dcm4che / dcm4che

DICOM Implementation in JAVA

dcm4che DICOM Toolkit & Library

Sources: https://github.com/dcm4che/dcm4che
Binaries: https://sourceforge.net/projects/dcm4che/files/dcm4che3
Issue Tracker: https://github.com/dcm4che/dcm4che/issues
Build Status:

This is a complete rewrite of dcm4che-2.x.

One main focus was to minimize the memory footprint of the DICOM data sets. It already provides modules to store/fetch configuration data to/from LDAP, compliant to the DICOM Application Configuration Management Profile, specified in DICOM PS 3.15, Annex H.

dcm4che uses a native library for the compression and decompression of images. Here is the list of supported systems and architectures:

System	Architecture	Package	Requirement
Linux	x86 64-bit	linux-x86-64	GLIBC_2.17
Linux	ARM 64-bit	linux-aarch64	GLIBC_2.27
Linux	ARM 32-bit	linux-armv7a	GLIBC_2.28
Windows	x86 64-bit	windows-x86-64	Windows 7 or higher
Windows	x86 32-bit	windows-x86	Windows 7 or higher
Mac OS	x86 64-bit	macosx-x86-64	Mac OS 10.13 or higher
Mac OS	ARM 64-bit	macosx-aarch64	Mac OS 11 or higher

Build

Make sure you have Java 17 (JDK) or newer installed.

Run the Maven Wrapper script for building:

./mvnw install

or on Windows:

.\mvnw install

Modules

• dcm4che-audit
• dcm4che-audit-keycloak
• dcm4che-conf
  • dcm4che-conf-api
  • dcm4che-conf-api-hl7
  • dcm4che-conf-json
  • dcm4che-conf-json-schema
  • dcm4che-conf-ldap
  • dcm4che-conf-ldap-audit
  • dcm4che-conf-ldap-hl7
  • dcm4che-conf-ldap-imageio
  • dcm4che-conf-ldap-schema
• dcm4che-core
• dcm4che-dcmr
• dcm4che-deident
• dcm4che-dict
• dcm4che-dict-priv
• dcm4che-emf
• dcm4che-hl7
• dcm4che-image
• dcm4che-imageio
• dcm4che-imageio-opencv
• dcm4che-imageio-rle
• dcm4che-js-dict
• dcm4che-json
• dcm4che-mime
• dcm4che-net
• dcm4che-net-audit
• dcm4che-net-hl7
• dcm4che-net-imageio
• dcm4che-soundex
• dcm4che-ws-rs
• dcm4che-xdsi
• dcm4che-jboss-modules

