mrcImageZPad - Revision history

Kinoshita: Created page with "'''mrcImageZPad''' is Eos's Command that performs padding of mrcImage(3D) along with z-axis. == List of option == === Main option ===
2014-08-04T07:23:16Z

Created page with "'''mrcImageZPad''' is Eos's Command that performs padding of mrcImage(3D) along with z-axis. == List of option == === Main option === <table border="1"> <tr..."

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'''mrcImageZPad''' is [[Eos]]'s [[Command]] that performs padding of [[mrcImage]](3D) along with z-axis.

== 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>rmax = height of z window * 0.5</td>
<td>0</td>
</tr>
<tr>
<td>-w</td>
<td>Optional</td>
<td>Width of slope.(For mode 1)(Usually w>=3 is good enough)</td>
<td>1</td>
</tr>
<tr>
<td>-v</td>
<td>Optional</td>
<td>Padding value</td>
<td>0</td>
</tr>
<tr>
<td>-Nx</td>
<td>Optional</td>
<td>Number x of Output</td>
<td>Number x of Input</td>
</tr>
<tr>
<td>-Ny</td>
<td>Optional</td>
<td>Number y of Output</td>
<td>Number y of Input</td>
</tr>
<tr>
<td>-Nz</td>
<td>Optional</td>
<td>Number z of Output</td>
<td>Number z of Input</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>Calculation method of padding value</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</table>

===-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.</td>
</tr>
<tr>
<td>1</td>
<td>Mulplying cos function.</td>
</tr>
</table>

<div>About padding value, -v takes priority.</div>

== 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>

=== Option -m===
====Case: m=1, r=20====
<div>Output</div>
<pre>
Tailer: 0
Program Start
av :0.00324832
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1r-mrcImageZPad.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1r-mrcImageZPad.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">-0.302611 (10, 14, 59)<br>
1.52145 (47, 41, 47)<br>
0.00427721<br>
0.0683816<br>
9.91038e-05<br></p>
</td>
</tr>
</table>

<div>In the following, Setting at m=1, r=20</div>

=== Option -w===
====Case: w=10====
<div>Output</div>
<pre>
Tailer: 0
Program Start
av :0.00028809
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1w-mrcImageZPad.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1w-mrcImageZPad.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">-0.302611 (10, 14, 59)<br>
1.52145 (47, 41, 47)<br>
0.00272471<br>
0.0715415<br>
0.000103683<br></p>
</td>
</tr>
</table>

=== Option -v===
====Case: v=0.1, w=10====
<div>Output</div>
<pre>
Tailer: 0
Program Start
av :0.1
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1v-mrcImageZPad.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1v-mrcImageZPad.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">-0.302611 (10, 14, 59)<br>
1.52145 (47, 41, 47)<br>
0.0498431<br>
0.0831128<br>
0.000120453<br></p>
</td>
</tr>
</table>

=== Option -Floating===
<div>Output</div>
<pre>
Tailer: 0
Program Start
av :0.00324832
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1Floating-mrcImageZPad.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1Floating-mrcImageZPad.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">-0.30586 (10, 14, 59)<br>
1.5182 (47, 41, 47)<br>
0.0010289<br>
0.0683816<br>
9.91038e-05<br></p>
</td>
</tr>
</table>

=== Option -Nx, -Ny, -Nz===
====Case: Nx=40, Ny=40, Nz=50====
<div>Output</div>
<pre>
Tailer: 0
Program Start
av :0.00324832
</pre>
<div>Output file's image</div>
<table>
<tr>
<td><p align="Center">[[File:Outdata-m1NxNyNz-mrcImageZPad.png]]<br>
xy-plane<br></p>
</td>
<td><p align="Center">[[File:Outdata1-m1NxNyNz-mrcImageZPad.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">-0.289995 (10, 3, 38)<br>
1.52145 (33, 27, 22)<br>
0.015069<br>
0.138822<br>
0.000490811<br></p>
</td>
</tr>
</table>