[Imgcif-l] RE: CBFlib status
Herbert J. Bernstein yaya at bernstein-plus-sons.comMon Apr 17 15:06:21 BST 2006
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Dear Chris,
Until a new convert_image is ready, the following script will
do the necessary edit, if it has not already been done:
================= CUT HERE =========================
#!/bin/csh
grep 'diffrn_data_frame' $1
if ( $status == 0) then
ex $1 << 'EOF_EOF_EOF'
1,$s/diffrn_data_frame/diffrn_frame_data/
w
q
'EOF_EOF_EOF'
endif
grep '_diffrn_detector.sample_detector_distance' $1
if ( $status == 0) then
ex $1 << 'EOF_EOF_EOF'
1,$s/_diffrn_detector.sample_detector_distance/_diffrn_measurement.sample_detector_distance/
w
q
'EOF_EOF_EOF'
endif
================= CUT HERE =========================
Running that script on a modern linux box on a file
that does not need to be changed took 0.025 seconds
and is 100% CPU bound. Running that script on a file
that does need to be changed took .77 seconds cpu
time and 1.56 seconds wall clock time.
Just put the code between the CUT HERE lines into a file,
check that the first line is not blank, but begins with
#!/bin/csh
save it as FixMosflmCBF.csh, do a
chmod 755 FixMosflmCBF.csh
and run it with one argument -- the CBF to be modified in place.
I know this would be cleaner and faster with sed, but this way it is just a
fixup on one file as an easy insert into a script, and also provides
a simple template of what needs to be changed in convert_image for
mosflm, and a quick check to see if a cbf is ready for the unpatched
mosflm.
Regards,
Herbert
At 9:03 AM -0700 4/17/06, Chris Nielsen wrote:
> Hi Herbert,
>
> I'll probably make the changes to convert_image right now and
>not change mosflm. Recompiling it is (sometimes) an adventure. Sort
>of like remaking CCP4, especially after a new release.
>
> Best,
>
> Chris
>
>
>-----Original Message-----
>From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>Sent: Mon 4/17/2006 5:06 AM
>To: Chris Nielsen
>Cc: imgCIF-l at iucr.org
>Subject: RE: CBFlib status
>Dear Chris,
>
> I am copying this to the imgcif list, since this might be
>useful to others working with mosflm and CBF:
>
> If you are running a version of mosflm without the following
>patch,
>
> http://arcib.dowling.edu/~bernsteh/cbfwrap.patch
>
>you will need to use an editor (e.g. ex or sed) to apply
>the following correction to any CBF produced by convert_image:
>
>1,$s/diffrn_data_frame/diffrn_frame_data/
>
> You will also want to make the following edit pass to
>put the sample detector distance where mosflm expects it
>instead of where I mistakenly put it:
>
>1,$s/_diffrn_detector.sample_detector_distance/_diffrn_measurement.sample_detector_distance/
>
>With just the first change, ipmosflm runs, but with some warnings.
>With both changes, ipmosflm seems to just run for the adsc
>images.
>
>Once we have collected a few more comments, I will provide internal
>hooks for both these changes in a patch for convert_image.
>
> Thanks for you patience with all this.
>
> Regards,
> Herbert
>
>At 6:26 AM -0400 4/17/06, Herbert J. Bernstein wrote:
>>Dear Chris,
>>
>> It looks like you are using a version of ipmosflm
>>that still insists on diffrn_frame_data instead
>>of diffrn_data_frame. You need to do one of the
>>following:
>>
>> 0. Apply the patch
>>
>> http://arcib.dowling.edu/~bernsteh/cbfwrap.patch
>>
>>to mosflm.
>>
>> 1. Edit your cbf to have an extra copy
>>of the diffrn_data_frame loop as a
>>diffrn_frame_data loop and to ensure that
>>it contains the sample_detector_distance.
>>
>>If this is too much of a nuisance, I'll just add
>>an option to convert image to do the mapping
>>fromn diffrn_data_frame to diffrn_frame_data
>>on output. All the pieces to do that are
>>there, but Harry seems to be willing to
>>accept the patch.
