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20110907. DAC.
This is the PixelMed Publishing pure Java DICOM toolkit. All the
class and supporting files are included in a single jar file,
pixelmed.jar.
Installation.
A JRE of 1.5.0 or more recent is required.
The following additional jar files from other freely available packages
may be required, depending on which components of the toolkit are used:
junit-4.8.1.jar
Required for compilation but currently only required at runtime
for the tests related to the dose packages (doseocr and test);
however, future versions of the toolkit will likely make more
extensive use of junit for unit testing.
hsqldb.jar
The HypersonicSQL database. The recommended version is
1.8.0.7 or later. Versions prior to 1.8.0 will not work.
See "http://hsqldb.org/".
Required at runtime for applications that use a database (such
as DicomImageViewer and the various servers).
Required for building from source.
xmlpack.jar [no longer required]
Since the components used for xml and xslt during translation
and validation are now included in the 1.5 JRE, this package
is no longer necessary at compilation or run time.
excalibur-bzip2-1.0.jar
A pure Java implementation of the bzip2 compression algorithm. Even
though this is only used to support a private PixelMed compression
transfer syntax, the jar file is required at runtime regardless. It
is available from the Apache project:
"http://www.apache.org/dist/avalon/excalibur/components/deprecated/bzip2/"
It was formerly part of the Apache Jakarta Avalon Excalibur project
as a component, but has now been folded into the Ant distribution,
which is why it is flagged as deprecated.
Required at runtime for applications that want to support bzip2
transfer syntaxes ... absence will be detected dynamically and
these transfer syntaxes will not be offered or accepted.
Not required for building from source.
vecmath1.2-1.14.jar
The computation of geometric information (such as for posting localizers
and reporting 3D cursor positions) for cross-sectional images depends
on the Java 3D API, and since this isn't available for all platforms,
the code makes use of the routines in this free 3rd party implementation
of the vector math (only) parts of the 3D API written by Kenji Hiranabe:
"http://objectclub.esm.co.jp/vecmath/"
The official Sun Java 3D implementation also works, if it is available
for your hardware platform.
Required at runtime for applications that want use 3D localization, such
as DicomImageViewer.
Required for building from source unless Java3D installed.
commons-codec-1.3.jar
Contains encoding of person name using phonetic mechanisms such as Soundex
and Metaphone; used for person name matching in database queries. See:
"http://jakarta.apache.org/commons/codec/"
Required at runtime for applications that want to support phonetic matching;
absense will result in trapped exceptions and default use of canonical as
phonetic name (i.e., the exceptions are harmless).
Not required for building from source.
commons-net-ftp-2.0
Contains ftp and secure ftp clients.
For use with IHE REM Dose Information Reporter transaction for transfer to
registry (which is via ftp over TLS (RFC 4217) rather than DICOM).
jmdns.jar
Contains support for Multicast DNS (mDNS) and DNS Self Discovery (DNS-SD)
used for zeroconf network configuration (aka. Apple's Bonjour):
"http://sourceforge.net/projects/jmdns/"
"http://jmdns.sourceforge.net/"
Tested with version jmdns-3.4.1 from sourceforge unmodified (2.x versions
will no longer work, since some 3.x API changes and features are now used).
Required at runtime for all DICOM network applications that want to perform
self discovery ... absence will be detected dynamically and self discovery
will not be performed.
Required for building from source.
jpedalSTD.jar
Contains support for reading and rendering PDF:
"http://www.jpedal.org/"
Tested with 2007/06/14 GPL version.
Note that there are also commercial (non-GPL) versions that should work.
Also, additional jar files are available from the JPedal site, including
the BouncyCastle cryptography provider (bcprov-jdk14-119.jar, which is open
source) and the jdom XML provider (jdom.jar, also open source); neither of
these appear to be necessary for decoding PDF files as used in the
pixelmed toolkit,given the faciities of contemporary JVMs.
There is also at the JPedal site a jar file that is not open source but is
free for non-commercial use (only), which provides support for rendering of
embedded fonts (pjes.jar); this is not necessary for the function of the
tools, but may improve the quality of the rendering.
******** GPL Alert ********
NB. JPedal is GPL - PixelMed is not - consider this with respect to using
and or distributing PixelMed-based source and/or binary code that depends
on the JPedal functionality - the only thing that will not work if JPedal
is not included is rendering of PDF (com.pixelmed.dicom.PDFToDicomImage)
Not required for building from source (reflection is used to detect if
present at runtime when necessary).
NOT INCLUDED IN PIXELMED DISTRIBUTION - DOWNLOAD IT YOURSELF AS REQUIRED.
AiViewer
Though not a dependency per se, the web server does support the use of
Takahiro Katoji's AiViewer open source GPL Java applet from Akira Iwata's
laboratory at the Nagoya Institute of Technology with the web server.
It is available from "http://mars.elcom.nitech.ac.jp/dicom".
To use it, make sure that the class files are in the "dicomviewer" folder
in the root of the web server folder (where the stylesheet is), as specified
in the web server properties. The DICOM dictionary is not necessary but can
be put in the same location. Then set the RequestTypeToUseForInstances
web server property to APPLETDISPLAY. Alternatively, include a jar file
in the classpath that contains the dicomviewer/*.class files.
Alternatively, one could modify the AppletDisplayTemplate.tpl template to
directly get the class files from the Nagoya site, but then the local
java security policy file would need to be changed to allow the applet
to access images from a different server than that from which the class
files were obtained.
Not required for building from source.
Java Image I/O
Support for reading and displaying images with compressed transfer syntaxes
depends on the availability of native or pure Java Image I/O (JIIO) codecs.
Binary builds are available from:
http://download.java.net/media/jai-imageio/builds/release/
These can be used by either installing them into the JRE, or by including
the jar files in the classpath (and the native libraries in the path).
Not required for building from source.
Fonts and Internationalization
To support some international character sets, you need to be sure that your
JRE is installed with the charsets.jar file, which is optional on some
platforms. Make sure that during JRE install that you select the "custom
installation" and select the "Support for additional locales" feature. See:
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6329080
If you fail to do this, you may get an java.io.UnsupportedEncodingException.
As far as fonts are concerned, see the discussion in section 4.2.6 Fonts
of the docs/DicomImageViewer/UserManual.pdf user guide.
Invocation.
One the various jar files have been assembled, applications in the DICOM toolkit can be
invoked as follows, using the com.pixelmed.display.DicomImageViewer as an example:
java -Xmx512m -Xms512m -cp "./pixelmed.jar:./lib/additional/hsqldb.jar:./lib/additional/excalibur-bzip2-1.0.jar:./lib/additional/vecmath1.2-1.14.jar:./lib/additional/jmdns.jar:./lib/additional/commons-codec-1.3.jar:./lib/additional/jai_imageio.jar" com.pixelmed.display.DicomImageViewer
Note that for practical display or processing of large DICOM images a lot of heap
space is necessary, hence the "-Xmx512m -Xms512m".
On some Windows Java installations, the Direct3D drivers (e.g., Nvidia) are buggy,
and adding "-Dsun.java2d.d3d=false" will help; this can also be set from an
environment variable "_JAVA_OPTIONS" ; see also
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6762839
http://java.sun.com/j2se/1.5.0/docs/guide/2d/flags.html
Development Documentation.
To use the toolkit for your own applications, read the documentation of the classes
provided, both as traditional Javadoc (see docs/javadoc/index.html) and as Doxygen
(see docs/doxygen/html/index.html).
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