mrcImage(API)

DataManip/mrcImageは、mrcImage型's imageを取り扱うための低水準APIです。

定数

マスク処理

typedef unsigned int mrcStatusMask;
typedef unsigned int mrcStatusType;

#define  mrcStatusMask_ExitFailure  ((mrcStatusMask)0x80000000L)
#define  mrcStatusMask_Warning      ((mrcStatusMask)0x40000000L)
#define  mrcStatusMask_Information  ((mrcStatusMask)0x20000000L)
#define  mrcStatusMask_Message      ((mrcStatusMask)0x10000000L)
#define  mrcStatusMask_1B           ((mrcStatusMask)0x08000000L)
#define  mrcStatusMask_1A           ((mrcStatusMask)0x04000000L)
#define  mrcStatusMask_19           ((mrcStatusMask)0x02000000L)
#define  mrcStatusMask_18           ((mrcStatusMask)0x01000000L)
#define  mrcStatusMask_17           ((mrcStatusMask)0x00800000L)
#define  mrcStatusMask_16           ((mrcStatusMask)0x00400000L)
#define  mrcStatusMask_15           ((mrcStatusMask)0x00200000L)
#define  mrcStatusMask_14           ((mrcStatusMask)0x00100000L)
#define  mrcStatusMask_ReferMRCInfo ((mrcStatusMask)0x00080000L)
#define  mrcStatusMask_Mode         ((mrcStatusMask)0x00040000L)
#define  mrcStatusMask_ReferMemory  ((mrcStatusMask)0x00020000L)
#define  mrcStatusMask_ReferFile    ((mrcStatusMask)0x00010000L)

mrcファイルの状態

#define  MRC_Status_OK              ((mrcStatusType)0x00000000L)

#define  MRC_FileCanNotOpened       ((mrcStatusType)0x00000000L|mrcStatusMask_ReferFile)
#define  MRC_ImageHeaderCanNotRead  ((mrcStatusType)0x00000001L|mrcStatusMask_ReferFile)
#define  MRC_ImageDataCanNotRead    ((mrcStatusType)0x00000002L|mrcStatusMask_ReferFile)
#define  MRC_ImageHeaderCanNotWrite ((mrcStatusType)0x00000003L|mrcStatusMask_ReferFile)
#define  MRC_ImageDataCanNotWrite   ((mrcStatusType)0x00000004L|mrcStatusMask_ReferFile)
#define  MRC_FileCanNotClosed       ((mrcStatusType)0x00000005L|mrcStatusMask_ReferFile)

#define  MRC_MemoryNotAllocate      ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMemory)

#define  MRC_ModeNotSupported       ((mrcStatusType)0x00000000L|mrcStatusMask_Mode)
#define  MRC_ModeZNot1FFTMode       ((mrcStatusType)0x00000001L|mrcStatusMask_Mode)

#define  MRC_SizeOfZero             ((mrcStatusType)0x00000000L|mrcStatusMask_ReferMRCInfo)

extern char* mrcImageGeneralTypeList[];

サイズ

Headerサイズ

#define MRC_HEADER (1024)

トレイラサイズ

#define MRC_TAILER (1024)

画像Mode

mrcファイル互換のための定義

typedef	mrcImageParaTypeInteger mrcImageMode;
#define	MRC_char_image	    	 ((mrcImageMode)0)
#define	MRC_short_image	    	 ((mrcImageMode)1)
#define	MRC_float_image	    	 ((mrcImageMode)2)
#define	MRC_complex_short_ft     ((mrcImageMode)3)
#define	MRC_complex_float_ft     ((mrcImageMode)4)
#define	MRC_long_image	         ((mrcImageMode)101)
#define	MRC_double_image	     ((mrcImageMode)102)
#define	MRC_complex_long_ft      ((mrcImageMode)103)
#define	MRC_complex_double_ft    ((mrcImageMode)104)
#define	MRC_complex_short_fft    ((mrcImageMode)1003)
#define	MRC_complex_float_fft    ((mrcImageMode)1004)
#define	MRC_complex_long_fft     ((mrcImageMode)1103)
#define	MRC_complex_double_fft   ((mrcImageMode)1104)
#define	MRC_NotSuppotedMode      ((mrcImageMode)0xffffffffL)

#define	mrcCharImage	    	 ((mrcImageMode)0)
#define	mrcShortImage	    	 ((mrcImageMode)1)
#define	mrcFloatImage	    	 ((mrcImageMode)2)
#define	mrcComplexShortFT        ((mrcImageMode)3)
#define	mrcComplexFloatFT        ((mrcImageMode)4)
#define	mrcComplexFloatOneDimFT  ((mrcImageMode)5)

IMOD

#define	mrcUShortImage           ((mrcImageMode)6)
#define	mrcCharImageRGB          ((mrcImageMode)16)

IMOD: (6,7) -> (26,27)

#define	mrcFloatRadonImage       ((mrcImageMode)26)
#define	mrcFloatRadonFT          ((mrcImageMode)27)
#define	mrcLongImage	         ((mrcImageMode)101)
#define	mrcDoubleImage	         ((mrcImageMode)102)
#define	mrcComplexLongFT         ((mrcImageMode)103)
#define	mrcComplexDoubleFT       ((mrcImageMode)104)
#define	mrcComplexShortFFT       ((mrcImageMode)1003)
#define	mrcComplexFloatFFT       ((mrcImageMode)1004)
#define	mrcComplexLongFFT        ((mrcImageMode)1103)
#define	mrcComplexDoubleFFT      ((mrcImageMode)1104)
#define	mrcNotSuppotedMode       ((mrcImageMode)0xffffffffL)

#define MRC_MAX_LABEL_N    (10)
#define MRC_MAX_LABEL_LEN  (80)
#define MRC_MAX_EXTRA      (29)
#define MRC_MAX_EXTRA_CCP4 (15)

