com.pixelmed.dicom

Class JSONRepresentationOfDicomObjectFactory

java.lang.Object

com.pixelmed.dicom.JSONRepresentationOfDicomObjectFactory

public class JSONRepresentationOfDicomObjectFactory
extends java.lang.Object

A class to encode a representation of a DICOM object in a JSON form, and to convert it back again.

There are a number of characteristics of this form of output:

Note that a round trip from DICOM to JSON and back again does not always result in full fidelity, since:

• Binary floating point values will lose precision when converted to string representation and back again
• Leading and trailing white space and control characters in strings will be discarded
• Meta information header elements will be changed
• Structural elements such as group lengths will be removed and may or may not be replaced
• Physical offsets such as in the DICOMDIR will be invalidated
• Large attributes with OB and OW value representations will have their values discarded so as not to encode the bulk pixel data (probably should be added as an option)

A typical example of how to invoke this class to convert DICOM to JSON would be:

try {
    AttributeList list = new AttributeList();
    list.read("dicomfile",null,true,true);
    JsonArray document = new JSONRepresentationOfDicomObjectFactory().getDocument(list);
    JSONRepresentationOfDicomObjectFactory.write(System.out,document);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

or even simpler, if there is no further use for the JSON document:

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

A typical example of converting JSON back to DICOM would be:

try {
    AttributeList list = new JSONRepresentationOfDicomObjectFactory().getAttributeList("jsonfile");
    list.insertSuitableSpecificCharacterSetForAllStringValues();
    list.write(System.out,TransferSyntax.ExplicitVRLittleEndian,true,true);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

or if you need to handle the meta information properly:

try {
    AttributeList list = new JSONRepresentationOfDicomObjectFactory().getAttributeList("jsonfile");
    list.insertSuitableSpecificCharacterSetForAllStringValues();
    String sourceApplicationEntityTitle = Attribute.getSingleStringValueOrEmptyString(list,TagFromName.SourceApplicationEntityTitle);
    list.removeMetaInformationHeaderAttributes();
    FileMetaInformation.addFileMetaInformation(list,TransferSyntax.ExplicitVRLittleEndian,sourceApplicationEntityTitle);
    list.write(System.out,TransferSyntax.ExplicitVRLittleEndian,true,true);
} catch (Exception e) {
    slf4jlogger.error("",e);
 }
 

When the JSON is being converted to DICOM, the group, element and VR attributes are not needed if the element name is a keyword that can be found in the dictionary; if they are present, then their values are checked against the dictionary values.

Field Summary

Fields

Modifier and Type	Field and Description
protected static java.lang.String	reservedKeywordForPersonNameAlphabeticPropertyInJsonRepresentation
protected static java.lang.String	reservedKeywordForPersonNameIdeographicPropertyInJsonRepresentation
protected static java.lang.String	reservedKeywordForPersonNamePhoneticPropertyInJsonRepresentation

