Difference between revisions of "mrcImageSmoothing"

From EosPedia
Jump to: navigation, search
(Created page with "'''mrcImageSmoothing''' is Eos's Command that performs Nonlinear smoothing mrcImage. == List of option == === Main option === <table border="1"> <div align=...")
 
 
(4 intermediate revisions by the same user not shown)
Line 26: Line 26:
 
<td>-sx</td>  
 
<td>-sx</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>xのカーネルサイズ</td>  
+
<td>x of Kernel Size</td>  
 
<td>3</td>  
 
<td>3</td>  
 
</tr>  
 
</tr>  
Line 32: Line 32:
 
<td>-sy</td>  
 
<td>-sy</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>yのカーネルサイズ</td>  
+
<td>y of Kernel Size</td>  
 
<td>3</td>  
 
<td>3</td>  
 
</tr>  
 
</tr>  
Line 38: Line 38:
 
<td>-sz</td>  
 
<td>-sz</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>zのカーネルサイズ</td>  
+
<td>z of Kernel Size</td>  
 
<td>3</td>  
 
<td>3</td>  
 
</tr>  
 
</tr>  
Line 44: Line 44:
 
<td>-r</td>  
 
<td>-r</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>半径のカーネルサイズ</td>  
+
<td>Radius of Kernel Size</td>  
 
<td>1</td>  
 
<td>1</td>  
 
</tr>  
 
</tr>  
Line 50: Line 50:
 
<td>-sigma</td>  
 
<td>-sigma</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>Sigma (m=4で使用)</td>  
+
<td>Sigma (For m=4)</td>  
 
<td>2.0</td>  
 
<td>2.0</td>  
 
</tr>  
 
</tr>  
Line 74: Line 74:
 
<td>-M</td>  
 
<td>-M</td>  
 
<td>Optional</td>  
 
<td>Optional</td>  
−
<td>Mode2を設定</td>  
+
<td>Mode2</td>  
 
<td>0</td>  
 
<td>0</td>  
 
</tr>  
 
</tr>  
Line 84: Line 84:
 
</tr>  
 
</tr>  
 
</div>  
 
</div>  
−
</table>  
+
</table>
  
 
===-m  details===
 
===-m  details===
Line 111: Line 111:
 
</div>  
 
</div>  
 
</table>
 
</table>
−
<div>※Mode１はデフォルト＝０になっているが、Mode１の選択肢に<br>
+
<div>m=0, at the default setting. Therefore, It is error if -m isn't set.</div>
−
０は無いので、指定しなければエラーとなる。</div>
+
 
<br>
 
<br>
  
Line 123: Line 122:
 
<tr>  
 
<tr>  
 
<td>0</td>  
 
<td>0</td>  
−
<td>矩形: -sx, -sy, [-sz]の入力が必要</td>  
+
<td>Kernel is cube. : required argumnent: -sx, -sy, [-sz]</td>  
 
</tr>  
 
</tr>  
 
<tr>  
 
<tr>  
 
<td>1</td>  
 
<td>1</td>  
−
<td>球体(m=1のみ対応): -rの入力が必要</td>  
+
<td>Kernel is sphere.(Only mode 1 supported) : required argumnent: -r </td>  
 
</tr>  
 
</tr>  
−
</table>  
+
</table>
 +
 
 
== Execution example ==
 
== Execution example ==
  
−
-h によるヘルプの例
+
Example of Option -h
  
 
  $ mrcImageSmoothing  -h
 
  $ mrcImageSmoothing  -h
Line 157: Line 157:
  
  
−
===------Input file's image------===
+
===Input file's image===
 
<table>
 
<table>
 
<tr>
 
<tr>
Line 175: Line 175:
 
</tr>
 
</tr>
 
</table>
 
</table>
−
+
<br>
−
===------Mode１の1～3での処理画像------===
+
 
 +
===Option -m, -M===
 +
====Case: m=1====
 
<table>
 
<table>
−
<tr><td>Mode１:1</td></tr>
 
 
<tr>
 
<tr>
 
<td>[[File:Smo.m1.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m1.center-mrcImageSmoothing.png]]</td>
Line 193: Line 194:
 
0.178854<br></p>
 
0.178854<br></p>
 
</td>
 
</td>
−
<td>Mode２:0を選択<br>
+
<td>Case: M=0<br>
−
-sx=9,-sy=9に変更<br>
+
with -sx=9,-sy=9<br>
 
　　－－－－－－＞</td>
 
　　－－－－－－＞</td>
 
<td>[[File:Smo.m1M0x9y9.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m1M0x9y9.center-mrcImageSmoothing.png]]</td>
Line 214: Line 215:
 
<td></td>
 
<td></td>
 
<td></td>
 
<td></td>
−
<td>Mode２:1を選択<br>
+
<td>Case: M=1<br>
−
-r=5に変更<br>
+
with -r=5<br>
 
　　－－－－－－＞</td>
 
　　－－－－－－＞</td>
 
<td>[[File:Smo.m1M1r5.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m1M1r5.center-mrcImageSmoothing.png]]</td>
Line 231: Line 232:
 