2D投影Mode

#define  mrcImageTailerMode2DProjection 0

画像情報

統計データの算出Mode

typedef enum mrcImageInformationMode {
	meanOfAll             = 0,
	meanOfSphereSurface   = 1,
	meanOfCylinderSurface = 2,
	meanOfEdge            = 3, 
	meanOfCentre          = 4,
	meanOfSparse          = 5,
	meanOf2DEdgeY         = 6,
	RMSofAllPixels       = 7
} mrcImageInformationMode;

平均値などを算出する関数(lmrcImageInformation、lmrcImageSolventFlattening(API)など)のModeとして設定します。
mrcImageInformation.modeの値として使用します。

ピクセルデータ

データの種類

typedef enum mrcPixelDataType {
    mrcPixelRePart = 0,
    mrcPixelImPart,
    mrcPixelMag,
    mrcPixelPow,
    mrcPixelLogMag,
    mrcPixelLogPow,
    mrcPixelPhase
} mrcPixelDataType;

設定・取得するピクセルデータのタイプで、mrcPixselDataSetやmrcPixselDataGetの引数(mode)として使用します。

Value	実画像	FT画像
mrcPixelRePart	データ	実部データ
mrcPixelImPart	対応無し	虚部データ
mrcPixelMag	データ	振幅: (実部^2 + 虚部^2)^(1/2)
mrcPixelPow	データ^2	強度: 実部^2 + 虚部^2
mrcPixelLogMag	対応無し	ログ振幅: (log10(実部^2 + 虚部^2)) / 2
mrcPixelLogPow	対応無し	ログ強度: log10(実部^2 + 虚部^2)
mrcPixelPhase	対応無し	位相

Interpolation方法

typedef enum mrcPixelDataHowToGet {
    mrcPixelHowNearest = 0,
    mrcPixelHowLinear,
    mrcPixelHowCubicConv,
    mrcPixelHowPolySig
} mrcPixelDataHowToGet;

ピクセルデータのInterpolation方法で、mrcPixselDataGetの引数(how)として使用します。

Value	設定値	Interpolation方法
mrcPixelHowNearest	0	Nearest neighbor method
mrcPixelHowLinear	1	Bi-linear interpolation method
mrcPixelHowCubicConv	2	Cubic convolution method
mrcPixelHowPolySig	3	Polynomial interpolation method

構造体

マスク処理

typedef union MRC_Status_t {
   mrcStatusType all;
   struct Content {
#ifdef M68
       unsigned char level;
       unsigned char category;
       short detail;
#else
       short detail;
       unsigned char category;
       unsigned char level;
#endif
	} status;
} MRC_Status_t;

#ifdef M68
typedef int mrcImageParaTypeInteger;
#else
typedef int mrcImageParaTypeInteger;
#endif

typedef float mrcImageParaTypeReal;
typedef unsigned char mrcImageParaTypeCharacter;

座標

整数: ピクセルデータなどを扱うときに使用します。

typedef struct mrcImageParaTypeIntegerCoord {
	mrcImageParaTypeInteger x;
	mrcImageParaTypeInteger y;
	mrcImageParaTypeInteger z;
} mrcImageParaTypeIntegerCoord;

実数: 実データやPDBデータなどを扱うときに使用します。

typedef struct mrcImageParaTypeRealCoord {
	mrcImageParaTypeReal x;
	mrcImageParaTypeReal y;
	mrcImageParaTypeReal z;
} mrcImageParaTypeRealCoord;

mrcImageの構造

typedef struct mrcImage {
	mrcImageHeader          Header;
	size_t BytePerImage;
	mrcImageParaTypeInteger BytePerBand;
	mrcImageParaTypeInteger BandPerPixel;
	size_t PixelPerImage;
	mrcStatusType           status;
	char*           Image;
	unsigned char*  ImageCharImage;
	unsigned short* ImageShortImage;
	unsigned long*  ImageLongImage;
	float*          ImageFloatImage;
	double*         ImageDoubleImage;

	/* Tailer */
	mrcImageTailer*         Tailer;	
	mrcImageParaTypeInteger numTailer;

	/* FEIextendedHeader */
	FEIextendedHeader*      FEIHeader;
	mrcImageParaTypeInteger numFEIHeader;

 	/* Dummy */
	char*     dummyHeader;
	mrcImageParaTypeInteger dummyHeaderByte;

	/* Swap Bytes */
	mrcImageParaTypeInteger flagByteSwap;

	/* flag CCP4-2000 */
	mrcImageParaTypeInteger   flagCCP4;
	mrcImageParaTypeInteger   ImageOffset; 
	mrcImageSymmetryOperator* SymmetryOperator;
} mrcImage;

構成	対応メンバ	役割
Header情報	Header	画像Mode、サイズなど
隠しデータ	BytePerImage, BytePerBand, BandPerPixel, PixelPerImage	1ピクセル当たりのオングストロームなど
ステータス	status	ファイルの状態
画像データ	Image, ImageCharImage, ... , ImageDoubleImage	画像データ本体(実体はImage、他メンバはポインタで管理)
トレイラ情報	Tailer, numTailer	角度情報など
FEIHeader	FEIHeader, numFEIHeader	FEI用の拡張Header
ダミー	dummyHeaderByte	ダミーデータ
バイトスワップ	flagByteSwap	処理系によったエンディアン関連のフラグ
CCP4-2000	flagCCP4, ImageOffset, SymmetryOperator	CCP4-2000用

