subtom_shape

Creates a simple shape of a user-specified type that can be used for masking purposes.

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

shape_exec

Shape executable

File Options

output_fn

Relative path and name of the output volume to write.

ref_fn

Relative path and name of a reference to apply the mask to, which can be useful for checking. If you want to skip this check just leave it set to “”.

Shape Options

shape
The shape to place into the volume. The available options are:
  • sphere,

  • sphere_shell

  • ellipsoid

  • ellipsoid_shell

  • cylinder

  • tube

  • elliptic_cylinder

  • elliptic_tube

  • cuboid

box_size

Size of the volume in pixels. The volume will be a cube with this side length.

radius
For the shapes:
  • sphere

  • cylinder

Defines the radius of the shape. If you are not creating one of the listed shapes leave this set to “”.

inner_radius
For the shapes:
  • sphere_shell

  • tube

Defines the inner radius of the shape. If you are not creating one of the listed shapes leave this set to “”.

outer_radius
For the shapes:
  • sphere_shell

  • tube

Defines the outer radius of the shape. If you are not creating one of the listed shapes leave this set to “”.

radius_x
For the shapes:
  • ellipsoid

  • elliptic_cylinder

Defines the radius of the shape about the X-axis. If you are not creating one of the listed shapes leave this set to “”.

radius_y
For the shapes:
  • ellipsoid

  • elliptic_cylinder

Defines the radius of the shape about the Y-axis. If you are not creating one of the listed shapes leave this set to “”.

radius_z
For the shapes:
  • ellipsoid

  • elliptic_cylinder

Defines the radius of the shape about the Z-axis. If you are not creating one of the listed shapes leave this set to “”.

inner_radius_x
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the inner radius of the shape about the X-axis. If you are not creating one of the listed shapes leave this set to “”.

inner_radius_y
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the inner radius of the shape about the Y-axis. If you are not creating one of the listed shapes leave this set to “”.

inner_radius_z
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the inner radius of the shape about the Z-axis. If you are not creating one of the listed shapes leave this set to “”.

outer_radius_x
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the outer radius of the shape about the X-axis. If you are not creating one of the listed shapes leave this set to “”.

outer_radius_y
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the outer radius of the shape about the Y-axis. If you are not creating one of the listed shapes leave this set to “”.

outer_radius_z
For the shapes:
  • ellipsoid_shell

  • elliptic_tube

Defines the outer radius of the shape about the Z-axis. If you are not creating one of the listed shapes leave this set to “”.

length_x
For the shape:
  • cuboid

Defines the length of the cuboid about the X-axis. If you are not creating one of the listed shapes leave this set to “”.

length_y
For the shape:
  • cuboid

Defines the length of the cuboid about the Y-axis. If you are not creating one of the listed shapes leave this set to “”.

length_z
For the shape:
  • cuboid

Defines the length of the cuboid about the Z-axis. If you are not creating one of the listed shapes leave this set to “”.

height
For the shape:
  • cylinder

  • tube

  • elliptic_cylinder

  • elliptic_tube

Defines the height of the shape. If you are not creating one of the listed shapes leave this set to “”.

center_x

For all shapes. Defines the X-coordinate of the center of the shape. The default center is defined as:

center_x = floor(box_size / 2) + 1;

If you do not want to modify the default value leave this set to “”.

center_y

For all shapes. Defines the Y-coordinate of the center of the shape. The default center is defined as:

center_y = floor(box_size / 2) + 1;

If you do not want to modify the default value leave this set to “”.

center_z

For all shapes. Defines the Z-coordinate of the center of the shape. The default center is defined as:

center_z = floor(box_size / 2) + 1;

If you do not want to modify the default value leave this set to “”.

shift_x

For all shapes. Defines a shift along the X-axis after any given rotations. This shift is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

shift_y

For all shapes. Defines a shift along the Y-axis after any given rotations. This shift is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

shift_z

For all shapes. Defines a shift along the Z-axis after any given rotations. This shift is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

rotate_phi

For all shapes. Defines an inplane rotation about the Z-axis. This rotation is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

rotate_psi

For all shapes. Defines an azimuthal rotation about the Z-axis. This rotation is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

rotate_theta

For all shapes. Defines a zenithal rotation about the X-axis. This rotation is part of an affine transformation about the given center that is applied to the coordinates before the shape is determined. If you do not want to modify the default value leave this set to “”.

sigma

For all shapes. Defines the sigma of a Gaussian falloff away from the hard edges of the shape. If you do not want to modify the default value leave this set to “”.

Example

scratch_dir="${PWD}"

mcr_cache_dir="${scratch_dir}/mcr"

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

shape_exec="${exec_dir}/utils/subtom_shape"

output_fn="otherinputs/mask.em"

ref_fn="ref/ref_1.em"

shape="sphere"

box_size="128"

radius="32"

inner_radius=""

outer_radius=""

radius_x=""

radius_y=""

radius_z=""

inner_radius_x=""

inner_radius_y=""

inner_radius_z=""

outer_radius_x=""

outer_radius_y=""

outer_radius_z=""

length_x=""

length_y=""

length_z=""

height=""

center_x=""

center_y=""

center_z=""

shift_x=""

shift_y=""

shift_z=""

rotate_phi=""

rotate_psi=""

rotate_theta=""

sigma="3"