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Re: [Imgcif-l] Goniometer axis question

Dear Herbert,

I have just made a clean installation of everything with your 0.9.2.2 version and I got sensible 2-theta offsets. Now working with Ralf W G K to update the version bundled in cctbx. It seems that when I tried to install a newer version over the top it did not work!

D'oh.

Best wishes,

Graeme

-----Original Message-----
From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Herbert J. Bernstein
Sent: 05 July 2011 14:53
To: The Crystallographic Binary File and its imgCIF application to image data
Subject: Re: [Imgcif-l] Goniometer axis question

Thanks -- Herbert

=====================================================
  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  +1-631-244-3035
                  yaya@dowling.edu
=====================================================

On Tue, 5 Jul 2011, Graeme.Winter@Diamond.ac.uk wrote:

> It seems that in fact I do not attach it, as the list does not allow attachments.
>
> It can be found at
>
> http://www.ccp4.ac.uk/xia/2t_header.cbf
>
> Best wishes,
>
> Graeme
>
> -----Original Message-----
> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Graeme.Winter@Diamond.ac.uk
> Sent: 05 July 2011 13:55
> To: imgcif-l@iucr.org
> Subject: Re: [Imgcif-l] Goniometer axis question
>
> Dear Herbert,
>
> I attach the CIF header, which I have been using with pycbf.
>
> Best wishes,
>
> Graeme
>
> -----Original Message-----
> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On Behalf Of Herbert J. Bernstein
> Sent: 05 July 2011 13:14
> To: The Crystallographic Binary File and its imgCIF application to image data
> Subject: Re: [Imgcif-l] Goniometer axis question
>
> Dear Graeme,
>
>   Strange.  I'll take a look.
>
>   Herbert
>
>
> =====================================================
>  Herbert J. Bernstein, Professor of Computer Science
>    Dowling College, Kramer Science Center, KSC 121
>         Idle Hour Blvd, Oakdale, NY, 11769
>
>                  +1-631-244-3035
>                  yaya@dowling.edu
> =====================================================
>
> On Tue, 5 Jul 2011, Graeme.Winter@Diamond.ac.uk wrote:
>
>> Dear Herbert,
>>
>> I have stumbled across what may be either a more significant problem
>> in the library or a more substantial error on my part: I am attempting
>> to introduce a two-theta offset into the detector arm.
>>
>> The axes are defined:
>>
>> # category DIFFRN_DETECTOR
>> loop_
>> _diffrn_detector.diffrn_id
>> _diffrn_detector.id
>> _diffrn_detector.type
>> _diffrn_detector.number_of_axes
>> DLS_I04-1 i04-1-p2m 'Pilatus2M' 4
>>
>> loop_
>> _diffrn_detector_axis.detector_id
>> _diffrn_detector_axis.axis_id
>> i04-1-p2m DETECTOR_2T
>> i04-1-p2m DETECTOR_X
>> i04-1-p2m DETECTOR_Y
>> i04-1-p2m DETECTOR_Z
>>
>> loop_
>> _axis.id
>> _axis.type
>> _axis.equipment
>> _axis.depends_on
>> _axis.vector[1] _axis.vector[2] _axis.vector[3] _axis.offset[1]
>> _axis.offset[2] _axis.offset[3] GONIOMETER_FRED  rotation goniometer .
>> 0.643 -0.766 0 . . .
>> GONIOMETER_OMEGA rotation goniometer GONIOMETER_FRED 1 0 0 . . .
>> SOURCE           general source . 0 0 1 . . .
>> GRAVITY          general gravity . 0 -1 0 . . .
>> DETECTOR_2T      rotation    detector . 1 0 0 0 0 0
>> DETECTOR_Z       translation detector DETECTOR_2T 0 0 -1 0 0 0
>> DETECTOR_Y       translation detector DETECTOR_Z 0 1 0 0 0 0
>> DETECTOR_X       translation detector DETECTOR_Y 1 0 0 0 0 0
>> ELEMENT_X        translation detector DETECTOR_X 1 0 0 -126.30 144.39 0
