[474] | 1 | %'merge_proj': project and concatene fields |
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| 2 | % can be used as a template for applying an operation (here projection and concatenation) on each field of an input series |
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[457] | 3 | %------------------------------------------------------------------------ |
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[464] | 4 | % function ParamOut=merge_proj(Param) |
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[457] | 5 | %------------------------------------------------------------------------ |
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[222] | 6 | |
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[457] | 7 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[169] | 8 | % |
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[457] | 9 | % This function is used in four modes by the GUI series: |
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| 10 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 11 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 12 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 13 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 14 | % |
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| 15 | % This function is used in four modes by the GUI series: |
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| 16 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 17 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 18 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 19 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 20 | % |
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[169] | 21 | %OUTPUT |
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| 22 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 23 | % |
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| 24 | %INPUT: |
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[457] | 25 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 26 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 27 | % In the absence of input (as activated when the current Action is selected |
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| 28 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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[169] | 29 | % |
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[457] | 30 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 31 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 32 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 33 | % .OutputSubDir: name of the subdirectory for data outputs |
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[474] | 34 | % .OutputDirExt: directory extension for data outputs |
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[457] | 35 | % .Action: .ActionName: name of the current activated function |
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| 36 | % .ActionPath: path of the current activated function |
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| 37 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 38 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 39 | % .TransformPath: path of the selected transform function |
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| 40 | % .TransformHandle: corresponding function handle |
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| 41 | % .InputFields: sub structure describing the input fields withfields |
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| 42 | % .FieldName: name of the field |
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| 43 | % .VelType: velocity type |
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| 44 | % .FieldName_1: name of the second field in case of two input series |
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| 45 | % .VelType_1: velocity type of the second field in case of two input series |
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| 46 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 47 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 48 | |
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[462] | 49 | function ParamOut=merge_proj(Param) |
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[29] | 50 | |
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[457] | 51 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 52 | if ~exist('Param','var') % case with no input parameter |
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[474] | 53 | ParamOut={'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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[462] | 54 | 'WholeIndexRange';'off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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[29] | 55 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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[462] | 56 | 'VelType';'one';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 57 | 'FieldName';'one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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[457] | 58 | 'FieldTransform'; 'on';...%can use a transform function |
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| 59 | 'ProjObject';'on';...%can use projection object(option 'off'/'on', |
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[462] | 60 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 61 | 'OutputDirExt';'.mproj';...%set the output dir extension |
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[29] | 62 | ''}; |
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[457] | 63 | return |
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[29] | 64 | end |
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| 65 | |
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[457] | 66 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 67 | %% select different modes, RUN, parameter input, BATCH |
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| 68 | % BATCH case: read the xml file for batch case |
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| 69 | if ischar(Param) |
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| 70 | Param=xml2struct(Param); |
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| 71 | checkrun=0; |
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| 72 | % RUN case: parameters introduced as the input structure Param |
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| 73 | else |
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[374] | 74 | hseries=guidata(Param.hseries);%handles of the GUI series |
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[457] | 75 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
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[462] | 76 | if isfield(Param,'Specific')&& strcmp(Param.Specific,'?') |
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| 77 | checkrun=1;% will only search interactive input parameters (preparation of BATCH mode) |
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| 78 | else |
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| 79 | checkrun=2; % indicate the RUN option is used |
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| 80 | end |
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[374] | 81 | end |
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[462] | 82 | ParamOut=Param; %default output |
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[474] | 83 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt]; |
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[457] | 84 | |
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| 85 | %% root input file(s) and type |
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| 86 | RootPath=Param.InputTable(:,1); |
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| 87 | RootFile=Param.InputTable(:,3); |
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| 88 | SubDir=Param.InputTable(:,2); |
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| 89 | NomType=Param.InputTable(:,4); |
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| 90 | FileExt=Param.InputTable(:,5); |
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[374] | 91 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[474] | 92 | %%%%%%%%%%%% |
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| 93 | % The cell array filecell is the list of input file names, while |
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| 94 | % filecell{iview,fileindex}: |
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[457] | 95 | % iview: line in the table corresponding to a given file series |
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| 96 | % fileindex: file index within the file series, |
