http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=mrcImageClusterAnalysis
mrcImageClusterAnalysis - Revision history
2026-05-14T14:23:45Z
Revision history for this page on the wiki
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http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageClusterAnalysis&diff=3441&oldid=prev
Kinoshita at 01:15, 19 August 2014
2014-08-19T01:15:43Z
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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 01:15, 19 August 2014</td>
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<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>'''mrcImageClusterAnalysis''' is [[Eos]]'s [[Command]] that performs [[Cluster <del class="diffchange diffchange-inline">analysis</del>]] each [[mrcImage]].</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>'''mrcImageClusterAnalysis''' is [[Eos]]'s [[Command]] that performs [[Cluster <ins class="diffchange diffchange-inline">Analysis</ins>]] each [[mrcImage]].</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;"></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;"></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;"></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;"></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageClusterAnalysis&diff=959&oldid=prev
Kinoshita: Created page with "'''mrcImageClusterAnalysis''' is Eos's Command that performs Cluster analysis each mrcImage. == List of option == === Main option === <table border="1">..."
2014-07-23T01:32:36Z
<p>Created page with "'''mrcImageClusterAnalysis''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that performs <a href="/Eos/index.php?title=Cluster_analysis&action=edit&redlink=1" class="new" title="Cluster analysis (page does not exist)">Cluster analysis</a> each <a href="/Eos/index.php/mrcImage" title="mrcImage">mrcImage</a>. == List of option == === Main option === <table border="1">..."</p>
<p><b>New page</b></p><div>'''mrcImageClusterAnalysis''' is [[Eos]]'s [[Command]] that performs [[Cluster analysis]] each [[mrcImage]].<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>Essential</td> <br />
<td>Input: [[ASCII]]</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>-O</td> <br />
<td>Optional</td> <br />
<td>Output(averaged images): filename: (Input file's name).avg</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-N</td> <br />
<td>Optional</td> <br />
<td>Number of clusters</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-Min</td> <br />
<td>Optional</td> <br />
<td>Minimum: Correlation: Conditions for ending</td> <br />
<td>0.0</td> <br />
</tr> <br />
<tr> <br />
<td>-Iter</td> <br />
<td>Optional</td> <br />
<td>IterationFlag</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-AR</td> <br />
<td>Optional</td> <br />
<td>AutoRotation: rotation divided by this value</td> <br />
<td>72</td> <br />
</tr> <br />
<tr> <br />
<td>-ARange</td> <br />
<td>Optional</td> <br />
<td>AutoRotationRange: (ARMin, ARMax)</td> <br />
<td>(0, 360)</td> <br />
</tr> <br />
<tr> <br />
<td>-ARiter</td> <br />
<td>Optional</td> <br />
<td>AutoRotationIteration</td> <br />
<td>2</td> <br />
</tr> <br />
<tr> <br />
<td>-ARMethod</td> <br />
<td>Optional</td> <br />
<td>Method for Correlation for Auto Rotation</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-M</td> <br />
<td>Optional</td> <br />
<td>Correlation Mode for AutoRotation</td> <br />
<td>19</td> <br />
</tr> <br />
<tr> <br />
<td>-pvm</td> <br />
<td>Optional</td> <br />
<td>Parallel Analysis by PVM</td> <br />
<td></td> <br />
</tr> <br />
<tr> <br />
<td>-pvmList</td> <br />
<td>Optional</td> <br />
<td>Input: pvmList: [[ASCII]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-Log</td> <br />
<td>Optional</td> <br />
<td>Output: Log(All):[[ASCII]]</td> <br />
<td>stdout</td> <br />
</tr> <br />
<tr> <br />
<td>-Log2</td> <br />
<td>Optional</td> <br />
<td>Output: Log2(ClusterNode Only): [[ASCII]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-LogIn</td> <br />
<td>Optional</td> <br />
<td>Input: previousLog: [[ASCII]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-prevF</td> <br />
<td>Optional</td> <br />
<td>Input: previousLogFileNum</td> <br />
