[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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| 5 | %OUTPUT |
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| 6 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 7 | % |
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| 8 | %INPUT: |
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[374] | 9 | % Param: structure containing all the parameters read on the GUI series |
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| 10 | % or name of the xml file containing these parameters (BATCH case) |
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[169] | 11 | % |
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[361] | 12 | function GUI_input=aver_stat(Param) |
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[27] | 13 | %---------------------------------------------------------------------- |
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| 14 | % --- make average on a series of files |
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| 15 | %---------------------------------------------------------------------- |
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| 16 | %INPUT: |
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[374] | 17 | %i1_series: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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[27] | 18 | %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ) |
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[374] | 19 | %j1_series: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ ) |
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[27] | 20 | %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ) |
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| 21 | %OTHER INPUTS given by the structure Series |
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| 22 | % Series.Time: |
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| 23 | % Series.GeometryCalib:%requests for the visibility of input windows in the GUI series (activated directly by the selection in the menu ACTION) |
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[361] | 24 | if ~exist('Param','var') |
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[27] | 25 | GUI_input={'RootPath';'two';...%nbre of possible input series (options 'on'/'two'/'many', default:'one') |
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| 26 | 'SubDir';'on';... % subdirectory of derived files (PIV fields), ('on' by default) |
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| 27 | 'RootFile';'on';... %root input file name ('on' by default) |
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| 28 | 'FileExt';'on';... %input file extension ('on' by default) |
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| 29 | 'NomType';'on';...%type of file indexing ('on' by default) |
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| 30 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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| 31 | 'VelTypeMenu';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 32 | 'FieldMenu';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 33 | 'CoordType'; 'on';...%can use a transform function |
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| 34 | 'GetObject';'on';...%can use projection object(option 'off'/'one'/'two', |
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| 35 | %'GetMask';'on'...%can use mask option |
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| 36 | %'PARAMETER'; %options: name of the user defined parameter',repeat a line for each parameter |
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| 37 | ''}; |
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| 38 | return |
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| 39 | end |
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| 40 | |
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| 41 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[41] | 42 | |
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[374] | 43 | %% input parameters |
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| 44 | % read the xml file for batch case |
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[361] | 45 | if ischar(Param) && ~isempty(find(regexp('Param','.xml$'))) |
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| 46 | Param=xml2struct(Param); |
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[442] | 47 | checkrun=0; |
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[374] | 48 | else % RUN case: parameters introduced as the input structure Param |
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| 49 | hseries=guidata(Param.hseries);%handles of the GUI series |
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[361] | 50 | WaitbarPos=get(hseries.waitbar_frame,'Position'); |
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[442] | 51 | checkrun=1; |
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[361] | 52 | end |
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[374] | 53 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[361] | 54 | |
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[255] | 55 | %% projection object |
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[41] | 56 | test_object=get(hseries.GetObject,'Value'); |
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| 57 | if test_object%isfield(Series,'sethandles') |
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[76] | 58 | hset_object=findobj(allchild(0),'tag','set_object'); |
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[381] | 59 | ProjObject=read_GUI(hset_object); |
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[394] | 60 | answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type ' before averaging']); |
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[41] | 61 | if ~isequal(answeryes,'Yes') |
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| 62 | return |
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| 63 | end |
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| 64 | end |
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| 65 | |
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[255] | 66 | %% root input file and type |
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[361] | 67 | RootPath=Param.InputTable(:,1); |
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| 68 | RootFile=Param.InputTable(:,3); |
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| 69 | SubDir=Param.InputTable(:,2); |
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| 70 | NomType=Param.InputTable(:,4); |
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| 71 | FileExt=Param.InputTable(:,5); |
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[27] | 72 | ext=FileExt{1}; |
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| 73 | form=imformats(ext([2:end]));%test valid Matlab image formats |
