source: trunk/src/series/ima_levels.m @ 590

Last change on this file since 590 was 590, checked in by sommeria, 8 years ago

ima_levels: bug correction
check_peaklock: adapated to new conventions, not finished

File size: 9.3 KB
Line 
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%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
8% This function is used in four modes by the GUI series:
9%           1) config GUI: with no input argument, the function determine the suitable GUI configuration
10%           2) interactive input: the function is used to interactively introduce input parameters, and then stops
11%           3) RUN: the function itself runs, when an appropriate input  structure Param has been introduced.
12%           4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input.
13%
14%OUTPUT
15% GUI_input=list of options in the GUI series.fig needed for the function
16%
17%INPUT:
18% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
19% In batch mode, Param is the name of the corresponding xml file containing the same information
20% In the absence of input (as activated when the current Action is selected
21% in series), the function ouput GUI_input set the activation of the needed GUI elements
22%
23% Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param)
24%    .InputTable: cell of input file names, (several lines for multiple input)
25%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
26%    .OutputSubDir: name of the subdirectory for data outputs
27%    .OutputDir: directory for data outputs, including path
28%    .Action: .ActionName: name of the current activated function
29%             .ActionPath:   path of the current activated function
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%                     .TransformHandle: corresponding function handle
34%    .InputFields: sub structure describing the input fields withfields
35%              .FieldName: name of the field
36%              .VelType: velocity type
37%              .FieldName_1: name of the second field in case of two input series
38%              .VelType_1: velocity type of the second field in case of two input series
39%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
40%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
41 
42function GUI_input=ima_levels (Param)
43
44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
45if ~exist('Param','var') % case with no input parameter
46    GUI_input={'NbViewMax';1;...% max nbre of input file series (default='' , no limitation)
47        'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default)
48        'NbSlice';'off'; ...%nbre of slices ('off' by default)
49        'VelType';'off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
50        'FieldName';'off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
51        'FieldTransform'; 'off';...%can use a transform function
52        'ProjObject';'off';...%can use projection object(option 'off'/'on',
53        'Mask';'off';...%can use mask option   (option 'off'/'on', 'off' by default)
54        'OutputDirExt';'.lev';...%set the output dir extension
55               ''};
56        return
57end
58
59%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
60%% select different modes,  RUN, parameter input, BATCH
61% BATCH  case: read the xml file for batch case
62if ischar(Param)
63    if strcmp(Param,'input?')
64        checkrun=1;% will inly search input parameters (preparation of BATCH mode)
65    else
66        Param=xml2struct(Param);
67        checkrun=0;
68    end
69% RUN case: parameters introduced as the input structure Param
70else
71    hseries=guidata(Param.hseries);%handles of the GUI series
72    checkrun=2; % indicate the RUN option is used
73end
74
75%% root input file(s) and type
76RootPath=Param.InputTable(:,1);
77RootFile=Param.InputTable(:,3);
78SubDir=Param.InputTable(:,2);
79NomType=Param.InputTable(:,4);
80FileExt=Param.InputTable(:,5);
81OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
82
83% get the set of input file names (cell array filecell), and the lists of
84% input file or frame indices i1_series,i2_series,j1_series,j2_series
85[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
86% filecell{iview,fileindex}: cell array representing the list of file names
87%        iview: line in the table corresponding to a given file series
88%        fileindex: file index within  the file series,
89% 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
90% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
91% set of frame indices used for movie or multimage input
92% numbers of slices and file indices
93
94NbSlice=1;%default
95if isfield(Param.IndexRange,'NbSlice')
96    NbSlice=Param.IndexRange.NbSlice;
97end
98nbview=numel(i1_series);%number of input file series (lines in InputTable)
99nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
100nbfield_i=size(i1_series{1},2); %nb of fields for the i index
101nbfield=nbfield_j*nbfield_i; %total number of fields
102nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
103nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
104
105%determine the file type on each line from the first input file
106ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
107
108[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
109CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
110if ~isempty(j1_series{1})
111    frame_index{1}=j1_series{1};
112else
113    frame_index{1}=i1_series{1};
114end
115
116%% calibration data and timing: read the ImaDoc files
117%not relevant for this function
118
119%% check coincidence in time for several input file series
120%not relevant for this function
121
122%% coordinate transform or other user defined transform
123%not relevant for this function
124
125%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
126 % EDIT FROM HERE
127
128 %% check the validity of  input file types
129if CheckImage{1}
130    FileExtOut='.png'; % write result as .png images for image inputs
131    if strcmp(lower(NomType{1}(end)),'a')
132        NomTypeOut=NomType{1};
133    else
134        NomTypeOut='_1_1';
135    end
136else
137    msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
138    return
139end
140
141%% Set field names and velocity types
142%not relevant for this function
143
144%% Initiate output fields
145%not relevant for this function
146
147%% set processing parameters
148% not needed for this function
149
150%% update the xml file
151% not needed for this function
152
153%% main loop on images
154j1=[];%default
155for ifile=1:nbfield
156    if checkrun
157        update_waitbar(hseries.Waitbar,ifile/nbfield)
158        stopstate=get(hseries.RUN,'BusyAction');
159    else
160        stopstate='queue';
161    end
162    if isequal(stopstate,'queue') % enable STOP command
163        if ~isempty(j1_series)&&~isequal(j1_series,{[]})
164            j1=j1_series{1}(ifile);
165        end
166        filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
167        A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
168        if ndims(A)==3;%color images
169            A=sum(double(Aread),3);% take the sum of color components
170        end
171        % operation on images
172        A=levels(A);
173        filename_new=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
174        imwrite(A,filename_new)
175        display([filename_new ' written'])
176    end
177end
178%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
179
180
181function C=levels(A)
182%whos A;
183B=double(A(:,:,1));
184windowsize=round(min(size(B,1),size(B,2))/20);
185windowsize=floor(windowsize/2)*2+1;
186ix=[1/2-windowsize/2:-1/2+windowsize/2];%
187%del=np/3;
188%fct=exp(-(ix/del).^2);
189fct2=cos(ix/(windowsize-1)/2*pi/2);
190%Mfiltre=(ones(5,5)/5^2);
191%Mfiltre=fct2';
192Mfiltre=fct2'*fct2;
193Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
194
195C=filter2(Mfiltre,B);
196C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
197C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
198C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
199C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
200C=tanh(B./(2*C));
201[n,c]=hist(reshape(C,1,[]),100);
202% figure;plot(c,n);
203
204[m,i]=max(n);
205c_max=c(i);
206[dummy,index]=sort(abs(c-c(i)));
207n=n(index);
208c=c(index);
209i_select = find(cumsum(n)<0.95*sum(n));
210if isempty(i_select)
211    i_select = 1:length(c);
212end
213c_select=c(i_select);
214n_select=n(i_select);
215cmin=min(c_select);
216cmax=max(c_select);
217C=(C-cmin)/(cmax-cmin)*256;
218C=uint8(C);
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