| 1 | %'time_series': extract a time series, used with series.fig |
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| 2 | % this function can be used as a template for applying a global operation on a series of input fields |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | % function GUI_input=time_series(Param) |
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| 5 | % |
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| 6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 7 | % |
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| 8 | % This function is used in four modes by the GUI series: |
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| 9 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 10 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 11 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 12 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 13 | % |
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| 14 | % This function is used in four modes by the GUI series: |
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| 15 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 16 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 17 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 18 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 19 | % |
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| 20 | %OUTPUT |
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| 21 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 22 | % |
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| 23 | %INPUT: |
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| 24 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 25 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 26 | % In the absence of input (as activated when the current Action is selected |
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| 27 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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| 28 | % |
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| 29 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 30 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 31 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 32 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 33 | % .OutputDir: directory for data outputs, including path |
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| 34 | % .Action: .ActionName: name of the current activated function |
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| 35 | % .ActionPath: path of the current activated function |
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| 36 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 37 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 38 | % .TransformPath: path of the selected transform function |
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| 39 | % .TransformHandle: corresponding function handle |
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| 40 | % .InputFields: sub structure describing the input fields withfields |
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| 41 | % .FieldName: name of the field |
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| 42 | % .VelType: velocity type |
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| 43 | % .FieldName_1: name of the second field in case of two input series |
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| 44 | % .VelType_1: velocity type of the second field in case of two input series |
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| 45 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 46 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 47 | % |
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| 48 | function ParamOut=time_series(Param) |
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| 49 | |
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| 50 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 51 | if ~exist('Param','var') % case with no input parameter |
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| 52 | ParamOut={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation) |
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| 53 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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| 54 | 'WholeIndexRange';'off';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 55 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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| 56 | 'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 57 | 'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 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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| 60 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 61 | 'OutputDirExt';'.tseries';...%set the output dir extension |
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| 62 | ''}; |
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| 63 | return |
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| 64 | end |
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| 65 | |
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| 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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| 74 | hseries=guidata(Param.hseries);%handles of the GUI series |
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| 75 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
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| 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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| 81 | end |
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| 82 | ParamOut=Param; %default output |
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| 83 | |
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| 84 | %% root input file(s) and type |
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| 85 | RootPath=Param.InputTable(:,1); |
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| 86 | RootFile=Param.InputTable(:,3); |
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| 87 | SubDir=Param.InputTable(:,2); |
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| 88 | NomType=Param.InputTable(:,4); |
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| 89 | FileExt=Param.InputTable(:,5); |
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| 90 | |
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| 91 | % get the set of input file names (cell array filecell), and the lists of |
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| 92 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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| 93 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 94 | % filecell{iview,fileindex}: cell array representing the list of file names |
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| 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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| 99 | % set of frame indices used for movie or multimage input |
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| 100 | % numbers of slices and file indices |
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| 101 | |
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| 102 | NbSlice=1;%default |
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| 103 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 104 | NbSlice=Param.IndexRange.NbSlice; |
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| 105 | end |
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| 106 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 107 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 108 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 109 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 110 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 111 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 112 | |
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| 113 | %determine the file type on each line from the first input file |
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| 114 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 115 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 116 | for iview=1:nbview |
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| 117 | if ~exist(filecell{iview,1}','file') |
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| 118 | msgbox_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist']) |
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| 119 | return |
