TRiP98 Oxygenation command

Oxygenation | file / import()   list      dim()             debug
            export()   delete    steps()
            read       display   po2()
            write      inspect  
            slice()    swap
            window() 

Purpose

Parameters

file

For read/write specifies the stem of the oxygenation cube's file name (without extension) for input/output, respectively.
Since oxygenation cubes are data cubes they come as a binary <file>.oxy data file together with an associated header text file, <file>.hed.
For export <file> is taken as a prefix.
For the creation of oxygenation cubes with dim() and steps() <file> is used as a patient name.

import()

Not yet implemented.

export(fmt)

Exports the current oxygenation cube in some other format.
With gd
data are exported 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:
<prefix>po2.gd,
and
<prefix>po2.um<yyyyyy>.gd,
for 1D and 2D files, respectively, where <yyyyyy> is the slice coordinate (centre) in micrometers. <prefix> is either given by file or, if omitted, derived from either the patient name or, if omitted, from the original input file name.

read

Read oxygenation data specified by file

write

Writes the current oxygenation cube as specified by file File naming convention is
<file>.oxy, <file>.hed,
or, if file is omitted:
<patient-id>000.oxy, <patient-id>000.hed,

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

Consider only the specified interval of oxygenation-coordinates for export(). A * may be used to specify the lower/upper limit, respectively.
The voxel range considered is determined by the voxels in which the respective coordinate limits are located.

slice(interval)

Consider only the specified interval of slice numbers for export(). <interval> might be

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

where * stands for "all" or the lower/upper limit, respectively.

list

Show some internal info about the currently loaded oxygenation data.

delete

Deletes the current oxygenation cube from memory (not from file).

display

Displays the current oxygenation cube. Not yet implemented.

inspect

Show some internal info about the current oxygenation cube.

swap

When a oxygenation cube is written, the bytes are swapped.

dim(nx,ny,nz) steps(dx,dy,dz)

When used together with either the num() or the eqvpathlength() parameters a oxygenation cube is generated in memory. <nx,ny,nz> specifies a list of three numbers denoting the number of voxels in the three dimensions. <dx,dy,dz> specifies a list of three numbers denoting the voxel sizes (in mm) in the three dimensions. Note that the file parameter must also be given in order to assign a patient name.

num(hf)

When used together with the dim() and the steps() parameters a oxygenation cube is generated in memory. If <hf> can be interpreted as a reasonable Hounsfield number (hf>=-1000) it will be assumed as a constant value for all oxygenation voxels. Otherwise <hf> is assumed to be the name of a user-supplied executable (plug-in) which calculates the Hounsfield numbers.

eqvpathlength(len)

When used together with the dim() and the steps() parameters a oxygenation cube is generated in memory. If <len> can be interpreted as a reasonable equivalent path length (len>0) it will be assumed as a constant value for all oxygenation voxels. Otherwise <len> is assumed to be the name of a user-supplied executable (plug-in) which calculates the equivalent path lengths.

debug

Debug switch. Lots of output!

Remark

Examples

1.    oxy OTTOT3000 / read
   

   Reads oxygenation data (files OTTOT3000.oxy and OTTOT3000.HED) for patient "OTTOT3".

2.    oxy xxxxxx /dim(8,4,2) steps(1,1,1) num(17)
   

   Creates a oxygenation data cube with size 8x4x2, a voxel size of 1 mm in either direction and a constant Hounsfield number of 17.