[953]  1  %'ima2vol': concatene image series to form a 'volume' image, make vertical cuts along x and y


[171]  2  %


 3  % function GUI_input=ima2vol(num_i1,num_i2,num_j1,num_j2,Series)


 4  %


 5  %OUTPUT


 6  % GUI_input=list of options in the GUI series.fig needed for the function


 7  %


 8  %INPUT:


 9  %num_i1: series of first indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)


 10  %num_i2: series of second indices i (given from the series interface as first_i:incr_i:last_i, mode and list_pair_civ)


 11  %num_j1: series of first indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ )


 12  %num_j2: series of second indices j (given from the series interface as first_j:incr_j:last_j, mode and list_pair_civ)


 13  %Series: Matlab structure containing information set by the series interface


 14  %


[41]  15  %


[810]  16 


 17  %=======================================================================


[924]  18  % Copyright 20082016, LEGI UMR 5519 / CNRS UGA GINP, Grenoble, France


[810]  19  % http://www.legi.grenobleinp.fr


 20  % Joel.Sommeria  Joel.Sommeria (A) legi.cnrs.fr


 21  %


 22  % This file is part of the toolbox UVMAT.


 23  %


 24  % UVMAT is free software; you can redistribute it and/or modify


 25  % it under the terms of the GNU General Public License as published


 26  % by the Free Software Foundation; either version 2 of the license,


 27  % or (at your option) any later version.


 28  %


 29  % UVMAT is distributed in the hope that it will be useful,


 30  % but WITHOUT ANY WARRANTY; without even the implied warranty of


 31  % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the


 32  % GNU General Public License (see LICENSE.txt) for more details.


 33  %=======================================================================


 34 


[953]  35  function ParamOut=ima2vol(Param)


 36 


 37  %% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed


 38  if isstruct(Param) && isequal(Param.Action.RUN,0)


 39  ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)


 40  ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)


 41  ParamOut.NbSlice='off'; %nbre of slices ('off' by default)


 42  ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two', 'off' by default)


 43  ParamOut.FieldName='one';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)


 44  ParamOut.FieldTransform = 'on';%can use a transform function


 45  ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)


 46  ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',


 47  ParamOut.Mask='on';%can use mask option (option 'off'/'on', 'off' by default)


[956]  48  ParamOut.OutputDirExt='.vol';%set the output dir extension


[953]  49  ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice


 50  %check the input files


 51  ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)


 52  first_j=[];


 53  if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end


 54  PairString='';


 55  if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end


 56  [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);


 57  FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...


 58  Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);


 59  return


[41]  60  end


 61 


[953]  62  %%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%


 63  %% read input parameters from an xml file if input is a file name (batch mode)


 64  ParamOut=[];


 65  RUNHandle=[];


 66  WaitbarHandle=[];


 67  checkrun=1;


 68  if ischar(Param)


 69  Param=xml2struct(Param);% read Param as input file (batch case)


 70  checkrun=0;


 71  else% interactive mode in Matlab


 72  hseries=findobj(allchild(0),'Tag','series');


 73  RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series


 74  WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series


 75  end


[41]  76 


[953]  77  %% subdirectory for output files


 78  SubdirOut=[Param.OutputSubDir Param.OutputDirExt];


[41]  79 


[953]  80  %% root input file names and nomenclature type (cell arrays with one element)


 81  RootPath=Param.InputTable(:,1);


 82  RootFile=Param.InputTable(:,3);


 83  SubDir=Param.InputTable(:,2);


 84  NomType=Param.InputTable(:,4);


 85  FileExt=Param.InputTable(:,5);


[41]  86 


 87 


[953]  88  %% get the set of input file names (cell array filecell), and file indices


 89  [filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);


 90  % filecell{iview,fileindex}: cell array representing the list of file names


 91  % iview: line in the table corresponding to a given file series


 92  % fileindex: file index within the file series,


 93  % 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


 94  % i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices


 95  nbfield_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)


 96  nbfield_i=size(i1_series{1},2); %nb of fields for the i index


 97  nbfield=nbfield_j*nbfield_i; %total number of fields


 98  [FileInfo{1},VideoObject{1}]=get_file_info(filecell{1,1});% type of input file


 99  FileType{1}=FileInfo{1}.FileType;


[41]  100 


[953]  101  %% calibration data and timing: read the ImaDoc files


 102  [XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);


 103  if ~isempty(errormsg)


 104  disp_uvmat('WARNING',errormsg,checkrun)


