Note
Click here to download the full example code
Scan a grid around each sample in a grid¶
Problem¶
Examples are arranged on a substrate. There are two motors, x and y, for moving a detector over the subtrate. Scan a grid of readings around the center position of each sample.
Approach¶
Specify the samples and their arrangement as a mapping of sample names to
(x, y) positions, like {'A': (1, 1), 'B': (1, 2)}. Write a custom plan that
loops through the samples. For each sample, move to sample’s center position
and perform a bluesky.plans.relative_outer_product_scan() (i.e., grid
scan) around that position. For each sample, one run will be saved. Include the
sample name in the metadata.
Example Solution¶
Out:
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:46.7 | 0.527 | 0.800 | 0.800 | 0.800 | 0.800 |
| 2 | 21:00:46.8 | 0.484 | 0.800 | 0.800 | 0.900 | 0.900 |
| 3 | 21:00:46.8 | 0.440 | 0.800 | 0.800 | 1.000 | 1.000 |
| 4 | 21:00:46.8 | 0.397 | 0.800 | 0.800 | 1.100 | 1.100 |
| 5 | 21:00:46.9 | 0.353 | 0.800 | 0.800 | 1.200 | 1.200 |
| 6 | 21:00:46.9 | 0.325 | 0.900 | 0.900 | 1.200 | 1.200 |
| 7 | 21:00:46.9 | 0.364 | 0.900 | 0.900 | 1.100 | 1.100 |
| 8 | 21:00:47.0 | 0.405 | 0.900 | 0.900 | 1.000 | 1.000 |
| 9 | 21:00:47.0 | 0.445 | 0.900 | 0.900 | 0.900 | 0.900 |
| 10 | 21:00:47.0 | 0.484 | 0.900 | 0.900 | 0.800 | 0.800 |
| 11 | 21:00:47.1 | 0.440 | 1.000 | 1.000 | 0.800 | 0.800 |
| 12 | 21:00:47.1 | 0.405 | 1.000 | 1.000 | 0.900 | 0.900 |
| 13 | 21:00:47.1 | 0.368 | 1.000 | 1.000 | 1.000 | 1.000 |
| 14 | 21:00:47.2 | 0.331 | 1.000 | 1.000 | 1.100 | 1.100 |
| 15 | 21:00:47.2 | 0.295 | 1.000 | 1.000 | 1.200 | 1.200 |
| 16 | 21:00:47.2 | 0.266 | 1.100 | 1.100 | 1.200 | 1.200 |
| 17 | 21:00:47.3 | 0.298 | 1.100 | 1.100 | 1.100 | 1.100 |
| 18 | 21:00:47.3 | 0.331 | 1.100 | 1.100 | 1.000 | 1.000 |
| 19 | 21:00:47.4 | 0.364 | 1.100 | 1.100 | 0.900 | 0.900 |
| 20 | 21:00:47.4 | 0.397 | 1.100 | 1.100 | 0.800 | 0.800 |
| 21 | 21:00:47.4 | 0.353 | 1.200 | 1.200 | 0.800 | 0.800 |
| 22 | 21:00:47.5 | 0.325 | 1.200 | 1.200 | 0.900 | 0.900 |
| 23 | 21:00:47.5 | 0.295 | 1.200 | 1.200 | 1.000 | 1.000 |
| 24 | 21:00:47.5 | 0.266 | 1.200 | 1.200 | 1.100 | 1.100 |
| 25 | 21:00:47.6 | 0.237 | 1.200 | 1.200 | 1.200 | 1.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['ed3e7375'] (scan num: 1)
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:47.7 | 0.144 | 0.800 | 0.800 | 1.800 | 1.800 |
