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Arrayed Mode 2D processing

Arrayed Mode 2D processing

NUTS Help

Arrayed Mode 2D processing

This is included in NUTS Professional version only.   

May 2003 – A preliminary 4D arrayed mode was created.

May 2002 – arrayed mode was modified to allow phase correction of processed data in both dimension.  See details.

The entire 2D data set is placed into memory, resulting in much faster 2D processing (a factor of ~12 in our tests on Windows, and a factor of ~40 on Macs).  The "normal" way of processing 2D data is by looping through a command string, applying the commands to each slice in turn.  With the Arrayed Mode, the entire data set is placed into memory, and each command operates on the entire 2D data set; i.e., typing FT one time transforms the all slices.

The amount of available memory needed is ~2.5 times size of the 2D data set being processed.  If sufficient memory is not available, NUTS will use virtual memory, which is very slow.

As new 2D processing features are added to NUTS, many function only in the arrayed mode.

See step-by-step processing instructions for different types of 2D data, including sample macros.

Using Arrayed Mode

The AR command (not yet in menus) is a toggle, and turns on/off arrayed mode.  In a macro, you can also use

Set array_on 
Set array_off
Set array_pairwisecomplex

The only indication you will have that Arrayed Mode has successfully been entered is the appearance of the words "Complex Arrayed" or "Pairwise Complex Arrayed" on the gray status bar.  On exiting the Arrayed Mode, this will change to say "Non-Arrayed".

http://www.acornnmr.com/content/uploads/ar.gif (11058 bytes)

Most commands are "array-aware", meaning that if in arrayed mode, NUTS will apply the command to all slices.  However, some commands apply only to the displayed slice.  It is important to keep track of when NUTS is in the arrayed mode, and understand whether a given operation affects the entire data set or a single slice.

Type AR to enter Arrayed Mode.  Process in the first dimension with commands such as

GA BC MS FT

These commands can be typed directly, or can be executed as a Link or a Macro.  Note that there is no SC command and no IN command. 

Phasing using any of the phasing commands will display just one slice while phasing, but on exiting the phasing subroutine (PE or PH), the correction is applied to all slices. See phasing details.

Next, execute TD to rotate the matrix in preparation for processing in the second dimension.  Execute an appropriate series of commands, such as

MS FT MC

Typing AR exits Arrayed Mode.  You will be asked if you want to save the data before exiting Arrayed Mode, which you should do, or you will lose the processing just completed. 

Note that you cannot go back to the previous step, as the data is not saved at each step, as is the case when processing in the "regular" mode.  Of course, the original data is unchanged, so it is always possible to go back and start over.  If UnDo is turned on, typing Ctrl-Z will undo the last command.  However, it is not recommended to use UnDo in arrayed mode because of the large amount of memory required.

After processing the second dimension, you can execute another TD command to view the data with the first dimension displayed horizontally.

** Starting in May, 2002, the Arrayed Mode can be configured for different Processing Types, depending on what kind of 2D data is to be processed.  This allows phase-sensitive data acquired as TPPI,  hypercomplex, echo-antiecho or States-TPPI to be processed while maintaining complex data correctly in both dimensions, so that the data can be phased in both dimensions after processing.

In the past, NUTS discarded the imaginary half of the data following FT in the direct dimension.  This made it impossible to phase the data in the direct dimension after further processing.   Ability to phase the frequency-domain data requires that the imaginary half of the data be carried through the entire processing operation, and that the Transpose operation correctly sort the data to maintain complex data pairs in each dimension.

For hypercomplex, echo-antiecho and States-TPPI data, before entering Arrayed Mode, type PT (Processing Type), which displays this dialog box:

The important changes involve setting Processing Type to either 2D_HyperComplex or 2D_EchoAntiecho, for processing the corresponding type of phase-sensitive data.  

2D_HyperComplex is for processing hypercomplex data (method of States, et al).

2D_EchoAntiecho is for processing gradient data acquired as echo-antiecho (also referred to as pn data).

2D_StatesTPPI functions the same as 2D_HyperComplex.

By default, 1D is chosen if the data set consists of only 1 slice, or 2D_Magnitude if the data contains more than 1 slice.  2D Magnitude is identical to the Arrayed Mode in previous versions.

