[457] | 1 | %'merge_proj': project and concatene fieldsmerge_proj |
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| 2 | % can be used as a template for applying an operation (here projection and concateantion) on each field of an input series |
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| 3 | %------------------------------------------------------------------------ |
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| 4 | % function GUI_config=merge_proj(Param) |
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| 5 | %------------------------------------------------------------------------ |
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[222] | 6 | |
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[457] | 7 | %%%%%%%%%%% GENERAL TO ALL SERIES ACTION FCTS %%%%%%%%%%%%%%%%%%%%%%%%%%% |
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[169] | 8 | % |
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[457] | 9 | % This function is used in four modes by the GUI series: |
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| 10 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 11 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 12 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 13 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 14 | % |
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| 15 | % This function is used in four modes by the GUI series: |
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| 16 | % 1) config GUI: with no input argument, the function determine the suitable GUI configuration |
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| 17 | % 2) interactive input: the function is used to interactively introduce input parameters, and then stops |
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| 18 | % 3) RUN: the function itself runs, when an appropriate input structure Param has been introduced. |
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| 19 | % 4) BATCH: the function itself proceeds in BATCH mode, using an xml file 'Param' as input. |
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| 20 | % |
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[169] | 21 | %OUTPUT |
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| 22 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 23 | % |
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| 24 | %INPUT: |
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[457] | 25 | % In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series. |
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| 26 | % In batch mode, Param is the name of the corresponding xml file containing the same information |
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| 27 | % In the absence of input (as activated when the current Action is selected |
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| 28 | % in series), the function ouput GUI_input set the activation of the needed GUI elements |
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[169] | 29 | % |
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[457] | 30 | % Param contains the elements:(use the menu bar command 'export/GUI config' in series to see the current structure Param) |
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| 31 | % .InputTable: cell of input file names, (several lines for multiple input) |
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| 32 | % each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension} |
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| 33 | % .OutputSubDir: name of the subdirectory for data outputs |
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| 34 | % .OutputDir: directory for data outputs, including path |
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| 35 | % .Action: .ActionName: name of the current activated function |
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| 36 | % .ActionPath: path of the current activated function |
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| 37 | % .IndexRange: set the file or frame indices on which the action must be performed |
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| 38 | % .FieldTransform: .TransformName: name of the selected transform function |
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| 39 | % .TransformPath: path of the selected transform function |
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| 40 | % .TransformHandle: corresponding function handle |
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| 41 | % .InputFields: sub structure describing the input fields withfields |
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| 42 | % .FieldName: name of the field |
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| 43 | % .VelType: velocity type |
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| 44 | % .FieldName_1: name of the second field in case of two input series |
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| 45 | % .VelType_1: velocity type of the second field in case of two input series |
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| 46 | % .ProjObject: %sub structure describing a projection object (read from ancillary GUI set_object) |
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| 47 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
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| 48 | |
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[374] | 49 | function GUI_input=merge_proj(Param) |
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[29] | 50 | |
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[457] | 51 | %% set the input elements needed on the GUI series when the action is selected in the menu ActionName |
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| 52 | if ~exist('Param','var') % case with no input parameter |
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| 53 | GUI_input={'NbViewMax';2;...% max nbre of input file series (default='' , no limitation) |
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| 54 | 'AllowInputSort';'off';...% allow alphabetic sorting of the list of input files (options 'off'/'on', 'off' by default) |
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[29] | 55 | 'NbSlice';'on'; ...%nbre of slices ('off' by default) |
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[457] | 56 | 'VelType';'two';...% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default) |
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| 57 | 'FieldName';'two';...% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default) |
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| 58 | 'FieldTransform'; 'on';...%can use a transform function |
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| 59 | 'ProjObject';'on';...%can use projection object(option 'off'/'on', |
