public class JSONRepresentationOfStructuredReportObjectFactory
extends java.lang.Object
A class to encode a representation of a DICOM Structured Report object in a JSON form, suitable for analysis as human-readable text.
Note that JSON 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 JSONRepresentationOfDicomObjectFactory.
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);
JsonArray document = new JSONRepresentationOfStructuredReportObjectFactory().getDocument(sr);
JSONRepresentationOfStructuredReportObjectFactory.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);
JsonArray document = new JSONRepresentationOfStructuredReportObjectFactory().getDocument(sr,list);
JSONRepresentationOfStructuredReportObjectFactory.write(System.out,document);
} catch (Exception e) {
slf4jlogger.error("",e);
}
or even simpler, if there is no further use for the JSON document or the SR tree model:
try {
AttributeList list = new AttributeList();
list.read("dicomsrfile",null,true,true);
JSONRepresentationOfStructuredReportObjectFactory.createDocumentAndWriteIt(list,System.out);
} catch (Exception e) {
slf4jlogger.error("",e);
}
StructuredReport,
JSONRepresentationOfDicomObjectFactory,
XPathQuery,
Document| Constructor and Description |
|---|
JSONRepresentationOfStructuredReportObjectFactory()
Construct a factory object, which can be used to get JSON documents from DICOM objects.
|
| Modifier and Type | Method and Description |
|---|---|
protected void |
addCodedSequenceItemPropertyFromBusinessName(javax.json.JsonObject businessNamePayload,
AttributeList csilist,
AttributeTag tag,
java.lang.String reservedKeywordInBusinessNamesFile) |
static void |
createDocumentAndWriteIt(AttributeList list,
java.io.OutputStream out)
Serialize a JSON document created from a DICOM Structured Report.
|
static void |
createDocumentAndWriteIt(StructuredReport sr,
AttributeList list,
java.io.File outputFile)
Serialize a JSON document created from a DICOM attribute list.
|
static void |
createDocumentAndWriteIt(StructuredReport sr,
AttributeList list,
java.io.OutputStream out)
Serialize a JSON document created from a DICOM attribute list.
|
static void |
createDocumentAndWriteIt(StructuredReport sr,
AttributeList list,
java.lang.String outputPath)
Serialize a JSON document created from a DICOM attribute list.
|
static void |
createDocumentAndWriteIt(StructuredReport sr,
java.io.OutputStream out)
Serialize a JSON document created from a DICOM Structured Report.
|
protected java.lang.String |
determineUnknownRelationshipType(java.lang.String parentValueType,
java.lang.String childValueType,
javax.json.JsonValue childObjectValue) |
protected java.lang.String |
determineUnknownValueType(java.lang.String parentValueType,
javax.json.JsonValue childObjectValue) |
AttributeList |
getAttributeList(java.io.File file)
Given a DICOM SR object encoded as a JSON document in a file
convert it to a list of attributes.
|
AttributeList |
getAttributeList(java.io.InputStream stream)
Given a DICOM SR object encoded as a JSON document in a stream
convert it to a list of attributes.
|
AttributeList |
getAttributeList(javax.json.JsonArray document)
Given a DICOM SR object encoded as a JSON document
convert it to a list of attributes.
|
AttributeList |
getAttributeList(javax.json.JsonObject topLevelObject)
Given a DICOM SR object encoded in a JSON document
convert it to a list of attributes.
|
AttributeList |
getAttributeList(java.lang.String name)
Given a DICOM SR object encoded as a JSON document in a named file
convert it to a list of attributes.
|
javax.json.JsonArray |
getBusinessNamesDocument() |
CodedSequenceItem |
getCodedSequenceItemForBusinessName(java.lang.String businessName,
java.lang.String location,
boolean roleIsAsConceptName) |
CodedSequenceItem |
getCodedSequenceItemForBusinessNameUsedAsConceptName(java.lang.String businessName,
java.lang.String location) |
CodedSequenceItem |
getCodedSequenceItemForBusinessNameUsedAsUnits(java.lang.String businessName,
java.lang.String location) |
CodedSequenceItem |
getCodedSequenceItemForBusinessNameUsedAsValue(java.lang.String businessName,
java.lang.String location) |
protected ContentItem |
getContentItemAndChildrenFromJSONObjectValue(java.lang.String businessName,
CodedSequenceItem concept,
java.lang.String valueType,
java.lang.String relationshipType,
javax.json.JsonValue contentItemValue,
java.lang.String location) |
protected javax.json.JsonObject |
getContentItemAttributesObject(javax.json.JsonArray contentItemAttributesAndChildrenArray) |
javax.json.JsonArray |
getDocument(AttributeList list)
Given a DICOM attribute list encoding a Structured Report, get a JSON document.
