Re: [IMP-dev] [IMP-commits] r903 - in trunk/modules/misc: include pyext src test/transformation

29 Nov 2008


      On Nov 29, 2008, at 5:33 PM, Keren Lasker wrote:
> sure Daniel - I would like to update that tomorrow.
> can you work with these classes in the meantime ( for fixing the  
> broken build) ?
The main think breaking the build is in the kernel. Actually, now that  
I think about it, we probably can't use them in anything in core until  
they get moved into the kernel, so we are probably still waiting on  
Ben. Especially since rotation and and all would be part of the  
TransformedPairScore interface.
>
> On Nov 30, 2008, at 3:32 AM, Daniel Russel wrote:
>
>> Couple quick comments:
>> - we are mostly avoiding abbreviations, so get_trans should  
>> probably be "get_translation". It is a bit weird just having that  
>> (and no get_matrix or "get_rotation")
>> - The function on Rotation3D shouldn't be mult (since it isn't  
>> necessarily multiplication as it is not necessarily a matrix).  
>> "transform" taken from Transformation3D or "rotate" are probably  
>> the best options.
>> - I still don't like exposing the various methods on Matrix3D  
>> having to do with rotation. I think they should be hidden (and some  
>> classes made friends if outside classes need them).
>>
>> Otherwise, looks good. THanks.
>>
>> On Nov 29, 2008, at 6:14 PM, Notification of IMP commits wrote:
>>
>>> Author: kerenl@SALILAB.ORG
>>> Date: 2008-11-29 18:14:37 -0800 (Sat, 29 Nov 2008)
>>> New Revision: 903
>>>
>>> Modified:
>>>   trunk/modules/misc/include/Rotation3D.h
>>>   trunk/modules/misc/include/Transformation3D.h
>>>   trunk/modules/misc/pyext/misc.i
>>>   trunk/modules/misc/src/SConscript
>>>   trunk/modules/misc/test/transformation/ 
>>> test_particles_transformation.py
>>>   trunk/modules/misc/test/transformation/ 
>>> test_rigid_transformation.py
>>> Log:
>>> Update interface for Rotation3D class
>>>
>>> Modified: trunk/modules/misc/include/Rotation3D.h
>>> ===================================================================
>>> --- trunk/modules/misc/include/Rotation3D.h	2008-11-29 04:49:09  
>>> UTC (rev 902)
>>> +++ trunk/modules/misc/include/Rotation3D.h	2008-11-30 02:14:37  
>>> UTC (rev 903)
>>> @@ -9,122 +9,98 @@
>>> #define IMPMISC_ROTATION_3D_H
>>>
>>> #include "misc_exports.h"
>>> -
>>> -#include "Matrix3D.h"
>>> +#include "IMP/Vector3D.h"
>>> +#include <iostream>
>>> IMPMISC_BEGIN_NAMESPACE
>>>
>>> //! 3D rotation class.
>>> -/** Holds a 3-dimensional rotation compactly using a quaternions  
>>> (4 numbers).
>>> -    For a given axis and angle, one can easily construct the  
>>> corresponding
>>> -    quaternion, and conversely, for a given quaternion one can  
>>> easily read
>>> -    off the axis and the angle.
>>> -    Another advantage is robustness to rounding errors.
>>> -    The quaternions representation does not harm the performance  
>>> too much.
>>> +/** Holds a three dimensional rotation compactly using a  
>>> quaternion (4 numbers).
>>> +    Advantages using quaternion:
>>> +    1. Easy convertion between axis/angle to quaternion  
>>> reprsentation
>>> +    2. Robustness to rounding errors.
>>> +    3. Is not subject to "Gimbal lock" (i.e. attempts to rotate an
>>> +       object fail to appear as expected, due to the order in  
>>> which the
>>> +       rotations are performed) like Euler angles.
>>> +    4. Can be interpolated
>>> +    5. The quaternions representation does not harm the  
>>> performance too much.
>>> +    http://www.euclideanspace.com/maths/algebra/matrix/orthogonal/rotation/index...
