http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=mrcImagePCA
mrcImagePCA - Revision history
2026-05-04T16:19:54Z
Revision history for this page on the wiki
MediaWiki 1.23.6
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImagePCA&diff=1871&oldid=prev
Kinoshita at 01:28, 29 July 2014
2014-07-29T01:28:39Z
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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 01:28, 29 July 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>'''mrcImagePCA''' <del class="diffchange diffchange-inline">is複数画像から[[主成分分析]]を行い、主成分画像を生成する </del>[[Eos]]'s [[Command]].</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>'''mrcImagePCA''' <ins class="diffchange diffchange-inline">is </ins>[[Eos]]'s [[Command]] <ins class="diffchange diffchange-inline">that performs PCA(Principal components analysis) from multiple images and creates the PCA images</ins>.</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=mrcImagePCA&diff=1870&oldid=prev
Kinoshita: Created page with "'''mrcImagePCA''' is複数画像から主成分分析を行い、主成分画像を生成する Eos's Command. == List of option == === Main option === <table..."
2014-07-29T01:26:19Z
<p>Created page with "'''mrcImagePCA''' is複数画像から<a href="/Eos/index.php?title=%E4%B8%BB%E6%88%90%E5%88%86%E5%88%86%E6%9E%90&action=edit&redlink=1" class="new" title="主成分分析 (page does not exist)">主成分分析</a>を行い、主成分画像を生成する <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a>. == List of option == === Main option === <table..."</p>
<p><b>New page</b></p><div>'''mrcImagePCA''' is複数画像から[[主成分分析]]を行い、主成分画像を生成する [[Eos]]'s [[Command]].<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]](File List)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output: [[ASCII]](File List)</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-EPS</td> <br />
<td>Optional</td> <br />
<td>EPS: lambda<EPS, stop calculation.</td> <br />
<td>1e2</td> <br />
</tr> <br />
<tr> <br />
<td>-NX</td> <br />
<td>Optional</td> <br />
<td>Pixel: Nx</td> <br />
<td>30</td> <br />
</tr> <br />
<tr> <br />
<td>-NY</td> <br />
<td>Optional</td> <br />
<td>Pixel: Ny</td> <br />
<td>30</td> <br />
</tr> <br />
<tr> <br />
<td>-O</td> <br />
<td>Optional</td> <br />
<td>Output: vectorfile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-EPSO</td> <br />
<td>Optional</td> <br />
<td>Output: EPSOutput: caletimefile</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-E</td> <br />
<td>Optional</td> <br />
<td>Output: eigenImage</td> <br />
<td>eigen</td> <br />
</tr> <br />
<tr> <br />
<td>-numE</td> <br />
<td>Optional</td> <br />
<td>Number of eigenImages</td> <br />
<td>10</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 />
<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, -o format===<br />
<pre><br />
File1<br />
File2<br />
.<br />
.<br />
<br />
</pre><br />
<br><br />
<br />
== Execution example ==<br />
===Input file's data===<br />
<pre><br />
Input-121P-2D-P.mrc<br />
Input-121P-2D1-P.mrc<br />
Input-121P-2D2-P.mrc<br />
<br />
</pre><br />
<br />
<div>[[Media:Input-121P-2D-P.mrc | Input-121P-2D-P.mrc]]'s image</div><br />
<table> <br />
<tr> <br />
<td>[[File:Input-121P-2D-P.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">-1105.85 (0, 0, 0)<br> <br />
29741.8 (13, 23, 0)<br> <br />
5686.81<br> <br />
5820.04<br> <br />
145.501<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
<div>[[Media:Input-121P-2D1-P.mrc | Input-121P-2D1-P.mrc]]'s image</div><br />
<table> <br />
<tr> <br />
<td>[[File:Input-121P-2D1-P.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">-1105.85 (0, 0, 0)<br> <br />
30528.7 (8, 21, 0)<br> <br />
5656.23<br> <br />
6199.33<br> <br />
154.983<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
<div>[[Media:Input-121P-2D2-P.mrc | Input-121P-2D2-P.mrc]]'s image</div><br />
<table> <br />
<tr> <br />
<td>[[File:Input-121P-2D2-P.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">-1105.85 (0, 0, 0)<br> <br />
29425.9 (17, 12, 0)<br> <br />
5666.16<br> <br />
6154.34<br> <br />
153.858<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br><br />
<br />
<div>-o 's file</div><br />
<pre><br />
Outdata0-mrcImagePCA.mrc<br />
Outdata1-mrcImagePCA.mrc<br />
Outdata2-mrcImagePCA.mrc<br />
<br />
</pre><br />
<br><br />
<br />
=== Example of options only essential ===<br />
<div>-o 's image</div><br />