For 2D_TPPI mode, it is not necessary to set the Processing Type from this screen, because additional manipulations are needed.  See details

If one of the 3 modes, 2D_HyperComplex, 2D_EchoAntiecho or 2D_StatesTPPI, is selected, then when arrayed mode is entered, the data is sorted and displayed in "Pairwise Complex" arrayed mode.    

If PT is not set, entering arrayed mode with the AR command will treat the data as magnitude data, and phasing after processing will not be possible.

Previously, the value NUTS displayed for data size in the indirect dimension (number of slices) was the total number of slices, not number of complex slices.  Hypercomplex, echo-antiecho and States-TPPI data consist of pairs of FIDs (2 FIDs acquired for each t1 value).  For example, if 128 t1 values were collected, NUTS would display the total number of slices as 256 (2 FIDs for each of the 128 values).   In "Pairwise Complex" arrayed mode, NUTS reports the data size in the indirect dimension as 128 complex points, and would display only 128 points (the first of each pair of FIDs).

Important: As of Nov, 2002, Nuts will look at the PT value when a file is opened, and enter/exit arrayed mode, as appropriate.  

With previous versions, to open a data set that had been saved while in the "Pairwise Complex" arrayed mode, you must first re-enter arrayed mode.  This is because of the data sorting required to display the data properly.  Similarly, you must exit "Pairwise Complex" arrayed mode before importing or opening data that has not been saved from within that routine.  Exit AR, ope
n the data set, choose the correct processing type using PT, then type AR to enter the correct arrayed mode.

The details of the data sorting that is performed in Pairwise Complex arrayed mode, and some additional commands, can be found here.

In macros, the Processing Type can be set to any of the values shown in the figure above.  This must be done in the non-2-letter command mode.  For example,

2f
pt 2D_hypercomplex,
2n,

The comma at the end of lines while in non-2-letter command mode are interpreted as an <ENTER>, and are required.

Processing instructions (see also: Processing 2D data)

Hypercomplex data 

Import or open the 2D data file, type TP and select 2D_Hypercomplex.  Click on OK to close this box.  Type AR to enter the "Pairwise Complex" arrayed mode.  Apply an appropriate window function, FT and phase.  Type TD to transpose the data.  Apply an appropriate window function, zerofill if desired, FT and phase.  You can go back and forth between the dimensions with TD, and phase in each.  

A detailed sequence of processing commands can be found here.

Note that the "tr tr st" series of commands is not used in this mode.

States-TPPI data

Import or open the 2D data file, type TP and select 2D_StatesTPPI.  Click on OK to close this box.  Type AR to enter the "Pairwise Complex" arrayed mode.  Apply an appropriate window function, FT and phase.  

Before transposing, it is necessary to invert every other slice.  To do this, type 2f to exit the 2-letter command mode, and type invert even <ENTER>.  Then return to 2-letter command mode by typing 2n <ENTER>.

Type TD to transpose the data.  Apply an appropriate window function, zerofill if desired, FT and phase.  You can go back and forth between the dimensions with TD, and phase in each.

A detailed sequence of processing commands can be found here.

Note that the "tr tr st" series of commands is not used in this mode.

Echo-antiecho data

Import or open the 2D data file, type TP and select 2D_EchoAntiecho.  Click on OK to close this box.  Type AR to enter the "Pairwise Complex" arrayed mode.  Apply an appropriate window function, FT and phase.  
Type C2 to add and subtract each pair of spectra.
Type TD to transpose the data.  Apply an appropriate window function, zerofill if desired, FT and phase.  You can go back and forth between the dimensions with TD, and phase in each.

A detailed sequence of processing commands can be found here.

TPPI data

First be sure you are in non-arrayed mode, and open the unprocessed data.  Then type (in the non-2-letter command mode):

ar tppi2pairwise

This does 2 things.  The pairwise arrayed mode is entered, and zeroes are loaded into the "B" half of the data.  The process type is automatically set to “2D_TPPI”, and the TD will do no swapping of data pairs.   

Be sure to use RT (real transform) in the indirect dimension!

A detailed sequence of processing commands can be found here.

See also: 

Examples of 2D data processing.  Sample macros are available for processing common types of 2D data, with detailed explanation.
Comparing
multiple 2D data sets

 

Last updated: 7/20/04