source: trunk/src/series/merge_proj.m @ 883

Last change on this file since 883 was 883, checked in by sommeria, 10 years ago

bugs corrected in series, transform functions with input parameters introduced, civ/deformation corrected (sign)

File size: 21.3 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
41%=======================================================================
42% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
43%   http://www.legi.grenoble-inp.fr
44%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
45%
46%     This file is part of the toolbox UVMAT.
47%
48%     UVMAT is free software; you can redistribute it and/or modify
49%     it under the terms of the GNU General Public License as published
50%     by the Free Software Foundation; either version 2 of the license,
51%     or (at your option) any later version.
52%
53%     UVMAT is distributed in the hope that it will be useful,
54%     but WITHOUT ANY WARRANTY; without even the implied warranty of
55%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
56%     GNU General Public License (see LICENSE.txt) for more details.
57%=======================================================================
58
59function ParamOut=merge_proj(Param)
60
61%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
62if isstruct(Param) && isequal(Param.Action.RUN,0)
63    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
64    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
65    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
66    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
67    ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
68    ParamOut.FieldTransform = 'on';%can use a transform function
69    ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
70    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
71    ParamOut.Mask='on';%can use mask option   (option 'off'/'on', 'off' by default)
72    ParamOut.OutputDirExt='.mproj';%set the output dir extension
73    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
74      %check the input files
75    first_j=[];
76    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
77    PairString='';
78    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
79    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
80    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
81        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
82    if ~exist(FirstFileName,'file')
83        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
84    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
85        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
86    end
87    return
88end
89
90%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
91ParamOut=[]; %default output
92%% read input parameters from an xml file if input is a file name (batch mode)
93checkrun=1;
94if ischar(Param)
95    Param=xml2struct(Param);% read Param as input file (batch case)
96    checkrun=0;
97end
98hseries=findobj(allchild(0),'Tag','series');
99RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
100WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
101
102%% define the directory for result file (with path=RootPath{1})
103OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
104
105if ~isfield(Param,'InputFields')
106    Param.InputFields.FieldName='';
107end
108
109%% root input file type
110RootPath=Param.InputTable(:,1);
111RootFile=Param.InputTable(:,3);
112SubDir=Param.InputTable(:,2);
113NomType=Param.InputTable(:,4);
114FileExt=Param.InputTable(:,5);
115[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
116%%%%%%%%%%%%
117% The cell array filecell is the list of input file names, while
118% filecell{iview,fileindex}:
119%        iview: line in the table corresponding to a given file series
120%        fileindex: file index within  the file series,
121% 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
122% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
123%%%%%%%%%%%%
124% NbSlice=1;%default
125% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
126%     NbSlice=Param.IndexRange.NbSlice;
127% end
128NbView=numel(i1_series);%number of input file series (lines in InputTable)
129NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
130NbField_i=size(i1_series{1},2); %nb of fields for the i index
131NbField=NbField_j*NbField_i; %total number of fields
132
133%% determine the file type on each line from the first input file
134ImageTypeOptions={'image','multimage','mmreader','video'};
135NcTypeOptions={'netcdf','civx','civdata'};
136for iview=1:NbView
137    if ~exist(filecell{iview,1}','file')
138        disp_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
139        return
140    end
141    [FileInfo{iview},MovieObject{iview}]=get_file_info(filecell{iview,1});
