source: trunk/src/series/filter_time.m @ 1157

Last change on this file since 1157 was 1157, checked in by sommeria, 3 months ago

filter_time added

File size: 10.1 KB
Line 
1%'filter_time': apply a a sliding filter in a time series
2%------------------------------------------------------------------------
3% function ParamOut=filter_time(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, (several5.804 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%             900
28%    .IndexRange: set the file or frame indices on which the action must be performseriesed
29%    .FieldTransform: .TransformName: name of the select39ed 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%             uvmat .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% Copyright 2008-2022, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
42%   http://www.legi.grenoble-inp.fr
43%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
44%
45%     This file is part of the toolbox UVMAT.
46%
47%     UVMAT is free software; you can redistribute it and/or modify
48%     it under the terms of the GNU General Public License as published
49%     by the Free Software Foundation; either version 2 of the license,
50%     or (at your option) any later version.
51%
52%     UVMAT is distributed in the hope that it will be useful,
53%     but WITHOUT ANY WARRANTY; without even the implied warranty of
54%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
55%     GNU General Public License (see LICENSE.txt) for more details.
56%=======================================================================
57
58function ParamOut=filter_time(Param)
59
60%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
61if isstruct(Param) && isequal(Param.Action.RUN,0)
62    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
63    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to mseriesax (options 'off'/'on', 'off' by default)
64    ParamOut.NbSlice=1; %nbre of slices ('off' by default)
65    ParamOut.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
66    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
67    ParamOut.FieldTransform = 'off';%can use a transform function
68    ParamOut.ProjObject='off';%can use projection object39(option 'off'/'on',
69    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
70    ParamOut.OutputDirExt='.tfilter';%set the output dir extension
71    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
72   
73    %% check the first input file in the series
74    first_j=[];%
75    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
76    PairString='';
77    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
78    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
79    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
80        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
81    if exist(FirstFileName,'file')
82        FileInfo=get_file_info(FirstFileName);
83        if ~(isfield(FileInfo,'FileType')&& strcmp(FileInfo.FileType,'netcdf'))
84            msgbox_uvmat('ERROR','this fct works only on netcdf files (fields projected on a grid, notraw civ data)')
85            return
86        end
87    else
88        msgbox_uvmat('ERROR',['the input file ' FirstFileName ' does not exist'])
89        return
90    end
91   
92    %% setting the fltering window length
93    answer = msgbox_uvmat('INPUT_TXT','set the filering window length','3');
94    ParamOut.ActionInput.WindowLength=str2double(answer);
95    return
96end
97
98%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
99ParamOut=[];%default output
100%% read input parameters from an xml file if input is a file name (batch mode)
101checkrun=1;
102if ischar(Param)
103    Param=xml2struct(Param);% read Param as input file (batch case)
104    checkrun=0;
105end
106
107hseries=findobj(allchild(0),'Tag','series');
108RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
109WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
110
111
112%% root input file(s) name, type and index series
113RootPath=Param.InputTable(:,1);
114RootFile=Param.InputTable(:,3);
115SubDir=Param.InputTable(:,2);
116NomType=Param.InputTable(:,4);
117FileExt=Param.InputTable(:,5);
118[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
119%%%%%%%%%%%%
120% The cell array filecell is the list of input file names, while
121% filecell{iview,fileindex}:
122%        iview: line in the table corresponding to a given file series
123%        fileindex: file index within  the file series,
124% 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
125% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
126%%%%%%%%%%%% NbView=1 : a single input series
127
128NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
129NbField_i=size(i1_series{1},2); %nb of fields for the i index
130NbField=NbField_j*NbField_i; %total number of fields
131
132%% define the output file (unique for the whole series)
133OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
134OutputDir=[Param.OutputSubDir Param.OutputDirExt];
135first_j=[];last_j=[];% %% check the first input file in the series
136
137PairString='';
138if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
139
140
141% OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
142% RootFileOut=RootFile{1};
143% NomTypeOut='_1';
144
145%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
146disp('loop for filtering started')
147     
148for index=1:NbField
149    index
150   
151    Field= read_field(filecell{1,index},'netcdf',Param.InputFields);
152   
153    %%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
154    if index==1 %first field, initialisation output data
155
156        DataOut.ListGlobalAttribute= {'Conventions','Time'};
157        DataOut.Conventions='uvmat';
158        %DataOut.ListVarName={'coord_y','coord_x','Ufilter','Vfilter','Wfilter'};
159        ListFields=Param.InputFields.FieldName;
160        YName=Param.InputFields.Coord_y;
161        XName=Param.InputFields.Coord_x;
162        NbField=numel(ListFields);
163        for ilist=1:NbField
164            ListFilter{ilist}=[ListFields{ilist} '_filter'];
165            VarDimName{ilist}={YName,XName};
166        end
167       DataOut.ListVarName=[{YName,XName} ListFilter];
168        DataOut.VarDimName=[{YName,XName} VarDimName];
169        npy=numel(Field.(YName));
170        npx=numel(Field.(XName));
171        DataOut.(XName)=Field.(XName);
172        DataOut.(YName)=Field.(YName);
173        TimeBlock=zeros(Param.ActionInput.WindowLength,1);
174       
175        UVblock=zeros(Param.ActionInput.WindowLength,NbField,npy,npx);
176        % Vblock=zeros(Param.ActionInput.WindowLength,npy,npx);
177        % Wblock=zeros(Param.ActionInput.WindowLength,npy,npx);
178    end
179    TimeBlock=circshift(TimeBlock,[-1 0 ]);
180    UVblock=circshift(UVblock,[-1 0 0 0]); %shift U by ishift along the first index
181    % Vblock=circshift(Vblock,[-1 0 0 0]); %shift U by ishift along the first index
182    % Wblock=circshift(Wblock,[-1 0 0]); %shift U by ishift along the first index
183    TimeBlock(end)=Field.Time;
184    for ilist=1:NbField
185    UVblock(end,ilist,:,:)=Field.(ListFields{ilist});
186    end
187    % Vblock(end,:,:)=Field.V;
188    % Vblock(end,:,:)=Field.W;
189    sumindex=min(index,Param.ActionInput.WindowLength)-1;
190    DataOut.Timefilter=mean(TimeBlock(end-sumindex:end,:));%mid time
191    for ilist=1:NbField
192    DataOut.(ListFilter{ilist})=squeeze(mean(UVblock(end-sumindex:end,ilist,:,:),1,'omitnan'));
193    end
194    % DataOut.Vfilter=squeeze(mean(Vblock(end-sumindex:end,:,:),1,'omitnan'));
195    % DataOut.Wfilter=squeeze(mean(Wblock(end-sumindex:end,:,:),1,'omitnan'));
196    %updating output the netcdf file
197    [i1,i2,j1,j2] = get_file_index(i1_series{1}(index),[],PairString{1});
198    OutputFile=fullfile_uvmat(OutputPath,OutputDir,Param.InputTable{1,3},'.nc',NomType{1},i1,i2,j1,j2);
199    errormsg=struct2nc(OutputFile, DataOut);
200        if isempty(errormsg)
201            disp([OutputFile ' written'])
202        else
203            disp(errormsg)
204        end
205end
206    % writing the result file as netcdf file
207    %     i1=i1_series{1}(index)-ceil(NpTime/2);
208    %     OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1);
209
210'END'
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