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| 120 | end |
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| 121 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 122 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 123 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 124 | if ~isempty(j1_series{iview}) |
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| 125 | frame_index{iview}=j1_series{iview}; |
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| 126 | else |
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| 127 | frame_index{iview}=i1_series{iview}; |
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| 128 | end |
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| 129 | end |
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| 130 | |
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| 131 | %% calibration data and timing: read the ImaDoc files |
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| 132 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 133 | if size(time,1)>1 |
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| 134 | diff_time=max(max(diff(time))); |
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| 135 | if diff_time>0 |
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| 136 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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| 137 | end |
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| 138 | end |
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| 139 | |
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| 140 | %% coordinate transform or other user defined transform |
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| 141 | transform_fct='';%default |
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| 142 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle') |
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| 143 | transform_fct=Param.FieldTransform.TransformHandle; |
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| 144 | end |
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| 145 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 146 | % EDIT FROM HERE |
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| 147 | |
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| 148 | %% check the validity of input file types |
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| 149 | if CheckImage{1} |
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| 150 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 151 | elseif CheckNc{1} |
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| 152 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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| 153 | else |
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| 154 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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| 155 | return |
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| 156 | end |
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| 157 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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| 158 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
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| 159 | return |
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| 160 | end |
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| 161 | NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
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| 162 | if NbSlice~=nbfield_j |
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| 163 | answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); |
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| 164 | if ~strcmp(answer,'Yes') |
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| 165 | return |
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| 166 | end |
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| 167 | end |
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| 168 | |
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| 169 | %% Set field names and velocity types |
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| 170 | InputFields{1}=[];%default (case of images) |
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| 171 | if isfield(Param,'InputFields') |
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| 172 | InputFields{1}=Param.InputFields; |
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| 173 | end |
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| 174 | if nbview==2 |
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| 175 | InputFields{2}=[];%default (case of images) |
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| 176 | if isfield(Param,'InputFields') |
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| 177 | InputFields{2}=Param.InputFields{1};%default |
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| 178 | if isfield(Param.InputFields,'FieldName_1') |
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| 179 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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| 180 | if isfield(Param.InputFields,'VelType_1') |
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| 181 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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| 182 | end |
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| 183 | end |
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| 184 | end |
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| 185 | end |
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| 186 | %%% TO UPDATE |
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| 187 | if isequal(InputFields{1},'get_field...') |
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| 188 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
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| 189 | if numel(hget_field)>1 |
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| 190 | delete(hget_field(2:end)) % delete multiple occurerence of the GUI get_fioeld |
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| 191 | elseif isempty(hget_field) |
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| 192 | filename=filecell{1,1}; |
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| 193 | % filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),num_j2{1}(1),SubDir{1}); |
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| 194 | idetect(iview)=exist(filename,'file'); |
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| 195 | hget_field=get_field(filename); |
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| 196 | return |
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| 197 | end |
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| 198 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
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| 199 | if isempty(SubField) |
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| 200 | delete(hget_field) |
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| 201 | filename=filecell{1,1}; |
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| 202 | %filename=name_generator(filebase{1},i1_series{1}(1),j1_series{1}(1),FileExt{1},NomType{1},1,i2_series{1}(1),j2_series{1}(1),SubDir{1}); |
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| 203 | hget_field=get_field(filename); |
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| 204 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
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| 205 | end |
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| 206 | end |
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| 207 | %%%%%%% |
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| 208 | |
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| 209 | %% Initiate output fields |
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| 210 | %initiate the output structure as a copy of the first input one (reproduce fields) |
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| 211 | [DataOut,tild,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
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| 212 | if ~isempty(errormsg) |
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| 213 | msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg]) |
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| 214 | return |
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| 215 | end |
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| 216 | time_1=[]; |
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| 217 | if isfield(DataOut,'Time') |
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| 218 | time_1=DataOut.Time(1); |
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| 219 | end |
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| 220 | if CheckNc{iview} |
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| 221 | if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) |
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| 222 | DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; |
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| 223 | end |
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| 224 | DataOut.Conventions='uvmat'; |
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| 225 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; |
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| 226 | ActionKey='Action'; |
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| 227 | while isfield(DataOut,ActionKey) |
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| 228 | ActionKey=[ActionKey '_1']; |
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| 229 | end |
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| 230 | DataOut.(ActionKey)=Param.Action; |
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| 231 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; |
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| 232 | if isfield(DataOut,'Time') |
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| 233 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; |
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| 234 | end |
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| 235 | end |
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| 236 | |
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| 237 | %% LOOP ON SLICES |
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| 238 | nbmissing=0; %number of undetected files |
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| 239 | for i_slice=1:NbSlice |
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| 240 | dt=[]; |
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| 241 | %%%%%%%%%%%%%%%%%%%%%%%%%%%% LOOP ON FIELDS WITHIN A SLICE |
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| 242 | filecounter=0; |
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| 243 | for ifile=i_slice:NbSlice:nbfield |
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| 244 | if checkrun |
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| 245 | update_waitbar(hseries.waitbar_frame,WaitbarPos,ifile/nbfield) |
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| 246 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 247 | else |
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| 248 | stopstate='queue'; |
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| 249 | end |
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| 250 | errormsg=''; |
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| 251 | if isequal(stopstate,'queue')% enable STOP command |
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| 252 | % loop on views (in case of multiple input series) |
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| 253 | for iview=1:nbview |
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| 254 | filename=filecell{iview,ifile}; |
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| 255 | % filename=name_generator(filebase{iview},... |
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| 256 | % i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview}); |
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| 257 | if exist(filename,'file') |
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| 258 | try |
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| 259 | Data{iview}=[]; %default |
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| 260 | if ~isequal(FileType{iview},'netcdf') |
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| 261 | Data{iview}.ListVarName={'A'}; |
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| 262 | Data{iview}.AName='image'; |
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| 263 | switch FileType{iview} |
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| 264 | case 'movie' |
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| 265 | A=read(MovieObject{iview},i1_series{iview}(ifile)); |
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| 266 | case 'avi' |
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| 267 | mov=aviread(filename,i1_series{iview}(ifile)); |
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| 268 | A=frame2im(mov(1)); |
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| 269 | case 'vol' |
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| 270 | A=imread(filename); |
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| 271 | case 'multimage' |
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| 272 | A=imread(filename,i1_series{iview}(ifile)); |
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| 273 | case 'image' |
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| 274 | A=imread(filename); |
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| 275 | end |
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| 276 | Data{iview}.ListVarName={'AY','AX','A'}; % |
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| 277 | npy=size(A,1); |
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| 278 | npx=size(A,2); |
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| 279 | nbcolor=size(A,3); |
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| 280 | if nbcolor==3 |
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| 281 | Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; |
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| 282 | else |
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| 283 | Data{iview}.VarDimName={'AY','AX',{'AY','AX'}}; |
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| 284 | end |
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| 285 | Data{iview}.AY=[npy-0.5 0.5]; |
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| 286 | Data{iview}.AX=[0.5 npx-0.5]; |
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| 287 | Data{iview}.A=double(A); |
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| 288 | Data{iview}.CoordUnit='pixel'; |
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| 289 | elseif testcivx |
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| 290 | [Data{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
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| 291 | if ~isequal(FieldName,{''}) |
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| 292 | Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) |
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| 293 | end |
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| 294 | else |
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| 295 | [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
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| 296 | Data{iview}.VarAttribute=SubField.VarAttribute; |
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| 297 | end |
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| 298 | if ~isempty(NbSlice_calib) % z index |
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| 299 | Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1; |
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| 300 | end |
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| 301 | catch ME |
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| 302 | errormsg=ME.message; |
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| 303 | end |
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| 304 | else |
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| 305 | errormsg=[filename ' is missing']; |
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| 306 | end |
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| 307 | if isempty(errormsg) |
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| 308 | % coordinate transform (or other user defined transform) |
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| 309 | if ~isempty(transform_fct) |
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| 310 | if nbview==2 |
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| 311 | [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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| 312 | if isempty(Data{2}) |
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| 313 | Data(2)=[]; |