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| 60 | 'Mask';'on';...%can use mask option (option 'off'/'on', 'off' by default) |
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| 61 | 'OutputDirExt';'.proj';...%set the output dir extension |
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[29] | 62 | ''}; |
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[457] | 63 | return |
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[29] | 64 | end |
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| 65 | |
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[457] | 66 | %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 67 | %% select different modes, RUN, parameter input, BATCH |
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| 68 | % BATCH case: read the xml file for batch case |
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| 69 | if ischar(Param) |
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| 70 | if strcmp(Param,'input?') |
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| 71 | checkrun=1;% will inly search input parameters (preparation of BATCH mode) |
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| 72 | else |
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| 73 | Param=xml2struct(Param); |
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| 74 | checkrun=0; |
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| 75 | end |
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| 76 | % RUN case: parameters introduced as the input structure Param |
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| 77 | else |
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[374] | 78 | hseries=guidata(Param.hseries);%handles of the GUI series |
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[457] | 79 | WaitbarPos=get(hseries.waitbar_frame,'Position');%position of the waitbar on the GUI series |
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| 80 | checkrun=2; % indicate the RUN option is used |
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[374] | 81 | end |
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[457] | 82 | |
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| 83 | %% root input file(s) and type |
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| 84 | RootPath=Param.InputTable(:,1); |
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| 85 | RootFile=Param.InputTable(:,3); |
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| 86 | SubDir=Param.InputTable(:,2); |
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| 87 | NomType=Param.InputTable(:,4); |
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| 88 | FileExt=Param.InputTable(:,5); |
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| 89 | |
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| 90 | % get the set of input file names (cell array filecell), and the lists of |
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| 91 | % input file or frame indices i1_series,i2_series,j1_series,j2_series |
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[374] | 92 | [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param); |
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[457] | 93 | % filecell{iview,fileindex}: cell array representing the list of file names |
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| 94 | % iview: line in the table corresponding to a given file series |
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| 95 | % fileindex: file index within the file series, |
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| 96 | % 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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| 97 | % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices |
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| 98 | % set of frame indices used for movie or multimage input |
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| 99 | % numbers of slices and file indices |
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[29] | 100 | |
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[457] | 101 | NbSlice=1;%default |
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| 102 | if isfield(Param.IndexRange,'NbSlice') |
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| 103 | NbSlice=Param.IndexRange.NbSlice; |
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| 104 | end |
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| 105 | nbview=numel(i1_series);%number of input file series (lines in InputTable) |
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| 106 | nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices) |
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| 107 | nbfield_i=size(i1_series{1},2); %nb of fields for the i index |
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| 108 | nbfield=nbfield_j*nbfield_i; %total number of fields |
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| 109 | nbfield_i=floor(nbfield/NbSlice);%total number of indexes in a slice (adjusted to an integer number of slices) |
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| 110 | nbfield=nbfield_i*NbSlice; %total number of fields after adjustement |
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| 111 | |
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| 112 | %determine the file type on each line from the first input file |
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| 113 | ImageTypeOptions={'image','multimage','mmreader','video'};%allowed input file types(images) |
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| 114 | |
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| 115 | [FileType{1},FileInfo{1},MovieObject{1}]=get_file_type(filecell{1,1}); |
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| 116 | CheckImage{1}=~isempty(find(strcmp(FileType,ImageTypeOptions)));% =1 for images |
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| 117 | if ~isempty(j1_series{1}) |
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| 118 | frame_index{1}=j1_series{1}; |
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| 119 | else |
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| 120 | frame_index{1}=i1_series{1}; |
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| 121 | end |
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| 122 | |
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| 123 | %% calibration data and timing: read the ImaDoc files |
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| 124 | mode=''; %default |
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| 125 | timecell={}; |
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| 126 | itime=0; |
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| 127 | NbSlice_calib={}; |
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| 128 | for iview=1:nbview%Loop on views |
