Changeset 606 for trunk/src/series


Ignore:
Timestamp:
Apr 7, 2013, 10:14:45 AM (11 years ago)
Author:
sommeria
Message:

bug on compilation solved (still to test with transform_field fct). faster browser inrtroduced. Various bug corrections

Location:
trunk/src/series
Files:
4 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/series/civ_series.m

    r605 r606  
    4242path_series=fileparts(which('series'));
    4343addpath(fullfile(path_series,'series'))
    44 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
     44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
    4545if isstruct(Param) && isequal(Param.Action.RUN,0)
    4646    Data=civ_input(Param);% introduce the civ parameters using the GUI civ_input
    47     Data.Program=mfilename;
    48     Data.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
    49         Data.WholeIndexRange='off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
    50         Data.NbSlice='off'; ...%nbre of slices ('off' by default)
    51         Data.VelType='off';...% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
    52         Data.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    53         Data.FieldTransform = 'off';...%can use a transform function
    54         Data.ProjObject='off';...%can use projection object(option 'off'/'on',
    55         Data.Mask='off';...%can use mask option   (option 'off'/'on', 'off' by default)
    56         Data.OutputDirExt='.civ';%set the output dir extension
    57        
     47    Data.Program=mfilename;%gives the name of the current function
     48    Data.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
     49    Data.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
     50    Data.NbSlice='off'; %nbre of slices ('off' by default)
     51    Data.VelType='off';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
     52    Data.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
     53    Data.FieldTransform = 'off';%can use a transform function
     54    Data.ProjObject='off';%can use projection object(option 'off'/'on',
     55    Data.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
     56    Data.OutputDirExt='.civ';%set the output dir extension
     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    end
    5861    return
    5962end
    … …  
    115118   
    116119    NbField=numel(i1_series_Civ1);
    117     ImageTypeOptions={'image','multimage','mmreader','video'};
    118120    [FileType_A,FileInfo,MovieObject_A]=get_file_type(filecell{1,1});
    119121    FileType_B=FileType_A;
    … …  
    121123    if size(filecell,1)>=2 && ~strcmp(filecell{1,1},filecell{2,1})
    122124        [FileType_B,FileInfo,MovieObject_B]=get_file_type(filecell{2,1});
    123         CheckImage_B=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images
    124125    end
    125126end
    … …  
    141142check_patch1=0;%default
    142143
    143 
    144 
    145 
    146 
     144%% get timing from the ImaDoc file or input video
     145[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
     146%TODO: get time_A and time_B
     147% case of movies TODO TODO TODO
     148if isempty(time) && (strcmp(FileType,'video') || strcmp(FileType,'mmreader'))
     149    set(handles.ListPairMode,'Value',1);
     150    dt=1/get(MovieObject,'FrameRate');%time interval between successive frames
     151    if strcmp(NomTypeIma,'*')
     152        set(handles.ListPairMode,'String',{'series(Di)'})
     153        MaxIndex_i=get(MovieObject,'NumberOfFrames');
     154        time=(dt*(0:MaxIndex_i-1))';%list of image times
     155    else
     156        set(handles.ListPairMode,'String',[{'series(Dj)'};{'series(Di)'}])
     157        MaxIndex_i=max(i1_series(i1_series>0));
     158        MaxIndex_j=get(MovieObject,'NumberOfFrames');
     159        time=ones(MaxIndex_i,1)*(dt*(0:MaxIndex_j-1));%list of image times
     160        enable_j(handles,'on')
     161    end
     162    TimeUnit='s';
    147163%%%%% MAIN LOOP %%%%%%
    148164
    … …  
    164180            end
    165181        else
    166             %         if ~isfield(Param.Civ1,'ImageA')
    167182            ImageName_A=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i1_series_Civ1(ifield),[],j1_series_Civ1(ifield));
    168183            [par_civ1.ImageA,MovieObject_A] = read_image(ImageName_A,FileType_A,MovieObject_A,FrameIndex_A_Civ1(ifield));
    169             %         elseif ischar(Param.Civ1.ImageA)
    170             %             Param.Civ1.ImageA=regexprep(Param.Civ1.ImageA,'''','\');
    171             %             [par_civ1.ImageA,VideoObject] = read_image(Param.Civ1.ImageA,par_civ1.FileTypeA,MovieObject_A,par_civ1.FrameIndexA);
    172             %         end
    173             %         if ~isfield(Param.Civ1,'ImageB')
    174184            ImageName_B=fullfile_uvmat(RootPath,SubDir,RootFile,FileExt,NomType,i2_series_Civ1(ifield),[],j2_series_Civ1(ifield));
