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Re: [Imgcif-l] imgCIF X axis

  • To: "Herbert J. Bernstein" <yayahjb@gmail.com>
  • Subject: Re: [Imgcif-l] imgCIF X axis
  • From: James H via imgcif-l <imgcif-l@iucr.org>
  • Date: Thu, 23 Jun 2022 10:48:24 +1000
  • Cc: James H <jamesrhester@gmail.com>, The Crystallographic Binary File and its imgCIF application to image data<imgcif-l@iucr.org>
  • In-Reply-To: <CABcsX25Q33aGhFm-hBFOXk6vLuu-MkLZk9B7wkgioYWo_KZFEQ@mail.gmail.com>
  • References: <CAM+dB2c5Hv=g03gGkC4==awB_ygVL6Hvdp-vf6R86pVOoRSmYQ@mail.gmail.com><CABcsX25oGH95vP8RLOET9R=BQZHDoizOu4FDht2ZjbXuYyYw8g@mail.gmail.com><CAM+dB2cRnOFZA+6RLD4oBEbz769aJ2TU-02NpeSFPUaBUKty0Q@mail.gmail.com><CABcsX24zMJ8yU+JFVKLOxaQKy02cMwE2h5eobWc_4C+NRkxmjw@mail.gmail.com><CAM+dB2dqj7M_PEpftjo3H5zfV98=80XQC6Hf-qDQ2SoUOk-qHg@mail.gmail.com><CABcsX24roBmnZ5wtsqXctbgoF5EmxTkEYAaMKHGL7wQDOZKt6g@mail.gmail.com><CAM+dB2eub4fzZexSig9cZqBooR+iiVspOyzNy7yfAcZUpm-xrA@mail.gmail.com><CABcsX25Q33aGhFm-hBFOXk6vLuu-MkLZk9B7wkgioYWo_KZFEQ@mail.gmail.com>
But according to
https://github.com/yayahjb/cbflib/blob/main/doc/cif_img_1.8.6.dic#L3204 the
positioner axis used for X has to intersect the origin, so a translational
rail that travels in either of the two directions that do not intersect the
beam can't be used. So for a kappa on XY translation stages, with no omega
(as per your original example), it looks like the kappa axis should be the
X axis. Unless there is a deeper meaning of "principal axis" in this case,
which I suspect there might be - something like "the axis of rotation of an
omega stage if there was one installed".

On Thu, 23 Jun 2022 at 00:48, Herbert J. Bernstein <yayahjb@gmail.com>
wrote:

> Dear James,
>   I am used to omega at the bottom, not kappa, so it would be omega on top
> of
> a translational positioner.  I would expect one of the translational rails
> to be
> the principal axis.
>   Regards,
>     Herbert
>
> On Wed, Jun 22, 2022 at 10:36 AM James H <jamesrhester@gmail.com> wrote:
>
>> My comments in relation to kappa were simply in response to your apparent
>> suggestion that my working principle of the "bottom-most rotation axis"
>> being the principal axis might not work very well if a kappa axis is
>> sitting on top of translation stages. However, if there is an omega axis
>> somewhere underneath the kappa axis, as in the example you just provided,
>> then that working principle remains valid.
>>
>> If we return to your original example of a kappa axis sitting on top of
>> translation stages, with no further rotation axes underneath, can you
>> please explain what the principal axis must be in this case? The positive
>> direction of movement of the bottom-most translation stage perhaps?
>>
>> I agree that in a few places the documentation both in Vol G and the
>> dictionary does need to be improved. In my experience the concept of a
>> "principal axis" is not readily understood by the general reader (not just
>> me) so should be explained. Your kappa on translation stage example might
>> be very illuminating in this case. And emphasising that the direction of X
>> matches the direction of the principal axis (not just "aligns") might also
>> help.
>>
>> I would be very surprised if the issues with NSLS and DLS had anything to
>> do with the coordinate system as such. The laws of physics are invariant
>> against rotation and translation, so I suspect that the problem was more
>> likely to be that some axis somewhere was not given the correct components
>> relative to the chosen coordinate system.
>>
>> all the best,
>> James.
>>
>>
>> On Wed, 22 Jun 2022 at 22:26, Herbert J. Bernstein <yayahjb@gmail.com>
>> wrote:
>>
>>> Dear James,
>>>   Here is an example from the AXIS category i the dictionary:
>>>
>>>  Example 1.
>>>
>>>         This example shows the axis specification of the axes of a
>>>         kappa-geometry goniometer [see Stout, G. H. & Jensen, L. H.
>>>         (1989). X-ray structure determination. A practical
>>>         guide, 2nd ed. p. 134. New York: Wiley Interscience].
