source: trunk/src/series/aver_synchro.m @ 804

Last change on this file since 804 was 787, checked in by sommeria, 10 years ago

aver_synchro corrected

File size: 11.5 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
41function ParamOut=aver_synchro(Param)
42
43%% set the input elements needed on the GUI series when the action is selected in the menu ActionName
44if isstruct(Param) && isequal(Param.Action.RUN,0)
45    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
46    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
47    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
48    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
49    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
50    ParamOut.FieldTransform = 'on';%can use a transform function
51    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
52    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
53    ParamOut.OutputDirExt='.synchro';%set the output dir extension
54    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
55    %     filecell=get_file_series(Param);%check existence of the first input file
56    %     if ~exist(filecell{1,1},'file')
57    %         msgbox_uvmat('WARNING','the first input file does not exist')
58    %     end
59    def={'26'};
60    if isfield (Param,'ActionInput')&& isfield(Param.ActionInput,'WavePeriod')
61        def=Param.ActionInput.WavePeriod;
62       
63        def={num2str(def)};
64    end
65    prompt={'wave period'};
66    dlgTitle='primary period';
67    lineNo=1;
68    answer=inputdlg(prompt,dlgTitle,lineNo,def);
69    ParamOut.ActionInput.WavePeriod=str2num(answer{1});
70    return
71end
72
73%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
74ParamOut=[];%default output
75%% read input parameters from an xml file if input is a file name (batch mode)
76checkrun=1;
77if ischar(Param)
78    Param=xml2struct(Param);% read Param as input file (batch case)
79    checkrun=0;
80end
81hseries=findobj(allchild(0),'Tag','series');
82RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
83WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
84
85%% define the directory for result file (with path=RootPath{1})
86OutputDir=[Param.OutputSubDir Param.OutputDirExt];
87   
88%% root input file(s) name, type and index series
89RootPath=Param.InputTable(:,1);
90RootFile=Param.InputTable(:,3);
91SubDir=Param.InputTable(:,2);
92NomType=Param.InputTable(:,4);
93FileExt=Param.InputTable(:,5);
94[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
95FileInfo=get_file_info(filecell{1,1});
96 FileType=FileInfo.FileType;
97%%%%%%%%%%%%
98% The cell array filecell is the list of input file names, while
99% filecell{iview,fileindex}:
100%        iview: line in the table corresponding to a given file series
101%        fileindex: file index within  the file series,
102% 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
103% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
104%%%%%%%%%%%%
105nbview=numel(i1_series);%number of input file series (lines in InputTable)
106nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
107nbfield_i=size(i1_series{1},2); %nb of fields for the i index
108nbfield=nbfield_j*nbfield_i; %total number of fields
109
110%% determine the input file type
111% if ~strcmp(FileType{1},'netcdf')
112%     displ_uvmat('ERROR','netcdf file series with field projected on a regular mesh must be put as input')
113%     return
114% end
115
116%% calibration data and timing: read the ImaDoc files
117[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
118% if size(time,1)>1
119%     diff_time=max(max(diff(time)));
120%     if diff_time>0
121%         msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)])
122%     end   
123% end
124
125%% coordinate transform or other user defined transform
126transform_fct='';%default
127if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
128    addpath(Param.FieldTransform.TransformPath)
129    transform_fct=str2func(Param.FieldTransform.TransformName);
130    rmpath(Param.FieldTransform.TransformPath)
131end
132
133%% settings for the output file
134NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
135first_i=i1_series{1}(1);
136last_i=i1_series{1}(end);
137if isempty(j1_series{1})% if there is no second index j
138    first_j=1;last_j=1;
139else
140    first_j=j1_series{1}(1);
141    last_j=j1_series{1}(end);
142end
143
144%% Set field names and velocity types
145InputFields{1}=[];%default (case of images)
146if isfield(Param,'InputFields')
147    InputFields{1}=Param.InputFields;
148end
149
150% for i_slice=1:NbSlice
151% index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
152nbfiles=0;
153nbmissing=0;
154MeanU=0;
155MeanV=0;
156MinU=0;
157MaxU=0;
