Class MoveDicomFilesIntoHierarchy

java.lang.Object
com.pixelmed.dicom.MoveDicomFilesIntoHierarchy
Direct Known Subclasses:
TestHierarchicalFileName.InstanceNumberMoveDicomFilesIntoHierarchy

public class MoveDicomFilesIntoHierarchy extends Object

This class provides a main method that recursively searches the supplied paths for DICOM files and moves them into a folder hierarchy based on their attributes.

Various static utility methods that assist in this operation are also provided, such as to create the hierarchical path name from the attributes, etc., since these may be useful in their own right.

  • Field Details

    • defaultHierarchicalFolderName

      protected static String defaultHierarchicalFolderName
    • defaultDuplicatesFolderNamePrefix

      protected static String defaultDuplicatesFolderNamePrefix
    • folderNamingStrategyToUseIfUnspecified

      protected static int folderNamingStrategyToUseIfUnspecified
    • includeDateTimeInSeriesFolderName

      protected boolean includeDateTimeInSeriesFolderName
    • includeInConcatenationNumberWithInstanceNumber

      protected boolean includeInConcatenationNumberWithInstanceNumber
    • terminateAfterRelationshipGroup

      protected static final AttributeList.ReadTerminationStrategy terminateAfterRelationshipGroup
  • Constructor Details

    • MoveDicomFilesIntoHierarchy

      public MoveDicomFilesIntoHierarchy()
  • Method Details

    • processFilesRecursively

      protected static void processFilesRecursively(File file, String suffix) throws SecurityException, IOException, DicomException, NoSuchAlgorithmException
      Throws:
      SecurityException
      IOException
      DicomException
      NoSuchAlgorithmException
    • makePatientLabelFromAttributes

      public String makePatientLabelFromAttributes(AttributeList list, int folderNamingStrategy)

      Create a patient label based on the DICOM attributes of the form:

      PatientName [PatientID]
      If missing values defaults to
      NONAME [NOID]
      Non-static so that sub-classes can override it.
      Parameters:
      list - list of attributes
      folderNamingStrategy -
      Returns:
      the patient label
    • makeStudyLabelFromAttributes

      public String makeStudyLabelFromAttributes(AttributeList list, int folderNamingStrategy)

      Create a study label based on the DICOM attributes of the form:

      StudyDate StudyTime [StudyID - StudyDescription]
      Non-static so that sub-classes can override it.
      Parameters:
      list - list of attributes
      folderNamingStrategy -
      Returns:
      the study label
    • makeSeriesLabelFromAttributes

      public String makeSeriesLabelFromAttributes(AttributeList list, int folderNamingStrategy)

      Create a series label based on the DICOM attributes of the form:

      Series SeriesNumber [Modality - SeriesDescription]
      Non-static so that sub-classes can override it.
      Parameters:
      list - list of attributes
      folderNamingStrategy -
      Returns:
      the series label
    • makeInstanceLabelFromAttributes

      public String makeInstanceLabelFromAttributes(AttributeList list, int folderNamingStrategy)

      Create an instance label based on the DICOM attributes of the form:

      If no information to create an instance label (the SOPInstanceUID is missing), an empty String is returned.

      SOPInstanceUID.dcm
      Non-static so that sub-classes can override it.
      Parameters:
      list - list of attributes
      folderNamingStrategy -
      Returns:
      the instance label or an empty string
    • makeHierarchicalPathFromAttributes

      public String makeHierarchicalPathFromAttributes(AttributeList list, int folderNamingStrategy)

      Create a folder structure based on the DICOM attributes of the form:

      PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - SeriesDescription]/xxx.dcm

      SeriesNumber is zero padded to three digits to better sort in browser.

      The form of the instance level name is controlled by the folderNamingStrategy parameter.

      If no information to create an instance label (the SOPInstanceUID is missing), an empty String is returned.

      Non-static so that sub-classes can override it and callers can call this method rather than static version that will not use overridden subclasses.
      Parameters:
      list - list of attributes
      folderNamingStrategy -
      Returns:
      the folder structure as a path
    • makeHierarchicalPathFromAttributes

      public static String makeHierarchicalPathFromAttributes(AttributeList list)

      Create a folder structure based on the DICOM attributes of the form:

      PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - SeriesDescription]/SOPInstanceUID.dcm

      SeriesNumber is zero padded to three digits to better sort in browser.

      If no information to create an instance label (the SOPInstanceUID is missing), an empty String is returned.

      Static so will NOT use overridden label methods in sub-classes - use non-static makeHierarchicalPathFromAttributes() if necessary instead.
      Parameters:
      list - list of attributes
      Returns:
      the folder structure as a path
    • renameFileWithHierarchicalPathFromAttributes

      public String renameFileWithHierarchicalPathFromAttributes(File file, AttributeList list, String hierarchicalFolderName, String duplicatesFolderNamePrefix, int folderNamingStrategy) throws IOException, DicomException, NoSuchAlgorithmException

      Rename a DICOM file into a folder hierarchy based on its attributes that are already available.

