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mrcImageFOMCalc - Revision history
2026-05-04T17:09:57Z
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http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageFOMCalc&diff=1241&oldid=prev
Kinoshita: /* Execution example */
2014-07-24T02:58:26Z
<p><span dir="auto"><span class="autocomment">Execution example</span></span></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 02:58, 24 July 2014</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <tr></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <tr></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td><p align="Center">[[File:Input-121P-N1-FFT.png]]<br></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td><p align="Center">[[File:Input-121P-N1-FFT.png]]<br></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div> [[mrcFFTExpression]](m=1)<del class="diffchange diffchange-inline">にて表示</del><br></p>  </div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> <ins class="diffchange diffchange-inline">by using </ins>[[mrcFFTExpression]](m=1)<br></p>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </td>  </div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> </td>  </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td><p align="left">Min<br></div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div> <td><p align="left">Min<br></div></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageFOMCalc&diff=1240&oldid=prev
Kinoshita: Created page with "'''mrcImageFOMCalc''' is Eos's Command that calculates FOM(Figure of merit) of mrcImage(3DFFT). ==Algorithm== <div>Refer the references in the following about alg..."
2014-07-24T02:57:49Z
<p>Created page with "'''mrcImageFOMCalc''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that calculates FOM(Figure of merit) of <a href="/Eos/index.php/mrcImage" title="mrcImage">mrcImage</a>(3DFFT). ==Algorithm== <div>Refer the references in the following about alg..."</p>
<p><b>New page</b></p><div>'''mrcImageFOMCalc''' is [[Eos]]'s [[Command]] that calculates FOM(Figure of merit) of [[mrcImage]](3DFFT).<br />
<br />
==Algorithm==<br />
<div>Refer the references in the following about algorithm of FOM(Figure of merit).</div><br />
<br><br />
<br />
== List of option ==<br />
=== Main option ===<br />
<table border="1"><br />
<tr> <br />
<th>Option</th> <br />
<th>Essential/Optional</th> <br />
<th>Description</th> <br />
<th>Default</th> <br />
</tr> <br />
<tr> <br />
<td>-i</td> <br />
<td>Optional</td> <br />
<td>Input: [[mrcImage]](FFT)(3D)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-I</td> <br />
<td>Optional</td> <br />
<td>Input: [[ASCII]](File List)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-r</td> <br />
<td>Essential</td> <br />
<td>Reference: [[mrcImage]](FFT)(3D)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Optional</td> <br />
<td>Output: [[ASCII]]</td> <br />
<td>stdout</td> <br />
</tr> <br />
<tr> <br />
<td>-w</td> <br />
<td>Optional</td> <br />
<td>Weight</td> <br />
<td>1.0</td> <br />
</tr> <br />
<tr> <br />
<td>-RR</td> <br />
<td>Optional</td> <br />
<td>Ring Range (Rmin, Rmax)</td> <br />
<td>(0.0, 0.1)</td> <br />
</tr> <br />
<tr> <br />
<td>-dR</td> <br />
<td>Optional</td> <br />
<td>Ring Width</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-nS</td> <br />
<td>Optional</td> <br />
<td>Sector Number</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-dA</td> <br />
<td>Optional</td> <br />
<td>delta Alpha</td> <br />
<td>5</td> <br />
</tr> <br />
<tr> <br />
<td>-XMax</td> <br />
<td>Optional</td> <br />
<td>Xmax: If not set, one calc Xmax</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-AS</td> <br />
<td>Optional</td> <br />
<td>Auto Scaling</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-AAS</td> <br />
<td>Optional</td> <br />
<td>All Area Auto Scaling</td> <br />
<td>0.05</td> <br />
</tr> <br />
<tr> <br />
<td>-RS</td> <br />
<td>Optional</td> <br />
<td>R Scaling</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-c</td> <br />
<td>Optional</td> <br />
<td>ConfigurationFile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-m</td> <br />
<td>Optional</td> <br />
<td>Mode</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-h</td> <br />
<td>Optional</td> <br />
<td>Help</td> <br />
<td> </td> <br />
</tr> <br />
</table> <br />
<div>-i or -I is essential.</div><br />
<br><br />
<br />
=== -m details ===<br />
<table border="1"><br />
<tr> <br />
<th>Value</th> <br />
<th>Description</th> <br />
</tr> <br />
<tr> <br />
<td>0</td> <br />
<td></td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
===-I format===<br />
<pre><br />
3DFFT File<br />
3DFFT File<br />
.<br />
.<br />
<br />
</pre><br />
<br><br />
<br />
== Execution example ==<br />
=== Input file's image ===<br />
<div>[[:Media:Input-121P-N.fft|-i file]]'s image</div><br />
<table><br />
<tr><br />
<td><p align="Center">[[File:Input-121P-N-FFT.png]]<br><br />
by using [[mrcFFTExpression]](m=1)<br></p> <br />
</td> <br />
<td><p align="left">Min<br><br />
Max<br><br />
Mean<br><br />
SD<br><br />
SE<br></p><br />
</td><br />
