Author Topic: Classify feature, K-means clustering for phase identification  (Read 601 times)

John Donovan

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I just realized that we've never created a dedicated topic for discussing phase extraction calculations in CalcImage.  This feature is accessed from the Image Processing | Classify Image menu in CalcImage as seen here:



This phase classification utilizes a modified k-means clustering method which allows the user to specify the number of phases to detect and also a precision parameter (Iteration Tolerance) to trade off calculation speed for sensitivity in the detection of discrete phases. Here is an example of using 8 phases and an iteration tolerance of 0.1 (%):



I know that several users already take advantage of this feature, but feel free to comment or ask questions about this method.
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Probeman

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Re: Classify feature, K-means clustering for phase identification
« Reply #1 on: April 26, 2018, 12:57:24 pm »
It should be added that these phase extractions can be performed not only on the elemental concentrations, but also on any data type output from CalcImage, which would include not only net intensities and k-ratios, but also oxide concentrations, atomic percents, formula basis, etc.

I don't know how different the phase results will be by utilizing different data types for classification, but I do know they will be somewhat different.
« Last Edit: April 26, 2018, 03:26:35 pm by Probeman »
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John Donovan

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Re: Classify feature, K-means clustering for phase identification
« Reply #2 on: April 26, 2018, 01:00:32 pm »
And here is a k-means calculation on the same data as in the first post, but this time using 12 phases (which is probably a bit overkill):

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John Donovan

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Re: Classify feature, K-means clustering for phase identification
« Reply #3 on: April 28, 2018, 03:01:53 pm »
And here is a k-means phase classification with 10 phases which looks reasonable:



Then just for fun I ran the modal analysis feature in CalcImage (from the Image Processing | Calculate Modal Abundances menu) and after matching to the (default) DHZ mineral database, we get the following results:



When we click the Calculate Modal Parameters button we get this output from Surfer:



I just noticed that the above image looks a little funny, and the reason is because the default for Surfer (v. 13 and higher)  now is to have "hill shading" turned on, so I will fix that in the script, but in the meantime we simply uncheck this box and it looks more like *microanalysis*:



But in any case clearly the DHZ database is limited to rock forming minerals, so we'd probably want to utilize a more complete match database such as the the AMCSD.MDB mineral database which contains over 4000 (ideal) minerals. 

Anyway, just a quick review so you all know what is available already in CalcImage.  More details can be found by searching the CalcImage board.
« Last Edit: April 28, 2018, 10:38:36 pm by John Donovan »
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John Donovan

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Re: Classify feature, K-means clustering for phase identification
« Reply #4 on: April 16, 2019, 10:16:35 pm »
We made a small change to the Classify window in CalcImage to improve how images are handled when the current instrument configuration (JEOL vs. Cameca) loads a classify .DAT file which is from the "other" instrument.



For example, when installing Probe for EPMA on an off-line computer the default instrument configuration is JEOL. If one then opens a CalcImage classify .DAT file acquired on a Cameca instrument, this new code will now handle this situation properly.

Of course one can also simply use the File | Use JEOL Simulation Mode or File | Use Cameca Simulation Mode menus in Probe for EPMA to switch instrument configurations.

https://probesoftware.com/smf/index.php?topic=837.msg5978#msg5978

Also one can export their current instrument configuration from any recently acquired MDB file as described here:

https://probesoftware.com/smf/index.php?topic=76.msg2196#msg2196

In any case, the new Classify display code should handle all situations properly. Ready to update now.
« Last Edit: April 17, 2019, 08:36:05 am by John Donovan »
John J. Donovan, Pres. 
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"Not Absolutely Certain, Yet Reliable"