source: trunk/src/series/merge_proj.m @ 596

Last change on this file since 596 was 596, checked in by sommeria, 11 years ago

corrections done in civ

File size: 16.6 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 action is selected in the menu ActionName
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='on';...% 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.ProjObject='on';...%can use projection object(option 'off'/'on',
52    ParamOut.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
53    ParamOut.OutputDirExt='.mproj';%set the output dir extension
54return
55end
56
57%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
58
59
60%% read input parameters from an xml file if input is a file name (batch mode)
61checkrun=1;
62if ischar(Param)
63    Param=xml2struct(Param);% read Param as input file (batch case)
64    checkrun=0;
65end
66
67ParamOut=Param; %default output
68if ~isfield(Param,'InputFields')
69    Param.InputFields.FieldName='';
70end
71OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
72
73%% root input file type
74RootPath=Param.InputTable(:,1);
75RootFile=Param.InputTable(:,3);
76SubDir=Param.InputTable(:,2);
77NomType=Param.InputTable(:,4);
78FileExt=Param.InputTable(:,5);
79[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
80%%%%%%%%%%%%
81% The cell array filecell is the list of input file names, while
82% filecell{iview,fileindex}:
83%        iview: line in the table corresponding to a given file series
84%        fileindex: file index within  the file series,
85% 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
86% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
87%%%%%%%%%%%%
88NbSlice=1;%default
89if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
90    NbSlice=Param.IndexRange.NbSlice;
91end
92nbview=numel(i1_series);%number of input file series (lines in InputTable)
93nbfield_j=size(i1_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
96nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
97nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
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
118%% calibration data and timing: read the ImaDoc files
119[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
120if size(time,1)>1
121    diff_time=max(max(diff(time)));
122    if diff_time>0
123        displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun)
124    end   
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  input 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
147for iview=1:nbview
148        if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1})
149        displ_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
150    return
151    end
152end
153NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series
154% if checkrun==1
155%     ParamOut.Specific=[];%no specific parameter
156%     return %stop here for interactive input (option Param.Specific='?')
157% end
158
159%% Set field names and velocity types
160%use Param.InputFields for all views
161
162%% MAIN LOOP ON SLICES
163%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
164for i_slice=1:NbSlice
165    index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
166    nbfiles=0;
167    nbmissing=0;
168
169    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
170    for index=index_slice
171        if checkrun
172            stopstate=get(Param.RUNHandle,'BusyAction');
173            update_waitbar(Param.WaitbarHandle,index/nbfield)
174        else
175            stopstate='queue';
176        end
177        if ~isequal(stopstate,'queue')% enable STOP command
178            return
179        end
180        %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
181        Data=cell(1,nbview);%initiate the set Data
182        nbtime=0;
183        for iview=1:nbview
184            %% reading input file(s)
185            [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
186            if ~isempty(errormsg)
187                errormsg=['merge_proj/read_field/' errormsg];
188                display(errormsg)
189                break
190            end
191            timeread(iview)=0;
192            if isfield(Data{iview},'Time')
193                    timeread(iview)=Data{iview}.Time;
194                    nbtime=nbtime+1;
195                end
196            if ~isempty(NbSlice_calib)
197                Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
198            end
199           
200            %% transform the input field (e.g; phys) if requested
201            if ~isempty(transform_fct)
202                if nargin(transform_fct)>=2
203                    Data{iview}=transform_fct(Data{iview},XmlData{iview});
204                else
205                    Data{iview}=transform_fct(Data{iview});
206                end
207            end
208           
209            %% check whether tps is needed, then calculate tps coefficients if needed
210            check_tps=0;
211            if isfield(Param.InputFields,'FieldName')
212                if ischar(Param.InputFields.FieldName)
213                    Param.InputFields.FieldName={Param.InputFields.FieldName};
214                end
215            else
216                Param.InputFields.FieldName={};
217            end
218            for ilist=1:numel(Param.InputFields.FieldName)
219                switch Param.InputFields.FieldName{ilist}
220                    case {'vort','div','strain'}
221                        check_tps=1;
222                end
223            end
224               
225            %% calculate tps coeff if needed
226             check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps');
227            Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
228
229            %% projection on object (gridded plane)
230            if Param.CheckObject
231                [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
232                if ~isempty(errormsg)
233                    displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun)
234                    return
235                end
236            end
237        end
238        %----------END LOOP ON VIEWS----------------------
239       
240        %% merge the nbview fields
241        MergeData=merge_field(Data);
242        if isfield(MergeData,'Txt')