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| 74 | testima=0; |
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| 75 | if ~isempty(form)||isequal(lower(ext),'.avi')||isequal(lower(ext),'.vol') |
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| 76 | testima(1)=1; |
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| 77 | end |
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| 78 | if length(FileExt)>=2 |
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| 79 | ext_1=FileExt{2}; |
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| 80 | form=imformats(ext_1([2:end]));%test valid Matlab image formats |
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| 81 | if ~isempty(form)||isequal(lower(ext_1),'.avi')||isequal(lower(ext_1),'.vol') |
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| 82 | testima(2)=1; |
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| 83 | end |
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| 84 | if testima(2)~=testima(1) |
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| 85 | msgbox_uvmat('ERROR','images and netcdf files cannot be compared') |
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| 86 | return |
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| 87 | end |
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| 88 | end |
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| 89 | |
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[374] | 90 | |
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[255] | 91 | %% Number of input series: this function accepts two input file series at most (then it operates on the difference of fields) |
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[27] | 92 | nbview=length(RootPath); |
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| 93 | if nbview>2 |
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| 94 | RootPath=RootPath(1:2); |
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| 95 | set(hseries.RootPath,'String',RootPath) |
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| 96 | SubDir=SubDir(1:2); |
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| 97 | set(hseries.SubDir,'String',SubDir) |
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| 98 | RootFile=RootFile(1:2); |
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| 99 | set(hseries.RootFile,'String',RootFile) |
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| 100 | NomType=NomType(1:2); |
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| 101 | FileExt=FileExt(1:2); |
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| 102 | set(hseries.FileExt,'String',FileExt) |
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| 103 | nbview=2; |
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| 104 | end |
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[43] | 105 | |
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[255] | 106 | %% determine image type |
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[27] | 107 | hhh=which('mmreader'); |
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| 108 | for iview=1:nbview |
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[43] | 109 | if isequal(FileExt{iview},'.nc')||isequal(FileExt{iview},'.cdf') |
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| 110 | FileType{iview}='netcdf'; |
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| 111 | elseif isequal(lower(FileExt{iview}),'.avi') |
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| 112 | if ~isequal(hhh,'')&& mmreader.isPlatformSupported() |
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[27] | 113 | MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); |
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[43] | 114 | FileType{iview}='movie'; |
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| 115 | else |
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| 116 | FileType{iview}='avi'; |
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[27] | 117 | end |
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[43] | 118 | elseif isequal(lower(FileExt{iview}),'.vol') |
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| 119 | FileType{iview}='vol'; |
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| 120 | else |
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| 121 | form=imformats(FileExt{iview}(2:end)); |
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| 122 | if ~isempty(form)% if the extension corresponds to an image format recognized by Matlab |
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| 123 | if isequal(NomType{iview},'*'); |
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| 124 | FileType{iview}='multimage'; |
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| 125 | else |
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| 126 | FileType{iview}='image'; |
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| 127 | end |
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| 128 | end |
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| 129 | end |
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[27] | 130 | end |
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| 131 | |
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[255] | 132 | %% number of slices |
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[361] | 133 | NbSlice=Param.IndexRange.NbSlice; |
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[27] | 134 | |
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[255] | 135 | %% Field and velocity type (the same for the two views) |
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[27] | 136 | Field_str=get(hseries.FieldMenu,'String'); |
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| 137 | FieldName=[]; %default |
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| 138 | testfield=get(hseries.FieldMenu,'Visible'); |
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| 139 | if isequal(testfield,'on') |
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| 140 | val=get(hseries.FieldMenu,'Value'); |
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| 141 | FieldName=Field_str(val);%the same set of fields for all views |
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| 142 | if isequal(FieldName,{'get_field...'}) |
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| 143 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
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| 144 | if length(hget_field)>1 |
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| 145 | delete(hget_field(2:end)) |
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| 146 | elseif isempty(hget_field) |
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| 147 | filename=... |
