Felix User Guide

D       Data Transfer and Conversion

The data-conversion software for the most popular NMR spectrometers provide easy conversion of NMR data from the native spectrometer formats to Felix format. Data conversion for Bruker Aspect and X32 consoles and Varian Unity consoles can be conveniently accessed from within Felix by selecting the File/Data Filters menu item. The conversion software is located in a subdirectory named /foreign, which exists at the same level as the older /gifts subdirectory.

Data-conversion software for other spectrometer data formats is located in the /gifts subdirectory or can be obtained as described below.

GE/Nicolet 1X80

This includes many types of spectrometers produced by Nicolet and then GE.

Serial: Files can be transferred serially using Kermit, then converted to Felix format by software available from Acorn NMR, (415) 683-8595.

Ethernet: Ethernet hardware must be purchased from GE and used for transfer. GENET (donated by M. Summers) converts to Felix format.

JEOL Alpha

Conversion from the Jeol Alpha data format to the Felix data format is supported through the executable named jeol2felix.

Varian VXR

For UNIX systems, we distribute a program (donated by S. Silber, Texas A&M University) that reads VXR tapes. For PCs, another program is available directly from S. Silber.

The Felix data format

The "new" Felix data format has several advantages over the "old" Felix data format with respect to file structure and cross-platform compatibility. The source code for a program named wn (wn.f) and its associated C modules has been provided in the gifts/newformat subdirectory. This program provides a functional environment for demonstrating and elucidating the subtleties of conversion to/from the new Felix format.

Please also see Appendix E, Data Files, for a more detailed explanation of the Felix data format.

Table 28. Felix data file formats  

In this table, a word is a 4-byte (32-bit) unit of data. The file is logically broken down into three segments, while physically it is just a single stream of bytes. The file contains a pre-header, a header, and then one or more spectra.

Word	Format	Usage
0		Byte key: hexadecimal value 0x04030201.
Header Format:
0	int	Number of words in a header.
1	int	Number of frames (default: 1).
2	int	Data format (0=IEEE float, 1=32 bit integer).
3	int	Currently unused (default: 1).
4	int	Frame size in 32 bit words (default 32).
5	int	Felix version number.
6-94		Room for expansion.
First Frame of Header: D1 parameters
95	int	Number of datapoints.
96	int	Data type (0=real, 1=complex, 2=integer).
97	int	Domain (0=time, 1=frequency).
98	int	Axis type (0=none, 1=points, 3=ppm).
99-110		unused.
111	float	Spectral width.
112	float	Spectrometer frequency.
113	float	Reference shift.
114	float	Reference point.
116	float	Phase0.
117	float	Phase1.
118-126		unused.
Second Frame of Header: D2 parameters (currently unused)
127-158		Same as the first frame
Data Records:
0	int	Number of words in this data record
1	float	First word of data
2	float	Second word of data
3	float	Third word of data
4	float	Fourth word of data

When the data are complex, the real- and imaginary-number components are stored adjacently. Thus the data record looks like the examples given below.

For real data:

N_words, Real_1, Real_2, Real_3, Real_4, ...

For complex data:

N_words, Real_1, Imag_1, Real_2, Imag_2, ...

Built-in data filters

A few data filters are provided directly from the Felix menu interface. The filters currently available include:

• Bruker X32 with binary parameters.
• Bruker X32 with ASCII parameters.
• Bruker Aspect via Bruknet.
• Bruker Aspect via Kermit.
• Varian Unity.

Gift data transfer and conversion filters

With four major spectrometer vendors and several smaller ones, most using nonstandard computers, comprehensive data transfer and conversion is nearly impossible. In an effort to solve this problem, and allow you, the spectroscopist, to spend your time on spectroscopy rather than data conversion and transfer, we provide these programs to users of our software at no charge. Some of these programs were donated by users. All gift software is in the "copyrighted public domain" category. This means that there is no charge for these programs, and that they can be utilized for any nonprofit purposes. The gift software is not warranted or supported by Molecular Simulations.

Included with each directory is a brief README file that describes the conversion routine(s), and a Make script that builds the executable program(s) in that directory.

Table 29. Bruker spectrometer gifts

BRUKER/X32/	Converts Bruker AMX (X32) data w/binary parameters on SGI, SUN, IBM.
BRUKER/aspect/brtape/	Converts Bruker Aspect 9-track tapes on SGI.
BRUKER/aspect/bruknet/	Converts Bruker Aspect data transferred via Bruknet on SGI, SUN, IBM.
BRUKER/aspect/kraulis/	Converts Bruker Aspect data transferred via Ethernet on SGI, SUN.