source: trunk/src/read_civdata.m @ 589

Last change on this file since 589 was 582, checked in by sommeria, 8 years ago

various bugs corrected

File size: 9.3 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
62errormsg='';
63if ischar(FieldNames), FieldNames={FieldNames}; end;
64ProjModeRequest='';
65for ilist=1:length(FieldNames)
66    if ~isempty(FieldNames{ilist})
67        switch FieldNames{ilist}
68            case{'U','V','norm(U,V)'}
69                ProjModeRequest='interp_lin';
70            case {'curl(U,V)','div(U,V)','strain(U,V)'}
71                ProjModeRequest='interp_tps';
72        end
73    end
74end
75
76%% reading data
77Data=nc2struct(filename,'ListGlobalAttribute','CivStage');
78[varlist,role,VelTypeOut]=varcivx_generator(ProjModeRequest,VelType,Data.CivStage);
79if isempty(varlist)
80    erromsg=['error in read_civdata: unknow velocity type ' VelType];
81    return
82else
83    [Field,vardetect]=nc2struct(filename,varlist);%read the variables in the netcdf file
84end
85if isfield(Field,'Txt')
86    errormsg=Field.Txt;
87    return
88end
89if vardetect(1)==0
90     errormsg=[ 'requested field not available in ' filename '/' VelType ': need to run patch'];
91     return
92end
93switch VelTypeOut
94    case{'civ1','filter1'}
95        if isfield(Field,'Patch1_SubDomain')
96            Field.SubDomain=Field.Patch1_SubDomain;
97            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
98        end     
99        Field.Dt=Field.Civ1_Dt;
100        Field.Time=Field.Civ1_Time;
101    case{'civ2','filter2'}
102        if isfield(Field,'Patch2_SubDomain')
103            Field.SubDomain=Field.Patch2_SubDomain;
104            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
105        end
106        Field.Dt=Field.Civ2_Dt;
107        Field.Time=Field.Civ2_Time;
108end
109Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
110ivar_U_tps=[];
111ivar_V_tps=[];
112var_ind=find(vardetect);
113for ivar=1:numel(var_ind)
114    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
115    if strcmp(role{var_ind(ivar)},'vector_x')
116        Field.VarAttribute{ivar}.FieldName=FieldNames;
117        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
118        ivar_U=ivar;
119    end
120    if strcmp(role{var_ind(ivar)},'vector_x_tps')
121        Field.VarAttribute{ivar}.FieldName=FieldNames;
122        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
123        ivar_U_tps=ivar;
124    end
125    if strcmp(role{var_ind(ivar)},'vector_y')
126        Field.VarAttribute{ivar}.FieldName=FieldNames;
127        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
128        ivar_V=ivar;
129    end
130    if strcmp(role{var_ind(ivar)},'vector_y_tps')
131        Field.VarAttribute{ivar}.FieldName=FieldNames;
132        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
133        ivar_V_tps=ivar;
134    end
135    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
136end
137if ~isempty(ivar_U_tps)
138    Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
139end
140if ~isempty(ivar_V_tps)
141    Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
142end
143
144%% update list of global attributes
145Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
146Field.NbCoord=2;
147Field.NbDim=2;
148Field.TimeUnit='s';
149Field.CoordUnit='pixel';
150
151%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
152% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
153%INPUT:
154% FieldNames =cell of field names to get, which can contain the strings:
155%             'ima_cor': image correlation, vec_c or vec2_C
156%             'vort','div','strain': requires velocity derivatives DUDX...
157%             'error': error estimate (vec_E or vec2_E)
158%             
159% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
160%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
161
162function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
163
164%% default input values
165if ~exist('vel_type','var'),vel_type='';end;
166if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
167errormsg='';
168
169%% select the priority order for automatic vel_type selection
170if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
171    vel_type='filter2';
172elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
173    vel_type='filter1';
174end
175if isempty(vel_type)||strcmp(vel_type,'*')
176    switch CivStage
177        case {6} %filter2 available
178            vel_type='filter2';
179        case {4,5}% civ2 available but not filter2
180            if strcmp(ProjModeRequest,'derivatives')% derivatives needed
181                vel_type='filter1';
182            else
183                vel_type='civ2';
184            end
185        case 3
186            vel_type='filter1';
187        case {1,2}% civ1 available but not filter1
188            vel_type='civ1';
189    end
190end
191
192var={};
193switch vel_type
194    case 'civ1'
195        var={'X','Y','Z','U','V','W','C','F','FF';...
196            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
197        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
198    %    units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
199    case 'filter1'
200        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
201            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
202            'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentres','Civ1_NbSites'};
203        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
204            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
205     %  rmq: NbSites obsolete replaced by NbCentres, kept for consistency with previous data
206    case 'civ2'
207        var={'X','Y','Z','U','V','W','C','F','FF';...
208            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
209        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
210    case 'filter2'
211        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
212            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
213            'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentres','Civ2_NbSites'};
214        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
215            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
216end
217if ~strcmp(ProjModeRequest,'interp_tps')
218    var=var(:,1:9);%suppress tps if not needed
219end
220vel_type_out=vel_type;
221
222
223
224
225
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