Difference between revisions of "lctfDetermination(API)"

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(Created page with "DataManip/ctfInfo/src/'''lctfDetermination''' is API for ctfDetermine. == constant == == struct == typedef struct lctfDetermineInfo { ctfInfo initial; long Tho...")
 
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DataManip/ctfInfo/src/'''lctfDetermination''' is API for [[ctfDetermine]].
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DataManip/ctfInfo/src/'''lctfDetermination''' is [[API]] to determine [[CTF]], and it is used by [[ctfDetermine]].
  
 
== constant ==
 
== constant ==
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== API ==
 
== API ==
 +
=== CTF Determination ===
 +
==== Main ====
 +
Perform [[CTF]] Determination depending on mode(masked by 0x000000F0).<br>
 +
Basically, mode of called function is used with masking at 0x0000000Fでマスク.<br>
 +
Currently, [[ctfDetermine]] doesn't use this [[API]], and uses directly other [[API]]s.
 
  extern void lctfDetermine(ctfInfo* result, ctfInfo* var, mrcImage* mrc, lctfDetermineInfo* linfo, long mode);
 
  extern void lctfDetermine(ctfInfo* result, ctfInfo* var, mrcImage* mrc, lctfDetermineInfo* linfo, long mode);
−
extern void lctfDtermmineUsage(FILE* fpt);
+
<table border="1">
 +
<tr>
 +
<th>mode(& 0x000000F0)</th>
 +
<th>Used Function</th>
 +
</tr>
 +
<tr>
 +
<td>0</td>
 +
<td>lctfDeterminationbyMinMaxMethods</td>
 +
</tr>
 +
<tr>
 +
<td>16</td>
 +
<td>lctfDeterminationbyFittingMethods</td>
 +
</tr>
 +
<tr>
 +
<td>32</td>
 +
<td>lctfDeterminationbyDifferentialMethods</td>
 +
</tr>
 +
<tr>
 +
<td>64</td>
 +
<td>lctfDeterminationbyCovarianceMethods</td>
 +
</tr>
 +
<tr>
 +
<td>96</td>
 +
<td>lctfDeterminationbyMixMethods</td>
 +
</tr>
 +
<tr>
 +
<td>128</td>
 +
<td>lctfDeterminationbyMinSquareMethods</td>
 +
</tr>
 +
<tr>
 +
<td>160, 161, 163(uses also mask of 0x0000000F)</td>
 +
<td>lctfDeterminationbyMinSquareMethods<br>
 +
EnvelopeDetermine<br>
 +
</td>
 +
</tr>
 +
<tr>
 +
<td>167(uses also mask of 0x0000000F)</td>
 +
<td>lctfDeterminationbyMinSquareMethodsWithAcomp</td>
 +
</tr>
 +
<tr>
 +
<td>176</td>
 +
<td>lmrcFSInfoScatteringAngularDistributionAverageSection<br>
 +
lctfDeterminationbyMinSquareMethods<br>
 +
lctfDeterminationByTangent<br>
 +
lastigmatismDetection<br>
 +
</td>
 +
</tr>
 +
</table>
 +
<br>
  
 +
==== MinMax Methods ====
 
  extern void lctfDeterminationbyMinMaxMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long mode);
 
  extern void lctfDeterminationbyMinMaxMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long mode);
 +
 +
==== Fitting Methods ====
 
  extern void lctfDeterminationbyFittingMethods(ctfInfo* res, ctfInfo* var, mrcImage* mrc, ctfInfo* ini, long mode);
 
  extern void lctfDeterminationbyFittingMethods(ctfInfo* res, ctfInfo* var, mrcImage* mrc, ctfInfo* ini, long mode);
 +
 +
Angular Distribution
 
  extern void angularDistributionFunctionOfSignalAndNoise(float x, float p[], float* y, float dyda[], int na);
 
  extern void angularDistributionFunctionOfSignalAndNoise(float x, float p[], float* y, float dyda[], int na);
 +
Input: x, p<br>
 +
Output: y, dyda<br>
 +
<br>
 +
Elements of '''p''' and '''dyda''' are used as the following member in '''ctfinfo'''.
 +
<table border="1">
 +
<tr>
 +
<th>No.</th>
 +
<th>corresponded '''ctfInfo''''s member</th>
 +
</tr>
 +
<tr>
 +
<td>1</td>
 +
<td>I0</td>
 +
</tr>
 +
<tr>
 +
<td>2</td>
 +
<td>defocus</td>
 +
</tr>
 +
<tr>
 +
<td>3</td>
 +
<td>Cs</td>
 +
</tr>
 +
<tr>
 +
<td>4</td>
 +
<td>ratioOfAmpToPhase</td>
 +
</tr>
 +
<tr>
 +
<td>5</td>
 +
<td>Ain</td>
 +
</tr>
 +
<tr>
 +
<td>6</td>
 +
<td>Cc</td>
 +
</tr>
 +
<tr>
 +
<td>7</td>
 +
<td>dE</td>
 +
</tr>
 +
<tr>
 +
<td>8</td>
 +
<td>BofVibration</td>
 +
</tr>
 +
<tr>
 +
<td>9</td>
 +
<td>WhiteNoise</td>
 +
</tr>
 +
<tr>
 +
<td>10</td>
 +
<td>WhiteNoise2</td>
 +
</tr>
 +
<tr>
 +
<td>11</td>
 +
<td>BofMTF</td>
 +
</tr>
 +
<tr>
 +
<td>12</td>
 +
<td>MolecEnv</td>
 +
</tr>
 +
<tr>
 +
<td>13</td>
 +
<td>kV</td>
 +
</tr>
 +
<tr>
 +
<td>14</td>
 +
<td>(Constant value)511*1e3</td>
 +
</tr>
 +
<tr>
 +
<td>15</td>
 +
<td>(Function value)wavelengthOfElectron(ini->kV*1e3)</td>
 +
</tr>
 +
<tr>
 +
<td>16</td>
 +
<td>Magnification</td>
 +
</tr>
 +
</table>
 +
<br>
 +
 +
==== Differential Methods ====
 
  extern void lctfDeterminationbyDifferentialMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);
 
  extern void lctfDeterminationbyDifferentialMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);
 +
 +
==== Covariance Methods ====
 
  extern void lctfDeterminationbyCovarianceMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);
 
  extern void lctfDeterminationbyCovarianceMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);
 +
 +
==== Differential & covariance  Methods ====
 
  extern void lctfDeterminationbyMixMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long* ThonRing,long mode);
 
  extern void lctfDeterminationbyMixMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long* ThonRing,long mode);
 +
 +
==== MinSquare Methods ====
 
  extern void lctfDeterminationbyMinSquareMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);
 
  extern void lctfDeterminationbyMinSquareMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);
 +
 +
Add "Ratio of Amplitude to Phase"(0.05 ~ 1.00 (+0.01)) to the condition.
 
  extern void lctfDeterminationbyMinSquareMethodsWithAcomp(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);
 
  extern void lctfDeterminationbyMinSquareMethodsWithAcomp(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);
−
extern double lctfDeterminationByTangent(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);
+
 
 +
==== Determine envelope ====
 +
Output the determined envelope to '''res'''.
 
  extern void EnvelopeDetermine(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);
 
  extern void EnvelopeDetermine(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);
 +
 +
==== By using tan Function ====
 +
extern double lctfDeterminationByTangent(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);
 +
 +
=== Help ===
 +
Output the mode details
 +
extern void lctfDtermmineUsage(FILE* fpt);

Revision as of 07:33, 30 September 2014

DataManip/ctfInfo/src/lctfDetermination is API to determine CTF, and it is used by ctfDetermine.

constant

struct

typedef struct lctfDetermineInfo {
	ctfInfo initial;

	long    ThonRing; 	
	/* For Astigmatism */
	int     flagAstigmatism;
	int    section;

	int    degree;
	double step;
	double max;
	double min;
	float  firstRingDefocus;
	float  IntensityMin;
	float  IntensityMax;
	float* noise;
} lctfDetermineInfo;

API

CTF Determination

Main

Perform CTF Determination depending on mode(masked by 0x000000F0).
Basically, mode of called function is used with masking at 0x0000000Fでマスク.
Currently, ctfDetermine doesn't use this API, and uses directly other APIs. 

extern void lctfDetermine(ctfInfo* result, ctfInfo* var, mrcImage* mrc, lctfDetermineInfo* linfo, long mode);
mode(& 0x000000F0) Used Function
0 lctfDeterminationbyMinMaxMethods
16 lctfDeterminationbyFittingMethods
32 lctfDeterminationbyDifferentialMethods
64 lctfDeterminationbyCovarianceMethods
96 lctfDeterminationbyMixMethods
128 lctfDeterminationbyMinSquareMethods
160, 161, 163(uses also mask of 0x0000000F) lctfDeterminationbyMinSquareMethods

EnvelopeDetermine
167(uses also mask of 0x0000000F) lctfDeterminationbyMinSquareMethodsWithAcomp
176 lmrcFSInfoScatteringAngularDistributionAverageSection

lctfDeterminationbyMinSquareMethods
lctfDeterminationByTangent
lastigmatismDetection


MinMax Methods

extern void lctfDeterminationbyMinMaxMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long mode);

Fitting Methods

extern void lctfDeterminationbyFittingMethods(ctfInfo* res, ctfInfo* var, mrcImage* mrc, ctfInfo* ini, long mode);

Angular Distribution 

extern void angularDistributionFunctionOfSignalAndNoise(float x, float p[], float* y, float dyda[], int na);

Input: x, p
Output: y, dyda

Elements of p and dyda are used as the following member in ctfinfo.

No. corresponded ctfInfo's member
1 I0
2 defocus
3 Cs
4 ratioOfAmpToPhase
5 Ain
6 Cc
7 dE
8 BofVibration
9 WhiteNoise
10 WhiteNoise2
11 BofMTF
12 MolecEnv
13 kV
14 (Constant value)511*1e3
15 (Function value)wavelengthOfElectron(ini->kV*1e3)
16 Magnification


Differential Methods

extern void lctfDeterminationbyDifferentialMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);

Covariance Methods

extern void lctfDeterminationbyCovarianceMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing, long mode);

Differential & covariance Methods

extern void lctfDeterminationbyMixMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini, long* ThonRing,long mode);

MinSquare Methods

extern void lctfDeterminationbyMinSquareMethods(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);

Add "Ratio of Amplitude to Phase"(0.05 ~ 1.00 (+0.01)) to the condition. 

extern void lctfDeterminationbyMinSquareMethodsWithAcomp(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,long* ThonRing,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres ,long mode);

Determine envelope

Output the determined envelope to res. 

extern void EnvelopeDetermine(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);

By using tan Function

extern double lctfDeterminationByTangent(ctfInfo* res, mrcImage* mrc, ctfInfo* ini,lctfDetermineInfo* linfo,floatVector* defocus,floatVector* Eres, long mode);

Help

Output the mode details 

extern void lctfDtermmineUsage(FILE* fpt);
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