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| 314 | end |
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| 315 | else |
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| 316 | Data{1}=transform_fct(Data{1},XmlData{1}); |
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| 317 | end |
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| 318 | end |
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| 319 | if length(Data)==2 |
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| 320 | [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields |
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| 321 | else |
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| 322 | Field=Data{1}; |
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| 323 | end |
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| 324 | if Param.CheckObject |
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| 325 | [Field,errormsg]=proj_field(Field,Param.ProjObject); |
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| 326 | end |
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| 327 | end |
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| 328 | filecounter=filecounter+1; |
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| 329 | |
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| 330 | % initiate the time series at the first iteration |
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| 331 | if filecounter==1 |
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| 332 | % stop program if the first field reading is in error |
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| 333 | if ~isempty(errormsg) |
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| 334 | msgbox_uvmat('ERROR',['error in time_series/sub_field:' errormsg]) |
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| 335 | return |
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| 336 | end |
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| 337 | DataOut=Field;%default |
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| 338 | DataOut.NbDim=Field.NbDim+1; %add the time dimension for plots |
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| 339 | nbvar=length(Field.ListVarName); |
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| 340 | if nbvar==0 |
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| 341 | msgbox_uvmat('ERROR','no input variable selected in get_field') |
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| 342 | return |
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| 343 | end |
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| 344 | testsum=2*ones(1,nbvar);%initiate flag for action on each variable |
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| 345 | if isfield(Field,'VarAttribute') % look for coordinate and flag variables |
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| 346 | for ivar=1:nbvar |
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| 347 | if length(Field.VarAttribute)>=ivar && isfield(Field.VarAttribute{ivar},'Role') |
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| 348 | var_role=Field.VarAttribute{ivar}.Role;%'role' of the variable |
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| 349 | if isequal(var_role,'errorflag') |
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| 350 | msgbox_uvmat('ERROR','do not handle error flags in time series') |
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| 351 | return |
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| 352 | end |
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| 353 | if isequal(var_role,'warnflag') |
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| 354 | testsum(ivar)=0; % not recorded variable |
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| 355 | eval(['DataOut=rmfield(DataOut,''' Field.ListVarName{ivar} ''');']);%remove variable |
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| 356 | end |
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| 357 | if isequal(var_role,'coord_x')| isequal(var_role,'coord_y')|... |
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| 358 | isequal(var_role,'coord_z')|isequal(var_role,'coord') |
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| 359 | testsum(ivar)=1; %constant coordinates, record without time evolution |
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| 360 | end |
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| 361 | end |
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| 362 | % check whether the variable ivar is a dimension variable |
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| 363 | DimCell=Field.VarDimName{ivar}; |
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| 364 | if ischar(DimCell) |
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| 365 | DimCell={DimCell}; |
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| 366 | end |
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| 367 | if numel(DimCell)==1 && isequal(Field.ListVarName{ivar},DimCell{1})%detect dimension variables |
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| 368 | testsum(ivar)=1; |
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| 369 | end |
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| 370 | end |
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| 371 | end |
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| 372 | for ivar=1:nbvar |
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| 373 | if testsum(ivar)==2 |
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| 374 | eval(['DataOut.' Field.ListVarName{ivar} '=[];']) |
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| 375 | end |
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| 376 | end |
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| 377 | DataOut.ListVarName=[{'Time'} DataOut.ListVarName]; |
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| 378 | end |
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| 379 | |
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| 380 | % add data to the current field |
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| 381 | for ivar=1:length(Field.ListVarName) |
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| 382 | VarName=Field.ListVarName{ivar}; |
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| 383 | VarVal=Field.(VarName); |
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| 384 | if testsum(ivar)==2% test for recorded variable |
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| 385 | if isempty(errormsg) |
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| 386 | if isequal(Param.ProjObject.ProjMode,'inside')% take the average in the domain for 'inside' mode |
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| 387 | if isempty(VarVal) |
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| 388 | msgbox_uvmat('ERROR',['empty result at frame index ' num2str(i1_series{iview}(ifile))]) |
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| 389 | return |
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| 390 | end |
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| 391 | VarVal=mean(VarVal,1); |
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| 392 | end |
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| 393 | VarVal=shiftdim(VarVal,-1); %shift dimension |
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| 394 | DataOut.(VarName)=cat(1,DataOut.(VarName),VarVal);%concanete the current field to the time series |
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| 395 | else |
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| 396 | DataOut.(VarName)=cat(1,DataOut.(VarName),0);% put each variable to 0 in case of input reading error |
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| 397 | end |
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| 398 | elseif testsum(ivar)==1% variable representing fixed coordinates |
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| 399 | eval(['VarInit=DataOut.' VarName ';']); |
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| 400 | if isempty(errormsg) && ~isequal(VarVal,VarInit) |
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| 401 | msgbox_uvmat('ERROR',['time series requires constant coordinates ' VarName]) |
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| 402 | return |
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| 403 | end |
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| 404 | end |
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| 405 | end |
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| 406 | |
