tomodrgn.utils

Common utility functions pertaining to both data processing and script execution

Functions

calc_cc	Helper function to calculate the zero-mean correlation coefficient as defined in eq 2 in https://journals.iucr.org/d/issues/2018/09/00/kw5139/index.html vol1 and vol2 should be maps of the same box size, shape (boxsize, boxsize, boxsize)
calc_fsc	Calculate the FSC between two volumes with optional masking.
calc_lowpass_filter_mask	Calculate a binary mask to later be multiplied into a fourier space volume to lowpass filter said volume.
calc_real_space_mask	Generate a real space mask generated from up to two volumes
check_git_revision_hash	Get the git revision hash of a git repository.
check_memory_usage	Get the current memory usage of the specified device_type.
first_n_factors	Decorator.
flog	Write a string to outfile with a standardized datetime format.
get_default_device	Determine whether a CUDA-capable GPU is availble or not for torch operations.
get_latest_epoch	Detect the latest completed epoch of model training.
load_pkl	Convenience function to read a binary pickle file.
log	Write a string to STDOUT with a standardized datetime format.
lowpass_filter	Lowpass-filters a volume in reciprocal space.
prefix_paths	Test which of various modifications to the image .mrcs files correctly locates the files on disk.
print_progress_bar	Display an ASCII progress bar in STDOUT.
rot_3d_from_eman	Convert Euler angles from EMAN to a 3-D rotation matrix.
rot_3d_from_relion	Convert Euler angles from RELION to a 3-D rotation matrix.
rot_3d_from_relion_scipy	Convert a Nx3 array of RELION euler angles to rotation matrices using Scipy Rotations class.
rot_3d_to_relion_scipy	Convert an array of Nx3x3 rotation matrices to RELION euler angles using Scipy Rotations class.
save_pkl	Convenience function to write data to a binary pickle file.
vlog	Write a string to STDOUT with a standardized datetime format only if _verbose is True.
xrot	Return rotation matrix associated with rotation over the x-axis.
yrot	Return rotation matrix associated with rotation over the y-axis
zero_sphere	Set volume values outside of a sphere inscribed within a cube to zero.

Classes

Memoized

Decorator.