source: trunk/src/series/merge_proj.m @ 784

Last change on this file since 784 was 784, checked in by sommeria, 10 years ago

adpat uvmat to reading data from rdvision

File size: 19.3 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      %check the input files
57    first_j=[];
58    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
59    PairString='';
60    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
61    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
62    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
63        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
64    if ~exist(FirstFileName,'file')
65        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
66    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
67        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
68    end
69    return
70end
71
72%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
73ParamOut=[]; %default output
74%% read input parameters from an xml file if input is a file name (batch mode)
75checkrun=1;
76if ischar(Param)
77    Param=xml2struct(Param);% read Param as input file (batch case)
78    checkrun=0;
79end
80hseries=findobj(allchild(0),'Tag','series');
81RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
82WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
83
84%% define the directory for result file (with path=RootPath{1})
85OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
86
87if ~isfield(Param,'InputFields')
88    Param.InputFields.FieldName='';
89end
90
91%% root input file type
92RootPath=Param.InputTable(:,1);
93RootFile=Param.InputTable(:,3);
94SubDir=Param.InputTable(:,2);
95NomType=Param.InputTable(:,4);
96FileExt=Param.InputTable(:,5);
97[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
98%%%%%%%%%%%%
99% The cell array filecell is the list of input file names, while
100% filecell{iview,fileindex}:
101%        iview: line in the table corresponding to a given file series
102%        fileindex: file index within  the file series,
103% 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
104% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
105%%%%%%%%%%%%
106% NbSlice=1;%default
107% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
108%     NbSlice=Param.IndexRange.NbSlice;
109% end
110NbView=numel(i1_series);%number of input file series (lines in InputTable)
111NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
112NbField_i=size(i1_series{1},2); %nb of fields for the i index
113NbField=NbField_j*NbField_i; %total number of fields
114
115%% determine the file type on each line from the first input file
116ImageTypeOptions={'image','multimage','mmreader','video'};
117NcTypeOptions={'netcdf','civx','civdata'};
118for iview=1:NbView
119    if ~exist(filecell{iview,1}','file')
120        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
121        return
122    end
123    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
124    FileType{iview}=FileInfo{iview}.FileType;
125    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
126    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
127    if ~isempty(j1_series{iview})
128        frame_index{iview}=j1_series{iview};
129    else
130        frame_index{iview}=i1_series{iview};
131    end
132end
133if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
134    disp_uvmat('ERROR','projection on a common grid is needed to concatene images: use a Projection Object of type ''plane'' with ProjMode=''interp_lin''',checkrun)
135    return
136end
137
138%% calibration data and timing: read the ImaDoc files
139[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
140if size(time,1)>1
141    diff_time=max(max(diff(time)));
142    if diff_time>0
143        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
144    end   
145end
146if ~isempty(errormsg)
147    disp_uvmat('WARNING',erromsg,checkrun)
148end
149time=mean(time,1); %averaged time taken for the merged field
150
151%% coordinate transform or other user defined transform
152transform_fct='';%default fct handle
153if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
154        currentdir=pwd;
155        cd(Param.FieldTransform.TransformPath)
156        transform_fct=str2func(Param.FieldTransform.TransformName);
157        cd (currentdir)
158end
159%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
160 % EDIT FROM HERE
161
162%% check the validity of  input file types
163for iview=1:NbView
164    if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1)
165        disp_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
166        return
167    end
168end
169
170%% output file type
171if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
172    FileExtOut='.png'; %image output (input and proj result = image)
173    for iview=1:NbView
174        BitDepth(iview)=FileInfo{iview}.BitDepth;
175    end
176    BitDepth=max(BitDepth);
177else
178    FileExtOut='.nc'; %netcdf output
179end
180NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
181RootFileOut=RootFile{1};
182for iview=2:NbView
183    if ~strcmp(RootFile{iview},RootFile{1})
184        RootFileOut='mproj';
185        break
186    end
187end
188
189%% mask (TODO: case of multilevels)
190MaskData=cell(NbView,1);
191if Param.CheckMask
192    if ischar(Param.MaskTable)% case of a single mask (char chain)
193        Param.MaskTable={Param.MaskTable};
194    end
195    for iview=1:numel(Param.MaskTable)
196        if exist(Param.MaskTable{iview},'file')
197            [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image');
198            if ~isempty(transform_fct) && nargin(transform_fct)>=2
199                MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview});
200            end
201        end
202    end
203end
204
205%% Set field names and velocity types
206%use Param.InputFields for all views
207
208%% MAIN LOOP ON FIELDS
209%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
210% for i_slice=1:NbSlice
211%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
212%     NbFiles=0;
213%     nbmissing=0;
214
215    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
216for index=1:NbField
217        update_waitbar(WaitbarHandle,index/NbField)
218    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
219        disp('program stopped by user')
220        return
221    end
222   
223    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
224    Data=cell(1,NbView);%initiate the set Data
225    timeread=zeros(1,NbView);
226    for iview=1:NbView
227        %% reading input file(s)
228        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
229        if ~isempty(errormsg)
230            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
231            return
232        end
233        % get the time defined in the current file if not already defined from the xml file
234        if ~isempty(time) && isfield(Data{iview},'Time')
235            timeread(iview)=Data{iview}.Time;
236        end
237        if ~isempty(NbSlice_calib)
238            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
239        end
240       
241        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
242        if ~isempty(transform_fct)
243            if nargin(transform_fct)>=2
244                Data{iview}=transform_fct(Data{iview},XmlData{iview});
245            else
246                Data{iview}=transform_fct(Data{iview});
247            end
248        end
249       
250        %% calculate tps coefficients if needed
251        check_proj_tps= isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps');
252        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