|
javax.json.JsonArray |
getDocument(java.io.File file)
Given a DICOM object 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(StructuredReport sr)
Given a DICOM Structured Report, get a JSON document of the content tree only.
|
javax.json.JsonArray |
getDocument(StructuredReport sr,
AttributeList list)
Given a DICOM Structured Report, get a JSON document of the content tree and the top level DICOM elements.
|
protected java.lang.String |
getSingleStringValueOrNullFromJsonContentItemValue(javax.json.JsonValue entry,
java.lang.String valueType,
CodedSequenceItem concept) |
protected java.lang.String |
getSingleStringValueOrNullFromJsonStringOrNumberContentItemValue(javax.json.JsonValue entry,
java.lang.String valueType,
CodedSequenceItem concept) |
protected java.lang.String |
getStringFromSelectedContentItemValue(javax.json.JsonArray contentItemValues,
int which,
java.lang.String what,
java.lang.String valueType,
CodedSequenceItem concept) |
StructuredReport |
getStructuredReport(javax.json.JsonArray document)
Given a DICOM SR object encoded as a JSON document
convert it to a StructuredReport using the content tree and ignoring any header attributes.
|
StructuredReport |
getStructuredReport(javax.json.JsonObject topLevelObject)
Given a DICOM SR object encoded in a JSON document
convert it to a StructuredReport using the content tree and ignoring any header attributes.
|
protected boolean |
haveChildrenForSingleStringOrCodeJsonContentItemValue(javax.json.JsonValue contentItemValue,
javax.json.JsonObject contentItemAttributesObject) |
protected boolean |
isCommonAnnotationAttribute(java.lang.String attributeName) |
void |
loadBusinessNamesDocument(java.io.File file)
Load the business names encoded in a JSON document.
|
void |
loadBusinessNamesDocument(java.io.InputStream stream)
Load the business names encoded in a JSON document.
|
void |
loadBusinessNamesDocument(javax.json.JsonArray document)
Load the business names encoded in a JSON document.
|
void |
loadBusinessNamesDocument(java.lang.String name)
Load the business names encoded in a JSON document.
|
static void |
main(java.lang.String[] arg)
Read a DICOM dataset (that contains a structured report) and write a JSON representation of it to the standard output or specified path, or vice versa.
|
static java.lang.String |
makeBusinessNameFromCodeMeaning(CodedSequenceItem conceptName) |
static java.lang.String |
makeBusinessNameFromCodeMeaning(java.lang.String codeMeaning,
boolean upperCamelCase) |
protected java.lang.String |
selectFromAlternativeRelationshipTypesForBusinessName(java.lang.String childLocation,
java.lang.String childBusinessName,
java.lang.String parentValueType,
java.lang.String childValueType,
java.util.Set<java.lang.String> childRelationshipTypes) |
protected java.lang.String |
selectFromAlternativeValueTypesForBusinessName(java.lang.String childLocation,
java.lang.String childBusinessName,
java.lang.String parentValueType,
java.util.Set<java.lang.String> childValueTypes,
javax.json.JsonValue childObjectValue) |
protected static java.lang.String |
selectTheOtherOfTwoStringsInSet(java.lang.String method,
java.lang.String location,
java.util.Set<java.lang.String> theSet,
java.lang.String doNotWant) |
protected void |
walkTreeBuildingSimplifiedLabelsForReferencedContentItemIdentifiers(ContentItem node,
java.lang.String location)
Walk the tree starting at the specified node.
|
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.