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
static void	addPersonNameAsComponentsToJsonObject(javax.json.JsonObjectBuilder jsonPersonNameValue, java.lang.String value, java.lang.String alphabeticProperty, java.lang.String ideographicProperty, java.lang.String phoneticProperty)
static void	createDocumentAndWriteIt(AttributeList list, java.io.File outputFile) Serialize a JSON document created from a DICOM attribute list.
static void	createDocumentAndWriteIt(AttributeList list, java.io.OutputStream out) Serialize a JSON document created from a DICOM attribute list.
static void	createDocumentAndWriteIt(AttributeList list, java.lang.String outputPath) Serialize a JSON document created from a DICOM attribute list.
AttributeList	getAttributeList(java.io.File file) Given a DICOM instance encoded as a JSON document in a file convert it to a list of attributes.
AttributeList	getAttributeList(java.io.InputStream stream) Given a DICOM instance encoded as a JSON document in a stream convert it to a list of attributes.
AttributeList	getAttributeList(javax.json.JsonArray document) Given a DICOM instance encoded as a JSON document convert it to a list of attributes.
AttributeList	getAttributeList(javax.json.JsonArray document, boolean ignoreUnrecognizedTags, boolean ignoreSR) Given a DICOM instance encoded as a JsonObject in JsonArray in a JSON document convert it to a list of attributes.
AttributeList	getAttributeList(javax.json.JsonObject document) Given a DICOM instance encoded as a JSON document convert it to a list of attributes.
AttributeList	getAttributeList(javax.json.JsonObject topLevelObject, boolean ignoreUnrecognizedTags, boolean ignoreSR) Given a DICOM object encoded in a JSON document convert it to a list of attributes.
AttributeList	getAttributeList(java.lang.String name) Given a DICOM instance encoded as a JSON document in a named file convert it to a list of attributes.
protected static AttributeTag	getAttributeTagFromHexadecimalGroupElementValues(java.lang.String s) Parse an AttributeTag represented as an eight character hexadecimal representation as defined for the standard JSON or XML representation.
javax.json.JsonArray	getDocument(AttributeList list) Given a DICOM instance encoded as a list of attributes, get a JSON document.
javax.json.JsonArray	getDocument(AttributeList list, boolean useKeywordInsteadOfTag, boolean addTag, boolean addKeyword, boolean addVR, boolean collapseValueArrays, boolean collapseEmptyToNull, boolean ignoreSR, boolean substituteUIDKeywords, boolean useNumberForIntegerOrDecimalString) Given a DICOM instance encoded as a list of attributes, get a JSON document.
javax.json.JsonArray	getDocument(java.io.File file) Given a DICOM instance encoded as a list of attributes, get a JSON document.
javax.json.JsonArray	getDocument(java.io.File file, boolean useKeywordInsteadOfTag, boolean addTag, boolean addKeyword, boolean addVR, boolean collapseValueArrays, boolean collapseEmptyToNull, boolean ignoreSR, boolean substituteUIDKeywords, boolean useNumberForIntegerOrDecimalString) Given a DICOM instance encoded as a list of attributes, get a JSON document.
javax.json.JsonArray	getDocument(java.lang.String filename) Given a DICOM object encoded as a list of attributes, get a JSON document.
javax.json.JsonArray	getDocument(java.lang.String filename, boolean useKeywordInsteadOfTag, boolean addTag, boolean addKeyword, boolean addVR, boolean collapseValueArrays, boolean collapseEmptyToNull, boolean ignoreSR, boolean substituteUIDKeywords, boolean useNumberForIntegerOrDecimalString) Given a DICOM instance encoded as a list of attributes, get a JSON document.
static java.lang.String	getJsonPersonNameFromPropertiesInJsonObject(javax.json.JsonObject jsonObjectValue, java.lang.String alphabeticProperty, java.lang.String ideographicProperty, java.lang.String phoneticProperty)
static void	main(java.lang.String[] arg) Read a DICOM dataset and write a JSON representation of it to the standard output or specified path, or vice versa.
protected static java.lang.String	substituteKeywordForUIDIfPossible(java.lang.String value)
protected static java.lang.String	substituteKeywordForUIDIfPossibleAndAppropriateForVRAndRequested(java.lang.String value, byte[] vr, boolean substitute)
protected static java.lang.String	substituteKeywordForUIDIfPossibleAndRequested(java.lang.String value, boolean substitute)
protected static java.lang.String	substituteUIDForKeywordIfPossible(java.lang.String value)
protected static java.lang.String	substituteUIDForKeywordIfPossibleAndAppropriateForVR(java.lang.String value, byte[] vr)
static void	write(java.io.File outputFile, javax.json.JsonArray document) Serialize a JSON document.
static void	write(java.io.OutputStream out, javax.json.JsonArray document) Serialize a JSON document.
static void	write(java.lang.String outputPath, javax.json.JsonArray document) Serialize a JSON document.