| 2 | 21:00:47.8 | 0.119 | 0.800 | 0.800 | 1.900 | 1.900 |
| 3 | 21:00:47.8 | 0.098 | 0.800 | 0.800 | 2.000 | 2.000 |
| 4 | 21:00:47.9 | 0.080 | 0.800 | 0.800 | 2.100 | 2.100 |
| 5 | 21:00:47.9 | 0.065 | 0.800 | 0.800 | 2.200 | 2.200 |
| 6 | 21:00:47.9 | 0.059 | 0.900 | 0.900 | 2.200 | 2.200 |
| 7 | 21:00:48.0 | 0.074 | 0.900 | 0.900 | 2.100 | 2.100 |
| 8 | 21:00:48.0 | 0.090 | 0.900 | 0.900 | 2.000 | 2.000 |
| 9 | 21:00:48.0 | 0.110 | 0.900 | 0.900 | 1.900 | 1.900 |
| 10 | 21:00:48.1 | 0.132 | 0.900 | 0.900 | 1.800 | 1.800 |
| 11 | 21:00:48.1 | 0.120 | 1.000 | 1.000 | 1.800 | 1.800 |
| 12 | 21:00:48.1 | 0.100 | 1.000 | 1.000 | 1.900 | 1.900 |
| 13 | 21:00:48.2 | 0.082 | 1.000 | 1.000 | 2.000 | 2.000 |
| 14 | 21:00:48.2 | 0.067 | 1.000 | 1.000 | 2.100 | 2.100 |
| 15 | 21:00:48.3 | 0.054 | 1.000 | 1.000 | 2.200 | 2.200 |
| 16 | 21:00:48.3 | 0.049 | 1.100 | 1.100 | 2.200 | 2.200 |
| 17 | 21:00:48.3 | 0.060 | 1.100 | 1.100 | 2.100 | 2.100 |
| 18 | 21:00:48.4 | 0.074 | 1.100 | 1.100 | 2.000 | 2.000 |
| 19 | 21:00:48.4 | 0.090 | 1.100 | 1.100 | 1.900 | 1.900 |
| 20 | 21:00:48.5 | 0.108 | 1.100 | 1.100 | 1.800 | 1.800 |
| 21 | 21:00:48.5 | 0.096 | 1.200 | 1.200 | 1.800 | 1.800 |
| 22 | 21:00:48.5 | 0.080 | 1.200 | 1.200 | 1.900 | 1.900 |
| 23 | 21:00:48.6 | 0.066 | 1.200 | 1.200 | 2.000 | 2.000 |
| 24 | 21:00:48.6 | 0.054 | 1.200 | 1.200 | 2.100 | 2.100 |
| 25 | 21:00:48.6 | 0.043 | 1.200 | 1.200 | 2.200 | 2.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['f35b0a7d'] (scan num: 2)
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:48.8 | 0.014 | 0.800 | 0.800 | 2.800 | 2.800 |
| 2 | 21:00:48.8 | 0.011 | 0.800 | 0.800 | 2.900 | 2.900 |
| 3 | 21:00:48.8 | 0.008 | 0.800 | 0.800 | 3.000 | 3.000 |
| 4 | 21:00:48.9 | 0.006 | 0.800 | 0.800 | 3.100 | 3.100 |
| 5 | 21:00:48.9 | 0.004 | 0.800 | 0.800 | 3.200 | 3.200 |
| 6 | 21:00:48.9 | 0.004 | 0.900 | 0.900 | 3.200 | 3.200 |
| 7 | 21:00:49.0 | 0.005 | 0.900 | 0.900 | 3.100 | 3.100 |
| 8 | 21:00:49.0 | 0.007 | 0.900 | 0.900 | 3.000 | 3.000 |
| 9 | 21:00:49.0 | 0.010 | 0.900 | 0.900 | 2.900 | 2.900 |
| 10 | 21:00:49.0 | 0.013 | 0.900 | 0.900 | 2.800 | 2.800 |
| 11 | 21:00:49.1 | 0.012 | 1.000 | 1.000 | 2.800 | 2.800 |
| 12 | 21:00:49.1 | 0.009 | 1.000 | 1.000 | 2.900 | 2.900 |
| 13 | 21:00:49.1 | 0.007 | 1.000 | 1.000 | 3.000 | 3.000 |
| 14 | 21:00:49.2 | 0.005 | 1.000 | 1.000 | 3.100 | 3.100 |