Utilities

• agfa2dcm: Extract DICOM files from Agfa BLOB file
• agfa2sr: Extract concatenated XML Agfa Reports and convert them to DICOM SR Documents
• dcm2dcm: Transcode DICOM file according the specified Transfer Syntax
• dcm2jpg: Convert DICOM image to JPEG or other image formats
• dcm2json: Convert DICOM file in JSON presentation
• dcm2pdf: Extract encapsulated PDF, CDA or STL from DICOM file
• dcm2str: Apply Attributes Format Pattern to dicom file or command line parameters.
• dcm2xml: Convert DICOM file in XML presentation
• dcmbenchmark: Parse a DICOM file repetitively, measuring time and used memory
• dcmdir: Dump, create or update DICOMDIR file
• dcmdump: Dump DICOM file in textual form
• dcmldap: Insert/remove configuration entries for Network AEs into/from LDAP server
• dcmqrscp: Simple DICOM archive
• dcmvalidate: Validate DICOM object according a specified Information Object Definition
• deidentify: De-identify one or several DICOM files
• emf2sf: Convert DICOM Enhanced Multi-frame image to legacy DICOM Single-frame images
• findscu: Invoke DICOM C-FIND Query Request
• fixlo2un: Fixes length of private tags truncated to 2 bytes on conversion from implicit VR to explicit VR Transfer Syntax
• getscu: Invoke DICOM C-GET Retrieve Request
• hl72xml: Convert HL7 v2.x message in XML presentation
• hl7pdq: Query HL7 v2.x Patient Demographics Supplier
• hl7pix: Query HL7 v2.x PIX Manager
• hl7rcv: HL7 v2.x Receiver
• hl7snd: Send HL7 v2.x message
• ianscp: DICOM Instance Availability Notification receiver
• ianscu: Send DICOM Instance Availability Notification
• jpg2dcm: Convert JPEG images or MPEG videos in DICOM files
• json2dcm: Converts JSON file to DICOM file
• json2index: Creates search index for UI configuration from JSON schema files
• json2props: Convert Archive configuration schema JSON files to key/value properties files and vice versa
• json2rst: Generate ReStructuredText files from Archive configuration schema JSON files
• maskpxdata: Mask information burned into the Pixel Data
• mkkos: Make DICOM Key Object Selection Document
• modality: Simulates DICOM Modality
• movescu: Invoke DICOM C-MOVE Retrieve request
• mppsscp: DICOM Modality Performed Procedure Step Receiver
• mppsscu: Send DICOM Modality Performed Procedure Step
• pdf2dcm: Convert PDF file into DICOM file
• planarconfig: Detects the actual planar configuration of uncompressed pixel data of color images with Photometric Interpretation RGB or YBR_FULL and optionally correct non matching values of attribute Planar Configuration of the image
• qstar: QStar SOAP Client to prefetch/retrieve or fetch file information of specified files
• stgcmtscu: Invoke DICOM Storage Commitment Request
• storescp: DICOM Composite Object Receiver
• storescu: Send DICOM Composite Objects
• stowrs: Send DICOM Composite Objects or Bulkdata file over Web
• stowrsd: STOW-RS Server
• swappxdata: Swaps bytes of uncompressed pixel data in DICOM files
• syslog: Send Syslog messages via TCP/TLS or UDP to a Syslog Receiver
• syslogd: Receives RFC 5424 Syslog messages via TCP/TLS or UDP
• tpl2xml: Converts private dictionaries present in template file(s) to xml file(s).
• upsscu: Invokes services of Unified Procedure Step Service Class
• wadors: Wado RS Client Simulator
• wadows: Wado WS Client Simulator
• xml2dcm: Create/Update DICOM file from/with XML presentation
• xml2hl7: Create HL7 v2.x message from XML presentation
• xroad: XRoad SOAP Client to query Estonia National Patient Registry for Patient Demographics

License

• Mozilla Public License Version 1.1

dcm4che's Issues

LIB-452 org.dcm4che3.data.Attributes.trimToSize(boolean) throw exception

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-452

LIB-423 Sending/receiveing DICOM files in DeflatedLittleEndianExplicit TS

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-423

Export and Import Dicm Files

How can I export dicom files from my client machine to the pacs server, and how to download dicom files from pacs server to local machine ??

LIB-463 JPEG Baseline image incorrectly rendered

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-463

LIB-159 Support Sigmoid lookups

This issue was migrated from Jira.

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http://dcm4che.org/jira/browse/LIB-159

LIB-441 Reading first frame in large multiframe is very slow

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-441

LIB-357 Unable to make cmove when using dcmqrscp

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-357

LIB-455 Reading images from big multi-slice files takes forever

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-455

Wrong VR for SourceApplicationEntityTitle in Attributes created by Association.createFileMetaInformation(..)

On the master ( and on the other branches ), on line 1228 of Association.java in createFileMetatInformation ( project dcm4che-net ) we can find :
fmi.setString(Tag.SourceApplicationEntityTitle, VR.SH, getRemoteAET());

The VR use shall be AE and not SH see the following link
https://www.dabsoft.ch/dicom/6/7/#(0002,0016)

This shall be changed to
fmi.setString(Tag.SourceApplicationEntityTitle, VR.AE, getRemoteAET());

Modify Attributes.addAll() to preserve non-conflicting Private Creator ID tag positions

Attributes.addAll() should preserve non-conflicting Private Creator ID tag positions.

