com.pixelmed.apps

Class MergeCompositeContext

java.lang.Object

com.pixelmed.apps.MergeCompositeContext

public class MergeCompositeContext
extends java.lang.Object

A class containing an application for merging the patient composite context of multiple instances for consistency.

Patient identity is determined by being within the same study (having the same Study Instance UID), or referencing each others SOP Instance UIDs.

It is assumed that one patient's instances can only cross-reference those of the same patient and not other patients. If there are no instance cross-references, then no commonality can be established across studies and no contexts are merged across studies.

There is no assumption that any particular patient entity level key is the same (e.g., Patient ID).

Various known dummy values are treated as if they were zero length or absent if conflicting with non-dummy values.

See Also:

MergeCompositeContextForOneEntitySelectively

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MergeCompositeContext.Group
protected class	MergeCompositeContext.OurFirstPassMediaImporter
protected class	MergeCompositeContext.OurSecondPassMediaImporter

Field Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	dstFolderName
protected java.util.Set<MergeCompositeContext.Group>	groups
protected java.util.Map<java.lang.String,MergeCompositeContext.Group>	mapOfSOPInstanceUIDToGroup
protected java.util.Map<java.lang.String,java.lang.String>	mapOfSOPInstanceUIDToStudyInstanceUID
protected java.util.Map<java.lang.String,MergeCompositeContext.Group>	mapOfStudyInstanceUIDToGroup
protected int	nextSequenceNumber
protected java.lang.String	ourAETitle

Constructor Summary

Constructors

Constructor and Description
MergeCompositeContext(java.lang.String[] srcs, java.lang.String dstFolderName, MessageLogger logger) Merge the patient composite context of multiple instances for consistency.
MergeCompositeContext(java.lang.String src, java.lang.String dstFolderName, MessageLogger logger) Merge the patient composite context of multiple instances for consistency.

Method Summary

Modifier and Type	Method and Description
protected MergeCompositeContext.Group	addToGroups(AttributeList list)
protected java.lang.String	dumpGroups()
protected boolean	isNonZeroLengthDummyValue(java.lang.String value)
static void	main(java.lang.String[] arg) Merge the patient composite context of multiple instances for consistency.
protected void	mergeGroups(MergeCompositeContext.Group g1, MergeCompositeContext.Group g2)
protected CompositeInstanceContext	mergePatientContext(MergeCompositeContext.Group group, CompositeInstanceContext newContext)

Methods inherited from class java.lang.Object

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

Field Detail

dstFolderName

protected java.lang.String dstFolderName

groups

protected java.util.Set<MergeCompositeContext.Group> groups

mapOfSOPInstanceUIDToGroup

protected java.util.Map<java.lang.String,MergeCompositeContext.Group> mapOfSOPInstanceUIDToGroup

mapOfSOPInstanceUIDToStudyInstanceUID

protected java.util.Map<java.lang.String,java.lang.String> mapOfSOPInstanceUIDToStudyInstanceUID

mapOfStudyInstanceUIDToGroup

protected java.util.Map<java.lang.String,MergeCompositeContext.Group> mapOfStudyInstanceUIDToGroup

nextSequenceNumber

protected int nextSequenceNumber

ourAETitle

protected java.lang.String ourAETitle

Constructor Detail

MergeCompositeContext

public MergeCompositeContext(java.lang.String[] srcs,
                             java.lang.String dstFolderName,
                             MessageLogger logger)
                      throws java.io.IOException,
                             DicomException

Merge the patient composite context of multiple instances for consistency.

Parameters:

srcs - source folders or DICOMDIRs

dstFolderName - destination folder

logger - logger to send progress, warnings and errors

Throws:

java.io.IOException - if there is a problem reading or writing

DicomException - if there is a problem parsing or extracting required content

MergeCompositeContext

public MergeCompositeContext(java.lang.String src,
                             java.lang.String dstFolderName,
                             MessageLogger logger)
                      throws java.io.IOException,
                             DicomException

Merge the patient composite context of multiple instances for consistency.

Parameters:

src - source folder or DICOMDIR

dstFolderName - destination folder

logger - logger to send progress, warnings and errors

Throws:

java.io.IOException - if there is a problem reading or writing

DicomException - if there is a problem parsing or extracting required content

Method Detail

addToGroups

protected MergeCompositeContext.Group addToGroups(AttributeList list)
                                           throws DicomException

Throws:

DicomException

dumpGroups

protected java.lang.String dumpGroups()

isNonZeroLengthDummyValue

protected boolean isNonZeroLengthDummyValue(java.lang.String value)

main

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

Merge the patient composite context of multiple instances for consistency.

The files are processed in the order in which they are specified on the command line, and when there is a conflict, the first values are used. This can be used to make sure that all PatientIDs, for example are coerced to those first specified.

For example, if a folder of images for multiple patients is specified first, and then a folder of structured reports or presentation states referencing (some of) those images but with different patient level identifiers is specified second, then the latter (the reports or presentation states) will be cooerced to have the same patient context as the former (the images).

Parameters:

arg - array of 2 or more strings - one or more source folder or DICOMDIR (to merge and use as a source of context), and a destination folder

mergeGroups

protected void mergeGroups(MergeCompositeContext.Group g1,
                           MergeCompositeContext.Group g2)

mergePatientContext

protected CompositeInstanceContext mergePatientContext(MergeCompositeContext.Group group,
                                                       CompositeInstanceContext newContext)