| 15 | 21:00:49.2 | 0.004 | 1.000 | 1.000 | 3.200 | 3.200 |
| 16 | 21:00:49.2 | 0.003 | 1.100 | 1.100 | 3.200 | 3.200 |
| 17 | 21:00:49.3 | 0.004 | 1.100 | 1.100 | 3.100 | 3.100 |
| 18 | 21:00:49.3 | 0.006 | 1.100 | 1.100 | 3.000 | 3.000 |
| 19 | 21:00:49.3 | 0.008 | 1.100 | 1.100 | 2.900 | 2.900 |
| 20 | 21:00:49.4 | 0.011 | 1.100 | 1.100 | 2.800 | 2.800 |
| 21 | 21:00:49.4 | 0.010 | 1.200 | 1.200 | 2.800 | 2.800 |
| 22 | 21:00:49.4 | 0.007 | 1.200 | 1.200 | 2.900 | 2.900 |
| 23 | 21:00:49.5 | 0.005 | 1.200 | 1.200 | 3.000 | 3.000 |
| 24 | 21:00:49.5 | 0.004 | 1.200 | 1.200 | 3.100 | 3.100 |
| 25 | 21:00:49.5 | 0.003 | 1.200 | 1.200 | 3.200 | 3.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['81bb23f1'] (scan num: 3)
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:49.7 | 0.144 | 1.800 | 1.800 | 0.800 | 0.800 |
| 2 | 21:00:49.7 | 0.132 | 1.800 | 1.800 | 0.900 | 0.900 |
| 3 | 21:00:49.7 | 0.120 | 1.800 | 1.800 | 1.000 | 1.000 |
| 4 | 21:00:49.8 | 0.108 | 1.800 | 1.800 | 1.100 | 1.100 |
| 5 | 21:00:49.8 | 0.096 | 1.800 | 1.800 | 1.200 | 1.200 |
| 6 | 21:00:49.8 | 0.080 | 1.900 | 1.900 | 1.200 | 1.200 |
| 7 | 21:00:49.9 | 0.090 | 1.900 | 1.900 | 1.100 | 1.100 |
| 8 | 21:00:49.9 | 0.100 | 1.900 | 1.900 | 1.000 | 1.000 |
| 9 | 21:00:49.9 | 0.110 | 1.900 | 1.900 | 0.900 | 0.900 |
| 10 | 21:00:50.0 | 0.119 | 1.900 | 1.900 | 0.800 | 0.800 |
| 11 | 21:00:50.0 | 0.098 | 2.000 | 2.000 | 0.800 | 0.800 |
| 12 | 21:00:50.0 | 0.090 | 2.000 | 2.000 | 0.900 | 0.900 |
| 13 | 21:00:50.1 | 0.082 | 2.000 | 2.000 | 1.000 | 1.000 |
| 14 | 21:00:50.1 | 0.074 | 2.000 | 2.000 | 1.100 | 1.100 |
| 15 | 21:00:50.1 | 0.066 | 2.000 | 2.000 | 1.200 | 1.200 |
| 16 | 21:00:50.2 | 0.054 | 2.100 | 2.100 | 1.200 | 1.200 |
| 17 | 21:00:50.2 | 0.060 | 2.100 | 2.100 | 1.100 | 1.100 |
| 18 | 21:00:50.2 | 0.067 | 2.100 | 2.100 | 1.000 | 1.000 |
| 19 | 21:00:50.3 | 0.074 | 2.100 | 2.100 | 0.900 | 0.900 |
| 20 | 21:00:50.3 | 0.080 | 2.100 | 2.100 | 0.800 | 0.800 |
| 21 | 21:00:50.4 | 0.065 | 2.200 | 2.200 | 0.800 | 0.800 |
| 22 | 21:00:50.4 | 0.059 | 2.200 | 2.200 | 0.900 | 0.900 |
| 23 | 21:00:50.4 | 0.054 | 2.200 | 2.200 | 1.000 | 1.000 |
| 24 | 21:00:50.5 | 0.049 | 2.200 | 2.200 | 1.100 | 1.100 |
| 25 | 21:00:50.5 | 0.043 | 2.200 | 2.200 | 1.200 | 1.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['f30d034d'] (scan num: 4)
