Igor's Peak finding and Area features

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Tue, 09/15/2009 - 08:24 pm

Hi

I have got a diffraction pattern from an experiment, as shown in this image, I wish to determine positions of the peaks and work out the total area of the entire pattern.

[URL]http://i31.tinypic.com/14t0w9h.jpg[/URL]

I opened the PeakAreasUnipolar.ipf file that comes with Igor's Technical Note, and then I go in Igor's experiment window

->Macros

->Indentify And Measure Peaks in Steps

->Init Indentify Peaks...

in which I set the followings:

peak data wave: wave(Y)
X coordinates for peak data wave: wave(X)
baseline: W_BaselineFit
Peak Threshold: 150
Peak Start End Threshold: 100

and leave all other selections by deflaut.

But as you can see, from the image, that it has actually not indentified any peaks and no lines for thresholds or knots for the peaks are indicated.

So, have I missed something out in the process?


Also, in the diffraction pattern I've got, there's a certain amount of background noise that actually lift the whole pattern up by 100-200 in the y scale.

If I go Macros->Manual Areas->Area between Cursors, it'll automatically give the total area between under the pattern and a baseline as defined by the cursors.

But that area still includes some of the background.

So, if I want to define the baseline myself, how do I do it? Using Init Area Between Cursors...? How?
I think that rather than using PeakAreasUnipolar.ipf (which is better for measuring rather than fitting peaks), you should try TN020 Procedures.ipf (in the TN020 Peak Measurement folder).

I see you initialized using a baseline of W_BaselineFit without mentioning whether you'd created that baseline subtraction wave or not. If you didn't create it, you shouldn't be using one created as a left-over of some demo experiment.

Also, whenever possible, we recommend discarding any X wave and using X scaling instead. Most of Igor's analysis code (FFT, for example) works only on "waveforms" which are arrays of Y values and associated wave scaling. Use this command to explain about waveforms and wave scaling:

DisplayHelpTopic "Waveform Versus XY Data"


Software Engineer, WaveMetrics, Inc.

September 16, 2009 at 10:21 am - Permalink

JimProuty wrote:
I think that rather than using PeakAreasUnipolar.ipf (which is better for measuring rather than fitting peaks), you should try TN020 Procedures.ipf (in the TN020 Peak Measurement folder).

I see you initialized using a baseline of W_BaselineFit without mentioning whether you'd created that baseline subtraction wave or not. If you didn't create it, you shouldn't be using one created as a left-over of some demo experiment.

Also, whenever possible, we recommend discarding any X wave and using X scaling instead. Most of Igor's analysis code (FFT, for example) works only on "waveforms" which are arrays of Y values and associated wave scaling. Use this command to explain about waveforms and wave scaling:

DisplayHelpTopic "Waveform Versus XY Data"


Software Engineer, WaveMetrics, Inc.


Thanks Jim! I'll try that also.

But what does TN020 Procedures.ipf in "TN020 Peak Measurement" exactly do and what are the differences between these different procedures in the Igor Tech Notes folder?
TN020 Peak Measurement/TN020-B Peak Areas/TN020-C UniPolar Peak Areas/TN020-H Peak Meas Est & Hold

e.g Doesn't "TN020 Peak Measurement" already give you the peak areas?

September 16, 2009 at 06:39 pm - Permalink

See the "TN020s-Choosing a Right One.ifn" file in the Igor Tech Notes folder.

Software Engineer, WaveMetrics, Inc.

September 17, 2009 at 12:21 pm - Permalink