>>
>> Regards,
>> 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 at dowling.edu
>>=====================================================
>>
>>On Sun, 16 Apr 2006, Chris Nielsen wrote:
>>
>>>
>>> Hi Herbert,
>>>
>>> Still no joy. Downloaded the latest, ran convert_image, and I get
>>> the messages below from mosflm. There needs to be a quick index lookup
>>> for "Fatal Error" numbers. I don't find an easy way to find this in
>>> the source.
>>>
>>> Getting closer!
>>>
>>> Regards,
>>>
>>> Chris
>>>
>>> convert_image -i mb_LP_1_001.img -o mb_LP_1_001.cbf -d adscquantum315
>>> convert_image: template_name: template_adscquantum315_3072x3072.cbf
>>> HEADER_BYTES = 512;
>>> DIM = 2;
>>> BYTE_ORDER = big_endian;
>>> TYPE = unsigned_short;
>>> SIZE1 = 3072;
>>> SIZE2 = 3072;
>>> PIXEL_SIZE = 0.102588;
>>> BIN = 2x2;
>>> DETECTOR_SN = 901;
>>> TIME = 29.945155;
>>> DISTANCE = 200.000000;
>>> PHI = 85.000000;
>>> OSC_START = 85.000000;
>>> OSC_RANGE = 1.000000;
>>> WAVELENGTH = 0.979381;
>>> BEAM_CENTER_X = 157.500000;
>>> BEAM_CENTER_Y = 157.500000;
>>> PIXEL SIZE = 0.102588;
>>> OSCILLATION RANGE = 1;
>>> EXPOSURE TIME = 29.9452;
>>> TWO THETA = 0;
>>> BEAM CENTRE = 157.5 157.5;
>>> header pixel center indices: 1535.5 1535.5
>>> Element ID: ELEMENT1
>>> convert_image: beam center: 1535.5 1535.5 157.524 -157.524
> >> detector distance: 200
>>> Pixel area, projected area: 0.0105243 , 0.00703457
>>> [ccd at cnvaio2 wide]$ cd process_cbf
>>> [ccd at cnvaio2 process_cbf]$ mosflm
>>>
>>>
>>> ************ Version 6.2.5 for Image plate and CCD data 9th
>>>August 2005 ***********
>>> A.G.W. Leslie, MRC Laboratory Of Molecular Biology, HILLS ROAD,
>>>CAMBRIDGE CB2 2QH, UK
>>> E-mail andrew at mrc-lmb.cam.ac.uk
>>> New auto-indexing using DPS due to Ingo Steller Robert Bolotovsky
>>>and Michael Rossmann
>>> (1998) J. Appl. Cryst. 30, 1036-1040
>>> Original auto-indexing using REFIX due to Wolfgang Kabsch
>>>(Kabsch,W. (1993),
>>> J.Appl.Cryst. 24,795-800.)
>>> X-windows interface using xdl_view due to John Campbell
>>>(Daresbury Laboratory, UK.)
>> > (Campbell,J.W. (1995) J. Appl. Cryst. 28, 236-242.
>>>
>>>
>>> MOSFLM => @mosflm.inp
>>> Command filename: mosflm.inp
>>> MOSFLM => scanner CBF
>>> warning, warning, warning. This detector option has not been fully
>>>enabled yet.
>>>
>>> You should be prepared for unexpected results.
>>> MOSFLM => gain 0.2
>>> MOSFLM => synchrotron polar 0.99
>>> MOSFLM => dispersion 0.0002
>>> MOSFLM => divergence 0.001 0.001
>>> MOSFLM => genf genfile.gen
>>> MOSFLM => wavelength 0.9794
>>> MOSFLM => distance 199.43
>>> MOSFLM => beam 157.52 157.60
>>> MOSFLM => mosaic 0.234
>>> MOSFLM => directory ../
>>> MOSFLM => template mb_LP_1_###.cbf
>>> MOSFLM => extention cbf
>>> MOSFLM => image 1
>>> MOSFLM => go
>>>
>>> CBFlib fatal error 4000
>>>
>>> CBFlib fatal error 4000
>>>
>>> CBFlib fatal error 4
>>> [ccd at cnvaio2 process_cbf]$ ls -l ../mb_LP_1_001.cbf
>>> -rw-r--r-- 1 ccd games 5773811 Apr 16 22:35 ../mb_LP_1_001.cbf
>>> [ccd at cnvaio2 process_cbf]$
>> >
>>>
>>> -----Original Message-----
>>> From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>>> Sent: Sun 4/16/2006 3:54 PM
>>> To: Chris Nielsen
>>> Cc:
>>> Subject: RE: CBFlib status
>>> Dear Chris,
>>>
>>> The latest and greatest is now at:
>>>
>>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/
>>>
>>> The updated manual is at:
>>>
>>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/doc/CBFlib.html
>>>
>>> The tarball is at:
>>>
>>> http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5/CBFlib.tar.gz
>>>
>>> This is not final, but further changes will go into 0.7.6, so people
>>> will have this as a base to work against.
