source: trunk/src/series/aver_synchro.m @ 974

Last change on this file since 974 was 974, checked in by sommeria, 4 years ago

aver synchro updated

File size: 12.6 KB
Line 
1%'aver_stat': calculate field average over a time series
2%------------------------------------------------------------------------
3% function ParamOut=aver_stat(Param)
4%
5%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
6%
7%OUTPUT
8% ParamOut: sets options in the GUI series.fig needed for the function
9%
10%INPUT:
11% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
12% In batch mode, Param is the name of the corresponding xml file containing the same information
13% when Param.Action.RUN=0 (as activated when the current Action is selected
14% in series), the function ouput paramOut set the activation of the needed GUI elements
15%
16% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
17% see the current structure Param)
18%    .InputTable: cell of input file names, (several lines for multiple input)
19%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
20%    .OutputSubDir: name of the subdirectory for data outputs
21%    .OutputDirExt: directory extension for data outputs
22%    .Action: .ActionName: name of the current activated function
23%             .ActionPath:   path of the current activated function
24%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
25%             .RUN =0 for GUI input, =1 for function activation
26%             .RunMode='local','background', 'cluster': type of function  use
27%             
28%    .IndexRange: set the file or frame indices on which the action must be performed
29%    .FieldTransform: .TransformName: name of the selected transform function
30%                     .TransformPath:   path  of the selected transform function
31%    .InputFields: sub structure describing the input fields withfields
32%              .FieldName: name(s) of the field
33%              .VelType: velocity type
34%              .FieldName_1: name of the second field in case of two input series
35%              .VelType_1: velocity type of the second field in case of two input series
36%              .Coord_y: name of y coordinate variable
37%              .Coord_x: name of x coordinate variable
38%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
39%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
40
41%=======================================================================
42% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
43%   http://www.legi.grenoble-inp.fr
44%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
45%
46%     This file is part of the toolbox UVMAT.
47%
48%     UVMAT is free software; you can redistribute it and/or modify
49%     it under the terms of the GNU General Public License as published
50%     by the Free Software Foundation; either version 2 of the license,
51%     or (at your option) any later version.
52%
53%     UVMAT is distributed in the hope that it will be useful,
54%     but WITHOUT ANY WARRANTY; without even the implied warranty of
55%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
56%     GNU General Public License (see LICENSE.txt) for more details.
57%=======================================================================
58
59function ParamOut=aver_synchro(Param)
60
61%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
62if isstruct(Param) && isequal(Param.Action.RUN,0)
63    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
64    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
65    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
66    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
67    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
68    ParamOut.FieldTransform = 'on';%can use a transform function
69    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
70    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
71    ParamOut.OutputDirExt='.synchro';%set the output dir extension
72    ParamOut.OutputFileMode='NbSlice';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
73    %     filecell=get_file_series(Param);%check existence of the first input file
74    %     if ~exist(filecell{1,1},'file')
75    %         msgbox_uvmat('WARNING','the first input file does not exist')
76    %     end
77    def={'26'};
78    if isfield (Param,'ActionInput')&& isfield(Param.ActionInput,'WavePeriod')
79        def=Param.ActionInput.WavePeriod;
80       
81        def={num2str(def)};
82    end
83    prompt={'wave period'};
84    dlgTitle='primary period';
85    lineNo=1;
86    answer=inputdlg(prompt,dlgTitle,lineNo,def);
87    ParamOut.ActionInput.WavePeriod=str2num(answer{1});
88    return
89end
90
91%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
92ParamOut=[];%default output
93%% read input parameters from an xml file if input is a file name (batch mode)
94checkrun=1;
95if ischar(Param)
96    Param=xml2struct(Param);% read Param as input file (batch case)
97    checkrun=0;
98end
99hseries=findobj(allchild(0),'Tag','series');
100RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
101WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
102
103%% define the directory for result file (with path=RootPath{1})
104OutputDir=[Param.OutputSubDir Param.OutputDirExt];
