source: trunk/src/transform_field/phys.m @ 1061

Last change on this file since 1061 was 1061, checked in by g7moreau, 2 years ago
  • Update copyright to year 2019
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1%'phys': transforms image (Unit='pixel') to real world (phys) coordinates using geometric calibration parameters.  It acts if the input field contains the tag 'CoordTUnit' with value 'pixel'
2%------------------------------------------------------------------------
3%%%%  Use the general syntax for transform fields %%%%
4% OUTPUT:
5% DataOut:   output field structure
6%
7%INPUT:
8% DataIn:  first input field structure
9% XmlData: first input parameter structure,
10%        .GeometryCalib: substructure of the calibration parameters
11% DataIn_1: optional second input field structure
12% XmlData_1: optional second input parameter structure
13%         .GeometryCalib: substructure of the calibration parameters
14
15%=======================================================================
16% Copyright 2008-2019, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
17%   http://www.legi.grenoble-inp.fr
18%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
19%
20%     This file is part of the toolbox UVMAT.
21%
22%     UVMAT is free software; you can redistribute it and/or modify
23%     it under the terms of the GNU General Public License as published
24%     by the Free Software Foundation; either version 2 of the license,
25%     or (at your option) any later version.
26%
27%     UVMAT is distributed in the hope that it will be useful,
28%     but WITHOUT ANY WARRANTY; without even the implied warranty of
29%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
30%     GNU General Public License (see LICENSE.txt) for more details.
31%=======================================================================
32
33function DataOut=phys(DataIn,XmlData,DataIn_1,XmlData_1)
34%------------------------------------------------------------------------
35
36% A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'):
37% chercher ListVarAttribute, for each field (cell of variables):
38%   .CoordType: 'phys' or 'px'   (default==phys, no transform)
39%   .scale_factor: =dt (to transform displacement into velocity) default=1
40%   .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor)
41%   (default='coord' if .Role='coord_x,_y...,
42%            'D_i' if '.Role='vector_x,...',
43%              'scalar', else (thenno change except scale factor)
44
45DataOut=[];
46DataOut_1=[]; %default second  output field
47if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
48    if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit')
49        DataOut.CoordUnit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units
50    end
51    return
52end
53
54%% analyse input and set default output
55DataOut=DataIn;%default first output field
56if nargin>=2 % nargin =nbre of input variables
57    if isfield(XmlData,'GeometryCalib')
58        Calib{1}=XmlData.GeometryCalib;
59    else
60        Calib{1}=[];
61    end
62    if nargin>=3  %two input fields
63        DataOut_1=DataIn_1;%default second output field
64        if nargin>=4 && isfield(XmlData_1,'GeometryCalib')
65            Calib{2}=XmlData_1.GeometryCalib;
66        else
67            Calib{2}=Calib{1};
68        end
69    end
70end
71
72%% get the z index defining the section plane
73if isfield(DataIn,'ZIndex')&&~isempty(DataIn.ZIndex)&&~isnan(DataIn.ZIndex)
74    ZIndex=DataIn.ZIndex;
75else
76    ZIndex=1;
77end
78
79%% transform first field
80iscalar=0;% counter of scalar fields
81checktransform=0;
82if  ~isempty(Calib{1})
83    if isfield(Calib{1},'CalibrationType')&& isfield(Calib{1},'CoordUnit') && isfield(DataIn,'CoordUnit')&& strcmp(DataIn.CoordUnit,'pixel')   
84        DataOut=phys_1(DataIn,Calib{1},ZIndex);% transform coordinates and velocity components
85        %case of images or scalar: in case of two input fields, we need to project the transform  on the same regular grid
86        if isfield(DataIn,'A') && isfield(DataIn,'Coord_x') && ~isempty(DataIn.Coord_x) && isfield(DataIn,'Coord_y')&&...
87                ~isempty(DataIn.Coord_y) && length(DataIn.A)>1
88            iscalar=1;
89            A{1}=DataIn.A;
90        end
91        checktransform=1;
92    end
93end
94
95%% document the selected  plane position and angle if relevant
96if  checktransform && isfield(Calib{1},'SliceCoord')&&size(Calib{1}.SliceCoord,1)>=ZIndex
97    DataOut.PlaneCoord=Calib{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex
98    if isfield(Calib{1},'SliceAngle') % transfer the slice rotation angles
99        if isequal(size(Calib{1}.SliceAngle,1),1)% case of a unique angle
100            DataOut.PlaneAngle=Calib{1}.SliceAngle;
101        else  % case of multiple planes with different angles: select the plane with index ZIndex
102            DataOut.PlaneAngle=Calib{1}.SliceAngle(ZIndex,:);
103        end
104    end
105end
106
107%% transform second field if relevant
108checktransform_1=0;
109if ~isempty(DataOut_1)
110    if isfield(DataIn_1,'ZIndex') && ~isequal(DataIn_1.ZIndex,ZIndex)
111        DataOut_1.Txt='different plane indices for the two input fields';
112        return
113    end
114    if isfield(Calib{2},'CalibrationType')&&isfield(Calib{2},'CoordUnit') && isfield(DataIn_1,'CoordUnit')&& strcmp(DataIn_1.CoordUnit,'pixel')
115        DataOut_1=phys_1(DataOut_1,Calib{2},ZIndex);
116        if isfield(Calib{1},'SliceCoord')
117            if ~(isfield(Calib{2},'SliceCoord') && isequal(Calib{2}.SliceCoord,Calib{1}.SliceCoord))
118                DataOut_1.Txt='different plane positions for the two input fields';
119                return
120            end
121            DataOut_1.PlaneCoord=DataOut.PlaneCoord;% same plane position for the two input fields
122            if isfield(Calib{1},'SliceAngle')
123                if ~(isfield(Calib{2},'SliceAngle') && isequal(Calib{2}.SliceAngle,Calib{1}.SliceAngle))
124                    DataOut_1.Txt='different plane angles for the two input fields';
125                    return
126                end
127                DataOut_1.PlaneAngle=DataOut.PlaneAngle; % same plane angle for the two input fields
128            end
129        end
130        if isfield(DataIn_1,'A')&&isfield(DataIn_1,'Coord_x')&&~isempty(DataIn_1.Coord_x) && isfield(DataIn_1,'Coord_y')&&...
