com.pixelmed.dicom

Class XMLRepresentationOfStructuredReportObjectFactory

java.lang.Object

com.pixelmed.dicom.XMLRepresentationOfStructuredReportObjectFactory

public class XMLRepresentationOfStructuredReportObjectFactory
extends java.lang.Object

A class to encode a representation of a DICOM Structured Report object in an XML form, suitable for analysis as human-readable text, or for feeding into an XSLT-based validator.

Note that XML representations can either contain only the content tree, or also the additional top level DICOM attributes other than those that encode the content tree, as individual DICOM attributes, in the manner of XMLRepresentationOfDicomObjectFactory.

A typical example of usage to extract just the content tree would be:

try {
    AttributeList list = new AttributeList();
    list.read("dicomsrfile",null,true,true);
        StructuredReport sr = new StructuredReport(list);
    Document document = new XMLRepresentationOfStructuredReportObjectFactory().getDocument(sr);
    XMLRepresentationOfStructuredReportObjectFactory.write(System.out,document);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

or to include the top level attributes as well as the content tree, supply the attribute list as well as the parsed SR content to the write() method:

try {
    AttributeList list = new AttributeList();
    list.read("dicomsrfile",null,true,true);
        StructuredReport sr = new StructuredReport(list);
    Document document = new XMLRepresentationOfStructuredReportObjectFactory().getDocument(sr,list);
    XMLRepresentationOfStructuredReportObjectFactory.write(System.out,document);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

or even simpler, if there is no further use for the XML document or the SR tree model:

try {
    AttributeList list = new AttributeList();
    list.read("dicomsrfile",null,true,true);
    XMLRepresentationOfStructuredReportObjectFactory.createDocumentAndWriteIt(list,System.out);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

See Also:

StructuredReport, XMLRepresentationOfDicomObjectFactory, XPathQuery, Document

Field Summary

Fields

Modifier and Type	Field and Description
protected ContentItemFactory	contentItemFactory
protected static java.lang.String	contentItemIdentiferPrefix

Constructor Summary

Constructors

Constructor and Description
XMLRepresentationOfStructuredReportObjectFactory() Construct a factory object, which can be used to get XML documents from DICOM objects.

Method Summary

Modifier and Type	Method and Description
static void	createDocumentAndWriteIt(AttributeList list, java.io.OutputStream out) Serialize an XML document (DOM tree) created from a DICOM Structured Report.
static void	createDocumentAndWriteIt(StructuredReport sr, AttributeList list, java.io.OutputStream out) Serialize an XML document (DOM tree) created from a DICOM Structured Report.
static void	createDocumentAndWriteIt(StructuredReport sr, java.io.OutputStream out) Serialize an XML document (DOM tree) created from a DICOM Structured Report.
AttributeList	getAttributeList(org.w3c.dom.Document document) Given a DICOM SR object encoded as an XML document convert it to a list of attributes.
AttributeList	getAttributeList(java.io.InputStream stream) Given a DICOM SR object encoded as an XML document in a stream convert it to a list of attributes.
AttributeList	getAttributeList(java.lang.String name) Given a DICOM SR object encoded as an XML document in a named file convert it to a list of attributes.
protected CodedSequenceItem	getCodedSequenceItem(org.w3c.dom.Node node)
org.w3c.dom.Document	getDocument(AttributeList list) Given a DICOM attribute list encoding a Structured Report, get an XML document as a DOM tree.
org.w3c.dom.Document	getDocument(StructuredReport sr) Given a DICOM Structured Report, get an XML document of the content tree only as a DOM tree.
org.w3c.dom.Document	getDocument(StructuredReport sr, AttributeList list) Given a DICOM Structured Report, get an XML document of the content tree and the top level DICOM elements as a DOM tree.
static org.w3c.dom.Node	getNamedChildElement(org.w3c.dom.Node parent, java.lang.String name)
static java.lang.String	getNamedNodeAttributeOrNull(org.w3c.dom.NamedNodeMap attributes, java.lang.String name)
protected ContentItem	getNextContentItemFromXMLNodeSiblings(org.w3c.dom.Node node)
StructuredReport	getStructuredReport(org.w3c.dom.Document document) Given a DICOM SR object encoded as an XML document convert it to a StructuredReport using the content tree and ignoring any header attributes.
static java.lang.String	getTextValueOfNamedChildElementOrNull(org.w3c.dom.Node parent, java.lang.String name)
static void	main(java.lang.String[] arg) Read a DICOM dataset (that contains a structured report) and write an XML representation of it to the standard output, or vice versa.
static java.lang.String	toString(org.w3c.dom.Node documentNode)
static java.lang.String	toString(org.w3c.dom.Node documentNode, int indent)
static void	write(java.io.OutputStream out, org.w3c.dom.Document document) Serialize an XML document (DOM tree).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

contentItemFactory

protected ContentItemFactory contentItemFactory

contentItemIdentiferPrefix

protected static java.lang.String contentItemIdentiferPrefix

Constructor Detail

XMLRepresentationOfStructuredReportObjectFactory

public XMLRepresentationOfStructuredReportObjectFactory()
                                                 throws javax.xml.parsers.ParserConfigurationException

Construct a factory object, which can be used to get XML documents from DICOM objects.

Throws:

javax.xml.parsers.ParserConfigurationException

Method Detail

createDocumentAndWriteIt

public static void createDocumentAndWriteIt(AttributeList list,
                                            java.io.OutputStream out)
                                     throws java.io.IOException,
                                            DicomException

Serialize an XML document (DOM tree) created from a DICOM Structured Report.

