source: trunk/src/series/time_series.m @ 1071

Last change on this file since 1071 was 1071, checked in by g7moreau, 11 months ago
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1%'time_series': extract a time series after projection on an object (points , line..)
2% this function can be used as a template for applying a global operation on a series of input fields
3%------------------------------------------------------------------------
4% function GUI_input=time_series(Param)
5%
6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
8%OUTPUT
9% ParamOut: sets options in the GUI series.fig needed for the function
10%
11%INPUT:
12% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
13% In batch mode, Param is the name of the corresponding xml file containing the same information
14% when Param.Action.RUN=0 (as activated when the current Action is selected
15% in series), the function ouput paramOut set the activation of the needed GUI elements
16%
17% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
18% see the current structure Param)
19%    .InputTable: cell of input file names, (several lines for multiple input)
20%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
21%    .OutputSubDir: name of the subdirectory for data outputs
22%    .OutputDirExt: directory extension for data outputs
23%    .Action: .ActionName: name of the current activated function
24%             .ActionPath:   path of the current activated function
25%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
26%             .RUN =0 for GUI input, =1 for function activation
27%             .RunMode='local','background', 'cluster': type of function  use
28%             
29%    .IndexRange: set the file or frame indices on which the action must be performed
30%    .FieldTransform: .TransformName: name of the selected transform function
31%                     .TransformPath:   path  of the selected transform function
32%    .InputFields: sub structure describing the input fields withfields
33%              .FieldName: name(s) of the field
34%              .VelType: velocity type
35%              .FieldName_1: name of the second field in case of two input series
36%              .VelType_1: velocity type of the second field in case of two input series
37%              .Coord_y: name of y coordinate variable
38%              .Coord_x: name of x coordinate variable
39%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
40%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
41
42%=======================================================================
43% Copyright 2008-2020, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
44%   http://www.legi.grenoble-inp.fr
45%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
46%
47%     This file is part of the toolbox UVMAT.
48%
49%     UVMAT is free software; you can redistribute it and/or modify
50%     it under the terms of the GNU General Public License as published
51%     by the Free Software Foundation; either version 2 of the license,
52%     or (at your option) any later version.
53%
54%     UVMAT is distributed in the hope that it will be useful,
55%     but WITHOUT ANY WARRANTY; without even the implied warranty of
56%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
57%     GNU General Public License (see LICENSE.txt) for more details.
58%=======================================================================
59
60function ParamOut=time_series(Param)
61
62%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
63if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
64    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
65    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
66    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
67    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
68    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
69    ParamOut.FieldTransform = {'phys','phys_polar'};%can use a transform function, proposed list (needed for compilation)
70    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)   
71    if 1==2 % loop used to enforce compilation of transform fct, never entered.
72        phys
73        phys_polar
74    end
75    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
76    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
77    ParamOut.OutputDirExt='.tseries';%set the output dir extension
78    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
79    % check for selection of a projection object
80    hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
81    hhseries=guidata(hseries);
82    if  ~isfield(Param,'ProjObject')
83        answer=msgbox_uvmat('INPUT_Y-N','use a projection object for the time_series?');
84        if strcmp(answer,'Yes')
85            set(hhseries.CheckObject,'Visible','on')
86            set(hhseries.CheckObject,'Value',1)
87            series('CheckObject_Callback',hseries,[],hhseries); %file input with xml reading  in uvmat, show the image in phys coordinates
88        end
89    end
90   
91    % introduce bin size for histograms
92    if isfield(Param,'CheckObject') &&Param.CheckObject
93        SeriesData=get(hseries,'UserData');
94        if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
95            answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
96            ParamOut.ActionInput.VarMesh=str2num(answer);
97        end
98    end
99   
100    % test for subtraction