>> ELEMENT_Y        translation detector ELEMENT_X 0 1 0 0 0 0
>>
>> loop_
>> _diffrn_scan_frame_axis.frame_id
>> _diffrn_scan_frame_axis.axis_id
>> _diffrn_scan_frame_axis.angle
>> _diffrn_scan_frame_axis.displacement
>> FRAME1 GONIOMETER_FRED  30.0 0.0
>> FRAME1 GONIOMETER_OMEGA 24.4499 0.0
>> FRAME1 DETECTOR_2T 30.0 0.0
>> FRAME1 DETECTOR_Z 0.0 800.02
>> FRAME1 DETECTOR_Y 0.0 0.0
>> FRAME1 DETECTOR_X 0.0 0.0
>>
>> loop_
>> _diffrn_scan_axis.scan_id
>> _diffrn_scan_axis.axis_id
>> _diffrn_scan_axis.angle_start
>> _diffrn_scan_axis.angle_range
>> _diffrn_scan_axis.angle_increment
>> _diffrn_scan_axis.displacement_start
>> _diffrn_scan_axis.displacement_range
>> _diffrn_scan_axis.displacement_increment
>> SCAN1 GONIOMETER_FRED  30.0000 0.0 0.0 0.0 0.0 0.0
>> SCAN1 GONIOMETER_OMEGA 24.4499 0.0500 0.0500 0.0 0.0 0.0
>> SCAN1 DETECTOR_2T 30.0 0.0 0.0 0.0 0.0 0.0
>> SCAN1 DETECTOR_Z 0.0 0.0 0.0 800.02 0.0 0.0
>> SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.0 0.0 0.0
>> SCAN1 DETECTOR_X 0.0 0.0 0.0 0.0 0.0 0.0
>>
>> So, as well as I can tell it I should have introduced a two-theta
>> rotation (i.e. about 1 0 0) of 30 degrees, which should introduce a
>> change to the direction of the detector normal and the detector slow
>> axis. However, I do not see this when I ask for
>> detector.get_detector_normal() etc. - they are still aligned with 1 0
>> 0 and 0 1 0.
>>
>> Now I looked through the code and it does look as if all of the
>> correct translations & rotations should have been calculated (there is
>> complicated code buried in there with no FIXME type comments) so I
>> suspect I have made a typographical error. However I can see no easy
>> way to verify this or understand where this error has been made.
>>
>> Can you see what I have done wrong?
>>
>> Many thanks,
>>
>> Graeme
>>
>>
>> -----Original Message-----
>> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
>> Behalf Of Herbert J. Bernstein
>> Sent: 04 July 2011 14:18
>> To: The Crystallographic Binary File and its imgCIF application to
>> image data
>> Subject: Re: [Imgcif-l] Goniometer axis question
>>
>> Looks good. -- Herbert
>>
>> =====================================================
>>  Herbert J. Bernstein, Professor of Computer Science
>>    Dowling College, Kramer Science Center, KSC 121
>>         Idle Hour Blvd, Oakdale, NY, 11769
>>
>>                  +1-631-244-3035
>>                  yaya@dowling.edu
>> =====================================================
>>
>> On Mon, 4 Jul 2011, Graeme.Winter@Diamond.ac.uk wrote:
>>
>>> Dear Herbert,
>>>
>>> Sorry, I was vague. I meant that as a list of axes - i.e. 3x3
>>> identity matrix columns. So if I rotate the identity to the start and
>>> the end, compute the matrix from the start to the end this should
>>> give me the axis about which the scan was performed. This does of
>>> course assume that there was a single axis about which the scan was
>>> performed, which could be incorrect (though for diffraction
>>> experiments would be unusual)
>>>
>>> I have the python code for this here:
>>>
>>> def determine_effective_scan_axis(gonio):
>>>    x = gonio.rotate_vector(0.0, 1, 0, 0)
>>>    y = gonio.rotate_vector(0.0, 0, 1, 0)
>>>    z = gonio.rotate_vector(0.0, 0, 0, 1)
>>>
>>>    R = matrix.rec(x + y + z, (3, 3)).transpose()
>>>
>>>    x1 = gonio.rotate_vector(1.0, 1, 0, 0)
>>>    y1 = gonio.rotate_vector(1.0, 0, 1, 0)
>>>    z1 = gonio.rotate_vector(1.0, 0, 0, 1)
>>>
>>>    R1 = matrix.rec(x1 + y1 + z1, (3, 3)).transpose()
>>>
>>>    RA = R1 * R.inverse()
>>>