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| 97 | % 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 |
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| 98 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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[474] | 99 | %%%%%%%%%%%% |
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[457] | 100 | NbSlice=1;%default |
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[462] | 101 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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[457] | 102 | NbSlice=Param.IndexRange.NbSlice; |
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| 103 | end |
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| 104 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 105 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 106 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 107 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 108 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 109 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 110 | |
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| 111 | %determine the file type on each line from the first input file |
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[462] | 112 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 113 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 114 | for iview=1:nbview |
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| 115 | if ~exist(filecell{iview,1}','file') |
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[474] | 116 | displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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[462] | 117 | return |
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| 118 | end |
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| 119 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 120 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 121 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 122 | if ~isempty(j1_series{iview}) |
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| 123 | frame_index{iview}=j1_series{iview}; |
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| 124 | else |
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| 125 | frame_index{iview}=i1_series{iview}; |
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| 126 | end |
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[457] | 127 | end |
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| 128 | |
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[470] | 129 | |
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[457] | 130 | %% calibration data and timing: read the ImaDoc files |
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[470] | 131 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 132 | if size(time,1)>1 |
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[457] | 133 | diff_time=max(max(diff(time))); |
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[474] | 134 | if diff_time>0 |
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| 135 | displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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[457] | 136 | end |
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| 137 | end |
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| 138 | |
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[409] | 139 | %% coordinate transform or other user defined transform |
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[374] | 140 | transform_fct='';%default |
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[474] | 141 | if isfield(Param,'FieldTransform') |
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| 142 | addpath(Param.FieldTransform.TransformPath) |
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| 143 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 144 | rmpath(Param.FieldTransform.TransformPath) |
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[374] | 145 | end |
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[474] | 146 | |
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[457] | 147 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 148 | % EDIT FROM HERE |
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[116] | 149 | |
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[457] | 150 | %% check the validity of input file types |
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| 151 | if CheckImage{1} |
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| 152 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 153 | elseif CheckNc{1} |
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| 154 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[474] | 155 | else |
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| 156 | displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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[457] | 157 | return |
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| 158 | end |
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[462] | 159 | for iview=1:nbview |
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| 160 | if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1}) |
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[474] | 161 | displ_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) |
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[457] | 162 | return |
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[464] | 163 | end |
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[457] | 164 | end |
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[462] | 165 | NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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[474] | 166 | if checkrun==1 |
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| 167 | ParamOut.Specific=[];%no specific parameter |
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| 168 | return %stop here for interactive input (option Param.Specific='?') |
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| 169 | end |
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[457] | 170 | |
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| 171 | %% Set field names and velocity types |
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[462] | 172 | %use Param.InputFields for all views |
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[457] | 173 | |
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| 174 | %% MAIN LOOP ON SLICES |
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| 175 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 176 | for i_slice=1:NbSlice |
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| 177 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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| 178 | nbfiles=0; |
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| 179 | nbmissing=0; |
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[474] | 180 | |
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[457] | 181 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 182 | for index=index_slice |
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[470] | 183 | |
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[457] | 184 | if checkrun |
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| 185 | update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield)) |
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| 186 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 187 | else |
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| 188 | stopstate='queue'; |
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| 189 | end |
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[462] | 190 | |
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| 191 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 192 | Data=cell(1,nbview);%initiate the set Data |
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[464] | 193 | nbtime=0; |
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[29] | 194 | for iview=1:nbview |
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[462] | 195 | % reading input file(s) |
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[464] | 196 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); |
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[462] | 197 | if ~isempty(errormsg) |
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[474] | 198 | errormsg=['merge_proj/read_field/' errormsg]; |
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| 199 | display(errormsg) |
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[29] | 200 | break |
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| 201 | end |
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[464] | 202 | timeread(iview)=0; |
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| 203 | if isfield(Data{iview},'Time') |
