「ctfInfo(API)」の版間の差分

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(ページの作成:「DataManip/'''ctfInfo'''はCTF補正のためのAPI です。 == 定数 == == 構造体 == == API ==」)
 
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== 定数 ==
 
== 定数 ==
 +
#define ctfInfoModeWithAmplitudeContrast    0x0f
 +
#define ctfInfoModeWithMTF                  0x10
 +
#define ctfInfoModeWithIlluminationAngle    0x20
 +
#define ctfInfoModeWithEnergySpread        0x40
 +
#define ctfInfoModeAbsoluteValue            0x100
 +
 +
typedef enum ctfInfoMode {
 +
ctfInfoModePhaseCTFOnly  = 0,
 +
ctfInfoModePhaseAndAmpCTF = 1
 +
} ctfInfoMode;
 +
 +
typedef enum ctfInfoMTFMode {
 +
ctfInfoMTFModeSingleExp = 0,
 +
ctfInfoMTFModeSingleLorentzian = 1,
 +
ctfInfoMTFModeBoth      = 2,
 +
ctfInfoMTFModeLinear    = 3,
 +
ctfInfoMTFModeBothSum  = 4,
 +
ctfInfoMTFModePolynomial = 5
 +
} ctfInfoMTFMode;
  
 
== 構造体 ==
 
== 構造体 ==
 +
typedef struct moleculrEnvelope {
 +
char* filename;
 +
int  nR;
 +
float* R;
 +
float* Envelope;
 +
int    mode;
 +
} molecularEnvelope;
 +
 +
typedef struct ctfInfo {
 +
float kV;      /* kV */
 +
float defocus; /* A : Underfocus is plus, while overfocus is minus*/
 +
float Cc;      /* mm */
 +
float dE;
 +
float Cs;      /* mm */
 +
float Ain;    /* mrad : Illumination Angle */
 +
long  flagWin; /* Windowing */
 +
float CutLow;  /* Windowing: CutLow  A-1 */
 +
float CutHigh; /* Windowing: CutHigh A-1 */
 +
 +
float I0;      /* Intensity */
 +
float Isignal; /* Intensity of signal */
 +
 +
float ratioOfAmpToPhase; /* The ratio of amp to phase */
 +
 +
float Inoise;  /* Intensity of noise : Isignal*/
 +
long  flagWhiteNoise;
 +
float WhiteNoise;  /* Affected by MTF(R) */
 +
 +
long  flagWhiteNoiseRaising;
 +
float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */
 +
 +
float Inoise2; /* Intensity of noise */
 +
long  flagWhiteNoise2;
 +
float WhiteNoise2; /* Not Affected by MTF(R)*/
 +
 +
int  flagAstigmatism;
 +
float defocus2D[2];      /* A : Normally [0]: Max [1]: Min */
 +
float defocus0axis;      /* radian : angle of the defocus2D[0]-axis */
 +
 +
long mode;
 +
 +
long  flagMagnification;
 +
float Magnification;
 +
 +
/* MTF(R): Modulation Transfer Function */
 +
ctfInfoMTFMode MTFMode;
 +
float BofMTF;  /* Exponential: exp(-B R)  */
 +
float BofMTF2; /* Lorentzian : 1/(B*B+R*R) */
 +
float WeightOfSecondTermForMTF; /* 0 <-> 1 */
 +
/*for PolynomialExpNoise*//*d = degree*/
 +
float BofMTFd2;
 +
float BofMTFd3;
 +
float BofMTFd4;
 +
float BofMTFd5;
 +
float BofMTFd6;
 +
 +
/* Molecular Envelope: Scattering Factor */
 +
/* For Gaussian */
 +
float MolecEnv;                  /* A : */
 +
/* For Table */
 +
long  flagMolecEnvTable;
 +
molecularEnvelope MolecEnvTable;
 +
/* For Lorentzian */
 +
float flagElastic;
 +
float Elastic;
 +
float ElasticShift;
 +
float ElasticWidth;
 +
float ElasticRing;
 +
float ElasticRingPosition;
 +
float ElasticRingWidth;
 +
 +
/* Stage Vibration */
 +
long  flagVibration;
 +
long  VibrationMode;
 +
float BofVibration;
 +
 +
/* Aliasing and Sampling */
 +
long flagAliasing;
 +
float NyquistFrequency;
 +
long flagSampling;
 +
 +
/* Inelastic Signal */
 +
/* For Gaussian */
 +
long flagWithInElastic;
 +
float InElasticGaussian;
 +
/* For Table */
 +
long flagWithInElasticTable;
 +
molecularEnvelope InElasticEnvTable;
 +
/* Lorentzian */
 +
long flagInElastic;
 +
float InElastic;
 +
float InElasticShift;
 +
float InElasticWidth;
 +
float InElasticRing;
 +
float InElasticRingPosition;
 +
float InElasticRingWidth;
 +
} ctfInfo;
  