|
protected java.util.Map<java.lang.String,CodedSequenceItem> businessNames
protected static java.lang.String businessNameToUseForAnonymousContentItems
protected static boolean collapseAttributeValueArrays
protected static boolean collapseContentTreeArrays
protected static boolean collapseEmptyToNull
protected ContentItemFactory contentItemFactory
protected java.util.Map<ContentItem,java.lang.String> contentItemIdentifiersByContentItem
protected static boolean elideSeparateContinuityOfContent
protected java.util.Map<java.lang.String,java.lang.String> referencedContentItemIdentifiersBySimplifiedLabel
protected java.util.Map<java.lang.String,java.util.SortedSet<java.lang.String>> relationshipTypesByBusinessName
protected static java.lang.String reservedKeywordFor2DCoordinatesAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordFor3DCoordinatesAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordForAlphabeticPropertyInPersonNameContentItem
protected static java.lang.String reservedKeywordForCodeMeaningInBusinessNamesFile
protected static java.lang.String reservedKeywordForCodeValueInBusinessNamesFile
protected static java.lang.String reservedKeywordForCodingSchemeDesignatorInBusinessNamesFile
protected static java.lang.String reservedKeywordForCodingSchemeVersionInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextGroupExtensionCreatorUIDInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextGroupExtensionFlagInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextGroupLocalVersionInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextGroupVersionInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextIdentifierInBusinessNamesFile
protected static java.lang.String reservedKeywordForContextUIDInBusinessNamesFile
protected static java.lang.String reservedKeywordForContinuityOfContentAttributeInSRFile
protected static java.lang.String reservedKeywordForFiducialUIDAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordForFloatingPointValueAttributeInNumericContentItem
protected static java.lang.String reservedKeywordForGraphicTypeAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordForIdeographicPropertyInPersonNameContentItem
protected static java.lang.String reservedKeywordForLongCodeValueInBusinessNamesFile
protected static java.lang.String reservedKeywordForMappingResourceInBusinessNamesFile
protected static java.lang.String reservedKeywordForMappingResourceNameInBusinessNamesFile
protected static java.lang.String reservedKeywordForMappingResourceUIDInBusinessNamesFile
protected static java.lang.String reservedKeywordForMeasurementUnitsAttributeInNumericContentItem
protected static java.lang.String reservedKeywordForNumericValueQualifierAttributeInNumericContentItem
protected static java.lang.String reservedKeywordForObservationDateTimeAttributeInSRFile
protected static java.lang.String reservedKeywordForObservationUIDAttributeInSRFile
protected static java.lang.String reservedKeywordForPhoneticPropertyInPersonNameContentItem
protected static java.lang.String reservedKeywordForPixelOriginInterpretationAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordForPresentationStateSOPClassUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForPresentationStateSOPInstanceUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForRationalDenominatorAttributeInNumericContentItem
protected static java.lang.String reservedKeywordForRationalNumeratorAttributeInNumericContentItem
protected static java.lang.String reservedKeywordForRealWorldValueMappingSOPClassUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForRealWorldValueMappingSOPInstanceUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForReferencedFrameNumberAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForReferencedFrameOfReferenceUIDAttributeInCoordinatesContentItem
protected static java.lang.String reservedKeywordForReferencedSegmentNumberAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForReferencedSOPClassUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForReferencedSOPInstanceUIDAttributeInCompositeContentItem
protected static java.lang.String reservedKeywordForRelationshipTypeInBusinessNamesFile
protected static java.lang.String reservedKeywordForSimplifiedLabelAttributeInSRFile
protected static java.lang.String reservedKeywordForSimplifiedReferenceToLabelAttributeInSRFile
protected static java.lang.String reservedKeywordForTemplateIdentifierAttributeInSRFile
protected static java.lang.String reservedKeywordForTemplateMappingResourceAttributeInSRFile
protected static java.lang.String reservedKeywordForURNCodeValueInBusinessNamesFile
protected static java.lang.String reservedKeywordForValueTypeInBusinessNamesFile
protected java.util.Map<java.lang.String,java.lang.String> simplifiedLabelByReferencedContentItemIdentifiers
protected int simplifiedLabelCounter
protected static java.lang.String simplifiedLabelPrefix
protected static boolean substituteUIDKeywords
protected static java.lang.String symbolSignifyingReservedKeyword
protected static boolean useNumberForNumericContentItemValue
protected java.util.Map<java.lang.String,java.util.SortedSet<java.lang.String>> valueTypesByBusinessName
public JSONRepresentationOfStructuredReportObjectFactory()
Construct a factory object, which can be used to get JSON documents from DICOM objects.
protected void addCodedSequenceItemPropertyFromBusinessName(javax.json.JsonObject businessNamePayload,
AttributeList csilist,
AttributeTag tag,
java.lang.String reservedKeywordInBusinessNamesFile)
public static void createDocumentAndWriteIt(AttributeList list, java.io.OutputStream out) throws java.io.IOException, DicomException
Serialize a JSON document created from a DICOM Structured Report.
list - the attribute listout - the output stream to write tojava.io.IOExceptionDicomExceptionpublic static void createDocumentAndWriteIt(StructuredReport sr, AttributeList list, java.io.File outputFile) throws java.io.IOException, DicomException
Serialize a JSON document created from a DICOM attribute list.