>>> +
>>> +    Currently the rotation can be initialized from either:
>>> +    XYZ Euler angles
>>> +    Rotation Matrix
>>> +    Quaternion
>>> */
>>>
>>> class IMPMISCEXPORT Rotation3D {
>>> public:
>>> -  Rotation3D(){
>>> - }
>>> -  //! Initialize a rotation in x-y-z order from three angles
>>> -  /** \param[in] xr Rotation around the X axis in radians
>>> -      \param[in] yr Rotation around the Y axis in radians
>>> -      \param[in] zr Rotation around the Z axis in radians
>>> -  */
>>> -  Rotation3D(Float xr, Float yr, Float zr) {
>>> -    init_angles(xr,yr,zr);
>>> +  Rotation3D():a_(0.0),b_(0.0),c_(0.0),d_(0.0) {}
>>> +  Rotation3D(Float a, Float b, Float c, Float d){
>>> +    a_=a;b_=b;c_=c;d_=d;
>>>   }
>>> -  //! Initialize a rotation in x-y-z order from three identical  
>>> angles
>>> -  /** \param[in] e_angle Rotation around first the X axis, Y axis  
>>> and Z axis
>>> -                 in radians
>>> -  */
>>> -  Rotation3D(Float e_angle){
>>> -    init_angles(e_angle, e_angle, e_angle);
>>> +    //! Rotation by vector multiplication
>>> +  Vector3D mult(const Vector3D &o) const {
>>> +    return Vector3D((a_*a_+b_*b_-c_*c_-d_*d_)*o[0] +
>>> +                         2*(b_*c_-a_*d_)*o[1] + 2*(b_*d_ 
>>> +a_*c_)*o[2],
>>> +                     2*(b_*c_+a_*d_)*o[0] +
>>> +                         (a_*a_-b_*b_+c_*c_-d_*d_)*o[1] +  
>>> 2*(c_*d_-a_*b_)*o[2],
>>> +                     2*(b_*d_-a_*c_)*o[0] +
>>> +                         2*(c_*d_+a_*b_)*o[1] + (a_*a_-b_*b_-c_*c_ 
>>> +d_*d_)*o[2]);
>>>   }
>>> -  Matrix3D get_matrix() const {
>>> -  const Float a = quat_[0];
>>> -  const Float b = quat_[1];
>>> -  const Float c = quat_[2];
>>> -  const Float d = quat_[3];
>>> -  return Matrix3D(a*a+b*b-c*c-d*d, 2*(b*c-a*d)    , 2*(b*d+a*c),
>>> -                  2*(b*c+a*d)    , a*a-b*b+c*c-d*d, 2*(c*d-a*b),
>>> -                  2*(b*d-a*c)    , 2*(c*d+a*b)    , a*a-b*b-c*c 
>>> +d*d);
>>> +  void show(std::ostream& out = std::cout) const {
>>> +    out <<a_<<"|"<<b_<<"|"<<c_<<"|"<<d_<<'\n';
>>>   }
>>> -  //! Rotation by vector multiplication
>>> -  Vector3D operator*(const Vector3D &o) const {
>>> -  const Float a = quat_[0];
>>> -  const Float b = quat_[1];
>>> -  const Float c = quat_[2];
>>> -  const Float d = quat_[3];
>>> -  return Vector3D((a*a+b*b-c*c-d*d)*o[0] + 2*(b*c-a*d)*o[1] +  
>>> 2*(b*d+a*c)*o[2],
>>> -                  2*(b*c+a*d)*o[0] + (a*a-b*b+c*c-d*d)*o[1] +  
>>> 2*(c*d-a*b)*o[2],
>>> -                  2*(b*d-a*c)*o[0] + 2*(c*d+a*b)*o[1] + (a*a-b*b- 
>>> c*c+d*d)*o[2]);
>>> -  }
>>> -  //! Returns the rotation around the x-axis for a rotational  
>>> matrix assuming
>>> -  //! rotations are performed in the order of x-y-z.
>>> -  Float rotX() const{
>>> -    return atan2(matrix32(), matrix33());
>>> -  }
>>> +private:
>>> +  Float a_,b_,c_,d_;
>>> +};
>>>
>>> -  //! Returns the rotation around the y-axis for a rotational  
>>> matrix assuming
>>> -  //! rotations are performed in the order of x-y-z.
>>> -  Float rotY() const{
>>> -    return atan2(matrix31(), sqrt(sqr(matrix21()) 
>>> +sqr(matrix11())));
>>> -  }
>>>
>>> -  //! Returns the rotation around the z-axis for a rotational  
>>> matrix assuming
>>> -  //! rotations are performed in the order of x-y-z.