>>>    rot = r3_rotation_axis_and_angle_from_matrix(RA)
>>>
>>>    return rot.axis
>>>
>>> where
>>>
>>>    gonio = cbf_handle.construct_goniometer()
>>>
>>> and I am making extensive use of cctbx matrix functionality. However the only fiddly bit is getting the axis from the matrix.
>>>
>>> Best wishes,
>>>
>>> Graeme
>>>
>>> -----Original Message-----
>>> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
>>> Behalf Of Herbert J. Bernstein
>>> Sent: 04 July 2011 14:03
>>> To: The Crystallographic Binary File and its imgCIF application to
>>> image data
>>> Subject: Re: [Imgcif-l] Goniometer axis question
>>>
>>> That sounds sensible except in the strange case that (i,j,k) happens
>>> to be the axis of rotation -- not likely.
>>>
>>> =====================================================
>>>  Herbert J. Bernstein, Professor of Computer Science
>>>    Dowling College, Kramer Science Center, KSC 121
>>>         Idle Hour Blvd, Oakdale, NY, 11769
>>>
>>>                  +1-631-244-3035
>>>                  yaya@dowling.edu
>>> =====================================================
>>>
>>> On Mon, 4 Jul 2011, Graeme.Winter@Diamond.ac.uk wrote:
>>>
>>>> Dear Herbert,
>>>>
>>>> I found that this does indeed work - though there is the additional complication that the rotation axis may be (1, 0, 0) but there are other goniometer components which have been rotated, for example kappa or phi for a kappa gonio performing an omega scan.
>>>>
>>>> So, what I ended up coding was something along these lines:
>>>>
>>>>  Use cbf_rotate_vector on (i, j, k) -> generate rotation at start of
>>>> frame (0.0)  Use cbf_rotate_vector on (i, j, k) -> generate rotation
>>>> at end of frame (1.0)  Compute rotation performed as B = RA => R =
>>>> BA^-1  Decompose this to a rotation axis and angle
>>>>
>>>> Which appears to give the "right" result, from a known axis, and should be general as fixed rotations connected to the rotation axis would cancel out. CCTBX includes handy python code to do all of this. I expect that there are more efficient mechanisms to do this, however they would require properly reconstructing the goniometer and paying attention to the axes which are being used to perform the scan.
>>>>
>>>> Best wishes,
>>>>
>>>> Graeme
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org]
>>>> On Behalf Of Herbert J. Bernstein
>>>> Sent: 04 July 2011 12:32
>>>> To: The Crystallographic Binary File and its imgCIF application to
>>>> image data
>>>> Subject: Re: [Imgcif-l] Goniometer axis question
>>>>
>>>> Clearly a bug (incomplete implementation)
>>>>
>>>> Have you tried constructing a goniometer and then applying
>>>> cbf_rotate_vector to [1,0,0]?  That sounds like what we really want
>>>> cbf_get_rotation_axis to do.
>>>>
>>>> I'll cobble together a fix with two new routine names, one to return
>>>> the reference setting of the nth axis in a chain of axes in a
>>>> goniometer, and one to return the current setting.
>>>>
>>>> Let's say:
>>>>
>>>>   cbf_get_reference_goinimeter_axis(cbf_goniometer goniometer,
>>>>       unsigned int  reserved,
>>>>       int axis_number,
>>>>       double  *vector1,
>>>>       double  *vector2,
>>>>       double  *vector3)
>>>>
>>>>   cbf_get_goinimeter_axis(cbf_goniometer goniometer,
>>>>       unsigned int  reserved,
>>>>       int axis_number,
>>>>       double  *vector1,
>>>>       double  *vector2,
>>>>       double  *vector3)
>>>>
>>>> where axis number, starting from 1 is the axis number counting down
>>>> the chain (most deeply nested axis first) and, if negative, is
