Nabu reconstruction parameters

The reconstruction parameters are split along several sections:

• dataset

• output

• phase

• preproc

• reconstruction

This is the nabu configuration file provided as a dict.

You can obtain nabu default configuration directly from nabu

from nabu.pipeline.fullfield.nabu_config import nabu_config

dataset

• binning: int

• binning_z: int

• exclude_projections: str

• projections_subsampling

output

• file_format: str

• location: str

• output_dir_mode: str

  warning:

  this is a tomwer specific values. See

phase

• beam_shape: str

• ctf_advanced_params: str

• ctf_geometry: str

• ctf_translations_file: str

• method: str

• unsharp_coeff: int

• unsharp_sigma: int

preproc

• autotilt_options: str

• ccd_filter_enabled: int

• ccd_filter_threshold: float

• dff_sigma: float

• flatfield_enabled: int

• flatfield: int

• log_max_clip: float

• log_min_clip: float

• normalize_srcurrent: int

• rotate_projections_center: str

• sino_rings_correction: str

• sino_rings_options: str

• take_logarithm: bool

• tilt_correction: str

reconstruction

• angle_offset: float

• angles_file: str

• axis_correction_file: str

• centered_axis: int

• clip_outer_circle: int

• enable_halftomo: str

• end_x: int

• end_y: int

• end_z: int

• fbp_filter_type: str

• iterations: int

• method: str

• optim_algorithm: str

• padding_type: str

• positivity_constraint: int

• preconditioning_filter: int

• rotation_axis_position: str | float

• start_x: int

• start_y: int

• start_z: int

• translation_movements_file: str

• regularization_weight: float