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[ubuntu] install dcm4chee pacs server

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December 13th, 2011

#1

sqadree

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install dcm4chee pacs server

hi

i want to install dcm4chee (http://www.dcm4che.org/) pacs server installed on ubentu LAMP server please help me how to install this application on ubuntu server through command line. if possible provide step by step tutorial

installed process

========================

INSTALL INSTRUCTIONS FOR DCM4CHEE ARCHIVE:

=========================================

Minimum System Requirements

JDK 5 or higher.

512 MB RAM

200 MB hard disk space (additional to archive storage disk space)

400 MHz CPU

Supported Databases

PostgreSQL 8.1+

MySQL 4.1+

Oracle 9i/10g

SQL Server

DB2 8.1+

Firebird 2.1

Hypersonic SQL (Embedded in JBoss AS) - not suitable for production use!

For image compression/decompression, dcm4chee 2.17.0 utilize Sun's Java Advanced

Imaging Image I/O Tools 1.1. The binary distribution packages of dcm4chee

2.17.0 already includes necessary JARs and native libraries for Windows and

Linux i586. For Linux-amd64 or Solaris, you have to download the SW package

from Sun [https://jai-imageio.dev.java.net/binary-builds.html] yourself and

replace the Linux version of libclib_jiio.so in dcm4chee-2.17.0-xxx/bin/native

from the JAI Image IO package for Linux-amd64 or Solaris.

For MAC OS X there is no native Image I/O implementation available. There is an

open call on the jai-imageio webpage:

https://jai-imageio-core.dev.java.ne...bug.cgi?id=103

Because of the missing implementation you have to change 2 files in dcm4chee

if you want to have RID and WADO service running. Please have a look at point

8a. how to change the files.

Installation Procedure:

1. Extract the binary distribution package of dcm4chee for the database

of your choice. Avoid using a directory that has a name that contains spaces

as installation directory.

2. Download the binary distribution package of JBoss Application Server 4.2.3.GA

from http://labs.jboss.com/jbossas/downloads and extract it into a different

directory.

3. Move to the dcm4chee-2.17.0-xxx/bin directory and execute the

install_jboss.bat or install_jboss.sh script, as appropriate for your operating

system, with the path of your JBoss AS installation directory as parameter.

4. [4.-6. are not necessary with Hypersonic SQL] Install the Database SW - if

not already done. You also have to copy an apropriate JDBC Driver for the

Database to dcm4chee-2.17.0-xxx/server/default/lib/ - except for MySQL and

PostgreSQL, which binary distribution packages of dcm4chee already contains a

JDBC driver. Also ensure, that DB access via TCP/IP socket is enabled.

E.g. PostgresSQL:

$PGDATA/pg_hba.conf:

# IPv4 local connections:

host all all 127.0.0.1/32 trust

5. Initiate the archive database instance: pacsdb using create DDL script

dcm4chee-2.17.0-xxx/sql/create.xxx.

E.g.: PostgreSQL

> export PGUSER=postgres

> createdb pacsdb

> psql pacsdb -f dcm4chee-2.17.0-psql/sql/create.psql

E.g.: MySQL

> mysql -uroot

mysql> create database pacsdb;

mysql> grant all on pacsdb.* to 'pacs'@'localhost' identified by 'pacs';

mysql> \q

> mysql -upacs -ppacs pacsdb < dcm4chee-2.17.0-mysql/sql/create.mysql

6. Adjust the Database connection configuration (host, port, DB name, user

password) of the archive:

dcm4chee-2.17.0-xxx/server/default/deploy/pacs-xxx-ds.xml

according your Database configuration.

7. Set environment variable JAVA_HOME to JDK location.

8. Adjust maximum allocation of heap memory:

[Windows]: dcm4chee-2.17.0-xxx/bin/run.bat:

rem Sun JVM memory allocation pool parameters. Modify as appropriate.

set JAVA_OPTS=%JAVA_OPTS% -Xms128m -Xmx512m

[Linux/Unix/MAC OS X]: dcm4chee-2.17.0-xxx/bin/run.conf

# Specify options to pass to the Java VM.

if [ "x$JAVA_OPTS" = "x" ]; then

JAVA_OPTS="-Xms128m -Xmx512m ..

fi

according available RAM and memory requirements of other processes on this node.

E.g.: if only 512 MB RAM are available, you should decrease the default

value -Xmx512m to (e.g.) -Xmx300.

