Field Detail

• ourCalledAETitle

  protected static java.lang.String ourCalledAETitle

• failedSet

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

Constructor Detail

• 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

• 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)
                      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

Method Detail

• 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

• 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")