Probe Software Users Forum

Software => CalcImage => Topic started by: John Donovan on November 10, 2018, 05:37:12 pm

Title: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 10, 2018, 05:37:12 pm
So Gareth Seward and I have been havin' a bit of ye' ole' chin wag, and the upshot of it is... this new feature which is not yet out officially, as it needs another few days of tweaking and testing, but it seems to be going well.

That said it looks to be pretty useful to all, and especially for students processing quantitative element maps off-line *without* access to the Surfer application.

(https://probesoftware.com/smf/gallery/395_10_11_18_5_20_19.png)

The cool thing, this feature will work for any data type created in CalcImage, so not just elemental quant maps, but also oxide wt.% maps, atomic % maps, formula basis maps, detection limit maps, etc., etc.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 11, 2018, 04:39:32 pm
We're making progress.

(https://probesoftware.com/smf/gallery/1_11_11_18_4_38_12.png)

Another few days of work and it should get interesting.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 14, 2018, 01:55:31 pm
Our "first cut" at polygon extraction and pixel filtering is now available for download. Simply run the UPdate Probe for EPMA from the Help menu and you will obtain v. 12.5.2.  Then launch CalcImage and select the Image Processing menu, and select the new EXtract Polygon Areas and/or Filter Pixels menu.

Here is a screen shot of this new feature with the main operations highlighted:

(https://probesoftware.com/smf/gallery/1_14_11_18_1_44_33.png)

Gareth Seward will provide more operational details over the next few weeks, but it is quite usable already and we're sure you all will have many excellent suggestions to make (Gareth has already given me a list to work on for this weekend!).

Basically one starts with the Browse For Classify DAT File button to select an output file from the CalcImage quantitative mapping output, which is described here in detail (be sure to click the "Refresh" button in your browser if the in-line images are not visible!):

https://probesoftware.com/smf/index.php?topic=146.0

Then one selects the element data to display (remember, any data type output from the CalcImage quantification can be processed using this feature, including elemental, oxide, atomic, formula, etc., etc.). Then select either the Shape Extraction button (On) or the Digitize Polygon button to extract shape areas or polygon areas. 

Finally, simply click on the image with the shape tool to see extracted pixels or click the Perform Extraction/Filtering to see the polygon extraction results.  More details will be forthcoming.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 14, 2018, 06:47:57 pm
We re-arranged the GUI controls so they are a little more intuitive:

(https://probesoftware.com/smf/gallery/1_14_11_18_6_38_30.png)

This update is ready to download now using the Help | Update Probe for EPMA menu.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: glennpoirier on November 15, 2018, 12:45:58 pm
Just been playing with the new  CalcImage. I don't have a copy of Surfer installed on my desktop computer so this is really useful!
Excellent work!
Cheers
Glenn
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 15, 2018, 02:49:34 pm
Just been playing with the new  CalcImage. I don't have a copy of Surfer installed on my desktop computer so this is really useful!
Excellent work!
Cheers
Glenn

Hi Glenn,
Thank-you, thank-you.  Gareth and I worked pretty hard on this and we think it's pretty cool too.  We're adding several additional cool features today, probably release a new version later tonight or tomorrow.

In the meantime I should mention that Golden Software allows you to install and register a copy for use both "in the field and in the office".  I would interpret that to mean one copy in the lab and one in the office.  Here's their license info:

Quote
Strater, Surfer and Grapher offer two licensing options: single-user licenses and concurrent licenses.

A single-user standalone license is associated with one person and only that person can use the license.  Single-user licenses can be activated on up to two computers for use in the field and in the office, for example.

A concurrent-use license, also called a “network” or “floating” license, is tied to a network. A license server be setup on the network for license distribution.  The licenses are activated on the server computer and then the software on the user's computers connects to the server to see if a seat is available each time it is started. The product can be installed on as many client machines as desired.

So I think it's OK to install another copy of Surfer in your office if you want to.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: JonF on November 16, 2018, 08:40:57 am
To echo the earlier sentiments: this is really nice, thanks guys!