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| 129 | XmlData{iview}=[];%default |
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| 130 | filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); |
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| 131 | if exist([filebase{iview} '.xml'],'file') |
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| 132 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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| 133 | if isfield(XmlData{iview},'Time') |
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| 134 | itime=itime+1; |
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| 135 | timecell{itime}=XmlData{iview}.Time; |
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| 136 | end |
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| 137 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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| 138 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1);%nbre of slices for Zindex in phys transform |
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| 139 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 140 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 141 | end |
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| 142 | end |
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| 143 | elseif exist([filebase{iview} '.civ'],'file') |
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| 144 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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| 145 | itime=itime+1; |
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| 146 | timecell{itime}=time; |
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| 147 | XmlData{iview}.Time=time; |
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| 148 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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| 149 | GeometryCalib.Tx=0; |
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| 150 | GeometryCalib.Ty=0; |
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| 151 | GeometryCalib.Tz=1; |
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| 152 | GeometryCalib.dpx=1; |
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| 153 | GeometryCalib.dpy=1; |
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| 154 | GeometryCalib.sx=1; |
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| 155 | GeometryCalib.Cx=0; |
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| 156 | GeometryCalib.Cy=0; |
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| 157 | GeometryCalib.f=1; |
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| 158 | GeometryCalib.kappa1=0; |
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| 159 | GeometryCalib.CoordUnit='cm'; |
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| 160 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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| 161 | if error==1 |
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| 162 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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| 163 | end |
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| 164 | end |
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| 165 | end |
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| 166 | |
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| 167 | %% check coincidence in time for several input file series |
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| 168 | multitime=0; |
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| 169 | if isempty(timecell) |
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| 170 | time=[]; |
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| 171 | elseif length(timecell)==1 |
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| 172 | time=timecell{1}; |
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| 173 | elseif length(timecell)>1 |
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| 174 | multitime=1; |
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| 175 | for icell=1:length(timecell) |
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| 176 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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| 177 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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| 178 | time=timecell{1}; |
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| 179 | multitime=0; |
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| 180 | break |
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| 181 | end |
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| 182 | end |
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| 183 | end |
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| 184 | if multitime |
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| 185 | for icell=1:length(timecell) |
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| 186 | time(icell,:,:)=timecell{icell}; |
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| 187 | end |
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| 188 | diff_time=max(max(diff(time))); |
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| 189 | if diff_time>0 |
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| 190 | msgbox_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time)]) |
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| 191 | end |
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| 192 | end |
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| 193 | if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% time array absent or too short in ImaDoc xml file' |
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| 194 | time=[]; |
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| 195 | end |
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| 196 | |
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[409] | 197 | %% coordinate transform or other user defined transform |
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[374] | 198 | transform_fct='';%default |
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[457] | 199 | if isfield(Param,'FieldTransform')&&isfield(Param.FieldTransform,'TransformHandle') |
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| 200 | transform_fct=Param.FieldTransform.TransformHandle; |
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[374] | 201 | end |
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[457] | 202 | %%%%%%%%%%%% END STANDARD PART %%%%%%%%%%%% |
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| 203 | % EDIT FROM HERE |
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[116] | 204 | |
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[457] | 205 | %% check the validity of input file types |
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| 206 | if CheckImage{1} |
