FLUKA: 8.3} Voxel Geometry
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8.3} Voxel Geometry
It is possible to describe a complex geometry in terms of "voxels" (tiny
identical parallelepipeds forming a 3-dimensional grid). In principle this can
be done with any geometry but it is especially useful when translating a CT
scan of a human body into a dosimetry phantom [Zan01]. Therefore, we will use
loosely the word "organ" to indicate a contiguous group of voxels (or even
more than one group) made of the same material. The code handles each organ as
a Combinatorial Geometry region, possibly in addition to other conventional
"non-voxel" regions defined by the user, and assigns automatically to each
organ a new region number.
To describe a voxel geometry, the user must:
1) Assign an organ to each voxel. Each organ is identified by a unique integer
=< 32767. The numbering does not need to be contiguous, i.e. gaps in the
numbering sequence are allowed. One of the organs must have number 0 and
plays the role of the medium surrounding the voxels (usually vacuum or air).
The assignment is done via a special file where the organ corresponding to
each voxel is listed sequentially in Fortran list-oriented format, with the
x coordinate running faster than y, and y running faster than z (see example
below). In practice the file is always written by a program similar to the
one reported below. The user will need to modify the values of the
parameters DX, DY, DZ, NX, NY, NZ (respectively voxel size and number of
voxels for each coordinate), and possibly some other more trivial things
(file names, title, reading from the original CT scan file). The following
program takes also care of recompacting the original organ numbers by
eliminating all gaps in the sequence, and writes a translation table to the
screen:
WRITE(*,'(A,2I10)')' New number, old number: ', NO, IC
After having modified the program (assumed to be in a file writegolem.f),
compile it:
$FLUPRO/flutil/fff writegolem.f
link it with the FLUKA library:
$FLUPRO/flutil/lfluka -o writegolem writegolem.o
execute it:
./writegolem
The result will be a file golem.vxl (or equivalent name chosen by the user)
which will be referred to by a special command line in the geometry input
(see below).
PROGRAM WRITEGOLEM
INCLUDE '(DBLPRC)'
INCLUDE '(DIMPAR)'
INCLUDE '(IOUNIT)'
PARAMETER ( DX = 0.208D+00 )
PARAMETER ( DY = 0.208D+00 )
PARAMETER ( DZ =-0.8D+00 )
PARAMETER ( NX = 256 )
PARAMETER ( NY = 256 )
PARAMETER ( NZ = 220 )
DIMENSION GOLEM(NX,NY,NZ)
INTEGER*2 GOLEM
CHARACTER TITLE*80
DIMENSION IREG(1000), KREG(1000)
INTEGER*2 IREG, KREG
CALL CMSPPR
DO IC = 1, 1000
KREG(IC) = 0
END DO
OPEN(UNIT=30,FILE='ascii_segm_golem',STATUS='OLD')
READ(30,*) GOLEM
NO=0
MO=0
DO IZ=1,NZ
DO IY=1,NY
DO IX=1,NX
IF (GOLEM(IX,IY,IZ) .GT. 0) THEN
IC = GOLEM(IX,IY,IZ)
MO = MAX (MO,IC)
DO IR=1,NO
IF (IREG(IR) .EQ. IC) GO TO 1000
END DO
NO=NO+1
IREG(NO)=IC
KREG(IC)=NO
WRITE(*,'(A,2I10)')' New number, old number: ', NO, IC
1000 CONTINUE
END IF
END DO
END DO
END DO
WRITE(*,*) ' NO,MO',NO,MO
OPEN(UNIT=31,FILE='golem.vxl',STATUS='UNKNOWN',FORM='UNFORMATTED')
TITLE = 'Golem'
WRITE(31) TITLE
WRITE(31) NX,NY,NZ,NO,MO
WRITE(31) DX,DY,DZ
WRITE(31) GOLEM
WRITE(31) (KREG(IC),IC=1,MO)
STOP
END
*----------------------------------------------------------------------
Starting from Fluka2011.2b, the voxel files can contain an arbitrary
number of extra records of 80 characters each, which are read and
interpreted as ordinary input cards. This allows to embed in the
voxel files informations such as material definitions, material
assignments, correction factor etc, which are often generated
by automatic programs out of a CT scan. Flair contains tools for
reading CT scans in Dicom format, and automatically generates a
voxel file containing the material and correction factor
informations according to a Hounsfield number to material/density
translation algorithm which can be tuned by the user.
2) Prepare the usual FLUKA input file. The geometry must be written like
a normal Combinatorial Geometry input (in any of the allowed formats,
as part of the normal input stream or in a separate file), but
in addition must include:
* A VOXELS card as a first line, before the Geometry title card, with the
following information:
WHAT(1)
, WHAT(2)
, WHAT(3)
= x, y, z coordinates chosen as the origin of
the "voxel volume", i.e. of a region made of a single RPP body
which contains all the voxels
WHAT(4)
= index (or name) of the ROT-DEFIni card for an eventual
roto/translation of the VOXELs
WHAT(5)
: not used
WHAT(6)
: used mainly for debugging. If WHAT(6)
is not divisible by 10,
a voxel geometry test is carried out. The RPP-to-voxel,
voxel-to-organ, and organ-to-region correspondences are
checked. The program stops in case of inconsistency.
SDUM
= name of the voxel file (extension will be assumed to be .vxl).
* The usual list of NB bodies, not including the RPP corresponding to the
"voxel volume" (see VOXELS card above). This RPP will be generated and
added automatically by the code as the (NB+1)th body, with one corner in
the point indicated in the VOXELS card, and dimensions NX*DX, NY*DY
and NZ*DZ as read from the voxel file.
* The usual region list of NR regions, with the space occupied by body NB+1
(the "voxel volume") subtracted. In other words, the NR regions listed
must cover the whole available space, excepted the space corresponding to
the "voxel volume". This is easily obtained by subtracting body NB+1 in
the relevant region definitions, even though this body is not explicitly
input at the end of the body list. The code will automatically generate
and add several regions:
Name Number Description
-------- ------ -------------
VOXEL NR+1 this is a sort of "cage" for all the voxels. Nothing
(energy etc.) should ever be deposited in it: the user
shall assign VACUUM to it
VOXEL001 NR+2 containing all voxels belonging to organ number 0.
There must be at least 2 of such voxels, but in general
they should be many more. Typical material assignment
to region NR+2 is AIR.
VOXEL002 NR+3 corresponding to organ 1
VOXEL003 NR+4 corresponding to organ 2
........ .... ........................
VOX##### NR+2+NO corresponding to organ NO
where NO = number of non-zero organs
The assignment of materials shall be made by command ASSIGNMAt
(and in a similar way other region-dependent options) referring to
the first NR regions in the usual way, and to the additional regions
using the correspondence to organs as explained above.
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