source: trunk/src/read_civdata.m @ 611

Last change on this file since 611 was 594, checked in by sommeria, 8 years ago

bugs corrected. One step further for using compiled fcts and cluster with series

File size: 9.5 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        if isfield(Field,'Civ1_Dt')
100        Field.Dt=Field.Civ1_Dt;
101        end
102        if isfield(Field,'Civ1_Time')
103        Field.Time=Field.Civ1_Time;
104        end
105    case{'civ2','filter2'}
106        if isfield(Field,'Patch2_SubDomain')
107            Field.SubDomain=Field.Patch2_SubDomain;
108            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
109        end
110        if isfield(Field,'Civ2_Dt')
111        Field.Dt=Field.Civ2_Dt;
112        end
113        if isfield(Field,'Civ2_Time')
114        Field.Time=Field.Civ2_Time;
115        end
116end
117Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
118ivar_U_tps=[];
119ivar_V_tps=[];
120var_ind=find(vardetect);
121for ivar=1:numel(var_ind)
122    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
123    if strcmp(role{var_ind(ivar)},'vector_x')
124        Field.VarAttribute{ivar}.FieldName=FieldNames;
125        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
126        ivar_U=ivar;
127    end
128    if strcmp(role{var_ind(ivar)},'vector_x_tps')
129        Field.VarAttribute{ivar}.FieldName=FieldNames;
130        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
131        ivar_U_tps=ivar;
132    end
133    if strcmp(role{var_ind(ivar)},'vector_y')
134        Field.VarAttribute{ivar}.FieldName=FieldNames;
135        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
136        ivar_V=ivar;
137    end
138    if strcmp(role{var_ind(ivar)},'vector_y_tps')
139        Field.VarAttribute{ivar}.FieldName=FieldNames;
140        Field.VarAttribute{ivar}.ProjModeRequest=ProjModeRequest;
141        ivar_V_tps=ivar;
142    end
143    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
144end
145if ~isempty(ivar_U_tps)
146    Field.VarAttribute{ivar_U}.VarIndex_tps=ivar_U_tps;
147end
148if ~isempty(ivar_V_tps)
149    Field.VarAttribute{ivar_V}.VarIndex_tps=ivar_V_tps;
150end
151
152%% update list of global attributes
153Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
154Field.NbCoord=2;
155Field.NbDim=2;
156Field.TimeUnit='s';
157Field.CoordUnit='pixel';
158
159%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
160% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
161%INPUT:
162% FieldNames =cell of field names to get, which can contain the strings:
163%             'ima_cor': image correlation, vec_c or vec2_C
164%             'vort','div','strain': requires velocity derivatives DUDX...
165%             'error': error estimate (vec_E or vec2_E)
166%             
167% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
168%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
169
170function [var,role,vel_type_out,errormsg]=varcivx_generator(ProjModeRequest,vel_type,CivStage)
171
172%% default input values
173if ~exist('vel_type','var'),vel_type='';end;
174if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
175errormsg='';
176
177%% select the priority order for automatic vel_type selection
178if strcmp(vel_type,'civ2') && strcmp(ProjModeRequest,'derivatives')
179    vel_type='filter2';
180elseif strcmp(vel_type,'civ1') && strcmp(ProjModeRequest,'derivatives')
181    vel_type='filter1';
182end
183if isempty(vel_type)||strcmp(vel_type,'*')
184    switch CivStage
185        case {6} %filter2 available
186            vel_type='filter2';
187        case {4,5}% civ2 available but not filter2
188            if strcmp(ProjModeRequest,'derivatives')% derivatives needed
189                vel_type='filter1';
190            else
191                vel_type='civ2';
192            end
193        case 3
194            vel_type='filter1';
195        case {1,2}% civ1 available but not filter1
196            vel_type='civ1';
197    end
198end
199
200var={};
201switch vel_type
202    case 'civ1'
203        var={'X','Y','Z','U','V','W','C','F','FF';...
204            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
205        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
206    %    units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
207    case 'filter1'
208        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
209            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
210            'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbCentres','Civ1_NbSites'};
211        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
212            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
213     %  rmq: NbSites obsolete replaced by NbCentres, kept for consistency with previous data
214    case 'civ2'
215        var={'X','Y','Z','U','V','W','C','F','FF';...
216            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
217        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
218    case 'filter2'
219        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbCentres','NbCentres';...
220            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
221            'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbCentres','Civ2_NbSites'};
222        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
223            'vector_y_tps','vector_z_tps','ancillary','ancillary','ancillary'};
224end
225if ~strcmp(ProjModeRequest,'interp_tps')
226    var=var(:,1:9);%suppress tps if not needed
227end
228vel_type_out=vel_type;
229
230
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