>>> -  Float rotZ() const{
>>> -    return atan2(matrix21(), matrix11());
>>> -  }
>>> +//! Initialize a rotation in x-y-z order from three angles
>>> +/** \param[in] xr Rotation around the X axis in radians
>>> +      \param[in] yr Rotation around the Y axis in radians
>>> +      \param[in] zr Rotation around the Z axis in radians
>>> +      \note The three rotations are represented in the original  
>>> (fixed)
>>> +            coordinate frame. http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
>>> +*/
>>> +inline Rotation3D rotation_from_fixed_xyz(Float xr,Float yr,  
>>> Float zr)
>>> +{
>>> +  Float a,b,c,d;
>>> +  Float cx = cos(xr);  Float cy = cos(yr);  Float cz = cos(zr);
>>> +  Float sx = sin(xr);  Float sy = sin(yr);  Float sz = sin(zr);
>>> +  Float m00 = cz*cy;
>>> +  Float m11 = -sy*sx*sz + cx*cz;
>>> +  Float m22 = cy*cx;
>>> +  a = sqrt(1+m00+m11+m22)/2.0;
>>> +  b = sqrt(1+m00-m11-m22)/2.0;
>>> +  c = sqrt(1-m00+m11-m22)/2.0;
>>> +  d = sqrt(1-m00-m11+m22)/2.0;
>>> +  if (cy*sx + sy*cx*sz + sx*cz < 0.0) b = -b;
>>> +  if (sz*sx - sy*cx*cz - sy < 0.0)    c = -c;
>>> +  if (sz*cy + sy*sx*cz + sz*cx < 0.0) d = -d;
>>> +  return Rotation3D(a,b,c,d);
>>> +}
>>>
>>> -private:
>>> -  void init_angles(Float xr, Float yr, Float zr) {
>>> -    Float cx = cos(xr);  Float cy = cos(yr);  Float cz = cos(zr);
>>> -    Float sx = sin(xr);  Float sy = sin(yr);  Float sz = sin(zr);
>>> -    Float m00 = cz*cy;
>>> -    Float m11 = -sy*sx*sz + cx*cz;
>>> -    Float m22 = cy*cx;
>>> -    quat_[0] = sqrt(1+m00+m11+m22)/2.0;
>>> -    quat_[1] = sqrt(1+m00-m11-m22)/2.0;
>>> -    quat_[2] = sqrt(1-m00+m11-m22)/2.0;
>>> -    quat_[3] = sqrt(1-m00-m11+m22)/2.0;
>>> -    if (cy*sx + sy*cx*sz + sx*cz < 0.0) quat_[1] = -quat_[1];
>>> -    if (sz*sx - sy*cx*cz - sy < 0.0)    quat_[2] = -quat_[2];
>>> -    if (sz*cy + sy*sx*cz + sz*cx < 0.0) quat_[3] = -quat_[3];
>>> -  }
>>> +inline Rotation3D rotation_from_mat(Float m11,Float m12,Float m13,
>>> +                                    Float m21,Float m22,Float m23,
>>> +                                    Float m31,Float m32,Float  
>>> m33) {
>>> +  Float a,b,c,d;
>>> +  a = fabs(1+m11+m22+m33)/4;
>>> +  b = fabs(1+m11-m22-m33)/4;
>>> +  c = fabs(1-m11+m22-m33)/4;
>>> +  d = fabs(1-m11-m22+m33)/4;
>>>
>>> -  Float matrix11() const {
>>> -    return sqr(quat_[0]) + sqr(quat_[1]) - sqr(quat_[2]) -  
>>> sqr(quat_[3]);
>>> -  }
>>> -  Float matrix12() const {
>>> -    return 2*(quat_[1]*quat_[2] - quat_[0]*quat_[3]);
>>> -  }
>>> -  Float matrix13()  const{
>>> -    return 2*(quat_[2]*quat_[3] + quat_[0]*quat_[2]);
>>> -  }
>>> -  Float matrix21() const {
>>> -    return 2*(quat_[1]*quat_[2] + quat_[0]*quat_[3]);
>>> -  }
>>> -  Float matrix22() const {
>>> -    return sqr(quat_[0]) - sqr(quat_[1]) + sqr(quat_[2]) -  
>>> sqr(quat_[3]);
>>> -  }
>>> -  Float matrix23() const {
>>> -    return 2*(quat_[2]*quat_[3] - quat_[0]*quat_[1]);
>>> -  }
>>> -  Float matrix31() const {
>>> -    return 2*(quat_[1]*quat_[3] - quat_[0]*quat_[2]);
>>> -  }
>>> -  Float matrix32() const {
>>> -    return 2*(quat_[2]*quat_[3] + quat_[0]*quat_[1]);
>>> -  }
>>> -  Float matrix33() const {
>>> -    return sqr(quat_[0]) - sqr(quat_[1]) - sqr(quat_[2]) +  
>>> sqr(quat_[3]);
>>> -  }
>>> +  // make sure quat is normalized.
