source: trunk/src/series/time_series.m @ 1069

Last change on this file since 1069 was 1069, checked in by sommeria, 5 years ago

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[572]1%'time_series': extract a time series after projection on an object (points , line..)
[457]2% this function can be used as a template for applying a global operation on a series of input fields
[169]3%------------------------------------------------------------------------
[374]4% function GUI_input=time_series(Param)
[169]5%
[457]6%%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%%
7%
[169]8%OUTPUT
[596]9% ParamOut: sets options in the GUI series.fig needed for the function
[169]10%
11%INPUT:
[457]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
[596]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
[169]16%
[596]17% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
18% see the current structure Param)
[457]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
[474]22%    .OutputDirExt: directory extension for data outputs
[457]23%    .Action: .ActionName: name of the current activated function
24%             .ActionPath:   path of the current activated function
[596]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%             
[457]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
[596]33%              .FieldName: name(s) of the field
[457]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
[596]37%              .Coord_y: name of y coordinate variable
38%              .Coord_x: name of x coordinate variable
[457]39%    .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object)
40%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[596]41
[810]42%=======================================================================
[1061]43% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
[810]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
[457]60function ParamOut=time_series(Param)
[27]61
[606]62%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
[875]63if isstruct(Param) && isequal(Param.Action.RUN,0)% function activated from the GUI series but not RUN
[605]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)
[1001]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
[605]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
[871]79    % check for selection of a projection object
80    hseries=findobj(allchild(0),'Tag','series');% handles of the GUI series
[875]81    hhseries=guidata(hseries);
[871]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
[875]90   
[871]91    % introduce bin size for histograms
[872]92    if isfield(Param,'CheckObject') &&Param.CheckObject
[871]93        SeriesData=get(hseries,'UserData');
[872]94        if ismember(SeriesData.ProjObject.ProjMode,{'inside','outside'})
[875]95            answer=msgbox_uvmat('INPUT_TXT','set bin size for histograms (or keep ''auto'' by default)?','auto');
[880]96            ParamOut.ActionInput.VarMesh=str2num(answer);
[871]97        end
98    end
[875]99   
[874]100    % test for subtraction
[875]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,:))
[874]112        end
[875]113    end
114   
[871]115    % check the existence of the first and last file in the series
[875]116    first_j=[];
[716]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'])
[871]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
[605]134    end
[599]135    return
[27]136end
137
[526]138%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
[624]139ParamOut=[]; %default output
[592]140%% read input parameters from an xml file if input is a file name (batch mode)
141checkrun=1;
[457]142if ischar(Param)
[592]143    Param=xml2struct(Param);% read Param as input file (batch case)
144    checkrun=0;
[374]145end
[624]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
[592]149
[624]150%% define the directory for result file (with path=RootPath{1})
[474]151OutputDir=[Param.OutputSubDir Param.OutputDirExt];
[457]152
[609]153%% root input file(s) name, type and index series
[457]154RootPath=Param.InputTable(:,1);
155RootFile=Param.InputTable(:,3);
156SubDir=Param.InputTable(:,2);
157NomType=Param.InputTable(:,4);
158FileExt=Param.InputTable(:,5);
[960]159
[751]160hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
[960]161% gives the series of input file names and indices set by the input parameters:
[374]162[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
[526]163% filecell{iview,fileindex}:
[457]164%        iview: line in the table corresponding to a given file series
[960]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
[457]167% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
[960]168if ~isempty(hdisp),delete(hdisp),end;%end the waiting display
[374]169
[960]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
[609]175%% determine the file type on each line from the first input file
