[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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[222] | 5 | |
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[457] | 6 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[169] | 7 | % |
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[457] | 8 | % This function is used in four modes by the GUI series: |
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| 9 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 10 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 11 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 12 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 13 | % |
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| 14 | % This function is used in four modes by the GUI series: |
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| 15 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 16 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 17 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 18 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 19 | % |
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[169] | 20 | %OUTPUT |
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| 21 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 22 | % |
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| 23 | %INPUT: |
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[457] | 24 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 25 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 26 | % In the absence of input (as activated when the current Action is selected |
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| 27 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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[169] | 28 | % |
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[457] | 29 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 30 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 31 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 32 | % .OutputSubDir: name of the subdirectory for data outputs |
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[474] | 33 | % .OutputDirExt: directory extension for data outputs |
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[457] | 34 | % .Action: .ActionName: name of the current activated function |
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| 35 | % .ActionPath: path of the current activated function |
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| 36 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 37 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 38 | % .TransformPath: path of the selected transform function |
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| 39 | % .TransformHandle: corresponding function handle |
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| 40 | % .InputFields: sub structure describing the input fields withfields |
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| 41 | % .FieldName: name of the field |
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| 42 | % .VelType: velocity type |
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| 43 | % .FieldName_1: name of the second field in case of two input series |
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| 44 | % .VelType_1: velocity type of the second field in case of two input series |
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| 45 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 46 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 47 | |
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[462] | 48 | function ParamOut=merge_proj(Param) |
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[29] | 49 | |
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[457] | 50 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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[592] | 51 | if isstruct(Param) && isequal(Param.Action.RUN,0) |
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| 52 | ParamOut.AllowInputSort='off';...% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default) |
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| 53 | ParamOut.WholeIndexRange='on';...% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default) |
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| 54 | ParamOut.NbSlice='off'; ...%nbre of slices ('off' by default) |
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| 55 | ParamOut.VelType='one';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 56 | ParamOut.FieldName='one';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 57 | ParamOut.FieldTransform = 'on';...%can use a transform function |
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| 58 | ParamOut.ProjObject='on';...%can use projection object(option 'off'/'on', |
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| 59 | ParamOut.Mask='off';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 60 | ParamOut.OutputDirExt='.mproj';%set the output dir extension |
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| 61 | return |
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[29] | 62 | end |
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| 63 | |
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[457] | 64 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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[592] | 65 | %% read input parameters from an xml file if input is a file name (batch mode) |
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| 66 | checkrun=1; |
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[457] | 67 | if ischar(Param) |
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[592] | 68 | Param=xml2struct(Param);% read Param as input file (batch case) |
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| 69 | checkrun=0; |
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[374] | 70 | end |
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[592] | 71 | |
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[462] | 72 | ParamOut=Param; %default output |
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[550] | 73 | if ~isfield(Param,'InputFields') |
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| 74 | Param.InputFields.FieldName=''; |
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| 75 | end |
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[592] | 76 | OutputSubDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files |
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[457] | 77 | |
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[577] | 78 | %% root input file type |
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[457] | 79 | RootPath=Param.InputTable(:,1); |
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| 80 | RootFile=Param.InputTable(:,3); |
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| 81 | SubDir=Param.InputTable(:,2); |
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| 82 | NomType=Param.InputTable(:,4); |
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| 83 | FileExt=Param.InputTable(:,5); |
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[374] | 84 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[474] | 85 | %%%%%%%%%%%% |
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| 86 | % The cell array filecell is the list of input file names, while |
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| 87 | % filecell{iview,fileindex}: |
