com.pixelmed.apps

Class DeidentifyAndRedact.OurMediaImporter

java.lang.Object

com.pixelmed.dicom.MediaImporter

com.pixelmed.apps.DeidentifyAndRedact.OurMediaImporter

Enclosing class:

DeidentifyAndRedact

protected class DeidentifyAndRedact.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

Modifier and Type	Field and Description
protected boolean	canUseBzip

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 outputFolderName, DeidentifyAndRedact.RedactionRegions redactionRegions, boolean decompress, boolean keepAllPrivate, boolean addContributingEquipmentSequence, AttributeList replacementAttributes, java.util.Set<java.lang.String> failedSet) Deidentify both the DICOM Attributes and the Pixel Data using the RedactionRegions specified in the constructor.

Method Summary

Modifier and Type	Method and Description
protected void	doSomethingWithDicomFileOnMedia(java.lang.String dicomFileName, java.lang.String inputTransferSyntaxUID, java.lang.String sopClassUID) Deidentify both the DICOM Attributes and the Pixel Data using the RedactionRegions specified in the constructor.
java.util.Set<java.lang.String>	getFilePathNamesThatFailedToProcess() Get file names that failed to import.
protected boolean	isOKToImport(java.lang.String sopClassUID, java.lang.String transferSyntaxUID) Allows all types of DICOM files, images or not, uncompressed or compressed, with supported Transfer Syntaxes 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

Field Detail

canUseBzip

protected boolean canUseBzip

Constructor Detail

OurMediaImporter

public OurMediaImporter(MessageLogger logger,
                        java.lang.String outputFolderName,
                        DeidentifyAndRedact.RedactionRegions redactionRegions,
                        boolean decompress,
                        boolean keepAllPrivate,
                        boolean addContributingEquipmentSequence,
                        AttributeList replacementAttributes,
                        java.util.Set<java.lang.String> failedSet)

Deidentify both the DICOM Attributes and the Pixel Data using the RedactionRegions specified in the constructor.

Parameters:

logger -

outputFolderName - where to store all the processed output files

redactionRegions - which regions to redact in all the processed files

decompress - decompress JPEG rather than try to avoid loss in unredacted blocks

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

addContributingEquipmentSequence - whether or not to add ContributingEquipmentSequence

replacementAttributes - additional attributes with values to add or replace during de-identification

failedSet - set to add paths of files that failed to import (does not have to be empty; will be added to)

Method Detail

doSomethingWithDicomFileOnMedia

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

Deidentify both the DICOM Attributes and the Pixel Data using the RedactionRegions specified in the constructor.

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)

If the pixel data can be redacted without decompressing it (i.e., for Baseline JPEG), then that will be done, otherwise the pixel data will be decompressed and store in Explicit VR Little Endian Transfer Syntax.

The output file is stored in the outputFolderName specified in the constructor and is named by its SOP Instance UID, a suffix of _Anon" and an extension of ".dcm"

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

getFilePathNamesThatFailedToProcess

public java.util.Set<java.lang.String> getFilePathNamesThatFailedToProcess()

Get file names that failed to import.

Returns:

file names that failed to import (empty if did not fail)

isOKToImport

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

Allows all types of DICOM files, images or not, uncompressed or compressed, with supported Transfer Syntaxes to be processed

Overrides:

isOKToImport in class MediaImporter

Parameters:

sopClassUID -

transferSyntaxUID -

Returns:

true if is suitable