source: trunk/src/series/test_patch_tps.m @ 1142

Last change on this file since 1142 was 1142, checked in by sommeria, 5 months ago

filter parameter improved in filter_tps

File size: 12.2 KB
Line 
1%'test_patch_tps': test the optimum value for the spline smmoothing function used in civ_series
2%------------------------------------------------------------------------
3% Method:
4    %open a netcdf file with civ results.
5   
6% function ParamOut=test_patch_tps (Param)
7%
8%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
9%
10%OUTPUT
11% ParamOut: sets input parameters when the function is selected, not activated(input Param.Action.RUN=0),=[] when the function is running
12%
13%INPUT:
14% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
15% In batch mode, Param is the name of the corresponding xml file containing the same information
16% when Param.Action.RUN=0 (as activated when the current Action is selected
17% in series), the function ouput paramOut set the activation of the needed GUI elements
18%
19% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
20% see the current structure Param)
21%    .InputTable: cell of input file names, (several lines for multiple input)
22%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
23%    .OutputSubDir: name of the subdirectory for data outputs
24%    .OutputDirExt: directory extension for data outputs
25%    .Action: .ActionName: name of the current activated function
26%             .ActionPath:   path of the current activated function
27%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
28%             .RUN =0 for GUI input, =1 for function activation
29%             .RunMode='local','background', 'cluster': type of function  use
30%             
31%    .IndexRange: set the file or frame indices on which the action must be performed
32%    .InputFields: sub structure describing the input fields withfields
33%              .FieldName: name(s) of the field
34%              .VelType: velocity type
35
36%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
37
38%=======================================================================
39% Copyright 2008-2024, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
40%   http://www.legi.grenoble-inp.fr
41%   Joel.Sommeria - Joel.Sommeria (A) univ-grenoble-alpes.fr
42%
43%     This file is part of the toolbox UVMAT.
44%
45%     UVMAT is free software; you can redistribute it and/or modify
46%     it under the terms of the GNU General Public License as published
47%     by the Free Software Foundation; either version 2 of the license,
48%     or (at your option) any later version.
49%
50%     UVMAT is distributed in the hope that it will be useful,
51%     but WITHOUT ANY WARRANTY; without even the implied warranty of
52%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
53%     GNU General Public License (see LICENSE.txt) for more details.
54%=======================================================================
55
56function ParamOut=test_patch_tps (Param)
57
58%%%%%%%%%%%%%%%%%    INPUT PREPARATION MODE (no RUN)    %%%%%%%%%%%%%%%%%
59if isstruct(Param) && isequal(Param.Action.RUN,0)
60    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
61    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
62    ParamOut.NbSlice='off'; % edit box nbre of slices made active
63    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
64    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
65    ParamOut.FieldTransform = 'off';%can use a transform function
66    ParamOut.ProjObject='off';%cannot use projection object(option 'off'/'on',
67    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
68    ParamOut.OutputDirExt='.test_patch';%set the output dir extension
69    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
70   
71    %% root input file(s) and type
72    % check the existence of the first file in the series
73     first_j=[];% note that the function will propose to cover the whole range of indices
74    if isfield(Param.IndexRange,'MinIndex_j'); first_j=Param.IndexRange.MinIndex_j; end
75    last_j=[];
