[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
Re: [Imgcif-l] CBF adds new lines to character data
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] CBF adds new lines to character data
- From: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Wed, 15 Oct 2008 21:10:31 -0400 (EDT)
- In-Reply-To: <35A58E72-F608-49EC-84DB-52AC06E9D799@rayonix.com>
- References: <7DD4536D-404D-4EED-B19D-1DAD4E8C5CFB@rayonix.com><20081015192519.L91833@epsilon.pair.com><35A58E72-F608-49EC-84DB-52AC06E9D799@rayonix.com>
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
Reply to: [list | sender only]
- Follow-Ups:
- References:
- [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)
- Prev by Date: Re: [Imgcif-l] CBF adds new lines to character data
- Next by Date: [Imgcif-l] [SPAM] ASSP Re: CBF adds new lines to character data
- Prev by thread: Re: [Imgcif-l] CBF adds new lines to character data
- Next by thread: [Imgcif-l] [SPAM] ASSP Re: CBF adds new lines to character data
- Index(es):