View source for mrcImage3DPad

'''mrcImage3DPad''' is [[Eos]]'s [[Command]] that is padding the [[mrcImage]](3D) of particle or filament.


== 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's Nx</td> 
			</tr> 
			<tr> 
				<td>-Ny</td> 
				<td>Optional</td> 
				<td>Output's Ny</td> 
				<td>Input's Ny</td> 
			</tr> 
			<tr> 
				<td>-Nz</td> 
				<td>Optional</td> 
				<td>Output's Nz</td> 
				<td>Input's 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> 

===-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>

===-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> 


== 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> 


<div>[[Media:Input-121P-O-N.mrc | Input file]]'s image (for M=1)</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Input-121P-O-N.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Input1-121P-O-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">-2255.49 (1, 42, 21)<br> 
				4032.8 (49, 53, 30)<br> 
				12.0338<br> 
				475.034<br> 
				0.48225<br></p> 
			</td> 
		</tr> 
	</table> 


=== Example of options only essential ===
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 34 
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-mrcImage3DPad.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>


=== Option -Nx, -Ny, -Nz===
====Case: Nx=50, Ny=50, Nz=75==== 
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 50 50 75
TailerNum 0
r: 34 
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-NxNyNz-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-NxNyNz-mrcImage3DPad.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> 
				0.00688378<br> 
				0.1116<br> 
				0.000257729<br></p> 
			</td> 
		</tr> 
	</table> 


=== Option -r===
====Case: r=20==== 
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 20 
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-r-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-r-mrcImage3DPad.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> 


<div>In the following, setting at r=20.</div>


=== Option -v===
====Case: v=0.1==== 
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-v-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-v-mrcImage3DPad.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> 
				0.0766349<br> 
				0.0778349<br> 
				0.000112804<br></p> 
			</td> 
		</tr> 
	</table>


=== Option -Floating===
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: 20 
Floating avg:-0.000912
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-Floating-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-Floating-mrcImage3DPad.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">-0.294238 (32, 21, 71)<br> 
				1.52236 (47, 41, 47)<br> 
				0.00327779<br> 
				0.0675752<br> 
				9.79351e-05<br></p> 
			</td> 
		</tr> 
	</table>


=== Option -m===
====Case: m=1==== 
=====Case: No other settings=====
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: -0.000245498 
av: -0.000245498 
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m1-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m1-mrcImage3DPad.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> 
				0.00286168<br> 
				0.0672918<br> 
				9.75243e-05<br></p> 
			</td> 
		</tr> 
	</table>


=====Case: w=2=====
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 69 69 100
TailerNum 0
r: -0.000162708 
av: -0.000162708 
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-m1w-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-m1w-mrcImage3DPad.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">-0.255166 (37, 36, 69)<br> 
				1.06472 (47, 41, 47)<br> 
				0.00197785<br> 
				0.0497011<br> 
				7.20306e-05<br></p> 
			</td> 
		</tr> 
	</table>


=== Option -M===
====Case: M=1, r=30==== 
<div>Output</div>
<pre>
Tailer: 0
Program Start
N: 99 99 99
99 99 99
</pre>
<div>Output file's image</div>
	<table> 
		<tr> 
			<td><p align="Center">[[File:Outdata-M1-mrcImage3DPad.png]]<br>
				xy-plane<br></p> 
			</td> 
			<td><p align="Center">[[File:Outdata1-M1-mrcImage3DPad.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">-1991.84 (41, 38, 29)<br> 
				4032.8 (49, 53, 30)<br> 
				13.2658<br> 
				197.192<br> 
				0.200188<br></p> 
			</td> 
		</tr> 
	</table>