susan.modules.Averager

class susan.modules.Averager

Bases: object

Map reconstruction (averaging) engine for subtomogram averaging.

Wraps the susan_reconstruct binary. Configure the attributes, then call reconstruct() (single-node) or reconstruct_mpi() (multi-node MPI).

Attributes

list_gpus_ids

GPU device IDs to use. Default: [0].

Type:

list of int

bandpass

Frequency bandpass applied during back-projection. Default: bandpass(0, -1, 2) (full range, 2-pixel rolloff).

Type:

bandpass

extra_padding

Extra zero-padding (pixels) added on each side before FFT. Default: 0.

Type:

int

rec_halfsets

If True, reconstruct separate half-maps (needed for FSC). Default: False.

Type:

bool

padding_type

Fill value for the padded region: 'zero' or 'noise'. Default: 'zero'.

Type:

str

normalize_type

Per-substack normalisation. One of 'none', 'zero_mean', 'zero_mean_one_std' and 'zero_mean_unit_var'. Default: 'zero_mean_one_std'.

Type:

str

weighting_type

Particle weighting scheme. One of 'none', 'particle', 'projection', '3DCC', '2DCC'. Default: 'none'.

Type:

str

ctf_correction

CTF correction applied during back-projection. One of 'none', 'phase_flip', 'wiener', 'wiener_ssnr'; 'wiener_atan' and 'wiener_lgstc' are experimental. Default: 'wiener'.

Type:

str

gridding_type

Fourier-space gridding method: 'linear' or 'kb' (Kaiser–Bessel). Default: 'kb'.

Type:

str

splat_gain

Experimental. Angular-spread splatting. When greater than 0, the bandpass lowpass and the per-projection def_mres stop acting as a cutoff and instead set the width of a tangential gaussian insertion kernel, so every frequency up to Nyquist is inserted, progressively blurred rather than truncated. The width is clamp(splat_gain*0.4*R/R_ref, 0.4, 1.5) fourier pixels with R_ref = min(lowpass, def_mres), so it is flat (and equivalent to trilinear) up to R_ref/splat_gain and then grows. 1 is the physically anchored value; larger distrusts the stated resolution more and starts blurring earlier. Overrides gridding_type. Costs roughly 4x more time in the insertion stage than linear gridding. Default: 0 (disabled, ordinary reconstruction).

Type:

float

symmetry

Point-group symmetry applied to the reconstructed map. Default: 'c1'.

Value	Description
'c1' / 'none'	No symmetry (identity).
'cN' / 'CN'	Cyclic N-fold (e.g. 'c4').
'dN' / 'DN'	Dihedral N-fold (e.g. 'd2').
'cbo' / 'CBO'	Cuboctahedral (order 24).
'ico' / 'ICO' / 'i2' / 'I2'	Icosahedral, I2 convention (order 60; RELION default).
'i1' / 'I1'	Icosahedral, I1 convention.
'i3' / 'I3'	Icosahedral, I3 convention.
'i4' / 'I4'	Icosahedral, I4 convention.
'cone_flip' / 'y_180'	180° rotation about the Y axis.

Type:

str

ssnr

Ad-hoc SSNR model for Wiener filter denominator. Default: ssnr(1, 0.01).

Type:

ssnr

inversion

Parameters for iterative sampling-function inversion. A std of 0 or less selects it from the gridding method. Default: inversion_params(10, -1).

Type:

inversion_params

mpi

MPI launcher configuration used by reconstruct_mpi(). Default: mpi_params('srun -n %d ', 1).

Type:

mpi_params

verbosity

Verbosity level passed to the binary. Default: 1.

Type:

int

normalize_output

Normalise the output map to unit standard deviation. Default: True.

Type:

bool

ignore_classes

Ignore reference-class assignments; reconstruct all particles. Default: False.

Type:

bool

boost_lowfreq

Experimental. Optional low-frequency boost before reconstruction. Default: boost_lowfreq_params(0, 0, 0) (disabled).

Type:

boost_lowfreq_params

Methods

get_args(out_pfx, tomos_file, ptcls_in, box_size)

Build the command-line argument string for susan_reconstruct.

Parameters:

• out_pfx (str) – Output path prefix; maps are written as <out_pfx>_class001.mrc etc.

• tomos_file (str) – Path to the .tomostxt tomograms file.

• ptcls_in (str) – Path to the input .ptclsraw particles file.

• box_size (int) – Subvolume box size in pixels.

Returns:

Space-separated argument string ready to be appended to the susan_reconstruct command.

Return type:

str

reconstruct(out_pfx, tomos_file, ptcls_in, box_size)

Execute the reconstruction on a single node.

Parameters:

• out_pfx (str) – Output path prefix for the reconstructed maps.

• tomos_file (str) – Path to the .tomostxt tomograms file.

• ptcls_in (str) – Path to the input .ptclsraw particles file.

• box_size (int) – Subvolume box size in pixels.

Raises:

RuntimeError – If the susan_reconstruct binary returns a non-zero exit code.

reconstruct_mpi(out_pfx, tomos_file, ptcls_in, box_size)

Execute the reconstruction using MPI across multiple nodes.

The MPI command is taken from mpi.

Parameters:

• out_pfx (str) – Output path prefix for the reconstructed maps.

• tomos_file (str) – Path to the .tomostxt tomograms file.

• ptcls_in (str) – Path to the input .ptclsraw particles file.

• box_size (int) – Subvolume box size in pixels.

Raises:

RuntimeError – If the MPI binary returns a non-zero exit code.