source: trunk/src/series/aver_spectral.m @ 1085

Last change on this file since 1085 was 1085, checked in by sommeria, 4 months ago

aver_spectral added andsmall bug repairs

File size: 11.0 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 2008-2020, 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_multi';%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={''};
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
168main_period=Param.ActionInput.WavePeriod;
169main_frequency=2*pi/main_period;
170frequency=(0:main_frequency/16:3*main_frequency)';
171nbfrequency=numel(frequency);
172%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
173for index=1:nbfield
174    index
175    update_waitbar(WaitbarHandle,index/nbfield)
176    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
177        disp('program stopped by user')
178        break
179    end
180   
181    % reading input file(s)
182    [Data,tild,errormsg] = read_field(filecell{1,index},FileType,InputFields{1});
183    if ~isempty(errormsg)
184        displ_uvmat('ERROR',['error of input reading: ' errormsg],checkrun);
185        break
186    end
187    if ~isempty(NbSlice_calib)
188        Data.ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform
189    end
190    %initiate average
191    if index==1
192        nby=numel(Data.coord_y);
193        nbx=numel(Data.coord_x);
194        cos_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x));
195        sin_U=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x));
196        cos_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x));
197        sin_V=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x));
198        NbField=zeros(nbfrequency,numel(Data.coord_y),numel(Data.coord_x));
199    end
200    %update average
201    FF=isnan(Data.U)|isnan(Data.V);% check NaN values
202    Data.U(FF)=0;% set to zero the NaN values
203    Data.V(FF)=0;
204    for ifreq=1:nbfrequency
205        NbField(ifreq,:,:)=NbField(ifreq,:,:)+reshape(~FF,1,nby,nbx);%count the NaN values
206        cos_U(ifreq,:,:)=cos_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*cos(Data.Time*frequency(ifreq));
207        sin_U(ifreq,:,:)=sin_U(ifreq,:,:)+reshape(Data.U,1,nby,nbx)*sin(Data.Time*frequency(ifreq));
208        cos_V(ifreq,:,:)=cos_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*cos(Data.Time*frequency(ifreq));
209        sin_V(ifreq,:,:)=sin_V(ifreq,:,:)+reshape(Data.V,1,nby,nbx)*sin(Data.Time*frequency(ifreq));
210    end
211end
212
213%%%%%%%%%%%%%%%%%%%%%%%%
214Data.ListVarName={'coord_x','coord_y','frequency','cos_U','cos_V','sin_U','sin_V','a_U','a_V','phase_U','phase_V'};
215%Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName];
216Data.VarDimName={'coord_x', 'coord_y','frequency'};
217for ilist=1:numel(Data.ListVarName)-3
218    Data.VarDimName{ilist+3}={'frequency','coord_y','coord_x'};
219end
220Data.frequency=frequency;
221Data.cos_U=cos_U./NbField;
222Data.sin_U=sin_U./NbField;
223Data.cos_V=cos_V./NbField;
224Data.sin_V=sin_V./NbField;
225Data.a_U=sqrt(2)*sqrt(Data.cos_U.*Data.cos_U+Data.sin_U.*Data.sin_U);
226Data.a_V=sqrt(2)*sqrt(Data.cos_V.*Data.cos_V+Data.sin_V.*Data.sin_V);
227Data.phase_U=angle(Data.cos_U+1i*Data.sin_U);
228Data.phase_V=angle(Data.cos_V+1i*Data.sin_V);
229
230
231%% write the results
232OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','',1);
233errormsg=struct2nc(OutputFile,Data);% write the output file
234if isempty(errormsg)
235    disp_uvmat('CONFIRMATION',[OutputFile ' successfully written'],checkrun)
236else
237    disp_uvmat('ERROR',errormsg,checkrun)
238end
239   
240
241%% open the result file with uvmat (in RUN mode)
242% if checkrun
243%     uvmat(OutputFile)% open the last result file with uvmat
244% end
245'#### THE END ####'
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