Package gov.nih.mipav.view.dialogs

Class JDialogAnonymizeDirectory.AnonymizeDicomDirectories

java.lang.Object

java.lang.Thread

gov.nih.mipav.view.dialogs.JDialogAnonymizeDirectory.AnonymizeDicomDirectories

All Implemented Interfaces:

Runnable

Enclosing class:

JDialogAnonymizeDirectory

public class JDialogAnonymizeDirectory.AnonymizeDicomDirectories
extends Thread

This thread anonymization processes all the Dicom files in the submitted source directories and places them into the submitted destination directory. Note that these selected directories are processed serially.

When one directory is chosen as the source, all anonymized Dicom files in source are placed directly in the destination. Any images in any subdirectories (when chkChildren is selected) are sent into the children of the sub-directories.

More than one submitted source directory will be placed into discrete child directories of the submitted destination directory. As as example, /images/a, /images/b are selected, and /dest is the selected destination directory. They would get put into /dest/a, and /dest/b.

Naming can change the way the destination is made. Selecting a top-level randomisation, will randomate the output directory ofthe selected image directory. This isalong the lines in the above example as /images/a becoming /dest/abcde; and /images/b becoming /dest/12345. Selecting only one input directory will notmakea difference for top-level randomising. Child-directory randomising will give a random name when processing child direcories. this amounts to selecting /images (and recursive processing) and the destination directory /dest,and getting /images/a becoming /dest/abcde, and /images/b becoming /dest/12345.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Thread

Thread.Builder, Thread.State, Thread.UncaughtExceptionHandler

Field Summary

Fields

Modifier and Type	Field	Description
private JDialogAnonymizeDirectory	anonDialog	DOCUMENT ME!
private String	anonymousName	DOCUMENT ME!
private boolean	checkChildren	DOCUMENT ME!
private File[]	destDirs	DOCUMENT ME!
private File	destStub	DOCUMENT ME!
private boolean	doRename	DOCUMENT ME!
private String	genericName	portion of the file name for all anonymized images.
private FileIO	io	DOCUMENT ME!
private String	keyLog	DOCUMENT ME!
private ModelImage	mi	DOCUMENT ME!
private Vector<JTextArea>	notifierList	DOCUMENT ME!
private String	outputLog	DOCUMENT ME!
private int	randomizeTopLevelDir	DOCUMENT ME!
private int	sequence	DOCUMENT ME!
private int	sequenceStart	DOCUMENT ME!
private File[]	srcDirs	DOCUMENT ME!
private boolean	stopThreadRequest	DOCUMENT ME!
private FileWriteOptions	writeOpts	DOCUMENT ME!

Fields inherited from class java.lang.Thread

MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY

Constructor Summary

Constructors

Constructor	Description
AnonymizeDicomDirectories(File[] src, File dest, String aname, int startseq, int toprand, boolean do_rename)	sets up the anonymizer thread.

Method Summary

Modifier and Type	Method	Description
void	addProcessLoggingNotifier(JTextArea jta)	a list of JTextAreas to be notified when a change in the process/output log is made. this permits almost-real-time updates to output devices this method adds the selected list of JTextAreas to receieve the output logs.
private boolean	anonymizeImage(File imageFile, File destinationDirectory, int[] randomSuffixList, int numberOfSuffices)	actually does the grunt-work of reading the designaated image-file, anonymizing it, and writing the file to the deisgnated destination directory.
private boolean	exists(int rnum, int[] rlist, int rnumptr)	Checks for the existance of the number rnum in the unsorted array rlist.
private String	generateAnonymousName()	creates a string to use as a name out of the generic name, and the sequence.
String	getKeyLog()	provides the string key of translations between source filename and destination filename.
String	getProcessLog()	provides the string key of translations between source filename and destination filename.
private Vector<FileDicomSQItem>	getSequenceTags(ModelImage image)
private void	logWriting(File f)	convienience method to add the filename to the log-string.
private void	notifyProcessLogs(String logtext)	called when an update is made to the output log, this method updates all the process logging JTextAreas.
private void	processMainDirectory(File sourceDirectory, File destinationDirectory)	opens top-level image directory. anonymizes the images in the top directory, when the class has been set to dig in recursively, anonymizes the top directories and calls openSubDirectory(...) to anonymize the files below.
private void	processSubDirectory(File destParentDirectory, File sourceParentDirectory)	traverses the directory, anonymizing as it goes. the child directories are named after the source child-directory, and attempted to traverse (by calling processSubDirectory(File dest, File src)).
void	run()	Specified by Thread. processes each directory selected directory, pausing after processing each selected directory to allow other threads run.
void	setCheckChildren(boolean chk)	tells the anonymizer to check and anonymize the child directories of the selected source directories.
void	setFinishNotification(JDialogAnonymizeDirectory jsa)	no real need for complete listener capabilities, so this is to take its place.
private void	setGenericName(String aname, int seqStart)	sets the genericname, and the start sequence to use when generating the anonymousname.
void	stopProcess()	stopping a thread prematurely is a co-operative process where the Thread checks for a stop-flag periodically, and stops itself by coming to the end of its run() method early.
private void	writeToKey(String original, String newKey)	appends the original string, then two tabs then the newKey, followed by a newline to the keylog. old keylog is not overwritten.
private void	writeToLog(String anon_name)	appends the name string, in between parens trailed by a colon.
private void	writeToLog(String logappendage, boolean completeString)	Method to append the string to the log, adding a newline to the end, if requested, and appending a colon when not adding a newline.

Methods inherited from class java.lang.Thread

activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, isVirtual, join, join, join, join, ofPlatform, ofVirtual, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, sleep, start, startVirtualThread, stop, suspend, threadId, toString, yield

Methods inherited from class java.lang.Object

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

Field Details

anonDialog

private JDialogAnonymizeDirectory anonDialog

DOCUMENT ME!

anonymousName

private String anonymousName

DOCUMENT ME!

checkChildren

private boolean checkChildren

DOCUMENT ME!

destDirs

private File[] destDirs

DOCUMENT ME!

destStub

private File destStub

DOCUMENT ME!

doRename

private boolean doRename

DOCUMENT ME!

genericName

private String genericName

portion of the file name for all anonymized images.

io

private FileIO io

DOCUMENT ME!

keyLog

private String keyLog

DOCUMENT ME!

mi

private ModelImage mi

DOCUMENT ME!

notifierList

private Vector<JTextArea> notifierList

DOCUMENT ME!

outputLog

private String outputLog

DOCUMENT ME!

randomizeTopLevelDir

private int randomizeTopLevelDir

DOCUMENT ME!

sequence

private int sequence

DOCUMENT ME!

sequenceStart

private int sequenceStart

DOCUMENT ME!

srcDirs

private File[] srcDirs

DOCUMENT ME!

stopThreadRequest

private boolean stopThreadRequest

DOCUMENT ME!

writeOpts

private FileWriteOptions writeOpts

DOCUMENT ME!

Constructor Details

AnonymizeDicomDirectories

AnonymizeDicomDirectories(File[] src,
 File dest,
 String aname,
 int startseq,
 int toprand,
 boolean do_rename)

sets up the anonymizer thread.

Parameters:

src - the list of directories to anonymize. this may be as large or as small as needed

dest - the output directory. when the source-list lists but one file, the destination is the directory provided. If the list is more than one, then the destination is the root of the output directorues. How the output directories are named depends on the boolean, toprand.

aname - the name to use for all images processed.

startseq - number to start the sequence for all names in the sequence of anonymousnames.

toprand - determines which directory to anonymize, if any. When processing a list of more than one source, the top-level directory can be randomized (as if the selected list were the image-directories themselves), or the first sub-directory level of directories (as if the selected directories had held lists of patient directories).

• NO_RANDOM_NAMES indicates no directory names are to be changed.
• RANDOM_DIRECTORY_NAME indicates the top-level is to be randomised,
• RANDOM_SUBDIRECTORY_NAME indicates the first sub-directory level to be randomised.

There is (true has??) no effect when only one level randomised.

do_rename - DOCUMENT ME!

Method Details

addProcessLoggingNotifier

public void addProcessLoggingNotifier(JTextArea jta)

a list of JTextAreas to be notified when a change in the process/output log is made. this permits almost-real-time updates to output devices this method adds the selected list of JTextAreas to receieve the output logs.

Parameters:

jta - DOCUMENT ME!

getKeyLog

public String getKeyLog()

provides the string key of translations between source filename and destination filename. The string is formatted with newlines and tabs seperating the filenames.

Returns:

String the translation Strin as formatted by the anonymizer

getProcessLog

public String getProcessLog()

provides the string key of translations between source filename and destination filename. The string is formatted with newlines and tabs seperating the filenames.

Returns:

String the translation Strin as formatted by the anonymizer

run

public void run()

Specified by Thread. processes each directory selected directory, pausing after processing each selected directory to allow other threads run. Notifies the 'anonDialog' of completion.

Specified by:

run in interface Runnable

Overrides:

run in class Thread

setCheckChildren

public void setCheckChildren(boolean chk)

tells the anonymizer to check and anonymize the child directories of the selected source directories. Default is false;

Parameters:

chk - whether or not to check the child directories.

setFinishNotification

public void setFinishNotification(JDialogAnonymizeDirectory jsa)

no real need for complete listener capabilities, so this is to take its place.

Parameters:

jsa - the anonimizer dialog to notify of the anonymization being complete

stopProcess

public void stopProcess()

stopping a thread prematurely is a co-operative process where the Thread checks for a stop-flag periodically, and stops itself by coming to the end of its run() method early. This co-operative method of premature Thread stop permits the Thread to close any open system resources it needed, and will use the natural death procedures.

In this case, in order to accept death, the Thread must close its open files; it will then back out of its recursion.

anonymizeImage

private boolean anonymizeImage(File imageFile,
 File destinationDirectory,
 int[] randomSuffixList,
 int numberOfSuffices)

actually does the grunt-work of reading the designaated image-file, anonymizing it, and writing the file to the deisgnated destination directory. Note that the anonymous-name is class-public. don't overwrite it! This method contains a list to all the random numbers used in making the image destination due to problems in making File.exists() work correctly without a SecurityManager. (haven't tried WITH a SecurityManager).

Parameters:

imageFile - a File that could be a DICOM image. Non-DICOM images should fail and simply return out of this method without another thought. DIMC images will be processed and saved into the destination directory.

destinationDirectory - a File which is the directory where a processed DICOM image file will be saved.

randomSuffixList - array of ints, which are filled from 0 to max lengh of an unsorted numbers. each of which becomes the random name for the file.

numberOfSuffices - current number of used slots in randomSuffixList. not to be larger than randomSuffixList.length returns boolean if the given image file was properly written to the destination directory, this method returns true. false gets returned if the file either did not get written correctly (which would generate an exception), or if the file was non-DICOM, and was therefor ignored.

Returns:

DOCUMENT ME!

Throws:

IllegalArgumentException - when destinationDirectory.isDirecrtory() returns false

exists

private boolean exists(int rnum,
 int[] rlist,
 int rnumptr)

Checks for the existance of the number rnum in the unsorted array rlist. The elements of rlist exist from rlist[0] to rlist[rnumptr-1]. Of course, if rnumptr is greater than to rlist.length, an ArrayIndexOutOfBoundsException will be thrown. Check for it. This of course means that rnum is not in the full array. This method does not check the array against the length of the array, but rather the number of assigned members, because only a partially-full list would return unpredicatable results.

Parameters:

rnum - number we are interested in finding.

rlist - unsorted array of integers at the bottom elements.

rnumptr - index into the array to stop searching; also, indicates the number of elements with an assigned value.

Returns:

true when rnum is found between rlist[0] and rlist[rlistptr-1]. false when rnum is not in the array.

generateAnonymousName

private String generateAnonymousName()

creates a string to use as a name out of the generic name, and the sequence. When processed, the anonymous name will be genericname_[seq]. the following name will be genericname_[seq+1].

Returns:

the anonymous name.

getSequenceTags

private Vector<FileDicomSQItem> getSequenceTags(ModelImage image)

logWriting

private void logWriting(File f)

convienience method to add the filename to the log-string.

Appends a newline to the file.

Parameters:

f - -- file to note the conversion of the file to log.

notifyProcessLogs

private void notifyProcessLogs(String logtext)

called when an update is made to the output log, this method updates all the process logging JTextAreas.

Parameters:

logtext - DOCUMENT ME!

processMainDirectory

private void processMainDirectory(File sourceDirectory,
 File destinationDirectory)

opens top-level image directory. anonymizes the images in the top directory, when the class has been set to dig in recursively, anonymizes the top directories and calls openSubDirectory(...) to anonymize the files below.

Parameters:

sourceDirectory - DOCUMENT ME!

destinationDirectory - DOCUMENT ME!

processSubDirectory

private void processSubDirectory(File destParentDirectory,
 File sourceParentDirectory)

traverses the directory, anonymizing as it goes. the child directories are named after the source child-directory, and attempted to traverse (by calling processSubDirectory(File dest, File src)).

Parameters:

destParentDirectory - parent directory is the parent directory tree for the destination;

sourceParentDirectory - source name is the name of the source directory name

See Also:

• invalid reference

  JDialogAnonymizeDirectory#processSubDirectory(File, File)

setGenericName

private void setGenericName(String aname,
 int seqStart)

sets the genericname, and the start sequence to use when generating the anonymousname. When processed, the anonymous name will be genericname_[seq]. the following name will be genericname_[seq+1].

Parameters:

aname - the name to use for all images processed.

seqStart - number to start the sequence for all names in the sequence of anonymousnames.

See Also:

• invalid reference

  JDialogAnonymizeDirectory#generateAnonymousName()

writeToKey

private void writeToKey(String original,
 String newKey)

appends the original string, then two tabs then the newKey, followed by a newline to the keylog. old keylog is not overwritten.

Parameters:

original - DOCUMENT ME!

newKey - DOCUMENT ME!

writeToLog

private void writeToLog(String anon_name)

appends the name string, in between parens trailed by a colon. Eg., (anon_name:)". To be used before filtering the tags out of images (as those actions are logged in sequence.)

Parameters:

anon_name - DOCUMENT ME!

writeToLog

private void writeToLog(String logappendage,
 boolean completeString)

Method to append the string to the log, adding a newline to the end, if requested, and appending a colon when not adding a newline. The log is not replaced by the incoming string.

Parameters:

logappendage - string to write to the log

completeString - true writes a newline to the log. false makes this an unfinished string.