101    if size(Param.InputTable,1)>2
102        msgbox_uvmat('WARNING','''time_series'' uses only one or two input lines (two for substraction). To concatene fields first use ''merge_proj''');
103    end
104    if size(Param.InputTable,1)>=2
105        answer=msgbox_uvmat('INPUT_Y-N','substract the two input file series?');
106        if strcmp(answer,'Yes')
107            if isempty(Param.FieldTransform.TransformName)
108                set(hhseries.TransformName,'value',2) %select sub_field
109            end
110        else
111            set(hhseries.InputTable,'Data',Param.InputTable(1,:))
112        end
113    end
114   
115    % check the existence of the first and last file in the series
116    first_j=[];
117    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
118    last_j=[];
119    if isfield(Param.IndexRange,'last_j'); last_j=Param.IndexRange.last_j; end
120    PairString='';
121    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
122    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
123    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
124        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
125    if ~exist(FirstFileName,'file')
126        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
127    else
128        [i1,i2,j1,j2] = get_file_index(Param.IndexRange.last_i,last_j,PairString);
129        LastFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
130            Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
131        if ~exist(LastFileName,'file')
132            msgbox_uvmat('WARNING',['the last input file ' LastFileName ' does not exist'])
133        end
134    end
135    return
136end
137
138%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
139ParamOut=[]; %default output
140%% read input parameters from an xml file if input is a file name (batch mode)
141checkrun=1;
142if ischar(Param)
143    Param=xml2struct(Param);% read Param as input file (batch case)
144    checkrun=0;
145end
146hseries=findobj(allchild(0),'Tag','series');
147RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
148WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
149
150%% define the directory for result file (with path=RootPath{1})
151OutputDir=[Param.OutputSubDir Param.OutputDirExt];
152
153%% root input file(s) name, type and index series
154RootPath=Param.InputTable(:,1);
155RootFile=Param.InputTable(:,3);
156SubDir=Param.InputTable(:,2);
157NomType=Param.InputTable(:,4);
158FileExt=Param.InputTable(:,5);
159
160hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
161% gives the series of input file names and indices set by the input parameters:
162[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
163% filecell{iview,fileindex}:
164%        iview: line in the table corresponding to a given file series
165%        fileindex: file index with i and j reshaped as a 1D array
166% 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
167% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
168if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
169
170NbView=numel(i1_series);%number of input file series (lines in InputTable)
171NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
172NbField_i=size(i1_series{1},2); %nb of fields for the i index
173NbField=NbField_j*NbField_i; %total number of fields
174
175%% determine the file type on each line from the first input file
176ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};
177NcTypeOptions={'netcdf','civx','civdata'};
178FileType=cell(1,NbView);
179FileInfo=cell(1,NbView);
180MovieObject=cell(1,NbView);
181CheckImage=cell(1,NbView);
182CheckNc=cell(1,NbView);
183frame_index=cell(1,NbView);
184
185for iview=1:NbView
186    if ~exist(filecell{iview,1}','file')
187        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
188        return
189    end
190    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
191    FileType{iview}=FileInfo{iview}.FileType;
192    if strcmp(FileType{iview},'civdata')||strcmp(FileType{iview},'civx')
193        if ~isfield(Param.InputFields,'VelType')
194            FileType{iview}='netcdf';% civ data read as usual netcdf files
195        end
196    end
197    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
198    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
199    if isempty(j1_series{iview})
200        frame_index{iview}=i1_series{iview};
201    else
202        frame_index{iview}=j1_series{iview};
203    end
204end
205
206%% calibration data and timing: read the ImaDoc files
207[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
208if ~isempty(errormsg)
209    disp_uvmat('ERROR',['error in reading xmlfile: ' errormsg],checkrun)
210    return
211end
212if size(time,1)>1
213    diff_time=max(max(diff(time)));
214    if diff_time>0
215        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
216    end
217    time=time(1,:);% choose the time data from the first sequence
218end
219
220%% coordinate transform or other user defined transform
221transform_fct=[];%default
222if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
223    %addpath(Param.FieldTransform.TransformPath)
224    transform_fct=str2func(Param.FieldTransform.TransformName);
225    %rmpath(Param.FieldTransform.TransformPath)
226    if isfield(Param,'TransformInput')
227        XmlData{1}.TransformInput=Param.TransformInput;
228    end
229end
230
231%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
232% EDIT FROM HERE
233
