/*=========================================================================
 This file is part of the Horos Project (www.horosproject.org)
 
 Horos is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by
 the Free Software Foundation, Êversion 3 of the License.
 
 The Horos Project was based originally upon the OsiriX Project which at the time of
 the code fork was licensed as a LGPL project.  However, not all of the the source-code
 was properly documented and file headers were not all updated with the appropriate
 license terms. The Horos Project, originally was licensed under the  GNU GPL license.
 However, contributors to the software since that time have agreed to modify the license
 to the GNU LGPL in order to be conform to the changes previously made to the
 OsiriX Project.
 
 Horos is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE OR USE. ÊSee the
 GNU Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public License
 along with Horos. ÊIf not, see http://www.gnu.org/licenses/lgpl.html
 
 Prior versions of this file were published by the OsiriX team pursuant to
 the below notice and licensing protocol.
 ============================================================================
 Program: Ê OsiriX
 ÊCopyright (c) OsiriX Team
 ÊAll rights reserved.
 ÊDistributed under GNU - LGPL
 Ê
 ÊSee http://www.osirix-viewer.com/copyright.html for details.
 Ê Ê This software is distributed WITHOUT ANY WARRANTY; without even
 Ê Ê the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
 Ê Ê PURPOSE.
 ============================================================================*/

#ifndef DCMPIX_H_INCLUDED
#define DCMPIX_H_INCLUDED

#import <Foundation/Foundation.h>
#import <Cocoa/Cocoa.h>
#import <Accelerate/Accelerate.h>

#include "options.h"

#define ORIENTATION_SENSIBILITY 0.001

typedef struct {
    double x,y,z;
} XYZ;


#ifdef __cplusplus
extern "C"
{
#endif /*cplusplus*/
    extern XYZ ArbitraryRotate(XYZ p,double theta,XYZ r);
#ifdef __cplusplus
}
#endif /*cplusplus*/


@class ROI;
@class ThickSlabController;
@class DCMObject;
@class Point3D;
@class DicomImage;
@class DicomSeries;
@class DicomStudy;
@class DCMWaveform;
@class DCMTKFileFormat;

/** \brief Represents an image for display */

@interface DCMPix: NSObject <NSCopying>
{
    NSString            *_srcFile;  /**< source File */
    NSString            *URIRepresentationAbsoluteString;
    BOOL				isBonjour;
    BOOL                fileTypeHasPrefixDICOM;
    int                 numberOfFrames;
    
    NSArray				*pixArray;
    NSManagedObjectID	*imageObjectID;	/**< Core data object ID for image */
    float				*fImage /**< float buffer of image Data */, *fExternalOwnedImage;  /**< float buffer of image Data - provided by another source, not owned by this object, not release by this object */
    
    //DICOM TAGS
    
    //	orientation
    BOOL				isOriginDefined;
    double				originX /**< x position of image origin */ , originY /**< y Position of image origin */ , originZ /**< Z position of image origin*/;
    double				orientation[ 9];  /**< pointer to orientation vectors  */
    
    //	pixel representation
    BOOL				fIsSigned;
    short				bitsAllocated, bitsStored;
    long                height, width;
    float               slope, offset;
    
    //	window level & width
    float				savedWL, savedWW;
    
    //	planar configuration
    long				fPlanarConf;
    double				pixelSpacingX, pixelSpacingY, pixelRatio;
    double              estimatedRadiographicMagnificationFactor;
    BOOL				pixelSpacingFromUltrasoundRegions;
    
    //	photointerpretation
    BOOL				isRGB, inverseVal;
    
    //  US Regions
    NSMutableArray      *usRegions;
    
    //  Waveform data
    DCMWaveform         *waveform;
    
    //  image type
    NSString*           imageType;
    
    //--------------------------------------
    
    // DICOM params needed for SUV calculations
    float				patientsWeight;
    
    NSString            *repetitiontime, *echotime, *flipAngle;
    
    NSString			*laterality, *viewPosition, *patientPosition, *acquisitionDate, *SOPClassUID, *frameofReferenceUID, *rescaleType;
    BOOL				hasSUV, SUVConverted, displaySUVValue;
    NSString			*units, *decayCorrection;
    float				decayFactor, factorPET2SUV, radionuclideTotalDose, radionuclideTotalDoseCorrected;
    NSCalendarDate		*acquisitionTime, *radiopharmaceuticalStartTime;
    float				halflife, frameReferenceTime, philipsFactor;
    
