susan.modules.CropProjection¶

class susan.modules.CropProjection[source]¶

Bases: object

Projection-cropping engine for 2-D subtomogram alignment.

Wraps the susan_crop_projections binary. Crops 2-D projection patches around each particle position into out_dir for subsequent 2-D alignment. Configure the attributes, then call extract().

Attributes

num_threads¶

Number of CPU threads to use. Default: 1.

Type:: int

normalize_type¶

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

Type:: str

invert_contrast¶

Invert the sign of the cropped projections. Default: False.

Type:: bool

Methods

get_args(out_dir, tomos_file, ptcls_in, box_size)[source]¶

Build the command-line argument string for susan_crop_projections.

Parameters:

out_dir (str) – Output directory where cropped projection patches are written.
tomos_file (str) – Path to the .tomostxt tomograms file.
ptcls_in (str) – Path to the input .ptclsraw particles file.
box_size (int) – Patch size in pixels.

Returns:

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

Return type:

str

extract(out_pfx, tomos_file, ptcls_in, box_size)[source]¶

Crop projection patches for all particles.

Parameters:

out_pfx (str) – Output directory for the cropped patches.
tomos_file (str) – Path to the .tomostxt tomograms file.
ptcls_in (str) – Path to the input .ptclsraw particles file.
box_size (int) – Patch size in pixels.

Raises:

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