234%% check the validity of  the input file types
235if ~CheckImage{1}&&~CheckNc{1}
236    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
237    return
238end
239if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
240    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
241    return
242end
243
244%% settings for the output file
245FileExtOut='.nc';% write result as .nc files for netcdf inputs
246NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
247first_i=i1_series{1}(1);
248last_i=i1_series{1}(end);
249if isempty(j1_series{1})% if there is no second index j
250    first_j=1;last_j=1;
251else
252    first_j=j1_series{1}(1);
253    last_j=j1_series{1}(end);
254end
255
256%% Set field names and velocity types
257InputFields{1}=[];%default (case of images)
258if NbView==2
259    InputFields{2}=[];%default (case of images)
260end
261if isfield(Param,'InputFields')
262    InputFields{1}=Param.InputFields;
263    if NbView==2
264        InputFields{2}=Param.InputFields;%default
265        if isfield(Param.InputFields,'FieldName_1')
266            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
267            if isfield(Param.InputFields,'VelType_1')
268                InputFields{2}.VelType=Param.InputFields.VelType_1;
269            end
270        end
271    end
272end
273
274%% Initiate output fields
275%initiate the output structure as a copy of the first input one (reproduce fields)
276[DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
277if ~isempty(errormsg)
278    disp_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun)
279    return
280end
281time_1=[];
282if isfield(DataOut,'Time')
283    time_1=DataOut.Time(1);
284end
285if CheckNc{iview}
286    if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute))
287        DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute];
288    end
289    DataOut.Conventions='uvmat';
290    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}];
291    ActionKey='Action';
292    while isfield(DataOut,ActionKey)
293        ActionKey=[ActionKey '_1'];
294    end
295    DataOut.(ActionKey)=Param.Action;
296    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}];
297    if isfield(DataOut,'Time')
298        DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}];
299    end
300end
301
302nbfile=0;% not used , to check
303nbmissing=0;
304VarMesh=[];
305checkhisto=0;
306checkline=0;
307if isfield(Param,'ProjObject')
308    if ismember(Param.ProjObject.ProjMode,{'inside','outside'})
309    checkhisto=1;
310    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
311        VarMesh=Param.ActionInput.VarMesh;
312    else
313        VarMesh=[];
314        disp_uvmat('WARNING','automatic bin size for histograms, select time_series again to set the value',checkrun)
315    end
316    elseif ismember(Param.ProjObject.Type,{'line'})
317        checkline=1;
318    end
319end
320
321%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
322for index=1:NbField
323    update_waitbar(WaitbarHandle,index/NbField)
324    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
325        disp('program stopped by user')
326        break % leave the loop if stop is ordered
327    end
328    Data=cell(1,NbView);%initiate the set Data;
329    nbtime=0;
330    dt=[];
331    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
332    for iview=1:NbView
333        % reading input file(s)
334        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
335        if ~isempty(errormsg)
336            errormsg=['time_series / read_field / ' errormsg];
337            disp(errormsg)
338            break% exit the loop on iview
339        end
340        if ~isempty(NbSlice_calib)
341            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
342        end
343    end
344    if ~isempty(errormsg)
345        continue %in case of input error skip the current input field, go to next index
346    end
347    Field=Data{1}; % default input field structure
348    % coordinate transform (or other user defined transform)
349    if ~isempty(transform_fct)
350        switch nargin(transform_fct)
351            case 4
352                if length(Data)==2
353                    Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
354                else
355                    Field=transform_fct(Data{1},XmlData{1});
356                end
357            case 3
358                if length(Data)==2
359                    Field=transform_fct(Data{1},XmlData{1},Data{2});
360                else
361                    Field=transform_fct(Data{1},XmlData{1});
362                end
363            case 2
364                Field=transform_fct(Data{1},XmlData{1});
365            case 1
366                Field=transform_fct(Data{1});
367        end
368    end
369   
370    %field projection on an object
371    if Param.CheckObject
372        % calculate tps coefficients if needed
373        if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
374            Field=tps_coeff_field(Field,check_proj_tps);
375        end
376        [Field,errormsg]=proj_field(Field,Param.ProjObject,VarMesh);
377        if ~isempty(errormsg)
378            disp_uvmat('ERROR',['time_series / proj_field / ' errormsg],checkrun)
379            return
380        end
381    end
382    %         nbfile=nbfile+1;
383   
384    % initiate the time series at the first iteration
385    if index==1
386        % stop program if the first field reading is in error