    // DICOM params for Overlays - 0x6000 group
    BOOL                overlaysChannelON[16];
    int					oRows[16], oColumns[16], oType[16], oOrigin[16][ 2], oBits[16], oBitPosition[16];
    unsigned char		*oData[16];
    
    //	DSA-subtraction
    float				*subtractedfImage;
    NSPoint				subPixOffset, subMinMax;
    float				subtractedfPercent, subtractedfZ, subtractedfZero, subtractedfGamma;
    GammaFunction		subGammaFunction;
    
    long				maskID;
    float				maskTime, fImageTime;
    
    NSNumber			*positionerPrimaryAngle;
    NSNumber			*positionerSecondaryAngle;
    
    BOOL                shutterEnabled;
    NSRect              shutterRect;
    
    
    NSPoint             shutterCircular;
    long				shutterCircular_radius;
    
    
    NSPoint	 			*shutterPolygonal;
    long				shutterPolygonalSize;
    
    //-------------------------------------------------------
    long				frameNo, serieNo, imID, imTot;
    char                *baseAddr;
    
    //convolution
    BOOL				convolution, updateToBeApplied;
    short				kernelsize;
    float				normalization, kernel[25];
    float				cineRate;
    
    //slice
    double				sliceInterval, sliceLocation, sliceThickness, spacingBetweenSlices;
    
    //stack
    short				stack, stackMode, pixPos, stackDirection;
    //thickslab
    BOOL				thickSlabVRActivated;
    ThickSlabController *thickSlab;
    
    float				countstackMean;
    float				ww, wl;
    float				fullww, fullwl;
    BOOL				fixed8bitsWLWW;
    float               maxValueOfSeries, minValueOfSeries;
    
    BOOL				generated;
    NSString			*generatedName;
    NSRecursiveLock		*checking;
    
    BOOL				notAbleToLoadImage, VOILUTApplied;
    int					VOILUT_first;
    unsigned int		VOILUT_number, VOILUT_depth, *VOILUT_table;
    
    unsigned short *shortRed, *shortGreen, *shortBlue;
    
    char				blackIndex;
    
    NSData				*transferFunction;
    float				*transferFunctionPtr;
    
    /** custom annotations */
    NSMutableDictionary *annotationsDictionary, *annotationsDBFields;
    NSString            *yearOld, *yearOldAcquisition;
    
    /** 12 bit monitors */
    BOOL				isLUT12Bit;
    unsigned char		*LUT12baseAddr;
    
    BOOL				full32bitPipeline;
    BOOL				needToCompute8bitRepresentation;
    
    /** Papyrus Loading variables */
    
    NSString			*modalityString;
    unsigned short		clutEntryR, clutEntryG, clutEntryB;
    unsigned short		clutDepthR, clutDepthG, clutDepthB;
    unsigned char		*clutRed, *clutGreen, *clutBlue;
    BOOL				fSetClut, fSetClut16;
    
    int					savedHeightInDB, savedWidthInDB;
    
    id					retainedCacheGroup;
    
    // Ophtalmic fundus images
    
    NSString            *referencedSOPInstanceUID;
    float               referenceCoordinates[ 4];
    
    DCMTKFileFormat     *dcmtkDcmFileFormat;
}

@property long frameNo;
@property(setter=setID:) long ID;
@property (readonly) NSRecursiveLock *checking;
@property (nonatomic) float minValueOfSeries, maxValueOfSeries, factorPET2SUV;

@property(retain) NSString* imageType, *modalityString, *referencedSOPInstanceUID, *yearOld, *yearOldAcquisition;

// Dimensions in pixels
@property (nonatomic) long pwidth, pheight;

/** Is it an RGB image (ARGB) or float image?
 Note setter is different to not break existing usage. :-( */
@property(nonatomic, setter=setRGB:) BOOL isRGB;

/** Pointer to image data */
@property(setter=setfImage:) float* fImage;

/** WW & WL */
@property(readonly) float ww, wl, fullww, fullwl;
@property(nonatomic) float slope, offset, savedWW, savedWL, *subtractedfImage;

@property(readonly) BOOL notAbleToLoadImage, VOILUTApplied;
@property(readonly) NSPoint *shutterPolygonal;

