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If the axes have been set up correctly, the beam center information
is redundant, since the beam center is implied as the intersection
of the Z-axis with detector face. You are right to cross-check
with the set and get routines. You should look at both the
mm and pixel values. Let me know if you have problems.
Regards,
Herbert
At 5:26 PM -0700 10/15/07, Chris Nielsen wrote:
> Hi Herbert,
>
> I have discussed Andy's question (which seems to be the genesis
>of the
>current discussion) with him over the phone. We are going to see how
>consistent
>the mm definitions of the SLS header are with their idea of the pixel
>origin
>assuming the array is stored as described in the CBF header using the
>cbf_simple.c
>beam center get/put functions. Typically, the detector's beam center in
>terms
>of pixels is known, and the idea is to convert to mm as per the standard
>CBF definition.
>If the "set" followed by the "get" from cbf_simple is consistent, we
>have it.
>I would like to encourage the use of standard library functions to make
>the process of
>storing a useful beam center painless.
>
>
> Personally, I think the "pixel" definition is easiest for
>everyone to understand, and fastest to get something useful from just
>from "more"ing
>the header, and for that reason is desirable:
>
>>> # _diffrn_data_frame.center_fast
>>> # _diffrn_data_frame.center_slow
>>> # _diffrn_data_frame.center_units
>
>
> Was there a consensus in the May meeting regarding the pixel
>origin question?
>I may have left before the discussion was finished.
>
> Chris
>
>
>
>-----Original Message-----
>From: imgcif-l-bounces@iucr.org [mailto:imgcif-l-bounces@iucr.org] On
>Behalf Of Herbert J. Bernstein
>Sent: Monday, October 15, 2007 4:35 PM
>To: The Crystallographic Binary File and its imgCIF application to image
>data
>Cc: Miroslav Kobas
>Subject: Re: [Imgcif-l] question on beam center
>
>As long as there is a clear and consistent definition, either will work,
>i.e. either using the pixel origin for the bins or defining a new origin
>for bins. I would appreciate hearing from others on the list as to
>which one would be easier for them to work with. -- Herbert
>
>
>At 12:41 AM +0200 10/16/07, Jon Wright wrote:
>>Dear Herbert,
>>
>>The fast/slow/units seems like a good solution. Is there some reason
>>for this choice of definition?
>>
>> ... In all cases the
>> center distances are measured from the center of the
>> first pixel, i.e. in a 2x2 binning, the measuring origin
>> is offset from the centers of the bins by one half pixel
>> towards the first pixel.
>>
>>Why not measure from the centre of the bins in the case of bins?
>>
>>Best,
>>
>>Jon
>>
>>
>>
>>
>>
>>Herbert J. Bernstein wrote:
>>> Dear Miro,
>>>
>>> The problem is not what I like, but what processing programs can
>
>>> deal with. In the last round of proposed dictionary changes, we
>>> suggested:
>>>
>>> # _diffrn_data_frame.center_fast
>>> # _diffrn_data_frame.center_slow
>>> # _diffrn_data_frame.center_units
>>>
>>> which would allow you to specify the center in mm, pixels or bins.
>>> What we need now is general agreement on this approach.
>>>
>>> I am forwarding this message to the imgcif list to see if anyone
>
>>> objects.
>>>
>>> Regards,
>>> Herbert
>>>
>>>
>>>
>>> At 6:54 PM +0200 10/15/07, Miroslav Kobas wrote:
> >>> Dear Herbert,
>>>>
>>>> I think that Andy Arvai has already contacted you concerning this
>>>> topic. It is about the fullCBF header. I have made a recent dataset
>
>>>> available on our webpage (<http://pilatus.web.psi.ch/datasets.htm>
>>>> http://pilatus.web.psi.ch/datasets.htm) with the miniCBF and the
>>>> fullCBF header (conversion done with convert_minicbf). After
>>>> experiencing some problems with adxv, I asked Andy, Harry Powell,
>>>> Jim Pflugrath to adapt their programs such that they take all the
> >>> necessary information from the CBFheader.
>>>>
>>>> Andy had problems with the definition of coordinate systems and how
>
>>>> to get the beam center (units of mm) into a know coordinate system
>>>> (in units of pixels).
>>>>
>>>> These are the 3 lines defining the beam center in units of mm in
>>>> the full CBF header:
>>>> _diffrn_data_frame.center_slow 225.406000
>>>> _diffrn_data_frame.center_fast -211.577200
>>>> _diffrn_data_frame.center_units mm
>>>>
>>>> For our detector, they correspond to the following beam center in
>>>> units of pixels:
>>>> slow 225.406000 corresponds to y at 1310.50 fast -211.577200
>>>> corresponds to x at 1230.10
>>>>
>>>> This conversion can only be done, if one understands the definition
>
>>>> of coordinate systems properly. I have asked several people who have
>
>>>> experience with CBF if they understand how the coordinate systems
>>>> are defined, but they could no give me a unified solution.
>>>>
>>>> Andy has asked me to include the following lines in our header:
>>>> _diffrn_data_frame.adxv_beam_center_x 2463
>>>> _diffrn_data_frame.adxv_beam_center_y 2527
>>>>
>>>> But since we really head now for the standard, full CBF-header
>>>> (Eric is implementing the full CBF-header into our dataformat), we
>>>> only want to use items, which are defined therein. Therefor I have
>
>>>> suggested Andy to ask you, if it would be possible to add 2 more
>>>> items in the CBF header giving the beam center in x and y. Something
>>>> like:
>>>> _diffrn_data_frame.beam_center_x 2463
>>>> _diffrn_data_frame.beam_center_y 2527
>>>>
>>>> What do you think about that? The consequence would be that there
>>>> would also be changes in convert_minicbf and and in our header
>>>> structure. Eric has told me that it is not a problem for him to
>>>> include additional items in our header. But I would easily
>>>> understand that you would not like to include these items in the
>>>> full CBF header, since this information is already there in a
>> >> slightly different form.
>>>>
>>>> If you want to check the above values, I have attached you one of
>>>> our recent images with the full CBF-header.
>>>>
>>>> Thanks for everything and have a nice day.
>>>> kind regards
>>>> miro
>>>>
>>>> --
>>>> ________________________________________
>>>> Dr. Miroslav Kobas
>>>> DECTRIS Ltd.
>>>> OSRA 007
>>>> 5232 Villigen PSI
>>>> Switzerland
>>>>
>>>> <mailto:miroslav.kobas@dectris.com>miroslav.kobas@dectris.com
>>>> <http://www.dectris.com>http://www.dectris.com
>>>> <http://pilatus.web.psi.ch>http://pilatus.web.psi.ch
>>>> +41 56 310 3269 phone
>>>> +41 56 310 5454 fax
>>>> ________________________________________
>>>>
>>>> Content-Type: application/octet-stream; name="run2_1_FH_00001.cbf"
>>>> Content-Disposition: attachment; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"; filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf";
>>>> filename="run2_1_FH_00001.cbf"
>>>> X-Attachment-Id: f_f7t7fn8h
>>>>
>>>> Attachment converted: Macintosh HD:run2_1_FH_00001.cbf ( /
>>>>) (001C5C25)
>>>
>>>
>>
> >_______________________________________________
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>
>
>--
>=====================================================
> 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
>=====================================================
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>_______________________________________________
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--
=====================================================
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
=====================================================
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