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bruceravel committed Feb 9, 2024
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2 changes: 1 addition & 1 deletion docs/before.rst
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Expand Up @@ -63,7 +63,7 @@ on sample processing and any safety measures necessary.

.. caution:: An approved SAF is required on the first day of beamtime.
Without enough time for approval, you may lose your
beamtime beamtime.
beamtime.

To submit a SAF: https://pass.bnl.gov

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11 changes: 7 additions & 4 deletions docs/desktop.rst
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Expand Up @@ -18,8 +18,8 @@ BMM's Desktop
This section provides an explanation of how to recover BMM's data
collection workspace after restarting the computer.

This is made a hair easier if a couple of symbolic links are made in
``~/bin/``. Do this:
This is made a bit easier if a couple of symbolic links are made in
``~/bin/``. If not already done, do this at the command line:

.. code-block:: sh
Expand All @@ -30,8 +30,8 @@ Monitoring
----------

To have eyeballs on the operation of the beamline, we want ``Phoebus``
for engineering screen and the ``cadashboard`` application for the
heads-up overview of
for engineering screens and the ``cadashboard`` application for the
heads-up overview of the state of the beamline.

Phoebus (engineering screens)
There are two ways to start Phoebus.
Expand Down Expand Up @@ -127,3 +127,6 @@ experiment:
+ Slack
+ A dolphin (file browser) window with a tab open to the current
experiment

Note that there are buttons on the icon bar at the bottom of the
screen for Athena and Hephaestus.
11 changes: 10 additions & 1 deletion docs/index.rst
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Expand Up @@ -11,7 +11,16 @@
BMM Users Manual
================

BMM is NIST's Beamline for Materials Measurement
BMM is NIST's :red:`B`\ eamline for :red:`M`\ aterials :red:`M`\ easurement.

.. _fig-bananagrams:
.. figure:: _images/Beamline-bananagrams.jpg
:target: _images/Beamline-bananagrams.jpg
:width: 50%
:align: left

BMM at a glance!


**Contents:**

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23 changes: 19 additions & 4 deletions docs/intro.rst
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Expand Up @@ -57,6 +57,17 @@ TL;DR
<start_consumer>`


Essential links
---------------

:NSLS-II: https://www.bnl.gov/nsls2/
:BMM's page: https://www.bnl.gov/nsls2/beamlines/beamline.php?r=6-BM
:Operations schedule: https://www.bnl.gov/nsls2/schedule/
:Beamtime schedule: https://scheduler.nsls2.bnl.gov/
:NSLS Status: https://www.bnl.gov/nsls2/operating-status.php
:BMM's at Github: https://github.com/NSLS-II-BMM


The user experience
-------------------

Expand Down Expand Up @@ -283,8 +294,12 @@ BMM and Building 743
--------------------


BMM is on the south side of the NSLS-II building. You should park at
building 743 and enter through the main entrance of 743.
BMM is on the south side of the NSLS-II building: `what3words:
///width.corrugated.support
<https://what3words.com/width.corrugated.support>`__

You should park at building 743 and enter through the main entrance
of 743.

.. _fig-sitemap:
.. figure:: _images/map.png
Expand Down Expand Up @@ -400,8 +415,8 @@ written by Bruce. But this would not have happened without the help
of several members of NSLS-II's DSSI program. In particular, I want
to thank Dan Allan, Tom Caswell, Josh Lynch, Max Rakitin, Dmitri
Gavrilov, Stuart Campbell, Abby Giles, and Garrett Bishof. And I need
to thank every BMM user |nd| being a BMM user means being a bug tester
for this software!
to thank every BMM user |nd| being a BMM user and being a beta tester
for the beamline software are the same thing!

BMM makes use of `lots of great python tools
<https://speakerdeck.com/jakevdp/the-unexpected-effectiveness-of-python-in-science?slide=52>`__.
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18 changes: 13 additions & 5 deletions docs/plotting.rst
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Expand Up @@ -4,10 +4,10 @@
Plotting via Kafka at BMM
=========================

For years, plotting at BMM has made use of `a BlueSky preprocessor
For years, plotting at BMM used a `BlueSky preprocessor
<htps://github.com/bluesky/bluesky/blob/master/bluesky/preprocessors.py#L333>`__
and specially constructed functions for extracting data from Bluesky
event documents. This has been fine, providing useful real-time views
event documents. That was fine and provided useful real-time views
of data for our users.

The problem with using these modified BlueSky `LivePlots
Expand All @@ -18,8 +18,8 @@ As BMM began to use `BlueSky queueserver
typically `not` run on the same machine as ``bsui``, this plotting
scheme stopped being helpful.

The solution adopted was to move all plotting chores out of the main
data collection profile and into a Kafka consumer. Using the
The solution was to move all plotting chores out of the main data
collection profile and into a Kafka consumer. Using the
`bluesky-kafka producer and consumer
<https://github.com/bluesky/bluesky-kafka>`__ and with the help of
DSSI, the beamline computers were given access to the same Kafka
Expand Down Expand Up @@ -263,7 +263,7 @@ bottom left, and plot of the transmission |mu| (E) of the reference
material on the bottom right.

For a scan not using the fluorescence detector, the plot is a 3x1 grid
of transmission |mu| (E), I0, and the reference spectrum.
of transmission |mu| (E), I\ :sub:`0`, and the reference spectrum.


.. _fig-xafs_live_view:
Expand All @@ -274,6 +274,14 @@ of transmission |mu| (E), I0, and the reference spectrum.

An example of the XAFS live plot made for a fluorescence XAFS scan.

.. note:: I\ :sub:`0` is now normalized by the dwell time, thus is
plotting in units of amperes rather than ampere*seconds,
as shown.

Also, as of January 2024, the live plot at the end of the
scan sequence is posted to Slack and included in the
:numref:`dossier (Section %s) <dossier>`.


.. _xafssequence:

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13 changes: 13 additions & 0 deletions docs/profile.rst
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Expand Up @@ -29,6 +29,19 @@ At Dan Allan's suggestion, we took a different approach.
The startup folder
------------------

The startup folder is a symlink to a folder on Lustre where BMM's
profile is kept. If bsui does not start with BMM's profile, make that
symlink by doing the following:

.. code-block:: sh
cd ~/.ipython
ln -s /nsls2/data3/bmm/shared/config/bluesky/profile_collection
If a folder called ``profile_collection`` already exists at that
location |nd| which would be the case if you have already used bsui
or ipython |nd| go ahead and rename or delete that folder.

The top folder of the profile contains a single python file. It
follows the old convention in that it is named
``00-populate-namespace.py`` and is read as soon as IPython starts.
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