/**  X/Y ratio - non-square pixels */
@property(nonatomic) double pixelRatio;

/**  pixel size */
@property double pixelSpacingX, pixelSpacingY;

- (BOOL) identicalOrientationTo:(DCMPix*) c;

- (void)orientationDouble:(double*) c;
- (void)setOrientationDouble:(double*) c;

/** Slice location */
@property(readonly) double originX, originY, originZ;
@property(readonly) BOOL isOriginDefined;
@property(retain) NSString *frameofReferenceUID;

- (void)setOrigin :(float*) o;
- (void)setOriginDouble :(double*) o;
- (void)origin: (float*)o;
- (void)originDouble: (double*)o;

/**  Axial Location */
@property double sliceLocation;
/**  Slice Thickness */
@property double sliceThickness;
/**  Slice Interval */
@property double sliceInterval;
/**  Gap between slices */
@property(readonly) double spacingBetweenSlices;

/**  8-bit TransferFunction */
@property(nonatomic, retain) NSData *transferFunction;

@property(nonatomic) NSPoint subPixOffset;

@property(nonatomic) BOOL shutterEnabled;
@property(nonatomic) NSRect shutterRect;

@property(retain) NSString *repetitiontime, *echotime;
@property(readonly) NSString *flipAngle;

@property(readonly) NSString *laterality, *viewPosition, *patientPosition;

@property char* baseAddr;
@property unsigned char* LUT12baseAddr;

@property(readonly) long serieNo;
@property(readonly) NSArray *pixArray;
@property(readonly) float *transferFunctionPtr;
@property short pixPos;
@property short stackDirection;
@property float countstackMean;

@property(getter=Tot, setter=setTot:) long Tot;

@property(readonly) short stack, stackMode;
@property(readonly) BOOL generated;
@property(retain) NSString *generatedName;

@property(strong) NSString *srcFile;
- (NSString *)sourceFile __deprecated;
- (void)setSourceFile:(NSString *)sf __deprecated;

@property(readonly) unsigned int* VOILUT_table;

/** Database links */
@property(retain) NSManagedObjectID *imageObjectID;
@property(retain) NSString *SOPClassUID;
@property(retain) NSMutableDictionary *annotationsDictionary, *annotationsDBFields;

// Properties (aka accessors) needed for SUV calculations
@property(readonly) float philipsFactor;
@property float patientsWeight, halflife, radionuclideTotalDose, radionuclideTotalDoseCorrected;
@property(retain) NSCalendarDate *acquisitionTime;
@property(copy) NSString *acquisitionDate, *rescaleType;
@property(retain) NSCalendarDate *radiopharmaceuticalStartTime;
@property BOOL SUVConverted, needToCompute8bitRepresentation;

@property BOOL full32bitPipeline;
@property(retain) DCMTKFileFormat *dcmtkDcmFileFormat;

@property(readonly) BOOL hasSUV;
@property float decayFactor;
@property(retain) NSString *units, *decayCorrection;
@property BOOL displaySUVValue;
@property BOOL isLUT12Bit;

// Waveform
@property(readonly,strong) DCMWaveform* waveform;

// US Regions
@property(readonly) NSMutableArray *usRegions;
-(BOOL) hasUSRegions;

- (float) appliedFactorPET2SUV;
- (void) copySUVfrom: (DCMPix*) from;  /**< Copy the SUV from another DCMPic */
- (float) getPixelValueX: (long) x Y:(long) y;  /**< Get the pixel for a point with x,y coordinates */

- (void) checkSUV; /**< Makes sure all the necessary values for SUV calculation are present */

+ (void) checkUserDefaults: (BOOL) update;  /**< Check User Default for needed setting */
+ (void) resetUserDefaults;  /**< Reset the defaults */
/** Determine if a point is inside a polygon
 * @param x is the NSPoint to check.
 * @param  poly is a pointer to an array of NSPoints.
 * @param count is the number of
 * points in the polygon.
 */
+ (BOOL) IsPoint:(NSPoint) x inPolygon:(NSPoint*) poly size:(int) count;

- (void) compute8bitRepresentation;
- (void) changeWLWW:(float)newWL :(float)newWW;  /**< Change window level to window width to the new values */
- (void) computePixMinPixMax;  /**< Compute the min and max values in the image */