      Creates a folder structure in the current working directory of the form:

      hierarchicalFolderName/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      The form of the instance level name is controlled by the folderNamingStrategy parameter.

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate duplicatesFolderNamePrefix_n folder.

      Non-static so that sub-classes can override it and callers can call this method rather than static version that will not use overridden subclasses.
      Parameters:
      file - the DICOM file
      list - the attributes of the file (already read in)
      hierarchicalFolderName - where to store the renamed file
      duplicatesFolderNamePrefix - where to store the renamed file if it is a non-identical duplicate of the existing file
      folderNamingStrategy -
      Returns:
      the path to the new file if successful, null if not
      Throws:
      IOException - if an error occurs renaming the files
      DicomException - if there is an error parsing the attribute list
      NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
    • renameFileWithHierarchicalPathFromAttributes

      public static String renameFileWithHierarchicalPathFromAttributes(File file, AttributeList list, String hierarchicalFolderName, String duplicatesFolderNamePrefix) throws IOException, DicomException, NoSuchAlgorithmException

      Rename a DICOM file into a folder hierarchy based on its attributes that are already available.

      Creates a folder structure in the current working directory of the form:

      hierarchicalFolderName/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate duplicatesFolderNamePrefix_n folder.

      Static so will NOT use overridden label methods in sub-classes - use non-static renameFileWithHierarchicalPathFromAttributes() if necessary instead.
      Parameters:
      file - the DICOM file
      list - the attributes of the file (already read in)
      hierarchicalFolderName - where to store the renamed file
      duplicatesFolderNamePrefix - where to store the renamed file if it is a non-identical duplicate of the existing file
      Returns:
      the path to the new file if successful, null if not
      Throws:
      IOException - if an error occurs renaming the files
      DicomException - if there is an error parsing the attribute list
      NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
    • renameFileWithHierarchicalPathFromAttributes

      public static String renameFileWithHierarchicalPathFromAttributes(File file, String hierarchicalFolderName, String duplicatesFolderNamePrefix) throws IOException, DicomException, NoSuchAlgorithmException

      Rename a DICOM file into a folder hierarchy based on its attributes.

      Creates a folder structure in the current working directory of the form:

      hierarchicalFolderName/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate duplicatesFolderNamePrefix_n folder.

      Parameters:
      file - the DICOM file
      hierarchicalFolderName - where to store the renamed file
      duplicatesFolderNamePrefix - where to store the renamed file if it is a non-identical duplicate of the existing file
      Returns:
      the path to the new file if successful, null if not (e.g., if not a DICOM file)
      Throws:
      IOException - if an error occurs renaming the files
      DicomException - if there is an error parsing the attribute list
      NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
    • renameFileWithHierarchicalPathFromAttributes

      public static String renameFileWithHierarchicalPathFromAttributes(File file) throws IOException, DicomException, NoSuchAlgorithmException

      Rename a DICOM file into a folder hierarchy based on its attributes.

      Creates a folder structure in the current working directory of the form:

      Sorted/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate Duplicates_n folder.

      Parameters:
      file - the DICOM file
      Returns:
      the path to the new file if successful, null if not (e.g., if not a DICOM file)
      Throws:
      IOException - if an error occurs renaming the files
      DicomException - if there is an error parsing the attribute list
      NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
    • renameFileWithHierarchicalPathFromAttributes

      public static String renameFileWithHierarchicalPathFromAttributes(String fileName) throws IOException, DicomException, NoSuchAlgorithmException

      Rename a DICOM file into a folder hierarchy based on its attributes.

      Creates a folder structure in the current working directory of the form:

      Sorted/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate Duplicates_n folder.

      Parameters:
      fileName - the DICOM file
      Returns:
      the path to the new file if successful, null if not (e.g., if not a DICOM file)
      Throws:
      IOException - if an error occurs renaming the files
      DicomException - if there is an error parsing the attribute list
      NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
    • main

      public static void main(String[] arg)

      Recursively search the supplied paths for DICOM files and move them into a folder hierarchy based on their attributes.

      Creates a folder structure in the current working directory of the form:

      Sorted/PatientName [PatientID]/StudyDate StudyTime [StudyID - StudyDescription]/Series SeriesNumber [Modality - Series Description]/SOPInstanceUID.dcm

      If the destination file already exists and is identical in content, the original is removed.

      If the destination file already exists and is different in content, it is not overwritten, and the duplicate is moved into a separate Duplicates_n folder.

      Parameters:
      arg - array of one or more file or directory names