source: trunk/src/series/ima_levels.m @ 977

Last change on this file since 977 was 977, checked in by g7moreau, 4 years ago
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1%'ima_levels': rescale the image intensity to reduce strong luminosity peaks (their blinking effects often perturbs PIV))
2% this function can be used as a template for applying a transform (here 'levels.m') to each image of a series
3%------------------------------------------------------------------------
4% function GUI_input=ima_levels(Param)
5%
6%------------------------------------------------------------------------
7%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
8%
9%OUTPUT
10% ParamOut: sets options in the GUI series.fig needed for the function
11%
12%INPUT:
13% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
14% In batch mode, Param is the name of the corresponding xml file containing the same information
15% when Param.Action.RUN=0 (as activated when the current Action is selected
16% in series), the function ouput paramOut set the activation of the needed GUI elements
17%
18% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
19% see the current structure Param)
20%    .InputTable: cell of input file names, (several lines for multiple input)
21%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
22%    .OutputSubDir: name of the subdirectory for data outputs
23%    .OutputDirExt: directory extension for data outputs
24%    .Action: .ActionName: name of the current activated function
25%             .ActionPath:   path of the current activated function
26%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
27%             .RUN =0 for GUI input, =1 for function activation
28%             .RunMode='local','background', 'cluster': type of function  use
29%             
30%    .IndexRange: set the file or frame indices on which the action must be performed
31%    .FieldTransform: .TransformName: name of the selected transform function
32%                     .TransformPath:   path  of the selected transform function
33%    .InputFields: sub structure describing the input fields withfields
34%              .FieldName: name(s) of the field
35%              .VelType: velocity type
36%              .FieldName_1: name of the second field in case of two input series
37%              .VelType_1: velocity type of the second field in case of two input series
38%              .Coord_y: name of y coordinate variable
39%              .Coord_x: name of x coordinate variable
40%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42
43%=======================================================================
44% Copyright 2008-2017, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
45%   http://www.legi.grenoble-inp.fr
46%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
47%
48%     This file is part of the toolbox UVMAT.
49%
50%     UVMAT is free software; you can redistribute it and/or modify
51%     it under the terms of the GNU General Public License as published
52%     by the Free Software Foundation; either version 2 of the license,
53%     or (at your option) any later version.
54%
55%     UVMAT is distributed in the hope that it will be useful,
56%     but WITHOUT ANY WARRANTY; without even the implied warranty of
57%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
58%     GNU General Public License (see LICENSE.txt) for more details.
59%=======================================================================
60
61function ParamOut=ima_levels (Param)
62
63%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
64if isstruct(Param) && isequal(Param.Action.RUN,0)
65    ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
66    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
67    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
68    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
69    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
70    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
71    ParamOut.FieldTransform = 'off';%can use a transform function
72    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
73    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
74    ParamOut.OutputDirExt='.lev';%set the output dir extension
75    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
76    %check the type of the existence and type of the first input file:
77    Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
78    if isfield(Param.IndexRange,'first_j')
79    Param.IndexRange.last_j=Param.IndexRange.first_j;
80    end
81    filecell=get_file_series(Param);
82    if ~exist(filecell{1,1},'file')
83        msgbox_uvmat('WARNING','the first input file does not exist')
84    else
85        FileInfo=get_file_info(filecell{1,1});
86        FileType=FileInfo.FileType;
87        if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images
88            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed'])
89        end
90    end
91return
92end
93
94%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
95%% read input parameters from an xml file if input is a file name (batch mode)
