[573] | 1 | %'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates |
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[457] | 2 | %------------------------------------------------------------------------ |
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[464] | 3 | % function ParamOut=merge_proj(Param) |
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[457] | 4 | %------------------------------------------------------------------------ |
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| 5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[169] | 6 | % |
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| 7 | %OUTPUT |
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[596] | 8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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[169] | 9 | % |
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| 10 | %INPUT: |
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[457] | 11 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 12 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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[596] | 13 | % when Param.Action.RUN=0 (as activated when the current Action is selected |
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| 14 | % in series), the function ouput paramOut set the activation of the needed GUI elements |
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[169] | 15 | % |
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[596] | 16 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to |
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| 17 | % see the current structure Param) |
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[457] | 18 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 19 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 20 | % .OutputSubDir: name of the subdirectory for data outputs |
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[474] | 21 | % .OutputDirExt: directory extension for data outputs |
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[457] | 22 | % .Action: .ActionName: name of the current activated function |
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| 23 | % .ActionPath: path of the current activated function |
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[596] | 24 | % .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled Matlab fct |
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| 25 | % .RUN =0 for GUI input, =1 for function activation |
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| 26 | % .RunMode='local','background', 'cluster': type of function use |
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| 27 | % |
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[457] | 28 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 29 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 30 | % .TransformPath: path of the selected transform function |
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| 31 | % .InputFields: sub structure describing the input fields withfields |
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[596] | 32 | % .FieldName: name(s) of the field |
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[457] | 33 | % .VelType: velocity type |
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| 34 | % .FieldName_1: name of the second field in case of two input series |
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| 35 | % .VelType_1: velocity type of the second field in case of two input series |
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[596] | 36 | % .Coord_y: name of y coordinate variable |
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| 37 | % .Coord_x: name of x coordinate variable |
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[457] | 38 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 39 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 40 | |
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[462] | 41 | function ParamOut=merge_proj(Param) |
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[29] | 42 | |
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[457] | 43 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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[592] | 44 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 45 | ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 46 | ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 47 | ParamOut.NbSlice='off'; ...%nbre of slices ('off' by default) |
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| 48 | ParamOut.VelType='one';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 49 | ParamOut.FieldName='one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 50 | ParamOut.FieldTransform = 'on';...%can use a transform function |
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| 51 | ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on', |
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| 52 | ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 53 | ParamOut.OutputDirExt='.mproj';%set the output dir extension |
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| 54 | return |
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[29] | 55 | end |
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| 56 | |
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[457] | 57 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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[595] | 58 | |
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| 59 | |
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[592] | 60 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 61 | checkrun=1; |
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[457] | 62 | if ischar(Param) |
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[592] | 63 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 64 | checkrun=0; |
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[374] | 65 | end |
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[592] | 66 | |
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[462] | 67 | ParamOut=Param; %default output |
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[550] | 68 | if ~isfield(Param,'InputFields') |
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| 69 | Param.InputFields.FieldName=''; |
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| 70 | end |
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[592] | 71 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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[457] | 72 | |
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[577] | 73 | %% root input file type |
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[457] | 74 | RootPath=Param.InputTable(:,1); |
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| 75 | RootFile=Param.InputTable(:,3); |
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| 76 | SubDir=Param.InputTable(:,2); |
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| 77 | NomType=Param.InputTable(:,4); |
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| 78 | FileExt=Param.InputTable(:,5); |
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[374] | 79 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[474] | 80 | %%%%%%%%%%%% |
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| 81 | % The cell array filecell is the list of input file names, while |
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| 82 | % filecell{iview,fileindex}: |
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[457] | 83 | % iview: line in the table corresponding to a given file series |
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| 84 | % fileindex: file index within the file series, |
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| 85 | % 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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| 86 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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[474] | 87 | %%%%%%%%%%%% |
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[457] | 88 | NbSlice=1;%default |
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[462] | 89 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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[457] | 90 | NbSlice=Param.IndexRange.NbSlice; |
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| 91 | end |
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| 92 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 93 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 94 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 95 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 96 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 97 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 98 | |
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| 99 | %determine the file type on each line from the first input file |
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[462] | 100 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 101 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 102 | for iview=1:nbview |