105   
106%% root input file(s) name, type and index series
107RootPath=Param.InputTable(:,1);
108RootFile=Param.InputTable(:,3);
109SubDir=Param.InputTable(:,2);
110NomType=Param.InputTable(:,4);
111FileExt=Param.InputTable(:,5);
112[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
113FileInfo=get_file_info(filecell{1,1});
114 FileType=FileInfo.FileType;
115%%%%%%%%%%%%
116% The cell array filecell is the list of input file names, while
117% filecell{iview,fileindex}:
118%        iview: line in the table corresponding to a given file series
119%        fileindex: file index within  the file series,
120% 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
121% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
122%%%%%%%%%%%%
123nbview=numel(i1_series);%number of input file series (lines in InputTable)
124nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
125nbfield_i=size(i1_series{1},2); %nb of fields for the i index
126nbfield=nbfield_j*nbfield_i; %total number of fields
127
128%% determine the input file type
129% if ~strcmp(FileType{1},'netcdf')
130%     displ_uvmat('ERROR','netcdf file series with field projected on a regular mesh must be put as input')
131%     return
132% end
133
134%% calibration data and timing: read the ImaDoc files
135[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
136% if size(time,1)>1
137%     diff_time=max(max(diff(time)));
138%     if diff_time>0
139%         msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
140%     end   
141% end
142
143%% coordinate transform or other user defined transform
144transform_fct='';%default
145if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
146    addpath(Param.FieldTransform.TransformPath)
147    transform_fct=str2func(Param.FieldTransform.TransformName);
148    rmpath(Param.FieldTransform.TransformPath)
149end
150
151%% settings for the output file
152NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
153first_i=i1_series{1}(1);
154last_i=i1_series{1}(end);
155if isempty(j1_series{1})% if there is no second index j
156    first_j=1;last_j=1;
157else
158    first_j=j1_series{1}(1);
159    last_j=j1_series{1}(end);
160end
161
162%% Set field names and velocity types
163InputFields{1}=[];%default (case of images)
164if isfield(Param,'InputFields')
165    InputFields{1}=Param.InputFields;
166end
167
168% for i_slice=1:NbSlice
169% index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
170nbfiles=0;
171nbmissing=0;
172MeanU=0;
173MeanV=0;
174MinU=0;
175MaxU=0;
176MinV=0;
177MaxV=0;
178vec_X=0;
179vec_Y=0;
180vec_U=0; %initiate the sum
181vec_V=0;
182cos1_U=0;
183cos1_V=0;
184sin1_U=0;
185sin1_V=0;
186cos2_U=0;
187cos2_V=0;
188sin2_U=0;
189sin2_V=0;
190cos3_U=0;
191cos3_V=0;
192sin3_U=0;
193sin3_V=0;
194cossub_U=0;
195cossub_V=0;
196sinsub_U=0;
197sigma1=2*pi/Param.ActionInput.WavePeriod;%primary wave frequency
198sigma2=4*pi/Param.ActionInput.WavePeriod;%harmonic 2
199sigma3=6*pi/Param.ActionInput.WavePeriod;%harmonic 3
200sigma_sub=pi/Param.ActionInput.WavePeriod;%subharmonic
201sinsub_V=0;
202NbField=0;
203vec_C=0;
204 
205%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
206for index=1:nbfield
207    index
208    update_waitbar(WaitbarHandle,index/nbfield)
209    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
210        disp('program stopped by user')
211        break
212    end
213   
214    % reading input file(s)
215    [Data,tild,errormsg] = read_field(filecell{1,index},FileType,InputFields{1});
216    if ~isempty(errormsg)
217        displ_uvmat('ERROR',['error of input reading: ' errormsg],checkrun);
218        break
219    end
220    if ~isempty(NbSlice_calib)
221        Data.ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform
222    end
223    %update average
224    FF=isnan(Data.U)|isnan(Data.V);% chceck NaN values
225    Data.U(FF)=0;% set to zero the NaN values
226    Data.V(FF)=0;
227    NbField=NbField+~FF;%count the NaN values
228    MeanU=MeanU+Data.U;
229    MeanV=MeanV+Data.V;
230    MaxU=(MaxU>=Data.U).*MaxU+(MaxU<Data.U).*Data.U;
231    MinU=(MinU<=Data.U).*MinU+(MinU>Data.U).*Data.U;
232    MaxV=(MaxV>=Data.V).*MaxV+(MaxV<Data.V).*Data.V;
233    MinV=(MinV<=Data.V).*MinV+(MinV>Data.V).*Data.V;
234    cos1_U=cos1_U+Data.U*cos(Data.Time*sigma1);
235    cos1_V=cos1_V+Data.V*cos(Data.Time*sigma1);
236    sin1_U=sin1_U+Data.U*sin(Data.Time*sigma1);
237    sin1_V=sin1_V+Data.V*sin(Data.Time*sigma1);
238    cos2_U=cos2_U+Data.U*cos(Data.Time*sigma2);
239    cos2_V=cos2_V+Data.V*cos(Data.Time*sigma2);
240    sin2_U=sin2_U+Data.U*sin(Data.Time*sigma2);
241    sin2_V=sin2_V+Data.V*sin(Data.Time*sigma2);
242    cos3_U=cos3_U+Data.U*cos(Data.Time*sigma3);
243    cos3_V=cos3_V+Data.V*cos(Data.Time*sigma3);
244    sin3_U=sin3_U+Data.U*sin(Data.Time*sigma3);
245    sin3_V=sin3_V+Data.V*sin(Data.Time*sigma3);
246    cossub_U=cossub_U+Data.U*cos(Data.Time*sigma_sub);
247    cossub_V=cossub_V+Data.V*cos(Data.Time*sigma_sub);
248    sinsub_U=sinsub_U+Data.U*sin(Data.Time*sigma_sub);
249    sinsub_V=sinsub_V+Data.V*sin(Data.Time*sigma_sub);
250   
251   
252end
253
254%%%%%%%%%%%%%%%%%%%%%%%%
255Data.ListVarName={'coord_x','coord_y','MeanU','MeanV','cos1_U','cos1_V','a1_U','a1_V','a2_U','a2_V','a3_U','a3_V','asub_U','asub_V',...