sr - the Structured Report - may be null if list is not - will build an sr tree modellist - the list of DICOM attributesoutputFile - the output file to write tojava.io.IOExceptionDicomExceptionpublic static void createDocumentAndWriteIt(StructuredReport sr, AttributeList list, java.io.OutputStream out) throws DicomException
Serialize a JSON document created from a DICOM attribute list.
sr - the Structured Report - may be null if list is not - will build an sr tree modellist - the list of DICOM attributesout - the output stream to write toDicomExceptionpublic static void createDocumentAndWriteIt(StructuredReport sr, AttributeList list, java.lang.String outputPath) throws java.io.IOException, DicomException
Serialize a JSON document created from a DICOM attribute list.
sr - the Structured Report - may be null if list is not - will build an sr tree modellist - the list of DICOM attributesoutputPath - the output path to write tojava.io.IOExceptionDicomExceptionpublic static void createDocumentAndWriteIt(StructuredReport sr, java.io.OutputStream out) throws java.io.IOException, DicomException
Serialize a JSON document created from a DICOM Structured Report.
sr - the Structured Reportout - the output stream to write tojava.io.IOExceptionDicomExceptionprotected java.lang.String determineUnknownRelationshipType(java.lang.String parentValueType,
java.lang.String childValueType,
javax.json.JsonValue childObjectValue)
protected java.lang.String determineUnknownValueType(java.lang.String parentValueType,
javax.json.JsonValue childObjectValue)
public AttributeList getAttributeList(java.io.File file) throws java.io.IOException, DicomException
Given a DICOM SR object encoded as a JSON document in a file convert it to a list of attributes.
file - the input file containing the JSON documentjava.io.IOExceptionDicomExceptionpublic AttributeList getAttributeList(java.io.InputStream stream) throws java.io.IOException, DicomException
Given a DICOM SR object encoded as a JSON document in a stream convert it to a list of attributes.
stream - the input stream containing the JSON documentjava.io.IOExceptionDicomExceptionpublic AttributeList getAttributeList(javax.json.JsonArray document) throws DicomException
Given a DICOM SR object encoded as a JSON document convert it to a list of attributes.
document - the JSON documentDicomExceptionpublic AttributeList getAttributeList(javax.json.JsonObject topLevelObject) throws DicomException
Given a DICOM SR object encoded in a JSON document convert it to a list of attributes.
topLevelObject - the first object of the array that is the JSON documentDicomExceptionpublic AttributeList getAttributeList(java.lang.String name) throws java.io.IOException, DicomException
Given a DICOM SR object encoded as a JSON document in a named file convert it to a list of attributes.
name - the input file containing the JSON documentjava.io.IOExceptionDicomExceptionpublic javax.json.JsonArray getBusinessNamesDocument()
public CodedSequenceItem getCodedSequenceItemForBusinessName(java.lang.String businessName, java.lang.String location, boolean roleIsAsConceptName)
public CodedSequenceItem getCodedSequenceItemForBusinessNameUsedAsConceptName(java.lang.String businessName, java.lang.String location)
public CodedSequenceItem getCodedSequenceItemForBusinessNameUsedAsUnits(java.lang.String businessName, java.lang.String location)
public CodedSequenceItem getCodedSequenceItemForBusinessNameUsedAsValue(java.lang.String businessName, java.lang.String location)
protected ContentItem getContentItemAndChildrenFromJSONObjectValue(java.lang.String businessName, CodedSequenceItem concept, java.lang.String valueType, java.lang.String relationshipType, javax.json.JsonValue contentItemValue, java.lang.String location) throws DicomException
DicomExceptionprotected javax.json.JsonObject getContentItemAttributesObject(javax.json.JsonArray contentItemAttributesAndChildrenArray)
public javax.json.JsonArray getDocument(AttributeList list) throws DicomException
Given a DICOM attribute list encoding a Structured Report, get a JSON document.
list - the attribute listDicomExceptionpublic javax.json.JsonArray getDocument(java.io.File file)
throws java.io.IOException,
DicomException
Given a DICOM object encoded as a list of attributes, get a JSON document.
file - the DICOM filejava.io.IOExceptionDicomExceptionpublic 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.
filename - the DICOM file namejava.io.IOExceptionDicomExceptionpublic javax.json.JsonArray getDocument(StructuredReport sr) throws DicomException
Given a DICOM Structured Report, get a JSON document of the content tree only.
sr - the Structured ReportDicomExceptionpublic javax.json.JsonArray getDocument(StructuredReport sr, AttributeList list) throws DicomException
Given a DICOM Structured Report, get a JSON document of the content tree and the top level DICOM elements.
