source: trunk/src/series/sliding_average.m @ 1128

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1%'sliding_average_natalya'
2%------------------------------------------------------------------------
3% function ParamOut=sliding_average(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 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
42%   http://www.legi.grenoble-inp.fr
43%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.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=sliding_average(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 = 'on';%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%     filecell=get_file_series(Param);%check existence of the first input file
73%     if ~exist(filecell{1,1},'file')
74%         msgbox_uvmat('WARNING','the first input file does not exist')
75%     end
76    return
77end
78
79%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
80ParamOut=[];%default output
81%% read input parameters from an xml file if input is a file name (batch mode)
82checkrun=1;
83if ischar(Param)
84    Param=xml2struct(Param);% read Param as input file (batch case)
85    checkrun=0;
86end
87
88hseries=findobj(allchild(0),'Tag','series');
89RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
90WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
91
92%% define the directory for result file (with path=RootPath{1})
93OutputDir=[Param.OutputSubDir Param.OutputDirExt];
94   
95%% root input file(s) name, type and index series
96RootPath=Param.InputTable(:,1);
97RootFile=Param.InputTable(:,3);
98SubDir=Param.InputTable(:,2);
99NomType=Param.InputTable(:,4);
100FileExt=Param.InputTable(:,5);
101[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
102%%%%%%%%%%%%
103% The cell array filecell is the list of input file names, while
104% filecell{iview,fileindex}:
105%        iview: line in the table corresponding to a given file series
106%        fileindex: file index within  the file series,
107% 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
108% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
109%%%%%%%%%%%% NbView=1 : a single input series
110NbView=numel(i1_series);%number of input file series (lines in InputTable)
111NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
112NbField_i=size(i1_series{1},2); %nb of fields for the i index
113NbField=NbField_j*NbField_i; %total number of fields
114
115%% determine the file type on each line from the first input file
116ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};
117NcTypeOptions={'netcdf','civx','civdata'};
118for iview=1:NbView
119    if ~exist(filecell{iview,1}','file')
120        msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'])
121        return
122    end
123    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
124    FileType{iview}=FileInfo{iview}.FileType;
125    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
126    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
127    if ~isempty(j1_series{iview})
128        frame_index{iview}=j1_series{iview};
129    else
130        frame_index{iview}=i1_series{iview};
131    end
132end
133
134%% calibration data and timing: read the ImaDoc files
135XmlData=[];
136[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
137if size(time,1)>1
138    diff_time=max(max(diff(time)));
139    if diff_time>0
140        msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
141    end   
142end
143
144%% coordinate transform or other user defined transform
145transform_fct='';%default
146if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
147    addpath(Param.FieldTransform.TransformPath)
148    transform_fct=str2func(Param.FieldTransform.TransformName);
149    rmpath(Param.FieldTransform.TransformPath)
150end
151
152%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
153 % EDIT FROM HERE
154
155%% check the validity of  input file types
156if CheckImage{1}
157    FileExtOut='.png'; % write result as .png images for image inputs
158elseif CheckNc{1}
159    FileExtOut='.nc';% write result as .nc files for netcdf inputs
160else
161    msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}])
162    return
163end
164
165
166%% settings for the output file
167NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
168first_i=i1_series{1}(1);
169last_i=i1_series{1}(end);
170if isempty(j1_series{1})% if there is no second index j
171    first_j=1;last_j=1;
172else
173    first_j=j1_series{1}(1);
174    last_j=j1_series{1}(end);
175end
176
177%% Set field names and velocity types
178InputFields{1}=[];%default (case of images)series
179if isfield(Param,'InputFields')
180    InputFields{1}=Param.InputFields;
181end
182
183nbfiles=0;
184nbmissing=0;
185
186%% initialisation manip Coriolis
187char_index=regexp(SubDir{1},'waves_L1_');
188switch(SubDir{1}(char_index+9))
189    case '1'
190        amplitude=2.5 %oscillation amplitude
191        T=24.46;
192        t0=3 ;% dt=0.5 s, torus at its max x at the beginning of motion, i0=7
193    case '2'
194        amplitude=5 %oscillation amplitude
195        T=24.47;
196        t0=8.5; % dt=1/3 s -> image index of starting motion = 26, % torus at its max x at the beginning of motion
197    case '3'
198        amplitude=10 %oscillation amplitude
199        T=24.45;
200        t0=6.5-T/2;% dt=0.25, torus at its minimum x at the beginning of motion
201    case '4' 
202        amplitude=15 %oscillation amplitude
203        T=24.48;
204        t0=3.4;     %dt=0.2 -> i0=18 image index of starting motion, % torus at its max x at the beginning of motion
205end
206%NbPeriod=2; %number of periods for the sliding average
207NbPeriod=4; %number of periods for the sliding average
208omega=2*2*pi/T;%harmonic
209Lscale=15;%diameter of the torus, length scale for normalisation
210Uscale=amplitude*omega;
211
212DataOut.ListGlobalAttribute= {'Conventions','Time'};
213DataOut.Conventions='uvmat';
214DataOut.ListVarName={'coord_y','coord_x','Umean','Vmean','Ucos','Vcos','Usin','Vsin','DUDXsin','DUDXcos','DUDYsin','DVDXsin','DVDXcos'...
215    ,'DVDYsin','Ustokes','Vstokes'};
216DataOut.VarDimName={'coord_y','coord_x',{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},...
217    {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},...