387        if ~isempty(errormsg)
388            disp_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun)
389            return
390        end
391        if ~isfield(Field,'ListVarName')
392            disp_uvmat('ERROR','no variable in the projected field',checkrun)
393            return
394        end
395        DataOut=Field;%output reproduced the first projected field by default
396        nbvar=length(Field.ListVarName);
397        if nbvar==0
398            disp_uvmat('ERROR','no input variable selected',checkrun)
399            return
400        end
401        if checkhisto%case of histograms
402            testsum=zeros(1,nbvar);%initiate flag for action on each variable
403            for ivar=1:numel(Field.ListVarName)% list of variable names before projection (histogram)
404                VarName=Field.ListVarName{ivar};
405                if isfield(Data{1},VarName)
406                    DataOut.ListVarName=[DataOut.ListVarName {[VarName 'Histo']}];
407                    DataOut.VarDimName=[DataOut.VarDimName {{'Time',VarName}}];
408                    StatName=pdf2stat;% get the names of statistical quantities to calcuilate at each time
409                    for istat=1:numel(StatName)
410                        DataOut.ListVarName=[DataOut.ListVarName {[VarName StatName{istat}]}];
411                        DataOut.VarDimName=[DataOut.VarDimName {'Time'}];
412                    end
413                    testsum(ivar)=1;
414                    DataOut.(VarName)=Field.(VarName);
415                    DataOut.([VarName 'Histo'])=zeros([NbField numel(DataOut.(VarName))]);
416                    VarMesh=Field.(VarName)(2)-Field.(VarName)(1);
417                end
418            end
419            disp(['mesh for histogram = ' num2str(VarMesh)])
420        else
421            testsum=2*ones(1,nbvar);%initiate flag for action on each variable
422            if isfield(Field,'VarAttribute') % look for coordinate and flag variables
423                for ivar=1:nbvar
424                    if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role')
425                        var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable
426                        if isequal(var_role,'errorflag')
427                            disp_uvmat('ERROR','do not handle error flags in time series',checkrun)
428                            return
429                        end
430                        if isequal(var_role,'warnflag')
431                            testsum(ivar)=0;  % not recorded variable
432                            eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable
433                        end
434                        if strcmp(var_role,'coord_x')||strcmp(var_role,'coord_z')||strcmp(var_role,'coord')
435                            testsum(ivar)=1; %constant coordinates, record without time evolution
436                        end
437                        if strcmp(var_role,'coord_y')&& ~checkline
438                             testsum(ivar)=1;
439                        end
440                    end
441                    % check whether the variable ivar is a dimension variable
442                    DimCell=Field.VarDimName{ivar};
443                    if ischar(DimCell)
444                        DimCell={DimCell};
445                    end
446                    if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
447                        testsum(ivar)=1;
448                    end
449                end
450            end
451            for ivar=1:nbvar
452                if testsum(ivar)==2
453                    VarName=Field.ListVarName{ivar};
454                    siz=size(Field.(VarName));
455                    DataOut.(VarName)=zeros([NbField siz]);
456                end
457            end
458        end
459        DataOut.ListVarName=[{'Time'} DataOut.ListVarName];
460    end
461    % end initialisation for index==1
462   
463    % append data from the current field
464
465    if checkhisto % case of histogram (projection mode=inside or outside)
466        for ivar=1:length(Field.ListVarName)
467            VarName=Field.ListVarName{ivar};
468            if isfield(Data{1},VarName)
469                MaxValue=max(DataOut.(VarName));% current max of histogram absissa
470                MinValue=min(DataOut.(VarName));% current min of histogram absissa
471                MaxIndex=round(MaxValue/VarMesh);
472                MinIndex=round(MinValue/VarMesh);
473                MaxIndex_new=round(max(Field.(VarName)/VarMesh));% max of the current field
474                MinIndex_new=round(min(Field.(VarName)/VarMesh));
475                if MaxIndex_new>MaxIndex% the variable max for the current field exceeds the previous one
476                    DataOut.(VarName)=[DataOut.(VarName) VarMesh*(MaxIndex+1:MaxIndex_new)];% append the new variable values
477                    DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(NbField,MaxIndex_new-MaxIndex)]; % append the new histo values
478                end
479                if MinIndex_new <= MinIndex-1
480                    DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
481                    DataOut.([VarName 'Histo'])=[zeros(NbField,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
482                    ind_start=1;
483                else
484                    ind_start=MinIndex_new-MinIndex+1;
