[169] | 1 | %'aver_stat': calculate field average, used with series.fig |
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| 2 | %------------------------------------------------------------------------ |
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[374] | 3 | % function GUI_input=aver_stat(Param) |
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[169] | 4 | % |
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[447] | 5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[169] | 6 | %OUTPUT |
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| 7 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 8 | % |
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| 9 | %INPUT: |
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[447] | 10 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 11 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 12 | % In the absence of input (as activated when the current Action is selected |
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| 13 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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[169] | 14 | % |
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[447] | 15 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 16 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 17 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 18 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 19 | % .OutputDir: directory for data outputs, including path |
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| 20 | % .Action: .ActionName: name of the current activated function |
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| 21 | % .ActionPath: path of the current activated function |
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| 22 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 23 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 24 | % .TransformPath: path of the selected transform function |
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| 25 | % .TransformHandle: corresponding function handle |
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| 26 | % .InputFields: sub structure describing the input fields withfields |
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| 27 | % .FieldName: name of the field |
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| 28 | % .VelType: velocity type |
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| 29 | % .FieldName_1: name of the second field in case of two input series |
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| 30 | % .VelType_1: velocity type of the second field in case of two input series |
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| 31 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 32 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 33 | |
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[361] | 34 | function GUI_input=aver_stat(Param) |
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[447] | 35 | |
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| 36 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 37 | if ~exist('Param','var') % case with no input parameter |
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| 38 | GUI_input={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation) |
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| 39 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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[27] | 40 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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[447] | 41 | 'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 42 | 'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 43 | 'FieldTransform'; 'on';...%can use a transform function |
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| 44 | 'ProjObject';'on';...%can use projection object(option 'off'/'on', |
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| 45 | 'Mask';'off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 46 | 'OutputDirExt';'.stat';...%set the output dir extension |
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[27] | 47 | ''}; |
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| 48 | return |
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| 49 | end |
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| 50 | |
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[447] | 51 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 52 | %% get input parameters, file names and indices |
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| 53 | % BATCH case: read the xml file for batch case |
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[449] | 54 | if ischar(Param) && ~isempty(find(regexp(Param,'.xml$'))) |
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[361] | 55 | Param=xml2struct(Param); |
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[442] | 56 | checkrun=0; |
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[447] | 57 | % RUN case: parameters introduced as the input structure Param |
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| 58 | else |
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[374] | 59 | hseries=guidata(Param.hseries);%handles of the GUI series |
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[447] | 60 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
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| 61 | checkrun=1; % indicate the RUN option is used |
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[361] | 62 | end |
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[447] | 63 | % get the set of input file names (cell array filecell), and the lists of |
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| 64 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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[374] | 65 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[447] | 66 | % filecell{iview,fileindex}: cell array representing the list of file names |
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| 67 | % iview: line in the table corresponding to a given file series |
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| 68 | % fileindex: file index within the file series, |
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| 69 | % 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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| 70 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 71 | % set of frame indices used for movie or multimage input |
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| 72 | if ~isempty(j1_series) |
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| 73 | frame_index=j1_series; |
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| 74 | else |
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| 75 | frame_index=i1_series; |
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[41] | 76 | end |
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| 77 | |
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[447] | 78 | %% root input file(s) and type |
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| 79 | RootPath=Param.InputTable(:,1); |
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| 80 | RootFile=Param.InputTable(:,3); |
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| 81 | SubDir=Param.InputTable(:,2); |
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| 82 | NomType=Param.InputTable(:,4); |
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| 83 | FileExt=Param.InputTable(:,5); |
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[27] | 84 | |
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[447] | 85 | % numbers of slices and file indices |
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| 86 | NbSlice=1;%default |
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| 87 | if isfield(Param.IndexRange,'NbSlice') |
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| 88 | NbSlice=Param.IndexRange.NbSlice; |
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[27] | 89 | end |
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[447] | 90 | nbview=size(i1_series,1);%number of input file series (lines in InputTable) |
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| 91 | nbfield_j=size(i1_series,2); %nb of consecutive fields at each level(burst |
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| 92 | nbfield=nbfield_j*size(i1_series,3); %total number of files or frames |
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| 93 | nbfield_i=floor(nbfield/NbSlice);%total number of i indexes (adjusted to an integer number of slices) |
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| 94 | nbfield=nbfield_i*nbfield_j; %total number of fields after adjustement |
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[43] | 95 | |
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[447] | 96 | %determine the file type on each line from the first input file |
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| 97 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 98 | NcTypeOptions={'netcdf','civx','civdata'}; |
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[27] | 99 | for iview=1:nbview |
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[447] | 100 | [FileType{iview},FileInfo{iview},Object{iview}]=get_file_type(filecell{iview,1}); |