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| 103 | if ~exist(filecell{iview,1}','file') |
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[474] | 104 | displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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[462] | 105 | return |
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| 106 | end |
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| 107 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 108 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 109 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 110 | if ~isempty(j1_series{iview}) |
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| 111 | frame_index{iview}=j1_series{iview}; |
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| 112 | else |
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| 113 | frame_index{iview}=i1_series{iview}; |
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| 114 | end |
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[457] | 115 | end |
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| 116 | |
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[470] | 117 | |
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[457] | 118 | %% calibration data and timing: read the ImaDoc files |
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[470] | 119 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 120 | if size(time,1)>1 |
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[457] | 121 | diff_time=max(max(diff(time))); |
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[474] | 122 | if diff_time>0 |
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| 123 | displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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[457] | 124 | end |
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| 125 | end |
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| 126 | |
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[409] | 127 | %% coordinate transform or other user defined transform |
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[374] | 128 | transform_fct='';%default |
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[478] | 129 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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[474] | 130 | addpath(Param.FieldTransform.TransformPath) |
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| 131 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 132 | rmpath(Param.FieldTransform.TransformPath) |
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[374] | 133 | end |
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[474] | 134 | |
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[457] | 135 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 136 | % EDIT FROM HERE |
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[116] | 137 | |
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[457] | 138 | %% check the validity of input file types |
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| 139 | if CheckImage{1} |
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| 140 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 141 | elseif CheckNc{1} |
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| 142 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[474] | 143 | else |
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| 144 | displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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[457] | 145 | return |
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| 146 | end |
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[462] | 147 | for iview=1:nbview |
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| 148 | if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1}) |
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[474] | 149 | displ_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) |
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[457] | 150 | return |
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[464] | 151 | end |
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[457] | 152 | end |
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[462] | 153 | NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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[595] | 154 | % if checkrun==1 |
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| 155 | % ParamOut.Specific=[];%no specific parameter |
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| 156 | % return %stop here for interactive input (option Param.Specific='?') |
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| 157 | % end |
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[457] | 158 | |
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| 159 | %% Set field names and velocity types |
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[462] | 160 | %use Param.InputFields for all views |
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[457] | 161 | |
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| 162 | %% MAIN LOOP ON SLICES |
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| 163 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 164 | for i_slice=1:NbSlice |
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| 165 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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| 166 | nbfiles=0; |
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| 167 | nbmissing=0; |
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[474] | 168 | |
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[457] | 169 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 170 | for index=index_slice |
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| 171 | if checkrun |
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[595] | 172 | stopstate=get(Param.RUNHandle,'BusyAction'); |
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| 173 | update_waitbar(Param.WaitbarHandle,index/nbfield) |
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[457] | 174 | else |
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| 175 | stopstate='queue'; |
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| 176 | end |
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[595] | 177 | if ~isequal(stopstate,'queue')% enable STOP command |
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| 178 | return |
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| 179 | end |
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[462] | 180 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 181 | Data=cell(1,nbview);%initiate the set Data |
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[464] | 182 | nbtime=0; |
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[29] | 183 | for iview=1:nbview |
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[551] | 184 | %% reading input file(s) |
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[464] | 185 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); |
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[462] | 186 | if ~isempty(errormsg) |
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[474] | 187 | errormsg=['merge_proj/read_field/' errormsg]; |
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| 188 | display(errormsg) |
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[29] | 189 | break |
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| 190 | end |
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[464] | 191 | timeread(iview)=0; |
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| 192 | if isfield(Data{iview},'Time') |
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[470] | 193 | timeread(iview)=Data{iview}.Time; |
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[464] | 194 | nbtime=nbtime+1; |
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| 195 | end |
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[29] | 196 | if ~isempty(NbSlice_calib) |
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[462] | 197 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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[29] | 198 | end |
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[494] | 199 | |
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[551] | 200 | %% transform the input field (e.g; phys) if requested |
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[41] | 201 | if ~isempty(transform_fct) |
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[551] | 202 | if nargin(transform_fct)>=2 |
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| 203 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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| 204 | else |
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| 205 | Data{iview}=transform_fct(Data{iview}); |
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[550] | 206 | end |