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[470] | 204 | timeread(iview)=Data{iview}.Time; |
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[464] | 205 | nbtime=nbtime+1; |
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| 206 | end |
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[29] | 207 | if ~isempty(NbSlice_calib) |
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[462] | 208 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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[29] | 209 | end |
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[464] | 210 | %transform the input field (e.g; phys) if requested |
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[41] | 211 | if ~isempty(transform_fct) |
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[462] | 212 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); %transform to phys if requested |
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[29] | 213 | end |
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[464] | 214 | % field calculation (vort, div...) |
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| 215 | if strcmp(FileType{iview},'civx')||strcmp(FileType{iview},'civ') |
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[462] | 216 | Data{iview}=calc_field(Param.InputFields.FieldName,Data{iview});%calculate field (vort..) |
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[29] | 217 | end |
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[464] | 218 | |
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| 219 | %projection on object (gridded plane) |
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| 220 | if Param.CheckObject |
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| 221 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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[409] | 222 | if ~isempty(errormsg) |
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[474] | 223 | displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun) |
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[409] | 224 | return |
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| 225 | end |
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[29] | 226 | end |
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[464] | 227 | end |
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[222] | 228 | %----------END LOOP ON VIEWS---------------------- |
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[464] | 229 | |
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[222] | 230 | %% merge the nbview fields |
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[462] | 231 | MergeData=merge_field(Data); |
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[29] | 232 | if isfield(MergeData,'Txt') |
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[474] | 233 | displ_uvmat('ERROR',MergeData.Txt,checkrun) |
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[29] | 234 | return |
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[464] | 235 | end |
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[470] | 236 | |
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| 237 | % time of the merged field: |
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| 238 | if ~isempty(time)% time defined from ImaDoc |
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| 239 | timeread=time(:,index); |
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[29] | 240 | end |
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[470] | 241 | timeread=mean(timeread); |
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| 242 | |
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[464] | 243 | % generating the name of the merged field |
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| 244 | i1=i1_series{iview}(index); |
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| 245 | if ~isempty(i2_series{iview}) |
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| 246 | i2=i2_series{iview}(index); |
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| 247 | else |
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| 248 | i2=i1; |
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| 249 | end |
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| 250 | j1=1; |
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| 251 | j2=1; |
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| 252 | if ~isempty(j1_series{iview}) |
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| 253 | j1=j1_series{iview}(index); |
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| 254 | if ~isempty(j2_series{iview}) |
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| 255 | j2=j2_series{iview}(index); |
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| 256 | else |
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| 257 | j2=j1; |
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| 258 | end |
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| 259 | end |
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[474] | 260 | OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2); |
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[29] | 261 | |
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[464] | 262 | % recording the merged field |
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| 263 | if CheckImage{1} %in case of input images an image is produced |
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[29] | 264 | if isa(MergeData.A,'uint8') |
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| 265 | bitdepth=8; |
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| 266 | elseif isa(MergeData.A,'uint16') |
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| 267 | bitdepth=16; |
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| 268 | end |
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[464] | 269 | imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth); |
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[29] | 270 | %write xml calibration file |
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| 271 | siz=size(MergeData.A); |
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| 272 | npy=siz(1); |
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| 273 | npx=siz(2); |
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| 274 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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| 275 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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| 276 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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| 277 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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| 278 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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| 279 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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| 280 | else |
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| 281 | Rangx=[0.5 npx-0.5]; |
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| 282 | Rangy=[npy-0.5 0.5];%default |
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| 283 | end |
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| 284 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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| 285 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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| 286 | T_x=-pxcmx*Rangx(1)+0.5; |
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| 287 | T_y=-pxcmy*Rangy(2)+0.5; |
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| 288 | GeometryCal.focal=1; |
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| 289 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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| 290 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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| 291 | ImaDoc.GeometryCalib=GeometryCal; |
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| 292 | t=struct2xml(ImaDoc); |
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| 293 | t=set(t,1,'name','ImaDoc'); |
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[464] | 294 | save(t,[filebase_merge '.xml']) |
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[29] | 295 | display([filebase_merge '.xml saved']) |
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| 296 | else |
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[464] | 297 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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[422] | 298 | MergeData.Conventions='uvmat'; |
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[29] | 299 | MergeData.nb_coord=2; |