>>>
>>>         There are three axes specified, and no offsets.  The outermost axis,
>>>         omega, is pointed along the *X* axis.  The next innermost axis, kapp
a,
>>>         is at a 50 degree angle to the *X* axis, pointed away from the sourc
e.
>>>         The innermost axis, phi, aligns with the *X* axis when omega and
>>>         phi are at their zero points.  If T-omega, T-kappa and T-phi
>>>         are the transformation matrices derived from the axis settings,
>>>         the complete transformation would be:
>>>             *X*' = (T-omega) (T-kappa) (T-phi) *X*
>>> ;
>>> ;
>>>          loop_
>>>         _axis.id <http://www.bernstein-plus-sons.com/software/CBF/doc/cif_im
g_1.8.4.html#_axis.id>
>>>         _axis.type <http://www.bernstein-plus-sons.com/software/CBF/doc/cif_
img_1.8.4.html#_axis.type>
>>>         _axis.equipment <http://www.bernstein-plus-sons.com/software/CBF/doc
/cif_img_1.8.4.html#_axis.equipment>
>>>         _axis.depends_on <http://www.bernstein-plus-sons.com/software/CBF/do
c/cif_img_1.8.4.html#_axis.depends_on>
>>>         _axis.vector[1] <http://www.bernstein-plus-sons.com/software/CBF/doc
/cif_img_1.8.4.html#_axis.vector[1]> _axis.vector[2] <http://www.bernstein-plus-
sons.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vector[2]> _axis.vector[3] <h
ttp://www.bernstein-plus-sons.com/software/CBF/doc/cif_img_1.8.4.html#_axis.vect
or[3]>
>>>         omega rotation goniometer     .    1        0        0
>>>         kappa rotation goniometer omega    -.64279  0       -.76604
>>>         phi   rotation goniometer kappa    1        0        0
>>> ;
>>>
>>>
>>>
>>> Note that it is omega and phi that point along X, not kappa and omega is
>>> grounded, so I really
>>> did mean omega as the principal axis is this case.  I also do mean to
>>> suggest that a
>>> translation rail can define X.  Please tell me what in the dictionary
>>> you are seeing that
>>> says that "kappa axis to be the principal axis, no questions asked".
>>> It comes as a
>>> surprise to me.
>>>
>>> At NSLS-II and DLS the choice of coordinate system has had a definite
>>> impact on analysis
>>> of the data.  Flipping X messes up handling of the beam center, which
>>> leads to one
>>> of these annoying hunts through the 8 alternatives which can undo beam
>>> center flips.
>>>
>>> Please send me a copy of the documentation you are working from.  It
>>> sounds like we
>>> have some work to do to make sure this is really clear.
>>>
>>> Regards,
>>>     Herbert
>>> On Wed, Jun 22, 2022 at 3:35 AM James H <jamesrhester@gmail.com> wrote:
>>>
>>>> Thanks Herbert. I assume in your kappa example you mistyped and meant
>>>> that kappa (not omega) would be the principal axis according to my working
>>>> definition. Meanwhile, you seem to be implying that there may be some
>>>> flexibility in the choice of "principal axis" for certain goniometers. That
>>>> is, in your example a more intuitive choice of principal axis might be that
>>>> of an imaginary omega stage underneath the translation stages, at which
>>>> point you have the freedom to choose rotation direction and therefore X
>>>> axis orientation. However, my reading of the current definition in the AXIS
>>>> category would require the kappa axis to be the principal axis, no
>>>> questions asked, so I'm not sure how much freedom there actually is.
>>>>
>>>> I guess it's worth noting as well that the choice of coordinate system
>>>> makes zero difference to the analysis of the data, so ambiguity in the
>>>> definition of X is not a major issue. However I do think we need to be
>>>> clear if and when this freedom of choice does exist.
>>>>
>>>> all the best,
>>>> James.
>>>>
>>>> On Wed, 22 Jun 2022 at 11:30, Herbert J. Bernstein <yayahjb@gmail.com>
>>>> wrote:
>>>>
>>>>> Dear James,
>>>>>   To be clear, it usually works best to do as you say and to choose a
>>>>> goniometer
>>>>> axis that does not depend on any other axes, but that may conflict
>>>>> with your
>>>>> preference for a rotation axis, as when a kappa goniometer is mounted
>>>>> on
>>>>> an x,y,z translation stage, which means that one of the translations
>>>>> would
>>>>> be the one that depends on no other axes.  Then if you choose omega as
>>>>> the
>>>>> principal axis axis to stick to using a rotation axis you have to
>>>>> jigger all your
>>>>> software to deal with a variable coordinate frame -- not a terrible
>>>>> thing if your
>>>>> software is carefully written to follow robotics conventions, but a
>>>>> likely source
>>>>> of bugs in general.