142    FileType{iview}=FileInfo{iview}.FileType;
143    CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images
144    if CheckImage{iview}
145        ParamIn{iview}=MovieObject{iview};
146    else
147        ParamIn{iview}=Param.InputFields;
148    end
149    CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files
150    if ~isempty(j1_series{iview})
151        frame_index{iview}=j1_series{iview};
152    else
153        frame_index{iview}=i1_series{iview};
154    end
155end
156if NbView >1 && max(cell2mat(CheckImage))>0 && ~isfield(Param,'ProjObject')
157    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)
158    return
159end
160
161%% calibration data and timing: read the ImaDoc files
162[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
163if size(time,1)>1
164    diff_time=max(max(diff(time)));
165    if diff_time>0
166        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
167    end   
168end
169if ~isempty(errormsg)
170    disp_uvmat('WARNING',errormsg,checkrun)
171end
172time=mean(time,1); %averaged time taken for the merged field
173
174%% coordinate transform or other user defined transform
175transform_fct='';%default fct handle
176if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
177        currentdir=pwd;
178        cd(Param.FieldTransform.TransformPath)
179        transform_fct=str2func(Param.FieldTransform.TransformName);
180        cd (currentdir)
181        if isfield(Param,'TransformInput')
182            for iview=1:NbView
183            XmlData{iview}.TransformInput=Param.TransformInput;
184            end
185        end       
186end
187%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
188 % EDIT FROM HERE
189
190%% check the validity of  input file types
191for iview=1:NbView
192    if ~isequal(CheckImage{iview},1)&&~isequal(CheckNc{iview},1)
193        disp_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
194        return
195    end
196end
197
198%% output file type
199if min(cell2mat(CheckImage))==1 && (~Param.CheckObject || strcmp(Param.ProjObject.Type,'plane'))
200    FileExtOut='.png'; %image output (input and proj result = image)
201    for iview=1:NbView
202        BitDepth(iview)=FileInfo{iview}.BitDepth;
203    end
204    BitDepth=max(BitDepth);
205else
206    FileExtOut='.nc'; %netcdf output
207end
208if isempty(j1_series{1})
209    NomTypeOut='_1';
210else
211    NomTypeOut='_1_1';
212end
213%NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
214RootFileOut=RootFile{1};
215for iview=2:NbView
216    if ~strcmp(RootFile{iview},RootFile{1})
217        RootFileOut='mproj';
218        break
219    end
220end
221
222%% mask (TODO: case of multilevels)
223MaskData=cell(NbView,1);
224if Param.CheckMask
225    if ischar(Param.MaskTable)% case of a single mask (char chain)
226        Param.MaskTable={Param.MaskTable};
227    end
228    for iview=1:numel(Param.MaskTable)
229        if exist(Param.MaskTable{iview},'file')
230            [MaskData{iview},tild,errormsg] = read_field(Param.MaskTable{iview},'image');
231            if ~isempty(transform_fct) && nargin(transform_fct)>=2
232                MaskData{iview}=transform_fct(MaskData{iview},XmlData{iview});
233            end
234        end
235    end
236end
237
238%% Set field names and velocity types
239%use Param.InputFields for all views
240
241%% MAIN LOOP ON FIELDS
242%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
243% for i_slice=1:NbSlice
244%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
245%     NbFiles=0;
246%     nbmissing=0;
247
248    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
249tstart=tic; %used to record the computing time
250for index=1:NbField
251        update_waitbar(WaitbarHandle,index/NbField)
252    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
253        disp('program stopped by user')
254        return
255    end
256    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
257    Data=cell(1,NbView);%initiate the set Data
258    timeread=zeros(1,NbView);
259    for iview=1:NbView
260        %% reading input file(s)     
261        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},ParamIn{iview},frame_index{iview}(index));
262        if ~isempty(errormsg)
263            disp_uvmat('ERROR',['ERROR in merge_proj/read_field/' errormsg],checkrun)
264            return
265        end
266        ListVar=Data{iview}.ListVarName;
267        for ilist=1:numel(ListVar)
268            Data{iview}.(ListVar{ilist})=double(Data{iview}.(ListVar{ilist}));% transform all fields in double before all operations
269        end
270        % get the time defined in the current file if not already defined from the xml file
271        if ~isempty(time) && isfield(Data{iview},'Time')
272            timeread(iview)=Data{iview}.Time;
273        end
274        if ~isempty(NbSlice_calib)