<td>0</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 of the distance between the clusters</td> <br />
<td>2</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>-AR: Setting, calculated by the rotation there. (Using [[mrcImageAutoRotationCorrelation]])</div><br />
<br><br />
<br />
===-ARMethod, -M details===<br />
<div>cf [[mrcImageAutoRotationCorrelation]]<br><br />
-ARMethod to -Method, -M to -m</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>By Correlation</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>By Euclid Distance</td> <br />
</tr> <br />
<tr> <br />
<td>2</td> <br />
<td>By Ward Method: without -AR: Euclid Length, with -AR: its square</td> <br />
</tr> <br />
<tr> <br />
<td>3</td> <br />
<td>By Ward Method using Linear Correlation : (1 - Correlation)/(1 + Correlation)</td> <br />
</tr> <br />
<tr> <br />
<td>4</td> <br />
<td>By Linear Correlation : (1 - Correlation)/(1 + Correlation)</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
== Execution example ==<br />
===-I data===<br />
<pre><br />
Input-1VOM-N-2D.mrc<br />
Input-1VOM-N-Rot-2D.mrc<br />
Input-1VOM-N-Rot1-2D.mrc<br />
Input-1VOM-N-Rot2-2D.mrc<br />
Input-1VOM-N-Rot3-2D.mrc<br />
<br />
</pre><br />
<br />
<div>[[Media:Input-1VOM-N-2D.mrc|Input-1VOM-N-2D.mrc]]'s image</div><br />
<table> <br />
<tr> <br />
<td>[[File:Input-1VOM-N-2D.png]]</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">-18651.7 (10, 1, 0)<br> <br />
52942.7 (24, 39, 0)<br> <br />
7214.87<br> <br />
10067.6<br> <br />
125.845<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<div>[[Media:Input-1VOM-N-Rot-2D.mrc|Input-1VOM-N-Rot-2D.mrc]]'s image</div><br />
<table><br />
<tr><br />
<td>[[File:Input-1VOM-N-Rot-2D.png]]</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">-11367.8 (51, 62, 0)<br><br />
51939.8 (29, 26, 0)<br><br />
6580.18<br><br />
9247.8<br><br />
115.597<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
<div>[[:Media:Input-1VOM-N-Rot1-2D.mrc|Input-1VOM-N-Rot1-2D.mrc]]'s image</div><br />
<table><br />
<tr><br />
<td>[[File:Input-1VOM-N-Rot1-2D.png]]</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">-14918 (53, 17, 0)<br><br />
58621.8 (30, 26, 0)<br><br />
6579.96<br><br />
9022.72<br><br />
112.784<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
<div>[[:Media:Input-1VOM-N-Rot2-2D.mrc|Input-1VOM-N-Rot2-2D.mrc]]'s image</div><br />
<table><br />
<tr><br />
<td>[[File:Input-1VOM-N-Rot2-2D.png]]</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">-2.31309e-06 (29, 7, 0)<br><br />
49749.2 (52, 51, 0)<br><br />
6572.32<br><br />
8769.91<br><br />
109.624<br></p><br />
</td><br />
</tr><br />
</table><br />
<br />
<div>[[:Media:Input-1VOM-N-Rot3-2D.mrc|Input-N-1VOM-Rot3-2D.mrc]]'s image</div><br />
<table><br />
<tr><br />
<td>[[File:Input-1VOM-N-Rot3-2D.png]]</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">-1.70846e-06 (56, 57, 0)<br><br />
40287.6 (43, 43, 0)<br><br />
6509.38<br><br />
8494.21<br><br />
106.178<br></p><br />
</td><br />
</tr><br />
</table><br />
<br><br />
<br />
=== Example of options only essential ===<br />
<div>-o 's data</div><br />
<pre><br />
/Eos/Input-1VOM-N-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot1-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot2-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot3-2D.mrc 0<br />
</pre><br />
<br><br />
<br />
<div>-Log 's data</div><br />
<pre><br />
1 0 5 5 4.24643e+11<br />
2 0 5 5 4.71782e+11<br />
2 1 5 5 2.57991e+11<br />
3 0 5 5 6.14144e+11<br />
3 1 5 5 4.54881e+11<br />
3 2 5 5 4.2017e+11<br />
4 0 5 5 6.53985e+11<br />
4 1 5 5 5.09646e+11<br />
4 2 5 5 4.66033e+11<br />
4 3 5 5 3.09305e+11<br />
1 0 2 1 3.83715e+11<br />
2 0 2 1 6.14144e+11<br />
2 1 2 1 3.73028e+11<br />
3 0 2 1 6.53985e+11<br />
3 1 2 1 4.23342e+11<br />
3 2 2 1 3.09305e+11<br />
1 0 3 2 3.83715e+11<br />
2 0 3 2 5.56738e+11<br />
2 1 3 2 3.20859e+11<br />
1 0 2 1 3.90012e+11<br />
</pre><br />
<br><br />
<br />
<div>-Log2 's data</div><br />
<pre><br />
CLUST MIN 2 1 2.57991e+11 0<br />
CLUST MIN 4 3 3.09305e+11 0<br />
CLUST MIN 3 1 3.20859e+11 0<br />
CLUST MIN 1 0 3.90012e+11 0<br />
</pre><br />
<br><br />
<br />
<div>-O 's data</div><br />