    175185            [par_civ1.ImageB,MovieObject_B] = read_image(ImageName_B,FileType_B,MovieObject_B,FrameIndex_B_Civ1(ifield));
    176             %         elseif isfield(Param.Civ1,'ImageB')&& ischar(Param.Civ1.ImageB)
    177             %              Param.Civ1.ImageB=regexprep(Param.Civ1.ImageB,'''','\');
    178             %              if strcmp(Param.Civ1.ImageA,Param.Civ1.ImageB)% use the same movie object
    179             %                  [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,VideoObject,par_civ1.FrameIndexB);
    180             %              else
    181             %             [par_civ1.ImageB,VideoObject] = read_image(Param.Civ1.ImageB,par_civ1.FileTypeB,par_civ1.ImageB,par_civ1.FrameIndexB);
    182             %              end
    183             %         end
    184186        end
    185187        ncfile=fullfile_uvmat(RootPath,OutputDir,RootFile,'.nc',NomTypeNc,i1_series_Civ1(ifield),i2_series_Civ1(ifield),...
    … …  
    188190        par_civ1.ImageHeight=FileInfo.Height;
    189191        list_param=(fieldnames(Param.ActionInput.Civ1))';
    190         Civ1_param=list_param;%default
    191        
    192         %set the values of all the global attributes in list_param 
     192        Civ1_param=regexprep(list_param,'^.+','Civ1_$0');% insert 'Civ1_' before  each string in list_param
     193        Civ1_param=[{'Civ1_ImageA','Civ1_ImageB','Civ1_Time','Civ1_Dt'} Civ1_param]; %insert the names of the two input images
     194        %indicate the values of all the global attributes in the output data
     195        Data.Civ1_ImageA=ImageName_A;
     196        Data.Civ1_ImageB=ImageName_B;
     197        Data.Civ1_Time=((time(i2_civ1(ifile)+1,j2_civ1(j)+1)+time(i1_civ1(ifile)+1,j1_civ1(j)+1))/2);
     198        Data.Civ1_Dt=(time(i2_civ1(ifile)+1,j2_civ1(j)+1)-time(i1_civ1(ifile)+1,j1_civ1(j)+1));
    193199        for ilist=1:length(list_param)
    194             Civ1_param{ilist}=['Civ1_' list_param{ilist}];
    195             Data.(['Civ1_' list_param{ilist}])=Param.ActionInput.Civ1.(list_param{ilist});
     200            Data.(Civ1_param{4+ilist})=Param.ActionInput.Civ1.(list_param{ilist});
    196201        end
    197202        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ1_param];
    … …  
    391396        ibx2=ceil(par_civ2.CorrBoxSize(1)/2);
    392397        iby2=ceil(par_civ2.CorrBoxSize(2)/2);
    393         %     isx2=ibx2+4;% search ara +-4 pixels around the guess
    394         %     isy2=iby2+4;
    395398        par_civ2.SearchBoxSize(1)=2*ibx2+9;% search ara +-4 pixels around the guess
    396399        par_civ2.SearchBoxSize(2)=2*iby2+9;
    397         %par_civ2.SearchBoxSize(1)=2*isx2+1;
    398         %par_civ2.SearchBoxSize(2)=2*isy2+1;
    399400        par_civ2.SearchBoxShift=[Shiftx(nbval>=1)./nbval(nbval>=1) Shifty(nbval>=1)./nbval(nbval>=1)];
    400401        par_civ2.Grid=[GridX(nbval>=1)-par_civ2.SearchBoxShift(:,1)/2 GridY(nbval>=1)-par_civ2.SearchBoxShift(:,2)/2];% grid taken at the extrapolated origin of the displacement vectors
    … …  
    409410
    410411        list_param=(fieldnames(Param.ActionInput.Civ2))';
    411         list_remove={'pxcmx','pxcmy','npx','npy','gridflag','maskflag','term_a','term_b','T0'};
    412         for ilist=1:length(list_remove)
    413             index=strcmp(list_remove{ilist},list_param);
    414             if ~isempty(find(index,1))
    415                 list_param(index)=[];
    416             end
    417         end
     412        Civ2_param=regexprep(list_param,'^.+','Civ2_$0');% insert 'Civ2_' before  each string in list_param
     413        Civ2_param=[{'Civ2_ImageA','Civ2_ImageB','Civ2_Time','Civ2_Dt'} Civ2_param]; %insert the names of the two input images
     414        %indicate the values of all the global attributes in the output data
     415        Data.Civ2_ImageA=ImageName_A;
     416        Data.Civ2_ImageB=ImageName_B;
     417        Data.Civ2_Time=1;
     418        Data.Civ2_Dt=1;
    418419        for ilist=1:length(list_param)
    419             Civ2_param{ilist}=['Civ2_' list_param{ilist}];
    420             eval(['Data.Civ2_' list_param{ilist} '=Param.ActionInput.Civ2.' list_param{ilist} ';'])
    421         end
    422         if isfield(Data,'Civ2_gridname') && strcmp(Data.Civ1_gridname(1:6),'noFile')
    423             Data.Civ1_gridname='';
    424         end
    425         if isfield(Data,'Civ2_maskname') && strcmp(Data.Civ1_maskname(1:6),'noFile')
    426             Data.Civ2_maskname='';
    427         end
    428         Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param {'Civ2_Time','Civ2_Dt'}];
     420            Data.(Civ2_param{4+ilist})=Param.ActionInput.Civ2.(list_param{ilist});
     421        end
     422        Data.ListGlobalAttribute=[Data.ListGlobalAttribute Civ2_param];
     423       
