Kinoshita at 05:24, 16 July 2014

2014-07-16T05:24:30Z

Kinoshita: Created page with "'''mrcImage3DPad2''' is Eos's Command that is padding the mrcImage(3D) of particle or filament. 出力ファイルのzサイズがmrcImage3DPadと異なる。 ..."

2014-07-16T05:19:34Z

Created page with "'''mrcImage3DPad2''' is Eos's Command that is padding the mrcImage(3D) of particle or filament. 出力ファイルのzサイズがmrcImage3DPadと異なる。 ..."

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'''mrcImage3DPad2''' is [[Eos]]'s [[Command]] that is padding the [[mrcImage]](3D) of particle or filament. 出力ファイルのzサイズが[[mrcImage3DPad]]と異なる。

== 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>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-r</td>
<td>Optional</td>
<td>Threshold radius of signal.(cf: -M)</td>
<td>Nx</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Width of slope. (For m=1.)</td>
<td>1</td>
</tr>
<tr>
<td>-v</td>
<td>Optional</td>
<td>Pad value</td>
<td>0</td>
</tr>
<tr>
<td>-Nx</td>
<td>Optional</td>
<td>Output's Nx</td>
<td>InputのNx</td>
</tr>
<tr>
<td>-Ny</td>
<td>Optional</td>
<td>Output's Ny</td>
<td>InputのNy</td>
</tr>
<tr>
<td>-Nz</td>
<td>Optional</td>
<td>Output's Nz</td>
<td>InputのNz</td>
</tr>
<tr>
<td>-Floating</td>
<td>Optional</td>
<td>Floating</td>
<td></td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode of calculating pad value</td>
<td>0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>Mode of calculating -r</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>
<br>

===-m details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Out of threshold is avrage of threshold plain.(Default)</td>
</tr>
<tr>
<td>1</td>
<td>Mulplying cos function. Default: Out of threshold is avrage of threshold plain.</td>
</tr>
</table>

<div>About pad value, -v is precedence.</div>
<br>

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>For filaments. (R is calculated from its axis.)</td>
</tr>
<tr>
<td>1</td>
<td>For particles. (R is calculated from its center.)</td>
</tr>
</table>
<br>

== Execution example ==
===[[Media:Input-ThickFilaments0-N.mrc | Input file]] image===
<table>
<tr>
<td><p align="Center">[[File:Input-ThickFilaments0-N.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Input1-ThickFilaments0-N.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.307724 (52, 10, 79)<br>
1.52145 (47, 41, 47)<br>
0.00295664<br>
0.0916201<br>
0.000132783<br></p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<div>Output</div>
<pre>
Tailer: 0
Program Start
TailerNum 0
r: 34
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-mrcImage3DPad2.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-mrcImage3DPad2.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.307724 (52, 10, 79)<br>
1.52145 (47, 41, 47)<br>
0.00295664<br>
0.0916201<br>
0.000132783<br></p>
</td>
</tr>
</table>

<div>Image does not change almost by default.</div>
<br>

=== Option -Nx, -Ny, -Nz===
====Case: Nx=50, Ny=50, Nz=75====
<div>Output</div>
<pre>
Tailer: 0
Program Start
TailerNum 0
r: 34
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-NxNyNz-mrcImage3DPad2.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-NxNyNz-mrcImage3DPad2.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.295151 (23, 12, 71)<br>
1.52145 (38, 32, 47)<br>
0.0057768<br>
0.106019<br>
0.000212039<br></p>
</td>
</tr>
</table>
<br>

=== Option -r===
====Case: r=20====
<div>Output</div>
<pre>
Tailer: 0
Program Start
TailerNum 0
r: 20
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-r-mrcImage3DPad2.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-r-mrcImage3DPad2.png]]<br>
yz-plane<br></p>
</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-0.295151 (32, 21, 71)<br>
1.52145 (47, 41, 47)<br>
0.00236564<br>
0.0675752<br>
9.79351e-05<br></p>
</td>
</tr>
</table>
<br>

← Older revision		Revision as of 05:24, 16 July 2014
Line 1:		Line 1:
−	'''mrcImage3DPad2''' is [[Eos]]'s [[Command]] that is padding the [[mrcImage]](3D) of particle or filament. ~~出力ファイルのzサイズが~~[[mrcImage3DPad]]~~と異なる。~~	+	'''mrcImage3DPad2''' is [[Eos]]'s [[Command]] that is padding the [[mrcImage]](3D) of particle or filament. Z size of the output file is different from [[mrcImage3DPad]].

mrcImage3DPad2 - Revision history

Kinoshita at 05:24, 16 July 2014

Kinoshita: Created page with "'''mrcImage3DPad2''' is Eos's Command that is padding the mrcImage(3D) of particle or filament. 出力ファイルのzサイズがmrcImage3DPadと異なる。 ..."