com.pixelmed.dicom

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.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	MoveDicomFilesIntoHierarchy.FolderNamingStrategy
protected static class	MoveDicomFilesIntoHierarchy.OurReadTerminationStrategy

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	defaultDuplicatesFolderNamePrefix
protected static String	defaultHierarchicalFolderName
protected static int	folderNamingStrategyToUseIfUnspecified
protected boolean	includeDateTimeInSeriesFolderName
protected boolean	includeInConcatenationNumberWithInstanceNumber
protected static AttributeList.ReadTerminationStrategy	terminateAfterRelationshipGroup

Constructor Summary

Constructors

Constructor and Description
MoveDicomFilesIntoHierarchy()

Method Summary

Modifier and Type	Method and Description
static void	main(String[] arg) Recursively search the supplied paths for DICOM files and move them into a folder hierarchy based on their attributes.
static String	makeHierarchicalPathFromAttributes(AttributeList list) Create a folder structure based on the DICOM attributes of the form:
String	makeHierarchicalPathFromAttributes(AttributeList list, int folderNamingStrategy) Create a folder structure based on the DICOM attributes of the form:
String	makeInstanceLabelFromAttributes(AttributeList list, int folderNamingStrategy) Create an instance label based on the DICOM attributes of the form:
String	makePatientLabelFromAttributes(AttributeList list, int folderNamingStrategy) Create a patient label based on the DICOM attributes of the form:
String	makeSeriesLabelFromAttributes(AttributeList list, int folderNamingStrategy) Create a series label based on the DICOM attributes of the form:
String	makeStudyLabelFromAttributes(AttributeList list, int folderNamingStrategy) Create a study label based on the DICOM attributes of the form:
protected static void	processFilesRecursively(File file, String suffix)
static String	renameFileWithHierarchicalPathFromAttributes(File file) Rename a DICOM file into a folder hierarchy based on its attributes.
static String	renameFileWithHierarchicalPathFromAttributes(File file, AttributeList list, String hierarchicalFolderName, String duplicatesFolderNamePrefix) Rename a DICOM file into a folder hierarchy based on its attributes that are already available.
String	renameFileWithHierarchicalPathFromAttributes(File file, AttributeList list, String hierarchicalFolderName, String duplicatesFolderNamePrefix, int folderNamingStrategy) Rename a DICOM file into a folder hierarchy based on its attributes that are already available.
static String	renameFileWithHierarchicalPathFromAttributes(File file, String hierarchicalFolderName, String duplicatesFolderNamePrefix) Rename a DICOM file into a folder hierarchy based on its attributes.
static String	renameFileWithHierarchicalPathFromAttributes(String fileName) Rename a DICOM file into a folder hierarchy based on its attributes.

Methods inherited from class java.lang.Object

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

Field Detail

defaultDuplicatesFolderNamePrefix

protected static String defaultDuplicatesFolderNamePrefix

defaultHierarchicalFolderName

protected static String defaultHierarchicalFolderName

folderNamingStrategyToUseIfUnspecified

protected static int folderNamingStrategyToUseIfUnspecified

includeDateTimeInSeriesFolderName

protected boolean includeDateTimeInSeriesFolderName

includeInConcatenationNumberWithInstanceNumber

protected boolean includeInConcatenationNumberWithInstanceNumber

terminateAfterRelationshipGroup

protected static final AttributeList.ReadTerminationStrategy terminateAfterRelationshipGroup

Constructor Detail

MoveDicomFilesIntoHierarchy

public MoveDicomFilesIntoHierarchy()

Method Detail

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

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

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

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

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

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

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

processFilesRecursively

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

Throws:

SecurityException

IOException

DicomException

NoSuchAlgorithmException

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(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 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,
                                                                  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(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