And thanks for the hat tip about the second licence for Surfer
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on November 17, 2018, 08:43:29 am
We added some additional features to the polygon extract filtering feature in CalcImage for extraction of pixels from quantitative x-ray maps as seen here:

(https://probesoftware.com/smf/gallery/1_17_11_18_8_38_09.png)

In addition to the new GUI controls outlined in red, both the shape and polygon extraction method graphics can now be enumerated (graphically and also saved to text and files), using the Enumerate Shapes and Enumerate Polygons checkbox controls.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 01, 2018, 11:50:35 am
Gareth Seward requested that we display the filtered image and that is now implemented.  Here is the display with the normal default image data:

(https://probesoftware.com/smf/gallery/1_01_12_18_11_49_04.png)

Then I set the Si minimum value to 20 and here is the filtered image display:

(https://probesoftware.com/smf/gallery/1_01_12_18_11_49_21.png)

So now only the quartz grains are showing.

The image can be reverted to the unfiltered image by unchecking the element and re-extracting, or clicking on another element for display or re-loading the Classify .DAT file.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Gseward on December 03, 2018, 02:00:54 pm
John

Very handy to have this option directly in the Extraction window. Thanks!

Output of .GRD for each elements is very important too, and really is the more complete output option, but the filtered image display is an instant sanity check!

Cheers,

gareth
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 08, 2018, 03:05:26 pm
OK, we added a new Line Profile Extraction feature in the Pixel Extraction window in CalcImage.

This new feature allows one to define two end points and perform pixel averaging for "N" points in between:

(https://probesoftware.com/smf/gallery/1_08_12_18_3_03_27.png)

 8)
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on December 10, 2018, 09:06:54 am
Hi John,

I've just tried the line extract - this is really nice - I'm keen to use it. I'm having some teething problems with the export of points though, (a) the append to file does not seem to work, (b) it be nice to have data structured so that its ready to plot all points - each element forming a row or column, (c) copy clipboard as csv only copies last entry.

It would also be great to have the relative distance between points.

Thanks, I'll try to patient  :)

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 10, 2018, 09:19:30 am
Hi John,

I've just tried the line extract - this is really nice - I'm keen to use it. I'm having some teething problems with the export of points though,

(a) the append to file does not seem to work,

Hi Ben,
So the File Export works, but the Append does not?   I'll check into this ASAP.

(b) it be nice to have data structured so that its ready to plot all points - each element forming a row or column,

How is what you are suggesting different from what it's doing now?   It's complicated because there are two data types: averages and standard deviations only, and alternatively, averages and standard deviations and also all pixels.

(c) copy clipboard as csv only copies last entry.

When you say "last entry", do you mean the last pixel square?  I will check.

It would also be great to have the relative distance between points.

That makes sense.   I should also output the center stage coordinate for each extraction shape.

Thanks, I'll try to patient  :)

Ben

I appreciate your feedback!
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 10, 2018, 07:05:22 pm
Hi Ben,
We fixed the append file output code.  Sorry about that!

(https://probesoftware.com/smf/gallery/1_10_12_18_7_00_59.png)

We also fixed the tab delimited clipboard code.   Had to create an array of average structures and a 3 dimensional array for the pixel output too.

Next we will work on the relative distance output you requested. Good idea.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on December 11, 2018, 02:26:40 am
Hi John,

Thanks for fixing it, it all works well now.

I don't know if it be difficult but my ideal structure for the export file of averages - is shown below - where you export all the wt. % data together, and all the errors together so that its ready for plotting. You might want to flip rows and columns

(https://probesoftware.com/smf/gallery/453_11_12_18_2_30_59.png)

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 11, 2018, 08:27:31 am
Hi John,

Thanks for fixing it, it all works well now.

I don't know if it be difficult but my ideal structure for the export file of averages - is shown below - where you export all the wt. % data together, and all the errors together so that its ready for plotting. You might want to flip rows and columns

Hi Ben,
OK, but I'm not sure I see how this makes it more "ready for plotting".   I may also just add some graphics to this feature as well.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 14, 2018, 09:07:11 am
We added code to output the stage positions and relative distance for line profile extractions as seen here:

(https://probesoftware.com/smf/gallery/1_14_12_18_9_03_46.png)

Here is another plot. Note that one can export the plot data to a file using the Export Data button.

(https://probesoftware.com/smf/gallery/1_14_12_18_9_04_04.png)

If one looks at the average total (magenta circles), one can see that each pixel has low precision, but the average is quite accurate!

Please update using the Help menu in Probe for EPMA as usual.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on December 17, 2018, 03:04:02 am
Hi John,

I like the graphs you've added in - they are great!