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| 207 | FileExtOut='.png'; % write result as .png images for image inputs |
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| 208 | elseif CheckNc{1} |
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| 209 | FileExtOut='.nc';% write result as .nc files for netcdf inputs |
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| 210 | else |
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| 211 | msgbox_uvmat('ERROR',['invalid file type input ' FileType{1}]) |
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| 212 | return |
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| 213 | end |
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| 214 | if nbview==2 && ~isequal(CheckImage{1},CheckImage{2}) |
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| 215 | msgbox_uvmat('ERROR','input must be two image series or two netcdf file series') |
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| 216 | return |
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| 217 | end |
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| 218 | NomTypeOut='_1-2_1';% output file index will indicate the first and last ref index in the series |
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| 219 | if NbSlice~=nbfield_j |
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| 220 | answer=msgbox_uvmat('INPUT_Y-N',['will not average slice by slice: for so cancel and set NbSlice= ' num2str(nbfield_j)]); |
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| 221 | if ~strcmp(answer,'Yes') |
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| 222 | return |
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| 223 | end |
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| 224 | end |
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| 225 | |
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| 226 | %% Set field names and velocity types |
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| 227 | InputFields{1}=[];%default (case of images) |
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| 228 | if isfield(Param,'InputFields') |
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| 229 | InputFields{1}=Param.InputFields; |
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| 230 | end |
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| 231 | if nbview==2 |
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| 232 | InputFields{2}=[];%default (case of images) |
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| 233 | if isfield(Param,'InputFields') |
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| 234 | InputFields{2}=Param.InputFields{1};%default |
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| 235 | if isfield(Param.InputFields,'FieldName_1') |
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| 236 | InputFields{2}.FieldName=Param.InputFields.FieldName_1; |
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| 237 | if isfield(Param.InputFields,'VelType_1') |
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| 238 | InputFields{2}.VelType=Param.InputFields.VelType_1; |
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| 239 | end |
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| 240 | end |
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| 241 | end |
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| 242 | end |
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| 243 | |
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| 244 | %% Initiate output fields |
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| 245 | %initiate the output structure as a copy of the first input one (reproduce fields) |
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| 246 | [DataOut,ParamOut,errormsg] = read_field(filecell{1,1},FileType{1},InputFields{1},1); |
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| 247 | if ~isempty(errormsg) |
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| 248 | msgbox_uvmat('ERROR',['error reading ' filecell{1,1} ': ' errormsg]) |
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| 249 | return |
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| 250 | end |
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| 251 | time_1=[]; |
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| 252 | if isfield(DataOut,'Time') |
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| 253 | time_1=DataOut.Time(1); |
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| 254 | end |
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| 255 | if CheckNc{iview} |
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| 256 | if isempty(strcmp('Conventions',DataOut.ListGlobalAttribute)) |
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| 257 | DataOut.ListGlobalAttribute=['Conventions' DataOut.ListGlobalAttribute]; |
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| 258 | end |
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| 259 | DataOut.Conventions='uvmat'; |
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| 260 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {Param.Action}]; |
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| 261 | ActionKey='Action'; |
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| 262 | while isfield(DataOut,ActionKey) |
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| 263 | ActionKey=[ActionKey '_1']; |
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| 264 | end |
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| 265 | DataOut.(ActionKey)=Param.Action; |
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| 266 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {ActionKey}]; |
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| 267 | if isfield(DataOut,'Time') |
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| 268 | DataOut.ListGlobalAttribute=[DataOut.ListGlobalAttribute {'Time','Time_end'}]; |
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| 269 | end |
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| 270 | end |
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| 271 | |
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| 272 | %% MAIN LOOP ON SLICES |
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| 273 | %%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%% |
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| 274 | for i_slice=1:NbSlice |
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| 275 | index_slice=i_slice:NbSlice:nbfield;% select file indices of the slice |
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| 276 | nbfiles=0; |
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| 277 | nbmissing=0; |
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| 278 | |
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| 279 | %initiate result fields |
