source: trunk/src/series/time_series.m @ 609

Last change on this file since 609 was 609, checked in by sommeria, 11 years ago

various bugs corrected after tests with Windows OS.

File size: 18.4 KB
Line 
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
42function ParamOut=time_series(Param)
43
44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
45if isstruct(Param) && isequal(Param.Action.RUN,0)
46    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
47    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
48    ParamOut.NbSlice='on'; %nbre of slices ('off' by default)
49    ParamOut.VelType='two';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
50    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
51    ParamOut.FieldTransform = 'on';%can use a transform function
52    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
53    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
54    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
55    ParamOut.OutputDirExt='.tseries';%set the output dir extension
56    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
57    filecell=get_file_series(Param);%check existence of the first input file
58    if ~exist(filecell{1,1},'file')
59        msgbox_uvmat('WARNING','the first input file does not exist')
60    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
61        msgbox_uvmat('WARNING','a projection object  needs to be introduced for time_series')
62    end
63    return
64end
65
66%%%%%%%%%%%% STANDARD PART  %%%%%%%%%%%%
67%% read input parameters from an xml file if input is a file name (batch mode)
68checkrun=1;
69if ischar(Param)
70    Param=xml2struct(Param);% read Param as input file (batch case)
71    checkrun=0;
72end
73
74ParamOut=[]; %default output
75OutputDir=[Param.OutputSubDir Param.OutputDirExt];
76
77%% root input file(s) name, type and index series
78RootPath=Param.InputTable(:,1);
79RootFile=Param.InputTable(:,3);
80SubDir=Param.InputTable(:,2);
81NomType=Param.InputTable(:,4);
82FileExt=Param.InputTable(:,5);
83[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
84%%%%%%%%%%%%
85% The cell array filecell is the list of input file names, while
86% filecell{iview,fileindex}:
87%        iview: line in the table corresponding to a given file series
88%        fileindex: file index within  the file series,
89% 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
90% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
91%%%%%%%%%%%%
92nbview=numel(i1_series);%number of input file series (lines in InputTable)
93nbfield_j=size(j1_series{1},1); %nb of fields for the j index (bursts or volume slices)
94nbfield_i=size(i1_series{1},2); %nb of fields for the i index
95nbfield=nbfield_j*nbfield_i; %total number of fields
96[first_i,tild,last_i,first_j,tild,last_j,errormsg]=get_index_range(Param.IndexRange);
97if ~isempty(errormsg),display(errormsg),return,end
98
99%% determine the file type on each line from the first input file
100ImageTypeOptions={'image','multimage','mmreader','video'};
101NcTypeOptions={'netcdf','civx','civdata'};
102for iview=1:nbview
103    if ~exist(filecell{iview,1}','file')
104        displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
105        return
106    end
107    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
108    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
109    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
110    if ~isempty(j1_series{iview})
111        frame_index{iview}=j1_series{iview};
112    else
113        frame_index{iview}=i1_series{iview};
114    end
115end
116
117%% calibration data and timing: read the ImaDoc files
118[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
119if size(time,1)>1
120    diff_time=max(max(diff(time)));
121    if diff_time>0
122        displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
123    end
124    time=time(1,:);% choose the time data from the first sequence
125end
126
127%% coordinate transform or other user defined transform
128transform_fct=[];%default
129if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
130    addpath(Param.FieldTransform.TransformPath)
131    transform_fct=str2func(Param.FieldTransform.TransformName);
132    rmpath(Param.FieldTransform.TransformPath)
133end
134
135%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
136% EDIT FROM HERE
137
138%% check the validity of  ctinput file types
139if CheckImage{1}
140    FileExtOut='.png'; % write result as .png images for image inputs
141elseif CheckNc{1}
142    FileExtOut='.nc';% write result as .nc files for netcdf inputs
143else
144    displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun)
145    return
146end
147if nbview==2 && ~isequal(CheckImage{1},CheckImage{2})
148    displ_uvmat('ERROR','input must be two image series or two netcdf file series',checkrun)
149    return
150end
151NomTypeOut=nomtype2pair(NomType{1});% determine the index nomenclature type for the output file
152
153%% Set field names and velocity types
154InputFields{1}=[];%default (case of images)
155if isfield(Param,'InputFields')
156    InputFields{1}=Param.InputFields;
157end
158if nbview==2
159    InputFields{2}=[];%default (case of images)
160    if isfield(Param,'InputFields')
161        InputFields{2}=Param.InputFields{1};%default
162        if isfield(Param.InputFields,'FieldName_1')
163            InputFields{2}.FieldName=Param.InputFields.FieldName_1;
