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"