8a. MAC OS X specific changes for RID/WADO service:

Please edit the following files and exchange

"com.sun.media.imageioimpl.plugins.jpeg.CLibJPEGIm ageWriter" with

"com.sun.image.codec.jpeg.JPEGImageEncoder" for the ImageWriterClass:

$DCM4CHEE_HOME/server/default/conf/xmdesc/dcm4chee-rid-xmbean.xml:

@@ -124,7 +124,7 @@

<name>ImageWriterClass</name>

<type>java.lang.String</type>

<descriptors>

- <value value="com.sun.media.imageioimpl.plugins.jpeg.CLib JPEGImageWriter" />

+ <value value="com.sun.image.codec.jpeg.JPEGImageEncoder" />

</descriptors>

</attribute>

and $DCM4CHEE_HOME/server/default/conf/xmdesc/dcm4chee-wado-xmbean.xml:

@@ -128,7 +128,7 @@

<name>ImageWriterClass</name>

<type>java.lang.String</type>

<descriptors>

- <value value="com.sun.media.imageioimpl.plugins.jpeg.CLib JPEGImageWriter" />

+ <value value="com.sun.image.codec.jpeg.JPEGImageEncoder" />

</descriptors>

</attribute>

9. To test your installation, move to the dcm4chee-2.17.0-xxx/bin directory

and execute the run.bat or run.sh script, as appropriate for your operating

system. Your output should look like the following and contain no error or

exception messages:

================================================== =======================

JBoss Bootstrap Environment

JBOSS_HOME: /home/gunter/dcm4chee-2.17.0-psql

JAVA: /usr/lib/jvm/java-6-sun/bin/java

JAVA_OPTS: -Dprogram.name=run.sh -server -Xms128m -Xmx512m

-Dsun.rmi.dgc.client.gcInterval=3600000

-Dsun.rmi.dgc.server.gcInterval=3600000 -Djava.awt.headless=true

-Dapp.name=dcm4chee -Djava.net.preferIPv4Stack=true

-Djava.library.path=/home/gunter/dcm4chee-2.17.0-psql/bin/native

CLASSPATH: /home/gunter/dcm4chee-2.17.0-psql/bin/run.jar:

/usr/lib/jvm/java-6-sun/lib/tools.jar

================================================== =======================

17:18:49,573 INFO [Server] Starting JBoss (MX MicroKernel)...

17:18:49,574 INFO [Server] Release ID: JBoss [Trinity] 4.2.3.GA

(build: SVNTag=JBoss_4_2_3_GA date=200807181439)

:

17:19:11,496 INFO [Server] JBoss (MX MicroKernel) [4.2.3.GA

(build: SVNTag=JBoss_4_2_3_GA date=200807181439)] Started in 21s:919ms

10. Connect to the Web Interface at http://localhost:8080/dcm4chee-web/

of the archive using any Web Browser (most tested are Mozilla-Firefox and

Microsoft Internet Explorer v6.x). You should get the User Login Screen.

Login in using default Administrator account 'admin', with password 'admin'.

11. Connect to JBoss's JMX Console at http://localhost:8080/jmx-console/ and

login using also the Administrator account 'admin', with password 'admin'.

Follow the link "group=ONLINE_STORAGE,service=FileSystemMgt" under the

"dcm4chee.archive" heading to the configuration page for the File System

Management service associated to the File System Group "ONLINE_STORAGE".

Invoke the operation addRWFileSystem(), with argument dirPath specifying

the directory, where the Storage SCP Service shall store received

objects/images.

(If no Storage File System is configured, the archive will auto-configure

dcm4chee-2.17.0-xxx/server/default/archive as Storage File System, when

receiving the first object/image)

12. [Optional] Change the default AE Title

Connect to JBoss's JMX Console at http://localhost:8080/jmx-console/ and login

using also the Administrator account 'admin', with password 'admin'.

Follow the link "service=AE" to the configuration page for AE Configuration

Service under the "dcm4chee.archive" heading.

Invoke the operation "updateAETitle()" with "DCM4CHEE" as parameter "prevAET"

and the new AE Title as parameter newAET.

13. [Optional] At default configuration, received images are stored as received

- in particular, no compression is performed. Lossless compression of received

uncompressed images can be activated by attribute "CompressionRules" in the

configuration page for the Storage SCP Service (service=StoreScp). E.g. set it

to "JLSL", to compress all type of images received from any Storage SCU using

JPEG-LS Lossless codec.

14. [Optional] The directories used for caching generated JPEG representations

of archived images requested by Web Access to DICOM Persistent Objects (WADO)

can be specified by attributes "CacheDataRootDirectory" and

"CacheJournalRootDirectory" in the configuration page for the WADO Service

(service=WADOService).

