[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
Reply to: [list | sender only]
[Imgcif-l] proposed change in first line of imgcif files
- To: "The Crystallographic Binary File and its imgCIF application to image data" <imgcif-l@iucr.org>
- Subject: [Imgcif-l] proposed change in first line of imgcif files
- From: "James Hester" <jamesrhester@gmail.com>
- Date: Tue, 7 Oct 2008 14:06:01 +1000
- In-Reply-To: <279aad2a0810062105p4b6c2996u76d7ea7b2f5fd61d@mail.gmail.com>
- References: <20080826195337.H76753@epsilon.pair.com><279aad2a0809231659g560a410ds3e1bcdf3a6809ae3@mail.gmail.com><20080923224741.M51207@epsilon.pair.com><279aad2a0809232135y1522bf21g1105afcc984fb9c4@mail.gmail.com><20080924064800.D66789@epsilon.pair.com><279aad2a0809301721i52e5ae91i39083f29a52ef917@mail.gmail.com><a0624080bc508798078a4@192.168.2.103><279aad2a0810012343s5e904d96kb113c043e0a0b5ae@mail.gmail.com><20081002084239.E47913@epsilon.pair.com><279aad2a0810062105p4b6c2996u76d7ea7b2f5fd61d@mail.gmail.com>
---------- Forwarded message ---------- From: James Hester <jamesrhester@gmail.com> Date: Tue, Oct 7, 2008 at 2:05 PM Subject: Re: [Imgcif-l] proposed change in first line of imgcif files To: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com> Dear Herbert and Harry: Herbert's suggestion is a fine one which I agree with. What I took from Harry's email was that he would be prepared to live in a regime where the course of action to be taken if header and contents didn't match would be application-specific, so that's good. Perhaps we should nut out the technical details of the proposal in a new thread for tidyness. Best wishes, James. On Thu, Oct 2, 2008 at 11:39 PM, Herbert J. Bernstein < yaya@bernstein-plus-sons.com> wrote: > Dear James, > > I have read your remarks and Harry's. How about we say what we all seem > to agree on: > > If both a magic number and one or more CIF tags specify values for the > same or related parameter(s), those values should agree according to the > dictionary specified relationships among the parameter(s). Similarly, if > two CIF tags specify values for the same or related parameters, those values > should agree according to the dictionary specified relationships among the > parameter(s). In all dictionaries, those relationships should be clearly > explained in the explanatory text of the dictionaries. In DDLm > dictionaries, the ability to algorithmically specify those relationships > should be exploited where appropriate. > > This would clearly specify our common intent for clearly documented > agreement among multiple presentations of the same information, and leave > it to specific applications to follow whatever approach seems appropriate > to the application developer in dealing with the error case of > disagreement. > > Now what we really need to do is to agree in the CIF tags that should > agree with the imgCIF magic number. > > To get everything in the same place, here is the magic number proposal > along with a _ws... tag to allow the information to be referenced > algorithmically and, finally, a variant on James' specific tags for the > newly added style and style_version > > 1. What problem is being solved?. As the use of imgCIF has increased, two > very distinct sets of files have appeared: the "miniCBFs" used for the > Pilatus 6m detector and more fully populated imgCIF files, such as the ones > produced for ADSC detectors. While the information necessary for processing > can be discovered from context in handling a miniCBF, it may be necessary to > read fairly far into the file to discover that the file is indeed a miniCBF, > complicating the design of reading software. > > 2. The proposed solution. Currently CBF files begin with a magic number > comment line > 1 2 3 4 5 > 12345678901234567890123456789012345678901234567890 > ###CBF: VERSION n.m > > We propose to extend the magic number comment line with two optional fields > to read > > 1 2 3 4 5 > 12345678901234567890123456789012345678901234567890 > ###CBF: VERSION n.m style style_version > > where "style" is a unique CBF style identifier left justified as a single > word in columns 25-34 and "style_version" is a left justified integer in > columns 35-44. > > Each style will be registered in a central repository along with > information on the tags that will be carried for that style and a template > of the tags that would be needed to fully populate the file. > > 3. To faciltiate writing DDLm methods to work with this or any other magic > number convention, a pseudo-tag _ws.prologue would allow application > manipulation of the comments and whitespace from before a data block. The > prefix ws would be reserved for this purpose and for similar, related tags. > No parser would have to work with this tag. It is provided simply to have > an unambigous algorithmic way to state the relationship with the following > actual CIF tags. > > 4. James Hester has proposed two new tags to be carried within an imgCIF > file to agree with the style and style_version: _diffrn_detector.data_style > and _diffrn_detector.data_style_version. Ignoring the 0-base, vs. 1-base > indexing issues, just to state the relationship between the first comment > line and these tags in pseudocode: > > _diffrn_detector.data_style = trim(_ws.prologue[25:34]) > _diffrn_detector.data_style_version = trim(_ws.prologue[35:44]) > > I would suggest, however, that these two tags do not quite fit in the > diffrn_detector category, inasmuch as they do not really describe the > detector. They actually describe the format of the data block being used to > present the detector information. Therefore I suggest that we start a new > category: data_block_format and define > > _data_block_format.data_style = trim(_ws.prologue[25:34]) > _data_block_format.data_style_version = trim(_ws.prologue[35:44]) > > > Regards, > Herbert > > P.S. I think we should explore formally creating a standard following > the ISO processes, working under the IUCr, but seeing if we can > eventually get ISO to accept what we do. > > ===================================================== > 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 > ===================================================== > > -- T +61 (02) 9717 9907 F +61 (02) 9717 3145 M +61 (04) 0249 4148 -- T +61 (02) 9717 9907 F +61 (02) 9717 3145 M +61 (04) 0249 4148 _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
Reply to: [list | sender only]
- References:
- [Imgcif-l] proposed change in first line of imgcif files (Herbert J. Bernstein)
- Re: [Imgcif-l] proposed change in first line of imgcif files (James Hester)
- Re: [Imgcif-l] proposed change in first line of imgcif files (James Hester)
- Re: [Imgcif-l] proposed change in first line of imgcif files (James Hester)
- Re: [Imgcif-l] proposed change in first line of imgcif files (James Hester)
- Re: [Imgcif-l] proposed change in first line of imgcif files (Herbert J. Bernstein)
- Prev by Date: Re: [Imgcif-l] proposed change in first line of imgcif files
- Next by Date: [Imgcif-l] renaming a data block?
- Prev by thread: Re: [Imgcif-l] proposed change in first line of imgcif files
- Next by thread: [Imgcif-l] renaming a data block?
- Index(es):