Header情報

デフォルト

typedef struct _mrcImageHeader {
	mrcImageParaTypeIntegerCoord        N;	    /* Data Numbers */
	mrcImageMode                        Mode;   /* Data Type */
	mrcImageParaTypeIntegerCoord        StartN; /* First in map */
	mrcImageParaTypeIntegerCoord        M;	    /* Number of Intervals */
	mrcImageParaTypeRealCoord           Length; /* Cell Dimensions : Angstrom */
	mrcImageParaTypeReal                Alpha;  /* Cell Angle : Degree */
	mrcImageParaTypeReal                Beta;
	mrcImageParaTypeReal                Gamma;
	mrcImageParaTypeInteger             MAPC;   /* Which Axis Corresponds to Columns */
	mrcImageParaTypeInteger             MAPR;   /* Which Axis Corresponds to Rows */
	mrcImageParaTypeInteger             MAPS;   /* Which Axis Corresponds to Sections */
	mrcImageParaTypeReal                AMin;   /* Minimum Density Value */
	mrcImageParaTypeReal                AMax;   /* Maximum Density Value */
	mrcImageParaTypeReal                AMean;  /* Mean Density Value */
	mrcImageParaTypeInteger             ISPG;   /* Space Group */
	mrcImageParaTypeInteger             NSYMBT; /* Number of bytes */
	mrcImageParaTypeReal                EXTRA[MRC_MAX_EXTRA]; /* Extra, user defined storage space */
	mrcImageParaTypeReal                OriginX;
	mrcImageParaTypeReal                OriginY;
	mrcImageParaTypeInteger             LabelN;
	char                                Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
} _mrcImageHeader;

CCP4 2000

typedef struct _mrcImageHeaderCCP4 {
	mrcImageParaTypeIntegerCoord        N;	    /* Data Numbers */
	mrcImageMode                        Mode;   /* Data Type */
	mrcImageParaTypeIntegerCoord        StartN; /* First in map */
	mrcImageParaTypeIntegerCoord        NI;	    /* Number of Intervals */
	mrcImageParaTypeRealCoord           Length; /* Cell Dimensions : Angstrom */
	mrcImageParaTypeReal                Alpha;  /* Cell Angle : Degree */
	mrcImageParaTypeReal                Beta;
	mrcImageParaTypeReal                Gamma;
	mrcImageParaTypeInteger             MAPC;   /* Which Axis Corresponds to Columns */
	mrcImageParaTypeInteger             MAPR;   /* Which Axis Corresponds to Rows */
	mrcImageParaTypeInteger             MAPS;   /* Which Axis Corresponds to Sections */
	mrcImageParaTypeReal                AMin;   /* Minimum Density Value */
	mrcImageParaTypeReal                AMax;   /* Maximum Density Value */
	mrcImageParaTypeReal                AMean;  /* Mean Density Value */
	mrcImageParaTypeInteger             ISPG;   /* Space Group */
	mrcImageParaTypeInteger             NSYMBT; /* Number of bytes used for storing symmetry operators */
	mrcImageParaTypeInteger             LSKFLG; /* Flag for Skew transformation */
	mrcImageParaTypeReal 				SKWMAT[9]; /* Skew matrix S */
	mrcImageParaTypeReal 				SKWTRN[3]; /* Skew translation */
	mrcImageParaTypeReal                EXTRA[MRC_MAX_EXTRA_CCP4]; /* Extra, user defined storage space */
	mrcImageParaTypeCharacter  			MAP[4];
	mrcImageParaTypeInteger  			MARCHST;
	mrcImageParaTypeReal                ARMS;
	mrcImageParaTypeInteger             LabelN;
	char                                Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
} _mrcImageHeaderCCP4;

IMOD

typedef struct _mrcImageHeaderIMOD {
	mrcImageParaTypeIntegerCoord        N;	    /* Data Numbers */
	mrcImageMode                        Mode;   /* Data Type */
	mrcImageParaTypeIntegerCoord        StartN; /* First in map */
	mrcImageParaTypeIntegerCoord        M;	    /* Number of Intervals */
	mrcImageParaTypeRealCoord           Length; /* PixelSize=Len/M: Angstrom */
	mrcImageParaTypeReal                Alpha;  /* Cell Angle : Degree */
	mrcImageParaTypeReal                Beta;
	mrcImageParaTypeReal                Gamma;
	mrcImageParaTypeInteger             MAPC;   /* Which Axis Corresponds to Columns */
	mrcImageParaTypeInteger             MAPR;   /* Which Axis Corresponds to Rows */
	mrcImageParaTypeInteger             MAPS;   /* Which Axis Corresponds to Sections */
	mrcImageParaTypeReal                AMin;   /* Minimum Density Value */
	mrcImageParaTypeReal                AMax;   /* Maximum Density Value */
	mrcImageParaTypeReal                AMean;  /* Mean Density Value */
	mrcImageParaTypeInteger             ISPG;   /* Space Group */
	mrcImageParaTypeInteger             NSYMBT; /* Number of bytes used for extended header */
	short                               creatid; /* Flag for Skew transformation */
	short                               extra1[15]; /* Flag for Skew transformation */
	short                               nint;
	short                               nreal; /*l Skew matrix S */
	mrcImageParaTypeReal                extra2[5]; /* Extra, user defined storage space */
	mrcImageParaTypeInteger             imodStamp;   
	mrcImageParaTypeInteger             imodFlags;   
	short                               idtype;   
	short                               lnes;   
	short                               nd1;   
	short                               nd2;   
	short                               vd1;   
	short                               vd2;   
	mrcImageParaTypeReal                tiltangles[6]; /* Extra, user defined storage space */
	mrcImageParaTypeReal                xorg; /* Extra, user defined storage space */
	mrcImageParaTypeReal                yorg; /* Extra, user defined storage space */
	mrcImageParaTypeReal                zorg; /* Extra, user defined storage space */
	mrcImageParaTypeCharacter  			MAP[4];
	mrcImageParaTypeInteger  			MARCHST;
	mrcImageParaTypeReal                ARMS;
	mrcImageParaTypeInteger             LabelN;
	char                                Label[MRC_MAX_LABEL_N][MRC_MAX_LABEL_LEN];
} _mrcImageHeaderIMOD;

Headerの共用体

以上で定義したHeaderを共用体とします。

typedef union mrcImageHeader {
  unsigned char           All[MRC_HEADER];
  mrcImageParaTypeInteger Int[MRC_HEADER/4];
  mrcImageParaTypeReal    Real[MRC_HEADER/4];
  _mrcImageHeader         Cont;
  _mrcImageHeaderCCP4     ContCCP4;
  _mrcImageHeaderIMOD     ContIMOD;
} mrcImageHeader;