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:50.6 | 0.039 | 1.800 | 1.800 | 1.800 | 1.800 |
| 2 | 21:00:50.7 | 0.033 | 1.800 | 1.800 | 1.900 | 1.900 |
| 3 | 21:00:50.7 | 0.027 | 1.800 | 1.800 | 2.000 | 2.000 |
| 4 | 21:00:50.8 | 0.022 | 1.800 | 1.800 | 2.100 | 2.100 |
| 5 | 21:00:50.8 | 0.018 | 1.800 | 1.800 | 2.200 | 2.200 |
| 6 | 21:00:50.8 | 0.015 | 1.900 | 1.900 | 2.200 | 2.200 |
| 7 | 21:00:50.9 | 0.018 | 1.900 | 1.900 | 2.100 | 2.100 |
| 8 | 21:00:50.9 | 0.022 | 1.900 | 1.900 | 2.000 | 2.000 |
| 9 | 21:00:51.0 | 0.027 | 1.900 | 1.900 | 1.900 | 1.900 |
| 10 | 21:00:51.0 | 0.033 | 1.900 | 1.900 | 1.800 | 1.800 |
| 11 | 21:00:51.0 | 0.027 | 2.000 | 2.000 | 1.800 | 1.800 |
| 12 | 21:00:51.1 | 0.022 | 2.000 | 2.000 | 1.900 | 1.900 |
| 13 | 21:00:51.1 | 0.018 | 2.000 | 2.000 | 2.000 | 2.000 |
| 14 | 21:00:51.2 | 0.015 | 2.000 | 2.000 | 2.100 | 2.100 |
| 15 | 21:00:51.2 | 0.012 | 2.000 | 2.000 | 2.200 | 2.200 |
| 16 | 21:00:51.2 | 0.010 | 2.100 | 2.100 | 2.200 | 2.200 |
| 17 | 21:00:51.3 | 0.012 | 2.100 | 2.100 | 2.100 | 2.100 |
| 18 | 21:00:51.3 | 0.015 | 2.100 | 2.100 | 2.000 | 2.000 |
| 19 | 21:00:51.3 | 0.018 | 2.100 | 2.100 | 1.900 | 1.900 |
| 20 | 21:00:51.4 | 0.022 | 2.100 | 2.100 | 1.800 | 1.800 |
| 21 | 21:00:51.4 | 0.018 | 2.200 | 2.200 | 1.800 | 1.800 |
| 22 | 21:00:51.5 | 0.015 | 2.200 | 2.200 | 1.900 | 1.900 |
| 23 | 21:00:51.5 | 0.012 | 2.200 | 2.200 | 2.000 | 2.000 |
| 24 | 21:00:51.5 | 0.010 | 2.200 | 2.200 | 2.100 | 2.100 |
| 25 | 21:00:51.6 | 0.008 | 2.200 | 2.200 | 2.200 | 2.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['13a42d3f'] (scan num: 5)
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| seq_num | time | det4 | motor1 | motor1_setpoint | motor2 | motor2_setpoint |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
| 1 | 21:00:51.7 | 0.004 | 1.800 | 1.800 | 2.800 | 2.800 |
| 2 | 21:00:51.8 | 0.003 | 1.800 | 1.800 | 2.900 | 2.900 |
| 3 | 21:00:51.8 | 0.002 | 1.800 | 1.800 | 3.000 | 3.000 |
| 4 | 21:00:51.9 | 0.002 | 1.800 | 1.800 | 3.100 | 3.100 |
| 5 | 21:00:51.9 | 0.001 | 1.800 | 1.800 | 3.200 | 3.200 |
| 6 | 21:00:51.9 | 0.001 | 1.900 | 1.900 | 3.200 | 3.200 |
| 7 | 21:00:52.0 | 0.001 | 1.900 | 1.900 | 3.100 | 3.100 |
| 8 | 21:00:52.0 | 0.002 | 1.900 | 1.900 | 3.000 | 3.000 |
| 9 | 21:00:52.0 | 0.002 | 1.900 | 1.900 | 2.900 | 2.900 |
| 10 | 21:00:52.1 | 0.003 | 1.900 | 1.900 | 2.800 | 2.800 |
| 11 | 21:00:52.1 | 0.003 | 2.000 | 2.000 | 2.800 | 2.800 |
