TUTORIAL

Dr. Peter Blümler

Informations

• Publié par: Udru
• Nombre de lectures: 62
• Langue: English

Extrait

WAVE-Tutorial for NMR-Applications
Version: 1.0 / November 1995
© Peter Blümler, School of Physical Sciences, University of Kent at Canterbury,
Canterbury, Kent CT2 7NR, United Kingdom .
Tel.: ++44-(0)1227-82-3228 4-(0)1227-82-7558 email: [e-mail]
Contents:
1 . Introductio n ...................................................................................................................................... . 2
2 . Philosoph y ....................................................................................................................................... . 4
2.1 WAVE data and plottin g ........................................................................................................... . 4
2.2 NMR routines...............................................................................................................................4
3 . Principles of data handlin g .............................................................................................................. . 5
3.1 Data types and conversio n ........................................................................................................ . 5
3.2 Creation of vectors and array s ................................................................................................... . 6
3.3 Array handling and assignmen t ................................................................................................. . 7
3.4 Operators and mathematical function s .................................................................................... . 10
4 . Compiling the modules and the LIBCOMB Progra m ..................................................................... . 14
4.1 Compilation of single module s ................................................................................................. . 14
4.2 Installation of the program s ..................................................................................................... . 15
4.3 Combining modules to a librar y ............................................................................................... . 16
5. Description of the module s ............................................................................................................. . 18
5.1 Input/Output module s .............................................................................................................. . 18
5.2 Basic NMR module s ..................................................................................................................27
5.3 Imaging module s .......................................................................................................................37
5.4 Radial transformation module s ..................................................................................................41
5.5 Simulation module s ...................................................................................................................42
6. Graphic output and printin g ..............................................................................................................45
6.1 Graphic output: Plotting routine s ...............................................................................................45
6.2 Printing the plot s ........................................................................................................................46
7. Source code of the module s ................................................................................................................
FAX: ++4EM
ZZREAD
™
™
WAVE-Tutorial for NMR Applications page: 2
The concept of this tutorial is thought as an introduction for new users, who do not want to get an
„in-depth“ understanding of the programing language, but simply apply some data processing to
their NMR-data. The programms are written for the PV-WAVE PERSONAL EDITION ™ for
Microsoft Windows ™. However, in principle these routines should run in any „WAVE-environment“,
because as far as possible no specific calls of operating systems or displays were used. It should
be mentioned that a special UNIX version exists as well.
The aim of this tutorial is a brief introduction into data handling by WAVE and some of its plotting
routines. Additionally, the programm-libraries written for NMR applications are described and
explained. These libraries contain the following functions and procedures
Procedure
input, output and conversion of data
BRING reading Bruker ASPECT ™ data files
BRUKREAD reading Bruker ASPECT ™ data transferred by
BRUKNET
ESR_DOS reading Bruker OS9 ™ EPR data
reading Bruker UNIX ™ files (
LOAD loading of data written by STORE
MAC_DOS reading of data generated by TECMAG
spectrometers
ORIGIN writing data in ASCII format (for ORIGIN
SFREAD reading data stored in FORTRAN 77 (as used in
the old days of the Spiess-group)
STORE storing of max. 3D data set
reading Bruker ASPECT ™ data transferred by
ZZ-NET
Basic NMR basic NMR modules
exponential multiplication
FT Fast Fourier transform
gaussian multiplication
PHASEN application of phasing parameters to data
PHASIER phasing
PP peak picking
REDFFT FFT of data acquired by the Redfield method
SCALE scaling of data
ZS zeroshifts (left- or right-shifts)
Imaging
BP back projection
IMAGE calculation of magnitude images
MKPRO calculation of BP-like projections from a spin-
density
radial transformationsRadial Transf.
TWOPABEL two point inverse Abel transformation
THREEPABEL three point inverse Abel transformation
ONIONPEEL Inverse Abel transformation by onion peeling
CENTER centering of slices
IAT2D 2D Inverse Abel transformation
IAT3D 3D Inverse Abel transformation
Simulation simulation and fitting
MAKE_FID generation of arbitrary FID
T1FIT fitting exp. growth
T2FIT fitting exp. decay
Z_COIL B-field simulation of single loop coils
NMR imaging library
zero-filling ZF
GM
™)
uxnmr) UXNMR
Input/Output
Explanation Function Library
Introduction [e-mail]
WAVE-Tutorial for NMR Applications page: 3
The programms are shareware as long as they are given to non-commercial institutions, like
universities. Others should contact the author.
For further suggestions, comments and recognized mistakes or bugs please contact the author.
The most actual version of all programs and the tutorial as an PostScript-file can be ordered on
floppy from the author for a small handling fee of US$10,-- (please send cash).
If you want a printed manual, please add another US$10,--.
An actual update of all programs, libraries and this tutorial can be found on the following
web-page: (serve yourself, for free!)
All users are welcome to distribute own PV-WAVE-libraries from this server. I would prefer if you
attach them in an email to me (
Have fun,
Peter Blümler, Canterbury 1999
)
!! IMPORTANT !!WAVE-Tutorial for NMR Applications page: 4
2.1 WAVE data and plotting
WAVE is a high level programming language with very powerful plotting routines. The big
advantages are:
o interactive handling of variables which allows easy data processing for non-routine
applications,
o all routines exist in an easy access default mode, but can be controlled by additional
o the whole session is documented and can easily be converted into makros, functions or
procedures
o setting of the environment, generates a suitable output on printers
2.2 NMR routines
The NMR library is a collection of procedures and functions, which can be applied to the data by
typing in the process. This may appear somewhat inconvenient, but allows interactive controll and
analysis of the corresponding step in data processing. The construction of one „big program“ can
be done, but would restrict the flexibility in usage and increase the possibility of bugs.
Functions are preferred, because they can be incorporated into bigger command strings, while
holding the data temporary.
variables
Philosophy 2.text= ‘Hallo !’
res=BYTE (
res=STRING (
var= 2.43e2
res=COMPLEX ( real [, imaginary])
expr)
temp=2.

res=BYTSCL ( array)
var= 243D
var=255b
res=DOUBLE (
info
expr)
expr)
res=LONG (
res=FIX (
expr)
var = 243
var = 243L
expr)
expr n )

expr 1 , ... ,
res=FLOAT (
WAVE-Tutorial for NMR Applications page: 5
WAVE keeps all the defines variables, vectors and arrays stored in memory. The list of defined
data, their type and length can be listed by typing . A single variable (scalar) can be created
by a statement like . This defines the variable temp as a floating point with the entry
2.00000. If the dot is neglected than it would be an integer with the entry 2 . Some routines need
special types of input variables, but most of them are tolerant. It is important to know that there is
also a hierachy of variables, for instance if a floating point variable is mutiplied with an integer, the
result will be a floating point and not an integer.
3.1 Data types and conversion
a) BYTE
Creation: Creates a byte (0-255)
Converts an expression to byte data type.
Scales and converts an array to byte data typ e.
b) INTEGERS AND LONG-INTEGERS
Creation: from -32768 to 32767 (2 bytes)
Converts an expression to integer data type.
Creation: from -2147483647 to 2147483648 (4 bytes)
Converts an ex