ctfDetermine - Revision history

Kinoshita: /* Main option */

2014-09-05T07:25:19Z

‎Main option

Kinoshita: /* Main option */

2014-08-25T06:49:07Z

‎Main option

Kinoshita: Created page with "'''ctfDetermine''' is Eos's Command. == List of option == === Main option === ..."
2014-08-19T02:19:12Z
Created page with "'''ctfDetermine''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essential/Optional</th>..."
New page
'''ctfDetermine''' is [[Eos]]'s [[Command]].

== List of option ==
=== Main option ===
<table border="1">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]](Parameters)</td>
<td>NULL</td>
</tr>
<tr>
<td>-D</td>
<td>Optional</td>
<td>Initial Defocus: [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>Initial [[Spherical aberration coefficient]]: [mm]</td>
<td>1.7</td>
</tr>
<tr>
<td>-Cc</td>
<td>Optional</td>
<td>Initial Cs: [mm]</td>
<td>1.2</td>
</tr>
<tr>
<td>-dE</td>
<td>Optional</td>
<td>Initial dE: [mm]</td>
<td>0.2</td>
</tr>
<tr>
<td>-Ac</td>
<td>Optional</td>
<td>[[Acceleration voltage]]: [kV]</td>
<td>200</td>
</tr>
<tr>
<td>-CutLow</td>
<td>Optional</td>
<td>CutOffLowFrequncy[/A]</td>
<td>0.05</td>
</tr>
<tr>
<td>-CutHigh</td>
<td>Optional</td>
<td>CutOffHighFrequncy[/A]</td>
<td>0.5</td>
</tr>
<tr>
<td>-I0</td>
<td>Optional</td>
<td>I0</td>
<td>1.0</td>
</tr>
<tr>
<td>-ratio</td>
<td>Optional</td>
<td>ratioOfAmpToPhase</td>
<td>0.1</td>
</tr>
<tr>
<td>-Ai</td>
<td>Optional</td>
<td>[[Illumination Angle]]: [mrad]</td>
<td>0.03</td>
</tr>
<tr>
<td>-BofMTF</td>
<td>Optional</td>
<td>B of MTF [A]</td>
<td>15.0</td>
</tr>
<tr>
<td>-BofV</td>
<td>Optional</td>
<td>B of Vibration [A]</td>
<td>3.0</td>
</tr>
<tr>
<td>-Mag</td>
<td>Optional</td>
<td>Magnification</td>
<td>1.0</td>
</tr>
<tr>
<td>-Noise</td>
<td>Optional</td>
<td>Signal/Noise Ratio</td>
<td>0.0</td>
</tr>
<tr>
<td>-Noise2</td>
<td>Optional</td>
<td>Signal/Noise Ratio2</td>
<td>0.0</td>
</tr>
<tr>
<td>-MolcEnv</td>
<td>Optional</td>
<td>Gaussian: Molcular Envelop [A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-MolcEnv2</td>
<td>Optional</td>
<td>Table: Molcular Envelop</td>
<td>NULL</td>
</tr>
<tr>
<td>-min</td>
<td>Optional</td>
<td>min of coefficient area</td>
<td>-10</td>
</tr>
<tr>
<td>-max</td>
<td>Optional</td>
<td>max of coefficient area</td>
<td>10</td>
</tr>
<tr>
<td>-s</td>
<td>Optional</td>
<td>step of coefficient</td>
<td>0.01</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>agree of function</td>
<td>6</td>
</tr>
<tr>
<td>-S</td>
<td>Optional</td>
<td>section number of fft</td>
<td>4</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>MinMax Methods (Henderson-like CTF determination)</td>
</tr>
<tr>
<td>16</td>
<td>Fitting Methods</td>
</tr>
<tr>
<td>32</td>
<td>Differential Methods</td>
</tr>
<tr>
<td>64</td>
<td>Covariance Methods</td>
</tr>
<tr>
<td>96</td>
<td>Differential & covariance Methods</td>
</tr>
<tr>
<td>128</td>
<td>MinSquare Methods </td>
</tr>
<tr>
<td>160</td>
<td>Differential+MinSquare Methods by Imamura</td>
</tr>
<tr>
<td>161</td>
<td>Differential+MinSquare Methods+NoiseRemoval(+1) </td>
</tr>
<tr>
<td>163</td>
<td>Differential+MinSquare Methods+NoiseRemoval(+1)+EnvelopeFromLocalMaxima(+2) </td>
</tr>
</table>

== Execution example ==
===[[:Media:Input-3D-Data.ctf | Input file]] image===
<table>
<tr>
<td>[[File:Input-ctfDetermine.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-1.54801 (35, 32, 8)<br>
1.3162 (35, 0, 55)<br>
-7.58399e-11<br>
0.19545<br>
0.000279214<br></p>
</td>
</tr>
</table>

=== Case: Options only essential ===
<pre>
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
</pre>

=== Option -D===
====Case: D=1====
<pre>
defocus: 1
defocus2D0: 1
defocus2D1: 1
</pre>
<div>Other data doesn't change.</div>

=== Option -Cs===
====Case: Cs=2====
<pre>
Cs: 2
</pre>
<div>Other data doesn't change.</div>

=== Option -Cc===
====Case: Cc=1====
<pre>
Cc: 1
</pre>
<div>Other data doesn't change.</div>

=== Option -dE===
====Case: dE=0.5====
<pre>
dE: 0.5
</pre>
<div>Other data doesn't change.</div>

=== Option -Ac===
====Case: Ac=100====
<pre>
kV: 100
</pre>
<div>Other data doesn't change.</div>

=== Option -CutLow===
====Case: CutLow=0.1====
<pre>
CutLow: 0.1
</pre>
<div>Other data doesn't change.</div>

=== Option -CutHigh===
====Case: CutHigh=0.3====
<pre>
CutHigh: 0.3
</pre>
<div>Other data doesn't change.</div>

=== Option -I0===
====Case: I0=2====
<pre>
I: 2
Isignal: 2
</pre>
<div>Other data doesn't change.</div>

=== Option -ratio===
====Case: ratio=0.2====
<pre>
AoverP: 0.2
</pre>
<div>Other data doesn't change.</div>

=== Option -Ai===
====Case: Ai=0.01====
<pre>
Ai: 0.01
</pre>
<div>Other data doesn't change.</div>

=== Option -BofMTF===
====Case: BofMTF=20====
<pre>
MTF: 20
</pre>
<div>Other data doesn't change.</div>

=== Option -BofV===
====Case: BofV=5====
<pre>
flagVibration: 1
BofVibration: 5
</pre>
<div>Other data doesn't change.</div>

=== Option -Mag===
====Case: Mag=2====
<pre>
Magnification: 2
</pre>
<div>Other data doesn't change.</div>

=== Option -Noise===
====Case: Noise=0.1====
<pre>
flagSN: 1
SN: 0.1
Inoise: 0.1
</pre>
<div>Other data doesn't change.</div>

=== Option -Noise2===
====Case: Noise2=0.2====
<pre>
flagSN2: 1
SN2: 0.2
Inoise2: 0.2
</pre>
<div>Other data doesn't change.</div>

=== Option -MolcEnv2===
====Case: MolcEnv=(filename)====
<pre>
flagMolecEnvTable: 1
MET-File: (filename)
</pre>
<div>Other data doesn't change.</div>

Option Essential/Optional