On Nov 12, 2008, at 7:15 PM, Javier Ángel Velázquez Muriel wrote:

I don't like the convention x-y-z for the Euler angles and we
absolutely need to be consistent around IMP about them or enforce
clear specification. The most used one in EM by far is ZYZ and the one
that I am going to use.

Javi

2008/11/12 <imp-dev-request@salilab.org>:
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Today's Topics:

1. Re: [IMP-commits] r854 - trunk/modules/misc/include
    (Dina Schneidman)
2. Re: [IMP-commits] r854 - trunk/modules/misc/include
    (Daniel Russel)
3. Re: 2D geometry ( Javier ?ngel Vel?zquez Muriel )
4. Re: 2D geometry ( Javier ?ngel Vel?zquez Muriel )
5. Re: 2D geometry (Daniel Russel)
6. Re: 2D geometry (Daniel Russel)
7. Re: 2D geometry (Keren Lasker)

----------------------------------------------------------------------

Message: 1
Date: Wed, 12 Nov 2008 15:59:13 -0800
From: "Dina Schneidman" <duhovka@gmail.com>
Subject: Re: [IMP-dev] [IMP-commits] r854 - trunk/modules/misc/include
To: "List for IMP development" <imp-dev@salilab.org>
Message-ID:
      <55d63ce50811121559p4995f334kf9e9c1247f21d35f@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

I think these are Euler angles.
http://www.euclideanspace.com/maths/algebra/matrix/orthogonal/rotation/index.htm
Daniel, I agree that conceptually it is wrong to store them in Vector3D, but
it is very convenient in practice.

On Wed, Nov 12, 2008 at 10:33 PM, Keren Lasker <kerenl@salilab.org> wrote:

Daniel - the angles are not Euler angles but just three angles around
X/Y/Z axis.
Would you like the option to rotate around another axis, ,something
like:
(1,1,0),45 - meaning rotating around the diagonal of the XY plane in
45 degrees?
On Nov 12, 2008, at 5:43 PM, Daniel Russel wrote:

I don't like having two equivalent constructors from thevsame data or
using a vector to hold angles.

What I had meant with my suggestion is initialization from an axis and
an amount of rotation about that axis as that is a somewhat less
problematic basis than Euler angles (and one I use :-)

On Nov 12, 2008, at 2:31 PM, Notification of IMP commits <
imp-commits@salilab.org
wrote:

Author: kerenl@SALILAB.ORG
Date: 2008-11-12 14:31:59 -0800 (Wed, 12 Nov 2008)
New Revision: 854

Modified:
trunk/modules/misc/include/Rotation3D.h
Log:
1. Change protected to private
2. Add constructors from Vector3D and an angle
3. update documentation

Modified: trunk/modules/misc/include/Rotation3D.h
===================================================================
--- trunk/modules/misc/include/Rotation3D.h    2008-11-12 21:15:36
UTC (rev 853)
+++ trunk/modules/misc/include/Rotation3D.h    2008-11-12 22:31:59
UTC (rev 854)
@@ -19,26 +19,28 @@

class IMPMISCEXPORT Rotation3D {
public:
- //! Initialize a rotation in x-y-z order from three angles
+ Rotation3D(){
+ }
+ //! Initialize a rotation in x-y-z order from three Euler angles
/** \param[in] xr Rotation around the X axis
    \param[in] yr Rotation around the Y axis
    \param[in] zr Rotation around the Z axis
*/
Rotation3D(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];
+    init_angles(xr,yr,zr);
}
-
+ //! Initialize a rotation in x-y-z order from three identical
Euler angles
+ /** \param[in] e_angle Rotation around first the X axis, Y axis
and Z axis
+ */
+ Rotation3D(Float e_angle){
+    init_angles(e_angle, e_angle, e_angle);
+ }
+ //! Initialize a rotation in x-y-z order from three Euler angles
+ /** \param[in] v A vector that holds three Euler angles (x-y-z
order)
+ */
+ Rotation3D(const Vector3D &v){
+    init_angles(v[0],v[1],v[2]);
+ }
Matrix3D get_matrix() const {
const Float a = quat_[0];
const Float b = quat_[1];
@@ -76,7 +78,22 @@
  return atan2(matrix21(), matrix11());
}

