mrcImage1dShiftAverageByAnnealing - Revision history

Kinoshita: Created page with "'''mrcImage1dShiftAverageByAnnealing''' is Eos's Command. == List of option == === Main option ===

Option Essenti..."
2014-07-16T01:50:17Z

Created page with "'''mrcImage1dShiftAverageByAnnealing''' is Eos's Command. == List of option == === Main option === <table border="1"> <tr> <th>Option</th> <th>Essenti..."

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'''mrcImage1dShiftAverageByAnnealing''' 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</td>
<td>NULL</td>
</tr>
<tr>
<td>-s</td>
<td>Essential</td>
<td>File to define position of signal</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output</td>
<td>NULL</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Search range of shift.</td>
<td>Nx</td>
</tr>
<tr>
<td>-d</td>
<td>Optional</td>
<td>Spacing of molecule(Pixel).</td>
<td>1.0</td>
</tr>
<tr>
<td>-T</td>
<td>Optional</td>
<td>Initial temperature.</td>
<td>1.0</td>
</tr>
<tr>
<td>-iter</td>
<td>Optional</td>
<td>Number of iteration before reducing temperature.</td>
<td>1000</td>
</tr>
<tr>
<td>-eps</td>
<td>Optional</td>
<td>Temperature(T) reduced to (1-epsilon)T.</td>
<td>0.001</td>
</tr>
<tr>
<td>-tol</td>
<td>Optional</td>
<td>Number to identify convergence</td>
<td>1e-2</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>-M</td>
<td>Optional</td>
<td>Mode2</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>
<br>

===-m details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>All search </td>
</tr>
<tr>
<td>1</td>
<td>annealing method </td>
</tr>
<tr>
<td>2</td>
<td>mode 1 and refine by powel</td>
</tr>
<tr>
<td>3</td>
<td>mode 1 and refine by annealing</td>
</tr>
</table>
<br>

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>by amplitude </td>
</tr>
<tr>
<td>1</td>
<td>by power</td>
</tr>
<tr>
<td>2</td>
<td>by amplitude using only phase </td>
</tr>
<tr>
<td>3</td>
<td>by power using only phase </td>
</tr>
<tr>
<td>4</td>
<td>by amplitude using S/sqrt(S) </td>
</tr>
<tr>
<td>5</td>
<td>by power using only S/sqrt(S) </td>
</tr>
</table>
<br>

===-i format===
<pre>
1DFile1
1DFile2
.
.

</pre>
<br>

===-s format===
<pre>
sigpos0 sigval0
sigpos1 sigval1
.
.

</pre>
<br>

== Execution example ==
===Input file's data===
<pre>
Input-1VOM-1D.mrc
Input-1VOM-N-1D.mrc
Input-1VOM-N-Rot-1D.mrc

</pre>
<br>

<div>[[Media:Input-1VOM-1D.mrc|Input-1VOM-1D.mrc]]'s image</div>
<table>
<tr>
<td>[[File:Input-1VOM-1D.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">9528.98 (1, 0, 0)<br>
1.05166e+06 (41, 0, 0)<br>
577032<br>
281935<br>
22288.9<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:Input-1VOM-N-1D.mrc|Input-1VOM-N-1D.mrc]]'s image</div>
<table>
<tr>
<td>[[File:Input-1VOM-N-1D.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-24564.9 (1, 0, 0)<br>
1.12206e+06 (40, 0, 0)<br>
577190<br>
290698<br>
22981.7<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:Input-1VOM-N-Rot-1D.mrc|Input-1VOM-N-Rot-1D.mrc]]'s image</div>
<table>
<tr>
<td>[[File:Input-1VOM-N-Rot-1D.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-27531.3 (2, 0, 0)<br>
1.11446e+06 (37, 0, 0)<br>
526414<br>
325460<br>
25729.9<br></p>
</td>
</tr>
</table>
<br>

===-s data===
<pre>
0 1
1 1

</pre>
<br>

=== Example of options only essential ===
<div>Output</div>
<pre>
result 1 1 2 79 2.87532e+07
</pre>
<br>

<div>-o image</div>
<table>
<tr>
<td>[[File:Outdata-mrcImage1dShiftAverageByAnnealing.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-5553.38 (1, 0, 0)<br>
3.11413e+06 (41, 0, 0)<br>
1.68064e+06<br>
876078<br>
69260<br></p>
</td>
</tr>
</table>
<br>

=== Option -r===
====Case: r=78====
<div>Output</div>
<pre>
result 1 1 2 0 2.87481e+07
</pre>
<br>

<div>-o image</div>
<table>
<tr>
<td>[[File:Outdata-r-mrcImage1dShiftAverageByAnnealing.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-16386 (2, 0, 0)<br>
3.09391e+06 (38, 0, 0)<br>
1.68064e+06<br>
880057<br>
69574.6<br></p>
</td>
</tr>
</table>
<br>

=== Option -d===
====Case: d=3====
<div>Output</div>
<pre>
result 1 81 2 159 2.87532e+07
</pre>
<br>

<div>-o image</div>
<table>
<tr>
<td>[[File:Outdata-d-mrcImage1dShiftAverageByAnnealing.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-18002.3 (1, 1, 0)<br>
3.11413e+06 (41, 0, 0)<br>
1.68056e+06<br>
876228<br>
69271.9<br></p>
</td>
</tr>
</table>
<br>