Export masks for registration in python

3DIMC.xcodeproj/project.pbxproj

@@ -775,6 +775,7 @@
 		0D6720511E3FF3C800C19663 /* IMCTransformDictController.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = IMCTransformDictController.h; sourceTree = "<group>"; };
 		0D6720521E3FF3C800C19663 /* IMCTransformDictController.m */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.objc; path = IMCTransformDictController.m; sourceTree = "<group>"; };
 		0D6720541E3FF3E400C19663 /* IMCTransformDictController.xib */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = file.xib; path = IMCTransformDictController.xib; sourceTree = "<group>"; };
+		0D6AFD87244288E700B9BF38 /* histoCAT++3D.entitlements */ = {isa = PBXFileReference; lastKnownFileType = text.plist.entitlements; path = "histoCAT++3D.entitlements"; sourceTree = "<group>"; };
 		0D6F4F2A1E473CC200533127 /* libz.tbd */ = {isa = PBXFileReference; lastKnownFileType = "sourcecode.text-based-dylib-definition"; name = libz.tbd; path = usr/lib/libz.tbd; sourceTree = SDKROOT; };
 		0D7CB26B217755F200EA36A5 /* License-AGPL3.0.txt */ = {isa = PBXFileReference; lastKnownFileType = text; path = "License-AGPL3.0.txt"; sourceTree = "<group>"; };
 		0D7CB26F217756EB00EA36A5 /* SOFTWARE CONTRIBUTION AGREEMENT-UZH.doc */ = {isa = PBXFileReference; lastKnownFileType = file; path = "SOFTWARE CONTRIBUTION AGREEMENT-UZH.doc"; sourceTree = "<group>"; };
@@ -1524,6 +1525,7 @@
 		0DB37CD21E304D25002975E2 = {
 			isa = PBXGroup;
 			children = (
+				0D6AFD87244288E700B9BF38 /* histoCAT++3D.entitlements */,
 				0D7CB26F217756EB00EA36A5 /* SOFTWARE CONTRIBUTION AGREEMENT-UZH.doc */,
 				0D7CB26B217755F200EA36A5 /* License-AGPL3.0.txt */,
 				0D57600E1EB9CAC2008CAB94 /* Frameworks */,
@@ -1933,6 +1935,7 @@
 			developmentRegion = English;
 			hasScannedForEncodings = 0;
 			knownRegions = (
+				English,
 				en,
 				Base,
 			);
@@ -2762,6 +2765,7 @@
 				ASSETCATALOG_COMPILER_APPICON_NAME = AppIcon;
 				CLANG_ALLOW_NON_MODULAR_INCLUDES_IN_FRAMEWORK_MODULES = NO;
 				CLANG_ENABLE_MODULES = YES;
+				CODE_SIGN_ENTITLEMENTS = "histoCAT++3D.entitlements";
 				CODE_SIGN_IDENTITY = "";
 				COMBINE_HIDPI_IMAGES = YES;
 				DEVELOPMENT_TEAM = HA3BXXH796;
@@ -2825,6 +2829,7 @@
 				ASSETCATALOG_COMPILER_APPICON_NAME = AppIcon;
 				CLANG_ALLOW_NON_MODULAR_INCLUDES_IN_FRAMEWORK_MODULES = NO;
 				CLANG_ENABLE_MODULES = YES;
+				CODE_SIGN_ENTITLEMENTS = "histoCAT++3D.entitlements";
 				CODE_SIGN_IDENTITY = "";
 				COMBINE_HIDPI_IMAGES = YES;
 				DEVELOPMENT_TEAM = HA3BXXH796;

3DIMC/IMCComputationOnMask.h

@@ -28,6 +28,7 @@
 -(void)addFeaturesFromCellProfiler:(NSURL *)url;
 -(void)extractDataForMask:(NSIndexSet *)computations processedData:(BOOL)rawOrProcessedData;
 -(float *)createImageForMaskWithCellData:(float *)data maskOption:(MaskOption)option maskType:(MaskType)maskType maskSingleColor:(NSColor *)maskSingleColor;
+-(UInt8 *)createImageForCategoricalMaskWithCellDataIndex:(NSUInteger)index maskType:(MaskType)maskType;
 -(CGImageRef)coloredMaskForChannel:(NSInteger)channel color:(NSColor *)color maskOption:(MaskOption)maskOption maskType:(MaskType)maskType maskSingleColor:(NSColor *)maskSingleColor brightField:(BOOL)brightField;
 -(BOOL)hasBackData;
 -(void)saveData;

3DIMC/IMCComputationOnMask.m

@@ -786,6 +786,51 @@ -(float *)createImageForMaskWithCellData:(float *)data maskOption:(MaskOption)op
     return img;
 }
 
