com.pixelmed.apps

Class PseudonymizeAndSequester.OurMediaImporter

java.lang.Object

com.pixelmed.dicom.MediaImporter

com.pixelmed.apps.PseudonymizeAndSequester.OurMediaImporter

Enclosing class:

PseudonymizeAndSequester

protected class PseudonymizeAndSequester.OurMediaImporter
extends MediaImporter

A protected class that actually does all the work of finding and processing the files.

Nested Class Summary

Nested classes/interfaces inherited from class com.pixelmed.dicom.MediaImporter

MediaImporter.MediaImporterWithFileChooserDialogThread, MediaImporter.OurReadTerminationStrategy

Field Summary

Fields inherited from class com.pixelmed.dicom.MediaImporter

logger, mediaDirectoryPath, progressBar, progressBarUpdater, terminateAfterIdentifyingGroup

Constructor Summary

Constructors

Constructor and Description

OurMediaImporter(MessageLogger logger, java.lang.String inputPathName, java.lang.String outputFolderCleanName, java.lang.String outputFolderDirtyName, java.lang.String pseudonymizationControlFileName, java.lang.String pseudonymizationResulttByOriginalPatientIDFileName, java.lang.String pseudonymizationResultByOriginalStudyInstanceUIDFileName, java.lang.String failedFilesFileName, java.lang.String uidMapResultFileName, boolean keepAllPrivate, boolean addContributingEquipmentSequence, boolean keepDescriptors, boolean keepSeriesDescriptors, boolean keepProtocolName, boolean keepPatientCharacteristics, boolean keepDeviceIdentity, boolean keepInstitutionIdentity, int handleDates, int handleStructuredContent) De-identify the DICOM Attributes and pseudonymize them and sequester any files that may have risk of identity leakage.

Method Summary

Modifier and Type	Method and Description
protected void	doSomethingWithDicomFileOnMedia(java.lang.String dicomFileName, java.lang.String inputTransferSyntaxUID, java.lang.String sopClassUID) De-identify the DICOM Attributes and pseudonymize them and sequester if may have risk of identity leakage.
protected void	finish()
protected boolean	isOKToImport(java.lang.String sopClassUID, java.lang.String transferSyntaxUID) Allows all types of DICOM files, images or not, with any Transfer Syntax to be processed

Methods inherited from class com.pixelmed.dicom.MediaImporter

choosePathAndImportDicomFiles, choosePathAndImportDicomFiles, doSomethingWithDicomFileOnMedia, doSomethingWithUnwantedFileOnMedia, getDirectory, importDicomFiles, logLn, main

Methods inherited from class java.lang.Object

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

Constructor Detail

OurMediaImporter

public OurMediaImporter(MessageLogger logger,
                        java.lang.String inputPathName,
                        java.lang.String outputFolderCleanName,
                        java.lang.String outputFolderDirtyName,
                        java.lang.String pseudonymizationControlFileName,
                        java.lang.String pseudonymizationResulttByOriginalPatientIDFileName,
                        java.lang.String pseudonymizationResultByOriginalStudyInstanceUIDFileName,
                        java.lang.String failedFilesFileName,
                        java.lang.String uidMapResultFileName,
                        boolean keepAllPrivate,
                        boolean addContributingEquipmentSequence,
                        boolean keepDescriptors,
                        boolean keepSeriesDescriptors,
                        boolean keepProtocolName,
                        boolean keepPatientCharacteristics,
                        boolean keepDeviceIdentity,
                        boolean keepInstitutionIdentity,
                        int handleDates,
                        int handleStructuredContent)
                 throws java.io.FileNotFoundException,
                        java.io.IOException

De-identify the DICOM Attributes and pseudonymize them and sequester any files that may have risk of identity leakage.

Parameters:

logger -

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

pseudonymizationResulttByOriginalPatientIDFileName - 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

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:

java.io.FileNotFoundException

java.io.IOException

Method Detail

doSomethingWithDicomFileOnMedia

protected void doSomethingWithDicomFileOnMedia(java.lang.String dicomFileName,
                                               java.lang.String inputTransferSyntaxUID,
                                               java.lang.String sopClassUID)

De-identify the DICOM Attributes and pseudonymize them and sequester if may have risk of identity leakage.

Implements the following options of ClinicalTrialsAttributes.removeOrNullIdentifyingAttributes():

keepDescriptors, keepSeriesDescriptors, keepProtocolName, keepPatientCharacteristics, keepDeviceIdentity, keepInstitutionIdentity, ClinicalTrialsAttributes.HandleDates.keep

Also performs AttributeList.removeUnsafePrivateAttributes()

Also performs ClinicalTrialsAttributes.remapUIDAttributes(AttributeList)

The pixel data is not redacted.

The output file is stored in the outputFolderName specified in the constructor and is named ...

Any exceptions encountered during processing are logged to stderr, and processing of the next file will continue.

Overrides:

doSomethingWithDicomFileOnMedia in class MediaImporter

Parameters:

dicomFileName - the fully qualified path name to a DICOM file

inputTransferSyntaxUID - the Transfer Syntax of the Data Set if a DICOM file, from the DICOMDIR or Meta Information Header

sopClassUID - the SOP Class of the Data Set if a DICOM file, from the DICOMDIR or Meta Information Header

finish

protected void finish()
               throws java.io.IOException

Throws:

java.io.IOException

isOKToImport

protected boolean isOKToImport(java.lang.String sopClassUID,
                               java.lang.String transferSyntaxUID)

Allows all types of DICOM files, images or not, with any Transfer Syntax to be processed

Overrides:

isOKToImport in class MediaImporter

Parameters:

sopClassUID -

transferSyntaxUID -

Returns:

true if is suitable