This behavior was originally implemented in commit 7c1d8f4

Unfortunately it was broken with the bug fix for http://dcm4che.org/jira/browse/LIB-362 (Commit 764d9c4 ).

The behavior has to be restored (of course also preserving the bug fix for LIB-362).

New unit tests (AttributesTest) should be implemented to ensure that this behavior doesn't break again.

dcm2dcm fails to find ImageWriter for format jpeg

Mac

Windows

Tried this with various other syntaxes and got the same result. I'm looking for j2ki in particular. The input file is a multiframe mammo. Have also tried it with a single frame dicom file.

LIB-402 Compressor fails transcoding single frames with fragmented pixeldata

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-402

LIB-440 Binary data added to wrong tag after converting xml to dicom

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-440

createFileMetaInformation: throw IllegalArgumentException with specific message instead NPE on null arguments

LIB-437 dcmQRSCP: NPE while receiving data

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-437

LIB-285 add pdf2dcm & dcm2pdf to dcm4che3-tool

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-285

LIB-329 Refactor BulkData representation for encapsulated/fragmented Pixel Data

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Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-329

Javadoc failure for files created with XSLT in generated-sources directory

I was starting up with dcm4che again after a few years and was trying to create some Javadoc files. When I tried running man javadoc:javadoc on the modules, I received a long list of errors. I was using Javadoc 8 and many of the problems were due to the information in the javadoc comment related to the schema for the files in the generated-sources sections not having the greater than sign changed to >. I know that Javadoc 8 has a problem with this because it is much stricter on html syntax in the comments. You are using group:javax.xml.bind artifact:jaxb-api version:2.1. According tohttps://jaxb.java.net/2.2.5/docs/release-documentation.html, there was fix between 2.2.3u2 and 2.2.4 that may refer to this.

There are some other Javadoc problems but they appear to be related to the source code.

This is what I received when I ran man javadoc:javadoc
problems.txt

---

I changed the versions for the following dependencies in dcm4che-audit/pom.xml and that seemed to have removed the problems with the illegal HTML in the Javadoc comments.

javax.xml.bind jaxb-api 2.2.5 junit junit 4.12 jar test

The resulting Javadocs can be found at https://bradleyross.github.io/dcm4che/apidocs

LIB-409 dcm2jpg generates Incorrect jpegs from some dicom images

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-409

Idle timeout may wrongly expire in case of two consecutive C-MOVE operations

When using the same association for two C-MOVE operations, an idle timeout may expire before the (second) C-MOVE operation is finished.

We are using a Connection in SYNCHRONOUS_MODE, i.e. with maxOpsInvoked = 1, and try to trigger two consecutive C-MOVE operations by calling Association.cmove(String, String, int, Attributes, String, String, DimseRSPHandler). The second call blocks in Association.addDimseRSPHandler(DimseRSPHandler) until the first C-MOVE operation is finished.
As soon as the first C-MOVE operation is finished, a notification is sent out in Association.onDimseRSP(Dimse, Attributes, Attributes). This starts the second C-MOVE operation. After that, an idle timeout is scheduled (in the same method). However, the stopTimeout() method (for stopping the idle timeout) has already been called before the second call to the cmove(...) method has blocked. Therefore, if the second C-MOVE operation takes longer than the idle timeout, the association is wrongly aborted.

LIB-453 [Audit] Patient Record auditing message failed IHE validator due to misplacing attribute 'code' in element AuditSourceIdentification

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-453

LIB-413 No Presentation Context error

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http://dcm4che.org/jira/browse/LIB-413

dcm4che-conf-core-api jar contains extra classes

The dcm4che-conf-core-api-3.3.8.jar in Maven contains classes for the Apache Commons BeanUtils and Logging library. This can cause problems if an application is using different versions of these libraries.

