source: trunk/src/series/ima_levels.m @ 602

Last change on this file since 602 was 602, checked in by sommeria, 8 years ago

limit time increased for series with cluster, status improved

File size: 9.5 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
56    ParamOut.OutputFileMode='NbInput';%NbInput= 1 output file per input file index, NbInput_i=1 fileper input file index i,NbSlice= 1 file per slice
57return
58end
59
60%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
61%% read input parameters from an xml file if input is a file name (batch mode)
62checkrun=1;
63if ischar(Param)
64    Param=xml2struct(Param);% read Param as input file (batch case)
65    checkrun=0;
66end
67
68ParamOut=Param; %default output
69if ~isfield(Param,'InputFields')
70    Param.InputFields.FieldName='';
71end
72OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
73
74%% root input file(s) and type
75RootPath=Param.InputTable(:,1);
76RootFile=Param.InputTable(:,3);
77SubDir=Param.InputTable(:,2);
78NomType=Param.InputTable(:,4);
79FileExt=Param.InputTable(:,5);
80OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
81
82% get the set of input file names (cell array filecell), and the lists of
83% input file or frame indices i1_series,i2_series,j1_series,j2_series
84[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
85% filecell{iview,fileindex}: cell array representing the list of file names
86%        iview: line in the table corresponding to a given file series
87%        fileindex: file index within  the file series,
88% 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
89% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
90% set of frame indices used for movie or multimage input
91% numbers of slices and file indices
92
93NbSlice=1;%default
94if isfield(Param.IndexRange,'NbSlice')
95    NbSlice=Param.IndexRange.NbSlice;
96end
97nbview=numel(i1_series);%number of input file series (lines in InputTable)
98nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
99nbfield_i=size(i1_series{1},2); %nb of fields for the i index
100nbfield=nbfield_j*nbfield_i; %total number of fields
101nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
102nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
103
104%determine the file type on each line from the first input file
105ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images)
106
107[FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1});
108CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
109if ~isempty(j1_series{1})
110    frame_index{1}=j1_series{1};
111else
112    frame_index{1}=i1_series{1};
113end
114
115%% calibration data and timing: read the ImaDoc files
116%not relevant for this function
117
118%% check coincidence in time for several input file series
119%not relevant for this function
120
121%% coordinate transform or other user defined transform
122%not relevant for this function
123
124%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
125 % EDIT FROM HERE
126
127 %% check the validity of  input file types
128if CheckImage{1}
129    FileExtOut='.png'; % write result as .png images for image inputs
130    if strcmp(lower(NomType{1}(end)),'a')
131        NomTypeOut=NomType{1};
132    else
133        NomTypeOut='_1_1';
134    end
135else
136    msgbox_uvmat('ERROR',['invalid file type input: ' FileType{1} ' not an image'])
137    return
138end
139
140%% Set field names and velocity types
141%not relevant for this function
142
143%% Initiate output fields
144%not relevant for this function
145
146%% set processing parameters
147% not needed for this function
148
149%% update the xml file
150% not needed for this function
151
152%% main loop on images
153j1=[];%default
154for ifile=1:nbfield
155          if checkrun
156                stopstate=get(Param.RUNHandle,'BusyAction');
157                update_waitbar(Param.WaitbarHandle,ifile/nbfield)
158          else
159                stopstate='queue';
160          end
161    if isequal(stopstate,'queue') % enable STOP command
162        if ~isempty(j1_series)&&~isequal(j1_series,{[]})
163            j1=j1_series{1}(ifile);
164        end
165        filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(ifile),[],j1);
166        A=read_image(filename,FileType{1},MovieObject{1},frame_index{1}(ifile));
167        if ndims(A)==3;%color images
168            A=sum(double(Aread),3);% take the sum of color components
169        end
170        % operation on images
171        A=levels(A);
172        filename_new=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(ifile),[],j1);
173        imwrite(A,filename_new)
174        display([filename_new ' written'])
175    end
176end
177%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
178
179
180function C=levels(A)
181%whos A;
182B=double(A(:,:,1));
183windowsize=round(min(size(B,1),size(B,2))/20);
184windowsize=floor(windowsize/2)*2+1;
185ix=[1/2-windowsize/2:-1/2+windowsize/2];%
186%del=np/3;
187%fct=exp(-(ix/del).^2);
188fct2=cos(ix/(windowsize-1)/2*pi/2);
189%Mfiltre=(ones(5,5)/5^2);
190%Mfiltre=fct2';
191Mfiltre=fct2'*fct2;
192Mfiltre=Mfiltre/(sum(sum(Mfiltre)));
193
194C=filter2(Mfiltre,B);
195C(:,1:windowsize)=C(:,windowsize)*ones(1,windowsize);
196C(:,end-windowsize+1:end)=C(:,end-windowsize+1)*ones(1,windowsize);
197C(1:windowsize,:)=ones(windowsize,1)*C(windowsize,:);
198C(end-windowsize+1:end,:)=ones(windowsize,1)*C(end-windowsize,:);
199C=tanh(B./(2*C));
200[n,c]=hist(reshape(C,1,[]),100);
201% figure;plot(c,n);
202
203[m,i]=max(n);
204c_max=c(i);
205[dummy,index]=sort(abs(c-c(i)));
206n=n(index);
207c=c(index);
208i_select = find(cumsum(n)<0.95*sum(n));
209if isempty(i_select)
210    i_select = 1:length(c);
211end
212c_select=c(i_select);
213n_select=n(i_select);
214cmin=min(c_select);
215cmax=max(c_select);
216C=(C-cmin)/(cmax-cmin)*256;
217C=uint8(C);
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