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[Imgcif-l] [SPAM] ASSP Re: CBF adds new lines to character data
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: [Imgcif-l] [SPAM] ASSP Re: CBF adds new lines to character data
- From: Michael Blum <blum@rayonix.com>
- Date: Wed, 15 Oct 2008 21:08:49 -0500
- In-Reply-To: <20081015210503.T91833@epsilon.pair.com>
- References: <7DD4536D-404D-4EED-B19D-1DAD4E8C5CFB@rayonix.com><20081015192519.L91833@epsilon.pair.com><35A58E72-F608-49EC-84DB-52AC06E9D799@rayonix.com><20081015210503.T91833@epsilon.pair.com>
Hi Herb, Jeez, I had no idea what a deep subject this already was! I thought I was just citing a bug. Please don't go do a lot of work on this due to my question. I think the read/write_widefile() calls will fix my problem. My interest is solely to be able to write a file that faithfully represents our data and can be universally read. I think our files will be read only be "modern" programs that are being developed contemporaneously so I think wide files will be OK. I am going to assume that is true until I get a complaint. Thanks for your quick responses. regards, Michael On Oct 15, 2008, at 8:10 PM, Herbert J. Bernstein wrote: > Dear Michael, > > The only reason we don't do it, is that nobody thought to > ask for it in CBFlib. We have it in a separate utility called > CIFFOLD. I'll add that into CBFlib when I get back from a talk > I am giving in Dubuque this weekend. If you need it sooner, > the is at > > http://www.bernstein-plus-sons.com/software/ciffold/ > > but that one is not prepared for the image portion of a CBF. > I'll merge it into CBFlib, so it is image aware. > > 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@dowling.edu > ===================================================== > > On Wed, 15 Oct 2008, Michael Blum wrote: > >> >> Thanks Herb - I'll switch to using _widefile - that should solve my >> problem. >> >> But why doesn't cbflib "unfold" the lines again when it reads them? >> Isn't the point of >> escaping the extra newlines so they can be recognized and removed? >> >> Michael >> >> >> On Oct 15, 2008, at 6:32 PM, Herbert J. Bernstein wrote: >> >>> There are two flavors of CIF -- the original 80 character line >>> length CIFs that can be read by all parsers, and the newer 2048 >>> character line length CIFS that can be read by most newer parsers. >>> CBFlib can handle either line length, but, if you are in the 80 >>> character mode and give it longer lines, it folds them with the >>> backslash escape. To avoid this, you need to tell it you want >>> to use the longer line length, using cbf_write_widefile rather >>> than cbf_write_file, and cbf_read_widefile instead of cbf_read_file. >>> >>> ===================================================== >>> 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 Wed, 15 Oct 2008, Michael Blum wrote: >>> >>>> Hi Herb et al, >>>> >>>> For testing our production of CBF files, I am converting our marccd >>>> frames to CBF, converting the CBF back to marccd, and >>>> then doing a "diff" between the original and final marccd frame >>>> files. All interactions with the CBF file and data are done using >>>> CBFlib. >>>> >>>> I am having trouble getting some string values back intact. >>>> >>>> Long comments (strings) that are written to the CBF using >>>> set_value() get newlines (or carriage returns) added to them in >>>> the >>>> CBF file. >>>> When the text is extracted again, using cbf_get_value(), it has >>>> the >>>> extra newlines it. The original strings may or may not have their >>>> own >>>> newlines. The added newlines seem to be "escaped', using '\', but >>>> neither the escapes nor the escaped newlines get removed from the >>>> string. >>>> >>>> This a little more than just a cosmetic issue, as sometimes we have >>>> formatted text in the comments, with columns that line up and >>>> we would like to get the text back in a readable format. >>>> >>>> >>>> two real examples using CBFlib v0.7.9 on a redhat 5.2 linux box. >>>> ( BTW, CBFlib 0.7.9 writes "0.7.8" into the header prologue! ) >>>> >>>> -------------------------------- >>>> This is OK: >>>> >>>> C-string input: >>>> "file comments for a blank image on the marMosaic simulator with >>>> dummy >>>> values" >>>> >>>> CBF result: (with cbf_set_value() ) >>>> _diffrn_data_frame.details^M >>>> 'file comments for a blank image on the marMosaic simulator with >>>> dummy values'^M >>>> ^M >>>> >>>> C-string result of reading CBF: (with cbf_get_value()) >>>> "file comments for a blank image on the marMosaic simulator with >>>> dummy >>>> values" >>>> -------------------------------- >>>> -------------------------------- >>>> This is NOT OK: >>>> >>>> C-string input: >>>> "dataset comments for a blank image on the marMosaic simulator with >>>> dummy values" >>>> >>>> CBF result: ( of cbf_set_value() ) >>>> _diffrn_measurement.details^M >>>> ;\ >>>> dataset comments for a blank image on the marMosaic simulator with\ >>>> dummy values\ >>>> ; >>>> >>>> C-string result of parsing CBF: (with cbf_get_value()) >>>> "\ >>>> dataset comments for a blank image on the marMosaic simulator with\ >>>> dummy values\" >>>> >>>> -------------------------------- >>>> >>>> >>>> >>>> Note NEW Company name and email address! >>>> _______________ >>>> Michael L. Blum Toll Free: 877-627-XRAY >>>> (627-9729) >>>> Rayonix, LLC Tel: 847-869-1548 >>>> 1880 Oak Avenue Fax: 847-869-1587 >>>> Evanston, IL 60201 Email: blum@rayonix.com >>>> USA WWW: www.rayonix.com >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> Note NEW Company name and email address! >> _______________ >> Michael L. Blum Toll Free: 877-627-XRAY (627-9729) >> Rayonix, LLC Tel: 847-869-1548 >> 1880 Oak Avenue Fax: 847-869-1587 >> Evanston, IL 60201 Email: blum@rayonix.com >> USA WWW: www.rayonix.com >> >> >> >> >> >> _______________________________________________ >> 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 Note NEW Company name and email address! _______________ Michael L. Blum Toll Free: 877-627-XRAY (627-9729) Rayonix, LLC Tel: 847-869-1548 1880 Oak Avenue Fax: 847-869-1587 Evanston, IL 60201 Email: blum@rayonix.com USA WWW: www.rayonix.com _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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- [Imgcif-l] CBF adds new lines to character data (Michael Blum)
- Re: [Imgcif-l] CBF adds new lines to character data (Herbert J. Bernstein)
- Re: [Imgcif-l] CBF adds new lines to character data (Michael Blum)
- Re: [Imgcif-l] CBF adds new lines to character data (Herbert J. Bernstein)
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