source: trunk/src/series/aver_stat.m @ 924

Last change on this file since 924 was 924, checked in by g7moreau, 5 years ago
  • Update Copyright Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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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 2008-2016, 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_stat(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)% function activated from the GUI series but not RUN
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='.stat';%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     % check for selection of a projection object
74    hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
75    if  ~isfield(Param,'ProjObject')
76        answer=msgbox_uvmat('INPUT_Y-N','use a projection object?');
77        if strcmp(answer,'Yes')
78            hhseries=guidata(hseries);
79            set(hhseries.CheckObject,'Visible','on')
80            set(hhseries.CheckObject,'Value',1)
81            Param.CheckObject=1;
82            series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading  in uvmat, show the image in phys coordinates
83        end
84    end
85    % introduce bin size for histograms
86    if isfield(Param,'CheckObject') && Param.CheckObject
87        SeriesData=get(hseries,'UserData');
88        if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
89            answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
90            ParamOut.ActionInput.VarMesh=str2num(answer);
91        end
92    end
93    % check the existence of the first and last file in the series
94    first_j=[];
95    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
96    last_j=[];
97    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
98    PairString='';
99    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
100    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
101    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
102        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
103    if ~exist(FirstFileName,'file')
104        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
105    else
106        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
107        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
108        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
109        if ~exist(LastFileName,'file')
110             msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
111        end
112    end
113    return
114end
115
116%%%%%%%%%%%%  STANDARD PART  %%%%%%%%%%%%
117ParamOut=[];%default output
118%% read input parameters from an xml file if input is a file name (batch mode)
119checkrun=1;
120if ischar(Param)
121    Param=xml2struct(Param);% read Param as input file (batch case)
122    checkrun=0;
123end
124hseries=findobj(allchild(0),'Tag','series');
125RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
126WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
127
128%% define the directory for result file (with path=RootPath{1})
129OutputDir=[Param.OutputSubDir Param.OutputDirExt];
130   
131%% root input file(s) name, type and index series
132RootPath=Param.InputTable(:,1);
133RootFile=Param.InputTable(:,3);
134SubDir=Param.InputTable(:,2);
135NomType=Param.InputTable(:,4);
136FileExt=Param.InputTable(:,5);
137hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
138[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
139if ~isempty(hdisp),delete(hdisp),end;
140%%%%%%%%%%%%
141% The cell array filecell is the list of input file names, while
142% filecell{iview,fileindex}:
143%        iview: line in the table corresponding to a given file series
144%        fileindex: file index within  the file series,
145% 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
146% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
147%%%%%%%%%%%%
148NbView=numel(i1_series);%number of input file series (lines in InputTable)
149NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
150NbField_i=size(i1_series{1},2); %nb of fields for the i index
151NbField=NbField_j*NbField_i; %total number of fields
152
153%% determine the file type on each line from the first input file
154ImageTypeOptions={'image','multimage','mmreader','video'};
155NcTypeOptions={'netcdf','civx','civdata'};
156for iview=1:NbView
157    if ~exist(filecell{iview,1}','file')
158        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
159        return
160    end
161    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
162    FileType{iview}=FileInfo{iview}.FileType;
163    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
164    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
165    if ~isempty(j1_series{iview})
166        frame_index{iview}=j1_series{iview};
167    else
168        frame_index{iview}=i1_series{iview};
169    end
170end
171
172%% calibration data and timing: read the ImaDoc files
173[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
174if size(time,1)>1
175    diff_time=max(max(diff(time)));
176    if diff_time>0
177        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
178    end   
179end
180
181%% coordinate transform or other user defined transform
182transform_fct='';%default
183if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
184    addpath(Param.FieldTransform.TransformPath)
185    transform_fct=str2func(Param.FieldTransform.TransformName);
186    rmpath(Param.FieldTransform.TransformPath)
187    if isfield(Param,'TransformInput')
188            XmlData{1}.TransformInput=Param.TransformInput;
189    end     
190end
191
192%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
193 % EDIT FROM HERE
194
195%% check the validity of  input file types and set the output file type
196if CheckImage{1}
197    FileExtOut='.png'; % write result as .png images for image inputs
198elseif CheckNc{1}
199    FileExtOut='.nc';% write result as .nc files for netcdf inputs
200else