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[374] | 148 | name_generator(fullfile(RootPath{1},RootFile{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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[27] | 149 | get_field(filename); |
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| 150 | return |
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| 151 | end |
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| 152 | SubField=read_get_field(hget_field); %read the names of the variables to plot in the get_field GUI |
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| 153 | end |
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| 154 | end |
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[255] | 155 | |
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| 156 | %% get the velocity type |
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[27] | 157 | testcivx=0; |
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| 158 | if ~isequal(FieldName,{'get_field...'}) |
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[43] | 159 | testcivx=isequal(FileType{1},'netcdf'); |
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[27] | 160 | end |
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| 161 | if testcivx |
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| 162 | VelType_str=get(hseries.VelTypeMenu,'String'); |
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| 163 | VelType_val=get(hseries.VelTypeMenu,'Value'); |
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| 164 | VelType{1}=VelType_str{VelType_val}; |
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| 165 | if nbview==2 |
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| 166 | VelType_str=get(hseries.VelTypeMenu_1,'String'); |
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| 167 | VelType_val=get(hseries.VelTypeMenu_1,'Value'); |
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| 168 | VelType{2}=VelType_str{VelType_val}; |
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| 169 | end |
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| 170 | end |
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| 171 | |
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[255] | 172 | %% Calibration data and timing: read the ImaDoc files |
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[27] | 173 | mode=''; %default |
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| 174 | timecell={}; |
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| 175 | itime=0; |
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| 176 | NbSlice_calib={}; |
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| 177 | for iview=1:nbview%Loop on views |
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| 178 | XmlData{iview}=[];%default |
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| 179 | filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); |
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| 180 | if exist([filebase{iview} '.xml'],'file') |
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| 181 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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| 182 | if isfield(XmlData{iview},'Time') |
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| 183 | itime=itime+1; |
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| 184 | timecell{itime}=XmlData{iview}.Time; |
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| 185 | end |
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| 186 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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| 187 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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| 188 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 189 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 190 | end |
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| 191 | end |
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| 192 | elseif exist([filebase{iview} '.civ'],'file') |
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| 193 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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| 194 | itime=itime+1; |
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| 195 | timecell{itime}=time; |
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| 196 | XmlData{iview}.Time=time; |
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| 197 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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| 198 | GeometryCalib.Tx=0; |
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| 199 | GeometryCalib.Ty=0; |
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| 200 | GeometryCalib.Tz=1; |
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| 201 | GeometryCalib.dpx=1; |
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| 202 | GeometryCalib.dpy=1; |
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| 203 | GeometryCalib.sx=1; |
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| 204 | GeometryCalib.Cx=0; |
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| 205 | GeometryCalib.Cy=0; |
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| 206 | GeometryCalib.f=1; |
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| 207 | GeometryCalib.kappa1=0; |
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| 208 | GeometryCalib.CoordUnit='cm'; |
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| 209 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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| 210 | if error==1 |
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| 211 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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| 212 | end |
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| 213 | end |
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| 214 | end |
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| 215 | |
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[392] | 216 | %% check coincidence in time for several input file series |
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[27] | 217 | multitime=0; |
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[55] | 218 | if isempty(timecell) |
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[27] | 219 | time=[]; |
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| 220 | elseif length(timecell)==1 |
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| 221 | time=timecell{1}; |
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| 222 | elseif length(timecell)>1 |
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| 223 | multitime=1; |
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| 224 | for icell=1:length(timecell) |
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| 225 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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| 226 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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| 227 | time=timecell{1}; |
