mrcImageSymmetryFind - Revision history

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

Option Essential/Optional
2014-08-04T00:33:54Z

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

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'''mrcImageSymmetryFind''' 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>Optional</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-O</td>
<td>Optional</td>
<td>Output: [[ASCII]](Symmetry Infomation)</td>
<td>stdout</td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>Output: [[mrcImage]](Average)</td>
<td>NULL</td>
</tr>
<tr>
<td>-centreMode</td>
<td>Optional</td>
<td>centreMode</td>
<td>1</td>
</tr>
<tr>
<td>-t1</td>
<td>Optional</td>
<td>Threshold of CheckByAdd</td>
<td>1.8</td>
</tr>
<tr>
<td>-t2</td>
<td>Optional</td>
<td>Threshold in deciding the symmetry number</td>
<td>0.9</td>
</tr>
<tr>
<td>-m1</td>
<td>Optional</td>
<td>Mode of Check</td>
<td>3</td>
</tr>
<tr>
<td>-m2</td>
<td>Optional</td>
<td>Mode of Substruction</td>
<td>2</td>
</tr>
<tr>
<td>-dr</td>
<td>Optional</td>
<td>Delta r of outputfile.</td>
<td>1</td>
</tr>
<tr>
<td>-dtheta</td>
<td>Optional</td>
<td>Delta theta of outputfile. [degree]</td>
<td>1</td>
</tr>
<tr>
<td>-n</td>
<td>Optional</td>
<td>Check to the number</td>
<td>10</td>
</tr>
<tr>
<td>-nRange</td>
<td>Optional</td>
<td>Checkto the number: (nmin, nmax)</td>
<td>(2, 10)</td>
</tr>
<tr>
<td>-In</td>
<td>Optional</td>
<td>Input: (Image, Back)</td>
<td>(NULL, NULL)</td>
</tr>
<tr>
<td>-rangex</td>
<td>Optional</td>
<td>Input: (minx, maxx, delx)</td>
<td>(-3, 3, 1)</td>
</tr>
<tr>
<td>-rangey</td>
<td>Optional</td>
<td>Input: (miny, maxy, dely)</td>
<td>(-3, 3, 1)</td>
</tr>
<tr>
<td>-rangez</td>
<td>Optional</td>
<td>Input: (minz, maxz, delz)</td>
<td>(0, 0, 1)</td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

===-centreMode details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Centre is GC (gravity of centre)</td>
</tr>
<tr>
<td>1</td>
<td>Centre is Rotational Symmetry</td>
</tr>
</table>

===-m1 details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>1</td>
<td>Check by Add</td>
</tr>
<tr>
<td>2</td>
<td>Check by Correlation</td>
</tr>
<tr>
<td>4</td>
<td>Check by Fourier</td>
</tr>
<tr>
<td>8</td>
<td>Check by TTest</td>
</tr>
<tr>
<td>16</td>
<td>Check by SRP</td>
</tr>
</table>

===-m2 details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>No Subtraction</td>
</tr>
<tr>
<td>1</td>
<td>Mean Subtraction</td>
</tr>
<tr>
<td>2</td>
<td>Min Subtraction</td>
</tr>
</table>

===-In format===
<div>Image, Back's format</div>
<pre>
mrcFile1
mrcFile2
.
.

</pre>

== Execution example ==
===[[Media:Input-2D-Data1-s.mrc | Input file]] image===
<table>
<tr>
<td>[[File:Input-2D-Data1-s.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>
65535 (14, 1, 0)<br>
24950.9<br>
31821.5<br>
776.135<br></p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<div>Output</div>
<pre>
2 -> value: 1.000000 point: 33.333332
3 -> value: 0.000000 point: 0.000000
4 -> value: 3.000000 point: 100.000000
5 -> value: 1.000000 point: 33.333332
6 -> value: 1.000000 point: 33.333332
7 -> value: 1.000000 point: 33.333332
8 -> value: 0.000000 point: 0.000000
9 -> value: 1.000000 point: 33.333332
10 -> value: 0.000000 point: 0.000000
Symmetry number 4.(Check by add, MinSubtraction)
2 -> value: 0.754960 point: 25.118885
3 -> value: 0.747752 point: 5.859963
4 -> value: 0.782986 point: 100.000000
5 -> value: 0.754746 point: 24.546839
6 -> value: 0.757313 point: 31.407404
7 -> value: 0.745559 point: 0.000000
8 -> value: 0.776130 point: 81.683868
9 -> value: 0.751637 point: 16.241667
10 -> value: 0.744289 point: -3.392937
Symmetry number 4.(Check by add, MinSubtraction)
</pre>
<br>

<div>-o 's file (By [[mrcImageMakeDump]])</div>
<pre>
0 0 1
1 0 0.748045
2 0 0.757302
3 0 0.777038
4 0 0.751623
5 0 0.751097
6 0 0.751701
7 0 0.750209
8 0 0.744015
9 0 0.775344

...

350 0 0.745883
351 0 0.775344
352 0 0.744015
353 0 0.750209
354 0 0.751701
355 0 0.751097
356 0 0.751623
357 0 0.777038
358 0 0.757302
359 0 0.748045
</pre>
<br>

<div>-A 's image</div>
<table>
<tr>
<td>[[File:Outdata-mrcImageSymmetryFind.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>
65535 (14, 1, 0)<br>
42883.4<br>
31166<br>
760.147<br></p>
</td>
</tr>
</table>
<br>