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[457] | 88 | % iview: line in the table corresponding to a given file series |
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| 89 | % fileindex: file index within the file series, |
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| 90 | % 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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| 91 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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[474] | 92 | %%%%%%%%%%%% |
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[457] | 93 | NbSlice=1;%default |
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[462] | 94 | if isfield(Param.IndexRange,'NbSlice')&&~isempty(Param.IndexRange.NbSlice) |
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[457] | 95 | NbSlice=Param.IndexRange.NbSlice; |
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| 96 | end |
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| 97 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 98 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 99 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 100 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 101 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 102 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 103 | |
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| 104 | %determine the file type on each line from the first input file |
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[462] | 105 | ImageTypeOptions={'image','multimage','mmreader','video'}; |
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| 106 | NcTypeOptions={'netcdf','civx','civdata'}; |
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| 107 | for iview=1:nbview |
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| 108 | if ~exist(filecell{iview,1}','file') |
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[474] | 109 | displ_uvmat('ERROR',['the first input file ' filecell{iview,1} ' does not exist'],checkrun) |
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[462] | 110 | return |
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| 111 | end |
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| 112 | [FileType{iview},FileInfo{iview},MovieObject{iview}]=get_file_type(filecell{iview,1}); |
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| 113 | CheckImage{iview}=~isempty(find(strcmp(FileType{iview},ImageTypeOptions)));% =1 for images |
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| 114 | CheckNc{iview}=~isempty(find(strcmp(FileType{iview},NcTypeOptions)));% =1 for netcdf files |
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| 115 | if ~isempty(j1_series{iview}) |
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| 116 | frame_index{iview}=j1_series{iview}; |
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| 117 | else |
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| 118 | frame_index{iview}=i1_series{iview}; |
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| 119 | end |
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[457] | 120 | end |
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| 121 | |
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[470] | 122 | |
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[457] | 123 | %% calibration data and timing: read the ImaDoc files |
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[470] | 124 | [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series); |
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| 125 | if size(time,1)>1 |
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[457] | 126 | diff_time=max(max(diff(time))); |
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[474] | 127 | if diff_time>0 |
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| 128 | displ_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)],checkrun) |
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[457] | 129 | end |
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| 130 | end |
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| 131 | |
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[409] | 132 | %% coordinate transform or other user defined transform |
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[374] | 133 | transform_fct='';%default |
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[478] | 134 | if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName) |
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[474] | 135 | addpath(Param.FieldTransform.TransformPath) |
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| 136 | transform_fct=str2func(Param.FieldTransform.TransformName); |
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| 137 | rmpath(Param.FieldTransform.TransformPath) |
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[374] | 138 | end |
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[474] | 139 | |
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[457] | 140 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 141 | % EDIT FROM HERE |
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[116] | 142 | |
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[457] | 143 | %% check the validity of input file types |
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| 144 | if CheckImage{1} |
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| 145 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 146 | elseif CheckNc{1} |
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| 147 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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[474] | 148 | else |
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| 149 | displ_uvmat('ERROR',['invalid file type input ' FileType{1}],checkrun) |
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[457] | 150 | return |
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| 151 | end |
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[462] | 152 | for iview=1:nbview |
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| 153 | if ~isequal(CheckImage{iview},CheckImage{1})||~isequal(CheckNc{iview},CheckNc{1}) |
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[474] | 154 | displ_uvmat('ERROR','input set of input series: need either netcdf either image series',checkrun) |
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[457] | 155 | return |
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[464] | 156 | end |
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[457] | 157 | end |
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[462] | 158 | NomTypeOut=NomType;% output file index will indicate the first and last ref index in the series |
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[474] | 159 | if checkrun==1 |
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| 160 | ParamOut.Specific=[];%no specific parameter |
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| 161 | return %stop here for interactive input (option Param.Specific='?') |
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| 162 | end |
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[457] | 163 | |
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| 164 | %% Set field names and velocity types |
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[462] | 165 | %use Param.InputFields for all views |