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| 101 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 102 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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[27] | 103 | end |
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| 104 | |
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[255] | 105 | %% Calibration data and timing: read the ImaDoc files |
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[27] | 106 | mode=''; %default |
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| 107 | timecell={}; |
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| 108 | itime=0; |
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| 109 | NbSlice_calib={}; |
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| 110 | for iview=1:nbview%Loop on views |
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| 111 | XmlData{iview}=[];%default |
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| 112 | filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); |
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| 113 | if exist([filebase{iview} '.xml'],'file') |
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| 114 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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| 115 | if isfield(XmlData{iview},'Time') |
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| 116 | itime=itime+1; |
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| 117 | timecell{itime}=XmlData{iview}.Time; |
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| 118 | end |
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| 119 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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| 120 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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| 121 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 122 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 123 | end |
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| 124 | end |
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| 125 | elseif exist([filebase{iview} '.civ'],'file') |
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| 126 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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| 127 | itime=itime+1; |
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| 128 | timecell{itime}=time; |
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| 129 | XmlData{iview}.Time=time; |
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| 130 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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| 131 | GeometryCalib.Tx=0; |
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| 132 | GeometryCalib.Ty=0; |
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| 133 | GeometryCalib.Tz=1; |
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| 134 | GeometryCalib.dpx=1; |
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| 135 | GeometryCalib.dpy=1; |
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| 136 | GeometryCalib.sx=1; |
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| 137 | GeometryCalib.Cx=0; |
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| 138 | GeometryCalib.Cy=0; |
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| 139 | GeometryCalib.f=1; |
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| 140 | GeometryCalib.kappa1=0; |
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| 141 | GeometryCalib.CoordUnit='cm'; |
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| 142 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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| 143 | if error==1 |
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| 144 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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| 145 | end |
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| 146 | end |
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| 147 | end |
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| 148 | |
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[392] | 149 | %% check coincidence in time for several input file series |
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[27] | 150 | multitime=0; |
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[55] | 151 | if isempty(timecell) |
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[27] | 152 | time=[]; |
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| 153 | elseif length(timecell)==1 |
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| 154 | time=timecell{1}; |
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| 155 | elseif length(timecell)>1 |
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| 156 | multitime=1; |
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| 157 | for icell=1:length(timecell) |
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| 158 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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| 159 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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| 160 | time=timecell{1}; |
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| 161 | multitime=0; |
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| 162 | break |
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| 163 | end |
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| 164 | end |
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| 165 | end |
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| 166 | if multitime |
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| 167 | for icell=1:length(timecell) |
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| 168 | time(icell,:,:)=timecell{icell}; |
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| 169 | end |
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| 170 | diff_time=max(max(diff(time))); |
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| 171 | if diff_time>0 |
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[447] | 172 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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[27] | 173 | end |
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| 174 | end |
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[447] | 175 | if size(time,2) < i2_series(1,end) || size(time,3) < j2_series(1,end)% time array absent or too short in ImaDoc xml file' |
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[27] | 176 | time=[]; |
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| 177 | end |
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| 178 | |
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[447] | 179 | %% coordinate transform or other user defined transform |
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| 180 | transform_fct='';%default |
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| 181 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle') |
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| 182 | transform_fct=Param.FieldTransform.TransformHandle; |
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[27] | 183 | end |
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[447] | 184 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 185 | % EDIT FROM HERE |
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| 186 | |
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| 187 | %% check the validity of input file types |
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| 188 | if CheckImage{1} |
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| 189 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 190 | elseif CheckNc{1} |
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| 191 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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| 192 | else |
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| 193 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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| 194 | return |
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| 195 | end |
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| 196 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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| 197 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
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| 198 | return |
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| 199 | end |
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| 200 | NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
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| 201 | if NbSlice~=nbfield_j |
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| 202 | 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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| 203 | if ~strcmp(answer,'Yes') |
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| 204 | return |
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[255] | 205 | end |
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[218] | 206 | end |
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[442] | 207 | |
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[447] | 208 | %% Set field names and velocity types |