// Compute ROI data
/** Calculates the cofactor used Calcium scoring.
 * Depends on the threshold used for scoring
 * Threshold is usually 90 or 120 depending on whether the source is
 * Electron Beam or Multislice CT
 */
- (int)calciumCofactorForROI:(ROI *)roi threshold:(int)threshold;

/** returns calculated values for ROI:
 *  mean, total, deviation, min, max
 */
- (void) computeROI:(ROI*) roi :(float *)mean :(float *)total :(float *)dev :(float *)min :(float *)max :(float*) skewness :(float*) kurtosis;
- (void) computeROI:(ROI*) roi :(float *)mean :(float *)total :(float *)dev :(float *)min :(float *)max;

/** Fill a ROI with a value
 * @param roi  Selected ROI
 * @param newVal  The replacement value
 * @param minValue  Lower threshold
 * @param maxValue Upper threshold
 * @param outside  if YES replace outside the ROI
 * @param orientationStack
 * @param stackNo
 * @param restore
 * @param addition
 */
- (void) fillROI:(ROI*) roi newVal:(float) newVal minValue:(float) minValue maxValue:(float) maxValue outside:(BOOL) outside orientationStack:(long) orientationStack stackNo:(long) stackNo restore:(BOOL) restore addition:(BOOL) addition;
- (void) fillROI:(ROI*) roi newVal:(float) newVal minValue:(float) minValue maxValue:(float) maxValue outside:(BOOL) outside orientationStack:(long) orientationStack stackNo:(long) stackNo restore:(BOOL) restore addition:(BOOL) addition spline:(BOOL) spline;
- (void) fillROI:(ROI*) roi newVal :(float) newVal minValue :(float) minValue maxValue :(float) maxValue outside :(BOOL) outside orientationStack :(long) orientationStack stackNo :(long) stackNo restore :(BOOL) restore addition:(BOOL) addition spline:(BOOL) spline clipMin: (NSPoint) clipMin clipMax: (NSPoint) clipMax;

/** Fill a ROI with a value
 * @param roi  Selected ROI
 * @param newVal  The replacement value
 * @param minValue  lower threshold
 * @param maxValue  upper threshold
 * @param outside  if YES replace outside the ROI
 * @param orientationStack  ?
 * @param  stackNo
 * @param  restore
 */
- (void) fillROI:(ROI*) roi :(float) newVal :(float) minValue :(float) maxValue :(BOOL) outside :(long) orientationStack :(long) stackNo :(BOOL) restore;

/** Fill a ROI with a value
 * @param roi  Selected ROI
 * @param newVal  The replacement value
 * @param minValue  lower threshold
 * @param maxValue  upper threshold
 * @param outside  if YES replace outside the ROI
 * @param orientation
 * @param stackNo
 */
- (void) fillROI:(ROI*) roi :(float) newVal :(float) minValue :(float) maxValue :(BOOL) outside :(long) orientation :(long) stackNo;

/** Fill a ROI with a value.
 * @param roi Selected ROI
 * @param newVal  The replacement value
 * @param minValue  Lower threshold
 * @param maxValue  Upper threshold
 * @param outside  If YES replace outside the ROI
 */
- (void) fillROI:(ROI*) roi :(float) newVal :(float) minValue :(float) maxValue :(BOOL) outside;

- (unsigned char*) getMapFromPolygonROI:(ROI*) roi size:(NSSize*) size origin:(NSPoint*) origin; /**< Map from Polygon ROI */
+ (unsigned char*) getMapFromPolygonROI:(ROI*) roi size:(NSSize*) size origin:(NSPoint*) ROIorigin;

/** Is this Point (pt) in this ROI ? */
- (BOOL) isInROI:(ROI*) roi :(NSPoint) pt;

/** Returns a pointer with all pixels values contained in the current ROI
 * User must Free the pointer with the free() function
 * Returns reference number of pixels in numberOfValues
 * Returns a pointer to the pixel locations. Each point has the x position followed by the y position
 * Locations is malloced but not freed
 */
- (float*) getROIValue :(long*) numberOfValues :(ROI*) roi :(float**) locations;

/** Returns a pointer with all pixels values contained in the current ROI
 * User must Free the pointer with the free() function
 * Returns reference number of pixels in numberOfValues
 * Returns a pointer to the pixel locations. Each point has the x position followed by the y position
 * Locations is malloced but not freed
 */
- (float*) getLineROIValue :(long*) numberOfValues :(ROI*) roi;


