minor editing

docs/instruments.rst

@@ -54,6 +54,11 @@ photons, this versatility of setup is occasionally very helpful.
    silicon drift detector.
 
 
+.. note::
+   Thanks to funding from the CHIPS Act, BMM is the process of
+   procuring a new 7-element SDD!  Look for that in late 2024 or
+   early 2025. 
+
 
 Area detector
 -------------
@@ -267,8 +272,8 @@ automated.
    The glancing angle stage with 8 sample positions.
 
 
-While this can be used for standing wave experiments, the much more
-typical application is a simple glancing angle measurement in which
-the point of the shallow angle is to spread the beam out over the full
-length of the sample.  This significantly increases the number of
-atoms involved in the measurement.
+While a standing wave experiment might be feasible at BMM, the much
+more typical application is a simple glancing angle measurement in
+which the point of the shallow angle is to spread the beam out over
+the full length of the sample.  This significantly increases the
+number of atoms involved in the measurement.

docs/intro.rst

@@ -191,9 +191,16 @@ This will create that data folder and populate it with an
 write a :numref:`user log file (Section %s) <logfile>` for this
 experiment, set the GUP and SAF numbers as metadata for output files,
 set up :numref:`snapshot (Section %s) <snap>` and :numref:`dossier
-(Section %s) <dossier>` folders, and perfrom other experiment start-up
+(Section %s) <dossier>` folders, and perform other experiment start-up
 chores.
 
+.. note::
+
+   In the near future, the ``start_experiment()`` command will grab
+   metadata from PASS (or UPS, or whatever) and set access permissions
+   on data.  When that happens, the only argument needed will be the
+   SAF number.
+
 The ``name`` should be the PI's full name, preferably transliterated
 into normal ASCII.  The ``date`` should be the starting day of the
 experiment in the ``YYYY-MM-DD`` format.  The ```GUP`` and ``SAF``
@@ -411,12 +418,16 @@ from the `The Executable Book Project
 BMM's profile was mostly 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, and Stuart Campbell
+Lynch, Max Rakitin, Dmitri Gavrilov, and Stuart Campbell.  And I need
+to thank all every BMM user because there is no difference being a BMM
+user and being a bug tester for this software!
 
 BMM makes use of `lots of great python tools
 <https://speakerdeck.com/jakevdp/the-unexpected-effectiveness-of-python-in-science?slide=52>`__.
 Matt Newville's `Larch <http://xraypy.github.io/xraylarch/>`__ is used
-to process every XAS scan that gets measured.
+to process every XAS scan that gets measured and Matt's `lmfit
+<https://lmfit.github.io/lmfit-py/>`__ is used for many alignment
+chores.
 
 This project uses a GitHub action to build and deploy `(see details
 here)

docs/linescans.rst

@@ -29,32 +29,30 @@ In BMM's ``linescan()`` plan, the scan is always a relative scan
 around the current position of the motor being scanned.  It works like
 this::
 
-    RE(linescan('it', 'x', -4, 4, 81))
+    RE(linescan(xafs_x, 'it', -4, 4, 81))
 
 The arguments are:
 
-#. A string indicating the detector for the plotted signal.  The
-   choices are:
-
-   * ``it``: display the ratio of ``It/I0``
-   * ``if``: display the sum of four silicon drift channels normalized
-     by ``I0``
-   * ``i0``: display the signal on ``I0``
-   * ``ir``: display the ratio of ``Ir/I0``
-   * ``both``: display both ``It/I0`` *and* the sum of four silicon
-     drift channels normalized by ``I0``
-
 #. The motor axis to be scanned.  This can be either the motor's
    BlueSky name or the nickname string from :numref:`Table %s
    <xafs-stages>`.  So, these are equivalent::
 
-     RE(linescan('it', 'x', -4, 4, 81))
-     RE(linescan('it', xafs_x, -4, 4, 81))
+     RE(linescan('x', 'it', -4, 4, 81))
+     RE(linescan('xafs', it_x, -4, 4, 81))
 