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| 280 | for ivar=1:length(DataOut.ListVarName) |
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| 281 | DataOut.(DataOut.ListVarName{ivar})=0; % initialise all fields to zero |
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| 282 | end |
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| 283 | |
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| 284 | %%%%%%%%%%%%%%%% loop on field indices %%%%%%%%%%%%%%%% |
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| 285 | for index=index_slice |
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| 286 | if checkrun |
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| 287 | update_waitbar(hseries.waitbar_frame,WaitbarPos,index/(nbfield)) |
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| 288 | stopstate=get(hseries.RUN,'BusyAction'); |
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| 289 | else |
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| 290 | stopstate='queue'; |
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| 291 | end |
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| 292 | %OUTPUT |
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| 293 | % GUI_input=list of options in the GUI series.fig needed for the function |
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| 294 | % |
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| 295 | %INPUT: |
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| 296 | % Param: structure containing all the parameters read on the GUI series |
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| 297 | % or name of the xml file containing these parameters (BATCH case) |
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| 298 | % |
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| 299 | |
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| 300 | |
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[222] | 301 | %% projection object |
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[41] | 302 | test_object=get(hseries.GetObject,'Value'); |
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| 303 | if test_object |
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[76] | 304 | hset_object=findobj(allchild(0),'tag','set_object'); |
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[381] | 305 | %ProjObject=read_set_object(guidata(hset_object)); |
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| 306 | ProjObject=read_GUI(hset_object); |
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[401] | 307 | if ~isfield(ProjObject,'Type') |
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| 308 | msgbox_uvmat('ERROR','Undefined projection object type') |
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[41] | 309 | return |
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| 310 | end |
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[394] | 311 | if ~isequal(ProjObject.Type,'plane')|| isequal(ProjObject.ProjMode,'projection') |
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[222] | 312 | msgbox_uvmat('ERROR','The projection object must be a plane with projection mode interp or filter') |
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[41] | 313 | return |
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| 314 | end |
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[394] | 315 | answeryes=msgbox_uvmat('INPUT_Y-N',['field series projected on ' ProjObject.Type]); |
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[41] | 316 | if ~isequal(answeryes,'Yes') |
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| 317 | return |
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| 318 | end |
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| 319 | end |
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| 320 | |
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[374] | 321 | %% features of the input fields |
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| 322 | RootPath=Param.InputTable(:,1); |
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| 323 | RootFile=Param.InputTable(:,3); |
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| 324 | SubDir=Param.InputTable(:,2); |
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| 325 | NomType=Param.InputTable(:,4); |
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| 326 | FileExt=Param.InputTable(:,5); |
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| 327 | |
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| 328 | nbview=length(RootFile);%number of views (file series to merge) |
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| 329 | nbfield=size(i1_series{1},1)*size(i1_series{1},2);%number of fields in the time series |
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[29] | 330 | hhh=which('mmreader'); |
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| 331 | for iview=1:nbview |
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| 332 | test_movie(iview)=0; |
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[409] | 333 | if ~isempty(hhh) |
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[374] | 334 | if isequal(lower(FileExt{iview}),'.avi') |
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| 335 | MovieObject{iview}=mmreader(fullfile(RootPath{iview},[RootFile{iview} FileExt{iview}])); |
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[29] | 336 | test_movie(iview)=1; |
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| 337 | end |
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[374] | 338 | end |
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[29] | 339 | end |
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| 340 | |
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[222] | 341 | %% Calibration data and timing: read the ImaDoc files |
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[29] | 342 | timecell={}; |
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| 343 | itime=0; |
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| 344 | NbSlice_calib={}; %test for z index |
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| 345 | for iview=1:nbview%Loop on views |
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| 346 | XmlData{iview}=[];%default |
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[374] | 347 | filebase{iview}=fullfile(RootPath{iview},RootFile{iview}); |
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[29] | 348 | if exist([filebase{iview} '.xml'],'file') |
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| 349 | [XmlData{iview},error]=imadoc2struct([filebase{iview} '.xml']); |
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| 350 | if isfield(XmlData{iview},'Time') |
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| 351 | itime=itime+1; |
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| 352 | timecell{itime}=XmlData{iview}.Time; |