-protected:
+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];
+ }
+
Float matrix11() const {
  return sqr(quat_[0]) + sqr(quat_[1]) - sqr(quat_[2]) -
sqr(quat_[3]);
}

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Message: 2
Date: Wed, 12 Nov 2008 15:59:26 -0800
From: Daniel Russel <drussel@gmail.com>
Subject: Re: [IMP-dev] [IMP-commits] r854 - trunk/modules/misc/include
To: List for IMP development <imp-dev@salilab.org>
Message-ID: <9A27C079-74F3-4390-89F3-0630AEF130B7@gmail.com>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

look at the latest version of Rotation3D class - I added some
documentation on quaternions
Sure, but why do we support construction from the (possibly) Euler
angles at all?

------------------------------

Message: 3
Date: Wed, 12 Nov 2008 16:02:23 -0800
From: " Javier ?ngel Vel?zquez Muriel " <javi@salilab.org>
Subject: Re: [IMP-dev] 2D geometry
To: "Daniel Russel" <drussel@gmail.com>
Cc: List for IMP development <imp-dev@salilab.org>,
      embed-dev@salilab.org
Message-ID:
      <598e2cdc0811121602h32663187m52e14c51e0243e4a@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

2008/11/12 Daniel Russel <drussel@gmail.com>:
Or vector and matrix can be replaced by a single version templated on the
dimension. We definitely don't want separate code bases for the 2 and 3D
versions as it will be a pain to keep the set of operations in sync.

On Nov 12, 2008, at 10:50 PM, Keren Lasker wrote:

Javi,

For your 2D geometry classes (Vector2D, Matrix2D ...) - why not just
using the corresponding 3D classes and keeping Z fixed?
I think it is not too bad in performance and will save you a lot of
coding/debugging time.

Keren.
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------------------------------

Message: 4
Date: Wed, 12 Nov 2008 16:02:42 -0800
From: " Javier ?ngel Vel?zquez Muriel " <javi@salilab.org>
Subject: Re: [IMP-dev] 2D geometry
To: "Daniel Russel" <drussel@gmail.com>
Cc: List for IMP development <imp-dev@salilab.org>,
      embed-dev@salilab.org
Message-ID:
      <598e2cdc0811121602y4cacb332t7603c6b3f0bc519a@mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

- Vector2D is already done but I am fine with changes
- I am building a templated version of matrix for 1,2,3D. I didn't
know about matrix3d until yesterday
- Images are going to be 2D matrices and header.

2008/11/12 Daniel Russel <drussel@gmail.com>:
Or vector and matrix can be replaced by a single version templated on the
dimension. We definitely don't want separate code bases for the 2 and 3D
versions as it will be a pain to keep the set of operations in sync.

On Nov 12, 2008, at 10:50 PM, Keren Lasker wrote:

Javi,

For your 2D geometry classes (Vector2D, Matrix2D ...) - why not just
using the corresponding 3D classes and keeping Z fixed?
I think it is not too bad in performance and will save you a lot of
coding/debugging time.

Keren.
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------------------------------

Message: 5
Date: Wed, 12 Nov 2008 16:04:22 -0800
From: Daniel Russel <drussel@gmail.com>
Subject: Re: [IMP-dev] 2D geometry
To: "Javier ?ngel Vel?zquez-Muriel"     <javi.velazquez@gmail.com>
Cc: List for IMP development <imp-dev@salilab.org>,
      embed-dev@salilab.org
Message-ID: <15ADFC5D-2B21-4120-ABD2-87357AEB2FA0@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes

On Nov 12, 2008, at 3:58 PM, Javier ?ngel Vel?zquez-Muriel wrote:

- Vector2D is already done but I am fine with changes
Lets make a unified ND vector. I have wanted 4D a bunch of times.

- I am building a templated version of matrix for 1,2,3D. I didn't
know about matrix3d until yesterday
If you want nice constructors (from lists of values) you can use the
boost static assert functionality to make sure, at compile time, that
the correct constructor is called for the correct dimensional vector/
matrix.

