ctfInfo(API) - Revision history

Kinoshita: /* constant */

2014-09-25T08:55:33Z

‎constant

Kinoshita: /* struct */

2014-09-25T08:49:07Z

‎struct

Kinoshita: /* API */

2014-09-25T08:45:40Z

‎API

Kinoshita: /* API */

2014-09-25T08:42:04Z

‎API

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Kinoshita at 05:50, 29 July 2014

2014-07-29T05:50:24Z

Kinoshita: Created page with "DataManip/'''ctfInfo''' is API fo CTF Correration. == constant == #define ctfInfoModeWithAmplitudeContrast 0x0f #define ctfInfoModeWithMTF 0x10 #de..."

2014-07-29T05:49:46Z

Created page with "DataManip/'''ctfInfo''' is API fo CTF Correration. == constant == #define ctfInfoModeWithAmplitudeContrast 0x0f #define ctfInfoModeWithMTF 0x10 #de..."

New page

DataManip/'''ctfInfo''' is API fo [[CTF Correration]].

== constant ==
#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;

== struct ==
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);

@@ Line 312: / Line 312: @@
 			<tr>
 				<td>0</td>
-				<td>return 1(No correction)</td>
+				<td>return 1(No Correction)</td>
 			</tr>
 			<tr>
 				<td>1</td>
-				<td>ctf/|ctf| (逆位相)</td>
+				<td>ctf/|ctf| (phase flipping)</td>
 			</tr>
 			<tr>
 				<td>2</td>
-				<td>ctf (逆位相 x  CTF Correction)</td>
+				<td>ctf (phase flipping and ctf-multiplying)</td>
 			</tr>
 			<tr>
 				<td>3</td>
-				<td>1/ctf    (0.1<|ctf| ) ( CTF Correction / 逆位相)</td>
+				<td>1/ctf    (0.1<|ctf| ) (phase flipping and ctf-divided)</td>
 			</tr>
 			<tr>
@@ Line 346: / Line 346: @@
 <br>
-===== 2Dの場合 =====
+===== Case 2D =====
-X, YからRを求めて引数としてctfWeightForCorrectionを呼び出す
+Calculate R by X and Y. Then call ctfWeightForCorrection with it as argument.
   extern float ctfWeightForCorrection2D(ctfInfo* info, float X, float Y, long mode);
-==== 分子のEnvelope ====
+==== Molecular Envelope ====
-fileRead
+File Read
   extern void lmolecularEnvelopeFileRead(FILE* fpt, molecularEnvelope* mol, int mode);
-file書き出し
+File Write
   extern void lmolecularEnvelopeFileWrite(FILE* fpt, molecularEnvelope* mol, int mode);
 Resampling
   extern void lmolecularEnvelopeResampling(molecularEnvelope* dst, molecularEnvelope* src, float dR, float RMax, int mode);
-srcにおけるRのEnvelope値を取得
+Get the Envelope of src at R.
   extern float lmolecularEnvelopeDataGet(molecularEnvelope* src, float R, int mode);
 ==== CTFInformation ====
-fileRead
+File Read
   extern void ctfInfoRead(FILE* fpt, ctfInfo* ctf, char* pre, int mode);
-file書き出し
+File Write
   extern void ctfInfoWrite(FILE* fpt, ctfInfo ctf, char* pre, int mode);

← Older revision		Revision as of 05:50, 29 July 2014
Line 1:		Line 1:
−	DataManip/'''ctfInfo''' is API fo [[CTF ~~Correration~~]].	+	DataManip/'''ctfInfo''' is API fo [[CTF Correction]].

	== constant ==		== constant ==

@@ Line 2: / Line 2: @@
 == constant ==
   #define ctfInfoModeWithAmplitudeContrast    0x0f
   #define ctfInfoModeWithMTF                  0x10
@@ Line 7: / Line 9: @@
   #define ctfInfoModeWithEnergySpread         0x40
   #define ctfInfoModeAbsoluteValue            0x100
   typedef enum ctfInfoMode {
   	ctfInfoModePhaseCTFOnly   = 0,
   	ctfInfoModePhaseAndAmpCTF = 1
   } ctfInfoMode;
   typedef enum ctfInfoMTFMode {
   	ctfInfoMTFModeSingleExp = 0,
@@ Line 21: / Line 83: @@
   	ctfInfoMTFModePolynomial = 5
   } ctfInfoMTFMode;
 == struct ==

@@ Line 23: / Line 23: @@
 == struct ==
   typedef struct moleculrEnvelope {
   	char* filename;
@@ Line 31: / Line 32: @@
   } molecularEnvelope;
   typedef struct ctfInfo {
   	float kV;      /* kV */