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) >>> >>> >> > >_______________________________________________ >>imgcif-l mailing list >>imgcif-l@iucr.org >>http://scripts.iucr.org/mailman/listinfo/imgcif-l > > >-- >===================================================== > 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 >===================================================== >_______________________________________________ >imgcif-l mailing list >imgcif-l@iucr.org >http://scripts.iucr.org/mailman/listinfo/imgcif-l >_______________________________________________ >imgcif-l mailing list >imgcif-l@iucr.org >http://scripts.iucr.org/mailman/listinfo/imgcif-l -- ===================================================== 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 ===================================================== _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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