131                ~isempty(DataIn_1.Coord_y)&&length(DataIn_1.A)>1
132            iscalar=iscalar+1;
133            Calib{iscalar}=Calib{2};
134            A{iscalar}=DataIn_1.A;
135        end
136        checktransform_1=1;
137    end
138end
139
140%% transform the scalar(s) or image(s)
141if checktransform && iscalar~=0
142    [A,Coord_x,Coord_y]=phys_ima(A,XmlData,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima
143    if iscalar==1 && ~isempty(DataOut_1) % case for which only the second field is a scalar
144         DataOut_1.A=A{1};
145         DataOut_1.Coord_x=Coord_x;
146         DataOut_1.Coord_y=Coord_y;
147    else
148        DataOut.A=A{1};
149        DataOut.Coord_x=Coord_x;
150        DataOut.Coord_y=Coord_y;
151    end
152    if iscalar==2
153        DataOut_1.A=A{2};
154        DataOut_1.Coord_x=Coord_x;
155        DataOut_1.Coord_y=Coord_y;
156    end
157end
158
159% subtract fields
160if ~isempty(DataOut_1)
161    DataOut=sub_field(DataOut,[],DataOut_1);
162end
163%------------------------------------------------
164%--- transform a single field
165function DataOut=phys_1(Data,Calib,ZIndex)
166%------------------------------------------------
167%% set default output
168DataOut=Data;%default
169DataOut.CoordUnit=Calib.CoordUnit;% the output coord unit is set by the calibration parameters
170
171%% transform  X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima)
172if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y)
173  [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex);
174    Dt=1; %default
175    if isfield(Data,'dt')&&~isempty(Data.dt)
176        Dt=Data.dt;
177    end
178    if isfield(Data,'Dt')&&~isempty(Data.Dt)
179        Dt=Data.Dt;
180    end
181    if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V)
182        [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex);
183        [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex);
184        DataOut.U=(XOut_2-XOut_1)/Dt;
185        DataOut.V=(YOut_2-YOut_1)/Dt;
186    end
187end
188
189%% suppress tps
190list_tps={'Coord_tps'  'U_tps'  'V_tps'  'SubRange'  'NbSites'};
191ind_remove=[];
192for ilist=1:numel(list_tps)
193    ind_tps=find(strcmp(list_tps{ilist},Data.ListVarName));
194    if ~isempty(ind_tps)
195        ind_remove=[ind_remove ind_tps];
196        DataOut=rmfield(DataOut,list_tps{ilist});
197    end
198end
199if isfield(DataOut,'VarAttribute') && numel(DataOut.VarAttribute)>=3 && isfield(DataOut.VarAttribute{3},'VarIndex_tps')
200    DataOut.VarAttribute{3}=rmfield(DataOut.VarAttribute{3},'VarIndex_tps');
201end
202if isfield(DataOut,'VarAttribute')&& numel(DataOut.VarAttribute)>=4 && isfield(DataOut.VarAttribute{4},'VarIndex_tps')
203    DataOut.VarAttribute{4}=rmfield(DataOut.VarAttribute{4},'VarIndex_tps');
204end
205if ~isempty(ind_remove)
206    DataOut.ListVarName(ind_remove)=[];
207    DataOut.VarDimName(ind_remove)=[];
208    DataOut.VarAttribute(ind_remove)=[];
209end
210   
211%% transform of spatial derivatives: TODO check the case with plane angles
212if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)
213    % estimate the Jacobian matrix DXpx/DXphys
214    for ip=1:length(Data.X)
215        [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),ZIndex);
216        [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),ZIndex);
217        [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,ZIndex);
218        [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,ZIndex);
219        %Jacobian matrix DXpphys/DXpx
220        DjXi(1,1)=(Xp1-Xm1);
221        DjXi(2,1)=(Yp1-Ym1);
222        DjXi(1,2)=(Xp2-Xm2);
223        DjXi(2,2)=(Yp2-Ym2);
224        DjUi(:,:)=Data.DjUi(ip,:,:);
225        DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
226        DataOut.DjUi(ip,:,:)=DjUi';
227    end
228    DataOut.DjUi =  DataOut.DjUi/Dt;   %     min(Data.DjUi(:,1,1))=DUDX
229end
230
231
232%%%%%%%%%%%%%%%%%%%%
233
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