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[457] | 166 | |
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| 167 | %% MAIN LOOP ON SLICES |
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| 168 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 169 | for i_slice=1:NbSlice |
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| 170 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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| 171 | nbfiles=0; |
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| 172 | nbmissing=0; |
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[474] | 173 | |
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[457] | 174 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 175 | for index=index_slice |
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[470] | 176 | |
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[457] | 177 | if checkrun |
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[478] | 178 | update_waitbar(hseries.Waitbar,index/(nbfield)) |
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[457] | 179 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 180 | else |
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| 181 | stopstate='queue'; |
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| 182 | end |
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[462] | 183 | |
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| 184 | %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%% |
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| 185 | Data=cell(1,nbview);%initiate the set Data |
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[464] | 186 | nbtime=0; |
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[29] | 187 | for iview=1:nbview |
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[551] | 188 | %% reading input file(s) |
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[464] | 189 | [Data{iview},tild,errormsg] = read_field(filecell{iview,index},FileType{iview},Param.InputFields,frame_index{iview}(index)); |
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[462] | 190 | if ~isempty(errormsg) |
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[474] | 191 | errormsg=['merge_proj/read_field/' errormsg]; |
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| 192 | display(errormsg) |
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[29] | 193 | break |
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| 194 | end |
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[464] | 195 | timeread(iview)=0; |
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| 196 | if isfield(Data{iview},'Time') |
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[470] | 197 | timeread(iview)=Data{iview}.Time; |
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[464] | 198 | nbtime=nbtime+1; |
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| 199 | end |
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[29] | 200 | if ~isempty(NbSlice_calib) |
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[462] | 201 | Data{iview}.ZIndex=mod(i1_series{iview}(index)-1,NbSlice_calib{iview})+1;%Zindex for phys transform |
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[29] | 202 | end |
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[494] | 203 | |
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[551] | 204 | %% transform the input field (e.g; phys) if requested |
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[41] | 205 | if ~isempty(transform_fct) |
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[551] | 206 | if nargin(transform_fct)>=2 |
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| 207 | Data{iview}=transform_fct(Data{iview},XmlData{iview}); |
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| 208 | else |
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| 209 | Data{iview}=transform_fct(Data{iview}); |
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[550] | 210 | end |
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[29] | 211 | end |
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[494] | 212 | |
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| 213 | %% check whether tps is needed, then calculate tps coefficients if needed |
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| 214 | check_tps=0; |
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[577] | 215 | if isfield(Param.InputFields,'FieldName') |
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| 216 | if ischar(Param.InputFields.FieldName) |
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| 217 | Param.InputFields.FieldName={Param.InputFields.FieldName}; |
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| 218 | end |
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| 219 | else |
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| 220 | Param.InputFields.FieldName={}; |
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[494] | 221 | end |
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| 222 | for ilist=1:numel(Param.InputFields.FieldName) |
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| 223 | switch Param.InputFields.FieldName{ilist} |
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| 224 | case {'vort','div','strain'} |
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| 225 | check_tps=1; |
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| 226 | end |
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| 227 | end |
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[522] | 228 | |
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| 229 | %% calculate tps coeff if needed |
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| 230 | check_proj_tps= ~isempty(Param.ProjObject)&& strcmp(Param.ProjObject.ProjMode,'filter')&&~isfield(Data{iview},'Coord_tps'); |
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[585] | 231 | Data{iview}=tps_coeff_field(Data{iview},check_proj_tps); |
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[551] | 232 | |
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| 233 | %% projection on object (gridded plane) |
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[464] | 234 | if Param.CheckObject |
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| 235 | [Data{iview},errormsg]=proj_field(Data{iview},Param.ProjObject); |
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[409] | 236 | if ~isempty(errormsg) |
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[474] | 237 | displ_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg],checkrun) |
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[409] | 238 | return |
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| 239 | end |
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[29] | 240 | end |
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[464] | 241 | end |
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[222] | 242 | %----------END LOOP ON VIEWS---------------------- |
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[464] | 243 | |
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[222] | 244 | %% merge the nbview fields |
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[462] | 245 | MergeData=merge_field(Data); |
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[29] | 246 | if isfield(MergeData,'Txt') |
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[474] | 247 | displ_uvmat('ERROR',MergeData.Txt,checkrun) |
