Phantoms

Collaboration diagram for Phantoms:

Classes
class	Feature
class	Oriented_Feature
class	Sphere
class	Blob
class	Gaussian
class	Cylinder
class	DCylinder
class	Cube
class	Ellipsoid
class	Cone
class	Phantom

Detailed Description

Phantoms are mathematical description of volumes such that in the reconstruction process, we can know exactly which was the original volume in a mathematical way. In this package phantoms are considered to be a collection of features plus some more information about the background and the phantom size. A feature is a cone, a box, a cylinder, or any other geometrical figure described by its parameters and not as a volume with voxels at a given value.

The file format generated and accepted by this library is the following:

"#Phantom Xdim Ydim Zdim Background density [scale factor]\n"
"          64   64   64            0             1\n"
"#Type +/= Density X_Center Y_Center Z_Center\n"
" sph   +     1      <x0>     <y0>     <z0>    <radius>\n"
" blo   +     1      <x0>     <y0>     <z0>    <radius>   <alpha> <order>\n"
" gau   +     1      <x0>     <y0>     <z0>    <sigma>\n"
" cyl   +     1      <x0>     <y0>     <z0>    <xradius> <yradius> <height>               <rot> <tilt> <psi>\n"
" dcy   +     1      <x0>     <y0>     <z0>    <radius>            <height>  <separation> <rot> <tilt> <psi>\n"
" cub   =     1      <x0>     <y0>     <z0>    <xdim>     <ydim>    <zdim>                <rot> <tilt> <psi>\n"
" ell   =     1      <x0>     <y0>     <z0>    <xradius> <yradius> <zradius>              <rot> <tilt> <psi>\n"
" con   +     1      <x0>     <y0>     <z0>    <radius>            <height>               <rot> <tilt> <psi>\n"

where spheres, blobs, gaussians, cylinders, double cylinders, cubes, ellipsoids and cones are defined (in this order). The '+' sign means that this feature will be added at those positions of the volume ocuupied by it. '=' instead means that those voxels will be set to the value of the density of this feature (if two features overlap the density of the last one is kept in the overlapping voxels). The density is the grey level of voxels affected by that feature. In the preceding example the final volume is 64x64x64 and has got a background density of 0. The center of the features might be negative, and they represent mathematical positions in R3. The phantom dimension, instead, define the phantom in this case to go from -32 to 31, in this R3 space.

If the scale factor, which by default is 1, is not unity then the whole phantom is scaled (0.5 means to its half and 1.5 enlarged by one half) just after reading it.