485                end
486                DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)=...
487                    DataOut.([VarName 'Histo'])(index,ind_start:ind_start+MaxIndex_new-MinIndex_new)+Field.([VarName 'Histo']);
488                VarVal=pdf2stat((Field.(VarName))',(Field.([VarName 'Histo']))');% max of the current field
489                for istat=1:numel(VarVal)
490                    DataOut.([VarName StatName{istat}])(index)=VarVal(istat);
491                end
492            end
493        end
494    else % not histogram
495        for ivar=1:length(Field.ListVarName)
496            VarName=Field.ListVarName{ivar};
497            VarVal=Field.(VarName);
498            if testsum(ivar)==2% test for recorded variable
499                if isempty(errormsg)
500                    VarVal=shiftdim(VarVal,-1); %shift dimension
501                    DataOut.(VarName)(index,:,:)=VarVal;%concanete the current field to the time series
502                end
503            elseif testsum(ivar)==1% variable representing fixed coordinates
504                VarInit=DataOut.(VarName);
505                if isempty(errormsg) && ~isequal(VarVal,VarInit)
506                    disp_uvmat('ERROR',['time series requires constant coordinates ' VarName ': use projection mode interp'],checkrun)
507                    return
508                end
509            end
510        end
511    end
512   
513    % record the time:
514    if isempty(time)% time not set by xml filer(s)
515        if isfield(Data{1},'Time')
516            DataOut.Time(index,1)=Field.Time;
517        else
518            DataOut.Time(index,1)=index;%default
519        end
520    else % time from ImaDoc prevails  TODO: correct
521        DataOut.Time(index,1)=time(index);%
522    end
523    index
524    % record the number of missing input fields
525    if ~isempty(errormsg)
526        nbmissing=nbmissing+1;
527        display(['index=' num2str(index) ':' errormsg])
528    end
529end
530
531%%%%%%% END OF LOOP WITHIN A SLICE
532
533%remove time for global attributes if exists
534Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute));
535if ~isempty(Time_index)
536    DataOut.ListGlobalAttribute(Time_index)=[];
537end
538DataOut.Conventions='uvmat';
539for ivar=1:numel(DataOut.ListVarName)
540    VarName=DataOut.ListVarName{ivar};
541    eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons
542end
543
544% add time dimension
545for ivar=1:length(Field.ListVarName)
546    DimCell=Field.VarDimName{ivar};
547    if ischar(DimCell),DimCell={DimCell};end
548    if testsum(ivar)==2% variable for which time series is calculated
549        DataOut.VarDimName{ivar}=[{'Time'} DimCell];
550    elseif testsum(ivar)==1 % variable represneting a fixed coordinate
551        DataOut.VarDimName{ivar}=DimCell;
552    end
553end
554indexremove=find(~testsum);
555if ~isempty(indexremove)
556    DataOut.ListVarName(1+indexremove)=[];
557    DataOut.VarDimName(indexremove)=[];
558    if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs
559        DataOut.Role(1+indexremove)=[];
560    end
561end
562
563%shift variable attributes
564if isfield(DataOut,'VarAttribute')
565    DataOut.VarAttribute=[{[]} DataOut.VarAttribute];
566end
567DataOut.VarDimName=[{'Time'} DataOut.VarDimName];
568DataOut.Action=Param.Action;%name of the processing programme
569test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant)
570if ~test_time
571    DataOut.Time=1:NbField;
572end
573
574if ~isequal(nbmissing,0)
575    disp_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun)
576end
577
578%% name of result file
579OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
580errormsg=struct2nc(OutputFile,DataOut); %save result file
581if isempty(errormsg)
582    display([OutputFile ' written'])
583else
584    disp_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun)
585end
586
587%% plot the time series for  (the last one in case of multislices)
588if checkrun %&& isfield(Param,'ProjObject') && strcmp(Param.ProjObject.Type,'points')
589    %% open the result file with uvmat (in RUN mode)
590    uvmat(OutputFile)% open the last result file with uvmat
591end
592%     figure
593%     haxes=axes;
594%     plot_field(DataOut,haxes)
595%     
596%     %% display the result file using the GUI get_field
597%     hget_field=findobj(allchild(0),'name','get_field');
598%     if ~isempty(hget_field)
599%         delete(hget_field)
600%     end
601%     get_field(OutputFile,DataOut)
602% end
603
604
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