275            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
276        end
277       
278        %% transform the input field (e.g; phys) if requested (no transform involving two input fields)
279        if ~isempty(transform_fct)
280            if nargin(transform_fct)>=2
281                Data{iview}=transform_fct(Data{iview},XmlData{iview});
282            else
283                Data{iview}=transform_fct(Data{iview});
284            end
285        end
286       
287        %% calculate tps coefficients if needed
288        check_proj_tps= isfield(Param,'ProjObject')&&~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'interp_tps')&&~isfield(Data{iview},'Coord_tps');
289        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
290       
291        %% projection on object (gridded plane)
292        if Param.CheckObject
293            [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
294            if ~isempty(errormsg)
295                disp_uvmat('ERROR',['ERROR in merge_proge/proj_field: ' errormsg],checkrun)
296                return
297            end
298        end
299       
300        %% mask
301        if Param.CheckMask && ~isempty(MaskData{iview})
302             [Data{iview},errormsg]=mask_proj(Data{iview},MaskData{iview});
303        end
304    end
305    %%%%%%%%%%%%%%%% END LOOP ON VIEWS %%%%%%%%%%%%%%%%
306
307    %% merge the NbView fields
308    [MergeData,errormsg]=merge_field(Data);
309    if ~isempty(errormsg)
310        disp_uvmat('ERROR',errormsg,checkrun);
311        return
312    end
313
314    %% time of the merged field: take the average of the different views
315    if ~isempty(time)
316        timeread=time(index);   
317    elseif ~isempty(find(timeread))% time defined from ImaDoc
318        timeread=mean(timeread(timeread~=0));% take average over times form the files (when defined)
319    else
320        timeread=index;% take time=file index
321    end
322
323    %% generating the name of the merged field
324    i1=i1_series{1}(index);
325    if ~isempty(i2_series{end})
326        i2=i2_series{end}(index);
327    else
328        i2=i1;
329    end
330    j1=1;
331    j2=1;
332    if ~isempty(j1_series{1})
333        j1=j1_series{1}(index);
334        if ~isempty(j2_series{end})
335            j2=j2_series{end}(index);
336        else
337            j2=j1;
338        end
339    end
340    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFileOut,FileExtOut,NomTypeOut,i1,i2,j1,j2);
341
342    %% recording the merged field
343    if strcmp(FileExtOut,'.png')    %output as image
344        if BitDepth==8
345            imwrite(uint8(MergeData.A),OutputFile,'BitDepth',8)
346        else
347            imwrite(uint16(MergeData.A),OutputFile,'BitDepth',16)
348        end
349        if index==1
350            %write xml calibration file, using the first file
351            siz=size(MergeData.A);
352            npy=siz(1);
353            npx=siz(2);
354            if isfield(MergeData,'Coord_x') && isfield(MergeData,'Coord_y')
355                Rangx=MergeData.Coord_x;
356                Rangy=MergeData.Coord_y;
357            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
358                Rangx=[MergeData.AX(1) MergeData.AX(end)];
359                Rangy=[MergeData.AY(1) MergeData.AY(end)];
360            else
361                Rangx=[0.5 npx-0.5];
362                Rangy=[npy-0.5 0.5];%default
363            end
364            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
365            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
366            T_x=-pxcmx*Rangx(1)+0.5;
367            T_y=-pxcmy*Rangy(2)+0.5;
368            GeometryCal.CalibrationType='rescale';
369            GeometryCal.CoordUnit=MergeData.CoordUnit;
370            GeometryCal.focal=1;
371            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
372            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
373            ImaDoc.GeometryCalib=GeometryCal;
374            t=struct2xml(ImaDoc);
375            t=set(t,1,'name','ImaDoc');
376            save(t,[fileparts(OutputFile) '.xml'])
377        end
378       
379    else
380        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim'};
381        MergeData.Conventions='uvmat';
382        MergeData.nb_coord=2;
383        MergeData.nb_dim=2;
384        dt=[];
385        if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
386            dt=Data{1}.dt;
387        end
388        for iview =2:numel(Data)
389            if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
390                dt=[];%dt not the same for all fields
391            end
392        end
393        if ~isempty(timeread)
394            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'Time'}];
395            MergeData.Time=timeread;
