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Processing a Series of Spectra

Some experiments require the acquisition of many similar spectra. Kinetic experiments, variable temperature experiments, batch analysis, are typical examples.
At least a part of the processing is common to all the elements of the series and it's convenient to automate this task.
Here we show how to proceed when each spectrum is stored in its own file/folder and all of these files or folders are organized into a larger folder.

To Process All the Spectra into a Folder:

Step 1

Open a representative spectrum (often the first of the series) and process it in the way that's more correct for you. It will represent the model for the other elements.

Step 2

Choose Process > Process Folder.

In the dialog that appears, you are going to specify when and how the processing of the other spectra will differ from the processing of the model.

You'll also specify how the results will be shown.

Step 3

For the Phase Correction you have 4 choices:

Respect the correction that already exists in each document (if it has been already processed).

Copy the correction from the model: this rarely works, because spectrometers aren't stable enough.

Apply the simple algorithm for automatic correction.

Apply the advanced algorithm for automatic correction: this is normally the best choice.

Step 4

For the Baseline Correction you have two options:

You can choose “Automatic First Order Baseline Correction”, which is equivalent to the menu command “Straight Line”.

If you don't choose this option, and have already applied an automatic correction to the model, the same correction with the same parameters will be applied to the other spectra.

Step 5

Choose how to Reference the frequency scale:

The first option is doing nothing.

The second option is to look for a known reference peak into a given interval, centered around its correct frequency. The algorithm is simple: iNMR assumes that the highest peak of the interval is the reference peak and corrects the frequency scale accordingly. You need to specify the correct frequency of the reference peak and the interval to search into.

The last option is to align all the spectra to the model, edge to edge. The spectral width must be exactly the same in all the spectra.

Step 6

Do you need to combine the spectra together?

Normally you want to leave all the windows open for inspection, for further processing or for adding the external spectra, as overlays, to the window of the model. There's a limit, though: a computer becomes extremely slow when there are too many windows. iNMR, to prevent this problem, doesn't open more than 30 windows. You should try a different approach when the number of documents is higher.

You can, for example, visualize all the spectra into a single window (the model's window). These spectra are called Windowless Overlays because they have no window of their own. As long as a spectrum already behaves as a windowless overlay somewhere, you can't open the same document into another window.
If you save a spectrum with more than 20 normal overlays, the next time you open it, iNMR will transform them into windowless overlays.

With the windowless overlays you reduce the number of windows, but not the number of documents. You save more memory if you create a single, new, file. There's a requirement: the names of the starting spectra, all 1-D, must form a sequence of natural numbers. The result will be a real matrix, called Pseudo-2D Matrix. You have to open this resulting file by yourself.

Step 7

The remaining controls of the dialog are self-explanatory. The processing functions that are not mentioned (from solvent suppression to binning) are applied nonetheless (if they have been applied to the model, of course).

Overwrite Existing Processing is a sort of main switch, and should be leaved ON.
Turn it OFF is when you are only interested into creating windowless overlays, starting from documents that have already been processed.

Step 8

Click Run to start the calculations.

If you want to reprocess again with different options, you can do it how many times you want; there's no need to close or to reload the spectra.

Step 9

To save the windowless overlays, turn on the User Preference “Automatically Save Documents When Closing” (into the dialog iNMR > Preferences).

The overlays will be saved when you close the hosting window. When you choose Save, only the document that owns the window is saved.

There's no other way to save windowless documents.

A completely different approach consists into writing a script and running it from the console; the latter contains an option called “for all documents”.

If you simply want to open all the spectra contained into a folder: on Windows, use the command File > Open Folder; on the Mac, either drag the folder onto the iNMR icon or use the Open File dialog and select all the files simultaneously.

Related Topics

Plotting Many Spectra Together with the Overlay Manager

Tabulating the Integrals of a Series

The Console: Command Line and Script Editor


Web Tutorial

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