<td><p align="left">0.466157 (79, 38, 83)<br><br />
11101.8 (0, 0, 0)<br><br />
417.825<br><br />
227.083<br><br />
0.227083<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
<div>[[:Media:Input-121P-N1.fft|-r file]]'s image</div><br />
<table><br />
<tr><br />
<td><p align="Center">[[File:Input-121P-N1-FFT.png]]<br><br />
[[mrcFFTExpression]](m=1)にて表示<br></p> <br />
</td> <br />
<td><p align="left">Min<br><br />
Max<br><br />
Mean<br><br />
SD<br><br />
SE<br></p><br />
</td><br />
<td><p align="left">0.337695 (84, 41, 49)<br><br />
10881.2 (0, 0, 0)<br><br />
418.011<br><br />
227.229<br><br />
0.227229<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
<div>-I 's data</div><br />
<pre><br />
Input-121P-N.fft 1.0<br />
Input-121P-N2.fft 1.0<br />
<br />
</pre><br />
<div>Input-121P-N.fft is -i file.</div><br />
<br />
<div>[[:Media:Input-121P-N2.fft|Input-121P-N2.fft]]'s image</div><br />
<table><br />
<tr><br />
<td><p align="Center">[[File:Input-121P-N2-FFT.png]]<br><br />
by using [[mrcFFTExpression]](m=1)<br></p> <br />
</td> <br />
<td><p align="left">Min<br><br />
Max<br><br />
Mean<br><br />
SD<br><br />
SE<br></p><br />
</td><br />
<td><p align="left">-2175.23 (42, 93, 33)<br><br />
4252.65 (42, 64, 56)<br><br />
10.8573<br><br />
474.411<br><br />
0.474411<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
===-i data===<br />
====Case: No other settings====<br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6693 2588 1.5496e+05 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: w=2.0==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6078 2588 8.5440e+02 2.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: RR=(0.1, 0.6)==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
1.0000e-01 6.0000e-01 0.4923 408780 8.8144e+04 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: dR=0.01==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-02 nan 0 0.0000e+00 1.0000e+00<br />
1.0000e-02 2.0000e-02 0.9982 28 1.5495e+05 1.0000e+00<br />
2.0000e-02 3.0000e-02 0.9407 60 1.5496e+05 1.0000e+00<br />
3.0000e-02 4.0000e-02 0.8423 112 1.0873e+04 1.0000e+00<br />
4.0000e-02 5.0000e-02 0.7840 156 1.0872e+04 1.0000e+00<br />
5.0000e-02 6.0000e-02 0.7246 268 4.0601e+02 1.0000e+00<br />
6.0000e-02 7.0000e-02 0.7007 328 4.4218e+03 1.0000e+00<br />
7.0000e-02 8.0000e-02 0.6649 408 2.3074e+02 1.0000e+00<br />
8.0000e-02 9.0000e-02 0.6015 520 3.9558e+03 1.0000e+00<br />
9.0000e-02 1.0000e-01 0.6063 672 9.1944e+02 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: nS=10==== <br />
<pre><br />
##Sector index 0/ 10 0.00 9.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6914 552 1.5496e+05 1.0000e+00<br />
##Sector index 1/ 10 9.00 18.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6572 304 1.5496e+05 1.0000e+00<br />
##Sector index 2/ 10 18.00 27.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6687 376 1.5496e+05 1.0000e+00<br />
##Sector index 3/ 10 27.00 36.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6560 296 1.5496e+05 1.0000e+00<br />
##Sector index 4/ 10 36.00 45.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6729 296 1.5496e+05 1.0000e+00<br />
##Sector index 5/ 10 45.00 54.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.7008 232 1.5496e+05 1.0000e+00<br />
##Sector index 6/ 10 54.00 63.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6690 196 1.5496e+05 1.0000e+00<br />
##Sector index 7/ 10 63.00 72.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6572 176 1.5496e+05 1.0000e+00<br />
##Sector index 8/ 10 72.00 81.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.5504 92 1.5496e+05 1.0000e+00<br />
##Sector index 9/ 10 81.00 90.00 9.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6745 68 1.5496e+05 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: dA=3==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6691 2588 1.5496e+05 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: AAS=0.01==== <br />
<pre><br />
All Area Scaling Calc. Start: 1<br />
ScalingFactor 0: 0.995613 = 1.83391e+06/1.82586e+06<br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6693 2588 3.2948e+04 9.9561e-01<br />
</pre><br />
<br><br />
<br />
====-AS==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6693 2588 2.8993e+04 9.9509e-01<br />
</pre><br />
<br><br />
<br />
====-RS==== <br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.6289 2588 4.2090e+03 1.0000e+00<br />
</pre><br />
<br><br />
<br />
===-I data===<br />
====Case: No other settings====<br />
<pre><br />
sumPP is zero<br />
sumPP is zero<br />
<br />
...<br />
<br />
sumPP is zero<br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 1.0000e-01 0.8316 5176 2.6579e+05 1.0000e+00 1.0000e+00<br />
</pre><br />
<br><br />
<br />
====Case: -RS, RR=(0.0, 0.05)====<br />
<pre><br />
##Sector index 0/ 1 0.00 90.00 90.00<br />
## minR< <=maxR FOM Num XMax Scaling<br />
0.0000e+00 5.0000e-02 0.9090 784 9.9502e+02 1.0000e+00 1.0000e+00<br />
</pre><br />
<br><br />
<br />
== References ==<br />
* [http://www.nature.com/nature/journal/v424/n6949/full/nature01830.html Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy]</div>
Kinoshita