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Translation

Translation

NUTS Help

Data Translation

Before a FID or spectrum can be processed by NUTS, it must be translated into the NUTS file format, called the Common Data File format. Most files can be translated from within NUTS with the Import command (IM). IM automatically detects the origin of the file and applies the appropriate translation. Import is also available from the File menu.

The What’s New text file supplied with NUTS will list new and modified imports.

Nicolet 1180 and 1280 Dexter NT spectrometer data files
Nicolet/GE TMON data files from NT, QE and GN spectrometers
GE Omega spectrometer files exported with the GE Export command
Bruker Aspect 3000 data files
Bruker X32 and UNIX data files, including digitally filtered data
Varian VXR 5000, Unity and INOVA data
JEOL Delta, GX, EX, FX, Lambda, ALS and Alpha data files 
Chemagnetics files
WinNMR files
Tecmag MacFID, MacNMR and NT-NMRfiles
ATI ASCII and binary files
SMIS data files
Analogic files
PC-NMR files in Lybrics format
Process Control Technology data files
Felix new format
NMRi format
ASCII format — data should be in the form of (real, imaginary) pairs
JCAMP format
Galactic (Grams-32) files
AZARA 
Elcint 
Philips MRi Spectroscopy Data – Type II
Siemens 

It is possible to bypass the automatic translation process and "force" a specific type of translation.  This is not generally recommended because it is easy to select the wrong type, which can cause NUTS to hang or crash.  In all but rare cases, it is best to do IM and let NUTS do its own auto identification process.

If you MUST force a type, the user can enter the non-2-letter command mode and enter a command like:

IM -type "force_type"

where allow words for "force_type" are:

NTDEXTER
NTTMON
GN
QE
NTDEXTER_NICNET
NTTMON_NICNET
GN_NICNET
QE_NICNET
OMEGA_ONE_FILE
OMEGA_TWO_FILE
BRUKERASPECT
FELIXNEW
ASC
CDFFDOS
CDFFUNIX
JEOL
JEOL_GENERIC
ATI
BRUKERASPECTBS
BRUKERETHERNET
SMIS
VARUNIX
BRUKERUNIX1
BRUKERUNIX2
BRUKERUNIXSGI1
BRUKERUNIXSGI2
BRUKERX32_1D
BRUKERX32_2D
BRUKNET
PCT
FXQ
ANALOGIC
LYBRICS
CHEMAGNETICS1
CHEMAGNETICS2
CHEMAGNETICS3
GALACTIC
IRIS_FELIX
CDFFINT
MACFID1
MACFID2
MACNMR1
MACNMR2
GEMS
FLXAII
NMRI
PHILIP_MR
JEOL_LAMBDA
WINNMR1DOF     (Bruker WinNMR 1D Old Conversion FID)
WINNMR1DOS     (Bruker WinNMR 1D Old Conversion Spectrum)
WINNMR2DOF     (Bruker WinNMR 2D Old Conversion FID)
WINNMR2DOS     (Bruker WinNMR 2D Old Conversion Spectrum)
WINNMR1DNF     (Bruker WinNMR 1D New Conversion FID)
WINNMR1DNS     (Bruker WinNMR 1D New Conversion Spectrum)
WINNMR2DNF     (Bruker WinNMR 1D New Conversion)
WINNMR2DNS     (Bruker WinNMR 1D New Conversion)
WINNMRAQS_FID     (Bruker WinNMR using *.aqs file)
WINNMRAQS_R     (Bruker WinNMR using *.aqs file)
WINNMRAQS_I     (Bruker WinNMR using *.aqs file)
WINNMRAQS_SER     (Bruker WinNMR using *.aqs file)
WINNMR1D97     (Bruker WinNMR 1D year 1997)
WINNMR2D97     (Bruker WinNMR 2D year 1997)
BRUKER_24_to_32     (Bruker Aspect transfers with LightNet to X32)
BRUKER_1R     (Bruker Real Only data)
JEOL_ALS 
JEOL_ALPHA 
JEOL_DELTA 
JCAMP 
XWINNMR 
TECMAG_NT 
AZARA 
ELCINT 
PHILIPS2     (Philips MRi Spectroscopy Data – Type II)
SIEMENS 

Varian data from XL and older Gemini spectrometers, based on the older computer, is translated into the NUTS format using a separate translation program called V_Helper, written by Steve Silber at Texas A&M.  This program allows a PC to read a Varian floppy despite its foreign format.

It is usually best to use the auto-detect capability of the IM command and let NUTS identify the file type. It is possible to force NUTS to apply a specific translation, regardless of the file’s origin, by selecting the desired file type from the File / Import menu. However, this can result in errors, including termination of the NUTS program, if the chosen format does not match the actual file type.

See details about how NUTS identifies different file types. Some spectrometers create multiple files for one data set, and the user must be careful to transfer all relevant files to the PC. In some cases, this involves creation of multiple layers of subdirectories, and it is important to create the subdirectories correctly on the PC, or NUTS may fail to locate part of the data.