 
== API ==
 
== API ==
 +
extern void ctfInfoSendByPVM(ctfInfo* info, int tid, long mode);
 +
extern void ctfInfoRecieveByPVM(ctfInfo* info, int tid, long mode);
 +
extern float ctfSignalFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfNoiseFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfNoise2Function(ctfInfo* info, float R, long mode);
 +
extern float ctfSignalPowerFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfNoisePowerFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfNoise2PowerFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfScatteringFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfMolecularEnvelopeFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfMolecularEnvelopeInElasticFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfVibrationFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfFunctionSampling(float R, float Nyquist, long mode);
 +
extern void  ctfFunctionPVMStart(ctfInfo* info, float R, int tid, long mode);
 +
extern float ctfFunctionPVMEnd(ctfInfo* info, float R, int tid, long mode);
 +
extern void  ctfFunctionPVMServer();
 +
extern float ctfEnvelopFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfMTFFunction(ctfInfo* info, float R, long mode);
 +
extern float ctfFunction2D(ctfInfo* info, float X, float Y, long mode);
 +
extern float wavelengthOfElectron(float E);
 +
extern float defocusDeterminationFromThonRing(ctfInfo* info, float R, long n, long mode);
 +
extern void ctfWeightForCorrectionUsage(FILE* fpt);
 +
extern float ctfWeightForCorrection2D(ctfInfo* info, float X, float Y, long mode);
 +
extern float ctfWeightForCorrection(ctfInfo* info, float R, long mode);
 +
extern void lmolecularEnvelopeFileRead(FILE* fpt, molecularEnvelope* mol, int mode);
 +
extern void lmolecularEnvelopeFileWrite(FILE* fpt, molecularEnvelope* mol, int mode);
 +
extern void lmolecularEnvelopeResampling(molecularEnvelope* dst, molecularEnvelope* src, float dR, float RMax, int mode);
 +
extern float lmolecularEnvelopeDataGet(molecularEnvelope* src, float R, int mode);
 +
extern void ctfInfoRead(FILE* fpt, ctfInfo* ctf, char* pre, int mode);
 +
extern void ctfInfoWrite(FILE* fpt, ctfInfo ctf, char* pre, int mode);

2014年5月13日 (火) 02:31時点における版

DataManip/ctfInfoはCTF補正のためのAPI です。

定数

#define ctfInfoModeWithAmplitudeContrast    0x0f
#define ctfInfoModeWithMTF                  0x10
#define ctfInfoModeWithIlluminationAngle    0x20
#define ctfInfoModeWithEnergySpread         0x40
#define ctfInfoModeAbsoluteValue            0x100 

typedef enum ctfInfoMode {
	ctfInfoModePhaseCTFOnly   = 0,
	ctfInfoModePhaseAndAmpCTF = 1 
} ctfInfoMode;

typedef enum ctfInfoMTFMode {
	ctfInfoMTFModeSingleExp = 0,
	ctfInfoMTFModeSingleLorentzian = 1,
	ctfInfoMTFModeBoth      = 2,
	ctfInfoMTFModeLinear    = 3, 
	ctfInfoMTFModeBothSum   = 4,
	ctfInfoMTFModePolynomial = 5
} ctfInfoMTFMode;

構造体

typedef struct moleculrEnvelope {
	char* filename; 
	int   nR;
	float* R;
	float* Envelope;
	int    mode;	
} molecularEnvelope;

typedef struct ctfInfo {
	float kV;      /* kV */
	float defocus; /* A : Underfocus is plus, while overfocus is minus*/
	float Cc;      /* mm */
	float dE; 
	float Cs;      /* mm */
	float Ain;     /* mrad : Illumination Angle */
	long  flagWin; /* Windowing */ 
	float CutLow;  /* Windowing: CutLow  A-1 */
	float CutHigh; /* Windowing: CutHigh A-1 */

	float I0;      /* Intensity */
	float Isignal; /* Intensity of signal */

	float ratioOfAmpToPhase; /* The ratio of amp to phase */

	float Inoise;  /* Intensity of noise : Isignal*/
	long  flagWhiteNoise;
	float WhiteNoise;  /* Affected by MTF(R) */

	long  flagWhiteNoiseRaising; 	
	float WhiteNoiseRaising; /* WhiteNoise Raising depending upon R */

	float Inoise2; /* Intensity of noise */
	long  flagWhiteNoise2;
	float WhiteNoise2; /* Not Affected by MTF(R)*/

	int   flagAstigmatism;
	float defocus2D[2];      /* A : Normally [0]: Max [1]: Min */
	float defocus0axis;      /* radian : angle of the defocus2D[0]-axis */

	long mode;
	
	long  flagMagnification;	
	float Magnification;