>>>
>>> Actually, I have not yet done a complete job on the transforms.
>>> I only have the code working for square arrays, and I really
>>> should allow for the possibility of unequal x and y dimensions.
>>>
>>> I think you will find the centering in this version fairly
>>> reasonable. I rounded to the nearest half pixel. Let me
>>> know if you want me to put it back to the previous handling.
> >>
>>> I've told every on the imgCIF list about this release to get more
>>> testers. Do you want to be added to the imgCIF list? We moved
>>> it from BNL to the IUCr.
>>>
>>> Regards,
>>> Herbert
>>>
>>>
>>> At 3:05 PM -0700 4/16/06, Chris Nielsen wrote:
>>> > Hi Herb,
>>> >
>>> > I'll give this a try. Apropos the beam center, well, you always
>>> >worry about something missed when the math does not work out, so I'm
>>> >with you.
>>> >
>>> > When I can get things to process (which I expect, now) I will
>>> >be in a position to understand where we are with this format. Note
>>> >well that mosflm has always displayed "normal" adsc images mirrored
>>> >and rotated; that's because of its origin as a film processing
>>> >package. Everyone lives with that distinction when the images are
>>> >processed. Fortunately, you built in *all* necessary mirror and
>>> >rotations into the conversion, so we're set. Since mosflm's
>>> >view is not natural we may elect to output adsc images in the
>>> >"normal" orientation and continue to view mosflm images with its
>>> >mirror and rotation. Normally "detector adsc" takes care of
>>> >the origins, etc., for adsc images but this can be explicitly
>>> >set as well, since scanner (or detector) cbf will nor correspond
>>> >to the adsc convention.
> >> >
>>> > I am sure this will sort out shortly.
>>> >
>>> > Thanks again for the hard work,
>>> >
>>> > Chris
>>> >
>>> >
>>> >-----Original Message-----
>>> >From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>>> >Sent: Sat 4/15/2006 4:14 AM
>>> >To: Chris Nielsen
>>> >Cc:
>>> >Subject: RE: CBFlib status
>>> >Dear Chris,
>>> >
>>> > You need to say
>>> >
>>> > scanner CBF
>>> >
>>> >The entire script follows below, but I should mention that
>>> >the biggest problem I am now having on finishing the
>>> >beam center is the small variations in the beam centers
>>> >presented: 157.5, 157.5 in the image file header,
>>> >and 157.52, 157.60 in the ipmosflm script. Is the
>>> >center intended to be good to a small fraction of a pixel,
>>> >or good to the nearest half pixel (i.e. centered on a
>>> >pixel when an integer is given, centered between
>>> >pixels when a half pixel is given), or good to the
>> > >nearest whole pixel (always centered on a pixel). With
>>> >an even number of pixels, centered between pixels seems
>>> >a likely possibility. I know I should not fuss on
>>> >such small differences, but it bothers the matehmatician
>>> >in me.
