ctfDetermine
From EosPedia
ctfDetermine is Eos's Command.
Contents
- 1 List of option
- 2 Execution example
- 2.1 Input file image
- 2.2 Case: Options only essential
- 2.3 Option -D
- 2.4 Option -Cs
- 2.5 Option -Cc
- 2.6 Option -dE
- 2.7 Option -Ac
- 2.8 Option -CutLow
- 2.9 Option -CutHigh
- 2.10 Option -I0
- 2.11 Option -ratio
- 2.12 Option -Ai
- 2.13 Option -BofMTF
- 2.14 Option -BofV
- 2.15 Option -Mag
- 2.16 Option -Noise
- 2.17 Option -Noise2
- 2.18 Option -MolcEnv2
List of option
Main option
| Option | Essential/Optional | Description | Default |
|---|---|---|---|
| -i | Essential | Input: mrcImage | NULL |
| -o | Essential | Output: ASCII(Parameters) | NULL |
| -D | Optional | Initial Defocus: [A] | 0.0 |
| -Cs | Optional | Initial Spherical aberration coefficient: [mm] | 1.7 |
| -Cc | Optional | Initial Chromatic aberration coefficient: [mm] | 1.2 |
| -dE | Optional | Initial dE: [mm] | 0.2 |
| -Ac | Optional | Acceleration voltage: [kV] | 200 |
| -CutLow | Optional | CutOffLowFrequncy[/A] | 0.05 |
| -CutHigh | Optional | CutOffHighFrequncy[/A] | 0.5 |
| -I0 | Optional | I0 | 1.0 |
| -ratio | Optional | ratioOfAmpToPhase | 0.1 |
| -Ai | Optional | Illumination Angle: [mrad] | 0.03 |
| -BofMTF | Optional | B of MTF [A] | 15.0 |
| -BofV | Optional | B of Vibration [A] | 3.0 |
| -Mag | Optional | Magnification | 1.0 |
| -Noise | Optional | Signal/Noise Ratio | 0.0 |
| -Noise2 | Optional | Signal/Noise Ratio2 | 0.0 |
| -MolcEnv | Optional | Gaussian: Molcular Envelop [A] | 0.0 |
| -MolcEnv2 | Optional | Table: Molcular Envelop | NULL |
| -min | Optional | min of coefficient area | -10 |
| -max | Optional | max of coefficient area | 10 |
| -s | Optional | step of coefficient | 0.01 |
| -d | Optional | degree of function | 6 |
| -S | Optional | section number of fft | 4 |
| -c | Optional | ConfigurationFile | NULL |
| -m | Optional | Mode | 0 |
| -h | Optional | Help |
-m details
| Value | Description |
|---|---|
| 0 | MinMax Methods (Henderson-like CTF determination) |
| 16 | Fitting Methods |
| 32 | Differential Methods |
| 64 | Covariance Methods |
| 96 | Differential & covariance Methods |
| 128 | MinSquare Methods |
| 160 | Differential+MinSquare Methods by Imamura |
| 161 | Differential+MinSquare Methods+NoiseRemoval(+1) |
| 163 | Differential+MinSquare Methods+NoiseRemoval(+1)+EnvelopeFromLocalMaxima(+2) |
Execution example
Input file image
 |
Min Max |
-1.54801 (35, 32, 8) 1.3162 (35, 0, 55) |
Case: Options only essential
I: 1 Isignal: 1 Magnification: 1 defocus: 0 AoverP: 0.1 Cs: 1.7 Cc: 1.2 dE: 0.2 Ai: 0.03 MTFMode: 32767 MTF: 15 MTF2: 4.59163e-41 flagVibration: 0 BofVibration: 3 flagSN: 0 SN: 0 Inoise: 0 flagSN2: 0 SN2: 0 Inoise2: 0 flagMolecEnvTable: -1922289664 defocus2D0: 0 defocus2D1: 0 defocus0axis: 0 kV: 200 flagWin: -1906535056 CutLow: 0.05 CutHigh: 0.5
Option -D
Case: D=1
defocus: 1 defocus2D0: 1 defocus2D1: 1
Other data doesn't change.
Option -Cs
Case: Cs=2
Cs: 2
Other data doesn't change.
Option -Cc
Case: Cc=1
Cc: 1
Other data doesn't change.
Option -dE
Case: dE=0.5
dE: 0.5
Other data doesn't change.
Option -Ac
Case: Ac=100
kV: 100
Other data doesn't change.
Option -CutLow
Case: CutLow=0.1
CutLow: 0.1
Other data doesn't change.
Option -CutHigh
Case: CutHigh=0.3
CutHigh: 0.3
Other data doesn't change.
Option -I0
Case: I0=2
I: 2 Isignal: 2
Other data doesn't change.
Option -ratio
Case: ratio=0.2
AoverP: 0.2
Other data doesn't change.
Option -Ai
Case: Ai=0.01
Ai: 0.01
Other data doesn't change.
Option -BofMTF
Case: BofMTF=20
MTF: 20
Other data doesn't change.
Option -BofV
Case: BofV=5
flagVibration: 1 BofVibration: 5
Other data doesn't change.
Option -Mag
Case: Mag=2
Magnification: 2
Other data doesn't change.
Option -Noise
Case: Noise=0.1
flagSN: 1 SN: 0.1 Inoise: 0.1
Other data doesn't change.
Option -Noise2
Case: Noise2=0.2
flagSN2: 1 SN2: 0.2 Inoise2: 0.2
Other data doesn't change.
Option -MolcEnv2
Case: MolcEnv=(filename)
flagMolecEnvTable: 1 MET-File: (filename)
Other data doesn't change.