I notice that you don't plot the average of the 10x10 (or whatever) pixel spot but plot each extracted pixel. This gives the large scatter. I think it would be good if you could plot the average value for each extracted spot instead or as an alternative.

The graphs are also good because I can export the data from the plot for plotting in Excel.

Thanks

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 20, 2018, 09:56:19 am
Hi John,

Thanks for fixing it, it all works well now.

I don't know if it be difficult but my ideal structure for the export file of averages - is shown below - where you export all the wt. % data together, and all the errors together so that its ready for plotting. You might want to flip rows and columns

(https://probesoftware.com/smf/gallery/453_11_12_18_2_30_59.png)

Ben

So you would prefer the averages separate from the variances? Or would it be better to have the average and variance for each element in adjacent columns?

Come to think of it, I agree with you, I think it would it be better to have the elements as columns and the profiles listed as rows, right?

How do others feel about this format?    We're thinking about working on this average plot output over the weekend.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 21, 2018, 11:42:20 am
Hi Ben,
We think we have what you want for extraction of line profile averages from quantitative x-ray maps. 

Basically the plot line profile pixel code now checks the "Averages Only" checkbox, and if it is checked, the plot only displays the averages and variances as error bars in the line profile as seen here:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_24_03.png)

If the checkbox is unchecked you will get all the pixels plotted as before.  Also we modified the Export Data button code to export the averages and variances to a tab delimited ASCII file as seen here when imported into Excel:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_35_36.png)

We hope you will find this feature useful.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on December 27, 2018, 06:23:43 pm
We've released a new pixel extraction plotting feature in v. 12.5.6 of Probe for EPMA in the CalcImage image quantification and analysis application.

This is just an initial effort at this new feature, but we think it could be useful for quantitative image analysis. To utilize this feature simply check one of these two checkboxes for either the shape extraction or polygon extraction methods:

(https://probesoftware.com/smf/gallery/1_27_12_18_5_52_43.png)

Because the polygon extraction method defaults to the entire image area, simply clicking the Perform Extraction/Filtering button will output the quantitative average and/or pixel results to the text windows or files. And if the Plot Polygon Histogram checkbox is checked, the application will also display a quantitative histogram, or as Ed Vicenzi suggests, a "Quantigram" plot.   We like it. 

Here is a quantigram of a full quantitative x-ray map of an Fe-Mo-Cr alloy diffusion zone:

(https://probesoftware.com/smf/gallery/1_27_12_18_5_45_57.png)

And here is a quantigram of a polygon area in this x-ray map:

(https://probesoftware.com/smf/gallery/1_27_12_18_5_46_26.png)

Finally, here is an example from a multiphase material showing the quantitative distribution of pixels:

(https://probesoftware.com/smf/gallery/1_27_12_18_5_47_45.png)

Please update your Probe for EPMA and try out this latest pixel extraction plot feature in Calcimage and let us know what you think.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 07, 2019, 06:06:22 am
Hi Ben,
We think we have what you want for extraction of line profile averages from quantitative x-ray maps. 

Basically the plot line profile pixel code now checks the "Averages Only" checkbox, and if it is checked, the plot only displays the averages and variances as error bars in the line profile as seen here:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_24_03.png)

If the checkbox is unchecked you will get all the pixels plotted as before.  Also we modified the Export Data button code to export the averages and variances to a tab delimited ASCII file as seen here when imported into Excel:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_35_36.png)

We hope you will find this feature useful.
john

Thanks John, this is very good. Is the variance - the maximum variance in the pixels? Could we have standard deviation?

Thanks

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 07, 2019, 06:11:46 am
We've released a new pixel extraction plotting feature in v. 12.5.6 of Probe for EPMA in the CalcImage image quantification and analysis application.

This is just an initial effort at this new feature, but we think it could be useful for quantitative image analysis. To utilize this feature simply check one of these two checkboxes for either the shape extraction or polygon extraction methods:

Finally, here is an example from a multiphase material showing the quantitative distribution of pixels:

(https://probesoftware.com/smf/gallery/1_27_12_18_5_47_45.png)

Please update your Probe for EPMA and try out this latest pixel extraction plot feature in Calcimage and let us know what you think.

