More Detail

• Terms and Conditions of use
  (copyright and ownership)
   
  
• A quick tour of the ISO format
  • What the format checker does
  • How to "construct" ISO files
  
   
  
• For system administrators-
  a note on syntax, security,
  and MIME type.

The code from which the present applet was derived was written by Guillaume Cottenceau at Imperial College and that code is
Copyright © 1998 G. Cottenceau.

That applet was originally designed to display the extensive possibilities provided by the JCAMP-DX format for spectroscopic data from IR, UV, NMR and other techniques.
Virtually all the JCAMP facilities have been removed here.

The Java Applet is "public domain" and "free to use" but is not public property: Alan Carrick is the author. A copy of the Java source code can be obtained here, or in case of difficulty, from the author.

An introduction to the format is available in the scientific literature:

Surface and Interface Analysis, Vol. 27, (No. 7), pp. 693-694, (July, 1999) (ISSN 0142-2421)

"Summary of ISO/TC 201 Standard:1 ISO 14976:1998 - Surface Chemical Analysis - Data Transfer Format"
M.P.Seah.

and this provides an overview of the thinking behind the standard.

 

An original publication describing the "VAMAS" format in detail is also available in the literature:

Surface and Interface Analysis, Vol. 13, (Nos.2&3), pp. 63-123, (November 1988) (ISSN 0142-2421)

"VAMAS Surface Chemical Analysis Standard Data Transfer Format with Skeleton Decoding Programs"
W. A. Dench, L. B. Hazell, M.P.Seah, and the VAMAS Community.

Whilst this is no longer exactly the present ISO standard, this article contains a great deal of valuable background information, detailed formalism, and practical application guidance. It is certainly "recommended reading".

 

An annotated version of the ISO-14976 header information for the PET spectrum used in the applet examples in these pages can be displayed in a separate window now for reference. Use it alongside the sections below.

The ISO-14976 SDTF is text based, consisting of (unannotated) header information followed by (a number of blocks of) ordinate values (at regular x-increments) as data. The format proper accommodates all techniques commonly used in Surface Chemical Analysis.

Whilst all the header information has meaning and usefulness, only a few key items need be identified and used in simple spectrum display: this is the approach adopted here and described below.

The checking procedures in the applet are very simple, and concentrate on the "invariant" aspects of the format. Incoming information is divided into separate lines of (text) data, and each line's content examined. The first check is for the word "VAMAS" (no other part of the "format identifier" (other than "new line") is checked): successful location of the format identifier line signals the start of the SDTF proper and its header information. Everything before this is ignored.

The displayed spectrum title is derived from the "experiment i.d." (line 5).

The checker then looks for the "technique" identifier (line 27 in the example - but note that this line number could vary, depending on the "number of comment lines" and whether or not the spectrum implements the new (ISO-14975) "information formats" protocol). "XPS" is the only technique allowed here at present: others will cause the applet to fail.
Next, the "abscissa start" and "abscissa increment" are sought (lines 49, 50): these lie in fixed positions relative to the "technique" identifier. "abscissa label" (line 47) and "abscissa units" (line 48) are stored en passant. The applet y axis label is taken as the "corresponding variable label" (line 52: "no units" assumed). Finally line 62 is located ("# ordinate values") and from this other required values calculated. The next two items (lines 63 and 64) are skipped before the data points proper are read.

The ISO "end of experiment" terminator is not required since the applet will decode and display only a single spectrum or spectrum region: other information, which may be perfectly valid in terms of the full ISO specification, will be ignored.

If it is desired to "fabricate" a data file which can be displayed by the applet - for example for test purposes, or if a data system which writes valid ISO-14976 files is not available, it is a simple matter to copy a dummy ISO-14976 header (for example, from the PET spectrum here) and append a series of ordinate values to that, changing the x-start, x-increment, and no. of x values lines appropriately (lines 49, 50, and 62 in this example). No formal "end of experiment" terminator is required, as mentioned above.
Care should be taken when using files generated by text editors which are then transferred to web servers which might interpret "newline" characters differently than expected: the SDTF requires "CR-LF" as line terminator: some servers might view this as two lines - which is NOT valid for the applet's checking routine.

Note: this type of "cut and paste" procedure does NOT provide a valid ISO-14976 format spectrum, merely one that the applet checker will recognise and display. It is NOT a procedure for generating spectra in the correct format and is NOT RECOMMENDED for anything other than ad hoc experimentation.

Broadly "HTML 4.0" should be followed, avoiding the "proprietary" tags, thus in general only the following tags and attributes should be used:

<APPLET

ALIGN = TOP | MIDDLE | BOTTOM | LEFT | RIGHT

ALT = alternative text

ARCHIVE = URL of archive file

CLASS = class name(s)

CODE = URL of Java class file

CODEBASE = URL for base referencing

HEIGHT = pixels

HSPACE = pixels

VSPACE = pixels

WIDTH = pixels

>

<PARAM> elements
Alternative content

</APPLET>

 
The parameter types and their required elements are described elsewhere.

The applet is "unsigned" and so must be regarded formally as "insecure"; (the original JCAMP applet implemented Netscape security signatures)

The ".vms" file extension is used for the spectra and is in process of submission through the IETF as a "Chemical MIME" type. The present status is "experimental" (i.e. the type/sub-type) "chemical/x-vamas-iso14976" should be set. Since the format is solely text based, however, http systems (and browsers communicating with them) will in general react correctly if configured to serve (or read) unknown MIME types as "text/plain". In most cases this will be the default action.

 
"Java", "HotJava" and the "coffee-cup" logo are trademarks of Sun Microsystems Inc. and acknowledged.

Copyright © Acolyte 1999 Last Update: 00/01/24