* JNLP install * 1. set environment variables: export CERT_ALIAS="<insert alias here>" export CERT_KEYSTORE="<insert path to keystore (.p12) here>" export CERT_PASS="<insert keystore password here>" 2. build singed jar: ant sign 3. build demo-server cd demo-server mvn clean install 4. Run jar web server: java -jar target/demo-server-0.0.1-SNAPSHOT.jar 20170228. DAC.g 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 1.7.0 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. For your convenience, these are available packaged together in the "dependencies" file of the current release, to be used in combination with the "binaries" and/or "source" release file. The dependencies are: slf4j-api-1.7.22.jar slf4j-simple-1.7.22.jar All logging of errors, warning, information, debugging and tracing is now performed using the com.pixelmed.slf package, which is a very thin wrapper around a subset of the SLF4J facade classes and methods, rather than the previous approach of sending everything directly to System.err (stderr). All constructors and methods with "debugLevel" arguments have been deprecated and all "debugLevel" command line arguments have been removed. slf4j-api-*.jar is required at compilation time, but may be omitted at run time if no SLF implementation is used, and com.pixelmed.slf will log to System.err. A logging implementation of some kind may be supplied at runtime; the minimal approach is to supply slf4j-simple-*.jar, which also sends everything to stderr. The default log level for slf4j is INFO, but either the default for all classes can be changed by adding: -Dorg.slf4j.simpleLogger.defaultLogLevel=debug in the java command line invocation, or per class, e.g.,: -Dorg.slf4j.simpleLogger.log.com.pixelmed.doseocr.OCR=trace Other options are useful for logging background processes, e.g.: -Dorg.slf4j.simpleLogger.showDateTime=true -Dorg.slf4j.simpleLogger.dateTimeFormat="EEE MMM dd HH:mm:ss zzz yyyy" -Dorg.slf4j.simpleLogger.dateTimeFormat="yyyy-MM-dd'T'HH:mm:ss.SSSZ" See: http://www.slf4j.org/ http://www.slf4j.org/api/org/slf4j/impl/SimpleLogger.html https://github.com/qos-ch/slf4j/blob/master/slf4j-simple/src/test/resources/simplelogger.properties Even if slf4j-api-*.jar and an slf implementation are not supplied at runtime, a subset of the slf4j properties are still used (i.e., com.pixelmed.slf reuses the same properties as slf4j rather than defining its own). Specifically, the following properties (only) are supported by the com.pixelmed.slf implementation: org.slf4j.simpleLogger.defaultLogLevel (default logging detail level for all instances, default is info) org.slf4j.simpleLogger.log.xxxxx (logging detail level for a logger instance named "xxxxx") org.slf4j.simpleLogger.showDateTime (default is false) org.slf4j.simpleLogger.dateTimeFormat (default is ms since start) pixelmed_codec.jar Required for compilation but currently only required at runtime when selective redaction of baseline JPEG blocks is needed (e.g., when this feature of DicomCleaner or DicomImageBlackout or DeidentifyAndRedact is needed). Available from the PixelMed software site at: "http://www.dclunie.com/pixelmed/software/codec/" 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 2.3.3 or later. See "http://hsqldb.org/". Required at runtime for applications that use a database (such as DicomImageViewer, DicomCleaner, DoseUtility and the various servers). Required for building from source. commons-compress-1.12.jar A pure Java implementation of the bzip2 compression algorithm. Primarily used to support a private PixelMed compression transfer syntax, if available at runtime regardless. It is available from the Apache project: "http://commons.apache.org/proper/commons-compress/" It was formerly part of the Apache Jakarta Avalon Excalibur project as a component, was then folded into the Ant distribution, before being migrated into the commons family, together with other codecs. 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. javax.json-1.0.4.jar javax.json-api-1.0.jar Contains support for JSON parsing: "https://jsonp.java.net/" "https://jsonp.java.net/download.html" and look for the "non-Maven" links javax.json-1.0.4.jar is required at runtime for com.pixelmed.app package tools that use JSON files as input to describe DICOM attributes and values javax.json-api-1.0.jar is 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. Conversion from consumer formats (com.pixelmed.dicom.ImageToDicom) also depends on the JIIO codecs. The JRE has only a limited set of codecs (baseline JPEG, GIF, PNG and BMP), and additional pure Java codecs (JPEG 2000, TIFF, more robust baseline JPEG, PNM) and native codecs (faster JPEG 2000, extended 12 bit lossy JPEG, lossless JPEG, JPEG-LS) can be found in the Java Advanced Imaging Image I/O Tools (JAI IIO). Binary builds are available from: http://web.archive.org/web/20150318212755/http://download.java.net/media/jai-imageio/builds/release/1.1/ 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). Native libraries are not available on the Mac, but you can extract the jai_imageio.jar file from one of the Unix distributions and use it in the classpath. This has already been extracted and supplied in the "dependencies" file of the current release. Not required for building from source. For further documentation of the capabilities of the codecs, see: http://web.archive.org/web/20150318212755/http://download.java.net/media/jai-imageio/builds/release/1.1/jai_imageio-1_1-doc.zip 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/commons-compress-1.12.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). Acknowledgements. Development of block selective redaaction of lossy JPEG files supported by funding from MDDX Research and Informatics. Localization of DicomCleaner, DicomImageBlackout, ApplicationEntityConfigurationDialog and NetworkApplicationConfigurationDialog funded by GE Healthcare and localization performed by SDL plc.