source: trunk/src/series/ima_levels.m @ 624

Last change on this file since 624 was 624, checked in by sommeria, 8 years ago

waitbar system for series improved to aloow use as stand alone fcts.

to add at the head of series fcts:
hseries=findobj(allchild(0),'Tag','series');
RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
WaitbarHandle?=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series

call to waitbar:

update_waitbar(WaitbarHandle?,index/nbfield)
if ishandle(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction?'),'queue')

disp('program stopped by user')
break

end

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