Continuous integration using Travis CI

Enable automatic continuous builds and tests using travis-ci.org

Builds will be available on: https://travis-ci.org/dcm4che/dcm4che

LIB-462 Bulk Data URIs for Encapsulated Pixel Data Contain Reference to Basic Offset Fragment

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-462

dcm2jpg throws EOFException when converting deflated explicit VR little endian file

Platform: macOS Sierra 10.12.3
dcm4che version: 3.3.8

To reproduce: convert file with TS explicit VR little endian to deflated using dcm2dcm -t 1.2.840.10008.1.2.1.99 file.dcm file_defl.dcm. Create jpeg file using dcm2jpg file_defl.dcm file.jpg

Result:

Failed to convert file_defl.dcm: null
java.io.EOFException
	at javax.imageio.stream.ImageInputStreamImpl.readFully(ImageInputStreamImpl.java:353)
	at javax.imageio.stream.ImageInputStreamImpl.readFully(ImageInputStreamImpl.java:373)
	at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.readRaster(DicomImageReader.java:295)
	at org.dcm4che3.imageio.plugins.dcm.DicomImageReader.read(DicomImageReader.java:342)
	at org.dcm4che3.tool.dcm2jpg.Dcm2Jpg.readImage(Dcm2Jpg.java:381)
	at org.dcm4che3.tool.dcm2jpg.Dcm2Jpg.convert(Dcm2Jpg.java:360)
	at org.dcm4che3.tool.dcm2jpg.Dcm2Jpg.mconvert(Dcm2Jpg.java:345)
	at org.dcm4che3.tool.dcm2jpg.Dcm2Jpg.main(Dcm2Jpg.java:314)

Does dcm4che's DicomImageReader not support deflated datasets?

homer.jpg in binary distribution corrupted

only effected dcm4chee-arc-light branch

TLS connections broken, if no explicit TLS Protocol is specified

Introduced by http://www.dcm4che.org/jira/browse/LIB-467

LIB-424 C-Find not working when using StudyDate

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-424

LIB-398 Failure to compress all black images to JPEG-LS

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-398

LIB-417 Correctly quote Accept-Header for WADO tools

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-417

LIB-399 Get rid of dangerous SafeClose

The class SafeClose used throughout the library (and the archive) is a bad idea.
It just silently swallows IOExceptions that happen on close of streams/sockets.
But close usually also involves flushing the stream, and if exceptions are ignored for that it could mean that an incomplete object is written to the stream.

It is a better idea to replace all usages of SafeClose with Java 7 try-with-resources statements. (This would require depending on Java 7 for the library. Currently it is still compatible with Java 6.)
Update: The master branch is now on Java 7, so try-with-resources can be used.

(This issue was originally opened in Jira and migrated from there: http://dcm4che.org/jira/browse/LIB-399 )

LIB-252 unable to parse object

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-252

LIB-349 PixelData larger than 2 GB

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http://dcm4che.org/jira/browse/LIB-349

LIB-419 StowRS breaking for big files (~500 mb)

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http://dcm4che.org/jira/browse/LIB-419

LIB-380 Error sending study to storecp tool while using --filepath option

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-380

LIB-385 Decompressor doesn't work properly with single frame, multi fragment instances

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-385

LIB-458 Connection.reconfigure(from) does not clear the lazy initialized hostAddr

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-458

LIB-389 Merge changes from dcm4chee-arc-light branch of dcm4che

Review changes from @gunterze on the dcm4chee-arc-light branch of the dcm4che repo and merge them back to the master branch.

(This issue was originally opened in Jira and migrated from there: http://dcm4che.org/jira/browse/LIB-389 )

findscu: Unable to recover non-ASCII text from DICOM attributes

findscu: Unable to recover non-ASCII text from DICOM attributes

Our PACS stores information in several fields encoded as ISO-8859-1 (latin-1). So far, we were able to recover properly this information using dcmqr (from dcm4che2 toolset) but right now we are unable to recover these fields using findscu (from dcm4che3 toolset).

You can find the description of our problem in the last two messages of this (rather old) thread:
http://forums.dcm4che.org/jiveforums/thread.jspa?messageID=18779
Notice that we were able to solve the problem back in 2011 using dcmqr, but we pretend to use the new findscu software in a new project.

Our storage server does not store information about specific character set (the attribute (0008,0005) is empty), so, maybe our PACS server is not perfectly configured. Would it be possible to recover the proper strings using findscu?

