[8]  1  %'read_civxdata': reads civx data from netcdf files


 2  %


[159]  3  %


 4  % function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType)


 5  %


[8]  6  % OUTPUT:


[179]  7  % Field: structure representing the selected field, containing


[8]  8  % .Txt: (char string) error message if any


[179]  9  % .ListGlobalAttribute: list of global attributes containing:


 10  % .NbCoord: number of vector components


 11  % .NbDim: number of dimensions (=2 or 3)


 12  % .dt: time interval for the corresponding image pair


 13  % .Time: absolute time (average of the initial image pair)


 14  % .CivStage: =0,


 15  % =1, civ1 has been performed only


 16  % =2, fix1 has been performed


 17  % =3, pacth1 has been performed


 18  % =4, civ2 has been performed


 19  % =5, fix2 has been performed


 20  % =6, pacth2 has been performed


 21  % .CoordUnit: 'pixel'


 22  % .ListVarName: {'X' 'Y' 'U' 'V' 'F' 'FF'}


 23  % .X, .Y, .Z: set of vector coordinates


 24  % .U,.V,.W: corresponding set of vector components


 25  % .F: warning flags


 26  % .FF: error flag, =0 for good vectors


 27  % .C: scalar associated with velocity (used for vector colors)


 28  % .DijU; matrix of spatial derivatives (DijU(1,1,:)=DUDX,


 29  % DijU(1,2,:)=DUDY, Dij(2,1,:)=DVDX, DijU(2,2,:)=DVDY


[8]  30  %


[179]  31  % VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....


 32  %


[8]  33  % INPUT:


 34  % filename: file name (string).


 35  % FieldNames =cell of field names to get, which can contain the strings:


 36  % 'ima_cor': image correlation, vec_c or vec2_C


 37  % 'vort','div','strain': requires velocity derivatives DUDX...


 38  % 'error': error estimate (vec_E or vec2_E)


 39  %


 40  % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)


 41  % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending


 42  % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)


 43 


 44 


 45  % FUNCTIONS called:


 46  % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file


 47  % 'nc2struct': reads a netcdf file


 48 


[236]  49  function [Field,VelTypeOut,errormsg]=read_civxdata(filename,FieldNames,VelType)


 50  errormsg='';


[380]  51  DataTest=nc2struct(filename,'ListGlobalAttribute','Conventions','CivStage');


[247]  52  if isfield(DataTest,'Txt')


[380]  53  errormsg=DataTest.Txt;


 54  return


[247]  55  elseif isequal(DataTest.Conventions,'uvmat/civdata')%test for new civ format


[380]  56  [Field,VelTypeOut,errormsg]=read_civdata(filename,FieldNames,VelType,DataTest.CivStage);


 57  % if ~isempty(errormsg)


 58  % msgbox_uvmat('ERROR',errormsg)


 59  % end


[236]  60  return


 61  end


 62 


[206]  63  %% default input


[8]  64  if ~exist('VelType','var')


 65  VelType=[];


 66  end


 67  if isequal(VelType,'*')


 68  VelType=[];


 69  end


 70  if ~exist('FieldNames','var')


 71  FieldNames=[]; %default


 72  end


[206]  73 


 74  %% reading data


[8]  75  VelTypeOut=VelType;%default


 76  [var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read


[206]  77  [Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file


 78  if isfield(Field,'Txt')


[236]  79  errormsg=Field.Txt;


[206]  80  return


 81  end


[140]  82  if vardetect(1)==0


[236]  83  errormsg=[ 'requested field not available in ' filename '/' VelType];


[206]  84  return


[8]  85  end


 86  var_ind=find(vardetect);


 87  for ivar=1:length(var_ind)


 88  Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};


[206]  89  Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel


[8]  90  end


 91  VelTypeOut=VelType;


 92  if ~isempty(ichoice)


 93  VelTypeOut=vel_type_out_cell{ichoice};


 94  end


 95 


[206]  96  %% adjust for Djui:


[8]  97  if isfield(Field,'DjUi')


[404]  98  Field.ListVarName{end3}='DjUi';


 99  Field.VarDimName{end3}=[Field.VarDimName{end3} {'nb_coord'} {'nbcoord'}];


[8]  100  Field.ListVarName(end2:end)=[];


[156]  101  Field.VarDimName(end2:end)=[];


[8]  102  Field.VarAttribute(end2:end)=[];


 103  end


 104 


[206]  105  %% renaming for standard conventions


[179]  106  Field.NbCoord=Field.nb_coord;


 107  Field.NbDim=Field.nb_dim;


 108 


[206]  109  %% CivStage


[8]  110  if isfield(Field,'patch2')&& isequal(Field.patch2,1)


 111  Field.CivStage=6;


 112  elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)


 113  Field.CivStage=5;


 114  elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)


 115  Field.CivStage=4;


 116  elseif isfield(Field,'patch')&& isequal(Field.patch,1)


 117  Field.CivStage=3;


 118  elseif isfield(Field,'fix')&& isequal(Field.fix,1)


 119  Field.CivStage=2;


 120  else


 121  Field.CivStage=1;


 122  end


 123 


[180]  124  %determine the appropriate constant for time and dt for the PIV pair


 125  test_civ1=isequal(VelTypeOut,'civ1')isequal(VelTypeOut,'interp1')isequal(VelTypeOut,'filter1');


 126  test_civ2=isequal(VelTypeOut,'civ2')isequal(VelTypeOut,'interp2')isequal(VelTypeOut,'filter2');


 127  Field.Time=0; %default


[221]  128  Field.TimeUnit='s';