メンバー呼び出しの省略表記を定義

#define HeaderN       Header.Cont.N       
#define HeaderMode    Header.Cont.Mode    
#define HeaderStartN  Header.Cont.StartN  
#define HeaderM       Header.Cont.M       
#define HeaderLength  Header.Cont.Length  
#define HeaderAlpha   Header.Cont.Alpha   
#define HeaderBeta    Header.Cont.Beta    
#define HeaderGamma   Header.Cont.Gamma   
#define HeaderMAPC    Header.Cont.MAPC    
#define HeaderMAPR    Header.Cont.MAPR    
#define HeaderMAPS    Header.Cont.MAPS    
#define HeaderAMin    Header.Cont.AMin    
#define HeaderAMax    Header.Cont.AMax    
#define HeaderAMean   Header.Cont.AMean   
#define HeaderISPG    Header.Cont.ISPG    
#define HeaderNSYMBT  Header.Cont.NSYMBT  
#define HeaderLSKFLG  Header.ContCCP4.LSKFLG
#define HeaderEXTRA   Header.Cont.EXTRA
#define HeaderOriginX Header.Cont.OriginX 
#define HeaderOriginY Header.Cont.OriginY  
#define HeaderLabelN  Header.Cont.LabelN
#define HeaderLabel   Header.Cont.Label

FEI

#define FEI_EXTENDED_HEADER_EACH (128)

typedef struct _FEIextendedHeader {
	mrcImageParaTypeReal aTilt;   // Alpha tilt, in degrees
	mrcImageParaTypeReal bTilt;   // Beta tilt, in degrees 
	mrcImageParaTypeReal xStage;  // Stage x position. 
								  // Normally in SI units (meters), 
								  // but some older files may be in micrometers. 
								  // Check by looking at values for x,y,z. 
								  // If one of these exceeds 1, it will be micrometers.
	mrcImageParaTypeReal yStage;  // Stage y position. For testing of units see x_stage.
	mrcImageParaTypeReal zStage;  // Stage z position. For testing of units see x_stage.
	mrcImageParaTypeReal xShift;  // Image shift x. For testing of units see x_stage.
	mrcImageParaTypeReal yShift;  // Image shift y. For testing of units see x_stage.
	mrcImageParaTypeReal defocus;  
	mrcImageParaTypeReal expTime;  
	mrcImageParaTypeReal mean;  
	mrcImageParaTypeReal tiltAxis;  
	mrcImageParaTypeReal pixelSize;  
	mrcImageParaTypeReal magnification;  
	mrcImageParaTypeReal ht;  
	mrcImageParaTypeReal binning;  
	mrcImageParaTypeReal appliedDefocus;  
	mrcImageParaTypeReal reminder[FEI_EXTENDED_HEADER_EACH/4-16];  
} _FEIextendedHeader;

typedef union FEIextendedHeader {
	mrcImageParaTypeReal Real[FEI_EXTENDED_HEADER_EACH/4];
	_FEIextendedHeader   Cont;
} FEIextendedHeader;

トレイラ情報

typedef struct _mrcImageTailer {
	char                 		Code[4]; 
	mrcImageParaTypeInteger		Mode;  
	char                        EulerAngleMode[4];
	mrcImageParaTypeReal 		Rot1;   
	mrcImageParaTypeReal 		Rot2;
	mrcImageParaTypeReal 		Rot3;
	mrcImageParaTypeInteger 	Mirror;
} _mrcImageTailer;

typedef union mrcImageTailer {
  unsigned char           All[MRC_TAILER];
  mrcImageParaTypeInteger Int[MRC_TAILER/4];
  mrcImageParaTypeReal    Real[MRC_TAILER/4];
  _mrcImageTailer         Cont;
} mrcImageTailer;

typedef char mrcImageSymmetryOperator;

画像の統計データ

mrcImageの統計データを格納する構造体です。
データはmrcImageInformation(API)から取得して、主に入力情報として使用します。

typedef struct mrcImageInformation {
	double mean;
	double rootMeanSquare;
	double meanOfSphereSurface;
	double sdOfSphereSurface;
	double seOfSphereSurface;
	double meanOfCylinderSurface;
	double sdOfCylinderSurface;
	double seOfCylinderSurface;
	double meanOfEdge;
	double sdOfEdge;
	double seOfEdge;
	double max;
	mrcImageParaTypeRealCoord maxCoord;
	double min;
	mrcImageParaTypeRealCoord minCoord;
	double sd;
	double se;
	double rmax;
	long flagrmax;
	double RMS; /* Root mean square */
	int mode;

	/* For Search Area */
	int flagXrange;
	int flagYrange;
	int flagZrange;
	double XrangeMin; 
	double XrangeMax; 
	double YrangeMin; 
	double YrangeMax; 
	double ZrangeMin; 
	double ZrangeMax; 

	int flagCentre;
	double CentreX;
	double CentreY;
	double CentreZ;
} mrcImageInformation;

API毎の設定ファイル

lmrcImageSmoothingInfo

lmrcImageSmoothingIt is used for 's setting data.

typedef struct lmrcImageSmoothingInfo  {
	long mode;
	mrcImageParaTypeReal sx; /* Filter kernel size */
	mrcImageParaTypeReal sy;
	mrcImageParaTypeReal sz;
	double sigma;            /* for Lee-Sigma filter  */
} lmrcImageSmoothingInfo;

lmrcImageCVEInfo

lmrcImageCVEIt is used for 's setting data.

typedef struct lmrcImageCVEInfo {
	long sx; /* CVE domain size. */
	long sy; /* Apr.30,1996 */
	long sz;
} lmrcImageCVEInfo;

lmrcImageTfunctionInfo

lmrcImageTfunctionIt is used for 's setting data.

typedef struct lmrcImageTfunctionInfo {
	long sx; /* Tfunction domain size. */
	long sy; /* June 11,1996 */
	long sz;
} lmrcImageTfunctionInfo;

lmrcImageHighlightInfo

lmrcImageHighlightingIt is used for 's setting data.