201    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
202    return
203end
204if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
205    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
206    return
207end
208if isfield(Param,'ProjObject') && ~strcmp(Param.ProjObject.Type,'plane')
209      FileExtOut='.nc';% write result as .nc files (even for image input)
210end
211
212%% settings for the output file
213NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
214first_i=i1_series{1}(1);
215last_i=i1_series{1}(end);
216if isempty(j1_series{1})% if there is no second index j
217    first_j=1;last_j=1;
218else
219    first_j=j1_series{1}(1);
220    last_j=j1_series{1}(end);
221end
222
223%% Set field names and velocity types
224InputFields{1}=[];%default (case of images)
225if NbView==2
226    InputFields{2}=[];%default (case of images)
227end
228if isfield(Param,'InputFields')
229    InputFields{1}=Param.InputFields;
230    if NbView==2
231        InputFields{2}=Param.InputFields;%default
232        if isfield(Param.InputFields,'FieldName_1')
233            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
234            if isfield(Param.InputFields,'VelType_1')
235                InputFields{2}.VelType=Param.InputFields.VelType_1;
236            end
237        end
238    end
239end
240nbfiles=0;%counter of the successfully read files (bad files are skipped)
241VarMesh=[];
242if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
243    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
244     VarMesh=Param.ActionInput.VarMesh;
245    else
246       VarMesh=[];
247       disp_uvmat('WARNING','automatic bin size for histograms, select aver_stat again to set the value',checkrun)
248    end
249end
250%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
251for index=1:NbField
252    update_waitbar(WaitbarHandle,index/NbField)
253    if ~isempty(RUNHandle)&& ~strcmp(get(RUNHandle,'BusyAction'),'queue')
254        disp('program stopped by user')
255        break
256    end
257   
258    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
259    for iview=1:NbView
260        % reading input file(s)
261        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
262        if ~isempty(errormsg)
263            errormsg=['error of input reading: ' errormsg];
264            break
265        end
266        if ~isempty(NbSlice_calib)
267            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
268        end
269    end
270    %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%%
271    %%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
272    % EDIT FROM HERE
273   
274    if isempty(errormsg)
275        Field=Data{1}; % default input field structure
276        nbfiles=nbfiles+1; %increment the file counter
277        %% coordinate transform (or other user defined transform)
278        if ~isempty(transform_fct)
279            switch nargin(transform_fct)
280                case 4
281                    if length(Data)==2
282                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
283                    else
284                        Field=transform_fct(Data{1},XmlData{1});
285                    end
286                case 3
287                    if length(Data)==2
288                        Field=transform_fct(Data{1},XmlData{1},Data{2});
289                    else
290                        Field=transform_fct(Data{1},XmlData{1});
291                    end
292                case 2
293                    Field=transform_fct(Data{1},XmlData{1});
294                case 1
295                    Field=transform_fct(Data{1});
296            end
297        end
298       
299        %% field projection on an object
300        if Param.CheckObject
301            if strcmp(Param.ProjObject.ProjMode,'interp_tps')
302                Field=tps_coeff_field(Field,check_proj_tps);% calculate tps coefficients if needed
303            end
304            [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
305            if ~isempty(errormsg)
306                disp_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg],checkrun)
307                return
308            end
309        end
310             
311        %%%%%%%%%%%% MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
312        if nbfiles==1 %first field
313            time_1=[];
314            if isfield(Field,'Time')
315                time_1=Field.Time(1);
316            end
317            DataOut=Field;%outcome reproduces the first (projected) field by default
318            DataOut.Conventions='uvmat'; %suppress Conventions='uvmat/civdata' for civ input files         
319            if isfield(Param,'ProjObject')&& ismember(Param.ProjObject.ProjMode,{'inside','outside'})%case of histograms
320                for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
321                    VarName=Field.ListVarName{ivar};
322                    if isfield(Data{1},VarName)
323                        DataOut.(VarName)=Field.(VarName);
324                        DataOut.([VarName 'Histo'])=zeros(size(DataOut.(VarName)));
325                        VarMesh=DataOut.(VarName)(2)-DataOut.(VarName)(1);
326                    end
327                end
328                disp(['mesh for histogram = ' num2str(VarMesh)])
329            else
330                errorvar=zeros(numel(Field.ListVarName));%index of errorflag associated to each variable
331                if isfield(Field,'VarAttribute')
332                    for ivar=1:numel(Field.ListVarName)
333                        VarName=Field.ListVarName{ivar};
334                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
335                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
336                       
337                        for iivar=1:length(Field.VarAttribute)
338                            if isequal(Field.VarDimName{iivar},Field.VarDimName{ivar})&& isfield(Field.VarAttribute{iivar},'Role')...