- Images are going to be 2D matrices and header.
BTW, have you looked at Boost.GIL? It is a general C++ image library
in boost (which we are already linked against, in theory).

2008/11/12 Daniel Russel <drussel@gmail.com>:
Or vector and matrix can be replaced by a single version templated
on the
dimension. We definitely don't want separate code bases for the 2
and 3D
versions as it will be a pain to keep the set of operations in sync.

On Nov 12, 2008, at 10:50 PM, Keren Lasker wrote:

Javi,

For your 2D geometry classes (Vector2D, Matrix2D ...) - why not just
using the corresponding 3D classes and keeping Z fixed?
I think it is not too bad in performance and will save you a lot of
coding/debugging time.

Keren.
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------------------------------

Message: 6
Date: Wed, 12 Nov 2008 16:05:45 -0800
From: Daniel Russel <drussel@gmail.com>
Subject: Re: [IMP-dev] 2D geometry
To: "Javier ?ngel Vel?zquez Muriel" <javi@salilab.org>
Cc: List for IMP development <imp-dev@salilab.org>,
      embed-dev@salilab.org
Message-ID: <63DCF487-8D99-4325-A604-DC4EBF6E352D@gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes

I can templatize the current Vector3D tonight (actually, I had already
done so a while ago, so I just have to resuscitate it).

On Nov 12, 2008, at 4:02 PM, Javier ?ngel Vel?zquez Muriel wrote:

- Vector2D is already done but I am fine with changes
- I am building a templated version of matrix for 1,2,3D. I didn't
know about matrix3d until yesterday
- Images are going to be 2D matrices and header.

2008/11/12 Daniel Russel <drussel@gmail.com>:
Or vector and matrix can be replaced by a single version templated
on the
dimension. We definitely don't want separate code bases for the 2
and 3D
versions as it will be a pain to keep the set of operations in sync.

On Nov 12, 2008, at 10:50 PM, Keren Lasker wrote:

Javi,

For your 2D geometry classes (Vector2D, Matrix2D ...) - why not just
using the corresponding 3D classes and keeping Z fixed?
I think it is not too bad in performance and will save you a lot of
coding/debugging time.

Keren.
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https://salilab.org/mailman/listinfo/imp-dev

------------------------------

Message: 7
Date: Thu, 13 Nov 2008 02:08:34 -0500
From: Keren Lasker <kerenl@salilab.org>
Subject: Re: [IMP-dev] 2D geometry
To: List for IMP development <imp-dev@salilab.org>
Cc: "Javier ?ngel Vel?zquez Muriel"     <javi@salilab.org>,
      embed-dev@salilab.org
Message-ID: <CE87CC11-878D-4882-87EC-4CFD1F47106A@salilab.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes

sounds good !
Lets decide on an interface for the geometry classes.
Ben's Vector3D is a very good start.
I'll update the 3D geometry classes accordingly.
Javi - do you have any specific needs for the geometry classes or just
the basic needs? Maybe you can send your header file so Daniel can
take it into account writing the VectorD?
On Nov 12, 2008, at 7:05 PM, Daniel Russel wrote:

I can templatize the current Vector3D tonight (actually, I had already
done so a while ago, so I just have to resuscitate it).

On Nov 12, 2008, at 4:02 PM, Javier ?ngel Vel?zquez Muriel wrote:

- Vector2D is already done but I am fine with changes
- I am building a templated version of matrix for 1,2,3D. I didn't
know about matrix3d until yesterday
- Images are going to be 2D matrices and header.

2008/11/12 Daniel Russel <drussel@gmail.com>:
Or vector and matrix can be replaced by a single version templated
on the
dimension. We definitely don't want separate code bases for the 2
and 3D
versions as it will be a pain to keep the set of operations in sync.

On Nov 12, 2008, at 10:50 PM, Keren Lasker wrote:

Javi,

For your 2D geometry classes (Vector2D, Matrix2D ...) - why not
just
using the corresponding 3D classes and keeping Z fixed?
I think it is not too bad in performance and will save you a lot of
coding/debugging time.

Keren.
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