%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
75%     GNU General Public License (see LICENSE.txt) for more details.
76%=======================================================================
77
78function ParamOut=particle_tracking(Param)
79
80%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
81if isstruct(Param) && isequal(Param.Action.RUN,0)
82    % general settings of the GUI:
83    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
84    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
85    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
86    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
87    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
88    ParamOut.FieldTransform = 'off';%can use a transform function
89    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
90    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
91    ParamOut.OutputDirExt='.patch';%set the output dir extension
92    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
93    filecell=get_file_series(Param);%check existence of the first input file
94    if ~exist(filecell{1,1},'file')
95        msgbox_uvmat('WARNING','the first input file does not exist')
96    end
97    % parameters specific to the function
98    prompt = {'threshold value'};
99    dlg_title = 'get threshold';
100    num_lines= 1;
101    def     = { '0'};
102    answer = inputdlg(prompt,dlg_title,num_lines,def);
103    if isempty(answer)
104        return
105    end
106    ParamOut.ActionInput.LumThreshold=str2double(answer{1});
107   
108    return
109end
110
111%%%%%%%%%%%%  STANDARD RUN PART  %%%%%%%%%%%%
112ParamOut=[];
113%% read input parameters from an xml file if input is a file name (batch mode)
114checkrun=1;
115if ischar(Param)
116    Param=xml2struct(Param);% read Param as input file (batch case)
117    checkrun=0;
118end
119hseries=findobj(allchild(0),'Tag','series');
120RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
121WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
122
123%% define the directory for result file
124OutputDir=[Param.OutputSubDir Param.OutputDirExt];
125
126%% root input file(s) name, type and index series
127RootPath=Param.InputTable{1,1};
128RootFile=Param.InputTable{1,3};
129SubDir=Param.InputTable{1,2};
130NomType=Param.InputTable{1,4};
131FileExt=Param.InputTable{1,5};
132[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
133%%%%%%%%%%%%
134% The cell array filecell is the list of input file names, while
135% filecell{iview,fileindex}:
136%        iview: line in the table corresponding to a given file series
137%        fileindex: file index within  the file series,
138% 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
139% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
140%%%%%%%%%%%%
141nbview=numel(i1_series);%number of input file series (lines in InputTable)
142nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
143nbfield_i=size(i1_series{1},2); %nb of fields for the i index
144nbfield=nbfield_j*nbfield_i; %total number of fields
145
146%% frame index for movie or multimage file input 
147if ~isempty(j1_series{1})
148    frame_index=j1_series{1};
149else
150    frame_index=i1_series{1};
151end
152
153%% check the input file type 
154[FileInfo,VideoObject]=get_file_info(filecell{1,1});
155FileType=FileInfo.FileType;
156ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};
157if isempty(find(strcmp(FileType,ImageTypeOptions)))
158    disp('input file not images')
159    return
160end
161
162%% calibration data and timing: read the ImaDoc files
163[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
164
165%%%%%%%%%%%%   SPECIFIC PART (to edit) %%%%%%%%%%%%
166%filter for particle center of mass(luminosity)
167
168Threshold=Param.ActionInput.LumThreshold;% luminosity threshold for particle detection, < 0 for black particles, >0 for white particles
169
170%%  fixed mask to avoid tube image
171Amask=imread('/fsnet/project/coriolis/2015/15MINI_MEDDY/0_REF_FILES/mask_patch.png');
172
173%% initiate output statistics data
174Data.ListVarName={'Time','z','Area',  'MajorAxisLength' , 'MinorAxisLength'};
175Data.VarDimName={'Time','z',{'Time','z'},{'Time','z'},{'Time','z'}};
176Data.Time = 1:nbfield_i; %default
177Data.z=1:nbfield_j;
178Data.Area=zeros(nbfield_i,nbfield_j);
179Data.MajorAxisLength=zeros(nbfield_i,nbfield_j);
180Data.MinorAxisLength=zeros(nbfield_i,nbfield_j);
181
182%%%%%% MAIN LOOP ON FRAMES %%%%%%
183for ifile=1:nbfield
184    if checkrun
185        update_waitbar(WaitbarHandle,ifile/nbfield)
186        if ~isempty(RUNHandle) &&ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
187            disp('program stopped by user')
188            return
189        end
190    end
191    i1=i1_series{1}(ifile);
192    j1=1;
193    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
194        j1=j1_series{1}(ifile);
195    end
196    filename=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1,[],j1);
197    A=read_image(filename,FileType,VideoObject,frame_index(ifile));% read the current frame
198   
199    A=(A>Threshold) & Amask>100;%transform to binary image format
200    try
201        STATS = regionprops(A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList');
202        Area=zeros(size(STATS));
203        for iobj=1:numel(STATS)
204            Area(iobj)=STATS(iobj).FilledArea;
205        end
206        [Data.Area(i1,j1), main_obj]=max(Area);
207        Data.MajorAxisLength(i1,j1)=STATS(main_obj).MajorAxisLength;
208        Data.MinorAxisLength(i1,j1)=STATS(main_obj).MinorAxisLength;
209        for iobj=1:numel(STATS)
210            if iobj~=main_obj
211                A(STATS(iobj).PixelIdxList)=0;
212            end
213        end
214
215    catch ME
216        disp('image toolbox not available, program stopped')
217%         return
218    end
219            filename_out=fullfile_uvmat(RootPath,OutputDir,RootFile,'.png',NomType,i1,[],j1);
220        imwrite(255*A,filename_out,'BitDepth',8)
221        disp([filename_out ' written'])
222end
223   
224%% record time series of stat
225[filename_nc,idetect]=name_generator(RootPath,OutputDir,RootFile,'.nc','_i1-i2',1,nbfield_i)
226errormsg=struct2nc(filename_nc,Data);
227
228if isempty(errormsg)
229    [filename_nc ' written']
230else
231    disp(errormsg)
232end
233
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