Defaults: dcm4chee-2.17.0-xxx/server/default/wadocachedata and

dcm4chee-2.17.0-xxx/server/default/wadocachejournal.

The directory used for caching generated PDF representations of archived

Structured Report Documents requested by IHE Retrieve Information for Display

(RID) Services can be specified by modifying BASE_DIR=docstore/rid/store in

file conf/dcm4chee-docstore/dcm4chee-docstore-cfg.xml (this file will not

15. Send some object/images to the archive's Storage SCP, e.g. by using the

send utility of the dcm4che 2.0 core package available at Sourceforge

(http://www.sourceforge.net/projects/dcm4che). E.g:

> dcm4che-2.0.21/bin/dcmsnd DCM4CHEE@localhost:11112 ~/mesa/storage/modality/MR

Refresh the Web Interface (http://localhost:8080/dcm4chee-web/), which shall

now show the the list of received studies.

Expand one study row to show contained series. Expand one of these series

to show contained instances. In the case of images, you can follow the image

icon on the right, to invoke a http WADO request for a JPEG presentation of

this image, which will be displayed in a separate browser window.

16. To test object retrieval, you need an external Storage SCP acting as

Move Destination, e.g. by using the receiver utility of the dcm4che 2.0 core:

> dcm4che-2.0.21/bin/dcmrcv 11113

13:55:14,782 INFO - Start listening on 0.0.0.0/0.0.0.0:11113

Start Server listening on port 11113

You also need to configure an additional Application Entity Title identifying

this Move Destination using "AE Management" function of the Web Interface.

E.g. new AET

AE Title: DCMRCV

Hostname: localhost

Port: 11113

Switch back to the Study List ("Folder"), mark studies to retrieve using the

check box on the right, select "DCMRCV" as send destination in the combo box

above and click on the send button left from it.

17. If that works, you may stop the archive by Ctrl+C in the console you have

started it, and

[Windows]: install it as Windows service executing install_service.bat

or

[Redhat Linux]: copy the init script dcm4chee_init_redhat.sh to /etc/init.d/

and adjust it according your installation location of the archive and the JDK

and under which user the archive application shall run

or

[MAC OS X]: copy the init script dcm4chee.plist to /Library/LaunchDaemons and

register it with launchctl load /Library/LaunchDaemons/dcm4chee.plist

and adjust it according your installation location of the archive and the JDK

and under which user the archive application shall run.

For more information on launchd look at:

http://developer.apple.com/macosx/launchd.html

DEPLOY DCM4CHEE MEDIA CREATOR 2.17.0 with DCM4CHEE ARCHIVE:

================================================== ========

Starting with dcm4chee-2.13.0, Media Creator 2.x (dcm4chee-cdw-2.x) is

no longer included in the binary distribution package of the archive

application, but provided in a separate binary distribution package, also

available at http://sourceforge.net/projects/dcm4che .

You may deploy dcm4chee-cdw-2.17.0 in the same JBoss instance as dcm4che archive:

1. Download and extract the binary distribution package of dcm4chee-cdw-2.17.0.

2. Move to the dcm4chee-2.17.0-xxx/bin directory and execute the

install_cdw.bat or install_cdw.sh script, as appropriate for your operating

system, with the path of the dcm4chee-cdw-2.17.0 installation directory as

parameter.

DEPLOY DCM4CHEE XDS REPOSITORY 1.0.2 with DCM4CHEE ARCHIVE:

================================================== ========

There is a separate binary distribution packages for dcm4chee XDS Repository

1.0.2 (dcm4chee-xds-1.0.2) available at

http://sourceforge.net/projects/dcm4che .

You may deploy dcm4chee-xds-1.0.2 in the same JBoss instance as dcm4che

archive:

1. Download and extract the binary distribution package of dcm4chee-xds-1.0.2.

2. Download the binary distribution package of JBoss Web Service

jbossws-3.0.1-native-2.0.4.GA from http://www.jboss.org/jbossws/downloads

and extract it into a different directory.

3. Move to the dcm4chee-2.17.0-xxx/bin directory and execute the

install_xds.bat or install_xds.sh script, as appropriate for your operating

system, with the path of the dcm4chee-xds-1.0.2 installation directory as

parameter.