164            if isfield(Param.InputFields,'VelType_1')
165                InputFields{2}.VelType=Param.InputFields.VelType_1;
166            end
167        end
168    end
169end
170
171%% Initiate output fields
172%initiate the output structure as a copy of the first input one (reproduce fields)
173[DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1);
174if ~isempty(errormsg)
175    displ_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg],checkrun)
176    return
177end
178time_1=[];
179if isfield(DataOut,'Time')
180    time_1=DataOut.Time(1);
181end
182if CheckNc{iview}
183    if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute))
184        DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute];
185    end
186    DataOut.Conventions='uvmat';
187    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}];
188    ActionKey='Action';
189    while isfield(DataOut,ActionKey)
190        ActionKey=[ActionKey '_1'];
191    end
192    DataOut.(ActionKey)=Param.Action;
193    DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}];
194    if isfield(DataOut,'Time')
195        DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}];
196    end
197end
198
199nbmissing=0; %number of undetected files
200% for i_slice=1:NbSlice
201%index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
202nbfile=0;
203nbmissing=0;
204
205%%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
206for index=1:nbfield
207    if checkrun
208        stopstate=get(Param.RUNHandle,'BusyAction');
209        update_waitbar(Param.WaitbarHandle,index/nbfield)
210    else
211        stopstate='queue';
212    end
213    if ~isequal(stopstate,'queue')% enable STOP command
214        break
215    end
216    Data=cell(1,nbview);%initiate the set Data;
217    nbtime=0;
218    dt=[];
219    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
220    for iview=1:nbview
221        % reading input file(s)
222        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index{iview}(index));
223        if ~isempty(errormsg)
224            errormsg=['time_series / read_field / ' errormsg];
225            display(errormsg)
226            break
227        end
228        if ~isempty(NbSlice_calib)
229            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
230        end
231    end
232    if isempty(errormsg)
233        Field=Data{1}; % default input field structure
234        % coordinate transform (or other user defined transform)
235        if ~isempty(transform_fct)
236            switch nargin(transform_fct)
237                case 4
238                    if length(Data)==2
239                        Field=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2});
240                    else
241                        Field=transform_fct(Data{1},XmlData{1});
242                    end
243                case 3
244                    if length(Data)==2
245                        Field=transform_fct(Data{1},XmlData{1},Data{2});
246                    else
247                        Field=transform_fct(Data{1},XmlData{1});
248                    end
249                case 2
250                    Field=transform_fct(Data{1},XmlData{1});
251                case 1
252                    Field=transform_fct(Data{1});
253            end
254        end
255       
256        % calculate tps coefficients if needed
257        if isfield(Param.ProjObject,'ProjMode')&& strcmp(Param.ProjObject.ProjMode,'interp_tps')
258            Field=tps_coeff_field(Field,check_proj_tps);
259        end
260       
261        %field projection on an object
262        if Param.CheckObject
263            [Field,errormsg]=proj_field(Field,Param.ProjObject);
264            if ~isempty(errormsg)
265                msgbox_uvmat('ERROR',['time_series / proj_field / ' errormsg])
266                return
267            end
268        end
269        nbfile=nbfile+1;
270       
271        % initiate the time series at the first iteration
272        if nbfile==1
273            % stop program if the first field reading is in error
274            if ~isempty(errormsg)
275                displ_uvmat('ERROR',['time_series / sub_field / ' errormsg],checkrun)
276                return
277            end
278            DataOut=Field;%default
279            DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots
280            nbvar=length(Field.ListVarName);
281            if nbvar==0
282                displ_uvmat('ERROR','no input variable selected',checkrun)
283                return
284            end
285            testsum=2*ones(1,nbvar);%initiate flag for action on each variable
286            if isfield(Field,'VarAttribute') % look for coordinate and flag variables
287                for ivar=1:nbvar
288                    if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role')
289                        var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable
290                        if isequal(var_role,'errorflag')
291                            displ_uvmat('ERROR','do not handle error flags in time series',checkrun)
292                            return
293                        end
294                        if isequal(var_role,'warnflag')
295                            testsum(ivar)=0;  % not recorded variable
296                            eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable
297                        end
298                        if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|...