    For a motor that does not have a nickname, you must use the ophyd
-   object, as in::
+   symbol, as in::
 
-     RE(linescan('i0', slits3_outboard, -1, 1, 21))
+     RE(linescan(slits3.outboard, 'i0', -1, 1, 21))
+
+#. A string indicating the detector for the plotted signal.  The
+   choices are:
+
+   * ``it``: display the ratio of ``It/I0``
+   * ``if``: display the sum of four silicon drift channels normalized
+     by ``I0``
+   * ``i0``: display the signal on ``I0``
+   * ``ir``: display the ratio of ``Ir/It``
 
 #. The starting position of the motor scan, relative to the current
    position.
@@ -75,18 +73,6 @@ At the end of the scan, you are prompted with the following question::
 
     Pluck motor position from the plot? [Yn]
 
-
-
-..
-   If you answer :quote:`y` then :button:`Enter`, or simply hit
-   :button:`Enter`, you will be prompted to single click the left mouse
-   button :mark:`leftclick,.` on the plot.  The motor that was scanned
-   will then move to the motor position you clicked on.
-
-   You can skip the "click for motor position" step by typing
-   :button:`n` and hitting :button:`Enter`.
-
-
 If you answer :key:`y` then :key:`Enter`, or simply hit
 :key:`Enter`, you will be prompted to single click the left mouse
 button :mark:`leftclick,.` on the plot.  The motor that was scanned
@@ -107,16 +93,12 @@ motor to the click-upon point, do::
   RE(pluck())
 
 This will enable the left mouse :mark:`leftclick,.` click and
-subsequent motion on the most recent plot.  The ``pluck()`` command
-*only* works on the most recent plot.  You may not pluck from an older
-plot that is still displayed on the screen.
-
-Of course, an older plot remains active in the sense that you can pass
-the cursor over the plot and read the mouse coordinates in the bottom,
-left corner of the plot window.  You can find a point in this way,
-then do a movement command like::
+subsequent motion on the most recent plot.  
 
-  RE(mv(xafs_y, 28.31))
+.. warning::
+   The ``pluck()`` command works on any plot made through the Kafka
+   plotter.  Be sure you are clicking on the plot you intend to pluck
+   from!
 
 
 Revisit a line scan
@@ -182,10 +164,10 @@ arguments that they have special names.
 
      yield from slit_height()
 
-**Align ex situ sample holder**
+**Align ex situ sample holder** 
    If the *ex situ* sample wheel is in approximately the right
-   position such that X-rays are passing through the slot, you can
-   center the slot around the beam with::
+   position such that X-rays are passing through a slot on the outer
+   ring, you can center the slot around the beam with::
 
      RE(find_slot())
 
@@ -207,12 +189,12 @@ Area scans
 
 
 .. todo:: A raster scan type |nd| i.e. ``RE(raster())`` |nd| that does
-          an areascan as described here, makes a nice figure using
-          `matplotlib's contourf
-          <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.contourf.html>`_,
-          exports data in formats used by popular plotting programs,
-          and writes a dossier was tested in 2022-2.  Current status:
-          dossier is written, scan works, documentation needs to be written.
+   an areascan as described here, makes a nice figure using
+   `matplotlib's contourf
+   <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.contourf.html>`_,
+   exports data in formats used by popular plotting programs,
+   and writes a dossier was tested in 2022-2.  Current status:
+   dossier is written, scan works, documentation needs to be written.
 
 
 An area scan is a simple scan of a two motor axes with an on-screen

docs/motors.rst

@@ -90,19 +90,23 @@ are the same for all sample stage motors.
 **Querying position**
    The position of any motor can be queried with a command line like ::
 
-      %w xafs_y 
+     %w xafs_y 
+
+   or ::
+
+     xafs_y.position
 
 **Moving to a new position**
    Always move motors through the run engine, for example: ::
 
-      RE(mvr(xafs_y, 10))
+     RE(mvr(xafs_y, 10))
 
    ``mvr`` is the relative move command |nd| the numerical argument is
    the amount by which the motor will move from the current position.
 