typedef struct lmrcImageHighlightInfo {
	long mode;
	float Bias; /* May 1,1996 */
	float Grad;
} lmrcImageHighlightInfo;

lmrcImageLowPassFilterInfo

lmrcImageLowPassFilterIt is used for 's setting data.

typedef struct lmrcImageLowPassFilterInfo 
{
	long mode; /* June 4,1996 */
	float hvp, width;
} lmrcImageLowPassFilterInfo;

lmrcImageHighPassFilterInfo

lmrcImageHighPassFilterIt is used for 's setting data.

typedef struct lmrcImageHighPassFilterInfo 
{
	long mode; /* June 5,1996 */
	float hvp, width;
	float pathWindowLow;
	float pathWindowHigh;
} lmrcImageHighPassFilterInfo;

lmrcImageBandPassFilterInfo

lmrcImageBandPassFilterIt is used for 's setting data.

typedef struct lmrcImageBandPassFilterInfo 
{
	long mode; /* June 5,1996 */
	float hvl, hvh, wl, wh;
	int flagLowWeight;
	double lowWeight;
} lmrcImageBandPassFilterInfo;

mrcImageDataSet

typedef enum mrcImageDataSetMode {
	mrcImageDataSetModeCentre = 0,
	mrcImageDataSetModeOrigin = 1
} mrcImageDataSetMode;

lmrcImageMultiCTFCompensationInfo

lmrcImageMultiCTFCompensationIt is used for 's setting data.

typedef enum lmrcImageMultiCTFCompensationSolventFlatteningMode {
	lmrcImageMultiCTFCompensationSolventFlatteningModeDensityPeakIsSolvent=0,
	lmrcImageMultiCTFCompensationSolventFlatteningModeDefinedSTDIsSolvent=1
} lmrcImageMultiCTFCompensationSolventFlatteningMode;

typedef struct lmrcImageMultiCTFCompensationInfo {
	long   maxiteration;
	double okrms;
	long   diversefactor;
	double z;
	long   nhist;
	FILE*  logfile;
	lmrcImageMultiCTFCompensationSolventFlatteningMode solventMode;
	float  definedSTD;	 	
} lmrcImageMultiCTFCompensationInfo;

lmrcImageCTFSNInfo

lmrcImageCTFSNIt is used for 's setting data.

typedef struct lmrcImageCTFSNInfo
{
	long mode, deg1, deg2;
	ctfInfo ctf;
} lmrcImageCTFSNInfo;

lmrcImageFourierPowerSpectrumInfo

lmrcImageFourierPowerSpectrumIt is used for 's setting data.

typedef struct mrcImageFourierPowerSpectrum
{
	long n;
	double d, *h;
} mrcImageFourierPowerSpectrum;

typedef struct lmrcImageFourierPowerSpectrumInfo
{
	double dX, dY, dZ;
} lmrcImageFourierPowerSpectrumInfo;

API

初期化

画像データの初期化

extern mrcStatusType mrcInit(mrcImage* mrc, char* filaname);

Header情報(画像Modeやサイズ)を別のmrcファイルから読み出す場合はfilenameにファイル名を指定し、NULLの場合はデフォルト設定となります。画像データをmrcのメンバーImageに新規作成し, ポインタをImageXXXXImage(XXXX: Char, Shortなど)に格納されます。

※ このAPIは無条件でmrc->Imageにメモリを確保しますので、mrc->Imageが空であることが保証されるときのみ使用して下さい。(空でない場合はmrcImageFreeでメモリを解放してから確認します。)

Initialize Header information

extern mrcStatusType mrcDefaultHeaderValueSet(mrcImage* mrc);
extern mrcStatusType mrcDefaultHeaderValueSetOnlyFixedValue(mrcImage* mrc);

Setting Hidden data

extern mrcStatusType mrcHiddenDataSet(mrcImage* mrc, long mode);

Initialize Trailer information

extern void mrcTailerInit(mrcImage* mrc, long mode);

Release Image data

extern void mrcImageFree(mrcImage* mrc, char* message);

Release the Image data's substance(Image), and Change Pointers of Image, ImageXXXXImage(XXXX: Char, Short, ...) to NULL Pointer.

Read from file

Read filename, and store to mrc.

extern mrcStatusType mrcFileRead  (mrcImage* mrc, char* filename, char* message, long mode);

extern mrcStatusType mrcImageRead (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcHeaderRead(mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcTailerRead(mrcImage* mrc, char* filename, char* message, long mode);

extern mrcStatusType mrcFileReadGeneral  (mrcImage* mrc, char* filename, char* type, char* message, long mode);
extern mrcStatusType mrcImageReadGeneral  (mrcImage* mrc, char* filename, char* type, char* message, long mode);
extern mrcStatusType mrcHeaderReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
extern mrcStatusType mrcTailerReadGeneral(mrcImage* mrc, char* filename, char* type, char* message, long mode);
extern mrcStatusType mrcFileGeneralListPrint(FILE* fpt);

extern mrcStatusType mrcFileReadFEIextendedMRC  (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcImageReadFEIextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcHeaderReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcTailerReadFEIextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);

extern mrcStatusType mrcFileReadIMODextendedMRC  (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcImageReadIMODextendedMRC (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcHeaderReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcTailerReadIMODextendedMRC(mrcImage* mrc, char* filename, char* message, long mode);

message: for error message
mode: Read data 0: Not display, 1: Display

Write to file

extern mrcStatusType mrcFileWrite  (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcImageWrite (mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcHeaderWrite(mrcImage* mrc, char* filename, char* message, long mode);
extern mrcStatusType mrcTailerWrite(mrcImage* mrc, char* filename, char* message, long mode);

#define mrcFileWriteModeGet(x)     BYTE4GETBYTE(x,0)
#define mrcImageWriteModeGet(x)    BYTE4GETBYTE(x,1)
#define mrcHeaderWriteModeGet(x)   BYTE4GETBYTE(x,2)
#define mrcTailerWriteModeGet(x)   BYTE4GETBYTE(x,3)
#define mrcFileWriteMode_InfoPrint         1
#define mrcFileWriteMode_NoCallForStatData 2

message: for error message
mode: +1: Display written data, +2: Not Calculate Statistics data

