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<br>
"simtbx" is the name we are giving to my diffraction image
simulation codes. You may or may not of heard of their standalone
versions as MLFSOM, fastBragg (now nanoBragg), nonBragg and
nearBragg. Nick and I thought the capability of creating absolutely
realistic diffraction data from a completely independent code base
would be an excellent way to generate test data for cctbx, dials,
phenix, and even third-party packages. There is also the idea of
fitting a simulation directly to diffraction images, which I have
had some success doing independently, but we hope this will work
better under cctbx. Until recently, all this was standalone c code,
with home pages here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/mlfsom/">http://bl831.als.lbl.gov/~jamesh/mlfsom/</a><br>
<a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nanoBragg/">http://bl831.als.lbl.gov/~jamesh/nanoBragg/</a><br>
<a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nearBragg/">http://bl831.als.lbl.gov/~jamesh/nearBragg/</a><br>
<a class="moz-txt-link-freetext" href="http://bl831.als.lbl.gov/~jamesh/nonBragg/">http://bl831.als.lbl.gov/~jamesh/nonBragg/</a><br>
<br>
I have spent the bulk of my time for three months trying to wire
these codes into the boost/Python framework of cctbx. I put
docstrings into every single one of my objects, but since I am new
to Python I don't know where people look for documentation.<br>
<br>
Again, sorry this broke everything. It's been in there since
February and I was surprised to find that a new developer here
couldn't access it. This is why I've been asking so many questions
about tests I should perform before checking things in, but
apparently it was all for naught.<br>
<br>
-James<br>
<br>
<div class="moz-cite-prefix">On 5/3/2017 7:57 AM, Pavel Afonine
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:9925f9c7-59cc-1e4f-0b19-30e4a1963ed4@lbl.gov">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Same questions here as Markus asked.. What is simtbx? First time
hear about it. How cctbx can benefit from it?<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 5/3/17 07:53, <a
class="moz-txt-link-abbreviated"
href="mailto:markus.gerstel@diamond.ac.uk"
moz-do-not-send="true">markus.gerstel@diamond.ac.uk</a> wrote:<br>
</div>
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<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi
Nick,<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Sorry,
outsider perspective here. I don’t know what simtbx does
or is supposed to do.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">What
is the benefit of having code in a repository that,
according to your earlier mail, is explicitly not used in
the project?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Or
more bluntly: We (and ccp4) distribute dials and, as part
of it, the cctbx_project repository.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Why
should we ship dead code?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">-Markus<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"
moz-do-not-send="true"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
<span style="mso-bookmark:_MailEndCompose"></span>
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif"
lang="EN-US"> <a class="moz-txt-link-abbreviated"
href="mailto:cctbxbb-bounces@phenix-online.org"
moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>
[<a class="moz-txt-link-freetext"
href="mailto:cctbxbb-bounces@phenix-online.org"
moz-do-not-send="true">mailto:cctbxbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>Nicholas Sauter<br>
<b>Sent:</b> 03 May 2017 15:52<br>
<b>To:</b> cctbx mailing list <a
class="moz-txt-link-rfc2396E"
href="mailto:cctbxbb@phenix-online.org"
moz-do-not-send="true"><cctbxbb@phenix-online.org></a><br>
<b>Subject:</b> Re: [cctbxbb] simtbx<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Markus,<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">We want option c. simtbx should be
in the cctbx_project directory. No separate git
repository. We need to double check we've gotten all
the files in cctbx_project, then remove them from the
separate repo. James, could you look into this?<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Nick<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal">Nicholas K. Sauter, Ph.
D.<br>
Senior Scientist, Molecular Biophysics
& Integrated Bioimaging Division<o:p></o:p></p>
<div>
<p class="MsoNormal">Lawrence Berkeley
National Laboratory<br>
1 Cyclotron Rd., Bldg. 33R0345<br>
Berkeley, CA 94720<br>
(510) 486-5713<o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On Wed, May 3, 2017 at 7:49 AM, <<a
href="mailto:markus.gerstel@diamond.ac.uk"
target="_blank" moz-do-not-send="true">markus.gerstel@diamond.ac.uk</a>>
wrote:<o:p></o:p></p>
<blockquote style="border:none;border-left:solid #CCCCCC
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6.0pt;margin-left:4.8pt;margin-right:0cm">
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Hi James,</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">It looks that you now have
two separate places where simtbx code is kept.