396        end
397        if ~isempty(dt)
398            MergeData.ListGlobalAttribute=[MergeData.ListGlobalAttribute {'dt'}];
399            MergeData.dt=dt;
400        end
401        error=struct2nc(OutputFile,MergeData);%save result file
402        if isempty(error)
403            disp(['output file ' OutputFile ' written'])
404        else
405            disp(error)
406        end
407    end
408end
409disp(['total ellapsed time ' num2str(toc(tstart))])
410
411%'merge_field': concatene fields
412%------------------------------------------------------------------------
413function [MergeData,errormsg]=merge_field(Data)
414%% default output
415if isempty(Data)||~iscell(Data)
416    MergeData=[];
417    return
418end
419errormsg='';
420MergeData=Data{1};% merged field= first field by default, reproduces the global attributes of the first field
421NbView=length(Data);
422if NbView==1% if there is only one field, just reproduce it in MergeData
423    return
424end
425
426%% group the variables (fields of 'Data') in cells of variables with the same dimensions
427[CellInfo,NbDim,errormsg]=find_field_cells(Data{1});
428if ~isempty(errormsg)
429    return
430end
431
432%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
433for icell=1:length(CellInfo)
434    if NbDim(icell)~=1 % skip field cells which are of dim 1
435        switch CellInfo{icell}.CoordType
436            case 'scattered'  %case of input fields with unstructured coordinates: just concatene data
437                for ivar=CellInfo{icell}.VarIndex %  indices of the selected variables in the list FieldData.ListVarName
438                    VarName=Data{1}.ListVarName{ivar};
439                    for iview=2:NbView
440                        MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
441                    end
442                end
443            case 'grid'        %case of fields defined on a structured  grid
444                FFName='';
445                if isfield(CellInfo{icell},'VarIndex_errorflag') && ~isempty(CellInfo{icell}.VarIndex_errorflag)
446                    FFName=Data{1}.ListVarName{CellInfo{icell}.VarIndex_errorflag};% name of errorflag variable
447                    MergeData.ListVarName(CellInfo{icell}.VarIndex_errorflag)=[];%remove error flag variable in MergeData (will use NaN instead)
448                    MergeData.VarDimName(CellInfo{icell}.VarIndex_errorflag)=[];
449                    MergeData.VarAttribute(CellInfo{icell}.VarIndex_errorflag)=[];
450                end
451                % select good data on each view
452                for ivar=CellInfo{icell}.VarIndex  %  indices of the selected variables in the list FieldData.ListVarName
453                    VarName=Data{1}.ListVarName{ivar};
454                    for iview=1:NbView
455                        if isempty(FFName)
456                            check_bad=isnan(Data{iview}.(VarName));%=0 for NaN data values, 1 else
457                        else
458                            check_bad=isnan(Data{iview}.(VarName)) | Data{iview}.(FFName)~=0;%=0 for NaN or error flagged data values, 1 else
459                        end
460                        Data{iview}.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
461                        if iview==1
462                            %MergeData.(VarName)=Data{1}.(VarName);% initiate MergeData with the first field
463                            MergeData.(VarName)(check_bad)=0; %set to zero NaN or data marked by error flag
464                            NbAver=~check_bad;% initiate NbAver: the nbre of good data for each point
465                        elseif size(Data{iview}.(VarName))~=size(MergeData.(VarName))
466                            errormsg='sizes of the input matrices do not agree, need to interpolate on a common grid using a projection object';
467                            return
468                        else                             
469                            MergeData.(VarName)=MergeData.(VarName) +double(Data{iview}.(VarName));%add data
470                            NbAver=NbAver + ~check_bad;% add 1 for good data, 0 else
471                        end
472                    end
473                    MergeData.(VarName)(NbAver~=0)=MergeData.(VarName)(NbAver~=0)./NbAver(NbAver~=0);% take average of defined data at each point
474                    MergeData.(VarName)(NbAver==0)=NaN;% set to NaN the points with no good data
475                end
476        end
477%         if isempty(FFName)
478%             FFName='FF';
479%         end
480%         MergeData.(FFName)(NbAver~=0)=0;% flag to 1 undefined summed data
481%         MergeData.(FFName)(NbAver==0)=1;% flag to 1 undefined summed data
482    end
483end
484
485
486   
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