Writing by Lower Resolution

It is used by ip2mrc, ...

extern mrcStatusType mrcFileWriteLowerResolution(mrcImage* mrc, char* filename, char* message, long sample , long mode);

Copy data

Copy as: src -> dst

Copy Image data

extern void lmrcImageCopy(mrcImage* dst, mrcImage* src, mrcImageParaTypeRealCoord to);

to: Offset(Coordinate)

Copy Trailer information

extern void mrcTailerCopy(mrcImage* dst, mrcImage* src, long mode);

mode: +1: New create and Copy, Otherwise: Copy directly

Check Image mode

extern int IsFloatImage(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
extern int IsFloatFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
extern int IsImage(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
extern int IsFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);
extern int IsFFT(mrcImage* mrc, char* message, mrcImageParaTypeInteger mode);

Return value: 0: False, 1: True

Getting Pixel data

Getting Pixel data by Pixel

extern double mrcPixelDataGet(mrcImage* mrc,
                              mrcImageParaTypeReal x /* Pixel Unit */,
                              mrcImageParaTypeReal y /* Pixel Unit */,
                              mrcImageParaTypeReal z /* Pixel Unit */,
                              double* data,
                              mrcPixelDataType mode,
                              mrcPixelDataHowToGet how);

Get the data of Coordinate(x, y, z), and store to "data".
Gotten data is depending to mode and how.

Getting Pixel data by Angstrom

extern double mrcImageDataGetbyAU(mrcImage* mrc,
                              mrcImageParaTypeReal x /* Angstrom */,
                              mrcImageParaTypeReal y /* Angstrom */,
                              mrcImageParaTypeReal z /* Angstrom */,
                              double* data,
                              mrcPixelDataType mode,
                              mrcPixelDataHowToGet how);

Inline function Gets Pixel data

extern inline double mrcPixelDataGetFloatImage(mrcImage* img,
                mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)

extern inline double mrcPixelDataGetFloatFTRe(mrcImage* fft,
                mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)

extern inline double mrcPixelDataGetFloatFTIm(mrcImage* fft,
                mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z)

Setting Pixel data

Setting Image Information

extern void mrcInfoSet(mrcImage* mrc, FILE* fptIn, FILE* fptOut, mrcImageParaTypeInteger mode);

Setting Pixel Information

extern void mrcImageInfoSet(mrcImage* mrc, FILE* fptIn, FILE* fptOut, long mode);

Setting Pixel data

extern void mrcImageDataSet(mrcImage* out, 
							mrcImage* in, 
							mrcImageParaTypeReal x,
							mrcImageParaTypeReal y,
							mrcImageParaTypeReal z,
							float phi,
							mrcImageDataSetMode  mode);

Setting Pixel data by Pixel

extern double mrcPixelDataSet(mrcImage* mrc,
			      mrcImageParaTypeReal x /* Pixel Unit */,
			      mrcImageParaTypeReal y /* Pixel Unit */,
			      mrcImageParaTypeReal z /* Pixel Unit */,
			      double data,
			      mrcPixelDataType mode);

Setting Pixel data by Angstrom

extern double mrcImageDataSetbyAU(mrcImage* mrc,
			      mrcImageParaTypeReal x /* Angstrom */,
			      mrcImageParaTypeReal y /* Angstrom */,
			      mrcImageParaTypeReal z /* Angstrom */,
			      double data,
			      mrcPixelDataType mode);

Inline function Sets Pixel data

static inline void mrcPixelDataSetFloatImage(mrcImage* img, 
		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)

static inline void mrcPixelDataSetFloatFTRe(mrcImage* fft, 
		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)

static inline void mrcPixelDataSetFloatFTIm(mrcImage* fft, 
		mrcImageParaTypeInteger x, mrcImageParaTypeInteger y, mrcImageParaTypeInteger z, double data)

Statistics processing of Pixel data

Calculate Max, Min, Mean(Store mrc's Header Information)

extern void mrcStatDataSet(mrcImage* mrc, mrcImageParaTypeInteger mode);

Library of General image processing

Operation image(mrcImageOperation)

Unary operation

Add

void lmrcImageAddedByReal(mrcImage* img, double d);                       img := img+d

Subtraction

void lmrcImageMeanSubtraction(mrcImage* out, mrcImage* in)                      out  :=  in - mean
void lmrcImageMeanSubtraction(mrcImage* out, mrcImage* in)                      out  :=  in - mean
void lmrcImageSubtraction(mrcImage* out, mrcImage* in, double value)            out  :=  in - value

Devide

void lmrcImageDevidedByReal(mrcImage* img, double d);                     img := img/d
void lmrcImageDevidedByRealForOnlyPositive(mrcImage* img, double d);      img := img/d, if img>=0, else img:=img;
void lmrcImageDevidedByImage(mrcImage* img, mrcImage* i1, mrcImage* i2);        img := i1/i2, 0 := 0/0, 0 := x/0

Absolute value

void ImageAbs(mrcImage* out ,mrcImage* in);                               out := fabs(in);

Square, Root

void lmrcImageSquare(mrcImage* in);                                       in := in*in
void lmrcImageRoot(mrcImage* in ,double eps);                             in := sqrt(in), if in>eps else in:=0

Dyadic operation

Addition

void lmrcImageAdd(mrcImage* img2, mrcImage* img1, long* number);                img2 := img2 + img1, number++

Square Add

void lmrcSQRImageAdd(mrcImage* img2, mrcImage* img1, long* number);             img2 := img2 + img1*img1, number++

Subtraction

void lmrcImageSubtractionCalc(mrcImage* out, mrcImage* in1, mrcImage* in2)      out  :=  in1 - in2
void llmrcImageSub(mrcImage*out ,mrcImage* in1 ,mrcImage* in2)                  out  : = in1 - in2（上記と同じ機能）

Convolution

extern void lmrcImageConvolution(mrcImage* out, mrcImage* in,  mrcImage* kernel, int mode);

Statistics

void lmrcImagetMapForZero(mrcImage* t, mrcImage* avg, mrcImage* se);           t  := avg/se,  at present, avg, se must be given.
void lmrcImageSN(mrcImage* sn, mrcImage* avg, mrcImage* sig);                  sn := avg/sig, at present, avg, sig must be given.
void mrcImageStdDev(mrcImage* sig, mrcImage* avg, mrcImage* avg2, long number); sig:= sqrt(avg2 - avg*avg), at present, avg, avg2 must be given.
void mrcImageStdErr(mrcImage* se, mrcImage* avg, mrcImage* avg2, long number);  se := sqrt(avg2 - avg*avg)/number, at present, avg, avg2 must be given.