| 12 | 21:00:52.2 | 0.002 | 2.000 | 2.000 | 2.900 | 2.900 |
| 13 | 21:00:52.2 | 0.002 | 2.000 | 2.000 | 3.000 | 3.000 |
| 14 | 21:00:52.3 | 0.001 | 2.000 | 2.000 | 3.100 | 3.100 |
| 15 | 21:00:52.3 | 0.001 | 2.000 | 2.000 | 3.200 | 3.200 |
| 16 | 21:00:52.3 | 0.001 | 2.100 | 2.100 | 3.200 | 3.200 |
| 17 | 21:00:52.4 | 0.001 | 2.100 | 2.100 | 3.100 | 3.100 |
| 18 | 21:00:52.4 | 0.001 | 2.100 | 2.100 | 3.000 | 3.000 |
| 19 | 21:00:52.5 | 0.002 | 2.100 | 2.100 | 2.900 | 2.900 |
| 20 | 21:00:52.5 | 0.002 | 2.100 | 2.100 | 2.800 | 2.800 |
| 21 | 21:00:52.6 | 0.002 | 2.200 | 2.200 | 2.800 | 2.800 |
| 22 | 21:00:52.6 | 0.001 | 2.200 | 2.200 | 2.900 | 2.900 |
| 23 | 21:00:52.6 | 0.001 | 2.200 | 2.200 | 3.000 | 3.000 |
| 24 | 21:00:52.7 | 0.001 | 2.200 | 2.200 | 3.100 | 3.100 |
| 25 | 21:00:52.7 | 0.001 | 2.200 | 2.200 | 3.200 | 3.200 |
+-----------+------------+------------+------------+-----------------+------------+-----------------+
generator rel_grid_scan ['1129ae81'] (scan num: 6)
from bluesky.plans import relative_outer_product_scan
from bluesky.plan_stubs import abs_set, wait
from bluesky.preprocessors import (run_decorator, stage_decorator,
subs_decorator)
from bluesky.callbacks import LiveTable, LivePlot
from ophyd.sim import det4, motor1, motor2
from bluesky import RunEngine
def grid_in_grid(samples):
"""
Scan a grid around the neighborhood of each sample.
Parameters
----------
sample : dict
mapping each sample's name to its (x, y) position
"""
# In this example we hard-code the hardware and other parameters. For more
# flexibility, they could instead be parameters to the function.
detector = det4
x = motor1
y = motor2
x_range = y_range = 0.2
x_num = y_num = 5
@subs_decorator([LiveTable([detector, x, y]),
LivePlot('motor2', 'motor1')])
def plan():
for name, position in samples.items():
# Prepare metadata.
md = {'sample': name}
# Move to the cetner of the sample position.
x_pos, y_pos = position
yield from abs_set(x, x_pos)
yield from abs_set(y, y_pos)
yield from wait()
# Scan a grid around that position.
yield from relative_outer_product_scan([detector],
x, -x_range, x_range, x_num,
y, -y_range, y_range, y_num,
True, md=md)
yield from plan()
# Example usage:
RE = RunEngine({})
samples = {'A': (1, 1),
'B': (1, 2),
'C': (1, 3),
'D': (2, 1),
'E': (2, 2),
'F': (2, 3)}
RE(grid_in_grid(samples))
Total running time of the script: ( 0 minutes 6.399 seconds)