Sector 32-ID Scripts¶

General Features¶

All the scan scripts below can be executed in one of three ways.

Through the tomography.sh graphical user interface (GUI)
From the command line interface (CLI)
Directly from a python interpreter

The mechanisms behind the GUI and command-line interfaces are identical. Every argument in the GUI parameter panel is also present as a long argument on the command-line:

$ energy-scan --Energy_End 8.5 --Energy_Start 8.3 --ExposureTime 1.5 --SampleXOut 0.1

The programatic python versions start with run_. They often have slightly differet parameters to the GUI/CLI implementation, allowing for more precise control.

>>> import aps_32id
>>> import numpy as np
>>> aps_32id.run_energy(energies=np.linspace(8.3, 8.5, num=101))

Logging¶

These scripts (except for move_energy) uses the standard library logging module to save logs with file names matching the HDF5 data files. The default level is logging.INFO, but this can be changed by using the Log_Level variable:

$ energy-scan --Log_Level 10

or the log_level parameter:

>>> import numpy as np
>>> import logging
>>> import aps_32id
>>> aps_32id.run_energy_scan(energies=np.linspace(8.3, 8.5, 100), log_level=logging.DEBUG)

The log levels are the same as those defined in the logging module. They get set to the root logger, so logging.UNSET results in all messages being sent through. The special value -1 causes no changes to the logging configuration.

Logging levels for the `Log_Level` variable¶
Level	Value
(no change)	-1
logging.UNSET	0
logging.DEBUG	10
logging.INFO	20
logging.WARNING	30
logging.ERROR	40
logging.CRITICAL	50

Move Energy¶

GUI:	`run/move_energy.py`
Command-line:	`$ move-energy`
Python:	`>>> aps_32id.move_energy()`

The move_energy script provides a way to change the energy of the beamline. If the parameter constant_mag is truthy, the detector will move to maintain a constant level of magnification. The equivalent function move_energy() can be used programatically.

Energy Scan¶

GUI:	`run/energy_scan.py`
Command-line:	`$ energy-scan`
Python:	`>>> aps_32id.run_energy_scan()`

The energy_scan script collects 2D frames over a range of energies, as well as the corresponding flat-field and dark-field images. The equivalent function run_energy_scan() lets this script be called programatically. The variable dictionary contains parameters for Energy_Start, Energy_End and Energy_Step. If more control is needed (eg, non-evenly spaced energies), then the function should be used with the energies argument. The helper function energy_range() allows easy construction of a unique list of energies.

from aps_32id import run_energy_scan
from scanlib import energy_range
import numpy as np

# Create a list of energies from energy ranges
energies = energy_range(
    # (start, end, step)
    (8250, 8290, 10),
    (8290, 8300, 2),
    (8300, 8380, 1),
    (8380, 8500, 10),
)

# Describe position for sample and flat-field frames
# (x, y, z, θ°)
out_pos = (0.2, None, None, 0)
sample_pos = (0, None, None, 0)

# Execute the scan
run_energy_scan(energies=energies, out_pos=out_pos, sample_pos=sample_pos)

Tomography Step Scan¶

GUI:	`run/tomo_step_scan.py`
Command-line:	`$ tomo-step-scan`
Python:	`>>> aps_32id.run_tomo_step_scan()`

The tomo_step_scan script collects a tomogram as well as flat-field and dark-field images. The variable dictionary entries SampleStart_Rot, SampleEnd_Rot, Projections control which angles get run. If more control is needed, the run_tomo_step_scan() function with the angles parameter can be used. It is not a requirement that the angles be equally spaced.

import numpy as np

from aps_32id import run_tomo_step_scan

# Create the list of angles to scan
angles = np.linspace(0, 180, 361)

# Describe positions for sample and white-field position
# (x, y, z, θ°)
out_pos = (0.2, None, None, 0)
sample_pos = (0, None, None, 0)

# Execute the scan
run_tomo_step_scan(angles=angles, sample_pos=sample_pos, out_pos=out_pos)

Tomography Fly Scan¶

GUI:	`run/tomo_fly_scan.py`
Command-line:	`$ tomo-fly-scan`
Python:	`>>> aps_32id.run_tomo_fly_scan()`

The tomo_fly_scan script is similar to tomo_step_scan except it does not come to a complete stop when collecting projection. The timing must be uniform, so only equally spaced angles are allowed, even in the python function form.

Mosaic Tomography Fly Scan¶

Warning

This function has not yet replaced the “old style” script at the beamline.

The mosaic_tomo_fly_scan script and mosaic_tomo_fly_scan() are similar to tomo_step_scan except multiple fields of view are collected.

Roll-Your-Own Scripts¶

Those with a sense of adventure can write their own scripts for Sector 32. It’s highly recommended to become familiar with the Sector 32-ID TXM and Examples pages.