	/* MTF(R): Modulation Transfer Function */ 
	ctfInfoMTFMode MTFMode;
	float BofMTF;  /* Exponential: exp(-B R)   */
	float BofMTF2; /* Lorentzian : 1/(B*B+R*R) */	
	float WeightOfSecondTermForMTF; /* 0 <-> 1 */
	/*for PolynomialExpNoise*//*d = degree*/
	float BofMTFd2;
	float BofMTFd3;
	float BofMTFd4;
	float BofMTFd5;
	float BofMTFd6;

	/* Molecular Envelope: Scattering Factor */
	/* For Gaussian */
	float MolecEnv;                   /* A : */
	/* For Table */
	long  flagMolecEnvTable;
	molecularEnvelope MolecEnvTable;
	/* For Lorentzian */
	float flagElastic;
	float Elastic;
	float ElasticShift;
	float ElasticWidth;
	float ElasticRing;
	float ElasticRingPosition;
	float ElasticRingWidth;

	/* Stage Vibration */
	long  flagVibration;
	long  VibrationMode;
	float BofVibration;

	/* Aliasing and Sampling */
	long flagAliasing;
	float NyquistFrequency;
	long flagSampling; 

	/* Inelastic Signal */
	/* For Gaussian */
	long flagWithInElastic;
	float InElasticGaussian;
	/* For Table */
	long flagWithInElasticTable;
	molecularEnvelope InElasticEnvTable;	
	/* Lorentzian */	
	long flagInElastic;
	float InElastic;
	float InElasticShift;
	float InElasticWidth;
	float InElasticRing;
	float InElasticRingPosition;
	float InElasticRingWidth;
} ctfInfo;

API

extern void ctfInfoSendByPVM(ctfInfo* info, int tid, long mode);
extern void ctfInfoRecieveByPVM(ctfInfo* info, int tid, long mode);
extern float ctfSignalFunction(ctfInfo* info, float R, long mode);
extern float ctfNoiseFunction(ctfInfo* info, float R, long mode);
extern float ctfNoise2Function(ctfInfo* info, float R, long mode);
extern float ctfSignalPowerFunction(ctfInfo* info, float R, long mode);
extern float ctfNoisePowerFunction(ctfInfo* info, float R, long mode);
extern float ctfNoise2PowerFunction(ctfInfo* info, float R, long mode);
extern float ctfScatteringFunction(ctfInfo* info, float R, long mode);
extern float ctfMolecularEnvelopeFunction(ctfInfo* info, float R, long mode);
extern float ctfMolecularEnvelopeInElasticFunction(ctfInfo* info, float R, long mode);
extern float ctfVibrationFunction(ctfInfo* info, float R, long mode);
extern float ctfFunction(ctfInfo* info, float R, long mode);
extern float ctfFunctionSampling(float R, float Nyquist, long mode);
extern void  ctfFunctionPVMStart(ctfInfo* info, float R, int tid, long mode);
extern float ctfFunctionPVMEnd(ctfInfo* info, float R, int tid, long mode);
extern void  ctfFunctionPVMServer();
extern float ctfEnvelopFunction(ctfInfo* info, float R, long mode);
extern float ctfMTFFunction(ctfInfo* info, float R, long mode);
extern float ctfFunction2D(ctfInfo* info, float X, float Y, long mode);
extern float wavelengthOfElectron(float E);
extern float defocusDeterminationFromThonRing(ctfInfo* info, float R, long n, long mode);
extern void ctfWeightForCorrectionUsage(FILE* fpt);
extern float ctfWeightForCorrection2D(ctfInfo* info, float X, float Y, long mode);
extern float ctfWeightForCorrection(ctfInfo* info, float R, long mode);
extern void lmolecularEnvelopeFileRead(FILE* fpt, molecularEnvelope* mol, int mode);
extern void lmolecularEnvelopeFileWrite(FILE* fpt, molecularEnvelope* mol, int mode);
extern void lmolecularEnvelopeResampling(molecularEnvelope* dst, molecularEnvelope* src, float dR, float RMax, int mode);
extern float lmolecularEnvelopeDataGet(molecularEnvelope* src, float R, int mode);
extern void ctfInfoRead(FILE* fpt, ctfInfo* ctf, char* pre, int mode);
extern void ctfInfoWrite(FILE* fpt, ctfInfo ctf, char* pre, int mode);

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