Dose

dose file / import()   list      calculate     field(*)    debug
            export()   delete    biological    window(*)
            read       display                 slice()
            write      inspect   nolateral     subdivide()
            prefix()             nofragments   events()
	                         norbe         clipctnum()
	                         nosvv
	                         rbe
	                         svv
	                         dosemeanlet

Purpose

Parameters

file

Specifies the stem of the file name (without extension) for input and output of dosecubes. Since dose cubes are data cubes they come as a binary <file>.DOS data file together with a text <file>.HED header file.

import()

Not yet implemented.

export(fmt)

Exports current dose cube(s) in some non-native format. At present only gd is foreseen, to be plotted with the gd program. Depending on window() or slice() data are exported as a single 1-dim file, a 2-dim file or a series of 2-dim files. File naming convention is
<file><xxxx>.gd
and
<file><xxxx>.um<yyyyyy>.gd
for 1D and 2D files, respectively, where <xxxx> is "phys", "bio", "rbe" or "svv". <yyyyyy> is the slice coordinate in micrometers.

read

Read dose cube specified by file. The target cube is specified by the biological, RBE or svv parameters, respectively. If omitted, the absorbed (physical) dose cube is assumed. Only a single dose cube can be read at a time.

write

Writes the current dose cube(s) as specified by file. Naming convention:

• <file> contains the extension .DOS or .dos:
  <file> for the physical dose. For the biological dose: <file><xxxx>.DOS and <file><xxxx>.HED, where <xxxx> is "bio", "rbe" and "svv".
• otherwise:
  <file><xxxx>.dos and <file><xxxx>.hed, where <xxxx> is "phys", "bio", "rbe" or "svv".

list

List current dose cube(s).

delete

Deletes the current dose cube(s) from memory (not from file).

display

Displays the current dose cube(s). Not yet implemented.

inspect

Show some internal info about the current dose cube(s).

calculate

Triggers dose calculation, by default the physical dose. If biological is specified, the biological dose as well as the RBE and survival cubes are computed. If a file parameter is additionally given, the dose cube(s) are created externally as if write was specified. Dimension and voxel size are cloned from the current CT cube

nofragments

Not yet implemented.

biological

Selects biological dose as well as the RBE and survival cubes.

dosemeanlet

Calculates a dose-mean LET cube (keV/um).

nolateral

Do not consider lateral dose contributions from finite beam width or small angle scattering. This is for backward compatibility with the "old" TRiP versions.

norbe

nosvv

Do not compute or output cubes for RBE or survival distributions, respectively. These parameters are disk space savers.

rbe

svv

Select RBE or survival cubes as target for read operations.

events(nevt)

Not yet implemented.

field(fieldlist)

Specifies a (comma-separated) list of partial fields which should contribute. "*" means all fields. This is the default.

window(xmin,xmax,ymin,ymax,zmin,zmax)

Specifies a window in CT coordinates (mm) for which the dose computation (and export) should be performed. This is useful to avoid lengthy calculations when only a small part of the cube is needed. Note that the data cube itself has always the full size.
You may use this parameter to distribute the dose calculation across many computers. Use the cubemerge command to collect the different slices into a single dose cube.

slice(interval)

Consider only the specified interval of slice numbers for dose computation. <interval> might be

*
<slice-number>
<low-slice>,<high-slice>
*,<high-slice>
<low-slice>,*

where * stands for "all" or the lower/upper limit, respectively. Slicing is useful to avoid lengthy calculations when only a small part of the cube is needed. Note that the data cube itself has always the full size.
You may use this parameter to distribute the dose calculation across many computers. Use the cubemerge command to collect the different slices into a single dose cube.

clipctnum(lo,hi)

If given, specifies an interval of CT numbers for which dose voxels should be calculated.

subdivide(ndx,ndy,ndz)

Specifies a finer granularity of voxel-based calculations. Each voxel is divided into ndx, ndy, ndz subvoxels to calculate partial doses which are subsequently averaged.
At present implemented for physical dose only.

prefix(prefix)

Not yet implemented.

debug

Debug switch. Lots of output !

Remark

Examples

1. 
   

   dose MyDose. / calculate 
   dose MyDose. / write
   

   First calculates the physical dose, where the auxiliary file MyDose.phys.dos is memory-mapped. Then make it available to the public by simply unmapping it.

2. dose xyz. / bio write field(1,3)
   

   Compute and output biological dose, RBE and survival on xyx.bio.dos, xyx.rbe.dos and xyx.svv.dos (and the corresponding HED files). Only fields 1 and 3 contribute.

3.  dose z005. / window(*,*,*,*, 0, 10) calculate write
    dose z015. / window(*,*,*,*,10, 20) calculate write
    cubemerge merge.dos / infile(z0*.phys.dos)
   

   Calculate two slices of a dose cube separately and merge them into a single result dose cube.

4. dose phys.dos /read
   dose biol.dos /read bio
   dose export.  /export(gd) window(128,128,128,128,*,*) bio
   

   Read an absorbed and a biological dose cube and subsequently export a 1-dimensional cut along the z-Axis in gd format.