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Perhaps someone can reply Wen..<br>
<br>
Pavel<br>
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<td>Re: indexing diffraction pattern</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">Date: </th>
<td>Sat, 10 Nov 2018 09:30:53 -0500</td>
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<th valign="BASELINE" align="RIGHT" nowrap="nowrap">From: </th>
<td>Wen Jiang <a class="moz-txt-link-rfc2396E" href="mailto:jiang12@purdue.edu"><jiang12@purdue.edu></a></td>
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<td>Pavel Afonine <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a></td>
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<div dir="ltr">Pavel,
<div>Sorry for insufficient details. The scenario is that I have
a numpy 2D array of float values that represents an image of
"diffraction pattern" (generated by an image processing
operation, not actual X-ray diffraction). I need to determine
the peak positions and then find a 2D lattice (two 2D vectors)
going through these peaks. I have my own simple functions that
can detect the peaks and find a 2-D lattice to cross the peaks
but it often fails when the "diffraction pattern" is not very
clean. Thus, I want to find a more robust method that works
well when the peaks are relatively weak, not very sharp, and
when there are some spurious peaks off the lattice. I think
these tasks are exactly what cctbx has solved for indexing
X-ray diffraction images.</div>
<div>Hope that these explanations help clarify the problem.</div>
<div>Thanks,</div>
<div><br>
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<div>Wen</div>
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<div dir="ltr">Prof. Wen Jiang<br>
Department of Biological Sciences<br>
Department of Chemistry (Courtesy)<br>
Scientific Director, Purdue Cryo-EM Facility<br>
Purdue University<br>
Hockmeyer Hall of Structural Biology<br>
240 S. Martin Jischke Drive<br>
West Lafayette, IN 47907<br>
<a href="http://jiang.bio.purdue.edu" target="_blank"
moz-do-not-send="true">http://jiang.bio.purdue.edu</a></div>
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<div dir="ltr">On Sat, Nov 10, 2018 at 8:03 AM Pavel Afonine
<<a href="mailto:pafonine@lbl.gov" moz-do-not-send="true">pafonine@lbl.gov</a>>
wrote:<br>
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<div text="#000000" bgcolor="#FFFFFF"> Hi Wen,<br>
<br>
I'm not sure I fully understand your question... You say a
function that takes a numpy array.. Array of what? <br>
Then, "a list of diffraction spots" -- these are measured in
diffraction experiment.<br>
<br>
If you could provide more details as to what you are trying
to do as well as what exactly the inputs are then I will do
my best to see how to do this in CCTBX or forward your
questions to CCTBX mailing list so that others can comment.<br>
<br>
All the best,<br>
Pavel<br>
<br>
<div class="m_-2307008666740175415moz-cite-prefix">On
11/10/18 03:56, Wen Jiang wrote:<br>
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<div dir="ltr">Hi Pavel,
<div>I am looking for a function that takes a
numpy array and returns a list of diffraction spots
and lattice vectors. I think cctbx should have such a
function but I am not familiar with it. Can you point
me in the right direction?</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Wen<br>
<div><br clear="all">
<div>
<div dir="ltr"
class="m_-2307008666740175415gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">Prof. Wen Jiang<br>
Department of Biological Sciences<br>
Department of Chemistry (Courtesy)<br>
Scientific Director, Purdue Cryo-EM Facility<br>
Purdue University<br>
Hockmeyer Hall of Structural Biology<br>
240 S. Martin Jischke Drive<br>
West Lafayette, IN 47907<br>
<a href="http://jiang.bio.purdue.edu"
target="_blank" moz-do-not-send="true">http://jiang.bio.purdue.edu</a></div>
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