[180]  129  if test_civ1


 130  if isfield(Field,'absolut_time_T0')


 131  Field.Time=double(Field.absolut_time_T0);


 132  Field.dt=double(Field.dt);


 133  else


[236]  134  errormsg='the input file is not civx';


[180]  135  Field.CivStage=0;


 136  Field.dt=0;


 137  end


 138  elseif test_civ2


 139  Field.Time=double(Field.absolut_time_T0_2);


 140  Field.dt=double(Field.dt2);


 141  else


[236]  142  errormsg='the input file is not civx';


[180]  143  Field.CivStage=0;


 144  Field.dt=0;


 145  end


 146 


 147 


 148 


[179]  149  %% rescale fields to pixel coordinates


[8]  150  if isfield(Field,'pixcmx')


[140]  151  Field.pixcmx=double(Field.pixcmx);


 152  Field.pixcmy=double(Field.pixcmy);


 153  Field.U=Field.U*Field.pixcmx;


 154  Field.V=Field.V*Field.pixcmy;


 155  Field.X=Field.X*Field.pixcmx;


 156  Field.Y=Field.Y*Field.pixcmy;


[8]  157  end


 158  if ~isequal(Field.dt,0)


 159  Field.U=Field.U*Field.dt;%translate in px displacement


 160  Field.V=Field.V*Field.dt;


 161  if isfield(Field,'DjUi')


 162  Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1);


 163  Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2);


 164  Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2);


 165  Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1);


 166  end


 167  end


[179]  168 


 169  %% update list of global attributes


 170  List=Field.ListGlobalAttribute;


 171  ind_remove=[];


 172  for ilist=1:length(List)


 173  switch(List{ilist})


 174  case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}


 175  ind_remove=[ind_remove ilist];


 176  Field=rmfield(Field,List{ilist});


 177  end


 178  end


 179  List(ind_remove)=[];


[221]  180  Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','TimeUnit','CivStage','CoordUnit'}];


[8]  181  Field.CoordUnit='pixel';


 182 


 183 


 184  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


 185  % [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)


 186  %INPUT:


 187  % FieldNames =cell of field names to get, which can contain the strings:


 188  % 'ima_cor': image correlation, vec_c or vec2_C


 189  % 'vort','div','strain': requires velocity derivatives DUDX...


 190  % 'error': error estimate (vec_E or vec2_E)


 191  %


 192  % vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)


 193  % if vel_type=[] or'*', a priority choice, given by vel_type_out{1,2}, is done depending


 194  % if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)


 195 


 196  function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)


 197 


[206]  198  %% default input values


[8]  199  if ~exist('vel_type','var'),vel_type=[];end;


 200  if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed


 201  if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar


 202  if ischar(FieldNames), FieldNames={FieldNames}; end;


 203 


[206]  204  %% select the priority order for automatic vel_type selection


[8]  205  testder=0;


 206  for ilist=1:length(FieldNames)


 207  if ~isempty(FieldNames{ilist})


 208  switch FieldNames{ilist}


 209  case {'vort','div','strain'}


 210  testder=1;


 211  end


 212  end


 213  end


 214  if isempty(vel_type)  isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)


 215  if testder


 216  vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second


 217  vel_type_out{2}='filter1';


 218  else


 219  vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority


 220  vel_type_out{2}='civ1';


 221  end


 222  elseif isequal(vel_type,'filter')


 223  vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second


 224  vel_type_out{2}='filter1';


 225  if ~testder


 226  vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed


 227  end


 228  elseif testder


 229  test_civ1=isequal(vel_type,'civ1')isequal(vel_type,'interp1')isequal(vel_type,'filter1');


 230  if test_civ1


 231  vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives


 232  else


 233  vel_type_out{1}='filter2';


 234  end


 235  else


 236  vel_type_out{1}=vel_type;%imposed velocity field


 237  end


 238  vel_type_out=vel_type_out';


 239 


[206]  240  %% determine names of netcdf variables to read


[8]  241  var={'X','Y','Z','U','V','W','C','F','FF'};


 242  role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};


 243  units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};


 244  if testder


 245  var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];


 246  role=[role {'tensor','tensor','tensor','tensor'}];


 247  units=[units {'pixel','pixel','pixel','pixel'}];


 248  end


 249  for ilist=1:length(vel_type_out)


 250  var=[var;varname1(vel_type_out{ilist},FieldNames)];


 251  end


 252 


[206]  253  %


 254  % determine var names to read


[8]  255  function varin=varname1(vel_type,FieldNames)


[206]  256  %


[8]  257  testder=0;


 258  C1='';


 259  C2='';


 260  for ilist=1:length(FieldNames)


 261  if ~isempty(FieldNames{ilist})


 262  switch FieldNames{ilist}


 263  case 'ima_cor' %image correlation corresponding to a vel vector


 264  C1='vec_C';


 265  C2='vec2_C';


 266  case 'error'


 267  C1='vec_E';


 268  C2='vec2_E';


 269  case {'vort','div','strain'}


 270  testder=1;


 271  end


 272  end


 273  end


 274  switch vel_type


 275  case 'civ1'


 276  varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};


 277  case 'interp1'


 278  varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};


 279  case 'filter1'


 280  varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};


 281  case 'civ2'


 282  varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};


 283  case 'interp2'


 284  varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};


 285  case 'filter2'


 286  varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};


 287  end


 288  if testder


 289  switch vel_type


 290  case 'filter1'


 291  varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];


 292  case 'filter2'


 293  varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];


 294  end


 295  end 
