CT

ct | file / import()   list      dim()             debug
            export()   delete    steps()
            read       display   num()
            write      inspect   eqvpathlength()
            slice()    swap
            window() 

Purpose

Parameters

file

For read specifies the stem of the file name (without extension) for input or output of CT cubes.
For write specifies the stem of the file name (without extension) for input or output of CT cubes.
Since CT cubes are data cubes they come as a binary <file>.CTX data file together with a text <file>.HED header file.
For export <file> is taken as a prefix.
For the creation of CTs with dim() and steps() <file> is used as a patient name.

import()

Not yet implemented.

export(fmt)

Exports the current CT cube in some other 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:
<prefix>ct.gd,
and
<prefix>ct.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 CT data specified by file

write

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

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

Consider only the specified interval of CT-coordinates for export(). A * may be used to specify the lower/upper limit, respectively.

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 CT data.

delete

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

display

Displays the current CT cube. Not yet implemented.

inspect

Show some internal info about the current CT cube.

swap

When a CT 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 CT 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 CT 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 CT 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 CT 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 CT 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

ct OTTOT3000 / read

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