Re: [IMP-dev] [IMP-commits] r903 - in trunk/modules/misc: include pyext src test/transformation
To: List for IMP development <>
Subject: Re: [IMP-dev] [IMP-commits] r903 - in trunk/modules/misc: include pyext src test/transformation
From: Daniel Russel <>
Date: Sat, 29 Nov 2008 18:49:37 -0800
Reply-to: List for IMP development <>
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: "> 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
//! 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.htm + + 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); +}