    429424        nbvar=numel(Data.ListVarName);
    430425        Data.ListVarName=[Data.ListVarName {'Civ2_X','Civ2_Y','Civ2_U','Civ2_V','Civ2_F','Civ2_C'}];%  cell array containing the names of the fields to record

  • trunk/src/series/ima_levels.m

    r604 r606  
    4343function ParamOut=ima_levels (Param)
    4444
    45 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
     45%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
    4646if isstruct(Param) && isequal(Param.Action.RUN,0)
    4747    ParamOut.NbViewMax=1;% max nbre of input file series (default , no limitation)
    … …  
    5858    %check the type of the existence and type of the first input file:
    5959    Param.IndexRange.last_i=Param.IndexRange.first_i;%keep only the first index in the series
     60    if isfield(Param.IndexRange,'first_j')
    6061    Param.IndexRange.last_j=Param.IndexRange.first_j;
     62    end
    6163    filecell=get_file_series(Param);
    6264    if ~exist(filecell{1,1},'file')
    … …  
    7375%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
    7476%% read input parameters from an xml file if input is a file name (batch mode)
     77ParamOut=[]
    7578checkrun=1;
    7679if ischar(Param)

  • trunk/src/series/merge_proj.m

    r605 r606  
    4141function ParamOut=merge_proj(Param)
    4242
    43 %% set the input elements needed on the GUI series when the function is selected in the menu ActionName
     43%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
    4444if 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)
     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.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='off';%can use mask option   (option 'off'/'on', 'off' by default)
    5354    ParamOut.OutputDirExt='.mproj';%set the output dir extension
    5455    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
    … …  
    5758        msgbox_uvmat('WARNING','the first input file does not exist')
    5859    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
    59          msgbox_uvmat('WARNING','a projection object of type plane needs to be introduced for merge_proj')
    60     end
    61 return
     60        msgbox_uvmat('WARNING','a projection object of type plane needs to be introduced for merge_proj')
     61    end
     62    return
    6263end
    6364
    6465%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
    65 
    66 
    6766%% read input parameters from an xml file if input is a file name (batch mode)
    6867checkrun=1;
    … …  
    7271end
    7372
    74 ParamOut=Param; %default output
     73ParamOut=[] %default output
    7574if ~isfield(Param,'InputFields')
    7675    Param.InputFields.FieldName='';
    7776end
    78 OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
     77OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
    7978
    8079%% root input file type
    … …  
    9392% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
    9493%%%%%%%%%%%%
    95 NbSlice=1;%default
    96 if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
    97     NbSlice=Param.IndexRange.NbSlice;
    98 end
    99 nbview=numel(i1_series);%number of input file series (lines in InputTable)
    100 nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
    101 nbfield_i=size(i1_series{1},2); %nb of fields for the i index
    102 nbfield=nbfield_j*nbfield_i; %total number of fields
    103 nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
    104 nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
     94% NbSlice=1;%default
     95% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
     96%     NbSlice=Param.IndexRange.NbSlice;
     97% end
     98NbView=numel(i1_series);%number of input file series (lines in InputTable)
     99NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
     100NbField_i=size(i1_series{1},2); %nb of fields for the i index
     101NbField=NbField_j*NbField_i; %total number of fields
    105102
    106103%determine the file type on each line from the first input file
    107104ImageTypeOptions={'image','multimage','mmreader','video'};
    108105NcTypeOptions={'netcdf','civx','civdata'};
    109 for iview=1:nbview
     106for iview=1:NbView
    110107    if ~exist(filecell{iview,1}','file')
    111108        displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun)
    … …  
    122119end
    123120
    124 
    125121%% calibration data and timing: read the ImaDoc files
    126122[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
    … …  
    133129
    134130%% coordinate transform or other user defined transform
    135 transform_fct='';%default
     131% transform_fct='';%default fct handle
     132% if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
     133%     if isdeployed
     134%         transform_fct=Param.FieldTransform.TransformName;
     135%         dd=phys([]);%activate phys for compilation
     136%     else