>>>>>   I would leave the wording at "principal axis"
>>>>>   Regards,
>>>>>     Herbert
>>>>>
>>>>> On Tue, Jun 21, 2022 at 8:39 PM James H <jamesrhester@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Just to pick up on something else in Herbert's reply: I've noticed
>>>>>> some confusion when talking to people as to what exactly "the principal
>>>>>> axis of the goniometer" is. My current working definition is "the
>>>>>> bottom-most rotation axis of the goniometer".  In terms of the imgCIF AXI
S
>>>>>> category, this would be the goniometer rotation axis that depends_on no
>>>>>> other axis, typically omega on a 4-circle diffractometer, and so by
>>>>>> definition of X this axis would have axis vector of [1 0 0] in
>>>>>> non-pathological cases. Is my understanding correct? Are there subtleties
>>>>>> not covered by my working definition?
>>>>>>
>>>>>> thanks,
>>>>>> James.
>>>>>>
>>>>>> On Wed, 15 Jun 2022 at 21:34, Herbert J. Bernstein <yayahjb@gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Dear James,
>>>>>>>   This is a little tricky.  The relevant rules are:
>>>>>>>
>>>>>>> "Axis 1 (X): The X-axis is aligned to the mechanical axis pointing
>>>>>>> from
>>>>>>>      the sample or specimen along the  principal axis of the
>>>>>>> goniometer."
>>>>>>>
>>>>>>>   "If the axis involved is a rotation axis, it is right-handed, i.e.
>>>>>>> as
>>>>>>>      one views the object to be rotated from the origin (the tail)
>>>>>>> of the
>>>>>>>      unit vector, the rotation is clockwise.  If a translation axis
>>>>>>> is
>>>>>>>      specified, the direction of the unit vector specifies the sense
>>>>>>> of
>>>>>>>      positive translation"
>>>>>>>
>>>>>>> So, yes the x-axis starts from the sample, but where it point to in
>>>>>>> the
>>>>>>> goniometer depends on where in the goniometer the "principal"
>>>>>>> axis of the goniometer points _and_ in which direction the axis
>>>>>>> settings increase and whether the principal axis is a rotation
>>>>>>> axis or a translation axis.  The only way I have figured out to
>>>>>>> do this is to start from the engineering diagrams (or at least
>>>>>>> photos) of the goniometer, and even then, I once screwed up
>>>>>>> the x-axis for a beamline at DLS (ask Graeme Winter).
>>>>>>>
>>>>>>>   Regards,
>>>>>>>     Herbert
>>>>>>>
>>>>>>> On Wed, Jun 15, 2022 at 2:38 AM James H via imgcif-l <
>>>>>>> imgcif-l@iucr.org> wrote:
>>>>>>>
>>>>>>>> Dear imgCIF experts,
>>>>>>>>
>>>>>>>> Just to double-check, is it correct to say that the imgCIF X axis
>>>>>>>> always
>>>>>>>> points from the specimen towards the goniometer base? Closely
>>>>>>>> parsing the
>>>>>>>> dictionary and Volume G suggests that the X axis being "aligned"
>>>>>>>> with the
>>>>>>>> principal axis could also allow the X axis to point from the
>>>>>>>> specimen away
>>>>>>>> from the goniometer base, particularly if the sense of rotation of
>>>>>>>> the
>>>>>>>> principal goniometer axis is taken into account when defining X (is
>>>>>>>> it?).
>>>>>>>>
>>>>>>>> thanks,
>>>>>>>> James.
>>>>>>>> --
>>>>>>>> T +61 (02) 9717 9907
>>>>>>>> F +61 (02) 9717 3145
>>>>>>>> M +61 (04) 0249 4148
>>>>>>>> _______________________________________________
>>>>>>>> imgcif-l mailing list
>>>>>>>> imgcif-l@iucr.org
>>>>>>>> http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> T +61 (02) 9717 9907
>>>>>> F +61 (02) 9717 3145
>>>>>> M +61 (04) 0249 4148
>>>>>>
>>>>>
>>>>
>>>> --
>>>> T +61 (02) 9717 9907
>>>> F +61 (02) 9717 3145
>>>> M +61 (04) 0249 4148
>>>>
>>>
>>
>> --
>> T +61 (02) 9717 9907
>> F +61 (02) 9717 3145
>> M +61 (04) 0249 4148

--
T +61 (02) 9717 9907
F +61 (02) 9717 3145
M +61 (04) 0249 4148
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