158MinV=0;
159MaxV=0;
160vec_X=0;
161vec_Y=0;
162vec_U=0; %initiate the sum
163vec_V=0;
164cos1_U=0;
165cos1_V=0;
166sin1_U=0;
167sin1_V=0;
168cos2_U=0;
169cos2_V=0;
170sin2_U=0;
171sin2_V=0;
172cos3_U=0;
173cos3_V=0;
174sin3_U=0;
175sin3_V=0;
176cossub_U=0;
177cossub_V=0;
178sinsub_U=0;
179sigma1=2*pi/Param.ActionInput.WavePeriod;%primary wave frequency
180sigma2=4*pi/Param.ActionInput.WavePeriod;%harmonic 2
181sigma3=6*pi/Param.ActionInput.WavePeriod;%harmonic 3
182sigma_sub=pi/Param.ActionInput.WavePeriod;%subharmonic
183sinsub_V=0;
184vec_C=0;
185 
186%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
187for index=1:nbfield
188    update_waitbar(WaitbarHandle,index/nbfield)
189    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
190        disp('program stopped by user')
191        break
192    end
193   
194    % reading input file(s)
195    [Data,tild,errormsg] = read_field(filecell{1,index},FileType,InputFields{1});
196    if ~isempty(errormsg)
197        displ_uvmat('ERROR',['error of input reading: ' errormsg],checkrun);
198        break
199    end
200    if ~isempty(NbSlice_calib)
201        Data.ZIndex=mod(i1_series{1}(index)-1,NbSlice_calib{1})+1;%Zindex for phys transform
202    end
203    %update average
204    MeanU=MeanU+Data.U;
205    MeanV=MeanV+Data.V;
206    MaxU=(MaxU>=Data.U).*MaxU+(MaxU<Data.U).*Data.U;
207    MinU=(MinU<=Data.U).*MinU+(MinU>Data.U).*Data.U;
208    MaxV=(MaxV>=Data.V).*MaxV+(MaxV<Data.V).*Data.V;
209    MinV=(MinV<=Data.V).*MinV+(MinV>Data.V).*Data.V;
210    cos1_U=cos1_U+Data.U*cos(Data.Time*sigma1);
211    cos1_V=cos1_V+Data.V*cos(Data.Time*sigma1);
212    sin1_U=sin1_U+Data.U*sin(Data.Time*sigma1);
213    sin1_V=sin1_V+Data.V*sin(Data.Time*sigma1);
214    cos2_U=cos2_U+Data.U*cos(Data.Time*sigma2);
215    cos2_V=cos2_V+Data.V*cos(Data.Time*sigma2);
216    sin2_U=sin2_U+Data.U*sin(Data.Time*sigma2);
217    sin2_V=sin2_V+Data.V*sin(Data.Time*sigma2);
218    cos3_U=cos3_U+Data.U*cos(Data.Time*sigma3);
219    cos3_V=cos3_V+Data.V*cos(Data.Time*sigma3);
220    sin3_U=sin3_U+Data.U*sin(Data.Time*sigma3);
221    sin3_V=sin3_V+Data.V*sin(Data.Time*sigma3);
222    cossub_U=cossub_U+Data.U*cos(Data.Time*sigma_sub);
223    cossub_V=cossub_V+Data.V*cos(Data.Time*sigma_sub);
224    sinsub_U=sinsub_U+Data.U*sin(Data.Time*sigma_sub);
225    sinsub_V=sinsub_V+Data.V*sin(Data.Time*sigma_sub);
226   
227   
228end
229
230%%%%%%%%%%%%%%%%%%%%%%%%
231Data.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',...
232    'phase1_U','phase1_V','phase2_U','phase2_V','phase3_U','phase3_V'};
233%Data.ListVarName=[{'coord_y','coord_x'} Data.ListVarName];
234%Data.VarDimName={'coord_y', 'coord_x'};
235for ilist=1:numel(Data.ListVarName)-2
236    Data.VarDimName{ilist+2}={'coord_y','coord_x'};
237 %   Data.VarDimName{ilist}='nb_vectors';
238end
239Data.MeanU=MeanU/nbfield;
240Data.MeanV=MeanV/nbfield;
241Data.cos1_U=cos1_U/nbfield;
242Data.cos1_V=cos1_V/nbfield;
243sin1_U=sin1_U/nbfield;
244sin1_V=sin1_V/nbfield;
245cos2_U=cos2_U/nbfield;
246cos2_V=cos2_V/nbfield;
247sin2_U=sin2_U/nbfield;
248sin2_V=sin2_V/nbfield;
249cos3_U=cos3_U/nbfield;
250cos3_V=cos3_V/nbfield;
251sin3_U=sin3_U/nbfield;
252sin3_V=sin3_V/nbfield;
253cossub_U=cossub_U/nbfield;
254cossub_V=cossub_V/nbfield;
255sinsub_U=sinsub_U/nbfield;
256sinsub_V=sinsub_V/nbfield;
257Data.a1_U=sqrt(2)*sqrt(Data.cos1_U.*Data.cos1_U+sin1_U.*sin1_U);
258Data.a1_V=-sqrt(2)*sqrt(Data.cos1_V.*Data.cos1_V+sin1_V.*sin1_V);
259Data.a2_U=sqrt(2)*sqrt(cos2_U.*cos2_U+sin2_U.*sin2_U);
260Data.a2_V=-sqrt(2)*sqrt(cos2_V.*cos2_V+sin2_V.*sin2_V);
261Data.a3_U=sqrt(2)*sqrt(cos3_U.*cos3_U+sin3_U.*sin3_U);
262Data.a3_V=-sqrt(2)*sqrt(cos3_V.*cos3_V+sin3_V.*sin3_V);
263Data.asub_U=sqrt(2)*sqrt(cossub_U.*cossub_U+sinsub_U.*sinsub_U);
264Data.asub_V=-sqrt(2)*sqrt(cossub_V.*cossub_V+sinsub_V.*sinsub_V);
265clear i
266Data.phase1_U=(angle(cos1_U+i*sin1_U));
267Data.phase1_V=angle(cos1_V+i*sin1_V);
268Data.phase2_U=(angle(cos2_U+i*sin2_U));
269Data.phase2_V=(angle(cos2_V+i*sin2_V));
270Data.phase3_U=(angle(cos3_U+i*sin3_U));
271Data.phase3_V=(angle(cos3_V+i*sin3_V));
272Data.phasesub_U=(angle(cossub_U+i*sinsub_U));
273Data.phasesub_V=(angle(cossub_V+i*sinsub_V));
274
275%% write the results
276OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','',1);
277errormsg=struct2nc(OutputFile,Data);% write the output file
278if isempty(errormsg)
279    disp_uvmat('CONFIRMATION',[OutputFile ' successfully written'],checkrun)
280else
281    disp_uvmat('ERROR',errormsg,checkrun)
282end
283   
284
285%% open the result file with uvmat (in RUN mode)
286% if checkrun
287%     uvmat(OutputFile)% open the last result file with uvmat
288% end
289'#### THE END ####'
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