96ParamOut=[];
97RUNHandle=[];
98WaitbarHandle=[];
99checkrun=1;
100if ischar(Param)
101    Param=xml2struct(Param);% read Param as input file (batch case)
102    checkrun=0;
103else% interactive mode in Matlab
104    hseries=findobj(allchild(0),'Tag','series');
105    RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
106    WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
107end
108
109%% subdirectory for output files
110SubdirOut=[Param.OutputSubDir Param.OutputDirExt];
111
112%% root input file names and nomenclature type (cell arrays with one element)
113RootPath=Param.InputTable(:,1);
114RootFile=Param.InputTable(:,3);
115SubDir=Param.InputTable(:,2);
116NomType=Param.InputTable(:,4);
117FileExt=Param.InputTable(:,5);
118
119
120%% get the set of input file names (cell array filecell), and file indices
121[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
122% filecell{iview,fileindex}: cell array representing the list of file names
123%        iview: line in the table corresponding to a given file series
124%        fileindex: file index within  the file series,
125% 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
126% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
127nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
128nbfield_i=size(i1_series{1},2); %nb of fields for the i index
129nbfield=nbfield_j*nbfield_i; %total number of fields
130[FileInfo{1},VideoObject{1}]=get_file_info(filecell{1,1});% type of input file
131FileType{1}=FileInfo{1}.FileType;
132
133%% frame index for movie or multimage file input 
134if ~isempty(j1_series{1})
135    frame_index{1}=j1_series{1};
136else
137    frame_index{1}=i1_series{1};
138end
139
140%% calibration data and timing: read the ImaDoc files
141%not relevant for this function
142
143%% check coincidence in time for several input file series
144%not relevant for this function
145
146%% coordinate transform or other user defined transform
147%not relevant for this function
148
149%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
150 % EDIT FROM HERE
151
152 %% Extension and indexing nomenclature for output file
153 FileExtOut='.png'; % write result as .png images for image inputs
154 if strcmpi(NomType{1}(end),'a')
155     NomTypeOut=NomType{1};
156 else
157     NomTypeOut='_1_1';
158 end
159
160%% Set field names and velocity types
161%not relevant for this function
162
163%% Initiate output fields
164%not relevant for this function
165
166%% set processing parameters
167% not needed for this function
168
169%% coordinate transform or other user defined transform
170transform_fct='';%default fct handle
171if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
172        currentdir=pwd;
173        cd(Param.FieldTransform.TransformPath)
174        transform_fct=str2func(Param.FieldTransform.TransformName);
175        cd (currentdir)
176        if isfield(Param,'TransformInput')
177            for iview=1:NbView
178            XmlData{iview}.TransformInput=Param.TransformInput;
179            end
180        end       
181end
182
183%% main loop on images
184j1=[];%default
185for ifile=1:nbfield
186            update_waitbar(WaitbarHandle,ifile/nbfield)
187    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
188        disp('program stopped by user')
189        return
190    end
191    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
192        j1=j1_series{1}(ifile);
193    end
194    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
195    A=read_image(filename,FileType{1},VideoObject{1},frame_index{1}(ifile));
196    if ndims(A)==3;%color images
197        A=sum(double(Aread),3);% take the sum of color components
198    end
199    % operation on images
200    A=levels(A);
201    % write output file
202    filename_new=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
203    imwrite(A,filename_new)
204    display([filename_new ' written'])
205end
206%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
207
208
209function C=levels(A)
210%whos A;
211B=double(A(:,:,1));
212windowsize=round(min(size(B,1),size(B,2))/20);
213windowsize=floor(windowsize/2)*2+1;
214ix=[1/2-windowsize/2:-1/2+windowsize/2];%
215%del=np/3;
216%fct=exp(-(ix/del).^2);
217fct2=cos(ix/(windowsize-1)/2*pi/2);
218%Mfiltre=(ones(5,5)/5^2);
219%Mfiltre=fct2';
220Mfiltre=fct2'*fct2;
221Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
222
223C=filter2(Mfiltre,B);
224C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
225C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
226C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
227C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
228C=tanh(B./(2*C));
229[n,c]=hist(reshape(C,1,[]),100);
230% figure;plot(c,n);
231
232[m,i]=max(n);
233c_max=c(i);
234[dummy,index]=sort(abs(c-c(i)));
235n=n(index);
236c=c(index);
237i_select = find(cumsum(n)<0.95*sum(n));
238if isempty(i_select)
239    i_select = 1:length(c);
240end
241c_select=c(i_select);
242n_select=n(i_select);
243cmin=min(c_select);
244cmax=max(c_select);
245C=(C-cmin)/(cmax-cmin)*256;
246C=uint8(C);
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