>>> >
>>> > Regards,
>>> > Herbert
>>> >
>>> >
>>> >================================================================
>>> ># File Automaticaly generated by ProDC
>>> ># X-Ray data collected at ESRF_ID29
>>> ># Detector type: ADSC Quantum 210
>>> ># Date: Thu Feb 10 19:01:18 2005
>>> ># User comments: Move
>>> >
>>> ># Basic definitions
>>> > scanner CBF
>>> > gain 0.2
>>> > synchrotron polar 0.99
>>> > dispersion 0.0002
>>> > divergence 0.001 0.001
>>> > genf genfile.gen
>>> >
>>> ># Better have them
>>> > wavelength 0.9794
>>> > distance 199.43
>>> > beam 157.52 157.60
>>> >
>>> ># Just a guess
>>> > mosaic 0.234
>>> >
>>> ># Files
>>> > directory ../
>>> > template mb_LP_1_###.cbf
>>> > extention cbf
>>> > image 1
>> > ># phi 0.00 to 1.00
>>> >
>>> > go
>>> > ================================================
>>> >
>>> >
>>> >=====================================================
>>> > 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 at dowling.edu
>>> >=====================================================
>>> >
>>> >On Fri, 14 Apr 2006, Chris Nielsen wrote:
>>> >
>>> >> Hi Herb,
>>> >>
>>> >> Forgive the redundant question, but what is the protocol for
>>> >>telling mosflm that the images
>>> >> are cbf rather than adsc images? I can't dig this information out
>>> >>of my email and havn't got
>>> >> mosflm to run sucessfully on your latest convert_image. Your
> >> >>ipmosflm input script would
>>> >> be useful.
>>> >>
>>> >> Best, and thanks for putting up with it all,
>>> >>
>>> >> Chris
>>> >>
>>> >>
>>> >> -----Original Message-----
>>> >> From: Herbert J. Bernstein [mailto:yaya at bernstein-plus-sons.com]
>>> >> Sent: Thu 4/13/2006 9:10 PM
>>> >> To: Andrew HAMMERSLEY; Jon Wright
>>> >> Cc: sweet at bnl.gov; Chris Nielsen
>>> >> Subject: Re: CBFlib status
>>> >>
>>> >>
>>> >>
>>> >> I promised Chris a snapshot this evening, so before it is tomorrow,
>>> >> here is the latest:
>>> >>
>>> >>
>>> >>http://arcib.dowling.edu/~bernsteh/software/CBFlib_0.7.5_12Apr06.tar.gz
>>> >>
>>> >> The version of convert_image in this kit now dumps the full
>>> >>image header
>>> >> into a text field, which is put into
>>> >>
>>> >> _diffrn_data_frame.detail
>>> >>
>>> >> The PHI angle now seems to be set correctly. The beam center is close
>>> >> (off by less than half a pixel as an index, but has the sign inverted
>>> >> for the y component of the beam center in mm). I'll continue on
>>> >> that tomorrow, but comments on this version would be be appreciated.
>>> >>
>>> >> To test, you will need to place
>>> >>
>>> >> mb_LP_1_001.img (Chris's adsc test case) and
>>> >>
>>> >> example.mar2300 (the Mar test case) into the same directory that
> >> >> contains the snapshot (not into the directory it creates).
>>> >> Both are available in
>>> >>
>>> >> http://arcib.dowling.edu/~bernsteh/software/
>>> >>
>>> >> then
>>> >>
>>> >> make all
>>> >> make tests
>>> >>
>>> >> The manual is growing, but I still have code to write up and make
>>> >> test programs for.
>>> >>
>>> >> Regards,
>>> >> Herbert
>>> >>
>>> >>
>>> >> --
>>> >> =====================================================
>>> >> Herbert J. Bernstein, Professor of Computer Science
>>> >> Dowling College, Kramer Science Center, KSC 121
>>> >> Idle Hour Blvd, Oakdale, NY, 11769
>>> >>
>>> >> Office: +1-631-244-3035
>>> >> Lab (KSC 020): +1-631-244-3451
>>> >> yaya at dowling.edu
>>> >> =====================================================
>>> >>
>>> >>
>>> >>
>>>
>>>
>>> --
>>> =====================================================
>>> Herbert J. Bernstein, Professor of Computer Science
>>> Dowling College, Kramer Science Center, KSC 121
>>> Idle Hour Blvd, Oakdale, NY, 11769
>>>
>>> Office: +1-631-244-3035
>>> Lab (KSC 020): +1-631-244-3451
>>> yaya at dowling.edu
>> > =====================================================
>>>
>>>
>>>
>>>
>
>
>--
>=====================================================
> Herbert J. Bernstein, Professor of Computer Science
> Dowling College, Kramer Science Center, KSC 121
> Idle Hour Blvd, Oakdale, NY, 11769
>
> Office: +1-631-244-3035
> Lab (KSC 020): +1-631-244-3451
> yaya at dowling.edu
>=====================================================
--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
Office: +1-631-244-3035
Lab (KSC 020): +1-631-244-3451
yaya at dowling.edu
=====================================================
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