Scan surface example¶

Set up notebook to display interactive plots:¶

[1]:

%matplotlib notebook
import sys
# add our GitHub repository to the path
sys.path.append(r'C:\Users\BF4K\Documents\GitHub\scanning-squid\scanning-squid')
import utils

Import microscope class:¶

[2]:

from microscope.susceptometer import SusceptometerMicroscope

Initialize microscope object using configuration file:¶

Useful information will be printed to the screen and logged to ‘logs/scan_surface_example.log’

[3]:

config_file = 'config_microscope.json'
m = SusceptometerMicroscope(config_file, 'RT', log_name='scan_surface_example')

INFO:2018-06-14_16:52:05:microscope:Logging started.
INFO:2018-06-14_16:52:05:microscope:Initializing microscope object using file config_microscope.json.
INFO:2018-06-14_16:52:05:atto:Initializing Attocube controller.

attocube ANC300 controller version 1.1.0-1304 2013-10-17 08:16

INFO:2018-06-14_16:52:12:microscope:Attocube controller successfully added to microscope.
INFO:2018-06-14_16:52:12:scanner:Moved scanner from [-0.001, -0.0, -0.001] V to [-0.0, -0.0, -0.001] V.
INFO:2018-06-14_16:52:12:microscope:Scanner successfully added to microscope.
INFO:2018-06-14_16:52:12:microscope:Susceptometer(SQUID) successfully added to microscope.

Connected to: Stanford_Research_Systems SR830 (serial:s/n53956, firmware:ver1.07) in 0.06s

INFO:2018-06-14_16:52:12:microscope:SUSC_lockin successfully added to microscope.

Connected to: Stanford_Research_Systems SR830 (serial:s/n53182, firmware:ver1.07) in 0.08s

INFO:2018-06-14_16:52:13:microscope:CAP_lockin successfully added to microscope.

These are the instruments contained in the microscope. Their metadata will automatically be saved.¶

[4]:

m.components

[4]:

{'atto': <ANC300: atto>,
 'benders': <Scanner: benders>,
 'SQUID': <Susceptometer: SQUID>,
 'SUSC_lockin': <SR830: SUSC_lockin>,
 'CAP_lockin': <SR830: CAP_lockin>}

Get current scanner position (in DAQ voltage units):¶

(scanner.position() is equivalent to scanner.position.get())

[5]:

m.scanner.position()

[5]:

[0.0, -0.0, -0.001]

Retract scanner to \(z\)-position set in config_microscope.json¶

[6]:

m.scanner.retract()

INFO:2018-06-14_16:52:14:scanner:Moved scanner from [-0.001, -0.0, -0.001] V to [-0.001, -0.0, -2.0] V.

(scanner.goto([0,0,0]) is equivalent to scanner.position([0,0,0]) and scanner.position.set([0,0,0]))

[7]:

m.scanner.position()

[7]:

[-0.001, -0.0, -2.0]

[8]:

m.scanner.goto([0,0,0])

INFO:2018-06-14_16:52:15:scanner:Moved scanner from [-0.001, -0.0, -2.0] V to [-0.0, -0.0, -0.0] V.

In order to run scan_plane without acquiring a surface, we have to trick the microscope into thinking it has acquired a surface:

[9]:

m.scanner.metadata['plane'].update({'x': 0.1, 'y': 0.1, 'z': 0.1})
m.atto.surface_is_current = True

Load measurement configuration file:¶

[10]:

measurements = utils.load_json_ordered('config_measurements_susc.json')

Run the scan:¶

[11]:

m.scan_surface(measurements['scan'])

INFO:2018-06-14_16:52:21:utils:Scan parameters are valid. Starting scan.
INFO:2018-06-14_16:52:21:scanner:Moved scanner from [-0.001, -0.0, -0.0] V to [-1.5, -1.5009999999999999, -0.40000000000000002] V.
INFO:2018-06-14_16:52:21:microscope:Setting amplitude on SUSC_lockin to 1 V.
INFO:2018-06-14_16:52:21:microscope:Setting frequency on SUSC_lockin to 131.79 Hz.
INFO:2018-06-14_16:52:21:microscope:Setting amplitude on CAP_lockin to 1 V.
INFO:2018-06-14_16:52:21:microscope:Setting frequency on CAP_lockin to 18437.0 Hz.

Started at 2018-06-14 16:52:23

INFO:2018-06-14_16:55:13:scanner:Moved scanner from [1.4990000000000001, 1.4990000000000001, 0.20000000000000001] V to [-0.001, -0.0, -0.001] V.
INFO:2018-06-14_16:55:13:microscope:Scan completed. DataSet saved to data/2018-06-14/#001_scan_16-52-23.
INFO:2018-06-14_16:55:13:microscope:Removed daq_ai from microscope.

DataSet:
   location = 'data/2018-06-14/#001_scan_16-52-23'
   <Type>   | <array_id>             | <array.name> | <array.shape>
   Setpoint | benders_position_y_set | position_y   | (50,)
   Measured | daq_ai_voltage         | voltage      | (50, 4, 50)
Finished at 2018-06-14 16:55:13

We can change the scan fast axis from \(x\) to \(y\):¶

[12]:

measurements['scan']['fast_ax'] = 'y'

And run the scan again:¶

[13]:

data1, plot1 = m.scan_surface(measurements['scan'])

INFO:2018-06-14_16:55:14:utils:Scan parameters are valid. Starting scan.
INFO:2018-06-14_16:55:15:scanner:Moved scanner from [-0.0, -0.0, -0.0] V to [-1.5, -1.5, -0.40000000000000002] V.
INFO:2018-06-14_16:55:15:microscope:Setting amplitude on SUSC_lockin to 1 V.
INFO:2018-06-14_16:55:15:microscope:Setting frequency on SUSC_lockin to 131.79 Hz.
INFO:2018-06-14_16:55:15:microscope:Setting amplitude on CAP_lockin to 1 V.
INFO:2018-06-14_16:55:15:microscope:Setting frequency on CAP_lockin to 18437.0 Hz.

Started at 2018-06-14 16:55:17

INFO:2018-06-14_16:58:03:scanner:Moved scanner from [1.5, 1.5, 0.20000000000000001] V to [-0.0, -0.0, -0.001] V.
INFO:2018-06-14_16:58:03:microscope:Scan completed. DataSet saved to data/2018-06-14/#002_scan_16-55-17.
INFO:2018-06-14_16:58:03:microscope:Removed daq_ai from microscope.

DataSet:
   location = 'data/2018-06-14/#002_scan_16-55-17'
   <Type>   | <array_id>             | <array.name> | <array.shape>
   Setpoint | benders_position_x_set | position_x   | (50,)
   Measured | daq_ai_voltage         | voltage      | (50, 4, 50)
Finished at 2018-06-14 16:58:03

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