com.pixelmed.apps

Class PseudonymizeAndSequester

java.lang.Object

com.pixelmed.apps.PseudonymizeAndSequester

public class PseudonymizeAndSequester
extends java.lang.Object

A class to implement bulk de-identification and pseudonymization of DICOM files with sequesteration of files that may have risk of identity leakage.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	PseudonymizeAndSequester.OurMediaImporter A protected class that actually does all the work of finding and processing the files.

Field Summary

Fields

Modifier and Type	Field and Description
protected static java.util.Date	defaultEarliestDateInSet
protected java.util.Map<java.lang.String,java.util.Date>	earliestDateByOrignalPatientID
protected static java.util.Date	epochForDateModification
protected java.util.Map<java.lang.String,java.lang.String>	newPatientIDByOriginalPatientID
protected java.util.Map<java.lang.String,java.lang.String>	newPatientIDByOriginalStudyInstanceUID
protected java.util.Map<java.lang.String,java.lang.String>	newPatientNameByNewPatientID
protected static java.lang.String	ourCalledAETitle
protected static int	radixForRandomPseudonymousID
protected java.util.Random	random

Constructor Summary

Constructors

Constructor and Description

PseudonymizeAndSequester(java.lang.String inputPathName, java.lang.String outputFolderCleanName, java.lang.String outputFolderDirtyName, java.lang.String pseudonymizationControlFileName, java.lang.String pseudonymizationResultByOriginalPatientIDFileName, java.lang.String pseudonymizationResultByOriginalStudyInstanceUIDFileName, java.lang.String failedFilesFileName, java.lang.String uidMapResultFileName, java.lang.String seed, boolean keepAllPrivate, boolean addContributingEquipmentSequence, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, int handleStructuredContent) Read DICOM format image files, de-identify and pseudonymize them and sequester any files that may have risk of identity leakage.

Method Summary

Modifier and Type	Method and Description
protected static boolean	containsOverlay(AttributeList list)
protected java.lang.String	createNewPseudonymousPatientAndAddToMaps(java.lang.String originalPatientID, java.lang.String originalStudyInstanceUID) Create a new PatientID and PatientName and them to the maps.
protected static boolean	isDirty(AttributeList list)
static void	main(java.lang.String[] arg) Read DICOM format image files, de-identify and pseudonymize them and sequester any files that may have risk of identity leakage.
protected static java.lang.String	makeOutputFileName(java.lang.String outputFolderName, java.lang.String inputFileName, java.lang.String sopInstanceUID) Make a suitable file name to use for a deidentified and redacted input file.
protected void	readPseudonymizationControlFile(java.lang.String pseudonymizationControlFileName) Read a file mapping original PatientID or StudyInstanceUID to new PatientID and PatientName and add them to the maps.
protected void	writePseudonymizationResultByOriginalPatientID(java.io.PrintWriter w)
protected void	writePseudonymizationResultByOriginalStudyInstanceUID(java.io.PrintWriter w)
protected void	writeUIDMapResult(java.io.PrintWriter uidMapResultWriter)

Methods inherited from class java.lang.Object

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

Field Detail

defaultEarliestDateInSet

protected static java.util.Date defaultEarliestDateInSet

earliestDateByOrignalPatientID

protected java.util.Map<java.lang.String,java.util.Date> earliestDateByOrignalPatientID

epochForDateModification

protected static java.util.Date epochForDateModification

newPatientIDByOriginalPatientID

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

newPatientIDByOriginalStudyInstanceUID

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

newPatientNameByNewPatientID

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

ourCalledAETitle

protected static java.lang.String ourCalledAETitle

radixForRandomPseudonymousID

protected static int radixForRandomPseudonymousID

random

protected java.util.Random random

Constructor Detail

PseudonymizeAndSequester

public PseudonymizeAndSequester(java.lang.String inputPathName,
                                java.lang.String outputFolderCleanName,
                                java.lang.String outputFolderDirtyName,
                                java.lang.String pseudonymizationControlFileName,
                                java.lang.String pseudonymizationResultByOriginalPatientIDFileName,
                                java.lang.String pseudonymizationResultByOriginalStudyInstanceUIDFileName,
                                java.lang.String failedFilesFileName,
                                java.lang.String uidMapResultFileName,
                                java.lang.String seed,
                                boolean keepAllPrivate,
                                boolean addContributingEquipmentSequence,
                                boolean keepDescriptors,
                                boolean keepSeriesDescriptors,
                                boolean keepProtocolName,
                                boolean keepPatientCharacteristics,
                                boolean keepDeviceIdentity,
                                boolean keepInstitutionIdentity,
                                int handleDates,
                                int handleStructuredContent)
                         throws DicomException,
                                java.io.FileNotFoundException,
                                java.io.IOException

Read DICOM format image files, de-identify and pseudonymize them and sequester any files that may have risk of identity leakage.