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[29] | 248 | return |
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[464] | 249 | end |
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[470] | 250 | |
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| 251 | % time of the merged field: |
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| 252 | if ~isempty(time)% time defined from ImaDoc |
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| 253 | timeread=time(:,index); |
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[29] | 254 | end |
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[470] | 255 | timeread=mean(timeread); |
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| 256 | |
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[464] | 257 | % generating the name of the merged field |
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| 258 | i1=i1_series{iview}(index); |
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| 259 | if ~isempty(i2_series{iview}) |
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| 260 | i2=i2_series{iview}(index); |
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| 261 | else |
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| 262 | i2=i1; |
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| 263 | end |
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| 264 | j1=1; |
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| 265 | j2=1; |
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| 266 | if ~isempty(j1_series{iview}) |
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| 267 | j1=j1_series{iview}(index); |
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| 268 | if ~isempty(j2_series{iview}) |
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| 269 | j2=j2_series{iview}(index); |
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| 270 | else |
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| 271 | j2=j1; |
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| 272 | end |
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| 273 | end |
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[474] | 274 | OutputFile=fullfile_uvmat(RootPath{1},OutputSubDir,RootFile{1},FileExtOut,NomType{1},i1,i2,j1,j2); |
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[29] | 275 | |
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[464] | 276 | % recording the merged field |
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| 277 | if CheckImage{1} %in case of input images an image is produced |
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[29] | 278 | if isa(MergeData.A,'uint8') |
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| 279 | bitdepth=8; |
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| 280 | elseif isa(MergeData.A,'uint16') |
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| 281 | bitdepth=16; |
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| 282 | end |
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[464] | 283 | imwrite(MergeData.A,OutputFile,'BitDepth',bitdepth); |
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[29] | 284 | %write xml calibration file |
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| 285 | siz=size(MergeData.A); |
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| 286 | npy=siz(1); |
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| 287 | npx=siz(2); |
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| 288 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
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| 289 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
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| 290 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
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| 291 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
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| 292 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
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| 293 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
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| 294 | else |
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| 295 | Rangx=[0.5 npx-0.5]; |
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| 296 | Rangy=[npy-0.5 0.5];%default |
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| 297 | end |
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| 298 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
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| 299 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
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| 300 | T_x=-pxcmx*Rangx(1)+0.5; |
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| 301 | T_y=-pxcmy*Rangy(2)+0.5; |
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| 302 | GeometryCal.focal=1; |
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| 303 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
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| 304 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
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| 305 | ImaDoc.GeometryCalib=GeometryCal; |
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[550] | 306 | % t=struct2xml(ImaDoc); |
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| 307 | % t=set(t,1,'name','ImaDoc'); |
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| 308 | % save(t,[filebase_merge '.xml']) |
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| 309 | % display([filebase_merge '.xml saved']) |
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[29] | 310 | else |
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[464] | 311 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
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[422] | 312 | MergeData.Conventions='uvmat'; |
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[29] | 313 | MergeData.nb_coord=2; |
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| 314 | MergeData.nb_dim=2; |
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[93] | 315 | dt=[]; |
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[462] | 316 | if isfield(Data{1},'dt')&& isnumeric(Data{1}.dt) |
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| 317 | dt=Data{1}.dt; |
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[93] | 318 | end |
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[462] | 319 | for iview =2:numel(Data) |
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| 320 | if ~(isfield(Data{iview},'dt')&& isequal(Data{iview}.dt,dt)) |
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[93] | 321 | dt=[];%dt not the same for all fields |
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| 322 | end |
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| 323 | end |
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| 324 | if isempty(dt) |
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| 325 | MergeData.ListGlobalAttribute(6)=[]; |
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| 326 | else |
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[464] | 327 | MergeData.dt=dt; |
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[93] | 328 | end |
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[470] | 329 | MergeData.Time=timeread; |
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[462] | 330 | error=struct2nc(OutputFile,MergeData);%save result file |
