llExtractWithLayerSeparationFilamentInfo - Revision history

Kinoshita: Created page with "'''llExtractWithLayerSeparationFilamentInfo''' is Eos's Command. == List of option == === Main option ===

Option ..."
2014-08-25T01:56:25Z

Created page with "'''llExtractWithLayerSeparationFilamentInfo''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>..."

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'''llExtractWithLayerSeparationFilamentInfo''' 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]]([[FFT]])</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-oF</td>
<td>Optional</td>
<td>Output</td>
<td>NULL</td>
</tr>
<tr>
<td>-oI</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-truePitch</td>
<td>Optional</td>
<td>True Pitch</td>
<td>430</td>
</tr>
<tr>
<td>-PixelSize</td>
<td>Optional</td>
<td>PixelSize: [A]</td>
<td>5</td>
</tr>
<tr>
<td>-deltadY</td>
<td>Optional</td>
<td>A range of deltaY to determine dY.</td>
<td>0.5</td>
</tr>
<tr>
<td>-kV</td>
<td>Optional</td>
<td>AccVol: [kV]</td>
<td>200</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>Cs: [mm]</td>
<td>2.1</td>
</tr>
<tr>
<td>-df</td>
<td>Optional</td>
<td>Defocus: [A]: under(+)</td>
<td>27000</td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>AmplitudeContrast / PhaseContrast</td>
<td>0.1</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>
<div>-oF 's file name is used by -o .</div>
<br>

=== -m details ===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td></td>
</tr>
</table>
<br>

===Output file format===
<div>-o format</div>
<pre>
-oF'sFileName turn defocus Cs kV AmplitudeContrast Mag
</pre>
<br>

<div>-oI format</div>
<pre>
defocus Cs kV AmplitudeContrast
</pre>
<div>It can be used by [[mrcImageCTFCompensation]]</div>
<br>

== Execution example ==
===[[:Media:1ATOMFil.fft|Input file]] image===
<div>by [[mrcFFTExpression]](m=1)</div>
<table>
<tr>
<td><p align="Center">[[File:1ATOMFil-FFT.png]]<br>
Whole area<br></p>
</td>
<td><p align="Center">[[File:1ATOMFil-FFT1.png]]<br>
Around center<br></p>
</td>
<td><p align="left">Size<br>
Mode<br>
Length<br>
Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">( 512, 1146, 1)<br>
mrcComplexFloatFT <br>
( 2.000, 2.000, 0.000)<br>
4.08519e-10 (257, 572, 0)<br>
0.109661 (0, 0, 0)<br>
0.00909953<br>
0.00776913<br>
1.01425e-05<br></p>
</td>
</tr>
</table>
<br>

=== Case: Options only essential ===
<div>Output</div>
<pre>
LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 13.325582
CalculatedY 13.000000
deltadY 0.325582
</pre>
<br>

<div>-o 's data</div>
<pre>
oF-Outdata 13 27000.000000 2.100000 200.000000 0.100000 1.0
</pre>
<br>

<div>-oI 's data</div>
<pre>
27000.000000 2.100000 200.000000 0.100000
</pre>
<br>

=== Option -truePitch===
====Case: truePitch=364====
<div>Output</div>
<pre>
LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 15.741758
CalculatedY 16.000000
deltadY 0.258242
</pre>
<br>

<div>-o 's data</div>
<pre>
oF-Outdata 16 27000.000000 2.100000 200.000000 0.100000 1.0
</pre>
<br>

=== Option -PixelSize===
====Case: PixelSize=2====
<div>Output</div>
<pre>
LengthY 2292.000000 [A] = LengthY 1146 [Pixel] x PixelSize 2.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 5.330233
CalculatedY 5.000000
deltadY 0.330233
</pre>
<br>

<div>-o 's data</div>
<pre>
oF-Outdata 5 27000.000000 2.100000 200.000000 0.100000 1.0
</pre>
<br>

=== Option -deltadY===
====Case: deltadY=0.1====
<div>Output</div>
<pre>
LengthY 5730.000000 [A] = LengthY 1146 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 13.325582
CalculatedY 13.000000
deltadY 0.325582
The deltadY value 0.325582 is larger than permitted deltadY range 0.100000
dY could not be determined
</pre>
<br>

=== Option -kV===
====Case: kV=100====
<div>-o 's data</div>
<pre>
oF-Outdata 13 27000.000000 2.100000 100.000000 0.100000 1.0
</pre>
<br>

<div>-oI 's data</div>
<pre>
27000.000000 2.100000 100.000000 0.100000
</pre>
<br>

=== Option -Cs===
====Case: Cs=1.7====
<div>-o 's data</div>
<pre>
oF-Outdata 13 27000.000000 1.700000 200.000000 0.100000 1.0
</pre>
<br>

<div>-oI 's data</div>
<pre>
27000.000000 1.700000 200.000000 0.100000
</pre>
<br>

=== Option -df===
====Case: df=20000====
<div>-o 's data</div>
<pre>
oF-Outdata 13 20000.000000 2.100000 200.000000 0.100000 1.0
</pre>
<br>

<div>-oI 's data</div>
<pre>
20000.000000 2.100000 200.000000 0.100000
</pre>
<br>

=== Option -A===
====Case: A=0.2====
<div>-o 's data</div>
<pre>
oF-Outdata 13 27000.000000 2.100000 200.000000 0.200000 1.0
</pre>
<br>

<div>-oI 's data</div>
<pre>
27000.000000 2.100000 200.000000 0.200000
</pre>
<br>