/** Utility methods to convert user supplied pixel coords to DICOM patient coords float d[3] (in mm)
 * using current slice location and orientation
 */
- (void) convertPixX: (float) x pixY: (float) y toDICOMCoords: (float*) d;
- (void) convertPixX: (float) x pixY: (float) y toDICOMCoords: (float*) d pixelCenter: (BOOL) pixelCenter;

- (void) getSliceCenter3DCoords: (float*) center;

/** Utility methods to convert user supplied pixel coords to DICOM patient coords double d[3] (in mm)
 * using current slice location and orientation
 */
- (void) convertPixDoubleX: (double) x pixY: (double) y toDICOMCoords: (double*) d;
- (void) convertPixDoubleX: (double) x pixY: (double) y toDICOMCoords: (double*) d pixelCenter: (BOOL) pixelCenter;

/** convert DICOM coordinated to slice coordinates */
- (void) convertDICOMCoords: (float*) dc toSliceCoords: (float*) sc;
- (void) convertDICOMCoords: (float*) dc toSliceCoords: (float*) sc pixelCenter:(BOOL) pixelCenter;

/** convert DICOM coordinated to slice coordinates */
- (void) convertDICOMCoordsDouble: (double*) dc toSliceCoords: (double*) sc;
- (void) convertDICOMCoordsDouble: (double*) dc toSliceCoords: (double*) sc pixelCenter:(BOOL) pixelCenter;

/** Return index & sliceCoords */
+(int) nearestSliceInPixelList: (NSArray*)pixlist withDICOMCoords: (float*)dc sliceCoords: (float*) sc;

- (DicomImage*) imageObj;
- (DicomSeries*) seriesObj;
- (DicomStudy*) studyObj;

- (BOOL) thickSlabVRActivated; /**< Activate Thick Slab VR */

/** convert to Black and White.
 * @param mode values: 0 Use Red Channel, 1 use Green Channel 2 use Blue Channel  3 Merge and use RGB
 */
- (void) ConvertToBW:(long) mode;

/** convert to RGB.
 * @param mode values: 0 create Red Channel, 1 create Green Channel 2 create Blue Channel  3 create all channels
 * @param  cwl  = window level to use
 * @param cww = window width to use
 */
- (void) ConvertToRGB:(long) mode :(long) cwl :(long) cww;
- (void) setPixelX: (int) x Y:(int) y value:(float) v;
- (float) cineRate;  /**< Returns the Cine rate */
+ (int) maxProcessors;
- (NSRect) rectCoordinates;
// drag-drop subtraction-multiplication between series
- (void) imageArithmeticMultiplication:(DCMPix*) sub;
- (float*) multiplyImages :(float*) input :(float*) subfImage;
- (void) imageArithmeticSubtraction:(DCMPix*) sub;
- (void) imageArithmeticSubtraction:(DCMPix*) sub absolute:(BOOL) abs;
- (float*) arithmeticSubtractImages :(float*) input :(float*) subfImage;
-(float*) arithmeticSubtractImages :(float*) input :(float*) subfImage absolute:(BOOL) abs;
//DSA
- (void) setSubSlidersPercent: (float) p gamma: (float) g zero: (float) z;
- (void) setSubSlidersPercent: (float) p;
- (NSPoint) subMinMax:(float*)input :(float*)subfImage;
- (void) setSubtractedfImage:(float*)mask :(NSPoint)smm;
- (float*) subtractImages:(float*)input :(float*)subfImage;
- (void) fImageTime:(float)newTime;
- (float) fImageTime;
- (void) freefImageWhenDone:(BOOL) b;
- (void) maskID:(long)newID;
- (long) maskID;
- (void) maskTime:(float)newMaskTime;
- (float) maskTime;
- (void) getDataFromNSImage:(NSImage*) otherImage;

- (void) positionerPrimaryAngle:(NSNumber *)newPositionerPrimaryAngle;
- (NSNumber*) positionerPrimaryAngle;
- (void) positionerSecondaryAngle:(NSNumber*)newPositionerSecondaryAngle;
- (NSNumber*) positionerSecondaryAngle;