Parameters:

list - the attribute list

out - the output stream to write to

Throws:

java.io.IOException

DicomException

createDocumentAndWriteIt

public static void createDocumentAndWriteIt(StructuredReport sr,
                                            AttributeList list,
                                            java.io.OutputStream out)
                                     throws java.io.IOException,
                                            DicomException

Serialize an XML document (DOM tree) created from a DICOM Structured Report.

Parameters:

sr - the Structured Report may be null if list is not - will build an sr tree model

list - the attribute list may be null if only the sr content tree is to be written

out - the output stream to write to

Throws:

java.io.IOException

DicomException

createDocumentAndWriteIt

public static void createDocumentAndWriteIt(StructuredReport sr,
                                            java.io.OutputStream out)
                                     throws java.io.IOException,
                                            DicomException

Serialize an XML document (DOM tree) created from a DICOM Structured Report.

Parameters:

sr - the Structured Report

out - the output stream to write to

Throws:

java.io.IOException

DicomException

getAttributeList

public AttributeList getAttributeList(org.w3c.dom.Document document)
                               throws DicomException,
                                      javax.xml.parsers.ParserConfigurationException

Given a DICOM SR object encoded as an XML document convert it to a list of attributes.

Parameters:

document - the XML document

Returns:

the list of DICOM attributes

Throws:

DicomException

javax.xml.parsers.ParserConfigurationException

getAttributeList

public AttributeList getAttributeList(java.io.InputStream stream)
                               throws java.io.IOException,
                                      org.xml.sax.SAXException,
                                      javax.xml.parsers.ParserConfigurationException,
                                      DicomException

Given a DICOM SR object encoded as an XML document in a stream convert it to a list of attributes.

Parameters:

stream - the input stream containing the XML document

Returns:

the list of DICOM attributes

Throws:

java.io.IOException

org.xml.sax.SAXException

javax.xml.parsers.ParserConfigurationException

DicomException

getAttributeList

public AttributeList getAttributeList(java.lang.String name)
                               throws java.io.IOException,
                                      org.xml.sax.SAXException,
                                      javax.xml.parsers.ParserConfigurationException,
                                      DicomException

Given a DICOM SR object encoded as an XML document in a named file convert it to a list of attributes.

Parameters:

name - the input file containing the XML document

Returns:

the list of DICOM attributes

Throws:

java.io.IOException

org.xml.sax.SAXException

javax.xml.parsers.ParserConfigurationException

DicomException

getCodedSequenceItem

protected CodedSequenceItem getCodedSequenceItem(org.w3c.dom.Node node)
                                          throws DicomException

Throws:

DicomException

getDocument

public org.w3c.dom.Document getDocument(AttributeList list)

Given a DICOM attribute list encoding a Structured Report, get an XML document as a DOM tree.

Parameters:

list - the attribute list

getDocument

public org.w3c.dom.Document getDocument(StructuredReport sr)

Given a DICOM Structured Report, get an XML document of the content tree only as a DOM tree.

Parameters:

sr - the Structured Report

getDocument

public org.w3c.dom.Document getDocument(StructuredReport sr,
                                        AttributeList list)

Given a DICOM Structured Report, get an XML document of the content tree and the top level DICOM elements as a DOM tree.

Parameters:

sr - the Structured Report may be null if list is not - will build an sr tree model

list - the attribute list may be null if only the sr content tree is to be added

getNamedChildElement

public static org.w3c.dom.Node getNamedChildElement(org.w3c.dom.Node parent,
                                                    java.lang.String name)

getNamedNodeAttributeOrNull

public static java.lang.String getNamedNodeAttributeOrNull(org.w3c.dom.NamedNodeMap attributes,
                                                           java.lang.String name)

getNextContentItemFromXMLNodeSiblings

protected ContentItem getNextContentItemFromXMLNodeSiblings(org.w3c.dom.Node node)
                                                     throws DicomException

Throws:

DicomException

getStructuredReport

public StructuredReport getStructuredReport(org.w3c.dom.Document document)
                                     throws DicomException,
                                            javax.xml.parsers.ParserConfigurationException

Given a DICOM SR object encoded as an XML document convert it to a StructuredReport using the content tree and ignoring any header attributes.

Parameters:

document - the XML document

Returns:

the StructuredReport

Throws:

DicomException

javax.xml.parsers.ParserConfigurationException

getTextValueOfNamedChildElementOrNull

public static java.lang.String getTextValueOfNamedChildElementOrNull(org.w3c.dom.Node parent,
                                                                     java.lang.String name)

main

public static void main(java.lang.String[] arg)

Read a DICOM dataset (that contains a structured report) and write an XML representation of it to the standard output, or vice versa.

Parameters:

arg - either one filename of the file containing the DICOM dataset, or a direction argument (toDICOM or toXML, case insensitive) and an input filename

toString

public static java.lang.String toString(org.w3c.dom.Node documentNode)

Parameters:

documentNode -

toString

public static java.lang.String toString(org.w3c.dom.Node documentNode,
                                        int indent)

Parameters:

documentNode -

indent -

write

public static void write(java.io.OutputStream out,
                         org.w3c.dom.Document document)
                  throws java.io.IOException,
                         javax.xml.transform.TransformerConfigurationException,
                         javax.xml.transform.TransformerException

Serialize an XML document (DOM tree).

Parameters:

out - the output stream to write to

document - the XML document

Throws:

java.io.IOException

javax.xml.transform.TransformerConfigurationException

javax.xml.transform.TransformerException