243            displ_uvmat('ERROR',MergeData.Txt,checkrun)
244            return
245        end
246       
247        % time of the merged field:
248        if ~isempty(time)% time defined from ImaDoc
249            timeread=time(:,index);
250        end
251        timeread=mean(timeread);
252       
253        % generating the name of the merged field
254        i1=i1_series{iview}(index);
255        if ~isempty(i2_series{iview})
256            i2=i2_series{iview}(index);
257        else
258            i2=i1;
259        end
260        j1=1;
261        j2=1;
262        if ~isempty(j1_series{iview})
263            j1=j1_series{iview}(index);
264            if ~isempty(j2_series{iview})
265                j2=j2_series{iview}(index);
266            else
267                j2=j1;
268            end
269        end
270        OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2);
271       
272        % recording the merged field
273        if CheckImage{1}    %in case of input images an image is produced
274            if isa(MergeData.A,'uint8')
275                bitdepth=8;
276            elseif isa(MergeData.A,'uint16')
277                bitdepth=16;
278            end
279            imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth);
280            %write xml calibration file
281            siz=size(MergeData.A);
282            npy=siz(1);
283            npx=siz(2);
284            if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1')
285                Rangx=MergeData.VarAttribute{1}.Coord_2;
286                Rangy=MergeData.VarAttribute{1}.Coord_1;
287            elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
288                Rangx=[MergeData.AX(1) MergeData.AX(end)];
289                Rangy=[MergeData.AY(1) MergeData.AY(end)];
290            else
291                Rangx=[0.5 npx-0.5];
292                Rangy=[npy-0.5 0.5];%default
293            end
294            pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
295            pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
296            T_x=-pxcmx*Rangx(1)+0.5;
297            T_y=-pxcmy*Rangy(2)+0.5;
298            GeometryCal.focal=1;
299            GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
300            GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
301            ImaDoc.GeometryCalib=GeometryCal;
302%             t=struct2xml(ImaDoc);
303%             t=set(t,1,'name','ImaDoc');
304%             save(t,[filebase_merge '.xml'])
305%             display([filebase_merge '.xml saved'])
306        else
307            MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};
308            MergeData.Conventions='uvmat';
309            MergeData.nb_coord=2;
310            MergeData.nb_dim=2;
311            dt=[];
312            if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
313                dt=Data{1}.dt;
314            end
315            for iview =2:numel(Data)
316                if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
317                    dt=[];%dt not the same for all fields
318                end
319            end
320            if isempty(dt)
321                MergeData.ListGlobalAttribute(6)=[];
322            else
323                MergeData.dt=dt;
324            end
325            MergeData.Time=timeread;
326            error=struct2nc(OutputFile,MergeData);%save result file
327            if isempty(error)
328                display(['output file ' OutputFile ' written'])
329            else
330                display(error)
331            end
332        end
333    end
334end
335
336%'merge_field': concatene fields
337%------------------------------------------------------------------------
338function MergeData=merge_field(Data)
339%% default output
340if isempty(Data)||~iscell(Data)
341    MergeData=[];
342    return
343end
344MergeData=Data{1};%default
345error=0;
346nbview=length(Data);
347if nbview==1
348    return
349end
350
351%% group the variables (fields of 'Data') in cells of variables with the same dimensions
352[CellVarIndex,NbDim,VarTypeCell]=find_field_cells(Data{1});
353%LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS
354% CellVarIndex=cells of variable index arrays
355for icell=1:length(CellVarIndex)
356    if NbDim(icell)==1
357        continue
358    end
359    VarIndex=CellVarIndex{icell};%  indices of the selected variables in the list FieldData.ListVarName
360    VarType=VarTypeCell{icell};
361    ivar_X=VarType.coord_x;
362    ivar_Y=VarType.coord_y;
363    ivar_FF=VarType.errorflag;
364    if isempty(ivar_X)
365        test_grid=1;%test for input data on regular grid (e.g. image)coordinates
366    else
367        if length(ivar_Y)~=1
368                displ_uvmat('ERROR','y coordinate missing in proj_field.m',checkrun)
369                return
370        end
371        test_grid=0;
372    end
373    %case of input fields with unstructured coordinates
374    if ~test_grid
375        for ivar=VarIndex
376            VarName=MergeData.ListVarName{ivar};
377            for iview=1:nbview
378                MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
379            end
380        end
381    %case of fields defined on a structured  grid
382    else 
383        testFF=0;
384        for iview=2:nbview
385            for ivar=VarIndex
386                VarName=MergeData.ListVarName{ivar};
387                if isfield(MergeData,'VarAttribute')
388                    if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag')
389                        testFF=1;
390                    end
391                end
392                MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName);
393            end
394        end
395        if testFF
396            nbaver=nbview-MergeData.FF;
397            indgood=find(nbaver>0);
398            for ivar=VarIndex
399                VarName=MergeData.ListVarName{ivar};
400                MergeData.(VarName)(indgood)=double(MergeData.(VarName)(indgood))./nbaver(indgood);
401            end
402        else
403            for ivar=VarIndex
404                VarName=MergeData.ListVarName{ivar};
405                MergeData.(VarName)=double(MergeData.(VarName))./nbview;
406            end   
407        end
408    end
409end
410
411   
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