source: trunk/src/series/ima_levels.m @ 592

Last change on this file since 592 was 592, checked in by sommeria, 8 years ago

commit the series fcts with the new form

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 ParamOut=ima_levels (Param)
43
44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
45if isstruct(Param) && isequal(Param.Action.RUN,0)
46    ParamOut.NbViewMax=1;% max nbre of input file series (default='' , no limitation)
47    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
48    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
49    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
50    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
51    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
52    ParamOut.FieldTransform = 'off';%can use a transform function
53    ParamOut.ProjObject='off';%can use projection object(option 'off'/'on',
54    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
55    ParamOut.OutputDirExt='.lev';%set the output dir extension
56return
57end
58
59%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
60%% read input parameters from an xml file if input is a file name (batch mode)
61checkrun=1;
62if ischar(Param)
63    Param=xml2struct(Param);% read Param as input file (batch case)
64    checkrun=0;
65end
66
67ParamOut=Param; %default output
68if ~isfield(Param,'InputFields')
69    Param.InputFields.FieldName='';
70end
71OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
72
73%% root input file(s) and type
74RootPath=Param.InputTable(:,1);
75RootFile=Param.InputTable(:,3);
76SubDir=Param.InputTable(:,2);
77NomType=Param.InputTable(:,4);
78FileExt=Param.InputTable(:,5);
79OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
80
81% get the set of input file names (cell array filecell), and the lists of
82% input file or frame indices i1_series,i2_series,j1_series,j2_series
83[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
84% filecell{iview,fileindex}: cell array representing the list of file names
85%        iview: line in the table corresponding to a given file series
86%        fileindex: file index within  the file series,
87% 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
88% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
89% set of frame indices used for movie or multimage input
90% numbers of slices and file indices
91
92NbSlice=1;%default
93if isfield(Param.IndexRange,'NbSlice')
94    NbSlice=Param.IndexRange.NbSlice;
95end
96nbview=numel(i1_series);%number of input file series (lines in InputTable)
97nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
98nbfield_i=size(i1_series{1},2); %nb of fields for the i index
99nbfield=nbfield_j*nbfield_i; %total number of fields
100nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
101nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
102
103%determine the file type on each line from the first input file
104ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
105
106[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
107CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
108if ~isempty(j1_series{1})
109    frame_index{1}=j1_series{1};
110else
111    frame_index{1}=i1_series{1};
112end
113
114%% calibration data and timing: read the ImaDoc files
115%not relevant for this function
116
117%% check coincidence in time for several input file series
118%not relevant for this function
119
120%% coordinate transform or other user defined transform
121%not relevant for this function
122
123%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
124 % EDIT FROM HERE
125
126 %% check the validity of  input file types
127if CheckImage{1}
128    FileExtOut='.png'; % write result as .png images for image inputs
129    if strcmp(lower(NomType{1}(end)),'a')
130        NomTypeOut=NomType{1};
131    else
132        NomTypeOut='_1_1';
133    end
134else
135    msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
136    return
137end
138
139%% Set field names and velocity types
140%not relevant for this function
141
142%% Initiate output fields
143%not relevant for this function
144
145%% set processing parameters
146% not needed for this function
147
148%% update the xml file
149% not needed for this function
150
151%% main loop on images
152j1=[];%default
153for ifile=1:nbfield
154          if checkrun
155                stopstate=get(Param.RUNHandle,'BusyAction');
156                update_waitbar(Param.WaitbarHandle,ifile/nbfield)
157          else
158                stopstate='queue';
159          end
160    if isequal(stopstate,'queue') % enable STOP command
161        if ~isempty(j1_series)&&~isequal(j1_series,{[]})
162            j1=j1_series{1}(ifile);
163        end
164        filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
165        A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
166        if ndims(A)==3;%color images
167            A=sum(double(Aread),3);% take the sum of color components
168        end
169        % operation on images
170        A=levels(A);
171        filename_new=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
172        imwrite(A,filename_new)
173        display([filename_new ' written'])
174    end
175end
176%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
177
178
179function C=levels(A)
180%whos A;
181B=double(A(:,:,1));
182windowsize=round(min(size(B,1),size(B,2))/20);
183windowsize=floor(windowsize/2)*2+1;
184ix=[1/2-windowsize/2:-1/2+windowsize/2];%
185%del=np/3;
186%fct=exp(-(ix/del).^2);
187fct2=cos(ix/(windowsize-1)/2*pi/2);
188%Mfiltre=(ones(5,5)/5^2);
189%Mfiltre=fct2';
190Mfiltre=fct2'*fct2;
191Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
192
193C=filter2(Mfiltre,B);
194C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
195C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
196C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
197C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
198C=tanh(B./(2*C));
199[n,c]=hist(reshape(C,1,[]),100);
200% figure;plot(c,n);
201
202[m,i]=max(n);
203c_max=c(i);
204[dummy,index]=sort(abs(c-c(i)));
205n=n(index);
206c=c(index);
207i_select = find(cumsum(n)<0.95*sum(n));
208if isempty(i_select)
209    i_select = 1:length(c);
210end
211c_select=c(i_select);
212n_select=n(i_select);
213cmin=min(c_select);
214cmax=max(c_select);
215C=(C-cmin)/(cmax-cmin)*256;
216C=uint8(C);
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