76    if isfield(Param.IndexRange,'MaxIndex_j'); last_j=Param.IndexRange.MaxIndex_j; end
77    PairString='';
78    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
79    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
80    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
81        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
82    if ~exist(FirstFileName,'file')
83        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
84        return
85    else
86        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
87        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
88        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
89        if ~exist(FirstFileName,'file')
90             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
91        end
92    end
93
94    %% check the validity of  input file types
95    Data=nc2struct(FirstFileName,[]);
96    if isfield(Data,'CivStage')
97        switch Data.CivStage
98            case {1,2}
99                CivStage='civ1';
100                MaxDiff=1.5; SubDomainSize=250; FieldSmooth=10; %default
101            case 3
102                CivStage='civ1';
103                MaxDiff=Data.Patch1_MaxDiff;
104               SubDomainSize=Data.Patch1_SubDomainSize;
105               FieldSmooth=Data.Patch1_FieldSmooth;
106            case {4,5}
107                CivStage='civ2';
108                MaxDiff=1.5; SubDomainSize=250; FieldSmooth=5; %default
109            case 6
110                CivStage='civ2';
111                 MaxDiff=Data.Patch2_MaxDiff;
112               SubDomainSize=Data.Patch2_SubDomainSize;
113               FieldSmooth=Data.Patch2_FieldSmooth;
114        end
115    else
116        msgbox_uvmat('ERROR',['invalid file type input: ' FileType ' not a civ data'])
117        return
118    end
119
120    %% numbers of fields
121    incr_j=1;%default
122    if isfield(Param.IndexRange,'incr_j')&&~isempty(Param.IndexRange.incr_j)
123        incr_j=Param.IndexRange.incr_j;
124    end
125    if isempty(first_j)||isempty(last_j)
126        nbfield_j=1;
127    else
128        nbfield_j=numel(first_j:incr_j:last_j);%nb of fields for the j index (bursts or volume slices)
129    end
130    first_i=1;last_i=1;incr_i=1;%default
131    if isfield(Param.IndexRange,'MinIndex_i'); first_i=Param.IndexRange.MinIndex_i; end   
132    if isfield(Param.IndexRange,'MaxIndex_i'); last_i=Param.IndexRange.MaxIndex_i; end
133    if isfield(Param.IndexRange,'incr_i')&&~isempty(Param.IndexRange.incr_i)
134        incr_i=Param.IndexRange.incr_i;
135    end
136    nbfield_i=numel(first_i:incr_i:last_i);%nb of fields for the i index (bursts or volume slices)
137    nbfield=nbfield_j*nbfield_i; %total number of fields
138   
139    %% setting of intput parameters
140    ListParam={'CivStage';'FieldSmooth';'MaxDiff';'SubDomainSize'};
141    DefaultValue={CivStage;FieldSmooth;MaxDiff;SubDomainSize};
142    if isfield(Param,'ActionInput')
143        ParamIn=Param.ActionInput;
144    else
145        ParamIn=[];
146    end
147        [ParamOut.ActionInput,errormsg] = set_param_input(ListParam,DefaultValue,ParamIn);
148        if ~isempty(errormsg)
149            msgbox_uvmat('ERROR',errormsg)
150        end
151    return
152end
153%%%%%%%%%%%%%%%%%    STOP HERE FOR PAMETER INPUT MODE   %%%%%%%%%%%%%%%%%
154
155%% read input parameters from an xml file if input is a file name (batch mode)
156checkrun=1;
157RUNHandle=[];
158WaitbarHandle=[];
159if ischar(Param)
160    Param=xml2struct(Param);% read Param as input file (batch case)
161    checkrun=0;
162else
163hseries=findobj(allchild(0),'Tag','series');
164RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
165WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
166end
167
168%% input preparation
169RootPath=Param.InputTable{:,1};
170RootFile=Param.InputTable{:,3};
171NomType=Param.InputTable{:,4};
172[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
173% if ~isempty(hdisp),delete(hdisp),end;
174%%%%%%%%%%%%
175    % The cell array filecell is the list of input file names, while
176    % filecell{iview,fileindex}:
177    %        iview: line in the table corresponding to a given file series