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| 228 | multitime=0; |
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| 229 | break |
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| 230 | end |
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| 231 | end |
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| 232 | end |
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| 233 | if multitime |
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| 234 | for icell=1:length(timecell) |
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| 235 | time(icell,:,:)=timecell{icell}; |
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| 236 | end |
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| 237 | diff_time=max(max(diff(time))); |
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| 238 | if diff_time>0 |
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| 239 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
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| 240 | end |
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| 241 | end |
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[392] | 242 | if size(time,2) < i2_series{1}(end) || size(time,3) < num_j2{1}(end)% time array absent or too short in ImaDoc xml file' |
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[27] | 243 | time=[]; |
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| 244 | end |
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| 245 | |
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[255] | 246 | %% Name(s) of output file(s) |
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| 247 | filebase_out=filebase{1};% the result file has the same root name as the input file series (and the first one is chosen in case of two input series) |
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| 248 | %file extension of the result |
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| 249 | if testima %case of images |
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| 250 | ext_out='.png'; |
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| 251 | else |
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| 252 | ext_out='.nc'; |
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[27] | 253 | end |
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[442] | 254 | subdir_result=[SubDir{1} '.stat'];%subdirectory for the results |
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| 255 | pathdir=RootPath{1};% full subdirectory name, including path |
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| 256 | checkdetect=1; |
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| 257 | while checkdetect %create a new subdir if the netcdf files already exist |
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| 258 | checkdetect=exist(fullfile(pathdir,subdir_result)); |
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| 259 | if checkdetect% if a nesult dir already exists |
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| 260 | r=regexp(subdir_result,'(?<root>.*\D)(?<num1>\d+)$','names');%detect whether name ends by a number |
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| 261 | if isempty(r) |
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| 262 | r(1).root=[subdir_result '_']; |
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| 263 | r(1).num1='0'; |
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[255] | 264 | end |
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[442] | 265 | subdir_result=[r(1).root num2str(str2num(r(1).num1)+1)];%increment the index by 1 or put 1 |
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[255] | 266 | end |
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[218] | 267 | end |
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[442] | 268 | NomTypeOut='_1-2'; |
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| 269 | fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i1_series{1}(1),i1_series{1}(end),[],[]); |
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| 270 | |
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| 271 | % A REPRNDRE CAS MULTI-NIVEAU: |
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| 272 | % pathdir=fullfile(RootPath{1},subdir_result);% full subdirectory name, including path |
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| 273 | % if NbSlice==1% keep track of the first and lsat indices of the input files |
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| 274 | % %NomTypeOut=nomtype2pair(Param.InputTable{1,4},i2_series{end}(end)-i1_series{1}(1),j2_series{end}(end)-j1_series{1}(1)); |
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| 275 | % NomTypeOut='_1-2'; |
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| 276 | % fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i1_series{1}(1),i1_series{1}(end),[],[]); |
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| 277 | % testexist=exist(fileresult{1},'file'); |
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| 278 | % else % simplified indexing with i_slice for multiple slices |
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| 279 | % testexist=0; |
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| 280 | % for i_slice=1:NbSlice |
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| 281 | % fileresult{1}=fullfile_uvmat(RootPath{1},subdir_result,RootFile{1},ext_out,NomTypeOut,i_slice,[],[],[]); |
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| 282 | % if exist(fileresult{i_slice},'file') |
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| 283 | % testexist=1; |
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| 284 | % break |
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| 285 | % end |
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| 286 | % end |
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| 287 | % end |
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| 288 | % if testexist |
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| 289 | % subdir_result=[subdir_result '.0']; |
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| 290 | % end |
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| 291 | % end |
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[255] | 292 | % create result directory if needed |
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[442] | 293 | if ~exist(fullfile(RootPath{1},subdir_result),'dir') |
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| 294 | [m1,m2,m3]=mkdir(fullfile(RootPath{1},subdir_result)); |
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[255] | 295 | if ~isequal(m2,'') |
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| 296 | msgbox_uvmat('CONFIRMATION',m2);%error message for directory creation |
