source: trunk/src/series/ima_levels.m @ 606

Last change on this file since 606 was 606, checked in by sommeria, 8 years ago

bug on compilation solved (still to test with transform_field fct). faster browser inrtroduced. Various bug corrections

File size: 9.1 KB
RevLine 
[454]1%'ima_levels': rescale the image intensity to reduce strong luminosity peaks (their blinking effects often perturbs PIV))
[457]2% this function can be used as a template for applying a transform (here 'levels.m') to each image of a series
[171]3%------------------------------------------------------------------------
[454]4% function GUI_input=ima_levels(Param)
[171]5%
[604]6%------------------------------------------------------------------------
[454]7%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
[457]8%
[171]9%OUTPUT
[604]10% ParamOut: sets options in the GUI series.fig needed for the function
[171]11%
12%INPUT:
[454]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
[604]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
[454]17%
[604]18% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
19% see the current structure Param)
[454]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
[604]23%    .OutputDirExt: directory extension for data outputs
[454]24%    .Action: .ActionName: name of the current activated function
25%             .ActionPath:   path of the current activated function
[604]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%             
[454]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
[604]34%              .FieldName: name(s) of the field
[454]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
[604]38%              .Coord_y: name of y coordinate variable
39%              .Coord_x: name of x coordinate variable
[454]40%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42 
[592]43function ParamOut=ima_levels (Param)
[454]44
[606]45%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
[592]46if isstruct(Param) && isequal(Param.Action.RUN,0)
[604]47    ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
[592]48    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
49    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
50    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
51    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
52    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
53    ParamOut.FieldTransform = 'off';%can use a transform function
54    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
55    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
56    ParamOut.OutputDirExt='.lev';%set the output dir extension
[604]57    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
58    %check the type of the existence and type of the first input file:
59    Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
[606]60    if isfield(Param.IndexRange,'first_j')
[604]61    Param.IndexRange.last_j=Param.IndexRange.first_j;
[606]62    end
[604]63    filecell=get_file_series(Param);
64    if ~exist(filecell{1,1},'file')
65        msgbox_uvmat('WARNING','the first input file does not exist')
66    else
67        FileType=get_file_type(filecell{1,1});
68        if isempty(find(strcmp(FileType,{'image','multimage','mmreader','video'})));% =1 for images
69            msgbox_uvmat('ERROR',['bad input file type for ' mfilename ': an image is needed'])
70        end
71    end
[592]72return
[64]73end
74
[457]75%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
[592]76%% read input parameters from an xml file if input is a file name (batch mode)
[606]77ParamOut=[]
[592]78checkrun=1;
[457]79if ischar(Param)
[592]80    Param=xml2struct(Param);% read Param as input file (batch case)
81    checkrun=0;
[442]82end
[64]83
[604]84%% root input file names and nomenclature type (cell arrays with one element)
[454]85RootPath=Param.InputTable(:,1);
86RootFile=Param.InputTable(:,3);
87SubDir=Param.InputTable(:,2);
88NomType=Param.InputTable(:,4);
89FileExt=Param.InputTable(:,5);
90
[604]91%% subdirectory for output files
92SubdirOut=[Param.OutputSubDir Param.OutputDirExt];
93
94%% get the set of input file names (cell array filecell), and file indices
[457]95[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
96% filecell{iview,fileindex}: cell array representing the list of file names
97%        iview: line in the table corresponding to a given file series
98%        fileindex: file index within  the file series,
99% 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
100% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
[604]101nbfield_j=size(j1_series{1},1); %nb of fields for the j index (bursts or volume slices)
[457]102nbfield_i=size(i1_series{1},2); %nb of fields for the i index
103nbfield=nbfield_j*nbfield_i; %total number of fields
[604]104[FileType{1},FileInfo{1},VideoObject{1}]=get_file_type(filecell{1,1});% type of input file
[442]105
[604]106%% frame index for movie or multimage file input 
[454]107if ~isempty(j1_series{1})
108    frame_index{1}=j1_series{1};
109else
110    frame_index{1}=i1_series{1};
[442]111end
[454]112
113%% calibration data and timing: read the ImaDoc files
114%not relevant for this function
115
116%% check coincidence in time for several input file series
117%not relevant for this function
118
119%% coordinate transform or other user defined transform
120%not relevant for this function
121
122%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
123 % EDIT FROM HERE
124
[604]125 %% Extension and indexing nomenclature for output file
126 FileExtOut='.png'; % write result as .png images for image inputs
127 if strcmpi(NomType{1}(end),'a')
128     NomTypeOut=NomType{1};
129 else
130     NomTypeOut='_1_1';
131 end
[64]132
[454]133%% Set field names and velocity types
134%not relevant for this function
[64]135
[454]136%% Initiate output fields
137%not relevant for this function
138
139%% set processing parameters
140% not needed for this function
141
142%% update the xml file
143% not needed for this function
144
145%% main loop on images
146j1=[];%default
[64]147for ifile=1:nbfield
[604]148    if checkrun
149        stopstate=get(Param.RUNHandle,'BusyAction');
150        update_waitbar(Param.WaitbarHandle,ifile/nbfield)
151    else
152        stopstate='queue';
[64]153    end
[604]154    if ~isequal(stopstate,'queue') % enable STOP command
155        break
156    end
157    if ~isempty(j1_series)&&~isequal(j1_series,{[]})
158        j1=j1_series{1}(ifile);
159    end
160    filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
161    A=read_image(filename,FileType{1},VideoObject{1},frame_index{1}(ifile));
162    if ndims(A)==3;%color images
163        A=sum(double(Aread),3);% take the sum of color components
164    end
165    % operation on images
166    A=levels(A);
167    % write output file
168    filename_new=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
169    imwrite(A,filename_new)
170    display([filename_new ' written'])
[64]171end
[442]172%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[64]173
[454]174
[64]175function C=levels(A)
176%whos A;
177B=double(A(:,:,1));
178windowsize=round(min(size(B,1),size(B,2))/20);
179windowsize=floor(windowsize/2)*2+1;
180ix=[1/2-windowsize/2:-1/2+windowsize/2];%
181%del=np/3;
182%fct=exp(-(ix/del).^2);
183fct2=cos(ix/(windowsize-1)/2*pi/2);
184%Mfiltre=(ones(5,5)/5^2);
185%Mfiltre=fct2';
186Mfiltre=fct2'*fct2;
187Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
188
[71]189C=filter2(Mfiltre,B);
[64]190C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
191C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
192C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
193C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
194C=tanh(B./(2*C));
195[n,c]=hist(reshape(C,1,[]),100);
196% figure;plot(c,n);
197
198[m,i]=max(n);
199c_max=c(i);
200[dummy,index]=sort(abs(c-c(i)));
201n=n(index);
202c=c(index);
203i_select = find(cumsum(n)<0.95*sum(n));
204if isempty(i_select)
205    i_select = 1:length(c);
206end
207c_select=c(i_select);
208n_select=n(i_select);
209cmin=min(c_select);
210cmax=max(c_select);
211C=(C-cmin)/(cmax-cmin)*256;
212C=uint8(C);
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