[597] | 1 | %'merge_proj': concatene several fields from series, can project them on a regular grid in phys coordinates |
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| 2 | %------------------------------------------------------------------------ |
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| 3 | % function ParamOut=merge_proj(Param) |
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| 4 | %------------------------------------------------------------------------ |
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| 5 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 6 | % |
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| 7 | %OUTPUT |
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| 8 | % ParamOut: sets options in the GUI series.fig needed for the function |
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| 9 | % |
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| 10 | %INPUT: |
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| 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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| 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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| 15 | % |
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| 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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| 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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| 21 | % .OutputDirExt: directory extension for data outputs |
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| 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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| 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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| 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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| 32 | % .FieldName: name(s) of the field |
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| 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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| 36 | % .Coord_y: name of y coordinate variable |
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| 37 | % .Coord_x: name of x coordinate variable |
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| 38 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 39 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%civ_series |
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| 40 | |
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| 41 | function ParamOut=civ_series(Param) |
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| 42 | |
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| 43 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 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='off';...% 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='off';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 49 | ParamOut.FieldName='off';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 50 | ParamOut.FieldTransform = 'off';...%can use a transform function |
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| 51 | ParamOut.ProjObject='off';...%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='.civ';%set the output dir extension |
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| 54 | return |
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| 55 | end |
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| 56 | |
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| 57 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 58 | |
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| 59 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 60 | checkrun=1; |
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| 61 | if ischar(Param) |
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| 62 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 63 | checkrun=0; |
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| 64 | end |
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| 65 | |
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| 66 | ParamOut=Param; %default output |
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| 67 | if ~isfield(Param,'InputFields') |
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| 68 | Param.InputFields.FieldName=''; |
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| 69 | end |
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| 70 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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| 71 | |
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| 72 | %% root input file type |
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| 73 | RootPath=Param.InputTable(:,1); |
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| 74 | RootFile=Param.InputTable(:,3); |
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| 75 | SubDir=Param.InputTable(:,2); |
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| 76 | NomType=Param.InputTable(:,4); |
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| 77 | FileExt=Param.InputTable(:,5); |
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| 78 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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| 79 | %%%%%%%%%%%% |
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| 80 | % The cell array filecell is the list of input file names, while |
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| 81 | % filecell{iview,fileindex}: |
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| 82 | % iview: line in the table corresponding to a given file series |
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| 83 | % fileindex: file index within the file series, |
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| 84 | % 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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| 85 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 86 | %%%%%%%%%%%% |
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| 87 | NbSlice=1;%default |
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| 88 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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| 89 | NbSlice=Param.IndexRange.NbSlice; |
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| 90 | end |
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| 91 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 92 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 93 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 94 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 95 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 96 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 97 | |
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| 98 | %determine the file type on each line from the first input file |
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| 99 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 100 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 101 | for iview=1:nbview |
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| 102 | if ~exist(filecell{iview,1}','file') |
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| 103 | displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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| 104 | return |
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| 105 | end |
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| 106 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 107 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 108 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 109 | if ~isempty(j1_series{iview}) |
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| 110 | frame_index{iview}=j1_series{iview}; |
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| 111 | else |
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| 112 | frame_index{iview}=i1_series{iview}; |
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| 113 | end |
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| 114 | end |
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| 115 | |
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| 116 | |
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| 117 | %% calibration data and timing: read the ImaDoc files |
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| 118 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 119 | if size(time,1)>1 |
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| 120 | diff_time=max(max(diff(time))); |
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| 121 | if diff_time>0 |
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| 122 | displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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| 123 | end |
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| 124 | end |
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| 125 | |
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| 126 | %% coordinate transform or other user defined transform |
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| 127 | |
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| 128 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 129 | % EDIT FROM HERE |
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| 130 | |
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| 131 | %% check the validity of input file types |
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| 132 | if CheckImage{1} |
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| 133 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 134 | elseif CheckNc{1} |
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| 135 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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| 136 | else |
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| 137 | displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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| 138 | return |
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| 139 | end |
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| 140 | for iview=1:nbview |
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| 141 | if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1}) |
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| 142 | displ_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) |
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| 143 | return |
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| 144 | end |
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| 145 | end |
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| 146 | NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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| 147 | % if checkrun==1 |
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| 148 | % ParamOut.Specific=[];%no specific parameter |
