subtom_parallel_dmatrix
Calculates chunks of the D-matrix for processing.
subtom_parallel_dmatrix(
'all_motl_fn_prefix', all_motl_fn_prefix ('combinedmotl/allmotl'),
'dmatrix_fn_prefix', dmatrix_fn_prefix ('class/dmatrix_wmd'),
'ptcl_fn_prefix', ptcl_fn_prefix ('subtomograms/subtomo'),
'ref_fn_prefix', ref_fn_prefix ('ref/ref'),
'weight_fn_prefix', weight_fn_prefix ('otherinputs/ampspec'),
'mask_fn', mask_fn ('none'),
'high_pass_fp', high_pass_fp (0),
'high_pass_sigma', high_pass_sigma (0),
'low_pass_fp', low_pass_fp (0),
'low_pass_sigma', low_pass_sigma (0),
'nfold', nfold (1),
'iteration', iteration (1),
'tomo_row', tomo_row (7),
'prealigned', prealigned (0),
'num_dmatrix_batch', num_dmatrix_batch (1),
'process_idx', process_idx (1))
Aligns a subset of particles using the rotations and shifts in the file given by
all_motl_fn_prefix and iteration and then subtracts the particle from
the reference specified by ref_fn_prefix and iteration and places these
voxels of the difference as a 1-D row vector in a data sub-matrix which is
denoted as the D-matrix (See Heumann, et al. 2011 J. Struct. Biol.). The
particle and reference are also filtered by a bandpass filter specified by
high_pass_fp, high_pass_sigma, low_pass_fp and low_pass_sigma,
and optionally symmetrized with nfold C-symmetry, before subtracted.The
reference is masked in Fourier space using the weight specified by
weight_fn_prefix and tomo_row. The subset of particles compared is
specified by the number of particles in the motive list and the number of
requested batches specified by num_dmatrix_batch, with the specific subset
deteremined by process_idx. The D-matrix chunk will be written out as given
by dmatrix_fn_prefix, iteration, and process_idx. The location of
the particles is specified by ptcl_fn_prefix. If prealigned evaluates to
true as a boolean then the particles are assumed to be prealigned, which should
increase speed of computation of D-Matrix calculations. Particles in the
D-matrix will be masked by the file given by mask_fn. If the string ‘none’
is used in place of mask_fn, a default spherical mask is applied. This mask
should be a binary mask and only voxels within the mask are placed into the
D-matrix which can greatly speed up computations.
Example
subtom_parallel_dmatrix(
'all_motl_fn_prefix', 'combinedmotl/allmotl', ...
'dmatrix_fn_prefix', 'class/dmatrix', ...
'ptcl_fn_prefix', 'subtomograms/subtomo_ali', ...
'ref_fn_prefix', 'ref/ref', ...
'weight_fn_prefix', 'otherinputs/ampspec', ...
'mask_fn', 'combinedmotl/classification_mask.em', ...
'high_pass_fp', 1, ...
'high_pass_sigma', 2, ...
'low_pass_fp', 15, ...
'low_pass_sigma', 3, ...
'nfold', 1, ...
'iteration', 1, ...
'prealigned', 1, ...
'num_dmatrix_batch', 100, ...
'process_idx', 1)