source: trunk/src/series/merge_proj_special.m @ 712

Last change on this file since 712 was 712, checked in by sommeria, 10 years ago

merge_proj_special added for specific projection methods

File size: 19.0 KB
Line 
1%'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates
2%------------------------------------------------------------------------
3% function ParamOut=merge_proj(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
41function ParamOut=merge_proj(Param)
42
43%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
44if isstruct(Param) && isequal(Param.Action.RUN,0)
45    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
46    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
47    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
48    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
49    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
50    ParamOut.FieldTransform = 'on';%can use a transform function
51    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
52    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
53    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
54    ParamOut.OutputDirExt='.mproj';%set the output dir extension
55    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
56    filecell=get_file_series(Param);%check existence of the first input file
57    if ~exist(filecell{1,1},'file')
58        msgbox_uvmat('WARNING','the first input file does not exist')
59    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
60        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
61    end
62    return
63end
64
65%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
66ParamOut=[]; %default output
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
73hseries=findobj(allchild(0),'Tag','series');
74RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
75WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
76
77%% define the directory for result file (with path=RootPath{1})
78OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
79
80if ~isfield(Param,'InputFields')
81    Param.InputFields.FieldName='';
82end
83
84%% root input file type
85RootPath=Param.InputTable(:,1);
86RootFile=Param.InputTable(:,3);
87SubDir=Param.InputTable(:,2);
88NomType=Param.InputTable(:,4);
89FileExt=Param.InputTable(:,5);
90[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
91%%%%%%%%%%%%
92% The cell array filecell is the list of input file names, while
93% filecell{iview,fileindex}:
94%        iview: line in the table corresponding to a given file series
95%        fileindex: file index within  the file series,
96% 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
97% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
98%%%%%%%%%%%%
99% NbSlice=1;%default
100% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
101%     NbSlice=Param.IndexRange.NbSlice;
102% end
103NbView=numel(i1_series);%number of input file series (lines in InputTable)
104NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
105NbField_i=size(i1_series{1},2); %nb of fields for the i index
106NbField=NbField_j*NbField_i; %total number of fields
107
108%% determine the file type on each line from the first input file
109ImageTypeOptions={'image','multimage','mmreader','video'};
110NcTypeOptions={'netcdf','civx','civdata'};
111for iview=1:NbView
112    if ~exist(filecell{iview,1}','file')
113        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
114        return
115    end
116    [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1});
117    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
118    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
119    if ~isempty(j1_series{iview})
120        frame_index{iview}=j1_series{iview};
121    else
122        frame_index{iview}=i1_series{iview};
123    end
124end
125
126%% calibration data and timing: read the ImaDoc files
127[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
128if size(time,1)>1
129    diff_time=max(max(diff(time)));
130    if diff_time>0
131        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
132    end   
133end
134if ~isempty(errormsg)
135    disp_uvmat('WARNING',erromsg,checkrun)
136end
137time=mean(time,1); %averaged time taken for the merged field
138
139%% coordinate transform or other user defined transform
140transform_fct='';%default fct handle
141if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
142        currentdir=pwd;
143        cd(Param.FieldTransform.TransformPath)
144        transform_fct=str2func(Param.FieldTransform.TransformName);
145        cd (currentdir)
146end
147%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
148 % EDIT FROM HERE
149
150%% check the validity of  input file types
151for iview=1:NbView
152    if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1)
153        disp_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
154        return
155    end
156end
157
158%% output file type
159if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
160    FileExtOut='.png'; %image output (input and proj result = image)
161    for iview=1:NbView
162        BitDepth(iview)=FileInfo{iview}.BitDepth;
163    end
164    BitDepth=max(BitDepth);
165else
166    FileExtOut='.nc'; %netcdf output
167end
168NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
169RootFileOut=RootFile{1};
170for iview=2:NbView