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| 149 | % return %stop here for interactive input (option Param.Specific='?') |
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| 150 | % end |
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| 151 | |
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| 152 | %% Set field names and velocity types |
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| 153 | %use Param.InputFields for all views |
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| 154 | |
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| 155 | %% MAIN LOOP ON SLICES |
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| 156 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 157 | |
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| 158 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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| 159 | nbfiles=0; |
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| 160 | nbmissing=0; |
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| 161 | |
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| 162 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 163 | %TODO: call civ_matlab |
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| 164 | for index=index_slice |
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| 165 | if checkrun |
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| 166 | stopstate=get(Param.RUNHandle,'BusyAction'); |
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| 167 | update_waitbar(Param.WaitbarHandle,index/nbfield) |
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| 168 | else |
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| 169 | stopstate='queue'; |
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| 170 | end |
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| 171 | if ~isequal(stopstate,'queue')% enable STOP command |
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| 172 | return |
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| 173 | end |
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| 174 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 175 | Data=cell(1,nbview);%initiate the set Data |
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| 176 | nbtime=0; |
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| 177 | for iview=1:nbview |
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| 178 | %% reading input file(s) |
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| 179 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); |
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| 180 | if ~isempty(errormsg) |
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| 181 | errormsg=['merge_proj/read_field/' errormsg]; |
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| 182 | display(errormsg) |
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| 183 | break |
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| 184 | end |
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| 185 | timeread(iview)=0; |
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| 186 | if isfield(Data{iview},'Time') |
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| 187 | timeread(iview)=Data{iview}.Time; |
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| 188 | nbtime=nbtime+1; |
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| 189 | end |
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| 190 | if ~isempty(NbSlice_calib) |
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| 191 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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| 192 | end |
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| 193 | |
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| 194 | %% transform the input field (e.g; phys) if requested |
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| 195 | if ~isempty(transform_fct) |
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| 196 | if nargin(transform_fct)>=2 |
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| 197 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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| 198 | else |
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| 199 | Data{iview}=transform_fct(Data{iview}); |
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| 200 | end |
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| 201 | end |
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| 202 | |
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| 203 | %% check whether tps is needed, then calculate tps coefficients if needed |
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| 204 | check_tps=0; |
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| 205 | if isfield(Param.InputFields,'FieldName') |
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| 206 | if ischar(Param.InputFields.FieldName) |
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| 207 | Param.InputFields.FieldName={Param.InputFields.FieldName}; |
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| 208 | end |
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| 209 | else |
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| 210 | Param.InputFields.FieldName={}; |
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| 211 | end |
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| 212 | for ilist=1:numel(Param.InputFields.FieldName) |
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| 213 | switch Param.InputFields.FieldName{ilist} |
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| 214 | case {'vort','div','strain'} |
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| 215 | check_tps=1; |
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| 216 | end |
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| 217 | end |
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| 218 | |
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| 219 | %% calculate tps coeff if needed |
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| 220 | check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps'); |
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| 221 | Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); |
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| 222 | |
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| 223 | %% projection on object (gridded plane) |
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| 224 | if Param.CheckObject |
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| 225 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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| 226 | if ~isempty(errormsg) |
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| 227 | displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun) |
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| 228 | return |
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| 229 | end |
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| 230 | end |
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| 231 | end |
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| 232 | %----------END LOOP ON VIEWS---------------------- |
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| 233 | |
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| 234 | %% merge the nbview fields |
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| 235 | MergeData=merge_field(Data); |
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| 236 | if isfield(MergeData,'Txt') |
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| 237 | displ_uvmat('ERROR',MergeData.Txt,checkrun) |
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| 238 | return |
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| 239 | end |
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| 240 | |
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| 241 | % time of the merged field: |
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| 242 | if ~isempty(time)% time defined from ImaDoc |
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| 243 | timeread=time(:,index); |
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| 244 | end |
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| 245 | timeread=mean(timeread); |
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| 246 | |
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| 247 | % generating the name of the merged field |
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| 248 | i1=i1_series{iview}(index); |
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| 249 | if ~isempty(i2_series{iview}) |
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| 250 | i2=i2_series{iview}(index); |
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| 251 | else |
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| 252 | i2=i1; |
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| 253 | end |
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| 254 | j1=1; |
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| 255 | j2=1; |
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| 256 | if ~isempty(j1_series{iview}) |
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| 257 | j1=j1_series{iview}(index); |
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| 258 | if ~isempty(j2_series{iview}) |
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| 259 | j2=j2_series{iview}(index); |
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| 260 | else |
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| 261 | j2=j1; |
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| 262 | end |
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| 263 | end |
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| 264 | OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2); |
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| 265 | |
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| 266 | % recording the merged field |
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| 267 | if CheckImage{1} %in case of input images an image is produced |
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| 268 | if isa(MergeData.A,'uint8') |
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| 269 | bitdepth=8; |
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| 270 | elseif isa(MergeData.A,'uint16') |
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| 271 | bitdepth=16; |
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| 272 | end |
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| 273 | imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth); |
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| 274 | %write xml calibration file |
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| 275 | siz=size(MergeData.A); |
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| 276 | npy=siz(1); |
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| 277 | npx=siz(2); |