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[29] | 207 | end |
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[494] | 208 | |
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| 209 | %% check whether tps is needed, then calculate tps coefficients if needed |
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| 210 | check_tps=0; |
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[577] | 211 | if isfield(Param.InputFields,'FieldName') |
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| 212 | if ischar(Param.InputFields.FieldName) |
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| 213 | Param.InputFields.FieldName={Param.InputFields.FieldName}; |
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| 214 | end |
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| 215 | else |
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| 216 | Param.InputFields.FieldName={}; |
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[494] | 217 | end |
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| 218 | for ilist=1:numel(Param.InputFields.FieldName) |
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| 219 | switch Param.InputFields.FieldName{ilist} |
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| 220 | case {'vort','div','strain'} |
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| 221 | check_tps=1; |
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| 222 | end |
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| 223 | end |
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[522] | 224 | |
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| 225 | %% calculate tps coeff if needed |
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| 226 | check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps'); |
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[585] | 227 | Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); |
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[551] | 228 | |
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| 229 | %% projection on object (gridded plane) |
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[464] | 230 | if Param.CheckObject |
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| 231 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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[409] | 232 | if ~isempty(errormsg) |
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[474] | 233 | displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun) |
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[409] | 234 | return |
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| 235 | end |
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[29] | 236 | end |
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[464] | 237 | end |
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[222] | 238 | %----------END LOOP ON VIEWS---------------------- |
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[464] | 239 | |
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[222] | 240 | %% merge the nbview fields |
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[462] | 241 | MergeData=merge_field(Data); |
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[29] | 242 | if isfield(MergeData,'Txt') |
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[474] | 243 | displ_uvmat('ERROR',MergeData.Txt,checkrun) |
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[29] | 244 | return |
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[464] | 245 | end |
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[470] | 246 | |
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| 247 | % time of the merged field: |
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| 248 | if ~isempty(time)% time defined from ImaDoc |
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| 249 | timeread=time(:,index); |
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[29] | 250 | end |
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[470] | 251 | timeread=mean(timeread); |
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| 252 | |
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[464] | 253 | % generating the name of the merged field |
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| 254 | i1=i1_series{iview}(index); |
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| 255 | if ~isempty(i2_series{iview}) |
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| 256 | i2=i2_series{iview}(index); |
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| 257 | else |
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| 258 | i2=i1; |
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| 259 | end |
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| 260 | j1=1; |
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| 261 | j2=1; |
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| 262 | if ~isempty(j1_series{iview}) |
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| 263 | j1=j1_series{iview}(index); |
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| 264 | if ~isempty(j2_series{iview}) |
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| 265 | j2=j2_series{iview}(index); |
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| 266 | else |
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| 267 | j2=j1; |
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| 268 | end |
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| 269 | end |
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[474] | 270 | OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2); |
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[29] | 271 | |
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[464] | 272 | % recording the merged field |
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| 273 | if CheckImage{1} %in case of input images an image is produced |
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[29] | 274 | if isa(MergeData.A,'uint8') |
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| 275 | bitdepth=8; |
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| 276 | elseif isa(MergeData.A,'uint16') |
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| 277 | bitdepth=16; |
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| 278 | end |
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[464] | 279 | imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth); |
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[29] | 280 | %write xml calibration file |
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| 281 | siz=size(MergeData.A); |
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| 282 | npy=siz(1); |
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| 283 | npx=siz(2); |
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| 284 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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| 285 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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| 286 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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| 287 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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| 288 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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| 289 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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| 290 | else |
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| 291 | Rangx=[0.5 npx-0.5]; |
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| 292 | Rangy=[npy-0.5 0.5];%default |
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| 293 | end |
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| 294 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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| 295 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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| 296 | T_x=-pxcmx*Rangx(1)+0.5; |
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| 297 | T_y=-pxcmy*Rangy(2)+0.5; |
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| 298 | GeometryCal.focal=1; |
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| 299 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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| 300 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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| 301 | ImaDoc.GeometryCalib=GeometryCal; |
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[550] | 302 | % t=struct2xml(ImaDoc); |
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| 303 | % t=set(t,1,'name','ImaDoc'); |
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| 304 | % save(t,[filebase_merge '.xml']) |
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| 305 | % display([filebase_merge '.xml saved']) |
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[29] | 306 | else |
