com.pixelmed.apps

Class DeidentifyAndRedact

java.lang.Object

com.pixelmed.apps.DeidentifyAndRedact

Direct Known Subclasses:

DeidentifyAndRedactWithOriginalFileName

public class DeidentifyAndRedact
extends java.lang.Object

A class to implement bulk de-identification and redaction of DICOM files.

Development of this class was supported by funding from MDDX Research and Informatics.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected class	DeidentifyAndRedact.OurMediaImporter A protected class that actually does all the work of finding and processing the files.
protected class	DeidentifyAndRedact.RedactionRegions A protected class to store sets of rectangular redaction regions indexed by a String classname.

Field Summary

Fields

Modifier and Type	Field and Description
protected java.util.Set<java.lang.String>	failedSet
protected static java.lang.String	ourCalledAETitle

Constructor Summary

Constructors

Constructor and Description
DeidentifyAndRedact(java.lang.String inputPathName, java.lang.String outputFolderName, java.lang.String redactionControlFileName, boolean decompress, boolean keepAllPrivate) Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.
DeidentifyAndRedact(java.lang.String inputPathName, java.lang.String outputFolderName, java.lang.String redactionControlFileName, boolean decompress, boolean keepAllPrivate, AttributeList replacementAttributes) Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.
DeidentifyAndRedact(java.lang.String inputPathName, java.lang.String outputFolderName, java.lang.String redactionControlFileName, boolean decompress, boolean keepAllPrivate, boolean addContributingEquipmentSequence) Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.
DeidentifyAndRedact(java.lang.String inputPathName, java.lang.String outputFolderName, java.lang.String redactionControlFileName, boolean decompress, boolean keepAllPrivate, boolean addContributingEquipmentSequence, AttributeList replacementAttributes) Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Method Summary

Modifier and Type	Method and Description
java.util.Set<java.lang.String>	getFilePathNamesThatFailedToProcess() Get file names that failed to import.
static void	main(java.lang.String[] arg) Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.
protected 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.

Methods inherited from class java.lang.Object

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

Field Detail

failedSet

protected java.util.Set<java.lang.String> failedSet

ourCalledAETitle

protected static java.lang.String ourCalledAETitle

Constructor Detail

DeidentifyAndRedact

public DeidentifyAndRedact(java.lang.String inputPathName,
                           java.lang.String outputFolderName,
                           java.lang.String redactionControlFileName,
                           boolean decompress,
                           boolean keepAllPrivate)
                    throws DicomException,
                           java.lang.Exception,
                           java.io.IOException

Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Searches the specified input path recursively for suitable files.

If Baseline (sequential 8 bit) JPEG, can either redact without affecting other JPEG blocks or decompress JPEG entirely, redact and recompress (lossy)

For details of the processing, see DeidentifyAndRedact.OurMediaImporter.doSomethingWithDicomFileOnMedia(String,String,String).

For specification of the contents of the redaction control file, see DeidentifyAndRedact.RedactionRegions.

Adds ContributingEquipmentSequence by default.

Parameters:

inputPathName - the path to search for DICOM files

outputFolderName - where to store all the processed output files

redactionControlFileName - 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

Throws:

DicomException

java.io.IOException

java.lang.Exception

DeidentifyAndRedact

public DeidentifyAndRedact(java.lang.String inputPathName,
                           java.lang.String outputFolderName,
                           java.lang.String redactionControlFileName,
                           boolean decompress,
                           boolean keepAllPrivate,
                           AttributeList replacementAttributes)
                    throws DicomException,
                           java.lang.Exception,
                           java.io.IOException

Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Searches the specified input path recursively for suitable files.

If Baseline (sequential 8 bit) JPEG, can either redact without affecting other JPEG blocks or decompress JPEG entirely, redact and recompress (lossy)

For details of the processing, see DeidentifyAndRedact.OurMediaImporter.doSomethingWithDicomFileOnMedia(String,String,String).

For specification of the contents of the redaction control file, see DeidentifyAndRedact.RedactionRegions.

Adds ContributingEquipmentSequence by default.

Parameters:

inputPathName - the path to search for DICOM files

outputFolderName - where to store all the processed output files

redactionControlFileName - 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

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

Throws:

DicomException

java.io.IOException

java.lang.Exception

DeidentifyAndRedact

public DeidentifyAndRedact(java.lang.String inputPathName,
                           java.lang.String outputFolderName,
                           java.lang.String redactionControlFileName,
                           boolean decompress,
                           boolean keepAllPrivate,
                           boolean addContributingEquipmentSequence)
                    throws DicomException,
                           java.lang.Exception,
                           java.io.IOException

Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Searches the specified input path recursively for suitable files.

If Baseline (sequential 8 bit) JPEG, can either redact without affecting other JPEG blocks or decompress JPEG entirely, redact and recompress (lossy)

For details of the processing, see DeidentifyAndRedact.OurMediaImporter.doSomethingWithDicomFileOnMedia(String,String,String).

For specification of the contents of the redaction control file, see DeidentifyAndRedact.RedactionRegions.

Parameters:

inputPathName - the path to search for DICOM files

outputFolderName - where to store all the processed output files

redactionControlFileName - 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

Throws:

DicomException

java.io.IOException

java.lang.Exception

DeidentifyAndRedact

public DeidentifyAndRedact(java.lang.String inputPathName,
                           java.lang.String outputFolderName,
                           java.lang.String redactionControlFileName,
                           boolean decompress,
                           boolean keepAllPrivate,
                           boolean addContributingEquipmentSequence,
                           AttributeList replacementAttributes)
                    throws DicomException,
                           java.lang.Exception,
                           java.io.IOException

Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Searches the specified input path recursively for suitable files.

If Baseline (sequential 8 bit) JPEG, can either redact without affecting other JPEG blocks or decompress JPEG entirely, redact and recompress (lossy)

For details of the processing, see DeidentifyAndRedact.OurMediaImporter.doSomethingWithDicomFileOnMedia(String,String,String).

For specification of the contents of the redaction control file, see DeidentifyAndRedact.RedactionRegions.

Parameters:

inputPathName - the path to search for DICOM files

outputFolderName - where to store all the processed output files

redactionControlFileName - 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

Throws:

DicomException

java.io.IOException

java.lang.Exception

Method Detail

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)

main

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

Read DICOM format image files, de-identify them and apply any specified redactions to the Pixel Data.

Searches the specified input path recursively for suitable files If Baseline (sequential 8 bit) JPEG, can either redact without affecting other JPEG blocks or decompress JPEG entirely, redact and recompress (lossy)

Parameters:

arg - three, four or more parameters, the inputPath (file or folder), outputFolder, redactionControlFile, optionally the redaction method BLOCK|DECOMPRESS (default is BLOCK), optionally whether or not to keep all or just known safe private data elements KEEPALLPRIVATE|KEEPSAFEPRIVATE (default is KEEPSAFEPRIVATE), optionally whether or not to add ContributingEquipmentSequence ADDCONTRIBUTINGEQUIPMENT|DONOTADDCONTRIBUTINGEQUIPMENT (default is ADDCONTRIBUTINGEQUIPMENT), followed by optional pairs of keyword and value attribute replacements (e.g., PatientName "Doe^Jane")

makeOutputFileName

protected 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