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| 353 | end |
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| 354 | if isfield(XmlData{iview},'GeometryCalib') && isfield(XmlData{iview}.GeometryCalib,'SliceCoord') |
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| 355 | NbSlice_calib{iview}=size(XmlData{iview}.GeometryCalib.SliceCoord,1); |
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| 356 | if ~isequal(NbSlice_calib{iview},NbSlice_calib{1}) |
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| 357 | msgbox_uvmat('WARNING','inconsistent number of Z indices for the two field series'); |
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| 358 | end |
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| 359 | end |
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| 360 | elseif exist([filebase{iview} '.civ'],'file') |
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| 361 | [error,time,TimeUnit,mode,npx,npy,pxcmx,pxcmy]=read_imatext([filebase{iview} '.civ']); |
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| 362 | itime=itime+1; |
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| 363 | timecell{itime}=time; |
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| 364 | XmlData{iview}.Time=time; |
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| 365 | GeometryCalib.R=[pxcmx 0 0; 0 pxcmy 0;0 0 0]; |
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| 366 | GeometryCalib.Tx=0; |
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| 367 | GeometryCalib.Ty=0; |
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| 368 | GeometryCalib.Tz=1; |
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| 369 | GeometryCalib.dpx=1; |
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| 370 | GeometryCalib.dpy=1; |
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| 371 | GeometryCalib.sx=1; |
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| 372 | GeometryCalib.Cx=0; |
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| 373 | GeometryCalib.Cy=0; |
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| 374 | GeometryCalib.f=1; |
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| 375 | GeometryCalib.kappa1=0; |
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| 376 | GeometryCalib.CoordUnit='cm'; |
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| 377 | XmlData{iview}.GeometryCalib=GeometryCalib; |
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| 378 | if error==1 |
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| 379 | msgbox_uvmat('WARNING','inconsistent number of fields in the .civ file'); |
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| 380 | end |
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| 381 | end |
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| 382 | end |
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| 383 | |
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[222] | 384 | %% check coincidence in time |
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[29] | 385 | multitime=0; |
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[89] | 386 | if isempty(timecell) |
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[29] | 387 | time=[]; |
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| 388 | elseif length(timecell)==1 |
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| 389 | time=timecell{1}; |
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| 390 | elseif length(timecell)>1 |
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| 391 | multitime=1; |
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| 392 | for icell=1:length(timecell) |
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| 393 | if ~isequal(size(timecell{icell}),size(timecell{1})) |
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| 394 | msgbox_uvmat('WARNING','inconsistent time array dimensions in ImaDoc fields, the time for the first series is used') |
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| 395 | time=timecell{1}; |
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| 396 | multitime=0; |
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| 397 | break |
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| 398 | end |
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| 399 | end |
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| 400 | end |
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| 401 | if multitime |
---|
| 402 | for icell=1:length(timecell) |
---|
| 403 | time(icell,:,:)=timecell{icell}; |
---|
| 404 | end |
---|
| 405 | diff_time=max(max(diff(time))); |
---|
| 406 | if diff_time>0 |
---|
| 407 | msgbox_uvmat('WARNING',['times of series differ by more than ' num2str(diff_time)]) |
---|
| 408 | end |
---|
[427] | 409 | time=sqeeze(mean(time,1)); |
---|
[29] | 410 | end |
---|
[374] | 411 | % if size(time,2) < i2_series{1}(end) || size(time,3) < j2_series{1}(end)% ime array absent or too short in ImaDoc xml file' |
---|
| 412 | % time=[]; |
---|
| 413 | % end |
---|
[29] | 414 | |
---|
[222] | 415 | %% Field and velocity type (the same for all views) |
---|
[109] | 416 | FieldName=''; |
---|
[374] | 417 | if isfield(Param,'InputFields')&&isfield(Param.InputFields,'FieldMenu') |
---|
| 418 | FieldName=Param.InputFields.FieldMenu;%the same set of fields for all views |
---|
| 419 | VelType=Param.InputFields.VelTypeMenu; |
---|
[29] | 420 | end |
---|
[374] | 421 | % if strcmp(get(hseries.FieldMenu,'Visible'),'on') |
---|
| 422 | % Field_str=get(hseries.FieldMenu,'String'); |
---|
| 423 | % val=get(hseries.FieldMenu,'Value'); |
---|
| 424 | % FieldName=Field_str(val);%the same set of fields for all views |
---|
| 425 | % VelType_str=get(hseries.VelTypeMenu,'String'); |
---|
| 426 | % VelType_val=get(hseries.VelTypeMenu,'Value'); |
---|
| 427 | % VelType=VelType_str{VelType_val}; %the same for all views |
---|
| 428 | if strcmp(FieldName,'') |
---|
| 429 | msgbox_uvmat('ERROR','no input field defined in FieldMenu') |
---|
| 430 | elseif strcmp(FieldName,'get_field...') |
---|
| 431 | hget_field=findobj(allchild(0),'Name','get_field');%find the get_field... GUI |
---|
| 432 | SubField=get_field('read_get_field',hObject,eventdata,hget_field); %read the names of the variables to plot in the get_field GUI |
---|
| 433 | end |
---|
| 434 | % end |
---|
[29] | 435 | %detect whether all the files are 'images' or 'netcdf' |
---|
| 436 | testima=0; |
---|
| 437 | testvol=0; |
---|
| 438 | testcivx=0; |
---|
| 439 | testnc=0; |
---|
| 440 | for iview=1:nbview |
---|
| 441 | ext=FileExt{iview}; |
---|
[89] | 442 | form=imformats(ext(2:end)); |
---|
[29] | 443 | if isequal(lower(ext),'.vol') |
---|
| 444 | testvol=testvol+1; |
---|
| 445 | elseif ~isempty(form)||isequal(lower(ext),'.avi')% if the extension corresponds to an image format recognized by Matlab |
---|
| 446 | testima=testima+1; |