Methods inherited from class java.lang.Object

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

Field Detail

reservedKeywordForPersonNameAlphabeticPropertyInJsonRepresentation

protected static java.lang.String reservedKeywordForPersonNameAlphabeticPropertyInJsonRepresentation

reservedKeywordForPersonNameIdeographicPropertyInJsonRepresentation

protected static java.lang.String reservedKeywordForPersonNameIdeographicPropertyInJsonRepresentation

reservedKeywordForPersonNamePhoneticPropertyInJsonRepresentation

protected static java.lang.String reservedKeywordForPersonNamePhoneticPropertyInJsonRepresentation

Constructor Detail

JSONRepresentationOfDicomObjectFactory

public JSONRepresentationOfDicomObjectFactory()

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

Method Detail

addPersonNameAsComponentsToJsonObject

public static void addPersonNameAsComponentsToJsonObject(javax.json.JsonObjectBuilder jsonPersonNameValue,
                                                         java.lang.String value,
                                                         java.lang.String alphabeticProperty,
                                                         java.lang.String ideographicProperty,
                                                         java.lang.String phoneticProperty)

Parameters:

jsonPersonNameValue -

value -

alphabeticProperty -

ideographicProperty -

phoneticProperty -

createDocumentAndWriteIt

public static void createDocumentAndWriteIt(AttributeList list,
                                            java.io.File outputFile)
                                     throws java.io.IOException,
                                            DicomException

Serialize a JSON document created from a DICOM attribute list.

Parameters:

list - the list of DICOM attributes

outputFile - the output file to write to

Throws:

java.io.IOException

DicomException

createDocumentAndWriteIt

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

Serialize a JSON document created from a DICOM attribute list.

Parameters:

list - the list of DICOM attributes

out - the output stream to write to

Throws:

DicomException

createDocumentAndWriteIt

public static void createDocumentAndWriteIt(AttributeList list,
                                            java.lang.String outputPath)
                                     throws java.io.IOException,
                                            DicomException

Serialize a JSON document created from a DICOM attribute list.

Parameters:

list - the list of DICOM attributes

outputPath - the output path to write to

Throws:

java.io.IOException

DicomException

getAttributeList

public AttributeList getAttributeList(java.io.File file)
                               throws java.io.IOException,
                                      DicomException

Given a DICOM instance encoded as a JSON document in a file convert it to a list of attributes.

Parameters:

file - the input file containing the JSON document

Returns:

the list of DICOM attributes

Throws:

java.io.IOException

DicomException

getAttributeList

public AttributeList getAttributeList(java.io.InputStream stream)
                               throws java.io.IOException,
                                      DicomException

Given a DICOM instance encoded as a JSON document in a stream convert it to a list of attributes.

Parameters:

stream - the input stream containing the JSON document

Returns:

the list of DICOM attributes

Throws:

java.io.IOException

DicomException

getAttributeList

public AttributeList getAttributeList(javax.json.JsonArray document)
                               throws DicomException

Given a DICOM instance encoded as a JSON document convert it to a list of attributes.

Parameters:

document - the JSON document

Returns:

the list of DICOM attributes

Throws:

DicomException

getAttributeList

public AttributeList getAttributeList(javax.json.JsonArray document,
                                      boolean ignoreUnrecognizedTags,
                                      boolean ignoreSR)
                               throws DicomException

Given a DICOM instance encoded as a JsonObject in JsonArray in a JSON document convert it to a list of attributes.

Parameters:

document - the JSON document

ignoreUnrecognizedTags - whether or not to ignore unrecognized tags (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

ignoreSR - whether or not to ignore SR Content Items (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

Returns:

the list of DICOM attributes

Throws:

DicomException

getAttributeList

public AttributeList getAttributeList(javax.json.JsonObject document)
                               throws DicomException

Given a DICOM instance encoded as a JSON document convert it to a list of attributes.

Parameters:

document - the JSON document

Returns:

the list of DICOM attributes

Throws:

DicomException

getAttributeList

public AttributeList getAttributeList(javax.json.JsonObject topLevelObject,
                                      boolean ignoreUnrecognizedTags,
                                      boolean ignoreSR)
                               throws DicomException

Given a DICOM object encoded in a JSON document convert it to a list of attributes.