+ (NSPoint) originDeltaBetween:(DCMPix*) pix1 And:(DCMPix*) pix2;
+ (NSPoint) originCorrectedAccordingToOrientation: (DCMPix*) pix1;
- (void) setBlackIndex:(int) i;
+ (NSImage*) resizeIfNecessary:(NSImage*) currentImage dcmPix: (DCMPix*) dcmPix;

- (void) computeTotalDoseCorrected;
- (void) setRGB : (BOOL) val;
- (void) setConvolutionKernel:(float*)val :(short) size :(float) norm;
- (void) applyConvolutionOnSourceImage;
- (void) setArrayPix :(NSArray*) array :(short) i;
- (BOOL) updateToApply;
- (id) myinitEmpty;  /**< Returns an Empty object */
- (float*) kernel;
- (void) applyShutter;
- (BOOL) is3DPlane;
+ (NSPoint) rotatePoint:(NSPoint)pt aroundPoint:(NSPoint)c angle:(float)a;
- (float) normalization;
- (short) kernelsize;
- (DCMPix*) renderWithRotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF;
- (DCMPix*) renderWithRotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF backgroundOffset: (float) bgO;
- (NSRect) usefulRectWithRotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF;
- (DCMPix*) mergeWithDCMPix:(DCMPix*) o offset:(NSPoint) oo;
- (DCMPix*) renderInRectSize:(NSSize) rectSize atPosition:(NSPoint) oo rotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF;
- (DCMPix*) renderInRectSize:(NSSize) rectSize atPosition:(NSPoint) oo rotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF smartCrop: (BOOL) smartCrop;
- (NSImage*) renderNSImageInRectSize:(NSSize) rectSize atPosition:(NSPoint) oo rotation:(float) r scale:(float) scale xFlipped:(BOOL) xF yFlipped: (BOOL) yF;
/**  calls
 * myinit:(NSString*) s :(long) pos :(long) tot :(float*) ptr :(long) f :(long) ss isBonjour:(BOOL) hello imageObj: (NSManagedObject*) iO
 * with hello = NO and iO = nil
 */
- (id) myinit:(NSString*) s :(long) pos :(long) tot :(float*) ptr :(long) f :(long) ss;
- (id) initWithPath:(NSString*) s :(long) pos :(long) tot :(float*) ptr :(long) f :(long) ss;

/**  Initialize
 * doesn't load pix data, only initializes instance variables
 * @param s  filename
 * @param pos  imageID  Position in array.
 * @param tot  imTot  Total number of images.
 * @param ptr  pointer to volume
 * @param f  frame number
 * @param ss  series number
 * @param hello  flag to indicate remote bonjour file
 * @param iO  coreData image Entity for image
 */
- (id) myinit:(NSString*) s :(long) pos :(long) tot :(float*) ptr :(long) f :(long) ss isBonjour:(BOOL) hello imageObj: (NSManagedObject*) iO;
- (id) initWithPath:(NSString*) s :(long) pos :(long) tot :(float*) ptr :(long) f :(long) ss isBonjour:(BOOL) hello imageObj: (NSManagedObject*) iO;

/** init with data pointer
 * @param im  pointer to image data
 * @param pixelSize  pixelDepth in bits
 * @param xDim  image width
 * @param yDim =image height
 * @param xSpace  pixel width
 * @param ySpace  pxiel height
 * @param oX x position of origin
 * @param oY y position of origin
 * @param oZ z position of origin
 */
- (id) initwithdata :(float*) im :(short) pixelSize :(long) xDim :(long) yDim :(float) xSpace :(float) ySpace :(float) oX :(float) oY :(float) oZ;
- (id) initWithData :(float*) im :(short) pixelSize :(long) xDim :(long) yDim :(float) xSpace :(float) ySpace :(float) oX :(float) oY :(float) oZ;

/** init with data pointer
 * @param im = pointer to image data
 * @param pixelSize = pixelDepth in bits
 * @param xDim  image width
 * @param yDim  image height
 * @param xSpace  pixel width
 * @param ySpace  pxiel height
 * @param oX x position of origin
 * @param oY y position of origin
 * @param oZ z position of origin
 * @param volSize ?
 */
- (id) initwithdata :(float*) im :(short) pixelSize :(long) xDim :(long) yDim :(float) xSpace :(float) ySpace :(float) oX :(float) oY :(float) oZ :(BOOL) volSize;
- (id) initWithData :(float*) im :(short) pixelSize :(long) xDim :(long) yDim :(float) xSpace :(float) ySpace :(float) oX :(float) oY :(float) oZ :(BOOL) volSize;