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| 297 | end |
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| 298 | end |
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[442] | 299 | [xx,msg2] = fileattrib(fullfile(RootPath{1},subdir_result),'+w','g'); %yield writing access (+w) to user group (g) |
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[218] | 300 | if ~strcmp(msg2,'') |
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[442] | 301 | msgbox_uvmat('ERROR',['pb of permission for ' fullfile(RootPath{1},subdir_result) ': ' msg2])%error message for writting access |
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[218] | 302 | return |
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| 303 | end |
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[27] | 304 | |
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[255] | 305 | %% coordinate transform or other user defined transform |
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[374] | 306 | transform_fct='';%default |
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[392] | 307 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'fct_handle') |
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| 308 | transform_fct=Param.FieldTransform.fct_handle; |
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[41] | 309 | end |
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[27] | 310 | |
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[255] | 311 | %% main loop |
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[374] | 312 | siz=size(i1_series{1}); |
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[255] | 313 | nbfield2=siz(1); %nb of consecutive fields at each level(burst |
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| 314 | nbfield=siz(1)*siz(2); |
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| 315 | nbfield=floor(nbfield/(nbfield2*NbSlice));%total number of i indexes (adjusted to an integer number of slices) |
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[27] | 316 | |
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[255] | 317 | % loop on slices |
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[27] | 318 | for i_slice=1:NbSlice |
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[255] | 319 | for ifield=1:nbfield |
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| 320 | indselect(:,ifield)=((ifield-1)*NbSlice+(i_slice-1))*nbfield2+[1:nbfield2]';%selected indices on the list of files of a slice |
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| 321 | end |
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| 322 | S=0; %initiate the image sum S |
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| 323 | nbfiles=0; |
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| 324 | nbmissing=0; |
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| 325 | % averaging loop |
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| 326 | for index=1:nbfield*nbfield2 |
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[374] | 327 | % stopstate=get(hseries.RUN,'BusyAction'); |
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| 328 | % if isequal(stopstate,'queue') % enable STOP command |
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| 329 | % update_waitbar(hseries.waitbar,WaitbarPos,index/(nbfield*nbfield2)) |
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[442] | 330 | if checkrun |
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| 331 | update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield*nbfield2)) |
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| 332 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 333 | else |
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| 334 | stopstate='queue'; |
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| 335 | end |
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[255] | 336 | ifile=indselect(index); |
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| 337 | % reading input file(s) |
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| 338 | for iview=1:nbview |
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[374] | 339 | filename=filecell{iview,index}; |
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| 340 | if ~isequal(FileType{iview},'netcdf') |
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[27] | 341 | Data{iview}.ListVarName={'A'}; |
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| 342 | Data{iview}.AName='image'; |
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[43] | 343 | switch FileType{iview} |
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| 344 | case 'movie' |
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[374] | 345 | A=read(MovieObject{iview},i1_series{iview}(ifile)); |
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[43] | 346 | case 'avi' |
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[374] | 347 | mov=aviread(filename,i1_series{iview}(ifile)); |
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[43] | 348 | A=frame2im(mov(1)); |
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| 349 | case 'vol' |
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| 350 | A=imread(filename); |
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| 351 | case 'multimage' |
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[374] | 352 | A=imread(filename,i1_series{iview}(ifile)); |
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[43] | 353 | case 'image' |
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| 354 | A=imread(filename); |
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[255] | 355 | end |
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| 356 | Data{iview}.ListVarName={'AY','AX','A'}; % |
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[43] | 357 | Atype{iview}=class(A); |
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| 358 | npy=size(A,1); |
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| 359 | npx=size(A,2); |
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| 360 | nbcolor=size(A,3); |
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| 361 | if nbcolor==3 |
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[255] | 362 | Data{iview}.VarDimName={'AY','AX',{'AY','AX','rgb'}}; |
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[27] | 363 | else |
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[255] | 364 | Data{iview}.VarDimName={'AY','AX',{'AY','AX'}}; |
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| 365 | end |
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[107] | 366 | Data{iview}.AY=[npy-0.5 0.5]; |
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| 367 | Data{iview}.AX=[0.5 npx-0.5]; |
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[43] | 368 | Data{iview}.A=double(A); |
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[158] | 369 | Data{iview}.CoordUnit='pixel'; |