[984]176ImageTypeOptions={'image','multimage','mmreader','video','cine_phantom'};
[457]177NcTypeOptions={'netcdf','civx','civdata'};
[970]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);
[874]184
[970]185for iview=1:NbView
[457]186    if ~exist(filecell{iview,1}','file')
[668]187        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
[27]188        return
189    end
[784]190    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
[783]191    FileType{iview}=FileInfo{iview}.FileType;
[768]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
[457]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
[768]199    if isempty(j1_series{iview})
200        frame_index{iview}=i1_series{iview};
201    else
[457]202        frame_index{iview}=j1_series{iview};
203    end
[27]204end
205
[457]206%% calibration data and timing: read the ImaDoc files
[470]207[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
[768]208if ~isempty(errormsg)
209    disp_uvmat('ERROR',['error in reading xmlfile: ' errormsg],checkrun)
210    return
211end
[470]212if size(time,1)>1
[457]213    diff_time=max(max(diff(time)));
214    if diff_time>0
[668]215        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
[599]216    end
[531]217    time=time(1,:);% choose the time data from the first sequence
[457]218end
[27]219
[457]220%% coordinate transform or other user defined transform
[526]221transform_fct=[];%default
[478]222if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
[1001]223    %addpath(Param.FieldTransform.TransformPath)
[474]224    transform_fct=str2func(Param.FieldTransform.TransformName);
[1001]225    %rmpath(Param.FieldTransform.TransformPath)
[883]226    if isfield(Param,'TransformInput')
227        XmlData{1}.TransformInput=Param.TransformInput;
228    end
[457]229end
[474]230
[457]231%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
[599]232% EDIT FROM HERE
[27]233
[656]234%% check the validity of  the input file types
235if ~CheckImage{1}&&~CheckNc{1}
[668]236    disp_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
[457]237    return
[27]238end
[970]239if NbView==2 && ~isequal(CheckImage{1},CheckImage{2})
[668]240    disp_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
[259]241    return
242end
[635]243
244%% settings for the output file
[656]245FileExtOut='.nc';% write result as .nc files for netcdf inputs
[609]246NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
[635]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
[457]255
256%% Set field names and velocity types
257InputFields{1}=[];%default (case of images)
[970]258if NbView==2
[867]259    InputFields{2}=[];%default (case of images)
260end
[457]261if isfield(Param,'InputFields')
262    InputFields{1}=Param.InputFields;
[970]263    if NbView==2
[867]264        InputFields{2}=Param.InputFields;%default
[457]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
[27]273
[457]274%% Initiate output fields
275%initiate the output structure as a copy of the first input one (reproduce fields)
[464]276[DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
[457]277if ~isempty(errormsg)
[668]278    disp_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun)
[457]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
[871]302nbfile=0;% not used , to check
[599]303nbmissing=0;
[880]304VarMesh=[];
[871]305checkhisto=0;
[1069]306checkline=0;
307if isfield(Param,'ProjObject')
308    if ismember(Param.ProjObject.ProjMode,{'inside','outside'})
[871]309    checkhisto=1;
[880]310    if isfield(Param,'ActionInput') && isfield(Param.ActionInput,'VarMesh')%case of histograms
311        VarMesh=Param.ActionInput.VarMesh;
[884]312    else
313        VarMesh=[];
314        disp_uvmat('WARNING','automatic bin size for histograms, select time_series again to set the value',checkrun)
[871]315    end
[1069]316    elseif ismember(Param.ProjObject.Type,{'line'})
317        checkline=1;
318    end
[871]319end
[875]320
[599]321%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
[970]322for index=1:NbField
323    update_waitbar(WaitbarHandle,index/NbField)
[635]324    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
[624]325        disp('program stopped by user')
326        break % leave the loop if stop is ordered
[599]327    end
[970]328    Data=cell(1,NbView);%initiate the set Data;
[599]329    nbtime=0;
330    dt=[];
331    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
[970]332    for iview=1:NbView
[599]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];
[880]337            disp(errormsg)
338            break% exit the loop on iview
[442]339        end
[599]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
[880]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
[875]355                    Field=transform_fct(Data{1},XmlData{1});
[880]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});