Parameters:

topLevelObject - the first object of the array that is the JSON document

ignoreUnrecognizedTags - whether or not to ignore unrecognized tags (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

ignoreSR - whether or not to ignore SR Content Items (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

Returns:

the list of DICOM attributes

Throws:

DicomException

getAttributeList

public AttributeList getAttributeList(java.lang.String name)
                               throws java.io.IOException,
                                      DicomException

Given a DICOM instance encoded as a JSON document in a named file convert it to a list of attributes.

Parameters:

name - the input file containing the JSON document

Returns:

the list of DICOM attributes

Throws:

java.io.IOException

DicomException

getAttributeTagFromHexadecimalGroupElementValues

protected static final AttributeTag getAttributeTagFromHexadecimalGroupElementValues(java.lang.String s)

Parse an AttributeTag represented as an eight character hexadecimal representation as defined for the standard JSON or XML representation.

Hex digits may be upper or lower case (though tthe standard requires upper only).

Returns:

AttributeTag or null if not in expected format

getDocument

public javax.json.JsonArray getDocument(AttributeList list)
                                 throws DicomException

Given a DICOM instance encoded as a list of attributes, get a JSON document.

Parameters:

list - the list of DICOM attributes

Returns:

the JSON document

Throws:

DicomException

getDocument

public javax.json.JsonArray getDocument(AttributeList list,
                                        boolean useKeywordInsteadOfTag,
                                        boolean addTag,
                                        boolean addKeyword,
                                        boolean addVR,
                                        boolean collapseValueArrays,
                                        boolean collapseEmptyToNull,
                                        boolean ignoreSR,
                                        boolean substituteUIDKeywords,
                                        boolean useNumberForIntegerOrDecimalString)
                                 throws DicomException

Given a DICOM instance encoded as a list of attributes, get a JSON document.

Parameters:

list - the list of DICOM attributes

useKeywordInsteadOfTag - use the keyword from the DicomDictionary rather than the hexadecimal tag group and element

addTag - add the hexadecimal group and element as an additional attribute

addKeyword - add the DicomDictionary keyword as an additional attribute

addVR - add the value representation as an additional attribute

collapseValueArrays - whether or not to elide value object and array when a single value and no other objects

collapseEmptyToNull - whether or not to elide empty object as value and send null instead when zero length attribute

ignoreSR - whether or not to ignore SR Content Items (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

substituteUIDKeywords - whether or not to substitute keywords for recognized standard SOP Classes

useNumberForIntegerOrDecimalString - whether or not to use JSON Number instead of JSON String for IS and DS attributes

Returns:

the JSON document

Throws:

DicomException

getDocument

public javax.json.JsonArray getDocument(java.io.File file)
                                 throws java.io.IOException,
                                        DicomException

Given a DICOM instance encoded as a list of attributes, get a JSON document.

Parameters:

file - the DICOM file

Returns:

the JSON document

Throws:

java.io.IOException

DicomException

getDocument

public javax.json.JsonArray getDocument(java.io.File file,
                                        boolean useKeywordInsteadOfTag,
                                        boolean addTag,
                                        boolean addKeyword,
                                        boolean addVR,
                                        boolean collapseValueArrays,
                                        boolean collapseEmptyToNull,
                                        boolean ignoreSR,
                                        boolean substituteUIDKeywords,
                                        boolean useNumberForIntegerOrDecimalString)
                                 throws java.io.IOException,
                                        DicomException

Given a DICOM instance encoded as a list of attributes, get a JSON document.

Parameters:

file - the DICOM file

useKeywordInsteadOfTag - use the keyword from the DicomDictionary rather than the hexadecimal tag group and element

addTag - add the hexadecimal group and element as an additional attribute

addKeyword - add the DicomDictionary keyword as an additional attribute

addVR - add the value representation as an additional attribute

collapseValueArrays - whether or not to elide value object and array when a single value and no other objects

collapseEmptyToNull - whether or not to elide empty object as value and send null instead when zero length attribute

ignoreSR - whether or not to ignore SR Content Items (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

substituteUIDKeywords - whether or not to substitute keywords for recognized standard SOP Classes

useNumberForIntegerOrDecimalString - whether or not to use JSON Number instead of JSON String for IS and DS attributes

Returns:

the JSON document

Throws:

java.io.IOException

DicomException

getDocument

public javax.json.JsonArray getDocument(java.lang.String filename)
                                 throws java.io.IOException,
                                        DicomException

Given a DICOM object encoded as a list of attributes, get a JSON document.

