TRiP98 Dose command
| GSI Biophysics | TRiP98 long write-up |

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         voi()
	                         rbe           datatype()
	                         svv
	                         dosemeanlet meanlet
	                         alpha beta
                                 algorithm(cl)
                                 bioalgorithm(cl)

Purpose

Handles input, output and calculation of dose data cubes. Different dose cubes are foreseen for the physical dose, the biological dose, the RBE and the survival distributions, respectively.

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:

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).
meanlet
Calculates a mean LET cube (keV/um).
alpha
Calculates an alpha cube (1/Gy).
beta
Calculates a beta cube (1/Gy**2).
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.
algorithm(alg)
Selects algorithm for dose calculation. Same choices as for detector signal calculation:
bioalgorithm(alg)
Selects algorithm for biological effect calculation.
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.
voi()
Restricts dose calculation to voxels within the given VOI.
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.
datatype(dt)
Specifies datatype dt of output dose cube: The default type is short.
debug
Debug switch. Lots of output !

Remark

Whereever possible, dose cubes are mapped to external files, rather than keeping them directly in computer memory. This is a big memory saver !
Note that when file-mapped dose cubes are calculated they are created with their full size immediately. Thus the actual file size is no progress report !

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) voi(rand)
    
    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.
    To save calculation time, only voxels within VOI rand are considered.
  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.

| GSI Biophysics | TRiP98 long write-up |
Last updated:
$Id: trip98cmddose.html,v 1.13 2009/10/13 18:52:13 kraemer Exp $
M.Kraemer@gsi.de