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| 278 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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| 279 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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| 280 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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| 281 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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| 282 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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| 283 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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| 284 | else |
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| 285 | Rangx=[0.5 npx-0.5]; |
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| 286 | Rangy=[npy-0.5 0.5];%default |
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| 287 | end |
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| 288 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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| 289 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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| 290 | T_x=-pxcmx*Rangx(1)+0.5; |
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| 291 | T_y=-pxcmy*Rangy(2)+0.5; |
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| 292 | GeometryCal.focal=1; |
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| 293 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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| 294 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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| 295 | ImaDoc.GeometryCalib=GeometryCal; |
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| 296 | % t=struct2xml(ImaDoc); |
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| 297 | % t=set(t,1,'name','ImaDoc'); |
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| 298 | % save(t,[filebase_merge '.xml']) |
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| 299 | % display([filebase_merge '.xml saved']) |
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| 300 | else |
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| 301 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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| 302 | MergeData.Conventions='uvmat'; |
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| 303 | MergeData.nb_coord=2; |
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| 304 | MergeData.nb_dim=2; |
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| 305 | dt=[]; |
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| 306 | if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt) |
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| 307 | dt=Data{1}.dt; |
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| 308 | end |
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| 309 | for iview =2:numel(Data) |
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| 310 | if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt)) |
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| 311 | dt=[];%dt not the same for all fields |
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| 312 | end |
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| 313 | end |
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| 314 | if isempty(dt) |
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| 315 | MergeData.ListGlobalAttribute(6)=[]; |
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| 316 | else |
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| 317 | MergeData.dt=dt; |
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| 318 | end |
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| 319 | MergeData.Time=timeread; |
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| 320 | error=struct2nc(OutputFile,MergeData);%save result file |
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| 321 | if isempty(error) |
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| 322 | display(['output file ' OutputFile ' written']) |
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| 323 | else |
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| 324 | display(error) |
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| 325 | end |
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| 326 | end |
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| 327 | end |
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| 328 | |
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| 329 | %'merge_field': concatene fields |
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| 330 | %------------------------------------------------------------------------ |
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| 331 | function MergeData=merge_field(Data) |
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| 332 | %% default output |
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| 333 | if isempty(Data)||~iscell(Data) |
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| 334 | MergeData=[]; |
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| 335 | return |
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| 336 | end |
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| 337 | MergeData=Data{1};%default |
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| 338 | error=0; |
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| 339 | nbview=length(Data); |
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| 340 | if nbview==1 |
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| 341 | return |
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| 342 | end |
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| 343 | |
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| 344 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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| 345 | [CellVarIndex,NbDim,VarTypeCell]=find_field_cells(Data{1}); |
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| 346 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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| 347 | % CellVarIndex=cells of variable index arrays |
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| 348 | for icell=1:length(CellVarIndex) |
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| 349 | if NbDim(icell)==1 |
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| 350 | continue |
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| 351 | end |
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| 352 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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| 353 | VarType=VarTypeCell{icell}; |
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| 354 | ivar_X=VarType.coord_x; |
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| 355 | ivar_Y=VarType.coord_y; |
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| 356 | ivar_FF=VarType.errorflag; |
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| 357 | if isempty(ivar_X) |
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| 358 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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| 359 | else |
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| 360 | if length(ivar_Y)~=1 |
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| 361 | displ_uvmat('ERROR','y coordinate missing in proj_field.m',checkrun) |
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| 362 | return |
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| 363 | end |
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| 364 | test_grid=0; |
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| 365 | end |
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| 366 | %case of input fields with unstructured coordinates |
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| 367 | if ~test_grid |
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| 368 | for ivar=VarIndex |
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| 369 | VarName=MergeData.ListVarName{ivar}; |
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| 370 | for iview=1:nbview |
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| 371 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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| 372 | end |
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| 373 | end |
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| 374 | %case of fields defined on a structured grid |
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| 375 | else |
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| 376 | testFF=0; |
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| 377 | for iview=2:nbview |
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| 378 | for ivar=VarIndex |
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| 379 | VarName=MergeData.ListVarName{ivar}; |
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| 380 | if isfield(MergeData,'VarAttribute') |
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| 381 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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| 382 | testFF=1; |
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| 383 | end |
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| 384 | end |
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| 385 | MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName); |
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| 386 | end |
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| 387 | end |
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| 388 | if testFF |
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| 389 | nbaver=nbview-MergeData.FF; |
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| 390 | indgood=find(nbaver>0); |
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| 391 | for ivar=VarIndex |
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| 392 | VarName=MergeData.ListVarName{ivar}; |
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| 393 | MergeData.(VarName)(indgood)=double(MergeData.(VarName)(indgood))./nbaver(indgood); |
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| 394 | end |
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| 395 | else |
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| 396 | for ivar=VarIndex |
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| 397 | VarName=MergeData.ListVarName{ivar}; |
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| 398 | MergeData.(VarName)=double(MergeData.(VarName))./nbview; |
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| 399 | end |
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| 400 | end |
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| 401 | end |
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| 402 | end |
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| 403 | |
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| 404 | |
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