218    {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}};
219
220%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
221% First get time %
222[Data,tild,errormsg]=nc2struct(filecell{1,1});   
223Time_1=Data.Time;
224if ~isempty(errormsg)
225    disp_uvmat('ERROR',errormsg,checkrun)
226    return
227end
228[Data,tild,errormsg]=nc2struct(filecell{1,end});   
229Time_end=Data.Time;
230dt=(Time_end-Time_1)/(NbField-1); %time interval
231NpTime=round(NbPeriod*T/dt+1);
232
233OutputPath=fullfile(Param.OutputPath,num2str(Param.Experiment),num2str(Param.Device));
234RootFileOut=RootFile{1};
235NomTypeOut='_1';
236%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
237disp('loop for filtering started')
238for index=1:NbField
239    update_waitbar(WaitbarHandle,index/NbField)
240    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
241        disp('program stopped by user')
242        break
243    end
244    [Field,tild,~] = read_field(filecell{1,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
245   
246    %%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
247    if index==1 %first field
248        DataOut.coord_x=Field.coord_x/Lscale;
249        DataOut.coord_y=Field.coord_y/Lscale;
250        npy=numel(DataOut.coord_y);
251        npx=numel(DataOut.coord_x);
252        Umean=zeros(NpTime,npy,npx);
253        Vmean=zeros(NpTime,npy,npx);
254        Ucos=zeros(NpTime,npy,npx);
255        Vcos=zeros(NpTime,npy,npx);
256        Usin=zeros(NpTime,npy,npx);
257        Vsin=zeros(NpTime,npy,npx);
258        DUDXcos=zeros(NpTime,npy,npx);
259        DUDXsin=zeros(NpTime,npy,npx);
260        DUDYsin=zeros(NpTime,npy,npx);
261        DVDXcos=zeros(NpTime,npy,npx);
262        DVDXsin=zeros(NpTime,npy,npx);
263        DVDYsin=zeros(NpTime,npy,npx);
264    end
265    Time(index)=Field.Time-t0;%time from the start of the motion
266    Umean=circshift(Umean,[-1 0 0]); %shift U by ishift along the first index
267    Vmean=circshift(Vmean,[-1 0 0]); %shift U by ishift along the first index
268    Ucos=circshift(Ucos,[-1 0 0]); %shift U by ishift along the first index
269    Vcos=circshift(Vcos,[-1 0 0]); %shift U by ishift along the first index
270    Usin=circshift(Usin,[-1 0 0]); %shift U by ishift along the first index
271    Vsin=circshift(Vsin,[-1 0 0]); %shift U by ishift along the first index
272    DUDXcos=circshift(DUDXcos,[-1 0 0]);
273    DUDXsin=circshift(DUDXsin,[-1 0 0]);
274    DUDYsin=circshift(DUDYsin,[-1 0 0]);       
275    DVDXcos=circshift(DVDXcos,[-1 0 0]);
276    DVDXsin=circshift(DVDXsin,[-1 0 0]);
277    DVDYsin=circshift(DVDYsin,[-1 0 0]);       
278    Umean(end,:,:)=Field.U;
279    Vmean(end,:,:)=Field.V;
280    Ucos(end,:,:)=Field.U*cos(omega*Time(index));
281    Vcos(end,:,:)=Field.V*cos(omega*Time(index));
282    Usin(end,:,:)=Field.U*sin(omega*Time(index));
283    Vsin(end,:,:)=Field.V*sin(omega*Time(index));
284    DUDXcos(end,:,:)=Field.DUDX*cos(omega*Time(index));
285    DUDXsin(end,:,:)=Field.DUDX*sin(omega*Time(index));
286    DUDYsin(end,:,:)=Field.DUDY*sin(omega*Time(index));% ParamOut=[];%default output
287
288    DVDXcos(end,:,:)=Field.DVDX*cos(omega*Time(index));
289    DVDXsin(end,:,:)=Field.DVDX*sin(omega*Time(index));
290    DVDYsin(end,:,:)=Field.DVDY*sin(omega*Time(index));
291    DataOut.Time=(Time(index)-(NpTime-1)*dt/2)/T;%time inperiods from the beginning of the oscillation (torus at max abscissa)
292    DataOut.Umean=(1/Uscale)*squeeze(nanmean(Umean,1));
293    DataOut.Vmean=(1/Uscale)*squeeze(nanmean(Vmean,1));
294    DataOut.Ucos=2*(1/Uscale)*squeeze(nanmean(Ucos,1));
295    DataOut.Vcos=2*(1/Uscale)*squeeze(nanmean(Vcos,1));
296    DataOut.Usin=2*(1/Uscale)*squeeze(nanmean(Usin,1));
297    DataOut.Vsin=2*(1/Uscale)*squeeze(nanmean(Vsin,1));
298    DataOut.DUDXcos=2*squeeze(nanmean(DUDXcos,1));
299    DataOut.DUDXsin=2*squeeze(nanmean(DUDXsin,1));
300    DataOut.DUDYsin=2*squeeze(nanmean(DUDYsin,1));
301    DataOut.DVDXcos=2*squeeze(nanmean(DVDXcos,1));
302    DataOut.DVDXsin=2*squeeze(nanmean(DVDXsin,1));
303    DataOut.DVDYsin=2*squeeze(nanmean(DVDYsin,1));
304    DataOut.Ustokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DUDXsin+DataOut.Vcos.*DataOut.DUDYsin);
305    DataOut.Vstokes=(1/omega)*(1/Uscale)*(DataOut.Ucos.*DataOut.DVDXsin+DataOut.Vcos.*DataOut.DVDYsin);
306
307    % writing the result file as netcdf file
308    i1=i1_series{1}(index);
309    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,'.nc',NomTypeOut,i1);
310    errormsg=struct2nc(OutputFile, DataOut);
311    if isempty(errormsg)
312        disp([OutputFile ' written'])
313    else
314        disp(errormsg)
315    end
316end
317   
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