Examples:

dcmqr:

$ LANG=es_ES.iso-8859-1 /usr/local/dcm4che/dcm4che2/bin/dcmqr [email protected]:104 -q 00100020='80701'|iconv -f ISO-8859-1 -t UTF8 | grep '(0008,1030)'

(0008,1030) LO #6 [tórax] Study Description
(0008,1030) LO #6 [tórax] Study Description

Perfect!!!

findscu:

$ LANG=es_ES.iso-8859-1 /usr/local/dcm4che/dcm4che3/bin/findscu -b DCMQR -c [email protected]:104 -m 00100020='80701' -m 00080005='ISO-8859-1' | grep '(0008,1030)'

(0008,1030) LO [t�rax] StudyDescription
(0008,1030) LO [t�rax] StudyDescription

I have tried with different locales, as well as using different values for the SpecificCharacterSet attribute, but so far we have been unable to recover correctly any fields containing non-ASCII characters.

LIB-400 dcm2jpg tool produces black images for Photometric Interpretation YBR_FULL_422

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-400

LIB-369 Tool functionality as a Service

This issue was migrated from Jira.

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http://dcm4che.org/jira/browse/LIB-369

Use certficate issued by IHE CA for all tools by default

Certificate[1]:
Owner: CN=dcm4che-tools, O=dcm4che.org, C=AT
Issuer: CN=IHE Europe CA, O=IHE Europe, C=FR
Serial number: 587
Valid from: Sun Apr 02 08:44:33 CEST 2017 until: Fri Apr 02 08:44:33 CEST 2027
Certificate fingerprints:
	 MD5:  E2:19:A3:34:EF:92:97:4C:A2:9A:70:E5:98:78:A2:A8
	 SHA1: D7:5C:5B:EF:CF:A5:BA:37:20:45:C3:74:7A:FF:F4:36:C2:B4:6A:95
	 SHA256: 08:54:62:83:A9:85:B3:0D:1A:19:D7:68:83:D1:03:AF:E4:52:BF:D1:5C:5F:5F:D1:8B:B5:C5:7F:E1:88:2C:9C
	 Signature algorithm name: SHA512withRSA
	 Version: 3

LIB-407 Decompression of valid JPEG-LS image without APP/COM markers fails

This issue was migrated from Jira.

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http://dcm4che.org/jira/browse/LIB-407

LIB-298 etc/probetc/sampleTCFile.properties contains entries for all UIDs

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LIB-414 Incorrect TimeUnit Used In BasicRetrieveTask Class

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dcm4che can't store a particular CT

when trying to dump:

IOException during read of (7FE0,0010) #524288 @ 1254 java.io.EOFException at org.dcm4che3.util.StreamUtils.readFully(StreamUtils.java:63) at org.dcm4che3.io.DicomInputStream.readFully(DicomInputStream.java:384) at org.dcm4che3.io.DicomInputStream.readValue(DicomInputStream.java:730) at org.dcm4che3.tool.dcmdump.DcmDump.readValue(DcmDump.java:122) at org.dcm4che3.io.DicomInputStream.readAttributes(DicomInputStream.java:516) at org.dcm4che3.io.DicomInputStream.readDataset(DicomInputStream.java:444) at org.dcm4che3.tool.dcmdump.DcmDump.parse(DcmDump.java:87) at org.dcm4che3.tool.dcmdump.DcmDump.main(DcmDump.java:245)

00010ccd.dcm.zip

LIB-338 Dictionary to provide the most appropriate DB BLOB Level

This issue was migrated from Jira.

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http://dcm4che.org/jira/browse/LIB-338

WADO Implementation

What Interfaces or Methods I need to implement wado service to handle weasis requests in my Spring boot application?

LIB-415 BasicRetrieveTask.update() Method Uses Inverse Logic For Writing Status Update Responses When Observing Instance CMOVE Operations

This issue was migrated from Jira.

Please check the original Jira issue for additional information and the actual Reporter:
http://dcm4che.org/jira/browse/LIB-415