http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?action=history&feed=atom&title=mrcImage3DPad
mrcImage3DPad - Revision history
2026-05-14T00:42:19Z
Revision history for this page on the wiki
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http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImage3DPad&diff=201&oldid=prev
Kinoshita at 05:19, 16 July 2014
2014-07-16T05:19:47Z
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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 05:19, 16 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><div>About pad value, -v is precedence.</div></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><div>About pad value, -v is precedence.</div></div></td></tr>
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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;"></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;"><div>===-M  details===</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>===-M  details===</div></td></tr>
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Kinoshita
http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImage3DPad&diff=199&oldid=prev
Kinoshita: Created page with "'''mrcImage3DPad''' is Eos's Command that is padding the mrcImage(3D) of particle or filament. == List of option == === Main option === <table border="1"> <..."
2014-07-16T05:14:09Z
<p>Created page with "'''mrcImage3DPad''' is <a href="/Eos/index.php/Eos" title="Eos">Eos</a>'s <a href="/Eos/index.php/Command" title="Command">Command</a> that is padding the <a href="/Eos/index.php/mrcImage" title="mrcImage">mrcImage</a>(3D) of particle or filament. == List of option == === Main option === <table border="1"> <..."</p>
<p><b>New page</b></p><div>'''mrcImage3DPad''' is [[Eos]]'s [[Command]] that is padding the [[mrcImage]](3D) of particle or filament.<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: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-o</td> <br />
<td>Essential</td> <br />
<td>Output: [[mrcImage]]</td> <br />
<td>NULL</td> <br />
</tr> <br />
<tr> <br />
<td>-r</td> <br />
<td>Optional</td> <br />
<td>Threshold radius of signal.(cf: -M)</td> <br />
<td>Nx</td> <br />
</tr> <br />
<tr> <br />
<td>-w</td> <br />
<td>Optional</td> <br />
<td>Width of slope. (For m=1.)</td> <br />
<td>1</td> <br />
</tr> <br />
<tr> <br />
<td>-v</td> <br />
<td>Optional</td> <br />
<td>Pad value</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-Nx</td> <br />
<td>Optional</td> <br />
<td>Output's Nx</td> <br />
<td>Input's Nx</td> <br />
</tr> <br />
<tr> <br />
<td>-Ny</td> <br />
<td>Optional</td> <br />
<td>Output's Ny</td> <br />
<td>Input's Ny</td> <br />
</tr> <br />
<tr> <br />
<td>-Nz</td> <br />
<td>Optional</td> <br />
<td>Output's Nz</td> <br />
<td>Input's Nz</td> <br />
</tr> <br />
<tr> <br />
<td>-Floating</td> <br />
<td>Optional</td> <br />
<td>Floating</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 of calculating pad value</td> <br />
<td>0</td> <br />
</tr> <br />
<tr> <br />
<td>-M</td> <br />
<td>Optional</td> <br />
<td>Mode of calculating -r</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 />
===-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>Out of threshold is avrage of threshold plain.(Default)</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>Mulplying cos function. Default: Out of threshold is avrage of threshold plain.</td> <br />
</tr> <br />
</table> <br />
<br />
<div>About pad value, -v is precedence.</div><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>For filaments. (R is calculated from its axis.)</td> <br />
</tr> <br />
<tr> <br />
<td>1</td> <br />
<td>For particles. (R is calculated from its center.)</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
== Execution example ==<br />
===[[Media:Input-ThickFilaments0-N.mrc | Input file]] image===<br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Input-ThickFilaments0-N.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Input1-ThickFilaments0-N.png]]<br><br />
yz-plane<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">-0.307724 (52, 10, 79)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.00295664<br> <br />
0.0916201<br> <br />
0.000132783<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
<div>[[Media:Input-121P-O-N.mrc | Input file]]'s image (for M=1)</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Input-121P-O-N.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Input1-121P-O-N.png]]<br><br />
yz-plane<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">-2255.49 (1, 42, 21)<br> <br />
4032.8 (49, 53, 30)<br> <br />
12.0338<br> <br />
475.034<br> <br />
0.48225<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
=== Example of options only essential ===<br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
r: 34 <br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.307724 (52, 10, 79)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.00295664<br> <br />
0.0916201<br> <br />
0.000132783<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<div>Image does not change almost by default.</div><br />
<br />
<br />
=== Option -Nx, -Ny, -Nz===<br />
====Case: Nx=50, Ny=50, Nz=75==== <br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 50 50 75<br />
TailerNum 0<br />
r: 34 <br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-NxNyNz-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-NxNyNz-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.295151 (23, 12, 71)<br> <br />
1.52145 (38, 32, 47)<br> <br />
0.00688378<br> <br />
0.1116<br> <br />
0.000257729<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
=== Option -r===<br />
====Case: r=20==== <br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
r: 20 <br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-r-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-r-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.295151 (32, 21, 71)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.00236564<br> <br />
0.0675752<br> <br />
9.79351e-05<br></p> <br />
</td> <br />
</tr> <br />
</table> <br />
<br />
<br />
<div>In the following, setting at r=20.</div><br />
<br />
<br />
=== Option -v===<br />
====Case: v=0.1==== <br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-v-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-v-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.295151 (32, 21, 71)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.0766349<br> <br />
0.0778349<br> <br />
0.000112804<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -Floating===<br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
r: 20 <br />
Floating avg:-0.000912<br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-Floating-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-Floating-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.294238 (32, 21, 71)<br> <br />
1.52236 (47, 41, 47)<br> <br />
0.00327779<br> <br />
0.0675752<br> <br />
9.79351e-05<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -m===<br />
====Case: m=1==== <br />
=====Case: No other settings=====<br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
r: -0.000245498 <br />
av: -0.000245498 <br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m1-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m1-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.295151 (32, 21, 71)<br> <br />
1.52145 (47, 41, 47)<br> <br />
0.00286168<br> <br />
0.0672918<br> <br />
9.75243e-05<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=====Case: w=2=====<br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 69 69 100<br />
TailerNum 0<br />
r: -0.000162708 <br />
av: -0.000162708 <br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-m1w-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-m1w-mrcImage3DPad.png]]<br><br />
yz-plane<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">-0.255166 (37, 36, 69)<br> <br />
1.06472 (47, 41, 47)<br> <br />
0.00197785<br> <br />
0.0497011<br> <br />
7.20306e-05<br></p> <br />
</td> <br />
</tr> <br />
</table><br />
<br />
<br />
=== Option -M===<br />
====Case: M=1, r=30==== <br />
<div>Output</div><br />
<pre><br />
Tailer: 0<br />
Program Start<br />
N: 99 99 99<br />
99 99 99<br />
</pre><br />
<div>Output file's image</div><br />
<table> <br />
<tr> <br />
<td><p align="Center">[[File:Outdata-M1-mrcImage3DPad.png]]<br><br />
xy-plane<br></p> <br />
</td> <br />
<td><p align="Center">[[File:Outdata1-M1-mrcImage3DPad.png]]<br><br />
yz-plane<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">-1991.84 (41, 38, 29)<br> <br />
4032.8 (49, 53, 30)<br> <br />
13.2658<br> <br />
197.192<br> <br />
0.200188<br></p> <br />
</td> <br />
</tr> <br />
</table></div>
Kinoshita