Beamline Configuration¶

IPython profiles¶

Configuration can be done interactively or in a Python script. At NSLS-II, configuration is done by startup scripts that are part of an IPython profile . But note that it is not essential to use IPython or IPython profile in general – this is just a convenience.

Profiles are stored in (or soft-linked) from ~/.ipython in the user profile of individual users or shared beamline accounts.

The standard profile is called “collection,” and the startup scripts are located in ~/.ipython/profile_collection/startup/. As stated in the quick start page, they can be invoked by typing:

ipython --profile=collection

To refresh a script that has been edited, restart IPython or re-execute the script using %run -i ~/.ipython/profile_collection/startup/<FILENAME>. Do this for any file(s) that have been updated. (There is no way to run all files at once.)

Example Configuration File¶

This is a example IPython profile startup file.:

# Make ophyd listen to pyepics.
from ophyd import setup_ophyd
setup_ophyd()

# Subscribe metadatastore to documents.
# If this is removed, data is not saved to metadatastore.
import metadatastore.commands
from bluesky.global_state import gs
gs.RE.subscribe_lossless('all', metadatastore.commands.insert)

# At the end of every run, verify that files were saved and
# print a confirmation message.
from bluesky.callbacks.broker import verify_files_saved
gs.RE.subscribe('stop', post_run(verify_files_saved))

# Import matplotlib and put it in interactive mode.
import matplotlib.pyplot as plt
plt.ion()

# Make plots update live while scans run.
from bluesky.utils import install_qt_kicker
install_qt_kicker()

# Optional: set any metadata that rarely changes.
# RE.md['beamline_id'] = 'YOUR_BEAMLINE_HERE'

# convenience imports
from ophyd.commands import *
from bluesky.callbacks import *
from bluesky.spec_api import *
from bluesky.global_state import gs, abort, stop, resume
from databroker import (DataBroker as db, get_events, get_images,
                        get_table, get_fields, restream, process)
from time import sleep
import numpy as np

RE = gs.RE  # convenience alias

# Uncomment the following lines to turn on verbose messages for debugging.
# import logging
# ophyd.logger.setLevel(logging.DEBUG)
# logging.basicConfig(level=logging.DEBUG)

Configuring the Olog¶

Essential Configuration¶

pyOlog requires a configuration file to specify the connection settings. As root, create a file at /etc/pyOlog.conf with the following contents.:

[DEFAULT]
url = https://<beamline>-log.cs.nsls2.local:8181/Olog
logbooks = Commissioning   # use the name of an existing logbook
username = <username>
password = <password>

where <beamline> is the designation formatted like xf23id1.

Integration with Bluesky¶

Bluesky automatically logs basic scan information at the start of a scan. (All of this information is strictly a subset of what is also stored in metadatastore – this is just a convenience.)

Back in an IPython profile startup file, add:

from functools import partial
from pyOlog import SimpleOlogClient
from bluesky.callbacks.olog import logbook_cb_factory

# Set up the logbook. This configures bluesky's summaries of
# data acquisition (scan type, ID, etc.).

LOGBOOKS = ['Data Acquisition']  # list of logbook names to publish to
simple_olog_client = SimpleOlogClient()
generic_logbook_func = simple_olog_client.log
configured_logbook_func = partial(generic_logbook_func, logbooks=LOGBOOKS)

cb = logbook_cb_factory(configured_logbook_func)
RE.subscribe('start', cb)

Integration with Ophyd¶

Ophyd has as log_pos method that writes the current position of all positioners into the log. To enable this, add the following to an IPython profile startup file, add:

# This is for ophyd.commands.get_logbook, which simply looks for
# a variable called 'logbook' in the global IPython namespace.
logbook = simple_olog_client

The log entires will be written into the logbook specified in .pyOlog.conf (in our example, “Commissioning”), not the logbook used by bluesky (in our example, “Data Acquisition”).

Olog IPython “Magics”¶

“Magics” are special IPython commands (not part of Python itself). They begin with %. There are two IPython magics for conveniently writing to the Olog.

Type %logit to quickly type a text log entry.
Type %grabit, select an area of the screen to capture, and type in a text caption.

These require their own special configuration. In the profile directory, such as ~/.ipython/profile_collection, edit the file ipython_config.py.

Add the line:

c.InteractiveShellApp.extensions = ['pyOlog.cli.ipy']

The log entires will be written into the logbook specified in .pyOlog.conf (in our example, “Commissioning”), not the logbook used by bluesky (in our example, “Data Acquisition”).

Defining Hardware Objects¶

For example:

from ophyd import EpicsMotor

# the two-theta motor
tth = EpicsMotor('XF:28IDC-ES:1{Dif:1-Ax:2ThI}Mtr', name='tth')

See the ophyd documentation for more.

Set up Default (“Global State”)¶

Set attributes of gs. This can be done interactively or in a startup file.:

gs.DETS = [det1, det2]
gs.TABLE_COLS = ['det1']
gs.PLOT_Y = 'det1'

Customizing IPython¶

Running the following

In [1]: %config PromptManager.in_template = '\T In [\\#]: '
In [2]: %config PromptManager.out_template = '\T Out[\\#]: '

will make your terminal look like this:

01:40 In [49]: 1
01:42 Out[49]: 1
01:42 In [50]:
02:21 In [50]: a = 2
02:28 In [51]:

It is not much more work to customize that timestamp to be truncated, include date / day of week etc. See this section of the IPython documentation for details.