<div>Input-1VOM-N-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata5-mrcImageClusterAnalysis.png]]</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">-5026.5 (68, 63, 0)<br> <br />
28784 (40, 46, 0)<br> <br />
6685.03<br> <br />
7223.34<br> <br />
90.2917<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata6-mrcImageClusterAnalysis.png]]</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">-5026.5 (68, 63, 0)<br> <br />
28784 (40, 46, 0)<br> <br />
6685.03<br> <br />
7223.34<br> <br />
90.2917<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot1-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata7-mrcImageClusterAnalysis.png]]</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">-8305.58 (63, 47, 0)<br> <br />
44934.5 (29, 26, 0)<br> <br />
6580.07<br> <br />
8566.67<br> <br />
107.083<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot2-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata8-mrcImageClusterAnalysis.png]]</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">-4662.21 (68, 63, 0)<br> <br />
32714.4 (21, 49, 0)<br> <br />
6552.58<br> <br />
7209.85<br> <br />
90.1231<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot3-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata9-mrcImageClusterAnalysis.png]]</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">-8070.97 (31, 10, 0)<br> <br />
39082.1 (53, 39, 0)<br> <br />
6525.08<br> <br />
7459.33<br> <br />
93.2416<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
=== Option -AR===<br />
====Case: AR=72====<br />
<div>-o 's data</div><br />
<pre><br />
/Eos/Input-1VOM-N-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot1-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot2-2D.mrc 0<br />
/Eos/Input-1VOM-N-Rot3-2D.mrc 0<br />
</pre><br />
<br><br />
<br />
<div>-Log 's data</div><br />
<pre><br />
1 0 5 5 1.04435e+11<br />
2 0 5 5 1.90062e+11<br />
2 1 5 5 1.27924e+11<br />
3 0 5 5 2.70151e+11<br />
3 1 5 5 2.24399e+11<br />
3 2 5 5 2.00805e+11<br />
4 0 5 5 2.70277e+11<br />
4 1 5 5 2.23333e+11<br />
4 2 5 5 2.13958e+11<br />
4 3 5 5 1.54653e+11<br />
1 0 1 0 1.77375e+11<br />
2 0 1 0 2.92444e+11<br />
2 1 1 0 2.00805e+11<br />
3 0 1 0 2.95344e+11<br />
3 1 1 0 2.13958e+11<br />
3 2 1 0 1.54653e+11<br />
1 0 3 2 1.77375e+11<br />
2 0 3 2 3.71482e+11<br />
2 1 3 2 2.33577e+11<br />
1 0 1 0 3.72121e+11<br />
</pre><br />
<br><br />
<br />
<div>-Log2 's data</div><br />
<pre><br />
CLUST MIN 1 0 1.04435e+11 0.83054<br />
CLUST MIN 4 3 1.54653e+11 0.643245<br />
CLUST MIN 2 0 1.77375e+11 0.751614<br />
CLUST MIN 3 0 3.72121e+11 0.635649<br />
</pre><br />
<br><br />
<br />
<div>-O 's data</div><br />
<div>Input-1VOM-N-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata-mrcImageClusterAnalysis.png]]</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">-5248.9 (41, 3, 0)<br> <br />
37074.9 (26, 29, 0)<br> <br />
6687.62<br> <br />
7446.87<br> <br />
93.0859<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata1-mrcImageClusterAnalysis.png]]</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">-11857.7 (56, 22, 0)<br> <br />
46633.1 (27, 28, 0)<br> <br />
6897.66<br> <br />
9242.12<br> <br />
115.527<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot1-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata2-mrcImageClusterAnalysis.png]]</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">-9406.5 (41, 3, 0)<br> <br />
50054.7 (27, 28, 0)<br> <br />
6792.38<br> <br />
8652.36<br> <br />
108.155<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot2-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata3-mrcImageClusterAnalysis.png]]</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">-5248.9 (41, 3, 0)<br> <br />
37074.9 (26, 29, 0)<br> <br />
6687.62<br> <br />
7446.87<br> <br />
93.0859<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Input-1VOM-N-Rot3-2D.mrc.avg</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata4-mrcImageClusterAnalysis.png]]</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">-8070.97 (31, 10, 0)<br> <br />
39082.1 (53, 39, 0)<br> <br />
6525.08<br> <br />
7459.33<br> <br />
93.2416<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br></div>
Kinoshita