This looks interesting, might be more useful to show a single element per graph, otherwise a bit confusing.
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 07, 2019, 08:20:41 am
Hi Ben,
Yeah, at this point this is a completely new feature, so please play with it and see if you think it's useful for quant analysis.

I think it might possibly be useful for multi-phase x-ray maps, but you tell me.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 07, 2019, 08:24:05 am
Hi Ben,
We think we have what you want for extraction of line profile averages from quantitative x-ray maps. 

Basically the plot line profile pixel code now checks the "Averages Only" checkbox, and if it is checked, the plot only displays the averages and variances as error bars in the line profile as seen here:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_24_03.png)

If the checkbox is unchecked you will get all the pixels plotted as before.  Also we modified the Export Data button code to export the averages and variances to a tab delimited ASCII file as seen here when imported into Excel:

(https://probesoftware.com/smf/gallery/1_21_12_18_11_35_36.png)

We hope you will find this feature useful.
john

Thanks John, this is very good. Is the variance - the maximum variance in the pixels? Could we have standard deviation?

Thanks

Ben

Hi Ben,
The plotted +/- error bars are one standard deviation, the same as the +/- values printed to the text window.  The exported tab delimited data are also one standard deviation.

So, yes.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 09, 2019, 07:20:21 am


Hi Ben,
The plotted +/- error bars are one standard deviation, the same as the +/- values printed to the text window.  The exported tab delimited data are also one standard deviation.

So, yes.
john

Thanks for clarifying that. This will be a very useful feature - particularly for users who don't like imagej - plus its easier!

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 09, 2019, 11:42:40 am


Hi Ben,
The plotted +/- error bars are one standard deviation, the same as the +/- values printed to the text window.  The exported tab delimited data are also one standard deviation.

So, yes.
john

Thanks for clarifying that. This will be a very useful feature - particularly for users who don't like imagej - plus its easier!

Ben

I like easy!    But some might ask if we are making it *too* easy.   :)
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 10, 2019, 01:08:56 am
Hi,

Here's a puzzle, why is standard deviation not a suitable measure of the error when averaging pixels?

Here's two line profiles extracted using calcimage line profile - for P in olivine. The error bars (which are standard deviation of 100 pixels - correctly calculated) are too large for the actual error - this can be seen by comparing the 'traverse' profile and 'along' profile. In the 'along' profile the error is seen to be very small - as given by the variation in average along the homogeneous zone and yet the error bars are large.
(https://probesoftware.com/smf/gallery/453_09_01_19_8_19_56.png)
I wonder if its because the counts per pixel are very small? Would calculating the error (using the error formula) for the sum of the counts be more realistic?

Here's a way of conceptualizing the issue. Again along the homogeneous zone. I extract boxes of 10x10, 7x7 and 5x5 (without moving the positions). The std dev is the same for each, but the error on the analysis improves as the box size increases (assuming the composition within the box is homogeneous). This can be seen in the straighter line with less noise (points deviating away from the straight line)

(https://probesoftware.com/smf/gallery/453_10_01_19_3_06_06.png)

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 10, 2019, 02:30:05 am
I've just done a quick approximate calculation

(https://probesoftware.com/smf/gallery/453_10_01_19_2_24_42.png)

Extracting boxes of ca. 40 pixels using imagej, along the homogeneous band - shown above. Extract average and standard deviation for (1) raw counts and (2) quantified weight %). Then using the raw counts subtract the background which is constant (trace element variation in homogeneous olivine). Then using square root of total counts (avg counts*no. of pixels) to calculate the statistical error.

It can be seen that the statistic error based on the number of counts is the right order of magnitude (ca 1%). Whereas the standard deviation is much greater (ca. 20%). The average wt % data varies by 3.7%.

(https://probesoftware.com/smf/gallery/453_10_01_19_2_37_57.png)

Can we calulate the improvement in std dev as the number of pixels increases. If we increase the number of pixels by 45x. An increase in counts by 45x should reduce the error by 0.149 (sqrt of cts), thus 20% multiplied by 0.149 gives 2.98.