For detailed information about the file format, see CDFF.

Fortran code to write data in NUTS format (contributed by Todd Alam)

Data files can be displayed using the look (LO) command, useful for "hacking" apart data files.

IM — Import File

Performs data translation "on the fly" and opens the translated file. NUTS automatically detects the source of the file and applies the appropriate translation.

For data from Unix computers, in most cases, multiple files are created when the spectrum is acquired. A directory is created bearing the file name entered by the user, into which all relevant files are placed. NUTS expects this file structure when it searches for the necessary files, so when files are transferred to the PC, the directory structure created on the PC must match that of the original data.

There are also some issues specific to Bruker data which may be important.

If a File Open (GA) command is attempted on a file which has not been translated into the NUTS format, a message appears asking if an auto-detect import should be attempted. If an import operation is to be included in a Link, use the GA command and not IM. The reason for this is when the GA command is used in a Link, the user is prompted for the file name only once. NUTS is smart enough to perform an import if necessary.

When IM is used, the original file remains unchanged with its original name. The translated file is given a file name consisting of a dollar sign ( $ ) appended to the beginning of the original file name. This file is then loaded into NUTS and becomes File A. For 2D data, the translated file is always saved to the disk. For 1D files, whether or not the translated file is automatically saved to the disk depends on which version of NUTS is being used. It is saved in the Win95/NT version only. This file name is printed at the top of the NUTS screen and is printed on all plots. Because DOS can only handle files with file names up to 8 letters, appending an extra character to the file name can create problems for file names of greater than 7 letters (not including the extension). The user can always save the file under a new name with SB or chose Save As under the File menu.

The default directories for file importing (with
IM) and for the file Open and Save operations (eg, GA and SA) can be different and can also be set in the NUTS.INI file. (Note that this does not work correctly on the Mac.) The translated file is saved in the directory currently being used for Open and Save operations. The current settings for these directories can be viewed with the WP command.

ZZ – Auto importing

This command imports a file with a default file name, as defined in the NUTS.ini file. This is useful in cases where the file to be opened always has the same file name and path name, as might be the case with some file transfer programs. The file name, with full path name, and the file type are defined in the NUTS.ini file. The relevant lines in the NUTS.ini file are shown in the examples below:

ZZ_FILE_PATH = C:NUTSDATAFILE.QE

ZZ_FILE_TYPE = Lybrics

The path name must be the full path name. If ZZ_FILE_TYPE = Auto is used the imported file will be auto identified using NUTS standard file detection scheme.

BS — Byte Swap

Used mainly for debugging data import operations. Reverses the byte order of floating point data. Data from some spectrometers requires this operation.

BV — Byte Swap to VAX byte order

Used mainly for debugging data import operations. Reverses the byte order of floating point data. Data from some spectrometers requires this operation.

CX — Convert data

Used mostly in the course of identifying and debugging data import problems. Allows selection of one of 3 options for imported data:

Byte swap for floating point data
Convert data from integer to floating point
Convert data from integer to floating point with byte swap

These can be useful to try when data does not appear to have imported correctly.

LO — Look at data file

This is a keyboard command that displays the contents of a specified file, useful for "hacking" apart data file formats. The user specifies a format from the following choices, which controls how the file’s contents will be displayed. These choices are available from the Display menu or by typing T.

Binary
CDFF (the format for NUTS files)
Unix
Macintosh
Aspect
1280

The default starting position for displaying the file is at zero, the beginning of the file. This can be changed from the Edit or Display menu, or by typing P. Scrolling up and down through the file is possible using the Page Up, Page Down and arrow keys. The currently displayed information can be copied to the Windows clipboard using Control-C or from the Edit menu. A new file can be opened from the File menu or by typing F. To exit this subroutine, type<Enter> or choose Exit from the File menu.

SE — Visually inspect data file

This command was created to aid in the visual inspection of unknown data files.  In the 2-lettered command mode, the command SE first brings up a dialog box and allows the user to select the file to look at. After this selection, another dialog box comes up which allows the user to specify how he wants to view the data. After selecting all the options and clicking OK, the data is imported without translation in that manner as a 1D file thereby allowing the user to visually “see”. This can aid if finding actual NMR data in unknown files. Hint – It is often useful to first load an NMR file with NMR data of about the vertical scale size the user expects and then do an FS to fix the scale. This allows all the “junk” to be imported and go off-scale without shrinking smaller NMR data so small as not to be seen.

In the non-2-lettered command mode, the SEE command with no arguments behaves as above. The user can give arguments as shown below to directly import the specified file as instructed in the arguments:

SEE [Bytes2Skip] [WordType] [Complex] [Endian] [FileName]

where:
Bytes2Skip is the number of bytes to move into the file before starting to read the data
WordType is one of CHAR / SHORT / INT / FLOAT / DOUBLE
Complex is one of REAL / COMPLEX
Endian is one of BIG / LITTLE
FileName is the name of the file to import.

 

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Last updated 12/5/02.