>>>> counting up the chain (with the base axis having axis number -1, the
>>>> axis on top of that having axis number -2, etc.).  I know that
>>>> sounds backwards, but I think it will make the common default of 1
>>>> give you the axis you are most likely to really want.
>>>>
>>>> =====================================================
>>>>  Herbert J. Bernstein, Professor of Computer Science
>>>>    Dowling College, Kramer Science Center, KSC 121
>>>>         Idle Hour Blvd, Oakdale, NY, 11769
>>>>
>>>>                  +1-631-244-3035
>>>>                  yaya@dowling.edu
>>>> =====================================================
>>>>
>>>> On Mon, 4 Jul 2011, Graeme.Winter@Diamond.ac.uk wrote:
>>>>
>>>>> Dear All,
>>>>>
>>>>> In an effort to understand how multiple axes are handled in CBFlib I "faked up" a toy goniometer which I chose to call FRED, which has a lot in common with a 50 degree kappa axis:
>>>>>
>>>>> loop_
>>>>> _axis.id
>>>>> _axis.type
>>>>> _axis.equipment
>>>>> _axis.depends_on
>>>>> _axis.vector[1] _axis.vector[2] _axis.vector[3] _axis.offset[1]
>>>>> _axis.offset[2] _axis.offset[3] GONIOMETER_FRED  rotation
>>>>> goniometer . 0.643 -0.766 0 . . .
>>>>> GONIOMETER_OMEGA rotation goniometer GONIOMETER_FRED 1 0 0 . . .
>>>>> SOURCE           general source . 0 0 1 . . .
>>>>> GRAVITY          general gravity . 0 -1 0 . . .
>>>>> DETECTOR_Z       translation detector . 0 0 -1 0 0 0
>>>>> DETECTOR_Y       translation detector DETECTOR_Z 0 1 0 0 0 0
>>>>> DETECTOR_X       translation detector DETECTOR_Y 1 0 0 0 0 0
>>>>> ELEMENT_X        translation detector DETECTOR_X 1 0 0 -126.30 144.39 0
>>>>> ELEMENT_Y        translation detector ELEMENT_X 0 1 0 0 0 0
>>>>>
>>>>> loop_
>>>>> _diffrn_scan_frame_axis.frame_id
>>>>> _diffrn_scan_frame_axis.axis_id
>>>>> _diffrn_scan_frame_axis.angle
>>>>> _diffrn_scan_frame_axis.displacement
>>>>> FRAME1 GONIOMETER_FRED  30.0 0.0
>>>>> FRAME1 GONIOMETER_OMEGA 24.4499 0.0
>>>>> FRAME1 DETECTOR_Z 0.0 800.02
>>>>> FRAME1 DETECTOR_Y 0.0 0.0
>>>>> FRAME1 DETECTOR_X 0.0 0.0
>>>>>
>>>>> loop_
>>>>> _diffrn_scan_axis.scan_id
>>>>> _diffrn_scan_axis.axis_id
>>>>> _diffrn_scan_axis.angle_start
>>>>> _diffrn_scan_axis.angle_range
>>>>> _diffrn_scan_axis.angle_increment
>>>>> _diffrn_scan_axis.displacement_start
>>>>> _diffrn_scan_axis.displacement_range
>>>>> _diffrn_scan_axis.displacement_increment
>>>>> SCAN1 GONIOMETER_FRED  30.0000 0.0 0.0 0.0 0.0 0.0
>>>>> SCAN1 GONIOMETER_OMEGA 24.4499 0.0500 0.0500 0.0 0.0 0.0
>>>>> SCAN1 DETECTOR_Z 0.0 0.0 0.0 800.02 0.0 0.0
>>>>> SCAN1 DETECTOR_Y 0.0 0.0 0.0 0.0 0.0 0.0
>>>>> SCAN1 DETECTOR_X 0.0 0.0 0.0 0.0 0.0 0.0
>>>>>
>>>>> (I presume that cbflib is not upset by silly goniometer names, I got no errors). Anyway offsetting this axis by 30 degrees then asking for the rotation axis I got (1, 0, 0) not the offset axis I was expecting. Checking through the documentation in Tables G it seems that the cbf_get_rotation_axis which is used in pycbf *should* do this.
>>>>>
>>>>> Looking at the actual code in cbf_simple I do however see:
>>>>>
>>>>>    /* Currently just return the first rotation axis */
>>>>>
>>>>> Would I be right in thinking that this is an aspirational method which still needs implementing, or am I perhaps looking in the wrong place? It would be consistent with my observations.
>>>>>
>>>>> I checked it out from the code mentioned in Herbert's most recent email...
>>>>>
>>>>> Thanks in advance & best wishes,
>>>>>
>>>>> Graeme
>>>>>
>>>>> --
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