<div>View image was corrected by [[mrcImageWindowing]], because its first data far larger than others.</div><br />
<br><br />
<br />
<div>Outdata0-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata0-mrcImagePCA.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">-0.00138839 (2, 0, 0)<br> <br />
107098 (1, 0, 0)<br> <br />
200.692<br> <br />
4325.59<br> <br />
144.186<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 73525.2 <br />
1 0 107098 <br />
2 0 -0.00138839 <br />
3 0 -0.00137284 <br />
4 0 -0.00128583 <br />
5 0 0.000646963 <br />
6 0 -0.000642849 <br />
<br />
...<br />
<br />
8 10 -2.65457e-06 <br />
9 10 -6.40329e-06 <br />
10 10 -6.56773e-06 <br />
11 10 -9.83265e-05 <br />
12 10 8.96691e-07 <br />
<br />
...<br />
<br />
25 29 -1.81996e-06 <br />
26 29 -8.89436e-07 <br />
27 29 1.35051e-06 <br />
28 29 7.98696e-07 <br />
29 29 -7.37277e-07 <br />
</pre><br />
<br><br />
<br />
<div>Outdata1-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata1-mrcImagePCA.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">-105568 (1, 0, 0)<br> <br />
76769.3 (0, 0, 0)<br> <br />
-31.9984<br> <br />
4350.89<br> <br />
145.03<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 76769.3 <br />
1 0 -105568 <br />
2 0 0.00136864 <br />
3 0 0.00135261 <br />
4 0 0.00127105 <br />
5 0 0.000675541 <br />
6 0 -0.000672826 <br />
<br />
...<br />
<br />
8 10 -3.828e-06 <br />
9 10 -6.76705e-06 <br />
10 10 -6.8542e-06 <br />
11 10 -9.83877e-05 <br />
12 10 7.78496e-07 <br />
<br />
...<br />
<br />
25 29 1.8971e-06 <br />
26 29 -1.24502e-06 <br />
27 29 1.55392e-06 <br />
28 29 1.16343e-06 <br />
29 29 -1.05502e-06 <br />
</pre><br />
<br><br />
<br />
<div>Outdata2-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata2-mrcImagePCA.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">-150295 (0, 0, 0)<br> <br />
0.00131568 (6, 0, 0)<br> <br />
-168.694<br> <br />
5007.24<br> <br />
166.908<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 -150295 <br />
1 0 -1530.13 <br />
2 0 1.97447e-05 <br />
3 0 2.02311e-05 <br />
4 0 1.47764e-05 <br />
5 0 -0.0013225 <br />
6 0 0.00131568 <br />
7 0 0.00128579 <br />
<br />
...<br />
<br />
8 10 6.48256e-06 <br />
9 10 1.31703e-05 <br />
10 10 1.34219e-05 <br />
11 10 0.000196714 <br />
12 10 -1.67518e-06 <br />
<br />
...<br />
<br />
25 29 -7.71467e-08 <br />
26 29 2.13446e-06 <br />
27 29 -2.90443e-06 <br />
28 29 -1.96212e-06 <br />
29 29 1.7923e-06 <br />
</pre><br />
<br><br />
<br />
=== Option -NX, -NY===<br />
====NX=20, NY=20==== <br />
<div>-o 's image</div><br />
<div>View image was corrected by [[mrcImageWindowing]], because its first data far larger than others.</div><br />
<br><br />
<br />
<div>Outdata0-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata0-N-mrcImagePCA.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">-0.00138839 (2, 0, 0)<br> <br />
107098 (1, 0, 0)<br> <br />
451.558<br> <br />
6479.66<br> <br />
323.983<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 73525.2 <br />
1 0 107098 <br />
2 0 -0.00138839 <br />
3 0 -0.00137284 <br />
4 0 -0.00128583 <br />
5 0 0.000646963 <br />
6 0 -0.000642849 <br />
<br />
...<br />
<br />
8 15 -2.65457e-06 <br />
9 15 -6.40329e-06 <br />
10 15 -6.56773e-06 <br />
11 15 -9.83265e-05 <br />
12 15 8.96691e-07 <br />
<br />
...<br />
<br />
15 19 -5.82619e-07 <br />
16 19 4.00663e-07 <br />
17 19 6.01493e-07 <br />
18 19 7.07807e-06 <br />
19 19 6.33428e-06 <br />
</pre><br />
<br><br />
<br />
<div>Outdata1-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata1-N-mrcImagePCA.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">-105568 (1, 0, 0)<br> <br />
76769.3 (0, 0, 0)<br> <br />
-71.9964<br> <br />
6526.11<br> <br />
326.305<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 76769.3 <br />
1 0 -105568 <br />
2 0 0.00136864 <br />
3 0 0.00135261 <br />
4 0 0.00127105 <br />
<br />
...<br />
<br />
8 15 -3.828e-06 <br />
9 15 -6.76705e-06 <br />
10 15 -6.8542e-06 <br />
11 15 -9.83877e-05 <br />
12 15 7.78496e-07 <br />
<br />
...<br />
<br />
15 19 -3.87463e-07 <br />
16 19 4.56702e-07 <br />
17 19 8.39118e-07 <br />
18 19 7.15604e-06 <br />
19 19 6.71392e-06 <br />
</pre><br />
<br><br />
<br />
<div>Outdata2-mrcImagePCA.mrc</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata2-N-mrcImagePCA.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">-150295 (0, 0, 0)<br> <br />
