source: trunk/src/read_civdata.m @ 660

Last change on this file since 660 was 654, checked in by sommeria, 11 years ago

various bugs corrected

File size: 9.9 KB
RevLine 
[237]1%'read_civdata': reads new civ data from netcdf files
2%------------------------------------------------------------------
3%
[613]4% function [Field,VelTypeOut]=read_civdata(FileName,FieldNames,VelType)
[237]5%
6% OUTPUT:
7% Field: structure representing the selected field, containing
8%            .Txt: (char string) error message if any
9%            .ListGlobalAttribute: list of global attributes containing:
10%                    .NbCoord: number of vector components
11%                    .NbDim: number of dimensions (=2 or 3)
[515]12%                    .Dt: time interval for the corresponding image pair
[237]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%
29% VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
30%
31% INPUT:
[613]32% FileName: file name (string).
[237]33% FieldNames =cell of field names to get, which can contain the strings:
34%             'ima_cor': image correlation, vec_c or vec2_C
35%             'vort','div','strain': requires velocity derivatives DUDX...
36%             'error': error estimate (vec_E or vec2_E)
37%             
38% VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
39%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
40%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
41
42
43% FUNCTIONS called:
44% 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
45% 'nc2struct': reads a netcdf file
46
[613]47function [Field,VelTypeOut,errormsg]=read_civdata(FileName,FieldNames,VelType)
[406]48
[237]49%% default input
50if ~exist('VelType','var')
[246]51    VelType='';
[237]52end
53if isequal(VelType,'*')
[246]54    VelType='';
[237]55end
[246]56if isempty(VelType)
57    VelType='';
58end
[237]59if ~exist('FieldNames','var')
60    FieldNames=[]; %default
61end
[613]62Field=[];
63VelTypeOut=VelType;
[406]64errormsg='';
[613]65if ~exist(FileName,'file')
66    errormsg=['input file ' FileName ' does not exist'];
67    return
68end
[515]69if ischar(FieldNames), FieldNames={FieldNames}; end;
[581]70ProjModeRequest='';
[515]71for ilist=1:length(FieldNames)
72    if ~isempty(FieldNames{ilist})
73        switch FieldNames{ilist}
74            case{'U','V','norm(U,V)'}
[654]75                if ~strcmp(FieldNames{1},'vec(U,V)')% if the scalar is not used as color of vectors
[581]76                ProjModeRequest='interp_lin';
[654]77                end
[515]78            case {'curl(U,V)','div(U,V)','strain(U,V)'}
[581]79                ProjModeRequest='interp_tps';
[515]80        end
81    end
82end
[237]83
84%% reading data
[613]85Data=nc2struct(FileName,'ListGlobalAttribute','CivStage');
[612]86if isfield(Data,'Txt')
87     erromsg=['error in read_civdata: ' Data.Txt];
88    return
89end
[581]90[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage);
[406]91if isempty(varlist)
92    erromsg=['error in read_civdata: unknow velocity type ' VelType];
93    return
94else
[613]95    [Field,vardetect]=nc2struct(FileName,varlist);%read the variables in the netcdf file
[406]96end
[237]97if isfield(Field,'Txt')
98    errormsg=Field.Txt;
99    return
100end
101if vardetect(1)==0
[613]102     errormsg=[ 'requested field not available in ' FileName '/' VelType ': need to run patch'];
[237]103     return
104end
[380]105switch VelTypeOut
[494]106    case{'civ1','filter1'}
107        if isfield(Field,'Patch1_SubDomain')
108            Field.SubDomain=Field.Patch1_SubDomain;
109            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
[594]110        end
111        if isfield(Field,'Civ1_Dt')
[380]112        Field.Dt=Field.Civ1_Dt;
[594]113        end
114        if isfield(Field,'Civ1_Time')
[494]115        Field.Time=Field.Civ1_Time;
[594]116        end
[494]117    case{'civ2','filter2'}
118        if isfield(Field,'Patch2_SubDomain')
119            Field.SubDomain=Field.Patch2_SubDomain;
120            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
121        end
[594]122        if isfield(Field,'Civ2_Dt')
[380]123        Field.Dt=Field.Civ2_Dt;
[594]124        end
125        if isfield(Field,'Civ2_Time')
[494]126        Field.Time=Field.Civ2_Time;
[594]127        end
[372]128end
[494]129Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
[515]130ivar_U_tps=[];
[581]131ivar_V_tps=[];
[237]132var_ind=find(vardetect);
[389]133for ivar=1:numel(var_ind)
[237]134    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
[515]135    if strcmp(role{var_ind(ivar)},'vector_x')
[576]136        Field.VarAttribute{ivar}.FieldName=FieldNames;
