Toolkit for processing 4D STEM image data on HPC.
Singularity instructions may be found here.
Build instructions may be found here.
# Example of electron counting raw 4d Camera data
# See stempy/example/electron_count.py for a full version
>>> from pathlib import Path
>>> import stempy.io as stio
>>> import stempy.image as stim
>>> import matplotlib.pyplot as plt
>>> import numpy as np
>>> data_path = Path('/mnt/hdd1/2020.06.03')
>>> files = sorted(data_path.glob('data_scan0*015_*.data')) # raw data files
>>> sReader = stio.reader(files, stio.FileVersion.VERSION5)
>>> events = stim.electron_count(sReader, np.zeros((576,576),background_threshold_n_sigma=4.0))
>>> stio.save_electron_counts('/mnt/hdd1/data_scan15_electrons.h5', events)
# Now create a bright field STEM image from the data by summing pixels
# 0 to 110 radially
>>> bf = stim.create_stem_images(events, 0, 35)
# Create a summed diffraction pattern of the entire dataset
>>> dp = stim.calculate_sum_sparse(events.data,
events.frame_dimensions)
>>> fg, ax = plt.subplots(1,2)
>>> ax[0].imshow(bf[0,:,:])
>>> ax[1].imshow(dp)
Build repo and set PYTHONPATH:
export PYTHONPATH=<build dir>/lib/Interact with raw data
>>> import stempy.io as stio
>>> r = stio.reader('/data/4dstem/smallScanningDiffraction/data0000.dat')
>>> b = r.read()
>>> b.header.images_in_block
32
>>> b.header.image_numbers
[1, 33, 65, 97, 129, 161, 193, 225, 257, 289, 321, 353, 385, 417, 449, 481, 513, 545, 577, 609, 641, 673, 705, 737, 769, 801, 833, 865, 897, 929, 961, 993]
>>> b.data[0]
array([[ 0, 0, 0, ..., 0, 0, 0],
[ 0, 0, 0, ..., 0, 0, 0],
[ 0, 0, 0, ..., 0, 0, 0],
...,
[ 932, 1017, 976, ..., 984, 834, 1031],
[ 928, 1081, 1100, ..., 1020, 985, 969],
[ 989, 940, 1045, ..., 1010, 959, 887]], dtype=uint16)
>>>