178    %        fileindex: file index within  the file series,
179    % 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
180    % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
181%%%%%%%%%%%%
182
183%% output file naming
184FileExtOut='.nc'; % write result as .png images for image inputsFileInfo.FileType='image'
185NomTypeOut=NomType;
186OutputDir=[Param.OutputSubDir Param.OutputDirExt];
187OutputPath=fullfile(Param.OutputPath,Param.Experiment,Param.Device);
188RootFileOut=RootFile;
189
190%% file index parameters
191
192Param.InputFields.VelType=Param.ActionInput.CivStage;
193SubDomainSize=Param.ActionInput.SubDomainSize;
194MaxDiff=Param.ActionInput.MaxDiff;
195FieldSmooth=(Param.ActionInput.FieldSmooth)*[0.1 0.2 0.5 1 2 5 10];%scan the smoothing param from 1/10 to 10 current value
196NbSmooth=numel(FieldSmooth);
197for irho=1:NbSmooth
198    str=num2str(FieldSmooth(irho));
199    str=regexprep(str,'\.','p');
200    Ustr{irho}=['U_' str];
201    Vstr{irho}=['V_' str];
202    Xstr{irho}=['X_' str];
203    Ystr{irho}=['Y_' str];
204    Dimstr{irho}='NbVec';
205    str_i{irho}=str;
206end
207
208%% Prepare the structure of output netcdf file
209DataOut.ListGlobalAttribute={'CivStage','SubDomainSize','MaxDiff','CoordUnit'};
210DataOut.CivStage=Param.InputFields.VelType;
211DataOut.SubDomainSize=SubDomainSize;
212DataOut.MaxDiff=MaxDiff;
213DataOut.CoordUnit='pixel';
214DataOut.ListVarName=[{'FieldSmooth','Diff_rms','NbExclude','X','Y'} Ustr Vstr] ;
215DataOut.VarDimName=[{'FieldSmooth','FieldSmooth','FieldSmooth','NbVec','NbVec'} Dimstr Dimstr];
216DataOut.VarAttribute{4}.Role='falseflag';
217DataOut.FieldSmooth=FieldSmooth;
218
219%% MAIN LOOP
220for index=1:1%numel(filecell)
221    Data=read_field(filecell{1,index},'civdata',Param.InputFields);
222            ind_good=find(Data.FF==0|Data.FF==20);%keep good civ data, and also the ones excluded by the criterium of discrepancy betwween smoothed and raw fields (FF=20)
223        NbGood=numel(ind_good);
224        Xin=Data.X(ind_good);
225        Yin=Data.Y(ind_good);
226        Uin=Data.U(ind_good);
227        Vin=Data.V(ind_good);
228        tic
229    for irho=1:NbSmooth
230        [SubRange,NbCentres,Coord_tps,U_tps,V_tps,~,U_smooth, V_smooth,~,FFres]=...
231            filter_tps([Xin Yin],Uin,Vin,[],SubDomainSize,FieldSmooth(irho),MaxDiff);
232        if irho==1
233            DataOut.FF=zeros(size(Xin));
234            DataOut.X=Xin;
235            DataOut.Y=Yin;
236        figure(1)
237            cla
238            scatter(Xin,Yin,1)
239            for irec=1:size(SubRange,3)
240                rectangle('Position',[SubRange(:,1,irec)' SubRange(:,2,irec)'-SubRange(:,1,irec)'])
241            end       
242            title('subdomains for thin shell splines (tps)')
243        end
244        ind_good=find(FFres==0);
245        ind_false=find(FFres~=0);
246        U_Diff=Uin(ind_good)-U_smooth(ind_good);
247        V_Diff=Vin(ind_good)-V_smooth(ind_good);
248        DataOut.Diff_rms(irho)=sqrt(mean(U_Diff.*U_Diff+V_Diff.*V_Diff)/2);
249        DataOut.NbExclude(irho)=(NbGood-numel(ind_good))/NbGood;
250        U_smooth(ind_false)=NaN;
251        V_smooth(ind_false)=NaN;
252        DataOut.(['U_' str_i{irho}])=U_smooth;
253        DataOut.(['V_' str_i{irho}])=V_smooth;
254        % DataOut.FF(ind_false)=FieldSmooth(irho);
255    end
256    time=toc
257    OutputFile=fullfile_uvmat(OutputPath,OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1_series{1}(index),[],j1_series{1}(index),j2_series{1}(index))
258    errormsg=struct2nc(OutputFile,DataOut)
259end
260figure
261    semilogx(FieldSmooth,DataOut.Diff_rms,'b',FieldSmooth,DataOut.NbExclude,'r',FieldSmooth,0.1*ones(size(FieldSmooth)),'m')
262    grid on
263    title( [filecell{1,1} ':' Param.InputFields.VelType])
264    legend({'rms vel. diff. ' ;' ratio excluded vectors';'recommended diff'},'Location','northwest')
265    xlabel('smoothing parameter')
266    ylabel('rms (pixels) and exclusion ratio')
267    OutputFig=fullfile(OutputPath,OutputDir,'plot_rms_diff.png')
268    saveas(2,OutputFig)
269
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