171    if ~strcmp(RootFile{iview},RootFile{1})
172        RootFileOut='mproj';
173        break
174    end
175end
176
177%% mask (TODO: case of multilevels)
178MaskData=cell(NbView,1);
179if Param.CheckMask
180    if ischar(Param.MaskTable)% case of a single mask (char chain)
181        Param.MaskTable={Param.MaskTable};
182    end
183    for iview=1:numel(Param.MaskTable)
184        if exist(Param.MaskTable{iview},'file')
185            [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image');
186            if ~isempty(transform_fct) && nargin(transform_fct)>=2
187                MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview});
188            end
189        end
190    end
191end
192
193%% Set field names and velocity types
194%use Param.InputFields for all views
195
196%% MAIN LOOP ON FIELDS
197%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
198% for i_slice=1:NbSlice
199%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
200%     NbFiles=0;
201%     nbmissing=0;
202
203    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
204for index=1:NbField
205        update_waitbar(WaitbarHandle,index/NbField)
206    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
207        disp('program stopped by user')
208        return
209    end
210   
211    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
212    Data=cell(1,NbView);%initiate the set Data
213    timeread=zeros(1,NbView);
214    for iview=1:NbView
215        %% reading input file(s)
216        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
217        if ~isempty(errormsg)
218            disp(['ERROR in merge_proj/read_field/' errormsg])
219            return
220        end
221        % get the time defined in the current file if not already defined from the xml file
222        if ~isempty(time) && isfield(Data{iview},'Time')
223            timeread(iview)=Data{iview}.Time;
224        end
225        if ~isempty(NbSlice_calib)
226            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
227        end
228       
229        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
230        if ~isempty(transform_fct)
231            if nargin(transform_fct)>=2
232                Data{iview}=transform_fct(Data{iview},XmlData{iview});
233            else
234                Data{iview}=transform_fct(Data{iview});
235            end
236        end
237       
238        %% calculate tps coefficients if needed
239        check_proj_tps= isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps');
240        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
241       
242        %% projection on object (gridded plane)
243        if Param.CheckObject
244            [Data{iview},errormsg]=proj_field_special(Data{iview},Param.ProjObject);
245            if ~isempty(errormsg)
246                disp(['ERROR in merge_proge/proj_field: ' errormsg])
247                return
248            end
249        end
250       
251        %% mask
252        if Param.CheckMask && ~isempty(MaskData{iview})
253             [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview});
254        end
255    end
256    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
257
258    %% merge the NbView fields
259    MergeData=merge_field(Data);
260    if isfield(MergeData,'Txt')
261        disp(MergeData.Txt);
262        return
263    end
264
265    %% time of the merged field: take the average of the different views
266    if ~isempty(time)
267        timeread=time(index);   
268    elseif ~isempty(find(timeread))% time defined from ImaDoc
269        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
270    else
271        timeread=index;% take time=file index
272    end
273
274    %% generating the name of the merged field
275    i1=i1_series{1}(index);
276    if ~isempty(i2_series{end})
277        i2=i2_series{end}(index);
278    else
279        i2=i1;
280    end
281    j1=1;
282    j2=1;
283    if ~isempty(j1_series{1})
284        j1=j1_series{1}(index);
285        if ~isempty(j2_series{end})
286            j2=j2_series{end}(index);
287        else
288            j2=j1;
289        end
290    end
291    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomType{1},i1,i2,j1,j2);
292
293    %% recording the merged field
294    if strcmp(FileExtOut,'.png')    %output as image
295        if BitDepth==8
296            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
297        else
298            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
299        end
300        if index==1
301            %write xml calibration file, using the first file
302            siz=size(MergeData.A);
303            npy=siz(1);
304            npx=siz(2);
305            if isfield(MergeData,'coord_x') && isfield(MergeData,'coord_y')
306                Rangx=MergeData.coord_x;
307                Rangy=MergeData.coord_y;
308            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
309                Rangx=[MergeData.AX(1) MergeData.AX(end)];
310                Rangy=[MergeData.AY(1) MergeData.AY(end)];
311            else
312                Rangx=[0.5 npx-0.5];
313                Rangy=[npy-0.5 0.5];%default
314            end
315            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
316            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
317            T_x=-pxcmx*Rangx(1)+0.5;
318            T_y=-pxcmy*Rangy(2)+0.5;
