recovar.utils

General-purpose utilities for I/O, array manipulation, and timing.

helpers

recovar.utils.helpers

General-purpose utilities: I/O, array manipulation, timing.

AlgorithmOptions(volume_mask_option, zs_dim_to_test, contrast, ignore_zero_frequency, keep_intermediate) dataclass

Typed container for pipeline algorithm options.

RobustStreamHandler

Bases: StreamHandler

StreamHandler that silently handles stale NFS/GPFS file handles.

RobustFileHandler

Bases: FileHandler

FileHandler that reopens the file on stale NFS/GPFS handles.

make_radial_image_half(average_image_PS, image_shape, extend_last_frequency=True)

Like :func:make_radial_image but outputs rfft-packed half-spectrum.

Uses get_grid_of_radial_distances_real so the output has shape (H * (W//2+1),) instead of (H * W,).

set_gpu_memory_limit(gb)

Set the GPU memory limit (in GB) used for batch-size calculations.

safe_batch_size(raw_size)

Clamp a raw batch size to at least 1 and convert to int.

get_image_batch_size(grid_size, gpu_memory)

Calculate batch size for image processing.

Parameters:

Name	Type	Description	Default
grid_size		Size of the grid	required
gpu_memory		Available GPU memory in GB	required

Returns:

Type	Description
	Integer batch size with reasonable bounds

get_vol_batch_size(grid_size, gpu_memory)

Calculate batch size for volume processing.

get_column_batch_size(grid_size, gpu_memory)

Calculate batch size for column processing.

compute_batch_sizes(grid_size, gpu_memory)

Compute all batch sizes at once.

Returns a BatchSizes(image, volume, column) namedtuple.

R_to_relion(rot, degrees=True)

Convert rotation matrices to RELION Euler angles.

Converts rotation matrices to RELION's ZXZ Euler angle convention with appropriate coordinate frame transformations.

Parameters:

Name	Type	Description	Default
rot	ndarray	Rotation matrix or matrices of shape (3,3) or (N,3,3)	required
degrees	bool	If True, return angles in degrees; otherwise radians	True

Returns:

Type	Description
ndarray	Euler angles in RELION convention, shape (N,3)

R_from_relion(euler_, degrees=True)

Convert RELION Euler angles to rotation matrices.

Converts RELION's ZXZ Euler angle convention to rotation matrices with appropriate coordinate frame transformations.

Parameters:

Name	Type	Description	Default
euler_	ndarray	Euler angles of shape (3,) or (N,3) in RELION convention	required
degrees	bool	If True, input angles are in degrees; otherwise radians	True

Returns:

Type	Description
ndarray	Rotation matrices of shape (N,3,3)