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Reducing the Number of Dimensions

Examining a 2-D (or 3-D) matrix can be difficult, because the screen has two dimensions only. Sometimes it's better to examine a single row, a single column or a single plane, extracted from the bigger matrix. These extractions are possible both in frequency and in time domain.

Some arrayed experiments (e.g.: an inversion recovery experiment) are packaged in the form of a 2-D matrix. They appear as 2-D spectra. You can extract a single row, which corresponds to a single spectrum, and manipulate it as a normal 1-D spectrum.

The sub-spectrum (called extract) takes the place of the main spectrum, until you choose File > Close Extract.
To see the main spectrum and the extract together, it's necessary to save the latter as a separate document, with File > Export.



Visualization of a Selected Row
(in frequency domain)

Create a single horizontal mark with alt-click. If there is no external projection on the borders, the selected row will be displayed (like a projection) on top. You can drag the mark up and down to inspect other rows. To inspect the columns, create a vertical mark with ⌘-click (on the Mac) or Alt Gr-click (on Windows).

Extraction of a Column

Two methods exist:
(1) ⌘-click (on the Mac) or Alt Gr-click (on Windows) to create a mark on the column and choose File > Extract.
(2) Right-click and choose Extract Column.
To return to the whole spectrum, choose File > Close Extract.

Sum of Many Columns

Create as many vertical marks as the columns to add together and choose File > Extract.

Sum of All the Columns

Create one or more vertical marks, it doesn't matter where you place them and choose File > Collapse. On the Mac the command appears when you hold down the alt key.

Skyline Projection

This projection is constructed by selecting the highest point (in absolute value) from each row. Create one or more vertical marks, it doesn't matter where you place them, and choose File > Skyline. On the Mac the command appears when you hold down the control key.

Operations on the Rows

The commands seen so far can also operate on the rows. Delete all the vertical marks (if present) with ⌘-double click (on the Mac) or Alt Gr-double click (on Windows). Select the rows with alt-click.

Extraction of the First(Last) Row(Column)

Put the mark outside the margins of the plot. iNMR will automatically select the nearest row/column.

Extraction of Perpendicular Planes

When the starting spectrum has 3 dimensions, the same commands can extract a YZ plane, corresponding to a vertical mark, or a XZ plane, corresponding to an horizontal mark. From the extracted plane, you can still extract rows and columns in the same fashion.

Extraction of XY Planes

To extract a XY plane from a 3-D matrix, delete all the marks and choose File > Extract; a dialog will ask you which plane to extract: 0 is the first plane (first acquired if in time domain, at the highest frequency if in frequency domain); 1 the second plane, etc...

Moving to the Next Horizontal Plane

When the spectrum has 3 dimensions, press the keys r and t to inspect all the planes in succession.

Repeating the Last Extraction

Frequently you want to experiment with different processing parameters, applied on the same extract. It's not necessary to close and extract again. Just choose File > Repeat.

Exporting a Sub-Matrix

When a spectrum has 2 or 3 dimensions and is, at least partially, transformed, you can save (not extract) a reduced sub-matrix. Each axis will be shorter, but the total number of axes will be constant. You can also select a single point on any axis, thus reducing the number of dimensions. Instead of using the command Extract, choose File > Export and save into the format iNMR document. The sub-matrix will be saved as a distinct file (the bigger spectrum remains open).

You can see from the current window title if you are working with an extract.
The extract and the main spectrum share the same processing parameters, but the display parameters are different. When working with the extract, you cannot create new pages, nor turn page, because the 2-D pages of the document are not compatible with the 1-D extract.

Related Topics

Basic Manipulations