Relation to Endian

extern int mrcImageByteSwap(mrcImage* mrc, long mode);

Projection

extern void lmrcImageXSection(mrcImage* proj, mrcImage* img, double Y);
extern void lmrcImageYSection(mrcImage* proj, mrcImage* img, double X);
extern void lmrcImageXProjection(mrcImage* proj, mrcImage* img);
extern void lmrcImageYProjection(mrcImage* proj, mrcImage* img);
extern void lmrcImageZProjection(mrcImage* proj, mrcImage* img);
extern void lmrcImageXYProjection(mrcImage* proj, mrcImage* img);
extern void lmrcImageYZProjection(mrcImage* proj, mrcImage* img);
extern void lmrcImageZXProjection(mrcImage* proj, mrcImage* img);

Histogram

extern void lmrcImageHistgram(double** hist, unsigned long nlevel, mrcImage* img);
extern void lmrcImageHistgram2(double** hist, double delta, mrcImage* img);
extern void lmrcImageHistgram5(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);
extern void lmrcImageHistgram3(double** hist, unsigned long nlevel, mrcImage* img);
extern void lmrcImageHistgram4(double** hist, double delta, mrcImage* img);
extern void lmrcImageHistgram6(double** hist, unsigned long nlevel, double Low, double High, mrcImage* img);

Get Statistics data

Getting from mrcImage to Statistics data of image.

extern void lmrcImageInformation(mrcImageInformation* info, mrcImage* img);

Convert pixel data

Converting from pixel data to int type.

extern void lmrcImageToIntImage(mrcImage* dst, mrcImage* src, mrcImageParaTypeInteger mode);

Relation to FFT

extern void lfft2d(mrcImage* fft, mrcImage* img);

extern void lmrcImageFFT(mrcImage* fft, mrcImage* img, long mode);
extern void lmrcImageFFTFirstDimensionOnly(mrcImage* fft, mrcImage* img, long mode);
#ifdef FFTW
extern void lmrcImageFFTWFlagSet(unsigned int flag);
#endif
extern void lmrcFFTFGconj(mrcImage* out, mrcImage* in1, mrcImage* in2);
extern void lmrcFFTFxG(mrcImage* out, mrcImage* in1, mrcImage* in2);

Correlation of image data

extern void lmrcImageCorrelation(mrcImage* out, mrcImage* in, mrcImage* ref, long mode);
extern void lmrcImageCorrelationModePrint(FILE* fpt);

extern void lmrcImageCorrelationWithCTFCompensation(mrcImage* out, mrcImage* in, ctfInfo* inctf, mrcImage* ref, ctfInfo* refctf, long mode);

Error Process

extern mrcStatusType mrcError(char* message, char* inRtnName, char* callRtnName, mrcStatusType status);
extern mrcStatusType mrcErrorMsg(FILE* fpt, char* message, char* inRtnName, char* callRtnName, mrcStatusType status);

Process each command

lmrcFFTInfo

extern floatVector* lmrcFSInfoXAxisMag(mrcImage* fft);
extern floatVector* lmrcFSInfoXAxisPhase(mrcImage* fft);
extern floatVector* lmrcFSInfoYAxisMag(mrcImage* fft);
extern floatVector* lmrcFSInfoYAxisPhase(mrcImage* fft);

extern floatVector* lmrcFSInfoScatteringAngularDistribution(mrcImage* fft);
extern floatVector* lmrcFSInfoScatteringAngularDistributionAverage(mrcImage* fft);
extern floatVector* lmrcFSInfoScatteringAngularDistributionSD(mrcImage* fft);
extern floatVector* lmrcFSInfoSpacing(mrcImage* fft);

mrcImageCheckSameSize

extern void lmrcImageCheckSameSize(mrcImage* in, mrcImage* ref);

mrcImageCheckFFT

extern void lmrcImageCheckFFT(mrcImage* in, mrcImage* ref);

lmrcImageSmoothing

Use setting data as lmrcImageSmoothingInfo.

extern void lmrcImageSmoothingModeInfo(FILE* fpt);
extern void lmrcImageSmoothing(mrcImage* dst, mrcImage* src, lmrcImageSmoothingInfo* info, long mode);

lmrcImageCVE

Use setting data as lmrcImageCVEInfo.

extern void lmrcImageCVE(mrcImage* dst, mrcImage* src, lmrcImageCVEInfo* info);

lmrcImageTfunction

Use setting data as lmrcImageTfunctionInfo.

extern void lmrcImageTfunction(mrcImage* dst, mrcImage* src, lmrcImageTfunctionInfo* info, long mode);

lmrcImageHighlighting

Use setting data as lmrcImageHighlightInfo.

extern void lmrcImageHighlightingInfoPrint(FILE* fpt);
extern void lmrcImageHighlighting(mrcImage* dst, mrcImage* src, lmrcImageHighlightInfo* info);

lmrcImageLowPassFilter

Use setting data as lmrcImageLowPassFilterInfo.

extern void lmrcImageLowPassFilter(mrcImage* dst, mrcImage* src, lmrcImageLowPassFilterInfo* info, long mode);

lmrcImageHighPassFilter

Use setting data as lmrcImageHighPassFilterInfo.

