[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 


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


[206]  50  %% default input


[8]  51  if ~exist('VelType','var')


 52  VelType=[];


 53  end


 54  if isequal(VelType,'*')


 55  VelType=[];


 56  end


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


 58  FieldNames=[]; %default


 59  end


[206]  60 


 61  %% reading data


[8]  62  VelTypeOut=VelType;%default


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


[206]  64  [Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file


 65  if isfield(Field,'Txt')


 66  return


 67  end


[140]  68  if vardetect(1)==0


 69  Field.Txt=[ 'requested field not available in ' filename '/' VelType];


[206]  70  return


[8]  71  end


 72  var_ind=find(vardetect);


 73  for ivar=1:length(var_ind)


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


[206]  75  Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel


[8]  76  end


 77  VelTypeOut=VelType;


 78  if ~isempty(ichoice)


 79  VelTypeOut=vel_type_out_cell{ichoice};


 80  end


 81 


[206]  82  %% adjust for Djui:


[8]  83  if isfield(Field,'DjUi')


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


 85  Field.ListVarName{end}='DjUi';


[156]  86  Field.VarDimName(end2:end)=[];


[8]  87  Field.VarAttribute(end2:end)=[];


 88  end


 89 


[206]  90  %% renaming for standard conventions


[179]  91  Field.NbCoord=Field.nb_coord;


 92  Field.NbDim=Field.nb_dim;


 93 


[206]  94  %% CivStage


[8]  95  if isfield(Field,'patch2')&& isequal(Field.patch2,1)


 96  Field.CivStage=6;


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


 98  Field.CivStage=5;


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


 100  Field.CivStage=4;


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


 102  Field.CivStage=3;


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


 104  Field.CivStage=2;


 105  else


 106  Field.CivStage=1;


 107  end


 108 


[180]  109  %determine the appropriate constant for time and dt for the PIV pair


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


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


 112  Field.Time=0; %default


[221]  113  Field.TimeUnit='s';


[180]  114  if test_civ1


 115  if isfield(Field,'absolut_time_T0')


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


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


 118  else


 119  Field.Txt='the input file is not civx';


 120  Field.CivStage=0;


 121  Field.dt=0;


 122  end


 123  elseif test_civ2


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


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


 126  else


 127  Field.Txt='the input file is not civx';


 128  Field.CivStage=0;


 129  Field.dt=0;


 130  end


 131 


 132 


 133 


[179]  134  %% rescale fields to pixel coordinates


[8]  135  if isfield(Field,'pixcmx')


[140]  136  Field.pixcmx=double(Field.pixcmx);


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


 138  Field.U=Field.U*Field.pixcmx;


 139  Field.V=Field.V*Field.pixcmy;


 140  Field.X=Field.X*Field.pixcmx;


 141  Field.Y=Field.Y*Field.pixcmy;


[8]  142  end


 143  if ~isequal(Field.dt,0)


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


 145  Field.V=Field.V*Field.dt;


 146  if isfield(Field,'DjUi')


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


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


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


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


 151  end


 152  end


[179]  153 


 154  %% update list of global attributes


 155  List=Field.ListGlobalAttribute;


 156  ind_remove=[];


 157  for ilist=1:length(List)


 158  switch(List{ilist})


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


 160  ind_remove=[ind_remove ilist];


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


 162  end


 163  end


 164  List(ind_remove)=[];


[221]  165  Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','TimeUnit','CivStage','CoordUnit'}];


[8]  166  Field.CoordUnit='pixel';


 167 


 168 


 169  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


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


 171  %INPUT:


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


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


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


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


 176  %


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


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


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


 180 


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


 182 


[206]  183  %% default input values


[8]  184  if ~exist('vel_type','var'),vel_type=[];end;


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


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


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


 188 


[206]  189  %% select the priority order for automatic vel_type selection


[8]  190  testder=0;


 191  for ilist=1:length(FieldNames)


 192  if ~isempty(FieldNames{ilist})


 193  switch FieldNames{ilist}


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


 195  testder=1;


 196  end


 197  end


 198  end


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


 200  if testder


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


 202  vel_type_out{2}='filter1';


 203  else


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


 205  vel_type_out{2}='civ1';


 206  end


 207  elseif isequal(vel_type,'filter')


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


 209  vel_type_out{2}='filter1';


 210  if ~testder


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


 212  end


 213  elseif testder


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


 215  if test_civ1


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


 217  else


 218  vel_type_out{1}='filter2';


 219  end


 220  else


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


 222  end


 223  vel_type_out=vel_type_out';


 224 


[206]  225  %% determine names of netcdf variables to read


[8]  226  var={'X','Y','Z','U','V','W','C','F','FF'};


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


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


 229  if testder


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


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


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


 233  end


 234  for ilist=1:length(vel_type_out)


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


 236  end


 237 


[206]  238  %


 239  % determine var names to read


[8]  240  function varin=varname1(vel_type,FieldNames)


[206]  241  %


[8]  242  testder=0;


 243  C1='';


 244  C2='';


 245  for ilist=1:length(FieldNames)


 246  if ~isempty(FieldNames{ilist})


 247  switch FieldNames{ilist}


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


 249  C1='vec_C';


 250  C2='vec2_C';


 251  case 'error'


 252  C1='vec_E';


 253  C2='vec2_E';


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


 255  testder=1;


 256  end


 257  end


 258  end


 259  switch vel_type


 260  case 'civ1'


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


 262  case 'interp1'


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


 264  case 'filter1'


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


 266  case 'civ2'


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


 268  case 'interp2'


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


 270  case 'filter2'


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


 272  end


 273  if testder


 274  switch vel_type


 275  case 'filter1'


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


 277  case 'filter2'


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


 279  end


 280  end 