[581]137        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
[515]138        ivar_U=ivar;
139    end
140    if strcmp(role{var_ind(ivar)},'vector_x_tps')
[576]141        Field.VarAttribute{ivar}.FieldName=FieldNames;
[581]142        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
[515]143        ivar_U_tps=ivar;
144    end
[581]145    if strcmp(role{var_ind(ivar)},'vector_y')
146        Field.VarAttribute{ivar}.FieldName=FieldNames;
147        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
148        ivar_V=ivar;
149    end
150    if strcmp(role{var_ind(ivar)},'vector_y_tps')
151        Field.VarAttribute{ivar}.FieldName=FieldNames;
152        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
153        ivar_V_tps=ivar;
154    end
[237]155    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
156end
[515]157if ~isempty(ivar_U_tps)
158    Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
159end
[581]160if ~isempty(ivar_V_tps)
161    Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
162end
[515]163
[581]164%% update list of global attributes
[237]165Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
166Field.NbCoord=2;
167Field.NbDim=2;
168Field.TimeUnit='s';
169Field.CoordUnit='pixel';
170
171%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
172% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
173%INPUT:
174% FieldNames =cell of field names to get, which can contain the strings:
175%             'ima_cor': image correlation, vec_c or vec2_C
176%             'vort','div','strain': requires velocity derivatives DUDX...
177%             'error': error estimate (vec_E or vec2_E)
178%             
179% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
[380]180%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
[237]181
[581]182function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
[237]183
184%% default input values
[246]185if ~exist('vel_type','var'),vel_type='';end;
[237]186if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
[406]187errormsg='';
[237]188
189%% select the priority order for automatic vel_type selection
[581]190if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
[492]191    vel_type='filter2';
[581]192elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
[492]193    vel_type='filter1';
194end
[406]195if isempty(vel_type)||strcmp(vel_type,'*')
[380]196    switch CivStage
197        case {6} %filter2 available
[492]198            vel_type='filter2';
[380]199        case {4,5}% civ2 available but not filter2
[581]200            if strcmp(ProjModeRequest,'derivatives')% derivatives needed
[492]201                vel_type='filter1';
[380]202            else
203                vel_type='civ2';
204            end
[492]205        case 3
206            vel_type='filter1';
207        case {1,2}% civ1 available but not filter1
[380]208            vel_type='civ1';
209    end
210end
[492]211
[406]212var={};
[246]213switch vel_type
[389]214    case 'civ1'
[492]215        var={'X','Y','Z','U','V','W','C','F','FF';...
216            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
217        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
[515]218    %    units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
[389]219    case 'filter1'
[651]220        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
[389]221            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
[651]222            'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentre','Civ1_NbCentres','Civ1_NbSites'};
[497]223        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
[651]224            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary','ancillary'};
225     %  rmq: NbCentres and NbSites obsolete replaced by NbCentre, kept for consistency with previous data
[389]226    case 'civ2'
[492]227        var={'X','Y','Z','U','V','W','C','F','FF';...
228            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
229        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
[389]230    case 'filter2'
[651]231        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
[389]232            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
[651]233            'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentre','Civ2_NbCentres','Civ2_NbSites'};
[497]234        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
[651]235            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary','ancillary'};
[246]236end
[581]237if ~strcmp(ProjModeRequest,'interp_tps')
[515]238    var=var(:,1:9);%suppress tps if not needed
239end
[380]240vel_type_out=vel_type;
[237]241
242
243
[246]244
245
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