256    'phase1_U','phase1_V','phase2_U','phase2_V','phase3_U','phase3_V','phasesub_U','phasesub_V'};
257%Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName];
258%Data.VarDimName={'coord_y', 'coord_x'};
259for ilist=1:numel(Data.ListVarName)-2
260    Data.VarDimName{ilist+2}={'coord_y','coord_x'};
261 %   Data.VarDimName{ilist}='nb_vectors';
262end
263Data.MeanU=MeanU./NbField;
264Data.MeanV=MeanV./NbField;
265cos1_U=cos1_U./NbField;
266cos1_V=cos1_V./NbField;
267sin1_U=sin1_U./NbField;
268sin1_V=sin1_V./NbField;
269cos2_U=cos2_U./NbField;
270cos2_V=cos2_V./NbField;
271sin2_U=sin2_U./NbField;
272sin2_V=sin2_V./NbField;
273cos3_U=cos3_U./NbField;
274cos3_V=cos3_V./NbField;
275sin3_U=sin3_U./NbField;
276sin3_V=sin3_V./NbField;
277cossub_U=cossub_U./NbField;
278cossub_V=cossub_V./NbField;
279sinsub_U=sinsub_U./NbField;
280sinsub_V=sinsub_V./NbField;
281Data.cos1_U=cos1_U;
282Data.cos1_V=cos1_V;
283Data.a1_U=sqrt(2)*sqrt(cos1_U.*cos1_U+sin1_U.*sin1_U);
284Data.a1_V=-sqrt(2)*sqrt(cos1_V.*cos1_V+sin1_V.*sin1_V);
285Data.a2_U=sqrt(2)*sqrt(cos2_U.*cos2_U+sin2_U.*sin2_U);
286Data.a2_V=-sqrt(2)*sqrt(cos2_V.*cos2_V+sin2_V.*sin2_V);
287Data.a3_U=sqrt(2)*sqrt(cos3_U.*cos3_U+sin3_U.*sin3_U);
288Data.a3_V=-sqrt(2)*sqrt(cos3_V.*cos3_V+sin3_V.*sin3_V);
289Data.asub_U=sqrt(2)*sqrt(cossub_U.*cossub_U+sinsub_U.*sinsub_U);
290Data.asub_V=-sqrt(2)*sqrt(cossub_V.*cossub_V+sinsub_V.*sinsub_V);
291% clear i
292Data.phase1_U=(angle(cos1_U+i*sin1_U));
293
294Data.phase1_V=angle(cos1_V+i*sin1_V);
295Data.phase2_U=(angle(cos2_U+i*sin2_U));
296Data.phase2_V=(angle(cos2_V+i*sin2_V));
297Data.phase3_U=(angle(cos3_U+i*sin3_U));
298Data.phase3_V=(angle(cos3_V+i*sin3_V));
299Data.phasesub_U=(angle(cossub_U+i*sinsub_U));
300Data.phasesub_V=(angle(cossub_V+i*sinsub_V));
301
302%% write the results
303OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','',1);
304errormsg=struct2nc(OutputFile,Data);% write the output file
305if isempty(errormsg)
306    disp_uvmat('CONFIRMATION',[OutputFile ' successfully written'],checkrun)
307else
308    disp_uvmat('ERROR',errormsg,checkrun)
309end
310   
311
312%% open the result file with uvmat (in RUN mode)
313% if checkrun
314%     uvmat(OutputFile)% open the last result file with uvmat
315% end
316'#### THE END ####'
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