>>> +  Float sum = a+b+c+d;
>>> +  a = sqrt(a/sum);
>>> +  b = sqrt(b/sum);
>>> +  c = sqrt(c/sum);
>>> +  d = sqrt(d/sum);
>>>
>>> -private:
>>> -  Float sqr(Float a)const{return a*a;}
>>> -  Float quat_[4];
>>> -};
>>> +  if (m32-m23 < 0.0) b=-b;
>>> +  if (m13-m31 < 0.0) c=-c;
>>> +  if (m21-m12 < 0.0) d=-d;
>>> +}
>>> +/*
>>> +Rotation3D rotation_from_axis_angle(Vector3D axis, Float a){}
>>> +*/
>>> IMPMISC_END_NAMESPACE
>>> #endif  /* IMPMISC_ROTATION_3D_H */
>>>
>>> Modified: trunk/modules/misc/include/Transformation3D.h
>>> ===================================================================
>>> --- trunk/modules/misc/include/Transformation3D.h	2008-11-29  
>>> 04:49:09 UTC (rev 902)
>>> +++ trunk/modules/misc/include/Transformation3D.h	2008-11-30  
>>> 02:14:37 UTC (rev 903)
>>> @@ -23,24 +23,23 @@
>>> public:
>>>   // public for swig
>>>   typedef Transformation3D This;
>>> -  Transformation3D():rot_(1.0),trans_(){
>>> +  Transformation3D():rot_(),trans_(){
>>>   }
>>> -
>>>   Transformation3D(const Rotation3D& r, const Vector3D& t)
>>> -    : rot_(r.get_matrix()), trans_(t){}
>>> +    : rot_(r), trans_(t){}
>>>   //! transform
>>>   Vector3D transform(const Vector3D &o) const {
>>> -    return (rot_ * o) + trans_;
>>> +    return rot_.mult(o) + trans_;
>>>   }
>>>   Vector3D get_trans()const{return trans_;}
>>> -  Matrix3D get_mat()const{return rot_;}
>>> +  //  Matrix3D get_mat()const{return rot_;}
>>>   void show(std::ostream& out = std::cout) const {
>>>     rot_.show(out);
>>>     out<<" || "<<trans_<<"\n";
>>>   }
>>> private:
>>>   Vector3D trans_; //tranlation
>>> -  Matrix3D rot_;  //rotation
>>> +  Rotation3D rot_;  //rotation
>>> };
>>>
>>> IMPMISC_END_NAMESPACE
>>>
>>> Modified: trunk/modules/misc/pyext/misc.i
>>> ===================================================================
>>> --- trunk/modules/misc/pyext/misc.i	2008-11-29 04:49:09 UTC (rev  
>>> 902)
>>> +++ trunk/modules/misc/pyext/misc.i	2008-11-30 02:14:37 UTC (rev  
>>> 903)
>>> @@ -1,11 +1,11 @@
>>> %module(directors="1") IMP_misc
>>>
>>> %{
>>> -#include "IMP/misc.h"
>>> -#include "IMP/core.h"
>>> #include "IMP.h"
>>> +#include "IMP/misc.h"
>>> %}
>>>
>>> +
>>> %include "kernel/pyext/IMP_macros.i"
>>> %include "kernel/pyext/IMP_exceptions.i"
>>>
>>> @@ -17,7 +17,6 @@
>>>
>>> /* Get definitions of kernel base classes (but do not wrap) */
>>> %import "kernel/pyext/IMP.i"
>>> -%import "modules/core/pyext/core.i"
>>>
>>> namespace IMP {
>>>   typedef VectorD<3> Vector3D;
>>> @@ -37,8 +36,6 @@
>>> %include "IMP/misc/RefineOncePairScore.h"
>>> %include "IMP/misc/TunnelSingletonScore.h"
>>> %include "IMP/misc/LowestRefinedPairScore.h"
>>> -%include "IMP/misc/Matrix3D.h"
>>> %include "IMP/misc/Rotation3D.h"
>>> %include "IMP/misc/Transformation3D.h"
>>> -%include "IMP/misc/ParticleFunction.h"
>>> -%include "IMP/misc/TransformationFunction.h"
>>> +%include "IMP/misc/TransformationFunction.h"
>>> \ No newline at end of file
>>>
>>> Modified: trunk/modules/misc/src/SConscript