+-(UInt8 *)createImageForCategoricalMaskWithCellDataIndex:(NSUInteger)index maskType:(MaskType)maskType{
+    if(!self.mask.mask)
+        return NULL;
+
+    int * copy = copyMask(self.mask.mask, (int)self.mask.imageStack.width, (int)self.mask.imageStack.height);
+    UInt8 * img = calloc(self.mask.imageStack.numberOfPixels, sizeof(UInt8));
+
+    if(self.computedData == NULL)
+        return NULL;
+    float * data = self.computedData[index];
+
+    NSInteger pix = self.mask.imageStack.numberOfPixels;
+
+    for (NSInteger i = 0; i < pix; i++) {
+        if(copy[i] == 0)continue;
+        NSInteger index = abs(copy[i]) - 1;
+
+
+        if(maskType == MASK_ALL_CELL){
+            img[i] = data[index];
+            copy[i] = abs(copy[i]);
+        }
+
+        else if(maskType == MASK_CYT){
+            img[i] = MAX((copy[i] > 0) * data[index], 0);
+            copy[i] = copy[i] > 0?copy[i]:0;
+        }
+
+        else if(maskType == MASK_NUC){
+            img[i] = MAX((copy[i] < 0) * data[index], 0);
+            copy[i] = copy[i] < 0?-copy[i]:0;
+        }
+        else if(maskType == MASK_NUC_PLUS_CYT){
+            img[i] = (copy[i]/abs(copy[i])) * data[index];
+        }
+    }
+
+    for (NSInteger i = 0; i < pix; i++)
+        if(copy[i] == 0)
+            img[i] = 0;
+
+    free(copy);
+    return img;
+}
+
 -(CGImageRef)coloredMaskForChannel:(NSInteger)channel color:(NSColor *)color maskOption:(MaskOption)option maskType:(MaskType)maskType maskSingleColor:(NSColor *)maskSingleColor brightField:(BOOL)brightField{
     if(channel == NSNotFound)
         return NULL;

3DIMC/IMCFileExporter.h

@@ -12,6 +12,7 @@
 @class IMCScrollView;
 @class IMCComputationOnMask;
 @class IMCLoader;
+@class IMCPixelClassification;
 
 @interface IMCFileExporter : NSObject
 
@@ -26,6 +27,9 @@
 //this is a subroutine, but useful to expose
 +(void)writeArrayOfRefImages:(NSArray *)images withTitles:(NSArray *)titles atPath:(NSString *)path in16bits:(BOOL)sixteenBits;//Array of ImageRefs multipage
 
+//Mask saving
++(void)saveMask:(IMCComputationOnMask *)mask channel:(NSInteger)channel path:(NSString *)path;
+
 //JPEG quick saving
 +(void)saveJPEGFromScroll:(IMCScrollView *)scroll withPath:(NSString *)fullPath allOrZoomed:(BOOL)zoomed;
 +(void)copyToClipBoardFromScroll:(IMCScrollView *)scroll allOrZoomed:(BOOL)zoomed;

3DIMC/IMCFileExporter.m

@@ -86,10 +86,8 @@ +(void)writer:(TIFF *)tiff writeBuffer:(unsigned char *)buffer width:(int)width
         TIFFSetField(tiff, TIFFTAG_SUBFILETYPE, FILETYPE_PAGE);
     }
 
-    int bytesPix = 32/bitsPixel;//Improve RCF
-
+    int bytesPix = 8/bitsPixel;//Improve RCF
     for (int i = 0; i < height; i++) {
-
         TIFFWriteScanline(tiff, &buffer[i * width * bytesPix], i, 0);//1 because there is always a leading 0
     }
 
@@ -174,6 +172,21 @@ +(void)saveMultipageTiffAllChannels:(IMCImageStack *)stack path:(NSString *)path
     [IMCFileExporter writeArrayOfRefImages:arr withTitles:stack.channels atPath:path in16bits:YES];
 }
 
++(void)saveMask:(IMCComputationOnMask *)mask channel:(NSInteger)channel path:(NSString *)path{
+
+    UInt8 * bytes = [mask createImageForCategoricalMaskWithCellDataIndex:channel maskType:MASK_ALL_CELL];
+
+    TIFF *writer = TIFFOpen(path.UTF8String, "w");
+
+    NSInteger bitsPerPixel = 8;
+    int samples = 1;
+
+    [self writer:writer writeBuffer:bytes width:(int)mask.mask.imageStack.width height:(int)mask.mask.imageStack.height page:0 bpPixel:(int)bitsPerPixel samplesPerPixel:samples totalPages:1 imageName:[mask.channels objectAtIndex:channel]];
+
+    TIFFClose(writer);
+    free(bytes);
+}
+
 +(NSImage *)getNSImageForIMCScrollView:(IMCScrollView *)scroll zoomed:(BOOL)zoomed{
     NSImage *someImage;
     if(zoomed)