339                                    && strcmp(Field.VarAttribute{iivar}.Role,'errorflag')
340                                errorvar(ivar)=iivar; % index of the errorflag variable corresponding to ivar
341                            end
342                        end
343                    end
344                    DataOut.ListVarName(errorvar(errorvar~=0))=[]; %remove errorflag from result
345                    DataOut.VarDimName(errorvar(errorvar~=0))=[]; %remove errorflag from result
346                    DataOut.VarAttribute(errorvar(errorvar~=0))=[]; %remove errorflag from result
347                else
348                                   for ivar=1:numel(Field.ListVarName)
349                                       VarName=Field.ListVarName{ivar};
350                        DataOut.(VarName)=zeros(size(DataOut.(VarName)));% initiate each field to zero
351                        NbData.(VarName)=zeros(size(DataOut.(VarName)));% initiate the nbre of good data to zero
352                                   end
353                end
354               
355            end
356        end   %current field
357        for ivar=1:length(DataOut.ListVarName)
358            VarName=DataOut.ListVarName{ivar};
359            sizmean=size(DataOut.(VarName));
360            siz=size(Field.(VarName));
361            if isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'})
362                if isfield(Data{1},VarName)
363                    MaxValue=max(DataOut.(VarName));% current max of histogram absissa
364                    MinValue=min(DataOut.(VarName));% current min of histogram absissa
365%                     VarMesh=Field.VarAttribute{ivar}.Mesh;
366                    MaxIndex=round(MaxValue/VarMesh);
367                    MinIndex=round(MinValue/VarMesh);
368                    MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
369                    MinIndex_new=round(min(Field.(VarName)/VarMesh));
370                    if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
371                        DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
372                        DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(1,MaxIndex_new-MaxIndex)]; % append the new histo values                   
373                    end
374                    if MinIndex_new <= MinIndex-1
375                        DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
376                        DataOut.([VarName 'Histo'])=[zeros(1,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
377                        ind_start=1;
378                    else
379                        ind_start=MinIndex_new-MinIndex+1;
380                    end
381                    DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
382                        DataOut.([VarName 'Histo'])(ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);   
383                end
384            elseif ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean)
385                disp_uvmat('ERROR',['unequal size of input field ' VarName ', need to project  on a grid'],checkrun)
386                return
387            else
388                if errorvar(ivar)==0
389                    check_bad=isnan(Field.(VarName));%=0 for NaN data values, 1 else
390                else
391                    check_bad=isnan(Field.(VarName)) | Field.(Field.ListVarName{errorvar(ivar)})~=0;%=0 for NaN or error flagged data values, 1 else
392                end
393                Field.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
394                DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum
395                NbData.(VarName)=NbData.(VarName)+ ~check_bad;% records the number of data for each point
396            end
397        end
398        %%%%%%%%%%%%   END MAIN RUNNING OPERATIONS  %%%%%%%%%%%%
399    else
400        disp(errormsg)
401    end
402end
403%%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%%
404if ~(isfield(Param,'ProjObject') && ismember(Param.ProjObject.ProjMode,{'inside','outside'}))
405    for ivar=1:length(Field.ListVarName)
406        VarName=Field.ListVarName{ivar};
407        DataOut.(VarName)=DataOut.(VarName)./NbData.(VarName); % normalize the mean
408    end
409end
410nbmissing=NbField-nbfiles;
411if nbmissing~=0
412    disp_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipped'],checkrun)
413end
414if isempty(time) % time is read from files
415    if isfield(Field,'Time')
416        time_end=Field.Time(1);%last time read
417        if ~isempty(time_1)
418            DataOut.Time=time_1;
419            DataOut.Time_end=time_end;
420        end
421    end
422else  % time from ImaDoc prevails if it exists
423    DataOut.Time=time(1);
424    DataOut.Time_end=time(end);
425end
426
427%% writing the result file
428OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
429if strcmp(FileExtOut,'.png') %case of images
430    if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16))
431        DataOut.A=uint16(DataOut.A);
432        imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images
433    else
434        DataOut.A=uint8(DataOut.A);
435        imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images
436    end
437    disp([OutputFile ' written']);
438else %case of netcdf  file , determine global attributes
439    errormsg=struct2nc(OutputFile,DataOut); %save result file
440    if isempty(errormsg)
441        disp([OutputFile ' written']);
442    else
443        disp(['error in writting result file: ' errormsg])
444    end
445end  % end averaging  loop
446
447%% open the result file with uvmat (in RUN mode)
448if checkrun
449    uvmat(OutputFile)% open the last result file with uvmat
450end
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