>>> ===================================================================
>>> --- trunk/modules/misc/src/SConscript	2008-11-29 04:49:09 UTC (rev  
>>> 902)
>>> +++ trunk/modules/misc/src/SConscript	2008-11-30 02:14:37 UTC (rev  
>>> 903)
>>> @@ -4,11 +4,11 @@
>>> files = [
>>>          'ChildrenParticleRefiner.cpp',
>>>          'LowestRefinedPairScore.cpp',
>>> -         'Matrix3D.cpp',
>>>          'RefineOncePairScore.cpp',
>>>          'Rotation3D.cpp',
>>>          'Transformation3D.cpp',
>>>          'TunnelSingletonScore.cpp',
>>> +         'Rotation3D.cpp','Transformation3D.cpp'
>>>         ]
>>>
>>> # Build and install the shared library:
>>>
>>> Modified: trunk/modules/misc/test/transformation/ 
>>> test_particles_transformation.py
>>> ===================================================================
>>> --- trunk/modules/misc/test/transformation/ 
>>> test_particles_transformation.py	2008-11-29 04:49:09 UTC (rev 902)
>>> +++ trunk/modules/misc/test/transformation/ 
>>> test_particles_transformation.py	2008-11-30 02:14:37 UTC (rev 903)
>>> @@ -27,7 +27,8 @@
>>>                                                           
>>> 82.603,46.874,76.53))
>>>     def test_transformation(self):
>>>         """Test the TransformationFunction class"""
>>> -         
>>> t 
>>> = 
>>> IMP 
>>> .misc 
>>> .Transformation3D 
>>> (IMP.misc.Rotation3D(0.2,0.8,-0.4),IMP.Vector3D(20.0,-12.4,18.6))
>>> +        r = IMP.misc.rotation_from_fixed_xyz(0.2,0.8,-0.4)
>>> +         
>>> t=IMP.misc.Transformation3D(r,IMP.Vector3D(20.0,-12.4,18.6))
>>>         tf=IMP.misc.TransformationFunction(t)
>>>         r = tf.apply(self.particles)
>>>         tp=[]
>>>
>>> Modified: trunk/modules/misc/test/transformation/ 
>>> test_rigid_transformation.py
>>> ===================================================================
>>> --- trunk/modules/misc/test/transformation/ 
>>> test_rigid_transformation.py	2008-11-29 04:49:09 UTC (rev 902)
>>> +++ trunk/modules/misc/test/transformation/ 
>>> test_rigid_transformation.py	2008-11-30 02:14:37 UTC (rev 903)
>>> @@ -16,7 +16,8 @@
>>>
>>>     def test_transformation(self):
>>>         """Check that the rotation function is ok"""
>>> -         
>>> t 
>>> = 
>>> IMP 
>>> .misc 
>>> .Transformation3D 
>>> (IMP.misc.Rotation3D(0.2,0.8,-0.4),IMP.Vector3D(20.0,-12.4,18.6))
>>> +        rt = IMP.misc.rotation_from_fixed_xyz(0.2,0.8,-0.4)
>>> +         
>>> t=IMP.misc.Transformation3D(rt,IMP.Vector3D(20.0,-12.4,18.6))
>>>         v1_t = t.transform(self.v1)
>>>         v2_t = t.transform(self.v2)
>>>         v1_t_res=IMP.Vector3D(-62.517,86.209, 41.139)
>>>
>>> _______________________________________________
>>> IMP-commits mailing list
>>> IMP-commits@salilab.org
>>> https://salilab.org/mailman/listinfo/imp-commits
>>
>> _______________________________________________
>> IMP-dev mailing list
>> IMP-dev@salilab.org
>> https://salilab.org/mailman/listinfo/imp-dev
>
> _______________________________________________
> IMP-dev mailing list
> IMP-dev@salilab.org
> https://salilab.org/mailman/listinfo/imp-dev