Bio-medical Ontologies Maintenance and Change Management

2.3 Extracting Data from DICOM File
Multimedia Medical Databases 83
In order to extract data from the DICOM file, we are taking into account every tag
from the DICOM dictionary. The tag will be searched in the file and in case of
finding it the corresponding value will be extracted.
The steps of extracting information from DICOM files, designed at Software
Engineering Department, Faculty of Automation, Computers and Electronics,
Craiova, are:
1. Verifying the existence of the ‘D’,’I’,’C’,’M’ characters in the file prefix.
2. Establishing the type of VR (ExplicitVR or ImplicitVR). This information is
given by the UID (Unique Identifier), information stored in the value field corresponding
to the Transfer Syntax Tag.
3. Establishing the Byte Ordering (BigEndian or LittleEndian). The information
is also given by UID, stored in the value field of the same Transfer Syntax Tag.
The DICOM standard contains all the values that UID can have.
4. Searching a tag in DICOM file according to the VR type and ByteOrdering
5. Value extraction of the corresponding found tag.
DICOM Standard contains over 20 types of binary data or ASCII. The type of
information stored in the value field is given by VR. In accordance with this type
will be extracted strings, integer or byte type information.
Next it is described the problem of image extracting from the standard DICOM
files, taking into account the method of compression that was used: RLE, JPEG. A
single DICOM object can contain only one image, but that image may have
multiple “frames”, allowing storage of cine-loops or other multi-frame data.
The images from DICOM files can be classified using several criteria:
1. The number of images stored in a file: single frame or multi-frame.
2. Number of bits per pixel: 8 bits, 12 bits, 16 bits or 24 bits.
3. Compression: without compression (raw) or with compression (RLE JPEG,
JPEG Lossless, JPEG 2000. LZW (zip) compression can be used for the whole
data set (not just the pixel data) but is rarely implemented.
4. Photometric interpretation: gray scale images, color images, palette color
images.
In the images without compression, the extraction of pictures is made pixel-bypixel,
taking into account the number of bits stored for each pixel and the
photometric interpretation (for monochrome images a pixel is stored using
maximum 2 bytes and for color images, a pixel is stored using 3 bytes). In the
images that use compression it is necessary a decompression algorithm before
saving.
The pseudo code for retrieving the frames is:
Set variable number to 0
Loop until all frames are retrieved
Set file dimension as Rows*Columns*SamplePerPixel
Read all file dimension pixels from file starting
With (Header Length + number* file dimension)