subtom_plot_scanned_angles

Plots the angles searched for a user-specified set of alignment angles. The angles can also be centered about a given initial orientation. The marker of the plot can be adjusted and the plot can also be saved to disk.

This utility script uses one MATLAB compiled scripts below:

Options

Directories

scratch_dir

Absolute path to the folder with the input to be processed. Other paths are relative to this one.

mcr_cache_dir

Absolute path to MCR directory for the processing.

exec_dir

Directory for executables

Variables

plot_angles_exec

Plot scanned angles executable.

File Options

output_fn_prefix

Relative path and name prefix of the output plot. If you want to skip this output file leave this set to “”.

Plot Scanned Angles Options

psi_angle_step

Angular increment in degrees, applied during the cone-search, i.e. psi and theta (define as real e.g. psi_angle_step=3)

psi_angle_shells

Number of angular iterations, applied to psi and theta (define as integer e.g. psi_angle_shells=3)

phi_angle_step

Angular increment for phi in degrees, (define as real e.g. phi_angle_step=3)

phi_angle_shells

Number of angular iterations for phi, (define as integer e.g. phi_angle_shells=3)

initial_phi

Initial first Euler angle rotation around the Z-axis about which the scanned angles are centered. (define as real e.g. initial_phi=45).

initial_psi

Initial third Euler angle rotation around the Z-axis about which the scanned angles are centered. (define as real e.g. initial_psi=30).

initial_theta

Initial second Euler angle rotation around the X-axis about which the scanned angles are centered. (define as real e.g. initial_theta=135).

angle_fmt

If the above angles are specified as degress leave this set to ‘degrees’, but if the angles above are in radian format set this to ‘radians’.

marker_size

Set the marker size of the arrows that are drawn for the rotations, reasonable values seem to be around the range of 0.01 to 0.1.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

exec_dir="/net/dstore2/teraraid/dmorado/software/subTOM/bin"

plot_angles_exec="${exec_dir}/utils/subtom_plot_scanned_angles"

output_fn_prefix=""

psi_angle_step="6"

psi_angle_shells="7"

phi_angle_step="6"

phi_angle_shells="7"

initial_phi="0"

initial_psi="0"

initial_theta="0"

angle_fmt="degrees"

marker_size="0.02"