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Re: CIF or NOT CIF, (or nothing)
- To: Multiple recipients of list <imgcif-l@bnl.gov>
- Subject: Re: CIF or NOT CIF, (or nothing)
- From: Andy Hammersley <hammersl@esrf.fr>
- Date: Wed, 20 Dec 1995 06:53:08 -0500 (EST)
Hi Everyone, I have a few comments on the comments ! 1. The term archiving has come up a few times. i.e. "CIF is an archive" format, and Yves thinks that one of the aims of "imageNCIF" should be to archive images. My (limited) understanding on present CIF, is that it is mainly used as a standardized way of submitting (processed) crystallographic data to Acta Cryst. Of course this doesn't mean that Acta Cryst. and others don't archive the entries. What is meant and implied by "archive" ? Does it mean any more than: "The format must be supported (supportable) in the future, and must be appropriate for present and forseeable technology." ? 2. The difference between proposal 2 and 4. Proposal 2 involves a separate "header" file, and a separate "data" (binary) file. Proposal 4 (in at least one scenerio) would store both "header" information and "data" in the same file. An advantage of proposal 2 (compared to 4) would be that existing CIF tools would be able to work directly on the "header" file. For 4, if the "header" section is very similar to CIF, then an extraction tool could be used to extract the header section and create an ASCII file which could then be used with standard CIF tools. If the format used is well defined and simply related to CIF (whilst being "binary"), this extraction tool could be very simple to write, and be very portable. A disadvantage of proposal 2 is that a single "image" would be stored in two separate files. This provides the opportunity for the "header" information to be separated from the "data" (Remember Murphy's law) Depending on how a sequence of n "images" was stored, you might have 2*n files or n+1 files. Image formats of type 2 do exist (e.g. Hamburg OTOKO / BSL) format, but the vast majority of existing image formats fall into the category defined by proposal 4. 3. Is "BINARY" a dirty word ? 10 years ago I guess the answer was YES. Today I don't think it is. With internet/ftp/WWW, etc. many people pass pictures of naked women (and occasionally other things) around the world without even thinking of all the potential problems. TIFF and many other "binary" formats show that byte ordering differences etc. can be handled (I use TIFF as an example as it is entirely binary based, including the "header" information.) Personnally I'm still uneasy about floating point representations, but for integer based images practically there is no longer an issue. Yves says that "images should be easily transfered through the network." An aim with which I'm sure most of us would agree. However, this is NOT reality at present, at least not for the quantity and size of images which many scientists produce. From or to the ESRF I think around 10 Mbytes is the practical limit which can be successfully transferred over internet. This of course is a bandwidth/shared usage limitation and we can all hope will increase with time, and some of you may be luckier. What does this mean, if anything, for image formats: 1: Transfer by tape, WORMs, etc. will continue to be a major need; 2. Efficient compression is desirable. 4. Graphical Description of "image" data. I think that I understand the idea, and Brian has now given examples, however I can't see this working in practice. My main aim would be the transfer of raw detector data from acquisition point to analysis software. For this I don't want to loss any information whatsoever, so the value (and meaning) of every single pixel/bin needs to be preserved. The crystallographic information in the image, is much smaller than this, but if you want to check that the detector was working properly that day, it can be very useful to look at the exact distribution of pixel/bin values. Even if a suitable form could be developed for a Laue image, how could that be used for a small angle scattering image ? At present we are talking about crystallographic "images" of many different types. 5. The aim of ("imageNCIF") Yes, the aim is essentially the same as that of the IUCr CIF project. I added the word "experimental" on a re-wording, partly to make my definition different that of the CIF project ! So if the basic aims are exactly the same, why should the mechanism for achieving them be different ? 1. The world has changed (slightly) since CIF was set-up. See above. Whilst I agree that CIF must maintain backwards compatibility, it seems unwise to try to restrict an image format of today (and the future) to this past. 2. The scale of the problem is completely different. Once data is processed to a list of hkl's and I's, or somethingelse, the quantity of information is enormously reduced from the raw data. This is another reason that I feel that the word "experimental" is useful. One difference of the scale of information, is the desirability of human-readability and (ASCII) print-outs of image data. Most people (I believe) do not want text print-outs of the pixel values of 1000x1000 pixel images. False colour representations/ 3-d surface plots/ contour plots etc. are generally much more useful. Given both common aims and vast scale differences, is it not wise to develop separate, but related formats ? Thanks for the replies. Seasonal Greeting, Andy
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