     137%         currentdir=pwd;
     138%         cd(Param.FieldTransform.TransformPath)
     139%         transform_fct=str2func(Param.FieldTransform.TransformName);
     140%         cd (currentdir)
     141%     end
     142% end
     143transform_fct='';%default fct handle
    136144if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)
    137     addpath(Param.FieldTransform.TransformPath)
    138     transform_fct=str2func(Param.FieldTransform.TransformName);
    139     rmpath(Param.FieldTransform.TransformPath)
    140 end
    141 
     145        currentdir=pwd;
     146        cd(Param.FieldTransform.TransformPath)
     147        transform_fct=str2func(Param.FieldTransform.TransformName);
     148        cd (currentdir)
     149end
    142150%%%%%%%%%%%% END STANDARD PART  %%%%%%%%%%%%
    143151 % EDIT FROM HERE
    … …  
    152160    return
    153161end
    154 for iview=1:nbview
     162for iview=1:NbView
    155163        if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1})
    156164        displ_uvmat('ERROR','input set of input series: need  either netcdf either image series',checkrun)
    … …  
    169177%% MAIN LOOP ON SLICES
    170178%%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
    171 for i_slice=1:NbSlice
    172     index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice
    173     nbfiles=0;
    174     nbmissing=0;
     179% for i_slice=1:NbSlice
     180%     index_slice=i_slice:NbSlice:NbField;% select file indices of the slice
     181%     NbFiles=0;
     182%     nbmissing=0;
    175183
    176184    %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%%
    177     for index=index_slice
    178         if checkrun
    179             stopstate=get(Param.RUNHandle,'BusyAction');
    180             update_waitbar(Param.WaitbarHandle,index/nbfield)
    181         else
    182             stopstate='queue';
    183         end
    184         if ~isequal(stopstate,'queue')% enable STOP command
    185             return
    186         end
    187         %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
    188         Data=cell(1,nbview);%initiate the set Data
    189         nbtime=0;
    190         for iview=1:nbview
    191             %% reading input file(s)
    192             [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
     185for index=1:NbField
     186    if checkrun
     187        stopstate=get(Param.RUNHandle,'BusyAction');
     188        update_waitbar(Param.WaitbarHandle,index/NbField)
     189    else
     190        stopstate='queue';
     191    end
     192    if ~isequal(stopstate,'queue')% enable STOP command
     193        return
     194    end
     195    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
     196    Data=cell(1,NbView);%initiate the set Data
     197    nbtime=0;
     198    for iview=1:NbView
     199        %% reading input file(s)
     200        [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index));
     201        if ~isempty(errormsg)
     202            errormsg=['merge_proj/read_field/' errormsg];
     203            display(errormsg)
     204            break
     205        end
     206        timeread(iview)=0;
     207        if isfield(Data{iview},'Time')
     208            timeread(iview)=Data{iview}.Time;
     209            nbtime=nbtime+1;
     210        end
     211        if ~isempty(NbSlice_calib)
     212            Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
     213        end
     214
     215        %% transform the input field (e.g; phys) if requested
     216        if ~isempty(transform_fct)
     217            if nargin(transform_fct)>=2
     218                Data{iview}=transform_fct(Data{iview},XmlData{iview});
     219            else
     220                Data{iview}=transform_fct(Data{iview});
     221            end
     222        end
     223%          Data{iview}=phys(Data{iview},XmlData{iview});
     224        %% check whether tps is needed, then calculate tps coefficients if needed
     225        check_tps=0;
     226        if isfield(Param.InputFields,'FieldName')
     227            if ischar(Param.InputFields.FieldName)
     228                Param.InputFields.FieldName={Param.InputFields.FieldName};
     229            end
     230        else
     231            Param.InputFields.FieldName={};
     232        end
     233        for ilist=1:numel(Param.InputFields.FieldName)
     234            switch Param.InputFields.FieldName{ilist}
     235                case {'vort','div','strain'}
     236                    check_tps=1;
     237            end
     238        end
     239
     240        %% calculate tps coeff if needed
     241        check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps');
     242        Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
     243
     244        %% projection on object (gridded plane)
     245        if Param.CheckObject