---|
| 447 | elseif isequal(ext,'.nc') |
---|
| 448 | testnc=testnc+1; |
---|
| 449 | end |
---|
| 450 | end |
---|
| 451 | if testvol |
---|
| 452 | msgbox_uvmat('ERROR','volume images not implemented yet') |
---|
| 453 | return |
---|
| 454 | end |
---|
| 455 | if testnc~=nbview && testima~=nbview && testvol~=nbview |
---|
| 456 | msgbox_uvmat('ERROR','need a set of images or a set of netcdf files with the same fields as input') |
---|
| 457 | return |
---|
| 458 | end |
---|
| 459 | if ~isequal(FieldName,'get_field...') |
---|
| 460 | testcivx=testnc; |
---|
| 461 | end |
---|
[41] | 462 | |
---|
[222] | 463 | %% name of output files and directory: |
---|
[374] | 464 | ProjectDir=fileparts(fileparts(RootPath{1}));% preoject directory (GERK) |
---|
[29] | 465 | prompt={['result directory (in' ProjectDir ')']}; |
---|
[374] | 466 | % RootPath=get(hseries.RootPath,'String'); |
---|
| 467 | % SubDir=get(hseries.SubDir,'String'); |
---|
[29] | 468 | if isequal(length(RootPath),1) |
---|
| 469 | fulldir=RootPath{1}; |
---|
[41] | 470 | subdir='merge_proj'; |
---|
[29] | 471 | res_subdir=fullfile(fulldir,subdir); |
---|
| 472 | else |
---|
| 473 | def={fullfile(ProjectDir,'0_RESULTS')}; |
---|
| 474 | dlgTitle='result directory'; |
---|
| 475 | lineNo=1; |
---|
| 476 | answer=msgbox_uvmat('INPUT_TXT',dlgTitle,def); |
---|
| 477 | fulldir=answer{1}; |
---|
| 478 | subdir=[]; |
---|
[374] | 479 | dirlist=sort(RootFile); |
---|
[29] | 480 | for iview=1:nbview |
---|
| 481 | if ~isempty(subdir) |
---|
| 482 | subdir=[subdir '-']; |
---|
| 483 | end |
---|
| 484 | subdir=[subdir dirlist{iview}]; |
---|
| 485 | end |
---|
| 486 | res_subdir=fullfile(fulldir,subdir); |
---|
| 487 | end |
---|
| 488 | ext=FileExt{1}; |
---|
| 489 | if ~exist(fulldir,'dir') |
---|
| 490 | msgbox_uvmat('ERROR',['directory ' fulldir ' needs to be created']) |
---|
| 491 | return |
---|
| 492 | end |
---|
| 493 | if ~exist(res_subdir,'dir') |
---|
| 494 | dircur=pwd; |
---|
[116] | 495 | cd(fulldir); |
---|
| 496 | succeed=mkdir(subdir); |
---|
| 497 | if succeed |
---|
[128] | 498 | [xx,msg2] = fileattrib(res_subdir,'+w','g'); %yield writing access (+w) to user group (g) |
---|
| 499 | if ~strcmp(msg2,'') |
---|
| 500 | msgbox_uvmat('ERROR',['pb of permission for ' res_subdir ': ' msg2])%error message for directory creation |
---|
| 501 | cd(dircur) |
---|
| 502 | return |
---|
| 503 | end |
---|
| 504 | cd(dircur); |
---|
[116] | 505 | else |
---|
[128] | 506 | msgbox_uvmat('ERROR',['Cannot create directory ' fulldir]) |
---|
| 507 | return |
---|
| 508 | end |
---|
[29] | 509 | end |
---|
[374] | 510 | filebasesub=fullfile(res_subdir,RootFile{1}); |
---|
| 511 | %filebase_merge=fullfile(res_subdir,'merged');%root name for the merged files |
---|
[29] | 512 | |
---|
[222] | 513 | %% MAIN LOOP |
---|
[29] | 514 | for ifile=1:nbfield |
---|
| 515 | stopstate=get(hseries.RUN,'BusyAction'); |
---|
| 516 | if isequal(stopstate,'queue')% enable STOP command from the 'series' interface |
---|
| 517 | update_waitbar(hseries.waitbar,WaitbarPos,ifile/nbfield) |
---|
| 518 | |
---|
[222] | 519 | %% ----------LOOP ON VIEWS---------------------- |
---|
[29] | 520 | nbtime=0; |
---|
| 521 | for iview=1:nbview |
---|
[222] | 522 | %name of the current file |
---|
[374] | 523 | filename=filecell{iview,ifile}; |
---|
| 524 | % filename=name_generator(filebase{iview},i1_series{iview}(ifile),j1_series{iview}(ifile),FileExt{iview},NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile),SubDir{iview}); |
---|
[29] | 525 | if ~exist(filename,'file') |
---|
| 526 | msgbox_uvmat('ERROR',['missing input file' filename]) |
---|
| 527 | break |
---|
| 528 | end |
---|
[374] | 529 | timeread(iview)=0; |
---|
[222] | 530 | %reading the current file |
---|
[29] | 531 | if testima |
---|
| 532 | if test_movie(iview) |
---|
[374] | 533 | Field{iview}.A=read(MovieObject{iview},i1_series{iview}(ifile)); |
---|
[29] | 534 | else |
---|
[78] | 535 | Field{iview}.A=imread(filename); |
---|
[29] | 536 | end % TODO: introduce ListVarName |
---|
| 537 | npxy=size(Field{iview}.A); |
---|
[109] | 538 | Field{iview}.ListVarName={'AX','AY','A'}; |
---|
| 539 | Field{iview}.VarDimName={'AX','AY',{'AY','AX'}}; |
---|
[29] | 540 | Field{iview}.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers |
---|
| 541 | Field{iview}.AY=[npxy(1)-0.5 0.5]; |
---|
[158] | 542 | Field{iview}.CoordUnit='pixel'; |
---|
[29] | 543 | Field{iview}.AName='image'; |
---|
| 544 | else |
---|
| 545 | if testcivx |
---|
| 546 | [Field{iview},VelTypeOut]=read_civxdata(filename,FieldName,VelType); |
---|
| 547 | else |
---|
| 548 | [Field{iview},var_detect]=nc2struct(filename,SubField.ListVarName); %read the corresponding input data |
---|
| 549 | Field{iview}.VarAttribute=SubField.VarAttribute; |
---|
| 550 | end |
---|
[93] | 551 | if isfield(Field{iview},'Txt') |
---|
| 552 | msgbox_uvmat('ERROR',Field{iview}.Txt) |
---|
| 553 | return |
---|
| 554 | end |
---|
[29] | 555 | if isfield(Field{iview},'Time') |
---|
| 556 | timeread(iview)=Field{iview}.Time; |
---|
| 557 | nbtime=nbtime+1; |
---|
| 558 | end |
---|
| 559 | end |
---|
| 560 | if ~isempty(NbSlice_calib) |
---|
[374] | 561 | Field{iview}.ZIndex=mod(i1_series{iview}(ifile)-1,NbSlice_calib{1})+1; |
---|
[29] | 562 | end |
---|
[222] | 563 | %transform the input field (e.g; phys) if requested |
---|
[41] | 564 | if ~isempty(transform_fct) |
---|
[127] | 565 | Field{iview}=transform_fct(Field{iview},XmlData{iview}); %transform to phys if requested |
---|
[29] | 566 | end |
---|
| 567 | if testcivx |
---|
[109] | 568 | Field{iview}=calc_field(FieldName,Field{iview}); |
---|
[29] | 569 | end |
---|
[222] | 570 | %projection on object (gridded plane) |
---|
[41] | 571 | if test_object |
---|
[409] | 572 | [Field{iview},errormsg]=proj_field(Field{iview},ProjObject); |
---|
| 573 | if ~isempty(errormsg) |
---|
| 574 | msgbox_uvmat('ERROR',['error in merge_proge/proj_field: ' errormsg]) |
---|
| 575 | return |
---|
| 576 | end |
---|
[29] | 577 | end |
---|
| 578 | end |
---|
[222] | 579 | %----------END LOOP ON VIEWS---------------------- |
---|
[29] | 580 | |
---|
[222] | 581 | %% merge the nbview fields |
---|
[29] | 582 | MergeData=merge_field(Field); |
---|
| 583 | if isfield(MergeData,'Txt') |
---|
| 584 | msgbox_uvmat('ERROR',MergeData.Txt) |
---|
| 585 | return |
---|
[222] | 586 | end |
---|
| 587 | % generating the name of the merged field |
---|
[335] | 588 | if testima |
---|
| 589 | ResultExt='.png'; |
---|
| 590 | else |
---|
[374] | 591 | ResultExt=FileExt{iview}; |
---|
[335] | 592 | end |
---|
[374] | 593 | i1=i1_series{iview}(ifile); |
---|
| 594 | if ~isempty(i2_series{iview}) |
---|
| 595 | i2=i2_series{iview}(ifile); |
---|
| 596 | else |
---|
| 597 | i2=i1; |
---|
| 598 | end |
---|
| 599 | j1=1; |
---|
| 600 | j2=1; |
---|
| 601 | if ~isempty(j1_series{iview}) |
---|
