Package mgui.geometry.neuro.mesh

Class ScalpAndSkullModelOptions

java.lang.Object
mgui.interfaces.InterfaceOptions
mgui.geometry.neuro.mesh.ScalpAndSkullModelOptions
All Implemented Interfaces:
InterfaceObject, NamedObject, TreeObject, CleanableObject
public class ScalpAndSkullModelOptions
extends InterfaceOptions
Parameters for skull and scalp surface approximation. Default values are also specified here.
Since:
1.0
Version:
1.0
Author:
Andrew Reid
See Also:
NeuroMeshFunctions

  • Field Details

    • t1_volume

      public Volume3DInt t1_volume

    • brain_mask

      public java.lang.String brain_mask

    • ear_nasium_plane

      public Plane3D ear_nasium_plane

    • center_of_mass

      public org.jogamp.vecmath.Point3f center_of_mass

    • brain_surface

      public Mesh3D brain_surface

    • n_nodes

      public int n_nodes

    • initial_radius

      public float initial_radius

    • sample_rate

      public float sample_rate

    • min_dist_B_IS

      public float min_dist_B_IS

    • min_dist_OS_S

      public float min_dist_OS_S

    • min_intensity

      public double min_intensity

    • max_intensity_dist

      public float max_intensity_dist

    • min_slope

      public double min_slope

    • apply_gaussian

      public boolean apply_gaussian

    • sigma_normal

      public float sigma_normal

    • sigma_tangent

      public float sigma_tangent

    • gaussian_cutoff

      public float gaussian_cutoff

    • max_skull_int

      public double max_skull_int

    • stop_skull_int

      public double stop_skull_int

    • max_skull_width

      public float max_skull_width

    • min_skull_width

      public float min_skull_width

    • plateau_slope

      public double plateau_slope

    • min_plateau_length

      public int min_plateau_length

    • max_plateau_slope

      public double max_plateau_slope

    • average_neighbour_rays

      public boolean average_neighbour_rays

    • average_neighbour_weight

      public double average_neighbour_weight

    • gradient_AP_A

      public float gradient_AP_A

    • gradient_IS_S

      public float gradient_IS_S

    • threshold_stdev

      public float threshold_stdev

    • correction_stdev

      public float correction_stdev

    • shape_set

      public ShapeSet3DInt shape_set

    • template_rays

      public java.lang.String template_rays

    • subject_deviation_threshold

      public double subject_deviation_threshold

    • debug_output_dir

      public java.lang.String debug_output_dir

    • resample_n

      public int resample_n

    • bottom_z

      public float bottom_z

    • bottom_dist

      public float bottom_dist

    • generate_control_meshes

      public boolean generate_control_meshes

  • Constructor Details

    • ScalpAndSkullModelOptions

      public ScalpAndSkullModelOptions()

  • Method Details

    • setFromFile

      public void setFromFile​(java.lang.String file) throws java.io.IOException
      Sets the parameters from a parameter file, which is a text file where parameters are specified by the form:

      < param name >=< value >

      Only primivite-valued parameters (of type boolean, float, int, or double) will be set.

      Throws:
      java.io.IOException