4. Execute the patch_jbossws.bat or patch_jbossws.sh script, as appropriate

for your operating system, with the path of the dcm4chee-xds-1.0.2 installation

installation directory as parameter. Necessary to accept faulty

(AttachmentPart Id mismatch) SwA (SOAP with Attachment) requests from Axis2

based Web Service clients and to disable schema validation during deployment,

which requires internet access. If you need a http proxy for internet access

you can configure http.proxyHost! (see run.conf or run.bat)

5. Only applicable for JDK5 version of jboss-4.2.3.GA in a JDK6 environment:

Execute the patch_jdk6_jbossws.bat or patch_jdk6_jbossws.sh script, as appropriate for your operating system.

This copies several jar files to JBOSS endorsed directory to avoid conflicts between JDK Webservice Stack and JBOSS WS.

DEPLOY DCM4CHEE AUDIT RECORD REPOSITORY 3.0.11 with DCM4CHEE ARCHIVE:

================================================== =================

Starting with dcm4chee-2.12.0, the binary distribution package of the archive

application does NOT longer include dcm4chee Audit Record Repository 2.x

(dcm4chee-arr-2.x).

There are now a separate binary distribution packages for dcm4chee Audit Record

Repository 3.0.11 (dcm4chee-arr-3.0.11) available at

http://sourceforge.net/projects/dcm4che .

You may deploy dcm4chee-arr-3.0.11 in the same JBoss instance as dcm4che archive:

1. Download and extract the binary distribution package of dcm4chee-arr-3.0.11

for the database of your choice for storage of audit records. - It may differ

from the database used for dcm4chee archive.

2. Move to the dcm4chee-2.17.0-xxx/bin directory and execute the

install_arr.bat or install_arr.sh script, as appropriate for your operating

system, with the path of the dcm4chee-arr-3.0.11 installation directory as

parameter.

3a. If the Audit Record Repository shall use a different database instance than

the archive to store received Audit Records, create the audit record repository

database instance: arrdb, and grant sufficient privileges to the DB user,

configured in the datasource descriptor arr-xxx-ds.xml.

Optionally, you may also initialize the database using create DDL script

dcm4chee-arr-3.0.11-xxx/sql/dcm4chee-arr-xxx.ddl. Otherwise, the database will

be initialized automatically at first startup of the application.

4b. If the Audit Record Repository shall share the database instance already

used by the archive, you have to modify database name - but NOT the JNDI name!

-, user and password in the datasource descriptor arr-xxx-ds.xml, to match with

the values specified in the datasource descriptor pacs-xxx-ds.xml for the

archive database.

Optionally, you may update the database with dcm4chee-arr specific tables using

modified create DDL script dcm4chee-arr-3.0.11-xxx/sql/dcm4chee-arr-xxx.ddl:

you have to remove or comment out the creation of already exisiting 'code'

table. But missing tables will be also initialized automatically at first

startup of the application.

MIGRATE AUDIT RECORDS RECEIVED BY DCM4CHEE AUDIT RECORD REPOSITORY 2.x TO 3.x:

================================================== ===========================

Audit Records received by dcm4chee-arr-2.x and stored in database table

'audit_record_old' can be migrated to dcm4chee-arr-3.x by re-emission to the

new Audit Record Repository by service 'MigrateOldARR':

1. Connect to JBoss's JMX Console at http://localhost:8080/jmx-console/ and

login using the Administrator account 'admin', with password 'admin'.

Follow the link "service=MigrateOldARR" under the "dcm4chee.archive" heading.

Invoke the operation emitAuditRecords(), with argument num=1, to test the

migration on the first Audit Record in table audit_record_old.

Check in the Audit Record Repository Web Application

(http://localhost:8080/dcm4chee-arr) if the record is now stored by

dcm4chee-arr-3.x.

2. Determine the number of Audit Records to migrate by (e.g.) executing

SELECT count(*) FROM audit_record_old

using any SQL client of your database.

Estimate the migration time for all Audit Records by configured

EmissionInterval x count.

If the estimated time exeeds several hours, you may consider

- to split the migration in chunks of records, and/or

- decrease the configured EmissionInterval from default 100 ms (but which will

increase the load for the Database during the task is running)

3. Invoke the operation emitAuditRecords(), with argument num set to the

maximal number of audit records to migrate/emit by this operation, until no

further record will be migrated/emited (=value of attribute LastEmittedPk

matches the last record received by dcm4chee-arr 2.x.).

=============================

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December 14th, 2011

#2

sqadree

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Re: install dcm4chee pacs server

still no reploy

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January 17th, 2012

#3

manthony121

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Re: install dcm4chee pacs server

Don't bother with the long instructions listed above. Do this instead:

http://cdmedicpacsweb.sourceforge.ne..._PACS_WEB.html

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