3DIMC/IMCFileWrapper.m

@@ -132,12 +132,17 @@ -(void)populateJsonDictForSingleImageFile:(NSString *)path success:(BOOL *)succe
     }
     else
         imageStack = (IMCImageStack *)self.children.firstObject.children.firstObject;
-    NSLog(@"%@", path);
+
     if([imageStack hasTIFFBackstore]){
         path = [imageStack backStoreTIFFPath];
-        NSLog(@"%@", path);
+
     }
     NSData *data = [NSData dataWithContentsOfFile:path];
+    NSError * error = nil;
+    data = [NSData dataWithContentsOfFile:path options:0 error:&error];
+    if(error)
+        NSLog(@"Error ---- > %@ %@", error, error.userInfo);
+    NSLog(@"%@",data);
     [self loadSingleFiler:imageStack data:data path:path success:success];
 }
 

3DIMC/IMCImageGenerator.m

@@ -700,7 +700,7 @@ +(CGImageRef)imageRefWithArrayOfCGImages:(NSMutableArray *)array width:(NSIntege
             CGImageRef refi = (__bridge CGImageRef)last;
             CGRect framePaint = CGRectMake(0, 0, width, height);
             CGContextDrawImage(canvas, framePaint, refi);
-            CGImageRelease(refi);
+//            CGImageRelease(refi);
         }
 
         //ref = CGBitmapContextCreateImage (canvas); //This leaked a lot changed to...

3DIMC/IMCPixelClassification.m

@@ -127,6 +127,10 @@ -(BOOL)loadMask{
     return NO;
 }
 
+-(BOOL)saveMaskForExternalRegistration{
+    return YES;
+}
+
 -(BOOL)loadNuclearMask{
     if(!self.secondRelativePath)
         self.secondRelativePath =

3DIMC/IMCWorkSpace.mm

@@ -554,6 +554,40 @@ -(IBAction)saveMultiPageTIFFs:(NSButton *)sender{
             }
     }];
 }
+
+-(IBAction)savePixelClassificationsAsTIFFs:(NSButton *)sender{
+
+
+    NSOpenPanel *panel = [NSOpenPanel openPanel];
+    panel.canChooseFiles = NO;
+    panel.canChooseDirectories = YES;
+    panel.canCreateDirectories = YES;
+    [panel beginSheetModalForWindow:self.windowForSheet completionHandler:^(NSInteger result){
+        if (result == NSModalResponseOK)
+            for (IMCComputationOnMask *comp in self.inScopeComputations.copy) {
+                BOOL wasLoaded = comp.isLoaded;
+                if(!wasLoaded)
+                    [comp loadLayerDataWithBlock:nil];
+                while (!comp.isLoaded);
+                if([panel.URL.path isEqualToString:self.dataCoordinator.filePath])
+                {
+                    [General runAlertModalWithMessage:@"Choose a directory different to the main project directory"];
+                }else if(self.channels.selectedRow == NSNotFound){
+                    [General runAlertModalWithMessage:@"One channel must be selected"];
+                }
+                else
+                {
+                    NSLog(@"____");
+                    [IMCFileExporter saveMask:comp channel:self.channels.selectedRow path:[panel.URL.path
+                                   stringByAppendingPathComponent:[comp.mask.imageStack backStoreTIFFPath].lastPathComponent]];
+
+                    if(!wasLoaded)
+                        [comp unLoadLayerDataWithBlock:nil];
+                }
+            }
+    }];
+}
+
 -(IBAction)saveMultiPageTIFFsWithSelected:(NSButton *)sender{
 
     if(![self checkThereIsImageInScopeAndChannelsSelected:YES])

3DIMC/IMCWorkspaceSelector.m

@@ -408,10 +408,12 @@ -(NSMenu *)tableView:(NSTableView *)aTableView menuForRows:(NSIndexSet *)rows{
 
                 NSArray *titles = @[@"Export FCS file...",
                                     @"Add features from Cell Profiler file...",
+                                    @"Save mask..."
                                     //@"Convert to mask"
                                     ];
                 NSArray *selectors = @[@"exportFCSFile...",
                                        @"addFeaturesFromCP:",
+                                       @"savePixelClassificationsAsTIFFs:"
                                     //   @"convertToMask:"
                                     ];
                 [addingTitles addObjectsFromArray:titles];

histoCAT++3D.entitlements

@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict/>
+</plist>