Class MoveDicomFilesIntoHierarchy

  • Direct Known Subclasses:
    TestHierarchicalFileName.InstanceNumberMoveDicomFilesIntoHierarchy

    public class MoveDicomFilesIntoHierarchy
    extends java.lang.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 Detail

      • defaultHierarchicalFolderName

        protected static java.lang.String defaultHierarchicalFolderName
      • defaultDuplicatesFolderNamePrefix

        protected static java.lang.String defaultDuplicatesFolderNamePrefix
      • folderNamingStrategyToUseIfUnspecified

        protected static int folderNamingStrategyToUseIfUnspecified
      • includeDateTimeInSeriesFolderName

        protected boolean includeDateTimeInSeriesFolderName
      • includeInConcatenationNumberWithInstanceNumber

        protected boolean includeInConcatenationNumberWithInstanceNumber
    • Constructor Detail

      • MoveDicomFilesIntoHierarchy

        public MoveDicomFilesIntoHierarchy()
    • Method Detail

      • processFilesRecursively

        protected static void processFilesRecursively​(java.io.File file,
                                                      java.lang.String suffix)
                                               throws java.lang.SecurityException,
                                                      java.io.IOException,
                                                      DicomException,
                                                      java.security.NoSuchAlgorithmException
        Throws:
        java.lang.SecurityException
        java.io.IOException
        DicomException
        java.security.NoSuchAlgorithmException
      • makePatientLabelFromAttributes

        public java.lang.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 java.lang.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 java.lang.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 java.lang.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 java.lang.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]/SOPInstanceUID.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 java.lang.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 java.lang.String renameFileWithHierarchicalPathFromAttributes​(java.io.File file,
                                                                             AttributeList list,
                                                                             java.lang.String hierarchicalFolderName,
                                                                             java.lang.String duplicatesFolderNamePrefix,
                                                                             int folderNamingStrategy)
                                                                      throws java.io.IOException,
                                                                             DicomException,
                                                                             java.security.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:
        java.io.IOException - if an error occurs renaming the files
        DicomException - if there is an error parsing the attribute list
        java.security.NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
      • renameFileWithHierarchicalPathFromAttributes

        public static java.lang.String renameFileWithHierarchicalPathFromAttributes​(java.io.File file,
                                                                                    AttributeList list,
                                                                                    java.lang.String hierarchicalFolderName,
                                                                                    java.lang.String duplicatesFolderNamePrefix)
                                                                             throws java.io.IOException,
                                                                                    DicomException,
                                                                                    java.security.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:
        java.io.IOException - if an error occurs renaming the files
        DicomException - if there is an error parsing the attribute list
        java.security.NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
      • renameFileWithHierarchicalPathFromAttributes

        public static java.lang.String renameFileWithHierarchicalPathFromAttributes​(java.io.File file,
                                                                                    java.lang.String hierarchicalFolderName,
                                                                                    java.lang.String duplicatesFolderNamePrefix)
                                                                             throws java.io.IOException,
                                                                                    DicomException,
                                                                                    java.security.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:
        java.io.IOException - if an error occurs renaming the files
        DicomException - if there is an error parsing the attribute list
        java.security.NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
      • renameFileWithHierarchicalPathFromAttributes

        public static java.lang.String renameFileWithHierarchicalPathFromAttributes​(java.io.File file)
                                                                             throws java.io.IOException,
                                                                                    DicomException,
                                                                                    java.security.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:
        java.io.IOException - if an error occurs renaming the files
        DicomException - if there is an error parsing the attribute list
        java.security.NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
      • renameFileWithHierarchicalPathFromAttributes

        public static java.lang.String renameFileWithHierarchicalPathFromAttributes​(java.lang.String fileName)
                                                                             throws java.io.IOException,
                                                                                    DicomException,
                                                                                    java.security.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:
        java.io.IOException - if an error occurs renaming the files
        DicomException - if there is an error parsing the attribute list
        java.security.NoSuchAlgorithmException - if there is an error checking duplicate files contain identical content caused by absence of a hash algorithm
      • main

        public static void main​(java.lang.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