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[464] | 307 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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[422] | 308 | MergeData.Conventions='uvmat'; |
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[29] | 309 | MergeData.nb_coord=2; |
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| 310 | MergeData.nb_dim=2; |
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[93] | 311 | dt=[]; |
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[462] | 312 | if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt) |
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| 313 | dt=Data{1}.dt; |
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[93] | 314 | end |
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[462] | 315 | for iview =2:numel(Data) |
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| 316 | if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt)) |
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[93] | 317 | dt=[];%dt not the same for all fields |
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| 318 | end |
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| 319 | end |
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| 320 | if isempty(dt) |
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| 321 | MergeData.ListGlobalAttribute(6)=[]; |
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| 322 | else |
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[464] | 323 | MergeData.dt=dt; |
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[93] | 324 | end |
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[470] | 325 | MergeData.Time=timeread; |
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[462] | 326 | error=struct2nc(OutputFile,MergeData);%save result file |
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[29] | 327 | if isempty(error) |
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[462] | 328 | display(['output file ' OutputFile ' written']) |
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[29] | 329 | else |
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| 330 | display(error) |
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| 331 | end |
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| 332 | end |
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| 333 | end |
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| 334 | end |
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| 335 | |
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[222] | 336 | %'merge_field': concatene fields |
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| 337 | %------------------------------------------------------------------------ |
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[29] | 338 | function MergeData=merge_field(Data) |
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[222] | 339 | %% default output |
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[29] | 340 | if isempty(Data)||~iscell(Data) |
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| 341 | MergeData=[]; |
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| 342 | return |
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| 343 | end |
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| 344 | MergeData=Data{1};%default |
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| 345 | error=0; |
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| 346 | nbview=length(Data); |
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| 347 | if nbview==1 |
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| 348 | return |
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| 349 | end |
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[222] | 350 | |
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[522] | 351 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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| 352 | [CellVarIndex,NbDim,VarTypeCell]=find_field_cells(Data{1}); |
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[89] | 353 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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| 354 | % CellVarIndex=cells of variable index arrays |
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| 355 | for icell=1:length(CellVarIndex) |
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| 356 | if NbDim(icell)==1 |
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| 357 | continue |
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| 358 | end |
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| 359 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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| 360 | VarType=VarTypeCell{icell}; |
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| 361 | ivar_X=VarType.coord_x; |
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| 362 | ivar_Y=VarType.coord_y; |
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| 363 | ivar_FF=VarType.errorflag; |
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| 364 | if isempty(ivar_X) |
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| 365 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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| 366 | else |
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| 367 | if length(ivar_Y)~=1 |
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[474] | 368 | displ_uvmat('ERROR','y coordinate missing in proj_field.m',checkrun) |
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[89] | 369 | return |
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| 370 | end |
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| 371 | test_grid=0; |
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| 372 | end |
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| 373 | %case of input fields with unstructured coordinates |
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| 374 | if ~test_grid |
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| 375 | for ivar=VarIndex |
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| 376 | VarName=MergeData.ListVarName{ivar}; |
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| 377 | for iview=1:nbview |
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[522] | 378 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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[89] | 379 | end |
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| 380 | end |
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| 381 | %case of fields defined on a structured grid |
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| 382 | else |
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| 383 | testFF=0; |
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| 384 | for iview=2:nbview |
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| 385 | for ivar=VarIndex |
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| 386 | VarName=MergeData.ListVarName{ivar}; |
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| 387 | if isfield(MergeData,'VarAttribute') |
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| 388 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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| 389 | testFF=1; |
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| 390 | end |
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| 391 | end |
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[522] | 392 | MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName); |
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[89] | 393 | end |
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| 394 | end |
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| 395 | if testFF |
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| 396 | nbaver=nbview-MergeData.FF; |
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| 397 | indgood=find(nbaver>0); |
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| 398 | for ivar=VarIndex |
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| 399 | VarName=MergeData.ListVarName{ivar}; |
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[522] | 400 | MergeData.(VarName)(indgood)=double(MergeData.(VarName)(indgood))./nbaver(indgood); |
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[89] | 401 | end |
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| 402 | else |
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| 403 | for ivar=VarIndex |
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| 404 | VarName=MergeData.ListVarName{ivar}; |
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[522] | 405 | MergeData.(VarName)=double(MergeData.(VarName))./nbview; |
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[89] | 406 | end |
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| 407 | end |
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| 408 | end |
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| 409 | end |
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[222] | 410 | |
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[89] | 411 | |
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