One is in the simtbx repository, where you fixed
the sign earlier, and the other one is in the
cctbx repository, where you just now fixed it
again.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Simtbx repo: <a
href="https://github.com/dials/simtbx"
target="_blank" moz-do-not-send="true">https://github.com/dials/simtbx</a></span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">Simtbx folder in cctbx
repo: <a
href="https://github.com/cctbx/cctbx_project/tree/master/simtbx"
target="_blank" moz-do-not-send="true">
https://github.com/cctbx/cctbx_project/tree/master/simtbx</a> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">I guess suppose there are
three options here:</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span
style="color:#1F497D">a.</span><span
style="font-size:7.0pt;color:#1F497D"> </span><span
style="color:#1F497D">move simtbx into the
module directory, add simtbx to the bootstrap
script so it is initialised correctly.</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span
style="color:#1F497D">b.</span><span
style="font-size:7.0pt;color:#1F497D"> </span><span
style="color:#1F497D">leave simtbx inside the
cctbx_project directory and repository, but as
its own git repository (using git submodule)</span><o:p></o:p></p>
<p class="m-2651995399140751371msolistparagraph"><span
style="color:#1F497D">c.</span><span
style="font-size:7.0pt;color:#1F497D"> </span><span
style="color:#1F497D">leave simtbx inside the
cctbx_project directory, delete the separate git
repository</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">NB: This issue is
independent of resolving the dials-dependency
issue.</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="color:#1F497D">-Markus</span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a
name="m_-2651995399140751371__MailEndCompose"
moz-do-not-send="true"><span
style="color:#1F497D"> </span></a><o:p></o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
lang="EN-US">From:</span></b><span
lang="EN-US"> <a
href="mailto:cctbxbb-bounces@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>
[mailto:<a
href="mailto:cctbxbb-bounces@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb-bounces@phenix-online.org</a>]
<b>On Behalf Of </b>James Holton<br>
<b>Sent:</b> 03 May 2017 15:40<br>
<b>To:</b> Winter, Graeme (DLSLtd,RAL,LSCI)
<<a
href="mailto:Graeme.Winter@Diamond.ac.uk"
target="_blank" moz-do-not-send="true">Graeme.Winter@Diamond.ac.uk</a>>;
<a href="mailto:cctbxbb@phenix-online.org"
target="_blank" moz-do-not-send="true">cctbxbb@phenix-online.org</a><br>
<b>Subject:</b> Re: [cctbxbb] simtbx</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;margin-bottom:12.0pt"><br>
Yesterday, Aaron and I were trying to set
things up so that simtbx would be available to
people who aren't James Holton. It's been
checked in and working for over a month now,
and only a few days ago I discovered that a
fresh "bootstrap" has a broken simtbx, despite
my "git status" telling me all my files are up
to date. I asked Aaron and Nick for help with
this.<br>
<br>
I thought what we did was make cctbx.xfel
depends on simtbx, since fitting simulations
to stills is the whole reason for porting my
stuff into python. <br>
<br>
I set up simtbx with a constructor that takes
a dxtbx detector as input, but does that make
it depend on dials? I did not expect that.<br>
<br>
Sorry, didn't mean to break anything! Would
much appreciate any help on this. <br>
<br>
-James<o:p></o:p></p>
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On
5/3/2017 1:41 AM, <a
href="mailto:Graeme.Winter@Diamond.ac.uk"
target="_blank" moz-do-not-send="true">Graeme.Winter@Diamond.ac.uk</a>
wrote:<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hi
Folks<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">We
have noticed that simtbx, part of the core
cctbx now, depends on dials<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This
means if you do not have a dials build your
cctbx will be broken<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">This
is probably not the way we want things?<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
thought simtbx was a separate repo?<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Cheerio
Graeme<o:p></o:p></p>
<p> <o:p></o:p></p>
<p>-- <o:p></o:p></p>
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<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<pre wrap="">_______________________________________________
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<pre wrap="">_______________________________________________
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