0.00131568 (6, 0, 0)<br> <br />
-379.562<br> <br />
7505.53<br> <br />
375.276<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>By [[mrcImageMakeDump]]</div><br />
<pre><br />
0 0 -150295 <br />
1 0 -1530.13 <br />
2 0 1.97447e-05 <br />
3 0 2.02311e-05 <br />
4 0 1.47764e-05 <br />
5 0 -0.0013225 <br />
6 0 0.00131568 <br />
<br />
...<br />
<br />
8 15 6.48256e-06 <br />
9 15 1.31703e-05 <br />
10 15 1.34219e-05 <br />
11 15 0.000196714 <br />
12 15 -1.67518e-06 <br />
<br />
...<br />
<br />
15 19 9.70083e-07 <br />
16 19 -8.57366e-07 <br />
17 19 -1.4406e-06 <br />
18 19 -1.42341e-05 <br />
19 19 -1.30482e-05 <br />
</pre><br />
<br><br />
<br />
=== Option -O===<br />
<div>-O 's data</div><br />
<pre><br />
0 848 11295979840.68 59.97<br />
1 933 7538968371.30 100.00<br />
2 1077 0.00 100.00<br />
3 231 0.00 100.00<br />
4 122 0.00 100.00<br />
5 184 0.00 100.00<br />
6 1398 0.00 100.00<br />
<br />
...<br />
<br />
1595 450 -0.00 100.00<br />
1596 888 -0.00 100.00<br />
1597 1068 -0.00 100.00<br />
1598 1259 -0.00 100.00<br />
1599 1132 -0.00 100.00<br />
</pre><br />
<br><br />
<br />
=== Option -EPSO===<br />
<div>-EPSO 's data</div><br />
<pre><br />
1000/1279200 = 0.078174 % current 9.66421e+07 EPS 100 2 sec<br />
2000/1279200 = 0.156348 % current 7.96464e+07 EPS 100 4 sec<br />
3000/1279200 = 0.234522 % current 1.3266e+07 EPS 100 6 sec<br />
4000/1279200 = 0.312695 % current 2.07992e+06 EPS 100 9 sec<br />
5000/1279200 = 0.390869 % current 76309.2 EPS 100 11 sec<br />
6000/1279200 = 0.469043 % current 663.412 EPS 100 14 sec<br />
EPSbreak<br />
6080/1279200 = 0.475297 % current 99.6128 EPS 100 14 sec<br />
</pre><br />
<br><br />
<br />
=== Option -EPS===<br />
====Case: EPS=1e3====<br />
<div>-EPSO 's data</div><br />
<pre><br />
1000/1279200 = 0.078174 % current 9.66421e+07 EPS 1000 2 sec<br />
2000/1279200 = 0.156348 % current 7.96464e+07 EPS 1000 4 sec<br />
3000/1279200 = 0.234522 % current 1.3266e+07 EPS 1000 7 sec<br />
4000/1279200 = 0.312695 % current 2.07992e+06 EPS 1000 9 sec<br />
5000/1279200 = 0.390869 % current 76309.2 EPS 1000 11 sec<br />
EPSbreak<br />
5952/1279200 = 0.465291 % current 968.28 EPS 1000 13 sec<br />
</pre><br />
<br><br />
<br />
=== Option -E===<br />
<div>-E 's data</div><br />
<div>10 files are output, because numE=10 on default setting.</div><br />
<div>eigen.00000</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata10-mrcImagePCA.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">-0.0991027 (17, 12, 0)<br> <br />
0.0947194 (8, 21, 0)<br> <br />
2.23033e-05<br> <br />
0.025<br> <br />
0.000625<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>eigen.00001</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata11-mrcImagePCA.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">-0.0995859 (18, 23, 0)<br> <br />
0.092875 (12, 22, 0)<br> <br />
0.000144147<br> <br />
0.0249996<br> <br />
0.00062499<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>eigen.00002</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata12-mrcImagePCA.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">-0.000641438 (8, 21, 0)<br> <br />
0.999987 (37, 26, 0)<br> <br />
0.000625099<br> <br />
0.0249922<br> <br />
0.000624805<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
...<br />
<br />
<div>eigen.00009</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata19-mrcImagePCA.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">-0.00053598 (13, 23, 0)<br> <br />
0.999988 (14, 4, 0)<br> <br />
0.000624184<br> <br />
0.0249922<br> <br />
0.000624805<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br><br />
<br />
=== Option -numE===<br />
====Case: numE=2====<br />
<div>-E 's data</div><br />
<div>eigen.00000</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata20-mrcImagePCA.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">-0.0991027 (17, 12, 0)<br> <br />
0.0947194 (8, 21, 0)<br> <br />
2.23033e-05<br> <br />
0.025<br> <br />
0.000625<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>eigen.00001</div><br />
<table> <br />
<tr> <br />
<td>[[File:Outdata21-mrcImagePCA.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">-0.0995859 (18, 23, 0)<br> <br />
0.092875 (12, 22, 0)<br> <br />
0.000144147<br> <br />
0.0249996<br> <br />
0.00062499<br></p> <br />
</td> <br />
</tr> <br />
</table></div>
Kinoshita