Description of read

0001 %'read_civxdata': reads civx data from netcdf files
0002 %------------------------------------------------------------------
0003 % COMBINE ET REMPLACE read_ncfield, read_vel et read_scalar_new
0004 %------------------------------------------------------------------
0005 % OUTPUT:
0006 % nb_coord,nb_dim,
0007 % Civ: =0 or 1, indicates whether the data is civ (A SUPPRIMER ?)
0008 % CivStage: =0, ??? A UTILISER POUR REMPLACER civ
0009 %           =1, civ1 has been performed only
0010 %           =2, fix1 has been performed
0011 %           =3, pacth1 has been performed
0012 %           =4, civ2 has been performed
0013 %           =5, fix2 has been performed
0014 %           =6, pacth2 has been performed
0015 % time: absolute time
0016 % Field
0017 %            .Txt: (char string) error message if any
0018 %            .NbDim: number of dimensions (=0 by default)
0019 %            .NbCoord: number of vector components
0020 %            .CoordType: expresses the type of coordinate ('px' for image, 'sig' for instruments, or 'phys')
0021 %            .dt: time interval for the corresponding image pair
0022 %            .CivStage: =0, ??? A UTILISER POUR REMPLACER civ
0023         %           =1, civ1 has been performed only
0024         %           =2, fix1 has been performed
0025         %           =3, pacth1 has been performed
0026         %           =4, civ2 has been performed
0027         %           =5, fix2 has been performed
0028         %           =6, pacth2 has been performed
0029 %            .X, .Y, .Z: set of vector coordinates
0030 %            .U,.V,.W: corresponding set of vector components
0031 %            .F: warning flags
0032 %            .FF: false flag, =0 for good vectors
0033 %            .C: scalar associated with velocity (used for vector colors)
0034 %            .CoordType
0035 %            .DijU; matrix of spatial derivatives (DijU(1,1,:)=DUDX,
0036 %            DijU(1,2,:)=DUDY, Dij(2,1,:)=DVDX, DijU(2,2,:)=DVDY
0037 %            .A, .AX, .AY: additional scalar
0038 % dt:time interval of the image pair red from a single file, or vector with
0039  
0040 % pixcmx,pixcmy: scaling factors (from the first file)
0041 % vel_type_out: string representing the selected velocity type (civ1,civ2,filter1...)
0042 %
0043 % INPUT:
0044 % filename: file name (string).
0045 % FieldNames =cell of field names to get, which can contain the strings:
0046 %             'ima_cor': image correlation, vec_c or vec2_C
0047 %             'vort','div','strain': requires velocity derivatives DUDX...
0048 %             'error': error estimate (vec_E or vec2_E)
0049 %
0050 % VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
0051 %            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
0052 %            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
0053 
0054 
0055 % FUNCTIONS called:
0056 % 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
0057 % 'nc2struct': reads a netcdf file
0058 
0059 function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType)
0060 
0061 if ~exist('VelType','var')
0062     VelType=[];
0063 end
0064 if isequal(VelType,'*')
0065     VelType=[];
0066 end
0067 if ~exist('FieldNames','var') 
0068     FieldNames=[]; %default
0069 end
0070 
0071 VelTypeOut=VelType;%default
0072 [var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
0073 [Field,vardetect,ichoice]=nc2struct(filename,var);
0074 if isfield(Field,'Txt')
0075     return % error in file reading
0076 end
0077 if isequal(vardetect,0)
0078      Field.Txt=[FieldNames ' not accessible in ' filename '/' VelType];
0079      return
0080 end
0081 var_ind=find(vardetect);
0082 for ivar=1:length(var_ind)
0083     Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
0084 %     Field.VarAttribute{ivar}.units=units{var_ind(ivar)};% not necessary: set with calc_field
0085 end
0086 VelTypeOut=VelType;
0087 if ~isempty(ichoice)
0088     VelTypeOut=vel_type_out_cell{ichoice};
0089 end
0090 
0091 %adjust for Djui:
0092 if isfield(Field,'DjUi')
0093     Field.ListVarName(end-2:end)=[];
0094     Field.ListVarName{end}='DjUi';
0095     Field.VarDimIndex(end-2:end)=[];
0096     Field.VarAttribute(end-2:end)=[];
0097 end
0098 
0099 %determine the appropriate constant for time and dt for the PIV pair
0100 test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
0101 test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
0102 if test_civ1
0103     Field.Time=Field.absolut_time_T0;
0104 elseif test_civ2
0105     Field.Time=Field.absolut_time_T0_2;
0106     Field.dt=Field.dt2;
0107 else
0108     Field.Txt='the input file is not civx';
0109     display(Field.Txt)
0110 end
0111 
0112 % CivStage
0113 if isfield(Field,'patch2')&& isequal(Field.patch2,1)
0114     Field.CivStage=6;
0115 elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
0116     Field.CivStage=5;
0117 elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
0118     Field.CivStage=4; 
0119 elseif isfield(Field,'patch')&& isequal(Field.patch,1)
0120     Field.CivStage=3; 
0121 elseif isfield(Field,'fix')&& isequal(Field.fix,1)
0122     Field.CivStage=2;
0123 else
0124     Field.CivStage=1;
0125 end 
0126 
0127 %update list of global attributes
0128 List=Field.ListGlobalAttribute;
0129 ind_remove=[];
0130 for ilist=1:length(List)
0131     switch(List{ilist})
0132         case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2'}