Parameters:

filename - the DICOM file name

Returns:

the JSON document

Throws:

java.io.IOException

DicomException

getDocument

public javax.json.JsonArray getDocument(java.lang.String filename,
                                        boolean useKeywordInsteadOfTag,
                                        boolean addTag,
                                        boolean addKeyword,
                                        boolean addVR,
                                        boolean collapseValueArrays,
                                        boolean collapseEmptyToNull,
                                        boolean ignoreSR,
                                        boolean substituteUIDKeywords,
                                        boolean useNumberForIntegerOrDecimalString)
                                 throws java.io.IOException,
                                        DicomException

Given a DICOM instance encoded as a list of attributes, get a JSON document.

Parameters:

filename - the DICOM file name

useKeywordInsteadOfTag - use the keyword from the DicomDictionary rather than the hexadecimal tag group and element

addTag - add the hexadecimal group and element as an additional attribute

addKeyword - add the DicomDictionary keyword as an additional attribute

addVR - add the value representation as an additional attribute

collapseValueArrays - whether or not to elide value object and array when a single value and no other objects

collapseEmptyToNull - whether or not to elide empty object as value and send null instead when zero length attribute

ignoreSR - whether or not to ignore SR Content Items (e.g., when used with JSONRepresentationOfStructuredReportObjectFactory)

substituteUIDKeywords - whether or not to substitute keywords for recognized standard SOP Classes

useNumberForIntegerOrDecimalString - whether or not to use JSON Number instead of JSON String for IS and DS attributes

Returns:

the JSON document

Throws:

java.io.IOException

DicomException

getJsonPersonNameFromPropertiesInJsonObject

public static java.lang.String getJsonPersonNameFromPropertiesInJsonObject(javax.json.JsonObject jsonObjectValue,
                                                                           java.lang.String alphabeticProperty,
                                                                           java.lang.String ideographicProperty,
                                                                           java.lang.String phoneticProperty)

main

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

Read a DICOM dataset and write a JSON representation of it to the standard output or specified path, or vice versa.

Parameters:

arg - either one input path of the file containing the DICOM/JSON dataset, or a direction argument (toDICOM or toJSON, case insensitive, defaults to toJSON) and an input path, and optionally an output path

substituteKeywordForUIDIfPossible

protected static java.lang.String substituteKeywordForUIDIfPossible(java.lang.String value)

substituteKeywordForUIDIfPossibleAndAppropriateForVRAndRequested

protected static java.lang.String substituteKeywordForUIDIfPossibleAndAppropriateForVRAndRequested(java.lang.String value,
                                                                                                   byte[] vr,
                                                                                                   boolean substitute)

substituteKeywordForUIDIfPossibleAndRequested

protected static java.lang.String substituteKeywordForUIDIfPossibleAndRequested(java.lang.String value,
                                                                                boolean substitute)

substituteUIDForKeywordIfPossible

protected static java.lang.String substituteUIDForKeywordIfPossible(java.lang.String value)

substituteUIDForKeywordIfPossibleAndAppropriateForVR

protected static java.lang.String substituteUIDForKeywordIfPossibleAndAppropriateForVR(java.lang.String value,
                                                                                       byte[] vr)

write

public static void write(java.io.File outputFile,
                         javax.json.JsonArray document)
                  throws java.io.IOException

Serialize a JSON document.

Parameters:

outputFile - the output file to write to

document - the JSON document

Throws:

java.io.IOException

write

public static void write(java.io.OutputStream out,
                         javax.json.JsonArray document)
                  throws java.io.IOException

Serialize a JSON document.

Parameters:

out - the output stream to write to

document - the JSON document

Throws:

java.io.IOException

write

public static void write(java.lang.String outputPath,
                         javax.json.JsonArray document)
                  throws java.io.IOException

Serialize a JSON document.

Parameters:

outputPath - the output path to write to

document - the JSON document

Throws:

java.io.IOException