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[27] | 370 | elseif testcivx |
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[420] | 371 | [Data{iview},VelTypeOut,errormsg]=read_civxdata(filename,FieldName,VelType); |
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| 372 | if ~isempty(errormsg) |
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| 373 | msgbox_uvmat('ERROR',['error of input reading: ' errormsg]) |
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| 374 | return |
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| 375 | end |
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[27] | 376 | else |
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[255] | 377 | [Data{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
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[27] | 378 | Data{iview}.VarAttribute=SubField.VarAttribute; |
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[255] | 379 | end |
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[27] | 380 | if isfield(Data{iview},'Txt') |
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| 381 | msgbox_uvmat('ERROR',['error of input reading: ' Data{iview}.Txt]) |
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| 382 | return |
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| 383 | end |
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[255] | 384 | end |
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| 385 | |
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| 386 | % coordinate transform (or other user defined transform) |
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| 387 | if ~isempty(transform_fct) |
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[27] | 388 | if ~isempty(NbSlice_calib) |
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[374] | 389 | Data{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1;%Zindex for phys transform |
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[27] | 390 | end |
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| 391 | if nbview==2 |
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[41] | 392 | [Data{1},Data{2}]=transform_fct(Data{1},XmlData{1},Data{2},XmlData{2}); |
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[27] | 393 | if isempty(Data{2}) |
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| 394 | Data(2)=[]; |
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| 395 | end |
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| 396 | else |
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[80] | 397 | Data{1}=transform_fct(Data{1},XmlData{1}); |
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[27] | 398 | end |
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[255] | 399 | end |
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| 400 | |
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| 401 | % field calculation (vort, div...) |
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[27] | 402 | if testcivx |
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[255] | 403 | Data{iview}=calc_field(FieldName,Data{iview});%calculate field (vort..) |
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[27] | 404 | end |
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[255] | 405 | |
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| 406 | % field substration (for two input file series) |
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[27] | 407 | if length(Data)==2 |
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| 408 | [Field,errormsg]=sub_field(Data{1},Data{2}); %substract the two fields |
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| 409 | if ~isempty(errormsg) |
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| 410 | msgbox_uvmat('ERROR',['error in aver_stat/sub_field:' errormsg]) |
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| 411 | return |
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| 412 | end |
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| 413 | else |
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| 414 | Field=Data{1}; |
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| 415 | end |
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[41] | 416 | if test_object |
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| 417 | [Field,errormsg]=proj_field(Field,ProjObject); |
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[255] | 418 | if ~isempty(errormsg) |
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[27] | 419 | msgbox_uvmat('ERROR',['error in aver_stat/proj_field:' errormsg]) |
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| 420 | return |
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| 421 | end |
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[255] | 422 | end |
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| 423 | nbfiles=nbfiles+1; |
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| 424 | if nbfiles==1 %first field |
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| 425 | time_1=[]; |
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| 426 | if isfield(Field,'Time') |
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| 427 | time_1=Field.Time(1); |
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| 428 | end |
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| 429 | DataMean=Field;%default |
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| 430 | else |
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| 431 | for ivar=1:length(Field.ListVarName) |
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| 432 | VarName=Field.ListVarName{ivar}; |
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| 433 | eval(['sizmean=size(DataMean.' VarName ');']); |
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| 434 | eval(['siz=size(Field.' VarName ');']); |
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| 435 | if ~isequal(siz,sizmean) |
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| 436 | msgbox_uvmat('ERROR',['unequal size of input field ' VarName ', need to project on a grid']) |
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| 437 | return |
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| 438 | else |
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| 439 | eval(['DataMean.' VarName '=DataMean.' VarName '+ Field.' VarName ';']); % update the sum |
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[27] | 440 | end |
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| 441 | end |
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[255] | 442 | end |
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[374] | 443 | % end |
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[255] | 444 | end |
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| 445 | %end averaging loop |
