defocusDeterminationFromThonRing - Revision history

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

Option Essentia..."
2014-08-20T01:37:30Z

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

New page
'''defocusDeterminationFromThonRing''' 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>Optional</td>
<td>Input</td>
<td>stdin</td>
</tr>
<tr>
<td>-iN</td>
<td>Optional</td>
<td>InputNameInInformationFile</td>
<td>stdin</td>
</tr>
<tr>
<td>-iR</td>
<td>Optional</td>
<td>InputReferenceForLength: [[mrcImage]]</td>
<td>stdin</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: [[ASCII]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-oI</td>
<td>Optional</td>
<td>OutputInformationFile1: [[ASCII]](mrcImageMultiCTFCompensation and mrcImageCTFCompensation)</td>
<td>stdout</td>
</tr>
<tr>
<td>-oI2</td>
<td>Optional</td>
<td>OutputInformationFile2: [[ASCII]](llDataCTFCompensate -I2)</td>
<td>stdout</td>
</tr>
<tr>
<td>-oI3</td>
<td>Optional</td>
<td>OutputInformationFile3: [[ASCII]](llExtractWithLayerSeparation)<br>
Options: -truePitch, -PixelSize, -deltadY and -ctfMode</td>
<td>stdout</td>
</tr>
<tr>
<td>-kV</td>
<td>Optional</td>
<td>[[Acceleration voltage]]: [kV]</td>
<td>200</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>[[Spherical aberration coefficient]]: [mm]</td>
<td>2.1</td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>The ratio of amplitude contrast to phase contrast</td>
<td>0.05</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>Pixel Size [A]</td>
<td>5</td>
</tr>
<tr>
<td>-deltadY</td>
<td>Optional</td>
<td>A range of deltadY to determine dY.</td>
<td>0.5</td>
</tr>
<tr>
<td>-R</td>
<td>Optional</td>
<td>[[Variable]]: Thon Ring: [/A]</td>
<td>NULL ...</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>-ctfMode</td>
<td>Optional</td>
<td>CTFMode</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></td>
</tr>
</table>

===CTFMode details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Phase CTF </td>
</tr>
<tr>
<td>1</td>
<td>PhaseCTF + ratio*AmpCTF </td>
</tr>
</table>

== Execution example ==
=== Case: Options only essential ===
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
---------------------------------------------
Avg. nan [A] +- S.D. nan [A]
Avg. nan [um] +- S.D. nan [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
---------------------------------------------
Avg. nan [A] +- S.D. nan [A]
Avg. nan [um] +- S.D. nan [um]
</pre>

=== Option -R===
====Case: R=(0.001, 0.01, 0.1)====
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
</pre>

=== Option -o, -oI, -oI2===
====Case: o, oI, oI2 specify file, R=(0.001, 0.01, 0.1)====
<div>-o 's data</div>
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
</pre>

<div>-oI 's data</div>
<pre>
stdin 13352487.000000 2.100000 200.000000 0.050000
</pre>

<div>-oI2 's data</div>
<pre>
13352487.000000 2.100000 200.000000 0.050000
</pre>

=== Option -iR===
====Case: -iR specify file, R=(0.001, 0.01, 0.1)====
=====-iR image=====
<table>
<tr>
<td>[[File:Refer-defocusDeterminationFromThonRing.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (0, 0, 0)<br>
255 (49, 32, 0)<br>
21.0538<br>
47.6709<br>
0.595886<br></p>
</td>
</tr>
</table>

=====Case: -oI3 specify file=====
<div>Output </div>
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 400.000000 [A] = LengthY 80 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 0.930233
CalculatedY 1.000000
deltadY 0.069767
</pre>

<div>-oI3 data </div>
<pre>
stdin 1 13352487.000000 2.100000 200.000000 0.050000 0
</pre>

=====Case: truePitch=300=====
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 400.000000 [A] = LengthY 80 [Pixel] x PixelSize 5.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 1.333333
CalculatedY 1.000000
deltadY 0.333333
</pre>

=====Case: PixelSize=10=====
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196908e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335249e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196396e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891301e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
LengthY 800.000000 [A] = LengthY 80 [Pixel] x PixelSize 10.000000 [A/Pixel] x Mag 1.000000
Final CalculatedY 1.860465
CalculatedY 2.000000
deltadY 0.139535
</pre>

=== Option -kV===
====Case: kV=100, R=(0.001, 0.01, 0.1)====
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 2.659654e+07 : 1.000000e-03
2 5.362301e+05 : 1.000000e-02
3 8.208672e+03 : 1.000000e-01
---------------------------------------------
Avg. 9.046993e+06 [A] +- S.D. 1.241128e+07 [A]
Avg. 904.70 [um] +- S.D. 1241.13 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -2.745611e+07 : 1.000000e-03
-2 -5.448229e+05 : 1.000000e-02
-3 -8.007123e+03 : 1.000000e-01
---------------------------------------------
Avg. -9.336313e+06 [A] +- S.D. 1.281450e+07 [A]
Avg. -933.63 [um] +- S.D. 1281.45 [um]
</pre>

=== Option -Cs===
====Case: Cs=2.0, R=(0.001, 0.01, 0.1)====
<div>Output </div>
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.925407e+07 : 1.000000e-03
2 7.914252e+05 : 1.000000e-02
3 1.196594e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.335248e+07 [A] +- S.D. 1.831795e+07 [A]
Avg. 1335.25 [um] +- S.D. 1831.79 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.052272e+07 : 1.000000e-03
-2 -8.041104e+05 : 1.000000e-02
-3 -1.196710e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.377960e+07 [A] +- S.D. 1.891300e+07 [A]
Avg. -1377.96 [um] +- S.D. 1891.30 [um]
</pre>

<div>-oI 's data</div>
<pre>
stdin 13352485.000000 2.000000 200.000000 0.050000
</pre>

=== Option -A===
====Case: A=0.1, R=(0.001, 0.01, 0.1)====
<pre>
>>> Underfocus
Ring Number Amount of defocus[A] R[1/A]
1 3.862291e+07 : 1.000000e-03
2 7.851137e+05 : 1.000000e-02
3 1.190596e+04 : 1.000000e-01
---------------------------------------------
Avg. 1.313998e+07 [A] +- S.D. 1.802192e+07 [A]
Avg. 1314.00 [um] +- S.D. 1802.19 [um]
>>> Overfocus
Ring Number Amount of defocus[A] R[1/A]
-1 -4.115387e+07 : 1.000000e-03
-2 -8.104219e+05 : 1.000000e-02
-3 -1.202707e+04 : 1.000000e-01
---------------------------------------------
Avg. -1.399211e+07 [A] +- S.D. 1.920903e+07 [A]
Avg. -1399.21 [um] +- S.D. 1920.90 [um]
</pre>