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| 209 | InputFields{1}=[];%default (case of images) |
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| 210 | if isfield(Param,'InputFields') |
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| 211 | InputFields{1}=Param.InputFields; |
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| 212 | end |
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| 213 | if nbview==2 |
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| 214 | InputFields{2}=[];%default (case of images) |
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| 215 | if isfield(Param,'InputFields') |
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| 216 | InputFields{2}=Param.InputFields{1};%default |
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| 217 | if isfield(Param.InputFields,'FieldName_1') |
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| 218 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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| 219 | if isfield(Param.InputFields,'VelType_1') |
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| 220 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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| 221 | end |
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| 222 | end |
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[255] | 223 | end |
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| 224 | end |
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[447] | 225 | |
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| 226 | %% Initiate output fields |
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| 227 | %initiate the output structure as a copy of the first input one (reproduce fields) |
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| 228 | [DataOut,ParamOut,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
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| 229 | if ~isempty(errormsg) |
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| 230 | msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg]) |
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[218] | 231 | return |
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| 232 | end |
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[447] | 233 | time_1=[]; |
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| 234 | if isfield(DataOut,'Time') |
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| 235 | time_1=DataOut.Time(1); |
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[41] | 236 | end |
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[447] | 237 | if CheckNc{iview} |
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| 238 | if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) |
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| 239 | DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; |
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| 240 | end |
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| 241 | DataOut.Conventions='uvmat'; |
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| 242 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; |
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| 243 | ActionKey='Action'; |
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| 244 | while isfield(DataOut,ActionKey) |
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| 245 | ActionKey=[ActionKey '_1']; |
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| 246 | end |
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| 247 | DataOut.(ActionKey)=Param.Action; |
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| 248 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; |
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| 249 | if isfield(DataOut,'Time') |
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| 250 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; |
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| 251 | end |
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| 252 | end |
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[27] | 253 | |
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[447] | 254 | %% MAIN LOOP ON SLICES |
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| 255 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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[27] | 256 | for i_slice=1:NbSlice |
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[447] | 257 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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[255] | 258 | nbfiles=0; |
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| 259 | nbmissing=0; |
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[447] | 260 | |
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| 261 | %initiate result fields |
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| 262 | for ivar=1:length(DataOut.ListVarName) |
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| 263 | DataOut.(DataOut.ListVarName{ivar})=0; % initialise all fields to zero |
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| 264 | end |
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| 265 | |
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| 266 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 267 | for index=index_slice |
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| 268 | if checkrun |
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| 269 | update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield)) |
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| 270 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 271 | else |
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| 272 | stopstate='queue'; |
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| 273 | end |
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| 274 | |
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| 275 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 276 | for iview=1:nbview |
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[255] | 277 | % reading input file(s) |
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[447] | 278 | [Data{iview},ParamOut,errormsg] = read_field(filecell{iview,index},FileType{iview},InputFields{iview},frame_index(iview,index)); |
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| 279 | if ~isempty(errormsg) |
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| 280 | errormsg=['error of input reading: ' errormsg]; |
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| 281 | break |
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[255] | 282 | end |
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[447] | 283 | if ~isempty(NbSlice_calib) |
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| 284 | Data{iview}.ZIndex=mod(i1_series(iview,index)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
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| 285 | end |
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| 286 | end |
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| 287 | Field=[]; % initiate the current input field structure |
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| 288 | %%%%%%%%%%%%%%%% end loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 289 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 290 | % EDIT FROM HERE |
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| 291 | |
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| 292 | if isempty(errormsg) |
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[255] | 293 | % coordinate transform (or other user defined transform) |
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| 294 | if ~isempty(transform_fct) |
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[27] | 295 | if nbview==2 |
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[41] | 296 | [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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[27] | 297 | if isempty(Data{2}) |
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| 298 | Data(2)=[]; |
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| 299 | end |
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| 300 | else |
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[80] | 301 | Data{1}=transform_fct(Data{1},XmlData{1}); |
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[27] | 302 | end |
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[255] | 303 | end |
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| 304 | |
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| 305 | % field calculation (vort, div...) |
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[447] | 306 | if strcmp(FileType{1},'civx')||strcmp(FileType{1},'civ') |
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| 307 | Data{1}=calc_field(InputFields{1}.FieldName,Data{1});%calculate field (vort..) |
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[27] | 308 | end |
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[255] | 309 | |
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| 310 | % field substration (for two input file series) |
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[27] | 311 | if length(Data)==2 |
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[447] | 312 | if strcmp(FileType{2},'civx')||strcmp(FileType{2},'civ') |