If we apply this to the data in the previous post

(https://probesoftware.com/smf/gallery/453_10_01_19_3_30_39.png)

 - it seems to work (not sure if its mathematically sound). This is actually the standard error (as John points out in later post) https://probesoftware.com/smf/index.php?topic=1144.msg7973#msg7973 (https://probesoftware.com/smf/index.php?topic=1144.msg7973#msg7973). Standard error is given by:

(https://probesoftware.com/smf/gallery/453_14_01_19_4_41_04.png)

https://en.wikipedia.org/wiki/Standard_error (https://en.wikipedia.org/wiki/Standard_error)



Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 10, 2019, 10:06:32 am
Hi Ben,
Interesting stuff.

But your first question has me confused.  What do you mean by "long concentrations"?  For example, when you say: "why is standard deviation not a suitable measure of the error at long concentrations?".

I'm guessing that you are trying to see the difference between the actual variance of the concentrations (what CalcImage is reporting as the error), and the actual counting statistics those concentrations are based on?
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 10, 2019, 11:01:11 am
Ok, I think I might know what is going on.

In x-ray maps the statistics for a single pixel are essentially determined by the pixel dwell time.  So increasing the number of pixels doesn't much change the standard deviation (in a homogeneous material).

If you want to see the error decrease as a function of the (increasing) number of pixels, then what you want is the standard error (not the standard deviation) of the pixels.

This is because the standard error describes the error of the average, while the standard deviation describes the error for a single measurement.

Now as to why we (in science) routinely report the average and the standard deviation (rather than the average and the standard error), is a question I have asked several statisticians over the years, and the only answer I've heard is that "maybe because the standard deviation is larger and therefore a more conservative estimate"... but maybe one of you more mathematical types can enlighten us? 

I myself would sure like to hear why it is that we don't usually see the average and standard error reported together more often.

In any case, this pixel averaging situation may be a case in which the standard error is more applicable than the standard deviation?
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on January 14, 2019, 04:28:44 am
Hi John,

Thanks you've got it, I was describing the need for standard error (I'd calculated the standard error without realizing it) when averaging pixels.

Your previous question 'long concentrations' should have read 'low concentrations' but it is a problem for all concentrations. I'll modify the post

Ben
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 14, 2019, 11:38:23 am
Hi John,

Thanks you've got it, I was describing the need for standard error (I'd calculated the standard error without realizing it) when averaging pixels.

Your previous question 'long concentrations' should have read 'low concentrations' but it is a problem for all concentrations. I'll modify the post

Ben

Hi Ben,
OK, cool.

I can imagine that some might like to see the actual standard deviations and some might want to see the standard errors.

I'll see if we can squeeze in an additional option button or checkbox somewhere!   Won't be until this weekend though, sorry.
john
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on January 22, 2019, 07:00:38 pm
Hi John,

Thanks you've got it, I was describing the need for standard error (I'd calculated the standard error without realizing it) when averaging pixels.

Your previous question 'long concentrations' should have read 'low concentrations' but it is a problem for all concentrations. I'll modify the post

Ben

Hi Ben,
I think we've got what we need.  Check out this new control for average and standard deviations or average and standard errors:

(https://probesoftware.com/smf/gallery/1_21_01_19_10_46_02.png)

And here is a plot using the standard deviations:

(https://probesoftware.com/smf/gallery/1_21_01_19_11_04_47.png)

and here is the same data but using the standard errors:

(https://probesoftware.com/smf/gallery/1_21_01_19_11_04_58.png)

For those wondering what the standard error is, it's the standard deviation divided by the square root of (number of measurements minus one).  That's a big improvement in precision, but it makes sense since there are lots of pixels to average in a 10 x 10 pixel shape!

Remember, the standard deviation describes the variance of each point, while the standard error describes the variance of the average.  Bottom line, making more measurements of points *or* pixels, has its reward!    :D
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Probeman on January 23, 2019, 12:30:03 pm
With all this talk about averaging of pixels, it is important to keep in mind that pixel averaging only works when averaging quantitative x-ray map pixels (or points for that matter!). Now these x-ray maps could be elemental weight percents, oxide weight percents, atomic percents, formula atoms, detection limits, etc., etc., etc., but they must be already corrected for matrix effects prior to averaging.

Why?  Because we know from physics that matrix correction of x-ray intensities are extremely non-linear. If we instead average raw intensities of a heterogeneous interaction volume, whether that heterogeneity be due to scanning the beam or defocusing it, we will obtain inaccurate results, when that average is subsequently quantified.  See the attachments to this post here for additional details:

https://probesoftware.com/smf/index.php?topic=44.msg145#msg145

An easy way to think about this is to consider an interaction volume that is at the boundary of a pure Cu phase and a pure Al phase. From geometry we know that most of the copper x-rays are being emitted from pure Cu and most of the aluminum x-rays are being emitted from pure Al, but our software sees both emitted intensities and has to assume that this is (roughly) a 50-50 Cu-Al "alloy" (since the software knows nothing about the sample geometry).