Searches the specified input path recursively for suitable files.

The pseudonymizationControlFileName and pseudonymizationResultFileName files are three columns of tab delimited UTF-8 text, the original PatientID, the new PatientID and the new PatientName.

Parameters:

inputPathName - the path to search for DICOM files

outputFolderCleanName - where to store all the low risk processed output files (must already exist)

outputFolderDirtyName - where to store all the high risk processed output files (must already exist)

pseudonymizationControlFileName - values to use for pseudonymization, may be null or empty in which case random values are used

pseudonymizationResultByOriginalPatientIDFileName - file into which to store pseudonymization by original PatientID performed

pseudonymizationResultByOriginalStudyInstanceUIDFileName - file into which to store pseudonymization by original StudyInstanceUID performed

failedFilesFileName - file into which to store the paths of files that failed to process

uidMapResultFileName - file into which to store the map of original to new UIDs

seed - the initial seed to generate random pseudonymous identifiers, long integer as string or null or zero length if none (for deterministic creation of pseudonyms)

keepAllPrivate - retain all private attributes, not just known safe ones

addContributingEquipmentSequence - whether or not to add ContributingEquipmentSequence

keepDescriptors - if true, keep the text description and comment attributes

keepSeriesDescriptors - if true, keep the series description even if all other descriptors are removed

keepProtocolName - if true, keep protocol name even if all other descriptors are removed

keepPatientCharacteristics - if true, keep patient characteristics (such as might be needed for PET SUV calculations)

keepDeviceIdentity - if true, keep device identity

keepInstitutionIdentity - if true, keep institution identity

handleDates - keep, remove or modify dates and times

handleStructuredContent - keep, remove or modify structured content

Throws:

DicomException

java.io.IOException

java.io.FileNotFoundException

Method Detail

containsOverlay

protected static boolean containsOverlay(AttributeList list)

createNewPseudonymousPatientAndAddToMaps

protected java.lang.String createNewPseudonymousPatientAndAddToMaps(java.lang.String originalPatientID,
                                                                    java.lang.String originalStudyInstanceUID)

Create a new PatientID and PatientName and them to the maps.

Parameters:

originalPatientID - the old PatientID

originalStudyInstanceUID - the old StudyInstanceUID

Returns:

the new PatientID

isDirty

protected static boolean isDirty(AttributeList list)

main

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

Read DICOM format image files, de-identify and pseudonymize them and sequester any files that may have risk of identity leakage.

Searches the specified input path recursively for suitable files The pseudonymizationControlFile and pseudonymizationResultFile are tab delimited with a header row containing either: originalPatientID newPatientID newPatientName or originalStudyInstanceUID newPatientID newPatientName

Parameters:

arg - seven or eight parameters plus options, the inputPath (file or folder), outputFolderClean, outputFolderDirty, pseudonymizationControlFile, pseudonymizationResultByOriginalPatientIDFile, pseudonymizationResultByOriginalStudyInstanceUIDFile, failedFilesFile, uidMapResultFile, and optionally a random seed for deterministic creation of pseudonyms, then various options controlling de-identification

makeOutputFileName

protected static java.lang.String makeOutputFileName(java.lang.String outputFolderName,
                                                     java.lang.String inputFileName,
                                                     java.lang.String sopInstanceUID)
                                              throws java.io.IOException

Make a suitable file name to use for a deidentified and redacted input file.

The default is the UID plus "_Anon.dcm" in the outputFolderName (ignoring the inputFileName).

Override this method in a subclass if a different file name is required.

Parameters:

outputFolderName - where to store all the processed output files

inputFileName - the path to search for DICOM files

sopInstanceUID - the SOP Instance UID of the output file

Throws:

java.io.IOException - if a filename cannot be constructed

readPseudonymizationControlFile

protected void readPseudonymizationControlFile(java.lang.String pseudonymizationControlFileName)
                                        throws java.io.IOException

Read a file mapping original PatientID or StudyInstanceUID to new PatientID and PatientName and add them to the maps.

Type of file is detected based on header line of the form: originalPatientID newPatientID newPatientName or originalStudyInstanceUID newPatientID newPatientName

Parameters:

pseudonymizationControlFileName - the control file, if any

Throws:

java.io.IOException

writePseudonymizationResultByOriginalPatientID

protected void writePseudonymizationResultByOriginalPatientID(java.io.PrintWriter w)

writePseudonymizationResultByOriginalStudyInstanceUID

protected void writePseudonymizationResultByOriginalStudyInstanceUID(java.io.PrintWriter w)

writeUIDMapResult

protected void writeUIDMapResult(java.io.PrintWriter uidMapResultWriter)