     246            [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
    193247            if ~isempty(errormsg)
    194                 errormsg=['merge_proj/read_field/' errormsg];
    195                 display(errormsg)
    196                 break
    197             end
    198             timeread(iview)=0;
    199             if isfield(Data{iview},'Time')
    200                     timeread(iview)=Data{iview}.Time;
    201                     nbtime=nbtime+1;
    202                 end
    203             if ~isempty(NbSlice_calib)
    204                 Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform
    205             end
    206            
    207             %% transform the input field (e.g; phys) if requested
    208             if ~isempty(transform_fct)
    209                 if nargin(transform_fct)>=2
    210                     Data{iview}=transform_fct(Data{iview},XmlData{iview});
    211                 else
    212                     Data{iview}=transform_fct(Data{iview});
    213                 end
    214             end
    215            
    216             %% check whether tps is needed, then calculate tps coefficients if needed
    217             check_tps=0;
    218             if isfield(Param.InputFields,'FieldName')
    219                 if ischar(Param.InputFields.FieldName)
    220                     Param.InputFields.FieldName={Param.InputFields.FieldName};
    221                 end
    222             else
    223                 Param.InputFields.FieldName={};
    224             end
    225             for ilist=1:numel(Param.InputFields.FieldName)
    226                 switch Param.InputFields.FieldName{ilist}
    227                     case {'vort','div','strain'}
    228                         check_tps=1;
    229                 end
    230             end
    231                
    232             %% calculate tps coeff if needed
    233              check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps');
    234             Data{iview}=tps_coeff_field(Data{iview},check_proj_tps);
    235 
    236             %% projection on object (gridded plane)
    237             if Param.CheckObject
    238                 [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject);
    239                 if ~isempty(errormsg)
    240                     displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun)
    241                     return
    242                 end
    243             end
    244         end
    245         %----------END LOOP ON VIEWS----------------------
    246        
    247         %% merge the nbview fields
    248         MergeData=merge_field(Data);
    249         if isfield(MergeData,'Txt')
    250             displ_uvmat('ERROR',MergeData.Txt,checkrun)
    251             return
    252         end
    253        
    254         % time of the merged field:
    255         if ~isempty(time)% time defined from ImaDoc
    256             timeread=time(:,index);
    257         end
    258         timeread=mean(timeread);
    259        
    260         % generating the name of the merged field
    261         i1=i1_series{iview}(index);
    262         if ~isempty(i2_series{iview})
    263             i2=i2_series{iview}(index);
    264         else
    265             i2=i1;
    266         end
    267         j1=1;
    268         j2=1;
    269         if ~isempty(j1_series{iview})
    270             j1=j1_series{iview}(index);
    271             if ~isempty(j2_series{iview})
    272                 j2=j2_series{iview}(index);
    273             else
    274                 j2=j1;
    275             end
    276         end
    277         OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2);
    278        
    279         % recording the merged field
    280         if CheckImage{1}    %in case of input images an image is produced
    281             if isa(MergeData.A,'uint8')
    282                 bitdepth=8;
    283             elseif isa(MergeData.A,'uint16')
    284                 bitdepth=16;
    285             end
    286             imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth);
    287             %write xml calibration file
    288             siz=size(MergeData.A);
    289             npy=siz(1);
    290             npx=siz(2);
    291             if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1')
    292                 Rangx=MergeData.VarAttribute{1}.Coord_2;
    293                 Rangy=MergeData.VarAttribute{1}.Coord_1;
    294             elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
    295                 Rangx=[MergeData.AX(1) MergeData.AX(end)];
    296                 Rangy=[MergeData.AY(1) MergeData.AY(end)];
    297             else
    298                 Rangx=[0.5 npx-0.5];
    299                 Rangy=[npy-0.5 0.5];%default
    300             end
