Re: [Ifeffit] selection of pixels by criteria

[Will Bennett]

Hi all,

I use ImageJ with the ScatterJ and ScatterJn plugins to do this type of 
analysis of XRF maps.

https://openresearchsoftware.metajnl.com/articles/10.5334/jors.89/

https://onlinelibrary.wiley.com/doi/abs/10./jmi.12187

Cheers,

Will

Dr William W. Bennett

Senior Lecturer
Environmental Futures Research Institute
School of Environment and Science
Griffith University
Gold Coast, Queensland, Australia
M +61 401 186 488
w.benn...@griffith.edu.au

Assistant Professor
Nordcee, Department of Biology
University of Southern Denmark
Odense, Denmark
M +45 8193 8111
wbenn...@biology.sdu.dk


From: Matthew Marcus 
Sent: Friday, 22 November 2019 6:33 am
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] selection of pixels by criteria

A suggestion: Make a scatterplot available, plotting the pixel-by-pixel values 
of any two relevant quantities, and make it
possible to define a polygon mask on that scatterplot. That often allows 
separation of chemically-distinct areas.

Sincerely,
Matthew Marcus

On 11/21/2019 12:26 PM, Matt Newville wrote:
> HI Troy,
>
> Sorry for the late reply -- I think this sort of slipped off my radar screen.
>
>
> On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury  > wrote:
>
> I have used larch some for XRF maps. I like the feature for defining ROI's 
> and then looking at the statistics of the data. I have some samples that are 
> an intimate mix of two or more phases and I would like to extract pixels 
> based on a criteria- like high Sr or low Fe, etc, from across a whole map 
> region. I wonder if this feature is available, or would be easy to create on 
> larch?
>
>
> Like you say, this is not currently available in the Mapviewer GUI.  But it's 
> a good suggestion and might be possible to do with a small amount of code.
>
> Would it work for you to say "Make an Area with all pixels where Sr Counts is 
> above some value"?  I think that would be easy to generalize from "Sr Counts" 
> to
> "Ratio of ROI Counts"  (or "analyzed concentration" once I get that done - a 
> work in progress).  If that's right, I think it would be "not hard to add".
>
> --Matt
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: 
> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: 
http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Re: [Ifeffit] selection of pixels by criteria

[Matthew Marcus]

A suggestion:  Make a scatterplot available, plotting the pixel-by-pixel values 
of any two relevant quantities, and make it
possible to define a polygon mask on that scatterplot.  That often allows 
separation of chemically-distinct areas.

Sincerely,
Matthew Marcus

On 11/21/2019 12:26 PM, Matt Newville wrote:

HI Troy,

Sorry for the late reply -- I think this sort of slipped off my radar screen.


On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury mailto:troy.rasb...@stonybrook.edu>> wrote:

I have used larch some for XRF maps. I like the feature for defining ROI's 
and then looking at the statistics of the data. I have some samples that are an 
intimate mix of two or more phases and I would like to extract pixels based on 
a criteria- like high Sr or low Fe, etc, from across a whole map region. I 
wonder if this feature is available, or would be easy to create on larch?


Like you say, this is not currently available in the Mapviewer GUI.  But it's a 
good suggestion and might be possible to do with a small amount of code.

Would it work for you to say "Make an Area with all pixels where Sr Counts is above some 
value"?  I think that would be easy to generalize from "Sr Counts" to
"Ratio of ROI Counts"  (or "analyzed concentration" once I get that done - a work in 
progress).  If that's right, I think it would be "not hard to add".

--Matt


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Re: [Ifeffit] selection of pixels by criteria

[Matt Newville]

HI Troy,

Sorry for the late reply -- I think this sort of slipped off my radar
screen.


On Sat, Nov 16, 2019 at 2:09 PM E. Rasbury 
wrote:

> I have used larch some for XRF maps. I like the feature for defining ROI's
> and then looking at the statistics of the data. I have some samples that
> are an intimate mix of two or more phases and I would like to extract
> pixels based on a criteria- like high Sr or low Fe, etc, from across a
> whole map region. I wonder if this feature is available, or would be easy
> to create on larch?
>
>
Like you say, this is not currently available in the Mapviewer GUI.  But
it's a good suggestion and might be possible to do with a small amount of
code.

Would it work for you to say "Make an Area with all pixels where Sr Counts
is above some value"?  I think that would be easy to generalize from "Sr
Counts" to
"Ratio of ROI Counts"  (or "analyzed concentration" once I get that done -
a work in progress).  If that's right, I think it would be "not hard to
add".

--Matt
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit

Re: [Ifeffit] no plot window with Demeter on Ubuntu 18.04

[Ravel, Bruce]

Hi Joseph,

You did the first few troubleshooting steps.  Good to know that gnuplot 
works by itself.

What is the value of preferences->gnuplot->program ?  On a linux 
machine, this parameter should simply be set to "gnuplot".  That means 
that gnuplot needs to be in the execution path.  Perhaps gnuplot is in 
an unexpected place on your machine?  Or perhaps it is called by an 
unexpected name?  If it is not in the normal execution path, try setting 
that parameter to the full path to the gnuplot executable.

The Gtk-CRITICAL warning is almost certainly a red herring.  That has to 
do with how one of the widgets in the main display gets sized when 
Athena is created.  It is noisy and annoying, but almost certainly not 
harmful or related to your plotting problem.

B


On 11/19/19 11:37 AM, Joseph Zsombor-Pindera wrote:
> Dear mailing list members;
> 
> I've successfully built Demeter from source on my computer running 
> Ubuntu 18.04. Running "dathena", for example opens the familiar Athena 
> window. Once I try to plot something, however, I get no plot window. It 
> appears as if the program has done something, but the window just 
> doesn't appear.
> 
> I have installed gnuplot-x11.
> running 'gnuplot -e "plot sin(x)"' produces no window, but
> 'gnuplot -p -e "plot sin(x)"' produces a plot, and if I just run
> 'plot sin(x)' within gnuplot, then I get the plot, so it appears that 
> gnuplot itself is working correctly.
> 'show terminal' results in:
> terminal type is wxt 0 enhanced
> I have tried changing the terminal to 'wxt' under 
> preferences>gnuplot>terminal in Athena, which didn't fix the problem.
> I have also tried changing the terminal to 'qt' and installing 
> gnuplot-qt. This didn't work, so I purged it and switched back to 
> gnuplot-x11.
> I haven't managed to get gnuplot to run with x11 as its default 
> terminal. It seems that the default terminal of gnuplot-x11 is wxt.
> 
> I'm not sure if these matter, but when I run Athena, I get errors in the 
> terminal like this:
> (dathena:16207): Gtk-CRITICAL **: 11:55:29.414: 
> gtk_box_gadget_distribute: assertion 'size >= 0' failed in GtkCheckButton
> 
> thanks,
> Joseph
> -- 
> *Joseph Zsombor-Pindera, BSc*
> PhD Student, UBC Chemistry
> 
> C
> 
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
> 


-- 
  Bruce Ravel   bra...@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Lead Beamline Scientist, 6BM (BMM)
  Building 743, Room 114
  Upton NY, 11973

  Homepage:http://bruceravel.github.io/home/
  Beamline:https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM
  Software:https://github.com/bruceravel
  Demeter: http://bruceravel.github.io/demeter/

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit