#import "Anonymization.h"

#import "DCMAttributeTag.h"

#import "AnonymizationViewController.h"

#import "AnonymizationSavePanelController.h"

#import "NSFileManager+N2.h"

#import "NSDictionary+N2.h"

#import "DCMObject.h"

#import "DicomImage.h"

#import "DCMCalendarDate.h"

#import "DicomStudy.h"

#import "DicomSeries.h"

#import "BrowserController.h"

#import "AppController.h"

#import "Wait.h"

#import "DicomFile.h"

#import "DICOMToNSString.h"

#import "XMLController.h"

#import "DicomFileDCMTKCategory.h"

#import "XMLControllerDCMTKCategory.h"

#import "N2Debug.h"

static NSString *templateDicomFile = nil;

@interface AnonymizationPanelRepresentation : NSObject {

NSString* defaultsKey;

id representedObject;

id target;

SEL action;

}

@property(retain) NSString* defaultsKey;

@property(retain) id representedObject;

@property(retain) id target;

@property SEL action;

@implementation AnonymizationPanelRepresentation

@synthesize defaultsKey, representedObject, target, action;

-(void)dealloc {

self.defaultsKey = NULL;

self.representedObject = NULL;

self.target = NULL;

self.action = NULL;

[super dealloc];

}

@implementation Anonymization

+(DCMAttributeTag*)tagFromString:(NSString*)k {

static NSDictionary* oldKeys = [[NSDictionary alloc] initWithObjectsAndKeys:

@"PatientsName", @"Patient's Name",

@"PatientsSex", @"Patient's Sex",

@"PatientID", @"Patient's ID",

@"PatientsWeight", @"Patient's Weight",

@"PatientsAge", @"Patient's Age",

@"ClinicalTrialSponsorName", @"Trial Sponsor Name",

@"PatientsBirthDate", @"Patient's Date of Birth",

@"ClinicalTrialProtocolID", @"Trial Protocol ID",

@"InstitutionName", @"Institution Name",

@"ClinicalTrialProtocolName", @"Trial Protocol Name",

@"StudyID", @"Study ID",

@"ClinicalTrialSiteID", @"Trial Site ID",

@"StudyDate", @"Study Date",

@"ClinicalTrialSiteName", @"Trial Site Name",

@"StudyTime", @"Study Time",

@"ClinicalTrialSubjectReadingID", @"Trial Subject Reading ID",

@"AcquisitionDatetime", @"Aquisition Date/Time",

@"ClinicalTrialSubjectID", @"Trial Subject ID",

@"SeriesDate", @"Series Date",

@"ClinicalTrialTimePointID", @"Trial Time Point ID",

@"SeriesTime", @"Series Time",

@"ClinicalTrialTimePointDescription", @"Trial Time Point Description",

@"InstanceCreationDate", @"Image Date",

@"ClinicalTrialCoordinatingCenterName", @"Trial Coordinating Center Name",

@"InstanceCreationTime", @"Image Time",

@"PerformingPhysiciansName", @"Performing Physician",

@"ReferringPhysiciansName", @"Referring Physician",

@"PhysiciansofRecord", @"Physicians of Record",

@"AccessionNumber", @"AccessionNumber",

NULL];

// older versions of OsiriX stored anonymization descriptors using the spaced keys and linked those with the DICOM tags through tags in the xib views and code.

// here, through the oldKeys dictionary, we support these keys and directly translate them to standard dicom tag names.

NSString* k2 = [oldKeys objectForKey:k];

if (k2) k = k2;

DCMAttributeTag* tag = [DCMAttributeTag tagWithName:k];

if (!tag)

tag = [DCMAttributeTag tagWithTagString:k];

if (!tag)

NSLog(@"Warning: unrecognized DICOM attribute tag %@", k);

return tag;

}

+(NSArray*)tagsValuesArrayFromDictionary:(NSDictionary*)dic {

NSMutableArray* out = [[NSMutableArray alloc] initWithCapacity:dic.count];

for (NSString* k in dic) {

id v = [dic objectForKey:k];

DCMAttributeTag* tag = [self tagFromString:k];

if (!tag)

continue;

if ([v isKindOfClass:[NSNull class]])

v = NULL;

[out addObject:[NSArray arrayWithObjects: tag, v, NULL]]; // if v is null then array contains only 1 object

}

return [out autorelease];

}

+(NSDictionary*)tagsValuesDictionaryFromArray:(NSArray*)arr {

NSMutableDictionary* out = [[NSMutableDictionary alloc] initWithCapacity:arr.count];

for (NSArray* a in arr) {

DCMAttributeTag* tag = [a objectAtIndex:0];

id v = a.count>1? [a objectAtIndex:1] : @"";

NSString* k = tag.name;

if (!k) k = tag.stringValue;

[out setObject:v forKey:k];

}

return [out autorelease];

}

+(NSArray*)tagsArrayFromStringsArray:(NSArray*)strings {

NSMutableArray* out = [NSMutableArray arrayWithCapacity:strings.count];

for (NSString* s in strings) {

DCMAttributeTag* tag = [self tagFromString:s];

if (tag)

[out addObject:tag];

}

return [[out copy] autorelease];

}

+(NSArray*)stringArrayFromTagsArray:(NSArray*)tags {

NSMutableArray* out = [NSMutableArray arrayWithCapacity:tags.count];

for (DCMAttributeTag* tag in tags)

[out addObject:tag.stringValue];

return [[out copy] autorelease];

}

+(BOOL)tagsValues:(NSArray*)a1 isEqualTo:(NSArray*)a2 {

if (a1.count != a2.count)

return NO;

for (NSArray* a in a1) {

DCMAttributeTag* atag = [a objectAtIndex:0];

BOOL found = NO;

for (NSArray* b in a2) {

DCMAttributeTag* btag = [b objectAtIndex:0];

if ([atag isEqual:btag]) {

id aval = a.count>1? [a objectAtIndex:1] : @"";

id bval = b.count>1? [b objectAtIndex:1] : @"";

found = YES;

if (!(aval == bval || [aval isEqual:bval]))

return NO;

}

}

if (!found)

return NO;

}

return YES;

}

#pragma mark Panel

+(NSString*) templateDicomFile

{

return templateDicomFile;

}

+(id)showPanelClass:(Class)c forDefaultsKey:(NSString*)defaultsKey modalForWindow:(NSWindow*)window modalDelegate:(id)delegate didEndSelector:(SEL)sel representedObject:(id)representedObject {

@try

{

[templateDicomFile release];

templateDicomFile = nil;

templateDicomFile = [[[representedObject objectAtIndex: 0] objectAtIndex: [[representedObject objectAtIndex: 0] count]/2] retain];

}

@catch (NSException * e)

{

N2LogExceptionWithStackTrace(e);

}

NSArray* values = [Anonymization tagsValuesArrayFromDictionary:[[NSUserDefaultsController sharedUserDefaultsController] dictionaryForKey:defaultsKey]];

NSArray* tags = [self tagsArrayFromStringsArray:[[NSUserDefaultsController sharedUserDefaultsController] arrayForKey:[NSString stringWithFormat:@"%@All", defaultsKey]]];

AnonymizationPanelController* panelController = [[c alloc] initWithTags:tags values:values];

AnonymizationPanelRepresentation* ro = [[[AnonymizationPanelRepresentation alloc] init] autorelease];

ro.defaultsKey = defaultsKey;

ro.representedObject = representedObject;

ro.target = delegate;

ro.action = sel;

panelController.representedObject = ro;

[NSApp beginSheet:panelController.window modalForWindow:window modalDelegate:self didEndSelector:@selector(panelDidEnd:returnCode:contextInfo:) contextInfo:panelController];

[panelController.window orderFront:self];

if (!delegate)

[NSApp runModalForWindow:panelController.window];

return panelController;

}

+(AnonymizationPanelController*)showPanelForDefaultsKey:(NSString*)defaultsKey modalForWindow:(NSWindow*)window modalDelegate:(id)delegate didEndSelector:(SEL)sel representedObject:(id)representedObject {

return [self showPanelClass:[AnonymizationPanelController class] forDefaultsKey:defaultsKey modalForWindow:window modalDelegate:delegate didEndSelector:sel representedObject:representedObject];

}

+(AnonymizationSavePanelController*)showSavePanelForDefaultsKey:(NSString*)defaultsKey modalForWindow:(NSWindow*)window modalDelegate:(id)delegate didEndSelector:(SEL)sel representedObject:(id)representedObject {

return [self showPanelClass:[AnonymizationSavePanelController class] forDefaultsKey:defaultsKey modalForWindow:window modalDelegate:delegate didEndSelector:sel representedObject:representedObject];

}

+(void)panelDidEnd:(NSPanel*)panel returnCode:(NSInteger)returnCode contextInfo:(void*)contextInfo {

AnonymizationPanelController* panelController = (id)contextInfo;

AnonymizationPanelRepresentation* ro = panelController.representedObject;

if (panelController.end) { // save config

[[NSUserDefaults standardUserDefaults] setObject:[self stringArrayFromTagsArray:panelController.anonymizationViewController.tags] forKey:[NSString stringWithFormat:@"%@All", ro.defaultsKey]];

[[NSUserDefaults standardUserDefaults] setObject:[self tagsValuesDictionaryFromArray:panelController.anonymizationViewController.tagsValues] forKey:ro.defaultsKey];

}

[panel close];

[ro retain];

panelController.representedObject = ro.representedObject;

if (ro.target)

[ro.target performSelector:ro.action withObject:panelController];

else if (panelController.end)

[NSApp stopModal];

else [NSApp abortModal];

[ro release];

[panelController release];

}

#pragma mark Anonymization

+ (NSString*) cleanStringForFile: (NSString*) s

{

s = [s stringByReplacingOccurrencesOfString:@"/" withString:@"-"];

s = [s stringByReplacingOccurrencesOfString:@":" withString:@"-"];

return s;

}

+ (void) error: (NSString*) s

{

NSRunCriticalAlertPanel( NSLocalizedString( @"Error", nil), s, NSLocalizedString( @"OK", nil), nil, nil);

}

+(NSDictionary*)anonymizeFiles:(NSArray*)files dicomImages: (NSArray*) dicomImages toPath:(NSString*)dirPath withTags:(NSArray*)intags

{

if( [files count] != [dicomImages count])

{

NSLog( @"***** anonymizeFiles [files count] != [dicomImages count]");

return nil;

}

NSMutableArray* tags = [NSMutableArray arrayWithCapacity:intags.count];

for (NSArray* intag in intags)

{

DCMAttributeTag* tag = [intag objectAtIndex:0];

id val = intag.count>1? [intag objectAtIndex:1] : NULL;

if ([val isKindOfClass:[NSDate class]])

{

if ([tag.vr isEqualToString:@"DA"]) //Date String

val = [DCMCalendarDate dicomDateWithDate:val];

else if ([tag.vr isEqualToString:@"TM"]) //Time String

val = [DCMCalendarDate dicomTimeWithDate:val];

else if ([tag.vr isEqualToString:@"DT"]) //Date Time

val = [DCMCalendarDate dicomDateTimeWithDicomDate:[DCMCalendarDate dicomDateWithDate:val] dicomTime:[DCMCalendarDate dicomTimeWithDate:val]];

}

else if ([val isKindOfClass:[NSNumber class]])

{

if ([tag.vr isEqualToString:@"DS"]) //Decimal String representing floating point

val = [val stringValue];

else if ([tag.vr isEqualToString:@"IS"]) //Integer String

val = [val stringValue];

}

[tags addObject:[NSArray arrayWithObjects: tag, val, NULL]];

}

NSMutableDictionary* filenameTranslation = [NSMutableDictionary dictionaryWithCapacity:files.count];

NSString* tempDirPath = [dirPath stringByAppendingPathComponent:@".temp"];

@try {

[[NSFileManager defaultManager] confirmDirectoryAtPath:tempDirPath];

}

@catch (NSException *exception) {

[self performSelectorOnMainThread: @selector( error:) withObject: exception.description waitUntilDone: NO];

return nil;

}

Wait *splash = nil;

if( [NSThread isMainThread])

{

splash = [[[Wait alloc] initWithString: NSLocalizedString( @"Processing...", nil)] autorelease];

[[splash progress] setMaxValue: [files count] * 2];

[splash showWindow: self];

[splash setCancel: YES];

}

NSMutableArray* producedFiles = [NSMutableArray arrayWithCapacity: files.count];

if( [[NSUserDefaults standardUserDefaults] boolForKey: @"useDCMTKForAnonymization"])

{

NSInteger fileIndex = 0;

for( NSString* filePath in files)

{

NSAutoreleasePool *pool = [[NSAutoreleasePool alloc] init];

@try

{

NSString* ext = [filePath pathExtension];

if (!ext.length) ext = @"dcm";

NSString* tempFileName = [NSString stringWithFormat:@"%d.%@", (int) fileIndex, ext];

NSString* tempFilePath = [tempDirPath stringByAppendingPathComponent:tempFileName];

[[NSFileManager defaultManager] copyItemAtPath: filePath toPath: tempFilePath byReplacingExisting: YES error: nil];

[filenameTranslation setObject:tempFilePath forKey:filePath];

++fileIndex;

[producedFiles addObject: tempFilePath];

[splash incrementBy: 1];

}

@catch (NSException * e)

{

N2LogExceptionWithStackTrace(e);

}

[pool release];

if( [splash aborted]) break;

}

// Prepare the parameters

NSMutableArray *params = [NSMutableArray arrayWithObjects:@"dcmodify", @"--ignore-errors", nil];

for( NSArray *intag in tags)

{

DCMAttributeTag* tag = [intag objectAtIndex:0];

id val = intag.count>1? [intag objectAtIndex:1] : NULL;

if( val == nil || [[val description] length] == 0)