extern void lmrcImageHighPassFilter(mrcImage* dst, mrcImage* src, lmrcImageHighPassFilterInfo* info, long mode);

lmrcImageBandPassFilter

Use setting data as lmrcImageBandPassFilterInfo.

extern void lmrcImageBandPassFilter(mrcImage* dst, mrcImage* src, lmrcImageBandPassFilterInfo* info, long mode);

lmrcImageShrink

extern void lmrcImageShrink(mrcImage* dst, mrcImage* src, mrcImageParaTypeIntegerCoord S, long mode);

lmrcImageShift

extern void lmrcImageShift(mrcImage* out, mrcImage* in, mrcImageParaTypeRealCoord shift, mrcPixelDataHowToGet mode);
extern void lmrcImageShiftFollowingGC(mrcImage* out, mrcImage* in, int mode);

mrcImagePrint

extern  void mrcInfoPrint(FILE* fpt, mrcImage* mrc, mrcImageParaTypeInteger mode);

lmrcImageMultiCTFCompensation

Use setting data as lmrcImageMultiCTFCompensationInfo.

extern void lmrcImageMultiCTFCompensationInfoInit(lmrcImageMultiCTFCompensationInfo* info);
extern void lmrcImageMultiCTFCompensationInfoSet(lmrcImageMultiCTFCompensationInfo* info);
extern void lmrcImageMultiCTFCompensation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long nfile, lmrcImageMultiCTFCompensationInfo info, long mode);

lmrcImageCTFObservation

extern void lmrcImageCTFObservation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long mode);
extern void lmrcImagesCTFObservation(mrcImage* dst, mrcImage* src, ctfInfo* ctf, long mode);

lmrcImageCTFCompensation

extern void lmrcImageCTFCompensation(mrcImage* src, ctfInfo* ctf, long mode);

lmrcImageCTFSN

Use setting data as lmrcImageCTFSNInfo.

extern void lmrcImageCTFSN(mrcImage *outMrc, const mrcImage *inMrc, lmrcImageCTFSNInfo *info, long mode);

lmrcImageFourierPowerSpectrum

Use setting data as lmrcImageFourierPowerSpectrumInfo.

extern mrcImageFourierPowerSpectrum lmrcImageFourierPowerSpectrumMakeSpectrum(const mrcImage *inFFT, lmrcImageFourierPowerSpectrumInfo *info);
extern void lmrcImageFourierPowerSpectrumDeleteSpectrum(mrcImageFourierPowerSpectrum theSpectrum);
extern mrcImageFourierPowerSpectrum lmrcImageFourierPowerSpectrum(const mrcImage *inMrc, lmrcImageFourierPowerSpectrumInfo *info, long mode);

extern void lmrcImageRotation3DModePrint(FILE* fpt);
extern void lmrcImageRotation3DFollowingEulerAngle(mrcImage* dst, mrcImage* src, const char* m, 
	mrcImageParaTypeReal rot1, mrcImageParaTypeReal rot2, mrcImageParaTypeReal rot3, mrcPixelDataHowToGet mode, int mode2);

extern void lmrcImageRotation3DFollowingMatrix3D(mrcImage* dst, mrcImage* src, Matrix3D mat, mrcPixelDataHowToGet mode, int mode2);

extern void lmrcImageRotation3DZXY(mrcImage* dst, mrcImage* src,  
	mrcImageParaTypeReal rotx, mrcImageParaTypeReal roty, mrcImageParaTypeReal rotz, mrcPixelDataHowToGet mode, int mode2);

extern void lmrcImageRotation2D(mrcImage* dst, mrcImage* src, double angle, mrcPixelDataHowToGet mode);
extern void lmrcImageRotation2DPeriodicBoundary(mrcImage* dst, mrcImage* src, double angle, mrcPixelDataHowToGet mode);

mrcImageSectionGet

extern char* mrcImageSectionGetModeDescription(long mode);
extern void mrcImageSectionGet(mrcImage* dst, mrcImage* src, mrcImageParaTypeReal z, long mode);

mrcImageSectionSet

extern void mrcImageSectionSet(mrcImage* dst, mrcImage* src, mrcImageParaTypeReal z, long mode);
extern double lmrcImageMaxDataGet(mrcImage* src, long mode);

mrcImage(API)

Contents

定数

マスク処理

mrcファイルの状態

サイズ

画像Mode

mrcファイル互換のための定義

IMOD

IMOD: (6,7) -> (26,27)

2D投影Mode

画像情報

ピクセルデータ

データの種類

Interpolation方法

構造体

マスク処理

座標

mrcImageの構造

Header情報

デフォルト

CCP4 2000

IMOD

Headerの共用体

FEI

トレイラ情報

画像の統計データ

API毎の設定ファイル

lmrcImageSmoothingInfo

lmrcImageCVEInfo

lmrcImageTfunctionInfo

lmrcImageHighlightInfo

lmrcImageLowPassFilterInfo

lmrcImageHighPassFilterInfo

lmrcImageBandPassFilterInfo

mrcImageDataSet

lmrcImageMultiCTFCompensationInfo

lmrcImageCTFSNInfo

lmrcImageFourierPowerSpectrumInfo

API

初期化

画像データの初期化

Initialize Header information

Setting Hidden data

Initialize Trailer information

Release Image data

Read from file

Write to file

Writing by Lower Resolution

Copy data

Copy Image data

Copy Trailer information

Check Image mode

Getting Pixel data

Getting Pixel data by Pixel

Getting Pixel data by Angstrom

Inline function Gets Pixel data

Setting Pixel data

Setting Image Information

Setting Pixel Information

Setting Pixel data

Setting Pixel data by Pixel

Setting Pixel data by Angstrom

Inline function Sets Pixel data

Statistics processing of Pixel data

Library of General image processing

Operation image(mrcImageOperation)

Unary operation

Add

Subtraction

Devide

Absolute value

Square, Root

Dyadic operation

Addition

Square Add

Subtraction

Convolution

Statistics

Relation to Endian