299                                isequal(var_role,'coord_z')|isequal(var_role,'coord')
300                            testsum(ivar)=1; %constant coordinates, record without time evolution
301                        end
302                    end
303                    % check whether the variable ivar is a dimension variable
304                    DimCell=Field.VarDimName{ivar};
305                    if ischar(DimCell)
306                        DimCell={DimCell};
307                    end
308                    if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables
309                        testsum(ivar)=1;
310                    end
311                end
312            end
313            for ivar=1:nbvar
314                if testsum(ivar)==2
315                    eval(['DataOut.' Field.ListVarName{ivar} '=[];'])
316                end
317            end
318            DataOut.ListVarName=[{'Time'} DataOut.ListVarName];
319        end
320       
321        % add data to the current field
322        for ivar=1:length(Field.ListVarName)
323            VarName=Field.ListVarName{ivar};
324            VarVal=Field.(VarName);
325            if testsum(ivar)==2% test for recorded variable
326                if isempty(errormsg)
327                    if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode
328                        if isempty(VarVal)
329                            displ_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(index))],checkrun)
330                            return
331                        end
332                        VarVal=mean(VarVal,1);
333                    end
334                    VarVal=shiftdim(VarVal,-1); %shift dimension
335                    DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series
336                else
337                    DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error
338                end
339            elseif testsum(ivar)==1% variable representing fixed coordinates
340                VarInit=DataOut.(VarName);
341                if isempty(errormsg) && ~isequal(VarVal,VarInit)
342                    displ_uvmat('ERROR',['time series requires constant coordinates ' VarName],checkrun)
343                    return
344                end
345            end
346        end
347       
348        % record the time:
349        if isempty(time)% time not set by xml filer(s)
350            if isfield(Data{1},'Time')
351                DataOut.Time(nbfile,1)=Field.Time;
352            else
353                DataOut.Time(nbfile,1)=index;%default
354            end
355        else % time from ImaDoc prevails  TODO: correct
356            DataOut.Time(nbfile,1)=time(index);%
357        end
358       
359        % record the number of missing input fields
360        if ~isempty(errormsg)
361            nbmissing=nbmissing+1;
362            display(['index=' num2str(index) ':' errormsg])
363        end
364    end
365   
366end
367%%%%%%% END OF LOOP WITHIN A SLICE
368
369%remove time for global attributes if exists
370Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute));
371if ~isempty(Time_index)
372    DataOut.ListGlobalAttribute(Time_index)=[];
373end
374DataOut.Conventions='uvmat';
375for ivar=1:numel(DataOut.ListVarName)
376    VarName=DataOut.ListVarName{ivar};
377    eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons
378end
379
380% add time dimension
381for ivar=1:length(Field.ListVarName)
382    DimCell=Field.VarDimName(ivar);
383    if testsum(ivar)==2%variable used as time series
384        DataOut.VarDimName{ivar}=[{'Time'} DimCell];
385    elseif testsum(ivar)==1
386        DataOut.VarDimName{ivar}=DimCell;
387    end
388end
389indexremove=find(~testsum);
390if ~isempty(indexremove)
391    DataOut.ListVarName(1+indexremove)=[];
392    DataOut.VarDimName(indexremove)=[];
393    if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs
394        DataOut.Role(1+indexremove)=[];
395    end
396end
397
398%shift variable attributes
399if isfield(DataOut,'VarAttribute')
400    DataOut.VarAttribute=[{[]} DataOut.VarAttribute];
401end
402DataOut.VarDimName=[{'Time'} DataOut.VarDimName];
403DataOut.Action=Param.Action;%name of the processing programme
404test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant)
405if ~test_time
406    DataOut.Time=1:filecounter;
407end
408
409% display nbmissing
410if ~isequal(nbmissing,0)
411    displ_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display'],checkrun)
412end
413
414%% name of result file
415OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,first_i,last_i,first_j,last_j);
416errormsg=struct2nc(OutputFile,DataOut); %save result file
417if isempty(errormsg)
418    display([OutputFile ' written'])
419else
420    displ_uvmat('ERROR',['error in Series/struct2nc: ' errormsg],checkrun)
421end
422
423%% plot the time series (the last one in case of multislices)
424if checkrun
425    figure
426    haxes=axes;
427    plot_field(DataOut,haxes)
428   
429    %% display the result file using the GUI get_field
430    hget_field=findobj(allchild(0),'name','get_field');
431    if ~isempty(hget_field)
432        delete(hget_field)
433    end
434    get_field(OutputFile,DataOut)
435end
436
437
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