[599]367        end
[880]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);
[599]375        end
[880]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'}];
[871]412                    end
[880]413                    testsum(ivar)=1;
414                    DataOut.(VarName)=Field.(VarName);
[970]415                    DataOut.([VarName 'Histo'])=zeros([NbField numel(DataOut.(VarName))]);
[880]416                    VarMesh=Field.(VarName)(2)-Field.(VarName)(1);
[871]417                end
[880]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
[27]429                        end
[880]430                        if isequal(var_role,'warnflag')
431                            testsum(ivar)=0;  % not recorded variable
432                            eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable
[27]433                        end
[1069]434                        if strcmp(var_role,'coord_x')||strcmp(var_role,'coord_z')||strcmp(var_role,'coord')
[880]435                            testsum(ivar)=1; %constant coordinates, record without time evolution
[474]436                        end
[1069]437                        if strcmp(var_role,'coord_y')&& ~checkline
438                             testsum(ivar)=1;
439                        end
[27]440                    end
[880]441                    % check whether the variable ivar is a dimension variable
442                    DimCell=Field.VarDimName{ivar};
443                    if ischar(DimCell)
444                        DimCell={DimCell};
[474]445                    end
[880]446                    if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
447                        testsum(ivar)=1;
448                    end
[474]449                end
450            end
[880]451            for ivar=1:nbvar
452                if testsum(ivar)==2
453                    VarName=Field.ListVarName{ivar};
454                    siz=size(Field.(VarName));
[970]455                    DataOut.(VarName)=zeros([NbField siz]);
[330]456                end
[871]457            end
[880]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
[970]477                    DataOut.([VarName 'Histo'])=[DataOut.([VarName 'Histo']) zeros(NbField,MaxIndex_new-MaxIndex)]; % append the new histo values
[599]478                end
[880]479                if MinIndex_new <= MinIndex-1
480                    DataOut.(VarName)=[VarMesh*(MinIndex_new:MinIndex-1) DataOut.(VarName)];% insert the new variable values
[970]481                    DataOut.([VarName 'Histo'])=[zeros(NbField,MinIndex-MinIndex_new) DataOut.([VarName 'Histo'])];% insert the new histo values
[880]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']);
[881]488                VarVal=pdf2stat((Field.(VarName))',(Field.([VarName 'Histo']))');% max of the current field
[880]489                for istat=1:numel(VarVal)
490                    DataOut.([VarName StatName{istat}])(index)=VarVal(istat);
491                end
[27]492            end
[599]493        end
[880]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
[474]509            end
[27]510        end
[880]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
[27]519        end
[880]520    else % time from ImaDoc prevails  TODO: correct
521        DataOut.Time(index,1)=time(index);%
[330]522    end
[881]523    index
[880]524    % record the number of missing input fields
525    if ~isempty(errormsg)
526        nbmissing=nbmissing+1;
527        display(['index=' num2str(index) ':' errormsg])
528    end
[599]529end
[880]530
[599]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)
[751]546    DimCell=Field.VarDimName{ivar};
547    if ischar(DimCell),DimCell={DimCell};end
548    if testsum(ivar)==2% variable for which time series is calculated
[599]549        DataOut.VarDimName{ivar}=[{'Time'} DimCell];
[751]550    elseif testsum(ivar)==1 % variable represneting a fixed coordinate
[599]551        DataOut.VarDimName{ivar}=DimCell;
[330]552    end
[599]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)=[];
[330]560    end
[27]561end
[107]562
[599]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
[970]571    DataOut.Time=1:NbField;
[599]572end
573
574if ~isequal(nbmissing,0)
[668]575    disp_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun)
[599]576end
577
[609]578%% name of result file
579OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
[599]580errormsg=struct2nc(OutputFile,DataOut); %save result file
581if isempty(errormsg)
582    display([OutputFile ' written'])
583else
[668]584    disp_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun)
[599]585end
586
[880]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
[474]591end
[880]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
[27]603
604
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