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| 313 | Data{2}=calc_field(InputFields{2}.FieldName,Data{2});%calculate field (vort..) |
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| 314 | end |
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[27] | 315 | [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields |
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| 316 | if ~isempty(errormsg) |
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| 317 | msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg]) |
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| 318 | return |
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| 319 | end |
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| 320 | else |
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| 321 | Field=Data{1}; |
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| 322 | end |
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[447] | 323 | if Param.CheckObject |
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[41] | 324 | [Field,errormsg]=proj_field(Field,ProjObject); |
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[255] | 325 | if ~isempty(errormsg) |
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[27] | 326 | msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) |
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| 327 | return |
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| 328 | end |
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[255] | 329 | end |
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| 330 | nbfiles=nbfiles+1; |
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[447] | 331 | |
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| 332 | %%%%%%%%%%%% MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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| 333 | %update sum |
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| 334 | for ivar=1:length(Field.ListVarName) |
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| 335 | VarName=Field.ListVarName{ivar}; |
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| 336 | sizmean=size(DataOut.(VarName)); |
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| 337 | siz=size(Field.(VarName)); |
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| 338 | if ~isequal(DataOut.(VarName),0)&& ~isequal(siz,sizmean) |
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| 339 | msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid']) |
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| 340 | return |
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| 341 | else |
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| 342 | DataOut.(VarName)=DataOut.(VarName)+ double(Field.(VarName)); % update the sum |
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[255] | 343 | end |
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| 344 | end |
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[447] | 345 | %%%%%%%%%%%% END MAIN RUNNING OPERATIONS %%%%%%%%%%%% |
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| 346 | else |
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| 347 | display(errormsg) |
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| 348 | end |
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[255] | 349 | end |
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[447] | 350 | %%%%%%%%%%%%%%%% end loop on field indices %%%%%%%%%%%%%%%% |
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| 351 | |
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[27] | 352 | for ivar=1:length(Field.ListVarName) |
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| 353 | VarName=Field.ListVarName{ivar}; |
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[447] | 354 | DataOut.(VarName)=DataOut.(VarName)/nbfiles; % normalize the mean |
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[27] | 355 | end |
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| 356 | if nbmissing~=0 |
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| 357 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) |
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| 358 | end |
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| 359 | if isempty(time) % time read from files prevails |
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| 360 | if isfield(Field,'Time') |
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| 361 | time_end=Field.Time(1);%last time read |
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| 362 | if ~isempty(time_1) |
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[447] | 363 | DataOut.Time=time_1; |
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| 364 | DataOut.Time_end=time_end; |
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[27] | 365 | end |
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| 366 | end |
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| 367 | else % time from ImaDoc prevails |
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[447] | 368 | DataOut.Time=time(1,i1_series(1,1),j1_series(1,1)); |
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| 369 | DataOut.Time_end=time(end,i1_series(end,end),j1_series(end,end)); |
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[27] | 370 | end |
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[255] | 371 | |
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[27] | 372 | %writing the result file |
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[447] | 373 | 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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| 374 | if CheckImage{1} %case of images |
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| 375 | if isequal(FileInfo{1}.BitDepth,16)||(numel(FileInfo)==2 &&isequal(FileInfo{2}.BitDepth,16)) |
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| 376 | DataOut.A=uint16(DataOut.A); |
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| 377 | imwrite(DataOut.A,OutputFile,'BitDepth',16); % case of 16 bit images |
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[27] | 378 | else |
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[447] | 379 | DataOut.A=uint8(DataOut.A); |
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| 380 | imwrite(DataOut.A,OutputFile,'BitDepth',8); % case of 16 bit images |
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[27] | 381 | end |
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[447] | 382 | display([OutputFile ' written']); |
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[55] | 383 | else %case of netcdf input file , determine global attributes |
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[447] | 384 | errormsg=struct2nc(OutputFile,DataOut); %save result file |
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[27] | 385 | if isempty(errormsg) |
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[447] | 386 | display([OutputFile ' written']); |
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[27] | 387 | else |
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| 388 | msgbox_uvmat('ERROR',['error in writting result file: ' errormsg]) |
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| 389 | display(errormsg) |
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| 390 | end |
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[255] | 391 | end % end averaging loop |
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[447] | 392 | end |
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| 393 | %%%%%%%%%%%%%%%% end loop on slices %%%%%%%%%%%%%%%% |
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[255] | 394 | |
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| 395 | %% reproduce ImaDoc/GeometryCalib for image series |
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[447] | 396 | % if isfield(XmlData{1},'GeometryCalib') && ~isempty(XmlData{1}.GeometryCalib) |
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| 397 | % [tild,RootFile]=fileparts(filebase_out); |
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| 398 | % outputxml=fullfile(pathdir,[RootFile '.xml']); |
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| 399 | % errormsg=update_imadoc(XmlData{1}.GeometryCalib,outputxml);% introduce the calibration data in the xml file |
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| 400 | % if strcmp(errormsg,'') |
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| 401 | % display(['GeometryCalib transferred to ' outputxml]) |
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| 402 | % else |
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| 403 | % msgbox_uvmat('ERROR',errormsg); |
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| 404 | % end |
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| 405 | % end |
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[55] | 406 | |
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[255] | 407 | %% open the result file with uvmat |
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[27] | 408 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
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| 409 | delete(hget_field) |
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[447] | 410 | uvmat(OutputFile)% open the last result file with uvmat |
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