    ``mv``, as in::
 
-      RE(mv(xafs_y, 37.63))
+     RE(mv(xafs_y, 37.63))
 
    is the absolute move command.  The numerical argument is the
    position to which the motor will move.
@@ -125,9 +129,9 @@ are the same for all sample stage motors.
      yield from mvr(xafs_y, 5)
 
 **Querying soft limits**
-   To know the soft limits on a sample stage, do
-   ``xafs_y.llm.get()`` or ``xafs_y.hlm.get()`` for the low or
-   high limit. 
+   To know the soft limits on a sample stage, do ``xafs_y.limits`` or
+   ``xafs_y.llm.get()`` or ``xafs_y.hlm.get()`` to query the low or
+   high limits individually.
 
 **Setting soft limits**
    To set the soft limits on a sample stage, do something like
@@ -148,15 +152,16 @@ are the same for all sample stage motors.
 
    BMM has foils or stable oxides for each of these elements::
 
-      Ti V  Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Zr Nb Mo Pt Au Pb Bi Sr Y
+      Sc Ti V  Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Zr Nb Mo Pt Au Pb Bi Sr Y
       Cs La Ce Pr Nd Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Rb Ba Hf Ta W  Re Os Ir Ru
 
-   (A few of these |nd| Ba, Os, Ir |nd| are missing as of 23
-   December, 2022.  We are working to obtain the missing ones.)
+   (A few of these |nd| Ba, Os, Ir |nd| are missing as of 2
+   November, 2023.  We are working to obtain the missing ones.)
 
    `Here is a complete list of standards
    <https://nsls-ii-bmm.github.io/bmm-standards/BMM-standards.html>`__
-   in BMM's collection.
+   in BMM's collection.  These standards are mounted on sample wheels
+   and stored in the hutch for ready access by users.
 
 
 Sample wheel

docs/pds.rst

@@ -351,9 +351,9 @@ facilitating any actions a user should ever need.
 
       dcm.mode = 'channelcut'
 
-   In practice, the monochromator is normally left in fixed-exit
-   mode.  That way, the monochromator can be moved without worry about
-   the beam height and the monochromator exit aperture.  In the 
+   In practice, the monochromator is normally left in fixed-exit mode.
+   That way, the monochromator can be moved without having to worry
+   about the beam height and the monochromator exit aperture.  In the
    :numref:`XAFS scan plan (Section %s) <xafsscan>`, the monochromator
    first moves |nd| in fixed-exit mode |nd| to the center of the
    angular range of the scan, then sets ``dcm.mode`` to

docs/xafs.rst

@@ -15,7 +15,7 @@
 XAFS scans
 ==========
 
-The BMM step scan plan starts by editing an `INI file
+The simplest access to an XAFS scan starts by editing an `INI file
 <https://en.wikipedia.org/wiki/INI_file>`_.  This is a simple
 keyword/value system where the keyword is separated from the value by
 an equals sign and each line contains a single keyword/value pair.
@@ -645,11 +645,11 @@ INI file.
       yield from end_of_macro()
       BMM_log_info('Sample macro finished!')
 
-The gray lines at lines 13-16 and 28-30 are comments indicating that
-parts of the macro are intended for editing by the user while other
-parts are boilerplate that make the macro work correctly.  In general,
-you only want to edit the lines between those two comment blocks,
-leaving the lines above and below untouched.
+The commented (by ``#``) lines at lines 13-16 and 28-30 are comments
+indicating that parts of the macro are intended for editing by the
+user while other parts are boilerplate that make the macro work
+correctly.  In general, you only want to edit the lines between those
+two comment blocks, leaving the lines above and below untouched.
 
 The calls to ``BMM_info()`` at lines 11 and 35 insert lines in the
 :numref:`experiment log (Section %s) <log>` indicating the times that