sr - the Structured Report may be null if list is not - will build an sr tree modellist - the attribute list may be null if only the sr content tree is to be addedDicomExceptionprotected java.lang.String getSingleStringValueOrNullFromJsonContentItemValue(javax.json.JsonValue entry,
java.lang.String valueType,
CodedSequenceItem concept)
protected java.lang.String getSingleStringValueOrNullFromJsonStringOrNumberContentItemValue(javax.json.JsonValue entry,
java.lang.String valueType,
CodedSequenceItem concept)
protected java.lang.String getStringFromSelectedContentItemValue(javax.json.JsonArray contentItemValues,
int which,
java.lang.String what,
java.lang.String valueType,
CodedSequenceItem concept)
public StructuredReport getStructuredReport(javax.json.JsonArray document) throws DicomException
Given a DICOM SR object encoded as a JSON document convert it to a StructuredReport using the content tree and ignoring any header attributes.
document - the JSON documentDicomExceptionpublic StructuredReport getStructuredReport(javax.json.JsonObject topLevelObject) throws DicomException
Given a DICOM SR object encoded in a JSON document convert it to a StructuredReport using the content tree and ignoring any header attributes.
topLevelObject - the first object of the array that is the JSON documentDicomExceptionprotected boolean haveChildrenForSingleStringOrCodeJsonContentItemValue(javax.json.JsonValue contentItemValue,
javax.json.JsonObject contentItemAttributesObject)
protected boolean isCommonAnnotationAttribute(java.lang.String attributeName)
public void loadBusinessNamesDocument(java.io.File file)
throws java.io.IOException,
DicomException
Load the business names encoded in a JSON document.
file - the input file containing the JSON documentjava.io.IOExceptionDicomExceptionpublic void loadBusinessNamesDocument(java.io.InputStream stream)
throws java.io.IOException,
DicomException
Load the business names encoded in a JSON document.
stream - the input stream containing the JSON documentjava.io.IOExceptionDicomExceptionpublic void loadBusinessNamesDocument(javax.json.JsonArray document)
throws DicomException
Load the business names encoded in a JSON document.
document - the JSON documentDicomExceptionpublic void loadBusinessNamesDocument(java.lang.String name)
throws java.io.IOException,
DicomException
Load the business names encoded in a JSON document.
name - the input file containing the JSON documentjava.io.IOExceptionDicomExceptionpublic static void main(java.lang.String[] arg)
Read a DICOM dataset (that contains a structured report) and write a JSON representation of it to the standard output or specified path, or vice versa.
arg - either one input path of the file containing the DICOM/JSON dataset and a business name file path to read or write, or a direction argument (toDICOM or toJSON, case insensitive) and an input path and an input or output business name path, and optionally an output pathpublic static java.lang.String makeBusinessNameFromCodeMeaning(CodedSequenceItem conceptName)
public static java.lang.String makeBusinessNameFromCodeMeaning(java.lang.String codeMeaning,
boolean upperCamelCase)
protected java.lang.String selectFromAlternativeRelationshipTypesForBusinessName(java.lang.String childLocation,
java.lang.String childBusinessName,
java.lang.String parentValueType,
java.lang.String childValueType,
java.util.Set<java.lang.String> childRelationshipTypes)
protected java.lang.String selectFromAlternativeValueTypesForBusinessName(java.lang.String childLocation,
java.lang.String childBusinessName,
java.lang.String parentValueType,
java.util.Set<java.lang.String> childValueTypes,
javax.json.JsonValue childObjectValue)
protected static java.lang.String selectTheOtherOfTwoStringsInSet(java.lang.String method,
java.lang.String location,
java.util.Set<java.lang.String> theSet,
java.lang.String doNotWant)
protected void walkTreeBuildingSimplifiedLabelsForReferencedContentItemIdentifiers(ContentItem node, java.lang.String location)
Walk the tree starting at the specified node.
node - location - the dotted numeric string describing the location of the starting nodepublic static void write(java.io.File outputFile,
javax.json.JsonArray document)
throws java.io.IOException
Serialize a JSON document.
outputFile - the output file to write todocument - the JSON documentjava.io.IOExceptionpublic static void write(java.io.OutputStream out,
javax.json.JsonArray document)
throws java.io.IOException
Serialize a JSON document.
out - the output stream to write todocument - the JSON documentjava.io.IOExceptionpublic static void write(java.lang.String outputPath,
javax.json.JsonArray document)
throws java.io.IOException
Serialize a JSON document.
outputPath - the output path to write todocument - the JSON documentjava.io.IOException