| 602 | j1=j1_series{iview}(ifile); |
---|
| 603 | if ~isempty(j2_series{iview}) |
---|
| 604 | j2=j2_series{iview}(ifile); |
---|
| 605 | else |
---|
| 606 | j2=j1; |
---|
| 607 | end |
---|
| 608 | end |
---|
| 609 | mergename=fullfile_uvmat(res_subdir,'','merged',ResultExt,NomType{iview},i1,i2,j1,j2); |
---|
| 610 | % mergename=name_generator(filebase_merge,i1,j1_series{iview}(ifile),ResultExt,NomType{iview},1,i2_series{iview}(ifile),j2_series{iview}(ifile)); |
---|
[29] | 611 | |
---|
[222] | 612 | % time of the merged field: |
---|
[29] | 613 | time_i=0;%default |
---|
| 614 | if isempty(time)% time from ImaDoc prevails |
---|
| 615 | time_i=sum(timeread)/nbtime; |
---|
| 616 | else |
---|
[427] | 617 | % time_i=i1; |
---|
| 618 | time_i=(time(i1,j1)+time(i2,j2))/2; %TODO: upgrade |
---|
[29] | 619 | end |
---|
| 620 | |
---|
[222] | 621 | % recording the merged field |
---|
[29] | 622 | if testima %in case of input images an image is produced |
---|
| 623 | if isa(MergeData.A,'uint8') |
---|
| 624 | bitdepth=8; |
---|
| 625 | elseif isa(MergeData.A,'uint16') |
---|
| 626 | bitdepth=16; |
---|
| 627 | end |
---|
| 628 | imwrite(MergeData.A,mergename,'BitDepth',bitdepth); |
---|
| 629 | %write xml calibration file |
---|
| 630 | siz=size(MergeData.A); |
---|
| 631 | npy=siz(1); |
---|
| 632 | npx=siz(2); |
---|
| 633 | if isfield(MergeData,'VarAttribute')&&isfield(MergeData.VarAttribute{1},'Coord_2')&&isfield(MergeData.VarAttribute{1},'Coord_1') |
---|
| 634 | Rangx=MergeData.VarAttribute{1}.Coord_2; |
---|
| 635 | Rangy=MergeData.VarAttribute{1}.Coord_1; |
---|
| 636 | elseif isfield(MergeData,'AX')&& isfield(MergeData,'AY') |
---|
| 637 | Rangx=[MergeData.AX(1) MergeData.AX(end)]; |
---|
| 638 | Rangy=[MergeData.AY(1) MergeData.AY(end)]; |
---|
| 639 | else |
---|
| 640 | Rangx=[0.5 npx-0.5]; |
---|
| 641 | Rangy=[npy-0.5 0.5];%default |
---|
| 642 | end |
---|
| 643 | pxcmx=(npx-1)/(Rangx(2)-Rangx(1)); |
---|
| 644 | pxcmy=(npy-1)/(Rangy(1)-Rangy(2)); |
---|
| 645 | T_x=-pxcmx*Rangx(1)+0.5; |
---|
| 646 | T_y=-pxcmy*Rangy(2)+0.5; |
---|
| 647 | GeometryCal.focal=1; |
---|
| 648 | GeometryCal.R=[pxcmx,0,0;0,pxcmy,0;0,0,1]; |
---|
| 649 | GeometryCal.Tx_Ty_Tz=[T_x T_y 1]; |
---|
| 650 | ImaDoc.GeometryCalib=GeometryCal; |
---|
| 651 | t=struct2xml(ImaDoc); |
---|
| 652 | t=set(t,1,'name','ImaDoc'); |
---|
| 653 | save(t,[filebase_merge '.xml']) |
---|
| 654 | display([filebase_merge '.xml saved']) |
---|
| 655 | else |
---|
[422] | 656 | MergeData.ListGlobalAttribute={'Conventions','Project','InputFile_1','InputFile_end','nb_coord','nb_dim','dt','Time','civ'}; |
---|
| 657 | MergeData.Conventions='uvmat'; |
---|
[29] | 658 | MergeData.nb_coord=2; |
---|
| 659 | MergeData.nb_dim=2; |
---|
[93] | 660 | dt=[]; |
---|
| 661 | if isfield(Field{1},'dt')&& isnumeric(Field{1}.dt) |
---|
| 662 | dt=Field{1}.dt; |
---|
| 663 | end |
---|
| 664 | for iview =2:numel(Field) |
---|
| 665 | if ~(isfield(Field{iview},'dt')&& isequal(Field{iview}.dt,dt)) |
---|
| 666 | dt=[];%dt not the same for all fields |
---|
| 667 | end |
---|
| 668 | end |
---|
| 669 | if isempty(dt) |
---|
| 670 | MergeData.ListGlobalAttribute(6)=[]; |
---|
| 671 | else |
---|
| 672 | MergeData.dt=dt; |
---|
| 673 | end |
---|
[29] | 674 | MergeData.Time=time_i; |
---|
[116] | 675 | error=struct2nc(mergename,MergeData);%save result file |
---|
[29] | 676 | if isempty(error) |
---|
| 677 | display(['output file ' mergename ' written']) |
---|
| 678 | else |
---|
| 679 | display(error) |
---|
| 680 | end |
---|
| 681 | end |
---|
| 682 | end |
---|
| 683 | end |
---|
| 684 | |
---|
[222] | 685 | %'merge_field': concatene fields |
---|
| 686 | %------------------------------------------------------------------------ |
---|
[29] | 687 | function MergeData=merge_field(Data) |
---|
[222] | 688 | %% default output |
---|
[29] | 689 | if isempty(Data)||~iscell(Data) |
---|
| 690 | MergeData=[]; |
---|
| 691 | return |
---|
| 692 | end |
---|
| 693 | MergeData=Data{1};%default |
---|
| 694 | error=0; |
---|
| 695 | nbview=length(Data); |
---|
| 696 | if nbview==1 |
---|
| 697 | return |
---|
| 698 | end |
---|
[222] | 699 | |
---|
| 700 | %% group the variables (fields of 'FieldData') in cells of variables with the same dimensions |
---|
[89] | 701 | [CellVarIndex,NbDim,VarTypeCell]=find_field_indices(Data{1}); |
---|
| 702 | %LOOP ON GROUPS OF VARIABLES SHARING THE SAME DIMENSIONS |
---|
| 703 | % CellVarIndex=cells of variable index arrays |
---|
| 704 | ivar_new=0; % index of the current variable in the projected field |
---|
| 705 | for icell=1:length(CellVarIndex) |
---|
| 706 | if NbDim(icell)==1 |
---|
| 707 | continue |
---|
| 708 | end |
---|
| 709 | VarIndex=CellVarIndex{icell};% indices of the selected variables in the list FieldData.ListVarName |
---|
| 710 | VarType=VarTypeCell{icell}; |
---|
| 711 | ivar_X=VarType.coord_x; |
---|
| 712 | ivar_Y=VarType.coord_y; |
---|
| 713 | ivar_FF=VarType.errorflag; |
---|
| 714 | if isempty(ivar_X) |
---|
| 715 | test_grid=1;%test for input data on regular grid (e.g. image)coordinates |
---|
| 716 | else |
---|
| 717 | if length(ivar_Y)~=1 |
---|
| 718 | msgbox_uvmat('ERROR','y coordinate missing in proj_field.m') |
---|
| 719 | return |
---|
| 720 | end |
---|
| 721 | test_grid=0; |
---|
| 722 | end |
---|
| 723 | %case of input fields with unstructured coordinates |
---|
| 724 | if ~test_grid |
---|
| 725 | for ivar=VarIndex |
---|
| 726 | VarName=MergeData.ListVarName{ivar}; |
---|
| 727 | for iview=1:nbview |
---|
| 728 | eval(['MergeData.' VarName '=[MergeData.' VarName '; Data{iview}.' VarName '];']) |
---|
| 729 | end |
---|
| 730 | end |
---|
| 731 | %case of fields defined on a structured grid |
---|
| 732 | else |
---|
| 733 | testFF=0; |
---|
| 734 | for iview=2:nbview |
---|
| 735 | for ivar=VarIndex |
---|
| 736 | VarName=MergeData.ListVarName{ivar}; |
---|
| 737 | if isfield(MergeData,'VarAttribute') |
---|
| 738 | if length(MergeData.VarAttribute)>=ivar && isfield(MergeData.VarAttribute{ivar},'Role') && isequal(MergeData.VarAttribute{ivar}.Role,'errorflag') |
---|
| 739 | testFF=1; |
---|
| 740 | end |
---|
| 741 | end |
---|
| 742 | eval(['MergeData.' VarName '=MergeData.' VarName '+ Data{iview}.' VarName ';']) |
---|
| 743 | end |
---|
| 744 | end |
---|
| 745 | if testFF |
---|
| 746 | nbaver=nbview-MergeData.FF; |
---|
| 747 | indgood=find(nbaver>0); |
---|
| 748 | for ivar=VarIndex |
---|
| 749 | VarName=MergeData.ListVarName{ivar}; |
---|
| 750 | eval(['MergeData.' VarName '(indgood)=double(MergeData.' VarName '(indgood))./nbaver(indgood);']) |
---|
| 751 | end |
---|
| 752 | else |
---|
| 753 | for ivar=VarIndex |
---|
| 754 | VarName=MergeData.ListVarName{ivar}; |
---|
| 755 | eval(['MergeData.' VarName '=double(MergeData.' VarName ')./nbview;']) |
---|
| 756 | end |
---|
| 757 | end |
---|
| 758 | end |
---|
| 759 | end |
---|
[222] | 760 | |
---|
[89] | 761 | |
---|