+ (id) dcmPixWithImageObj: (DicomImage*) image;
- (id) initWithImageObj: (DicomImage *) image;

- (id) initWithContentsOfFile: (NSString *)file;
/** create an NSImage from the current pix
 * @param newWW  window width to use
 * @param newWL window level to use;
 */
- (NSImage*) generateThumbnailImageWithWW: (float)newWW WL: (float)newWL;
- (void) allocate8bitRepresentation;

/** create an NSImage from the current pix using the current ww/wl. Full size*/
- (NSImage*) image;

/** reeturns the current image. returns nil if no image has be previously created */
// - (NSImage*) getImage;

/** A pointer to the orientation.  9 values in length. 3 for each axis. */
- (void) orientation:(float*) c;

/** Sets the orientation.  9 values in length. 3 for each axis. */
- (void) setOrientation:(float*) c;

/** Compute slicelocation according to pixelSpacing values, slice origin and slice orientation: the location is the center of the slice */
- (void) computeSliceLocation;

/** Releases the current NSImage */
- (void) kill8bitsImage;

- (void) checkImageAvailble:(float)newWW :(float)newWL;

/** Load the DICOM image using the DCMFramework.
 * There should be no reason to call this. The class will call it when needed. */
#ifndef OSIRIX_LIGHT
- (BOOL)loadDICOMDCMFramework;
#endif

/** Load the DICOM image using Papyrus.
 * There should be no reason to call this. The class will call it when needed.
 */
- (BOOL) loadDICOMPapyrus;

/** Reset the Annotations */
- (void) reloadAnnotations;


/** Parses the file. Extracts necessary data. Load image data.
 * This class will be called by the class when necessay.
 * There should be no need to call it externally
 */
- (void) CheckLoadIn;

/** Calls CheckLoadIn when needed */
- (void) CheckLoad;
- (BOOL) isLoaded;

-(void) CheckLoadFromThread:(NSThread*) loadingThread;

/** Compute the float pointer for the image data */
- (float*) computefImage;

/** Sets fusion paramaters
 * @param m  stack mode
 * @param s stack
 * @param direction stack direction
 */
- (void) setFusion:(short) m :(short) s :(short) direction;

/** Sets updateToBeApplied to YES. It is called whenver a setting has been changed.
 * Should be called by the class automatically when needed */
- (void) setUpdateToApply;


/** Releases the fImage and sets all values to nil. */
- (void) revert;
- (void) revert:(BOOL) reloadAnnotations;

/** Sets the ThickSlabController */
- (void) setThickSlabController:( ThickSlabController*) ts;


/** Sets the fixed8bitsWLWW flag */
- (void) setFixed8bitsWLWW:(BOOL) f;

/** Creates a DCMPix with the original values and places it in the restore cache*/
- (void) prepareRestore;


/** Releases the restored DCMPix from the restoreCache */
- (void) freeRestore;

/** Sets flag for when OsiriX is running in protected mode */
+ (void) setRunOsiriXInProtectedMode:(BOOL) v;

/** Returns flag for protected mode */
+ (BOOL) isRunOsiriXInProtectedModeActivated;

/** Clears the papyrus group cache */
- (void) clearCachedDCMFrameworkFiles;

+ (void) purgeCachedDictionaries;

+ (double) moment: (float *) x length:(long) length mean: (double) mean order: (int) order;
+ (double) skewness: (float*) data length: (long) length mean: (double) mean;
+ (double) kurtosis: (float*) data length: (long) length mean: (double) mean;

#ifndef OSIRIX_LIGHT
/** create ROIs from RTSTRUCT */
- (void)createROIsFromRTSTRUCT: (DCMObject*)dcmObject;
#endif

#ifdef OSIRIX_VIEWER
/** Custom Annotations */
- (void)loadCustomImageAnnotationsDBFields: (DicomImage*) imageObj;

- (void)loadCustomImageAnnotationsPapyLink:(int)fileNb DCMLink:(DCMObject*)dcmObject;

- (NSString*) getDICOMFieldValueForGroup:(int)group element:(int)element DCMLink:(DCMObject*)dcmObject;
#endif

@end

#endif