1-      I was able to export calibration data ( wavelength, distance etc) to
other image files by using “copy” in “Image Controls”. Somehow checking the
“Use as defaults for all images?” does not work for me.

(Problem Solved)


2-      To export all the integrated data, I tried “export” , “powder data
as”. I was previously trying to export “text” data, in “text” data I don’t
see “select all” but for CSV, FXYE, XYE. I am able to select all and export
all data in a single go.

(Problem Solved)


3-      May be I am asking too much about this “feature request” . I agree
that by converting the wavelength of final data, some information will be
lost and one would not be able to perform “Rietveld Refinement etc”, but
still I believe it can be helpful to many users for easy comparison of data
with ICDD or other published data etc.







From: Andrzej Falenty [] 
Sent: Thursday, July 3, 2014 12:53 AM
To: Shoaib Muhammad
Subject: Re: [GSAS-II] Masking Bad Data Points In Image Data


Here is some further help



Am 02.07.2014 11:55, schrieb Shoaib Muhammad:

Dear All


Thanks all for the excellent help, I was able to calibrate, import all data
together, mask it and integrate it. Data qulity is not so good, so Rietveld
refinement is not meaningful. I have few more questions:



1-      First, I imported LaB6 image file to do the calibrations and saved
the “controls file”. Then I imported in situ image data files together but I
had to add “control file” (to add “sample to detector” distance and beam
center etc) individually to each image file. I have around 90 image files so
it took long to add control file to every image file. I tried different ways
but could not figure out any way to add control parameters to each image
file. In Fit2d usually after calibration, calibration data is exported to
all other image files. Is there any way to do this in GSAS2?

After finishing the calibration with LaB6 image you should select a box "Use
as default for all images" in the "Image controls" window . If I remember
correctly when you load your 2D data the image control settings should be
automatically applied to every image.


2-      After integrating all the image file, I could not find a way to
export all the integrated data together. I had to export each integrated
data file individually. How can I export all the integrated data together?


You can export all your 1D patterns in one go via GSASII data
tree>Export>Powder Data As>GSAS FXYE file. Then a window "Item Selector"
opens. There you can select your data for export individually or all of them
(Toggle All or Set All will do the job). The export of 2D images is
one-by-one only...

Feature Request:

Usually data recorded at synchrotron beamlines is not at CuKa wavelength but
one is supposed to report this data in CuKa for easy comparison. It would be
very helpful if GSAS2 users can export integrated diffraction image data,
directly to CuKa wavelength








Hi Shoaib,

I'm still working myself into the GSASII but I think I have figured of most
of the often used options. I'm not sure to what extent you are familiar with
the idea of masking but here are the basics. You can "draw" or select a
region of different shape (e.g spot, polygon, arc etc) and that area is
ignored in the integration. If you are familiar with masks in Fit2D program
you will find nearly the same functionality in GSASII.

1) there any way in GSAS2 to mask unwanted spots or sometimes even
unwanted peaks...

-In order to create a mask you should load an image and in "GSAS II data
tree" go to the sub tree: "Mask>Operations>Create new> ....." How to use
individual mask types is written on the bottom of the "Mask" window. You can
save, copy and load created masks. You can do it individually to selected
images apply it to all images.

-If you have an interference showing up always in the same area (e.g.  a
beam stop) you may also limit the angular range of the integrated area ("Set
Start/End azimuth" and "Inner/Outer 2-theta" in the "Image controls" window)

2) ...integrating this data and then make a sequence file to integrate...

Yeas you can. Prepare masks for your images and go: Image
Controls>Operations>Integrate all> (Select 2D images) and Integrate. You
will get a bunch of 1D diffraction patterns in the "GSAS II data tree".

3)...refine many image files together...

Hmm, this is a tough one and I had not opportunity to try this one out. An
option to sum up diffraction patterns might help here if there is no
crystallographic argument against it (like change in: T, detector-sample
distance, wavelength and so on.... )

Good luck!


From: Brian Toby []
Sent: Wednesday, July 2, 2014 10:47 AM
To: Shoaib Muhammad
Cc: Robert Von Dreele
Subject: Re: [GSAS-II] Masking Bad Data Points In Image Data

Yes, you can mask sections of the detector. You can read in a series of
images and then once you have settings you are happy with the masking and
integration for one image you can copy those settings to the rest of the
images and then integrate them while you get a cup of coffee. 


Yes. Go to the Mask data tree item for your 1st image & add spots where you
need them. Then change the size of the spot to fit. Use other masks as well;
frame outlines the image to remove edge features. Masks can be copied to
other images; they all can be integrated at once. Use sequential refinement
to fit a sequence of images.
Bob Von Dreele
On 7/1/2014 8:33 PM, Shoaib Muhammad wrote:


Dear All,


Recently I noticed many updates in GSAS2 about image plate diffraction data
integration and Rietveld refinement. I have some MAR345 type image plate
diffraction data which I can successfully read in GSAS2. Data is recorded in
situ on lithium ion battery cell so quality is not the best and has couple
of unwanted bright spots. I was wondering, is there any way in GSAS2 to mask
unwanted spots or sometimes even unwanted peaks while integrating this data
and then make a sequence file to integrate  and refine many image files






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Dr. Andrzej Falenty  <> <>
Abt. Kristallographie
GZG, Georg-August-Universität
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D-37077 Göttingen
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