319            GeometryCal.CalibrationType='rescale';
320            GeometryCal.CoordUnit=MergeData.CoordUnit;
321            GeometryCal.focal=1;
322            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
323            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
324            ImaDoc.GeometryCalib=GeometryCal;
325            t=struct2xml(ImaDoc);
326            t=set(t,1,'name','ImaDoc');
327            save(t,[fileparts(OutputFile) '.xml'])
328        end
329       
330    else
331        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim'};
332        MergeData.Conventions='uvmat';
333        MergeData.nb_coord=2;
334        MergeData.nb_dim=2;
335        dt=[];
336        if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
337            dt=Data{1}.dt;
338        end
339        for iview =2:numel(Data)
340            if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
341                dt=[];%dt not the same for all fields
342            end
343        end
344        if ~isempty(timeread)
345            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
346            MergeData.Time=timeread;
347        end
348        if ~isempty(dt)
349            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'dt'}];
350            MergeData.dt=dt;
351        end
352        error=struct2nc(OutputFile,MergeData);%save result file
353        if isempty(error)
354            display(['output file ' OutputFile ' written'])
355        else
356            display(error)
357        end
358    end
359end
360
361
362%'merge_field': concatene fields
363%------------------------------------------------------------------------
364function MergeData=merge_field(Data)
365%% default output
366if isempty(Data)||~iscell(Data)
367    MergeData=[];
368    return
369end
370error=0;
371MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
372NbView=length(Data);
373if NbView==1
374    return
375end
376
377%% group the variables (fields of 'Data') in cells of variables with the same dimensions
378[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
379
380%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
381for icell=1:length(CellInfo)
382    if NbDim(icell)~=1 % skip field cells which are of dim 1
383        switch CellInfo{icell}.CoordType
384            case 'scattered'  %case of input fields with unstructured coordinates: just concacene data
385                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
386                    VarName=Data{1}.ListVarName{ivar};
387                    %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
388                    for iview=2:NbView
389                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
390                    end
391                end
392            case 'grid'        %case of fields defined on a structured  grid
393                FFName='';
394                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
395                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
396                end
397                % select good data on each view
398                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
399                    VarName=Data{1}.ListVarName{ivar};
400                    for iview=1:NbView
401                        if isempty(FFName)
402                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
403                        else
404                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
405                        end
406                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data
407                        if iview==1
408                            MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData
409                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
410                        else
411                            MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data
412                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
413                        end
414                    end
415                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
416                end
417        end
418        if isempty(FFName)
419            FFName='FF';
420        end
421        MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
422        MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
423    end
424end
425
426function  [DataOut,errormsg]=proj_field_special(Data,Param,ProjObject)
427errormsg='';
428DataOut.ListVarName={'coord_x','coord_y','U','V'};
429DataOut.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'},{'coord_y','coord_x'}};
430DataOut.coord_x=Param.RangeX(1):Param.DX:Param.RangeX(2);
431DataOut.coord_y=Param.RangeY(1):Param.DY:Param.RangeY(2);
432[XI,YI]=meshgrid(DataOut.coord_x,DataOut.coord_y);%grid in the new coordinates
433ind_select=find(Data.FF==0 & Data.C>0.5);
434Data.X=Data.X(ind_select);
435Data.Y=Data.Y(ind_select);
436Data.U=Data.U(ind_select);
437Data.V=Data.V(ind_select);
438Coord=[Data.X Data.Y];
439F=TriScatteredInterp(Coord,Data.U);
440DataOut.U=F(XI,YI);
441F=TriScatteredInterp(Coord,Data.V);
442DataOut.V=F(XI,YI);
443F=TriScatteredInterp(Coord,Data.X,'nearest');
444Xinterp=F(XI,YI);
445F=TriScatteredInterp(Coord,Data.Y,'nearest');
446Yinterp=F(XI,YI);
447
448   
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