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Cookbook

Start Bluesky

From a terminal write 

bluesky_start

Start Phoebus GUI

To start the screens run this line in a terminal:

phoebus_start

To open the gui panels navigate to the folder /opt/phoebus/gui.

Move motors

If you want to move a motor, or a set of motors you can simply type:

mov motor1 position1 motor2 position2

or using relative motions

movr motor1 relative_motion1 motor2 relative_motion2

Change the PGM cff

To set the cff value to 2.5 use:

mov pgm.cff 2.5

Note that this will not produce any movement in the monochromator. The new cff will be set once you change the energy to a new one.

Scan

Select Plotted detector

One can choose a detector to be plotted using giving the command plotselect():

In [1]: plotselect()
Current detector: ['kth01']
Press enter to exit
Available detectors:
1. accelerator_current
2. kth01
Select detectors by one or more numbers (e.g., '1', '1 2', '1,2')

Scan Syntax

Command Usage Example
Take readings from detectors. count 5 delay=1
absolute scan one motor scan motor -1 1 10
absolute scan multiple motors scan motor -1 1 motor2 -2 3 10
relative scan one motor dscan motor -1 1 10
relative mesh multiple motors dmesh motor1 -1 1 10 motor2 -2 2 20
absolute mesh multiple motors amesh motor1 12 14 10 motor2 18 22 20

Settle Time (wait before measuring)

It is possible to define a settle time, which is a a number of seconds waited by a motor before reporting that the motion is completed. 

motor.axis.settle_time = 5

Average keithleys measurements

When measuring with the Keithleys, it is possible to instruct them to repeat the measurement n times, and return the averaged value. 

kth1.avg_type.set('Repeat')
kth1.avg_num.put(5)

Adding Custom Metadata to Scans

Custom metadata allows users to annotate scans with additional information that can be specific to the current context or experimental conditions. This metadata is added at the time of executing a scan plan by including a dictionary named md as a parameter in the scan command.

Below is an example of how to add custom metadata when executing a scan. In this example, the metadata includes the name of the operator and a description of the sample:

# Define the scan parameters and include custom metadata
scan motor 1 5 5 md={'operator':'John','sample':'gold'}

Abort Motion

Weather you are moving a motor or running a plan, the motion can be interrupted by pressing 

ctrl+c

Magics

Command Description
ct Shows a reading of all the detectors.
wa Shows all the motor positions. You can select which motors to show using their label.
where Draws a line of the current motor position in the last scan.
pic Moves the motor to the highest value of the signal from the detector in the last scan.
cen Moves the motor to the center of the signal from the detector in the last scan.
com Moves the motor to the center of mass of the signal from the detector in the last scan.
minimum Moves the motor to the minimum of the signal from the detector in the last scan.

Data

The data is exported in a subfolder of ~/bluesky/data.

The data is exported as specfiles (that can be visualized with PyMCA), and as individual csv files.

Before starting taking measurements, make sure that you are exporting the data in the right folder.

User Data

Change your user folder using the following command:

bds.change_user('<user_name>')

Create an additional subfolder for each sample/part of the experiment (you need at least one).

bds.change_sample('<sample_name>')

This is the folder structure that you create


    ├── ~/bluesky/data
    │   ├── user_name
    │   │   └── sample_name
    │   │   │   ├── csv
    │   │   │   │   ├── 00001_meta.json
    │   │   │   │   ├── 00001_primary.csv
    │   │   │   │   └── 00001_baseline.csv
    │   │   │   └── sample1.spec

Specfile

Specfiles can be visualized using PyMCA. To start the program click on it on the dock, or just write pymca in a terminal.

Individual csv files

The csv folder contains three files for each scan:

  • scanNumber_baseline.csv: the baseline
  • scanNumber_meta.json: the metadata
  • scanNumber_primary.csv: the data

Suspenders

Bluesky can automatically pause a measurement in case some conditions are met, by using suspenders.

Injection

This suspender pause the measurements two seconds before and after the injection happens. To activate it and deactivate it use:

wait_for_injection()