    301             pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
    302             pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
    303             T_x=-pxcmx*Rangx(1)+0.5;
    304             T_y=-pxcmy*Rangy(2)+0.5;
    305             GeometryCal.focal=1;
    306             GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
    307             GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
    308             ImaDoc.GeometryCalib=GeometryCal;
    309 %             t=struct2xml(ImaDoc);
    310 %             t=set(t,1,'name','ImaDoc');
    311 %             save(t,[filebase_merge '.xml'])
    312 %             display([filebase_merge '.xml saved'])
    313         else
    314             MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};
    315             MergeData.Conventions='uvmat';
    316             MergeData.nb_coord=2;
    317             MergeData.nb_dim=2;
    318             dt=[];
    319             if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
    320                 dt=Data{1}.dt;
    321             end
    322             for iview =2:numel(Data)
    323                 if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
    324                     dt=[];%dt not the same for all fields
    325                 end
    326             end
    327             if isempty(dt)
    328                 MergeData.ListGlobalAttribute(6)=[];
    329             else
    330                 MergeData.dt=dt;
    331             end
    332             MergeData.Time=timeread;
    333             error=struct2nc(OutputFile,MergeData);%save result file
    334             if isempty(error)
    335                 display(['output file ' OutputFile ' written'])
    336             else
    337                 display(error)
    338             end
    339         end
    340     end
    341 end
     248                displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun)
     249                return
     250            end
     251        end
     252    end
     253    %----------END LOOP ON VIEWS----------------------
     254
     255    %% merge the NbView fields
     256    MergeData=merge_field(Data);
     257    if isfield(MergeData,'Txt')
     258        displ_uvmat('ERROR',MergeData.Txt,checkrun)
     259        return
     260    end
     261
     262    % time of the merged field:
     263    if ~isempty(time)% time defined from ImaDoc
     264        timeread=time(:,index);
     265    end
     266    timeread=mean(timeread);
     267
     268    % generating the name of the merged field
     269    i1=i1_series{iview}(index);
     270    if ~isempty(i2_series{iview})
     271        i2=i2_series{iview}(index);
     272    else
     273        i2=i1;
     274    end
     275    j1=1;
     276    j2=1;
     277    if ~isempty(j1_series{iview})
     278        j1=j1_series{iview}(index);
     279        if ~isempty(j2_series{iview})
     280            j2=j2_series{iview}(index);
     281        else
     282            j2=j1;
     283        end
     284    end
     285    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2);
     286
     287    % recording the merged field
     288    if CheckImage{1}    %in case of input images an image is produced
     289        if isa(MergeData.A,'uint8')
     290            bitdepth=8;
     291        elseif isa(MergeData.A,'uint16')
     292            bitdepth=16;
     293        end
     294        imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth);
     295        %write xml calibration file
     296        siz=size(MergeData.A);
     297        npy=siz(1);
     298        npx=siz(2);
     299        if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1')
     300            Rangx=MergeData.VarAttribute{1}.Coord_2;
     301            Rangy=MergeData.VarAttribute{1}.Coord_1;
     302        elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY')
     303            Rangx=[MergeData.AX(1) MergeData.AX(end)];
     304            Rangy=[MergeData.AY(1) MergeData.AY(end)];
     305        else
     306            Rangx=[0.5 npx-0.5];
     307            Rangy=[npy-0.5 0.5];%default
     308        end
     309        pxcmx=(npx-1)/(Rangx(2)-Rangx(1));
     310        pxcmy=(npy-1)/(Rangy(1)-Rangy(2));
     311        T_x=-pxcmx*Rangx(1)+0.5;
     312        T_y=-pxcmy*Rangy(2)+0.5;
     313        GeometryCal.focal=1;
     314        GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1];
     315        GeometryCal.Tx_Ty_Tz=[T_x T_y 1];
     316        ImaDoc.GeometryCalib=GeometryCal;
     317        %             t=struct2xml(ImaDoc);
     318        %             t=set(t,1,'name','ImaDoc');
     319        %             save(t,[filebase_merge '.xml'])
     320        %             display([filebase_merge '.xml saved'])
     321    else
     322        MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'};
