Port Dicom files to ROOT

I made a pluging that allows manipulation of images stored in the Dicom
file format in ROOT. Basically, it is an IO (import/export) facility that reads and stores dicom images.

The software is loadable via git:

git clone http://www-f9.ijs.si/~studen/git/dicom2ROOT.git

Once extracted to a working directory, cd to that directory and run root. The software should compile.

Possible problems

A message saying

Dcmtk unset. Exit ROOT and do
 #>export DCMTK=/location/to/installed/dcmtk

appears if DCMTK is not found. If you haven't installed DCMTK yet, this would be a good time. Go to DCMTK and install following their instructions. Because I am working on a multiuser machine, I tend to install software away from the common locations, hence the DCMTK enviromental variable, which you can also use. The software assumes that $DCMTK/include points to location of headers and $DCMTK/lib to libraries.

Typical usage

Once the root is open without errors, you should be able to create an object of dicomHeader type:

root[0] dicomHeader hd;

The object can load and store dicom files, so you can do:

root[1] hd.read_dicom_file("fname");

where fname is the path to your dicom file. If you want to see the obtained image, do

root[2] TH2D h2;
root[3] hd.Draw(h2);
root[4] h2.Draw("COL");

Most often than not, the whole image is loaded as a series of slices in a single directory. To get the full set, do:

root[5] dicomList data;
root[6] readDataset("directory",data);

where "directory" is the path to the directory (and not to a particular file). The whole image should then be loaded in a 3D structure, so:

root[7] TH3D h3;
root[8] Draw(data,h3);

accomplishes that. A particular axial or trans-axial slice is then extracted via ROOT's TH3D manipulation routines. For example, getting I-th transaxial projection/slice, you should do:

root[9] h3.GetZaxis()->SetRange(I+1,I+1);
root[10] h3.Project3D("YX")->Draw("COL");

You can also store a particular image by:

root[11] hd.save_dicom_file("fname");

Usually, a subset of the original dicom parameters will be stored. If you require more, let me know and I can add them.

Todo

Just now I think that manipulation of the image in the dicomHeader might be useful, something like:

root[X] hd.Adopt(h2);

where h2 is a TH2D histogram. The actual content of the stored pixel $p_i$, stored in Uint16 format would be:

$$ p_i=\frac{h_i-O}{S} $$

where O is RescaleOffset and S RescaleSlope DICOM parameter. They can be directly manipulated via hd.rescale_slope and hd.rescale_offset parameters, say:

root[X] hd.rescale_slope=19.3;
root[X] hd.rescale_offset=100;

One probably shouldn't change their value between Adopt and save_dicom_file routines.

Using from other projects

This script lets you use Dicom2ROOT from different directories, if you don't want to add files to the Dicom2ROOT directory, say. From your project, you should first execute

root[0] .x loadDicom2ROOT.C

and you should have all functionality of the dicom2ROOT. You should again set shell enviromental variables prior to calling root:

DCMTK=/path/to/dcmtk
DICOM2ROOT=/path/to/dicom2ROOT