source: trunk/src/read_civdata.m @ 660

Last change on this file since 660 was 654, checked in by sommeria, 8 years ago

various bugs corrected

File size: 9.9 KB
Line 
1%'read_civdata': reads new civ data from netcdf files
2%------------------------------------------------------------------
3%
4% function [Field,VelTypeOut]=read_civdata(FileName,FieldNames,VelType)
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)
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%
29% VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
30%
31% INPUT:
32% FileName: file name (string).
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
47function [Field,VelTypeOut,errormsg]=read_civdata(FileName,FieldNames,VelType)
48
49%% default input
50if ~exist('VelType','var')
51    VelType='';
52end
53if isequal(VelType,'*')
54    VelType='';
55end
56if isempty(VelType)
57    VelType='';
58end
59if ~exist('FieldNames','var')
60    FieldNames=[]; %default
61end
62Field=[];
63VelTypeOut=VelType;
64errormsg='';
65if ~exist(FileName,'file')
66    errormsg=['input file ' FileName ' does not exist'];
67    return
68end
69if ischar(FieldNames), FieldNames={FieldNames}; end;
70ProjModeRequest='';
71for ilist=1:length(FieldNames)
72    if ~isempty(FieldNames{ilist})
73        switch FieldNames{ilist}
74            case{'U','V','norm(U,V)'}
75                if ~strcmp(FieldNames{1},'vec(U,V)')% if the scalar is not used as color of vectors
76                ProjModeRequest='interp_lin';
77                end
78            case {'curl(U,V)','div(U,V)','strain(U,V)'}
79                ProjModeRequest='interp_tps';
80        end
81    end
82end
83
84%% reading data
85Data=nc2struct(FileName,'ListGlobalAttribute','CivStage');
86if isfield(Data,'Txt')
87     erromsg=['error in read_civdata: ' Data.Txt];
88    return
89end
90[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage);
91if isempty(varlist)
92    erromsg=['error in read_civdata: unknow velocity type ' VelType];
93    return
94else
95    [Field,vardetect]=nc2struct(FileName,varlist);%read the variables in the netcdf file
96end
97if isfield(Field,'Txt')
98    errormsg=Field.Txt;
99    return
100end
101if vardetect(1)==0
102     errormsg=[ 'requested field not available in ' FileName '/' VelType ': need to run patch'];
103     return
104end
105switch VelTypeOut
106    case{'civ1','filter1'}
107        if isfield(Field,'Patch1_SubDomain')
108            Field.SubDomain=Field.Patch1_SubDomain;
109            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
110        end
111        if isfield(Field,'Civ1_Dt')
112        Field.Dt=Field.Civ1_Dt;
113        end
114        if isfield(Field,'Civ1_Time')
115        Field.Time=Field.Civ1_Time;
116        end
117    case{'civ2','filter2'}
118        if isfield(Field,'Patch2_SubDomain')
119            Field.SubDomain=Field.Patch2_SubDomain;
120            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
121        end
122        if isfield(Field,'Civ2_Dt')
123        Field.Dt=Field.Civ2_Dt;
124        end
125        if isfield(Field,'Civ2_Time')
126        Field.Time=Field.Civ2_Time;
127        end
128end
129Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
130ivar_U_tps=[];
131ivar_V_tps=[];
132var_ind=find(vardetect);
133for ivar=1:numel(var_ind)
134    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
135    if strcmp(role{var_ind(ivar)},'vector_x')
136        Field.VarAttribute{ivar}.FieldName=FieldNames;
137        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
138        ivar_U=ivar;
139    end
140    if strcmp(role{var_ind(ivar)},'vector_x_tps')
141        Field.VarAttribute{ivar}.FieldName=FieldNames;
142        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
143        ivar_U_tps=ivar;
144    end
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
155    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
156end
157if ~isempty(ivar_U_tps)
158    Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
159end
160if ~isempty(ivar_V_tps)
161    Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
162end
163
164%% update list of global attributes
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'...)
180%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
181
182function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
183
184%% default input values
185if ~exist('vel_type','var'),vel_type='';end;
186if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
187errormsg='';
188
189%% select the priority order for automatic vel_type selection
190if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
191    vel_type='filter2';
192elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
193    vel_type='filter1';
194end
195if isempty(vel_type)||strcmp(vel_type,'*')
196    switch CivStage
197        case {6} %filter2 available
198            vel_type='filter2';
199        case {4,5}% civ2 available but not filter2
200            if strcmp(ProjModeRequest,'derivatives')% derivatives needed
201                vel_type='filter1';
202            else
203                vel_type='civ2';
204            end
205        case 3
206            vel_type='filter1';
207        case {1,2}% civ1 available but not filter1
208            vel_type='civ1';
209    end
210end
211
212var={};
213switch vel_type
214    case 'civ1'
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'};
218    %    units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
219    case 'filter1'
220        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
221            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
222            'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentre','Civ1_NbCentres','Civ1_NbSites'};
223        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
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
226    case 'civ2'
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'};
230    case 'filter2'
231        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentre','NbCentre','NbCentre';...
232            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
233            'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentre','Civ2_NbCentres','Civ2_NbSites'};
234        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
235            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary','ancillary'};
236end
237if ~strcmp(ProjModeRequest,'interp_tps')
238    var=var(:,1:9);%suppress tps if not needed
239end
240vel_type_out=vel_type;
241
242
243
244
245
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