The matrix correction for copper in a CuAl alloy is similar to that of the pure element (because Cu Ka is very energetic and suffers little absorption in this "alloy"), but Al Ka is highly absorbed in such a composition, and is therefore is greatly overcorrected resulting in totals of around 150-160 wt%.

SAMPLE: 32767, TOA: 40, ITERATIONS: 0, Z-BAR: 24.23118

 ELEMENT  ABSCOR  FLUCOR  ZEDCOR  ZAFCOR STP-POW BKS-COR   F(x)u      Ec   Eo/Ec    MACs
   Cu ka   .9996  1.0000  1.0555  1.0551  1.0739   .9828   .9903  8.9790  1.6706 49.0723
   Al ka  2.0289  1.0000   .9199  1.8664   .8478  1.0851   .4374  1.5600  9.6154 3320.82

 ELEMENT   K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL                                       
   Cu ka  .00000  .66532  70.195   -----  50.000    .500   15.00                                       
   Al ka  .00000  .15969  29.805   -----  50.000    .500   15.00                                       
   TOTAL:                100.000   ----- 100.000   1.000

By the way, this is also why one cannot characterize thin film compositions if any substrate elements are detected. Because if the beam energy is sufficient, and the electrons penetrate to the substrate, not only will the homogeneous volume assumption be invalid, but the substrate can fluoresce elements in the thin film layer if any absorption edges of slightly lower energy than the substrate x-rays are present.

Unless of course one acquires intensities using multiple beam energies, and applies a  thin film geometry model such as Pouchou and Pichoir!  See here for more discussion on quantification of thin film geometries:

https://probesoftware.com/smf/index.php?topic=111.msg405#msg405
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: John Donovan on April 03, 2019, 10:57:02 am
Ben Buse mentions that the quantitative histogram feature, or Quantigram as Ed Vicenzi has termed it, described here:

https://probesoftware.com/smf/index.php?topic=1144.msg7951#msg7951

might be confusing when many elements are displayed at once.  We concur and we finally realized that there is a built-in feature of the Pro Essentials graphics library that allows the user to select specifically which data subsets to plot. To access this subset selection feature (and this applies to all plots in Probe for EPMA and CalcImage by the way!), simply right click on the plot and select the Customization Dialog menu as seen here:

(https://probesoftware.com/smf/gallery/1_03_04_19_10_08_02.png)

You will then see this dialog:

(https://probesoftware.com/smf/gallery/1_03_04_19_10_08_16.png)

Next, from this dialog select the subsets that you wish to plot and click the OK or Apply button as seen here:

(https://probesoftware.com/smf/gallery/1_03_04_19_10_08_32.png)

Here we selected only the Mg, Al and O subsets for clarity and the plot (after zooming in) in is much easier to read:

(https://probesoftware.com/smf/gallery/1_03_04_19_10_08_45.png)
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Ben Buse on April 04, 2019, 06:17:50 am
Thanks John,

This is nice.

Here's a plagioclase map

(https://probesoftware.com/smf/gallery/453_04_04_19_6_14_18.png)

You can see the Bytownite/Anorthite core and Andesine/Labradorite rim. It also shows the large error (as each pixel short time etc), which masks any further distinctions in the histogram
Title: Re: Polygon Extraction and/or Pixel Filtering
Post by: Probeman on April 06, 2019, 11:36:38 am
Thanks John,

This is nice.

Here's a plagioclase map

(https://probesoftware.com/smf/gallery/453_04_04_19_6_14_18.png)

You can see the Bytownite/Anorthite core and Andesine/Labradorite rim. It also shows the large error (as each pixel short time etc), which masks any further distinctions in the histogram

What a pretty sample. It's almost "art"!

Did you try seeing if you can "pull out" these zoned compositions using the Classify window in CalcImage:

https://probesoftware.com/smf/index.php?topic=1071.0

You might need to set the precision to a small number, maybe even zero, and try specifying 2, 3 or 4 phases.