253       
254        %% projection on object (gridded plane)
255        if Param.CheckObject
256            [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
257            if ~isempty(errormsg)
258                disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun)
259                return
260            end
261        end
262       
263        %% mask
264        if Param.CheckMask && ~isempty(MaskData{iview})
265             [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview});
266        end
267    end
268    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
269
270    %% merge the NbView fields
271    [MergeData,errormsg]=merge_field(Data);
272    if ~isempty(errormsg)
273        disp_uvmat('ERROR',errormsg,checkrun);
274        return
275    end
276
277    %% time of the merged field: take the average of the different views
278    if ~isempty(time)
279        timeread=time(index);   
280    elseif ~isempty(find(timeread))% time defined from ImaDoc
281        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
282    else
283        timeread=index;% take time=file index
284    end
285
286    %% generating the name of the merged field
287    i1=i1_series{1}(index);
288    if ~isempty(i2_series{end})
289        i2=i2_series{end}(index);
290    else
291        i2=i1;
292    end
293    j1=1;
294    j2=1;
295    if ~isempty(j1_series{1})
296        j1=j1_series{1}(index);
297        if ~isempty(j2_series{end})
298            j2=j2_series{end}(index);
299        else
300            j2=j1;
301        end
302    end
303    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomType{1},i1,i2,j1,j2);
304
305    %% recording the merged field
306    if strcmp(FileExtOut,'.png')    %output as image
307        if BitDepth==8
308            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
309        else
310            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
311        end
312        if index==1
313            %write xml calibration file, using the first file
314            siz=size(MergeData.A);
315            npy=siz(1);
316            npx=siz(2);
317            if isfield(MergeData,'coord_x') && isfield(MergeData,'coord_y')
318                Rangx=MergeData.coord_x;
319                Rangy=MergeData.coord_y;
320            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
321                Rangx=[MergeData.AX(1) MergeData.AX(end)];
322                Rangy=[MergeData.AY(1) MergeData.AY(end)];
323            else
324                Rangx=[0.5 npx-0.5];
325                Rangy=[npy-0.5 0.5];%default
326            end
327            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
328            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
329            T_x=-pxcmx*Rangx(1)+0.5;
330            T_y=-pxcmy*Rangy(2)+0.5;
331            GeometryCal.CalibrationType='rescale';
332            GeometryCal.CoordUnit=MergeData.CoordUnit;
333            GeometryCal.focal=1;
334            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
335            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
336            ImaDoc.GeometryCalib=GeometryCal;
337            t=struct2xml(ImaDoc);
338            t=set(t,1,'name','ImaDoc');
339            save(t,[fileparts(OutputFile) '.xml'])
340        end
341       
342    else
343        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim'};
344        MergeData.Conventions='uvmat';
345        MergeData.nb_coord=2;
346        MergeData.nb_dim=2;
347        dt=[];
348        if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
349            dt=Data{1}.dt;
350        end
351        for iview =2:numel(Data)
352            if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
353                dt=[];%dt not the same for all fields
354            end
355        end
356        if ~isempty(timeread)
357            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
358            MergeData.Time=timeread;
359        end
360        if ~isempty(dt)
361            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'dt'}];
362            MergeData.dt=dt;
363        end
364        error=struct2nc(OutputFile,MergeData);%save result file
365        if isempty(error)
366            disp(['output file ' OutputFile ' written'])
367        else
368            disp(error)
369        end
370    end
371end
372
373
374%'merge_field': concatene fields
375%------------------------------------------------------------------------
376function [MergeData,errormsg]=merge_field(Data)
377%% default output
378if isempty(Data)||~iscell(Data)
379    MergeData=[];
380    return
381end
382errormsg='';
383MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
384NbView=length(Data);
385if NbView==1
386    return
387end
388
389%% group the variables (fields of 'Data') in cells of variables with the same dimensions
390[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
391if ~isempty(errormsg)
392    return
393end
394
395%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
396for icell=1:length(CellInfo)
397    if NbDim(icell)~=1 % skip field cells which are of dim 1
398        switch CellInfo{icell}.CoordType
399            case 'scattered'  %case of input fields with unstructured coordinates: just concacene data
400                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
401                    VarName=Data{1}.ListVarName{ivar};
402                    %MergeData=Data{1};% merged field= first field by default, reproduces the glabal attributes of the first field
403                    for iview=2:NbView
404                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
405                    end
406                end
407            case 'grid'        %case of fields defined on a structured  grid
408                FFName='';
409                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
410                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
411                end
412                % select good data on each view
413                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
414                    VarName=Data{1}.ListVarName{ivar};
415                    for iview=1:NbView
416                        if isempty(FFName)
417                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
418                        else
419                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
420                        end
421                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or masked data
422                        if iview==1
423                            MergeData.(VarName)=Data{1}.(VarName);% correct the field of MergeData
424                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
425                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
426                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
427                            return
428                        else                     
429                            MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);%add data
430                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
431                        end
432                    end
433                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
434                end
435        end
436        if isempty(FFName)
437            FFName='FF';
438        end
439        MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
440        MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
441    end
442end
443
444
445   
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