     323        MergeData.Conventions='uvmat';
     324        MergeData.nb_coord=2;
     325        MergeData.nb_dim=2;
     326        dt=[];
     327        if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt)
     328            dt=Data{1}.dt;
     329        end
     330        for iview =2:numel(Data)
     331            if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt))
     332                dt=[];%dt not the same for all fields
     333            end
     334        end
     335        if isempty(dt)
     336            MergeData.ListGlobalAttribute(6)=[];
     337        else
     338            MergeData.dt=dt;
     339        end
     340        MergeData.Time=timeread;
     341        error=struct2nc(OutputFile,MergeData);%save result file
     342        if isempty(error)
     343            display(['output file ' OutputFile ' written'])
     344        else
     345            display(error)
     346        end
     347    end
     348end
     349
    342350
    343351%'merge_field': concatene fields
    … …  
    351359MergeData=Data{1};%default
    352360error=0;
    353 nbview=length(Data);
    354 if nbview==1
     361NbView=length(Data);
     362if NbView==1
    355363    return
    356364end
    … …  
    382390        for ivar=VarIndex
    383391            VarName=MergeData.ListVarName{ivar};
    384             for iview=1:nbview
     392            for iview=1:NbView
    385393                MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)];
    386394            end
    … …  
    389397    else 
    390398        testFF=0;
    391         for iview=2:nbview
     399        for iview=2:NbView
    392400            for ivar=VarIndex
    393401                VarName=MergeData.ListVarName{ivar};
    … …  
    401409        end
    402410        if testFF
    403             nbaver=nbview-MergeData.FF;
     411            nbaver=NbView-MergeData.FF;
    404412            indgood=find(nbaver>0);
    405413            for ivar=VarIndex
    … …  
    410418            for ivar=VarIndex
    411419                VarName=MergeData.ListVarName{ivar};
    412                 MergeData.(VarName)=double(MergeData.(VarName))./nbview;
     420                MergeData.(VarName)=double(MergeData.(VarName))./NbView;
    413421            end   
    414422        end

  • trunk/src/series/time_series.m

    r605 r606  
    4242function ParamOut=time_series(Param)
    4343
    44 %% set the input elements needed on the GUI series when the action is selected in the menu ActionName
     44%% set the input elements needed on the GUI series when the action is selected in the menu ActionName or InputTable refreshed
    4545if isstruct(Param) && isequal(Param.Action.RUN,0)
    4646    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
    … …  
    5050    ParamOut.FieldName='two';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
    5151    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)
    5253    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
    5354    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
    … …  
    7172end
    7273
    73 ParamOut=Param; %default output
     74ParamOut=[]; %default output
    7475OutputDir=[Param.OutputSubDir Param.OutputDirExt];
    7576
    … …  
    8990% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
    9091%%%%%%%%%%%%
    91 NbSlice=1;%default
    92 if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
    93     NbSlice=Param.IndexRange.NbSlice;
    94 end
     92% NbSlice=1;%default
     93% if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice)
     94%     NbSlice=Param.IndexRange.NbSlice;
     95% end
    9596nbview=numel(i1_series);%number of input file series (lines in InputTable)
    96 nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
     97nbfield_j=size(j1_series{1},1); %nb of fields for the j index (bursts or volume slices)
    9798nbfield_i=size(i1_series{1},2); %nb of fields for the i index
    9899nbfield=nbfield_j*nbfield_i; %total number of fields
    99 nbfield_i=floor(nbfield/NbSlice);%total number of  indexes in a slice (adjusted to an integer number of slices)
    100 nbfield=nbfield_i*NbSlice; %total number of fields after adjustement
    101100
    102101%determine the file type on each line from the first input file
    … …  
    153152end
    154153NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series
    155 if checkrun==1
    156     return % stop here for input checks
    157 end
    158154
    159155%% Set field names and velocity types
    … …  
    419415
    420416%name of result file
    421 OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]);
     417OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),j1_series{1}(1),j1_series{1}(end));
    422418errormsg=struct2nc(OutputFile,DataOut); %save result file
    423419if isempty(errormsg)
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