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| 407 | % record the time: |
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| 408 | if isempty(time)% time read in ncfiles |
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| 409 | if isfield(Field,'Time') |
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| 410 | DataOut.Time(filecounter,1)=Field.Time; |
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| 411 | else |
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| 412 | DataOut.Time(filecounter,1)=ifile;%default |
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| 413 | end |
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| 414 | else % time from ImaDoc prevails TODO: correct |
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| 415 | % DataOut.Time(filecounter,1)=time{1}(i1_series{1})(ifile),j1_series{1}(ifile))+time(end,i2_series{end}(ifile),j2_series{end}(ifile)))/2; |
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| 416 | DataOut.Time(filecounter,1)=i1_series{1}(ifile);% TODO : generalise |
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| 417 | end |
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| 418 | |
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| 419 | % record the number of missing input fields |
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| 420 | if ~isempty(errormsg) |
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| 421 | nbmissing=nbmissing+1; |
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| 422 | display(['ifile=' num2str(ifile) ':' errormsg]) |
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| 423 | end |
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| 424 | end |
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| 425 | end |
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| 426 | end |
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| 427 | %%%%%%% END OF LOOP WITHIN A SLICE |
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| 428 | |
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| 429 | %remove time for global attributes if exists |
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| 430 | Time_index=find(strcmp('Time',DataOut.ListGlobalAttribute)); |
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| 431 | if ~isempty(Time_index) |
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| 432 | DataOut.ListGlobalAttribute(Time_index)=[]; |
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| 433 | end |
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| 434 | DataOut.Conventions='uvmat'; |
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| 435 | for ivar=1:numel(DataOut.ListVarName) |
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| 436 | VarName=DataOut.ListVarName{ivar}; |
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| 437 | eval(['DataOut.' VarName '=squeeze(DataOut.' VarName ');']) %remove singletons |
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| 438 | end |
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| 439 | |
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| 440 | % add time dimension |
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| 441 | for ivar=1:length(Field.ListVarName) |
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| 442 | DimCell=Field.VarDimName(ivar); |
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| 443 | if testsum(ivar)==2%variable used as time series |
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| 444 | DataOut.VarDimName{ivar}=[{'Time'} DimCell]; |
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| 445 | elseif testsum(ivar)==1 |
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| 446 | DataOut.VarDimName{ivar}=DimCell; |
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| 447 | end |
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| 448 | end |
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| 449 | indexremove=find(~testsum); |
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| 450 | if ~isempty(indexremove) |
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| 451 | DataOut.ListVarName(1+indexremove)=[]; |
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| 452 | DataOut.VarDimName(indexremove)=[]; |
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| 453 | if isfield(DataOut,'Role') && ~isempty(DataOut.Role{1})%generaliser aus autres attributs |
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| 454 | DataOut.Role(1+indexremove)=[]; |
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| 455 | end |
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| 456 | end |
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| 457 | |
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| 458 | %shift variable attributes |
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| 459 | if isfield(DataOut,'VarAttribute') |
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| 460 | DataOut.VarAttribute=[{[]} DataOut.VarAttribute]; |
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| 461 | end |
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| 462 | DataOut.VarDimName=[{'Time'} DataOut.VarDimName]; |
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| 463 | DataOut.Action=Param.Action;%name of the processing programme |
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| 464 | test_time=diff(DataOut.Time)>0;% test that the readed time is increasing (not constant) |
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| 465 | if ~test_time |
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| 466 | DataOut.Time=[1:filecounter]; |
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| 467 | end |
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| 468 | |
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| 469 | % display nbmissing |
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| 470 | if ~isequal(nbmissing,0) |
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| 471 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' files skipped: missing files or bad input, see command window display']) |
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| 472 | end |
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| 473 | |
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| 474 | %name of result file |
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| 475 | % filemean=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},'.nc','_1',i1_series{1}(i_slice)); |
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| 476 | OutputFile=fullfile_uvmat(RootPath{1},Param.OutputSubDir,RootFile{1},FileExtOut,NomTypeOut,i1_series{1}(1),i1_series{1}(end),i_slice,[]); |
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| 477 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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| 478 | if isempty(errormsg) |
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| 479 | display([OutputFile ' written']) |
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| 480 | else |
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| 481 | msgbox_uvmat('ERROR',['error in Series/struct2nc: ' errormsg]) |
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| 482 | end |
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| 483 | end |
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| 484 | |
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| 485 | %% plot the time series (the last one in case of multislices) |
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| 486 | figure |
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| 487 | haxes=axes; |
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| 488 | plot_field(DataOut,haxes) |
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| 489 | |
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| 490 | %% display the result file using the GUI get_field |
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| 491 | hget_field=findobj(allchild(0),'name','get_field'); |
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| 492 | if ~isempty(hget_field) |
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| 493 | delete(hget_field) |
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| 494 | end |
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| 495 | get_field(OutputFile,DataOut) |
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| 496 | |
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| 497 | |
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| 498 | |
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