Miscellaneous Tools
Left Shift - LS
This command eliminates the first data point, and adds a zero point at the end to keep the data size the same. In the case of data containing multiple slices, by default, the operation is applied to all slices.
The command allows the following command line arguments:
LS this - apply the LS only to the displayed slice
LS n - where n is the number of points to shift; the default is 1
LS this n - apply a left shift of n data points to the currently displayed slice only
Right Shift - RS
This is similar to LS above, with the same options, except that points are eliminated from the right end of the data, and replaced with zeroes at the beginning.
Swap Real and Imaginary - RI
This can be performed on both FIDs and spectra. When performed on a FID, the spectrum after FT will look different, depending on whether the data were acquired by simultaneous acquisition of data points into the 2 quadrature channels or by sequential acquisition of data points alternately into the 2 channels (as is done on many Bruker spectrometers). In the former case, the spectrum will be reversed. In the latter case, artifacts will appear in the spectrum which resemble quadrature images.
Invert Imaginaries - II
Performs a 180 degree phase shift on the imaginary half of complex data. This is useful if the sense of direction with the mouse movements while phasing seems backwards. If performed on an FID, this will reverse the resulting spectrum after FT.
Extract
This command allows a user-defined region to be extracted from a spectrum. By default, the currently displayed zoom region is used, and both ends of the spectrum that are not displayed are lost. Parameters such as data size and spectral width are modified to reflect the new data. If the data are multi-dimensional, the same region is extracted for all slices.
This can also be used to extract a selected range of slices from a 2D data set. By default, the currently displayed zoom region is used, and slices that are not displayed are lost. Parameters such as data size and spectral width are modified to reflect the new data.
The command allows the following command line arguments:
extract 1D - extracts the currently displayed region; this is the default
extract 1D n m - where n and m are the data points defining the region the user desires to extract
extract 2D - extracts the currently displayed slices
extract 2D n m - where n and m are the slice numbers defining the region the user desires to extract
Decimate or Dec
This operates differently for time-domain data (FID) and for frequency-domain data (a spectrum).
For a spectrum, dec reduces the number of data points in the currently displayed dimension. By default, the size is reduced by half the number of points by discarding one-fourth of the data points from each end. A different number can be specified on the command line (dec n, where n is the number of points to be discarded from each end). Spectral width is adjusted.
For a FID, the data size is reduced by half by averaging pairs of data points.
Determine Ernst Angle - ernst
The Ernst angle (Richard R. Ernst, Nobel laureate in chemistry 1991) is the
optimum flip angle for a given recycle time (TR) and T1 relaxation time, giving
the maximum signal. The Ernst angle is derived by optimizing the three parameters relative to each other and can be calculated
by using the equation below (the expression is valid as long as TR < T1)
cos (TipAngle) = exp (-TR/T1)
Command syntax is
ernst x y where x is the recycle time and y is the T1 relaxation time.
High-Pass Filter - HFP
This routine allows the user to define a frequency limit and apply it to an FID. Signals above that frequency limit will remain unchanged and signals at lower frequencies will be filtered out from the currently displayed FID.
This is done by creating a function in the frequency domain which is equal to one for all frequencies greater than the cut-off value and equal to zero for all frequencies less than the cut-off. The function is converted to the time domain using a Hilbert transform. This time domain function is then correlated with the FID to remove high frequency components.
The user can adjust the order of the function, which is the number of pts in the correlation function. The more points, the sharper the cutoff, but the operation also becomes slower. As the order approaches the number of points in the FID, the filter approaches being perfectly square.
If the number of data points is not equal to a power of 2, it is important to execute a zero-fill to next higher power of 2 before executing the digital filter. Failure to do this will hang the program.
The command options are:
hfp - apply the filter using the current parameters
hfp order n - to set the order of the correlation function to n points
hfp cutoff f - to set the cut-off frequency to f
Low-Pass Filter - LFP
This routine allows the user to define a frequency limit and apply it to an FID. Signals below that frequency limit will remain unchanged and signals at higher frequencies (measured from the center of the spectrum) will be filtered out from the currently displayed FID.
This is done by creating a function in the frequency domain which is equal to one for all frequencies less than the cut-off value and equal to zero for all frequencies greater than the cut-off. The function is converted to the time domain using a Hilbert transform. This time domain function is then correlated with the FID to remove high frequency components.
The user can adjust the order of the function, which is the number of points in the correlation function. The more points, the sharper the cutoff, but the operation also becomes slower. As the order approaches the number of points in the FID, the filter approaches being perfectly square.
If the number of data points is not equal to a power of 2, it is important to execute a zero-fill to next higher power of 2 before executing the digital filter. Failure to do this will hang the program.
The command options are:
hlp - apply the filter using the current parameters
hlp order n - to set the order of the correlation function to n points
hlp cutoff f - to set the cut-off frequency to f
Last updated: 5/5/08