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[29] | 331 | if isempty(error) |
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[462] | 332 | display(['output file ' OutputFile ' written']) |
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[29] | 333 | else |
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| 334 | display(error) |
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| 335 | end |
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| 336 | end |
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| 337 | end |
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| 338 | end |
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| 339 | |
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[222] | 340 | %'merge_field': concatene fields |
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| 341 | %------------------------------------------------------------------------ |
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[29] | 342 | function MergeData=merge_field(Data) |
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[222] | 343 | %% default output |
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[29] | 344 | if isempty(Data)||~iscell(Data) |
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| 345 | MergeData=[]; |
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| 346 | return |
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| 347 | end |
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| 348 | MergeData=Data{1};%default |
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| 349 | error=0; |
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| 350 | nbview=length(Data); |
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| 351 | if nbview==1 |
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| 352 | return |
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| 353 | end |
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[222] | 354 | |
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[522] | 355 | %% group the variables (fields of 'Data') in cells of variables with the same dimensions |
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| 356 | [CellVarIndex,NbDim,VarTypeCell]=find_field_cells(Data{1}); |
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[89] | 357 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
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| 358 | % CellVarIndex=cells of variable index arrays |
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| 359 | for icell=1:length(CellVarIndex) |
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| 360 | if NbDim(icell)==1 |
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| 361 | continue |
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| 362 | end |
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| 363 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
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| 364 | VarType=VarTypeCell{icell}; |
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| 365 | ivar_X=VarType.coord_x; |
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| 366 | ivar_Y=VarType.coord_y; |
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| 367 | ivar_FF=VarType.errorflag; |
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| 368 | if isempty(ivar_X) |
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| 369 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
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| 370 | else |
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| 371 | if length(ivar_Y)~=1 |
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[474] | 372 | displ_uvmat('ERROR','y coordinate missing in proj_field.m',checkrun) |
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[89] | 373 | return |
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| 374 | end |
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| 375 | test_grid=0; |
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| 376 | end |
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| 377 | %case of input fields with unstructured coordinates |
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| 378 | if ~test_grid |
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| 379 | for ivar=VarIndex |
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| 380 | VarName=MergeData.ListVarName{ivar}; |
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| 381 | for iview=1:nbview |
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[522] | 382 | MergeData.(VarName)=[MergeData.(VarName); Data{iview}.(VarName)]; |
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[89] | 383 | end |
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| 384 | end |
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| 385 | %case of fields defined on a structured grid |
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| 386 | else |
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| 387 | testFF=0; |
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| 388 | for iview=2:nbview |
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| 389 | for ivar=VarIndex |
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| 390 | VarName=MergeData.ListVarName{ivar}; |
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| 391 | if isfield(MergeData,'VarAttribute') |
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| 392 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
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| 393 | testFF=1; |
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| 394 | end |
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| 395 | end |
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[522] | 396 | MergeData.(VarName)=MergeData.(VarName) + Data{iview}.(VarName); |
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[89] | 397 | end |
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| 398 | end |
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| 399 | if testFF |
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| 400 | nbaver=nbview-MergeData.FF; |
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| 401 | indgood=find(nbaver>0); |
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| 402 | for ivar=VarIndex |
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| 403 | VarName=MergeData.ListVarName{ivar}; |
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[522] | 404 | MergeData.(VarName)(indgood)=double(MergeData.(VarName)(indgood))./nbaver(indgood); |
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[89] | 405 | end |
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| 406 | else |
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| 407 | for ivar=VarIndex |
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| 408 | VarName=MergeData.ListVarName{ivar}; |
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[522] | 409 | MergeData.(VarName)=double(MergeData.(VarName))./nbview; |
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[89] | 410 | end |
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| 411 | end |
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| 412 | end |
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| 413 | end |
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[222] | 414 | |
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[89] | 415 | |
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