0133             ind_remove=[ind_remove ilist];
0134             Field=rmfield(Field,List{ilist});
0135     end
0136 end
0137 List(ind_remove)=[];
0138 Field.ListGlobalAttribute=[List {'Time','CivStage','CoordUnit'}];
0139 
0140 % rescale to pixel coordiantes
0141 Field.U=Field.U*Field.pixcmx;
0142 Field.V=Field.V*Field.pixcmy;
0143 Field.X=Field.X*Field.pixcmx;
0144 Field.Y=Field.Y*Field.pixcmy; 
0145 if ~isequal(Field.dt,0)
0146     Field.U=Field.U*Field.dt;%translate in px displacement
0147     Field.V=Field.V*Field.dt;
0148     if isfield(Field,'DjUi')
0149        Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1);
0150        Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2);
0151        Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2);
0152        Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1);
0153     end
0154 end
0155 Field.CoordType='px';% TODO: abandon, use COORdUnit instead ? (to adapt 'px' and 'phys')
0156 Field.CoordUnit='pixel';
0157 
0158 
0159 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0160 % [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
0161 %INPUT:
0162 % FieldNames =cell of field names to get, which can contain the strings:
0163 %             'ima_cor': image correlation, vec_c or vec2_C
0164 %             'vort','div','strain': requires velocity derivatives DUDX...
0165 %             'error': error estimate (vec_E or vec2_E)
0166 %
0167 % vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
0168 %            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
0169 %            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
0170 
0171 function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type) 
0172 
0173 %default input values
0174 if ~exist('vel_type','var'),vel_type=[];end;
0175 if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
0176 % if ~exist('display','var'),display=[];end;
0177 if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
0178 if ischar(FieldNames), FieldNames={FieldNames}; end;
0179 
0180 %select the priority order for automatic vel_type selection
0181 testder=0;
0182 for ilist=1:length(FieldNames)
0183     if ~isempty(FieldNames{ilist})
0184     switch FieldNames{ilist}
0185         case {'vort','div','strain'}
0186             testder=1;
0187     end
0188     end
0189 end      
0190 if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)
0191     if testder
0192          vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
0193         vel_type_out{2}='filter1';
0194     else
0195         vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority
0196         vel_type_out{2}='civ1';
0197     end
0198 elseif isequal(vel_type,'filter')
0199         vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
0200         vel_type_out{2}='filter1';
0201         if ~testder
0202             vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed
0203         end
0204 elseif testder
0205     test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1');
0206     if test_civ1
0207         vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives
0208     else
0209         vel_type_out{1}='filter2';
0210     end
0211 else   
0212     vel_type_out{1}=vel_type;%imposed velocity field
0213 end
0214 vel_type_out=vel_type_out';
0215 
0216 %determine names of netcdf variables to read
0217 var={'X','Y','Z','U','V','W','C','F','FF'};
0218 role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
0219 units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
0220 if testder
0221     var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];
0222     role=[role {'tensor','tensor','tensor','tensor'}];
0223     units=[units {'pixel','pixel','pixel','pixel'}];
0224 end
0225 for ilist=1:length(vel_type_out)
0226     var=[var;varname1(vel_type_out{ilist},FieldNames)];
0227 end
0228 
0229   
0230 %-------------------------
0231 %determine  var names to read
0232 %--------------------------------------
0233 function varin=varname1(vel_type,FieldNames)
0234 
0235 testder=0;
0236 C1='';
0237 C2='';
0238 for ilist=1:length(FieldNames)
0239     if ~isempty(FieldNames{ilist})
0240     switch FieldNames{ilist}
0241         case 'ima_cor' %image correlation corresponding to a vel vector
0242             C1='vec_C';
0243             C2='vec2_C';
0244         case 'error'
0245             C1='vec_E';
0246             C2='vec2_E';
0247         case {'vort','div','strain'}
0248             testder=1;
0249     end
0250     end
0251 end      
0252 switch vel_type
0253     case 'civ1'
0254         varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};
0255     case 'interp1'
0256         varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};
0257     case 'filter1'
0258         varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};
0259     case 'civ2'
0260         varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};
0261     case 'interp2'
0262         varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};
0263     case 'filter2'
0264         varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};
0265 end
0266 if testder
0267      switch vel_type
0268         case 'filter1'
0269             varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];
0270         case 'filter2'
0271             varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];
0272     end   
0273 end
read_civxdata

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SOURCE CODE