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| 300 | MergeData.nb_dim=2; |
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[93] | 301 | dt=[]; |
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[462] | 302 | if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt) |
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| 303 | dt=Data{1}.dt; |
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[93] | 304 | end |
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[462] | 305 | for iview =2:numel(Data) |
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| 306 | if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt)) |
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[93] | 307 | dt=[];%dt not the same for all fields |
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| 308 | end |
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| 309 | end |
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| 310 | if isempty(dt) |
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| 311 | MergeData.ListGlobalAttribute(6)=[]; |
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| 312 | else |
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[464] | 313 | MergeData.dt=dt; |
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[93] | 314 | end |
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[470] | 315 | MergeData.Time=timeread; |
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[462] | 316 | error=struct2nc(OutputFile,MergeData);%save result file |
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[29] | 317 | if isempty(error) |
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[462] | 318 | display(['output file ' OutputFile ' written']) |
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[29] | 319 | else |
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| 320 | display(error) |
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| 321 | end |
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| 322 | end |
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| 323 | end |
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| 324 | end |
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| 325 | |
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[222] | 326 | %'merge_field': concatene fields |
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| 327 | %------------------------------------------------------------------------ |
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[29] | 328 | function MergeData=merge_field(Data) |
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[222] | 329 | %% default output |
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[29] | 330 | if isempty(Data)||~iscell(Data) |
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| 331 | MergeData=[]; |
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| 332 | return |
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| 333 | end |
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| 334 | MergeData=Data{1};%default |
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| 335 | error=0; |
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| 336 | nbview=length(Data); |
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| 337 | if nbview==1 |
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| 338 | return |
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| 339 | end |
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[222] | 340 | |
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| 341 | %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions |
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[89] | 342 | [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); |
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| 343 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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| 344 | % CellVarIndex=cells of variable index arrays |
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| 345 | ivar_new=0; % index of the current variable in the projected field |
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| 346 | for icell=1:length(CellVarIndex) |
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| 347 | if NbDim(icell)==1 |
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| 348 | continue |
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| 349 | end |
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| 350 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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| 351 | VarType=VarTypeCell{icell}; |
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| 352 | ivar_X=VarType.coord_x; |
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| 353 | ivar_Y=VarType.coord_y; |
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| 354 | ivar_FF=VarType.errorflag; |
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| 355 | if isempty(ivar_X) |
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| 356 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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| 357 | else |
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| 358 | if length(ivar_Y)~=1 |
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[474] | 359 | displ_uvmat('ERROR','y coordinate missing in proj_field.m',checkrun) |
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[89] | 360 | return |
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| 361 | end |
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| 362 | test_grid=0; |
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| 363 | end |
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| 364 | %case of input fields with unstructured coordinates |
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| 365 | if ~test_grid |
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| 366 | for ivar=VarIndex |
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| 367 | VarName=MergeData.ListVarName{ivar}; |
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| 368 | for iview=1:nbview |
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| 369 | eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];']) |
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| 370 | end |
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| 371 | end |
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| 372 | %case of fields defined on a structured grid |
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| 373 | else |
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| 374 | testFF=0; |
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| 375 | for iview=2:nbview |
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| 376 | for ivar=VarIndex |
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| 377 | VarName=MergeData.ListVarName{ivar}; |
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| 378 | if isfield(MergeData,'VarAttribute') |
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| 379 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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| 380 | testFF=1; |
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| 381 | end |
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| 382 | end |
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| 383 | eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) |
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| 384 | end |
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| 385 | end |
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| 386 | if testFF |
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| 387 | nbaver=nbview-MergeData.FF; |
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| 388 | indgood=find(nbaver>0); |
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| 389 | for ivar=VarIndex |
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| 390 | VarName=MergeData.ListVarName{ivar}; |
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| 391 | eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) |
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| 392 | end |
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| 393 | else |
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| 394 | for ivar=VarIndex |
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| 395 | VarName=MergeData.ListVarName{ivar}; |
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| 396 | eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) |
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| 397 | end |
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| 398 | end |
---|
| 399 | end |
---|
| 400 | end |
---|
[222] | 401 | |
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[89] | 402 | |
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