 105  end


 106 


 107  %% coordinate transform or other user defined transform


 108  transform_fct='';%default fct handle


 109  if isfield(Param,'FieldTransform')&&~isempty(Param.FieldTransform.TransformName)


 110  currentdir=pwd;


 111  cd(Param.FieldTransform.TransformPath)


 112  transform_fct=str2func(Param.FieldTransform.TransformName);


 113  cd (currentdir)


 114  end


 115 


 116  %% main loop


 117  for ifile=1:nbfield_i


 118  update_waitbar(WaitbarHandle,ifile/nbfield)


 119  if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')


 120  disp('program stopped by user')


 121  return


 122  end


 123  for jfile=1:nbfield_j


 124  if ~isempty(j1_series)&&~isequal(j1_series,{[]})


 125  j1=j1_series{1}(jfile,ifile);


 126  end


 127  filename=fullfile_uvmat(RootPath{1},SubDir{1},RootFile{1},FileExt{1},NomType{1},i1_series{1}(jfile,ifile),[],j1)


 128  [Data,tild,errormsg] = read_field(filename,'image');


 129  % transform the input field (e.g; phys) if requested (no transform involving two input fields)


 130  if ~isempty(transform_fct)


 131  Data.ZIndex=jfile;


 132  Data=transform_fct(Data,XmlData{1});


 133  end


 134  if jfile==1


[956]  135  VolData.A=zeros(nbfield_j,size(Data.A,1),size(Data.A,2));


 136  VolData.Coord_z=1:nbfield_j;%default Z values


[953]  137  end


[956]  138  VolData.A(jfile,:,:)=Data.A;%concacene along y


 139  VolData.Coord_z(jfile)=Data.PlaneCoord(3);


[953]  140  end


[956]  141  % npx=size(Data.A,2);


 142  % npy=size(Data.A,1);


 143  % npz=256;


 144  % ind_x=round(npx/2)10:round(npx/2)+10;%image index at the mid x position


 145  % ind_y=round(npy/2)10:round(npy/2)+10;%image index at the mid y position


 146  % ind_y=ind_y100;% shift to avoid the injector


 147  % %write xml calibration file, using the first file


 148  % Rangx=Data.Coord_x;


 149  % Rangy=Data.Coord_y;


 150  % Rangz=[Z(end) Z(1)];


 151  %


 152  % GeometryCal.CalibrationType='rescale';


 153  % GeometryCal.CoordUnit=Data.CoordUnit;


 154  % GeometryCal.focal=1;


 155  % %scaling along x, y and z


 156  % pxcmx=(npx1)/(Rangx(2)Rangx(1));


 157  % pxcmy=(npy1)/(Rangy(1)Rangy(2));


 158  % pxcmz=(npz1)/(Rangz(2)Rangz(1));


 159  % T_x=pxcmx*Rangx(1)+0.5;


 160  % T_y=pxcmy*Rangy(2)+0.5;


 161  % T_z=pxcmz*Rangz(2)+0.5;


 162  % % xml file for x cut


 163  % GeometryCal.R=[pxcmx,0,0;0,pxcmz,0;0,0,1];


 164  % GeometryCal.Tx_Ty_Tz=[T_x T_z 1];


 165  % ImaDoc.GeometryCalib=GeometryCal;


 166  % t=struct2xml(ImaDoc);


 167  % t=set(t,1,'name','ImaDoc');


 168  % save(t,fullfile(RootPath{1},SubdirOut,'cut_x.xml'))


 169  % % xml file for y cut


 170  % GeometryCal.R=[pxcmy,0,0;0,pxcmz,0;0,0,1];


 171  % GeometryCal.Tx_Ty_Tz=[T_y T_z 1];


 172  % ImaDoc.GeometryCalib=GeometryCal;


 173  % t=struct2xml(ImaDoc);


 174  % t=set(t,1,'name','ImaDoc');


 175  % save(t,fullfile(RootPath{1},SubdirOut,'cut_y.xml'))


 176  % end


[41]  177 


[956]  178  filename=fullfile_uvmat(RootPath{1},SubdirOut,RootFile{1},'.nc','_1',i1_series{1}(jfile,ifile),[],j1);


 179  VolData.ListVarName={'Coord_z','Coord_y','Coord_x','A'};


 180  VolData.VarDimName={'Coord_z','Coord_y','Coord_x',{'Coord_z','Coord_y','Coord_x'}};


 181  VolData.Coord_x=Data.Coord_x;


 182  VolData.Coord_y=Data.Coord_y;


 183  struct2nc(filename,VolData)


 184  disp([filename ' written'])


[41]  185  end


 186 


 187 


 188 