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[27] | 446 | for ivar=1:length(Field.ListVarName) |
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| 447 | VarName=Field.ListVarName{ivar}; |
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| 448 | eval(['DataMean.' VarName '=DataMean.' VarName '/nbfiles;']); % normalize the mean |
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| 449 | end |
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| 450 | if nbmissing~=0 |
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| 451 | msgbox_uvmat('WARNING',[num2str(nbmissing) ' input files are missing or skipted']) |
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| 452 | end |
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| 453 | if isempty(time) % time read from files prevails |
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| 454 | if isfield(Field,'Time') |
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| 455 | time_end=Field.Time(1);%last time read |
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| 456 | if ~isempty(time_1) |
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| 457 | DataMean.Time=time_1; |
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| 458 | DataMean.Time_end=time_end; |
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| 459 | end |
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| 460 | end |
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| 461 | else % time from ImaDoc prevails |
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[374] | 462 | DataMean.Time=time(1,i1_series{1}(1),j1_series{1}(1)); |
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| 463 | DataMean.Time_end=time(end,i1_series{end}(end),j1_series{end}(end)); |
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[27] | 464 | end |
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[255] | 465 | |
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[27] | 466 | %writing the result file |
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[255] | 467 | if testima %case of images |
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[27] | 468 | if isequal(Atype{1},'uint16') |
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[255] | 469 | imwrite(uint16(DataMean.A),fileresult{i_slice},'BitDepth',16); % case of 16 bit images |
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[27] | 470 | else |
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[255] | 471 | imwrite(uint8(DataMean.A),fileresult{i_slice},'BitDepth',8); % case of 8 bit images |
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[27] | 472 | end |
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[255] | 473 | display([fileresult{i_slice} ' written']); |
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[55] | 474 | else %case of netcdf input file , determine global attributes |
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[374] | 475 | if isempty(strcmp('Conventions',DataMean.ListGlobalAttribute)) |
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| 476 | DataMean.ListGlobalAttribute=['Conventions' DataMean.ListGlobalAttribute]; |
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| 477 | end |
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| 478 | DataMean.Conventions='uvmat'; |
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[361] | 479 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {Param.Action}]; |
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[27] | 480 | ActionKey='Action'; |
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| 481 | while isfield(DataMean,ActionKey) |
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| 482 | ActionKey=[ActionKey '_1']; |
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| 483 | end |
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[374] | 484 | DataMean.(ActionKey)=Param.Action; |
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[27] | 485 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {ActionKey}]; |
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| 486 | if isfield(DataMean,'Time') |
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| 487 | DataMean.ListGlobalAttribute=[DataMean.ListGlobalAttribute {'Time','Time_end'}]; |
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[255] | 488 | end |
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| 489 | errormsg=struct2nc(fileresult{i_slice},DataMean); %save result file |
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[27] | 490 | if isempty(errormsg) |
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[255] | 491 | display([fileresult{i_slice} ' written']); |
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[27] | 492 | else |
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| 493 | msgbox_uvmat('ERROR',['error in writting result file: ' errormsg]) |
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| 494 | display(errormsg) |
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| 495 | end |
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[255] | 496 | end % end averaging loop |
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| 497 | end % end loop on slices |
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| 498 | |
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| 499 | %% reproduce ImaDoc/GeometryCalib for image series |
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| 500 | if isfield(XmlData{1},'GeometryCalib') && ~isempty(XmlData{1}.GeometryCalib) |
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[392] | 501 | [tild,RootFile]=fileparts(filebase_out); |
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| 502 | outputxml=fullfile(pathdir,[RootFile '.xml']); |
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[255] | 503 | errormsg=update_imadoc(XmlData{1}.GeometryCalib,outputxml);% introduce the calibration data in the xml file |
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| 504 | if strcmp(errormsg,'') |
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| 505 | display(['GeometryCalib transferred to ' outputxml]) |
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| 506 | else |
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| 507 | msgbox_uvmat('ERROR',errormsg); |
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| 508 | end |
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[27] | 509 | end |
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[55] | 510 | |
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[255] | 511 | %% open the result file with uvmat |
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[27] | 512 | hget_field=findobj(allchild(0),'name','get_field');%find the get_field... GUI |
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| 513 | delete(hget_field) |
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[255] | 514 | uvmat(fileresult{end}) |
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