[params addObjectsFromArray: [NSArray arrayWithObjects: @"-e", [NSString stringWithFormat: @"(%@)", tag.stringValue], nil]];

else

[params addObjectsFromArray: [NSArray arrayWithObjects: @"-i", [NSString stringWithFormat: @"(%@)=%@", tag.stringValue, [val description]], nil]];

}

[params addObjectsFromArray: producedFiles];

@try

{

NSStringEncoding encoding = [NSString encodingForDICOMCharacterSet: [[DicomFile getEncodingArrayForFile: [producedFiles lastObject]] objectAtIndex: 0]];

[XMLController modifyDicom: params encoding: encoding];

for( id loopItem in files)

[[NSFileManager defaultManager] removeFileAtPath: [loopItem stringByAppendingString:@".bak"] handler:nil];

}

@catch (NSException * e)

{

NSLog(@"**** DicomStudy setComment: %@", e);

}

}

else

{

NSInteger fileIndex = 0;

for( NSString* filePath in files)

{

NSAutoreleasePool *pool = [[NSAutoreleasePool alloc] init];

@try

{

NSString* ext = [filePath pathExtension];

if (!ext.length) ext = @"dcm";

NSString* tempFileName = [NSString stringWithFormat:@"%d.%@", (int) fileIndex, ext];

NSString* tempFilePath = [tempDirPath stringByAppendingPathComponent:tempFileName];

[DCMObject anonymizeContentsOfFile:filePath tags:tags writingToFile:tempFilePath];

[filenameTranslation setObject:tempFilePath forKey:filePath];

++fileIndex;

[producedFiles addObject: tempFilePath];

[splash incrementBy: 1];

}

@catch (NSException * e)

{

N2LogExceptionWithStackTrace(e);

}

[pool release];

if( [splash aborted]) break;

}

}

if( [producedFiles count] != [dicomImages count])

{

NSLog( @"***** anonymizeFiles [producedFiles count] != [dicomImages count]");

filenameTranslation = nil;

}

else

{

NSMutableArray* dicomSeries = [NSMutableArray array];

for (int i = 0; i < [dicomImages count]; i++)

{

DicomImage *image = [dicomImages objectAtIndex: i];

@try

{

if (![dicomSeries containsObject:image.series])

[dicomSeries addObject:image.series];

NSString* tempFilePath = [producedFiles objectAtIndex: i];

NSString* ext = [tempFilePath pathExtension];

NSString* fileDirPath = nil;

if( [image.series.study.patientID length] > 0)

fileDirPath = [dirPath stringByAppendingPathComponent: [NSString stringWithFormat: NSLocalizedString( @"Anonymized - %@", nil), [Anonymization cleanStringForFile:image.series.study.patientID]]];

else

fileDirPath = [dirPath stringByAppendingPathComponent: NSLocalizedString( @"Anonymized", nil)];

fileDirPath = [fileDirPath stringByAppendingPathComponent: [Anonymization cleanStringForFile: image.series.study.studyName]];

fileDirPath = [fileDirPath stringByAppendingPathComponent: [Anonymization cleanStringForFile: [NSString stringWithFormat:@"%@ - %@", image.series.name, image.series.id]]];

@try {

[[NSFileManager defaultManager] confirmDirectoryAtPath:fileDirPath];

}

@catch (NSException *exception) {

[self performSelectorOnMainThread: @selector( error:) withObject: exception.description waitUntilDone: NO];

break;

}

NSString* filePath;

NSInteger i = 0;

do

{

++i;

NSString* is = i ? [NSString stringWithFormat:@"-%4.4d", (int) i] : @"";

NSString* fileName = [NSString stringWithFormat:@"IM-%4.4d-%4.4d%@.%@", (int) dicomSeries.count, (int) [image.instanceNumber intValue], is, ext];

filePath = [fileDirPath stringByAppendingPathComponent:fileName];

} while ([[NSFileManager defaultManager] fileExistsAtPath:filePath]);

[[NSFileManager defaultManager] moveItemAtPath:tempFilePath toPath:filePath error:NULL];

NSString* k = [filenameTranslation keyForObject:tempFilePath];

if (k) [filenameTranslation setObject:filePath forKey: k];

else NSLog(@"Warning: anonymization file naming error: unknown original for %@ which should have changed to %@", tempFilePath, filePath);

}

@catch (NSException * e)

{

N2LogExceptionWithStackTrace(e);

}

[splash incrementBy: 1];

}

if( tempDirPath)

[[NSFileManager defaultManager] removeItemAtPath:tempDirPath error:NULL];

}

[splash close];

return [[filenameTranslation copy] autorelease];

}