</td>
 
</td>
 
</tr>
 
</tr>
−
+
</table>
−
<tr><td>Mode１:2</td></tr>
+
<br>
 +
 +
====Case: m=2====
 +
<table>
 
<tr>
 
<tr>
 
<td>[[File:Smo.m2.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m2.center-mrcImageSmoothing.png]]</td>
Line 247: Line 251:
 
0.17257<br></p>
 
0.17257<br></p>
 
</td>
 
</td>
−
<td>Mode２:0を選択<br>
+
<td>Case: M=0<br>
−
-sx=9,-sy=9に変更<br>
+
with -sx=9,-sy=9<br>
 
　　－－－－－－＞</td>
 
　　－－－－－－＞</td>
 
<td>[[File:Smo.m2M0x9y9.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m2M0x9y9.center-mrcImageSmoothing.png]]</td>
Line 264: Line 268:
 
</td>
 
</td>
 
</tr>
 
</tr>
 +
</table>
 +
<br>
  
−
<tr><td>Mode１:3</td></tr>
+
====Case: m=3====
 +
<table>
 
<tr>
 
<tr>
 
<td>[[File:Smo.m3.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m3.center-mrcImageSmoothing.png]]</td>
Line 280: Line 287:
 
0.21879<br></p>
 
0.21879<br></p>
 
</td>
 
</td>
−
<td>Mode２:0を選択<br>
+
<td>Case: M=0<br>
−
-sx=9,-sy=9に変更<br>
+
with -sx=9,-sy=9<br>
 
　　－－－－－－＞</td>
 
　　－－－－－－＞</td>
 
<td>[[File:Smo.m3M0x9y9.center-mrcImageSmoothing.png]]</td>
 
<td>[[File:Smo.m3M0x9y9.center-mrcImageSmoothing.png]]</td>
Line 298: Line 305:
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
<br>

Latest revision as of 06:08, 4 March 2015

mrcImageSmoothing is Eos's Command that performs Nonlinear smoothing mrcImage.

List of option

Main option

Option Essential/Optional Description Default
-i Essential Input名: mrcImage NULL
-o Optional Output名: mrcImage stdout(Standard output by default）
-sx Optional x of Kernel Size 3
-sy Optional y of Kernel Size 3
-sz Optional z of Kernel Size 3
-r Optional Radius of Kernel Size 1
-sigma Optional Sigma (For m=4) 2.0
-times Optional Repeat time 1
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-M Optional Mode2 0
-h Optional Help 　

-m details

Value Description
1 Median filter
2 Mean filter
3 Surface Fit filter
4 Lee-Sigma filter
m=0, at the default setting. Therefore, It is error if -m isn't set.


-M details

Value Description
0 Kernel is cube. : required argumnent: -sx, -sy, [-sz]
1 Kernel is sphere.(Only mode 1 supported) : required argumnent: -r

Execution example

Example of Option -h 

$ mrcImageSmoothing  -h
Usage: /home/people/tacyas/Eos/bin/X86LINUX64/mrcImageSmoothing
Options:
    [-i[nput]            In                  (NULL      )] :Essential :InputDataFile
    [-o[utput]           Out                 (NULL      )] :Essential :OutputDataFile
    [-sx                 sx                  (3         )] :Optional  :x of Kernel Size
    [-sy                 sy                  (3         )] :Optional  :y of Kernel Size
    [-sz                 sz                  (3         )] :Optional  :z of Kernel Size
    [-r                  r                   (1         )] :Optional  :Radius of Kernel Size
    [-sigma              sigma               (2.0       )] :Optional  :Sigma for Lee-Sigma
    [-m[ode]             mode                (0         )] :Optional  :Mode
    [-M[ode2]            mode2               (0         )] :Optional  :Mode
    [-c[onfig]           configFile          (NULL      )] :Optional  :ConfigurationFile
>>> Mode <<<< 
    1: Median filter
    2: Mean filter 
    3: Surface Fit filter
    4: Lee-Sigma filter
>>> Mode2 <<<< 
    0: Kernel is cube. : required argumnent: -sx, -sy, [-sz]
    1: Kernel is sphere.(Only mode 1 supported) : required argumnent: -r


Input file's image

B120.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-65.0178

94.4699
4.85274
20.4635

0.255794


Option -m, -M

Case: m=1

Smo.m1.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-41.8721

65.9659
4.7617
14.3083

0.178854

 Case: M=0

with -sx=9,-sy=9

　　－－－－－－＞		 Smo.m1M0x9y9.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-54.6403

54.0815
4.773
13.5848

0.16981
Case: M=1

with -r=5

　　－－－－－－＞		 Smo.m1M1r5.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-54.6403

55.7056
4.73966
13.9823

0.174779


Case: m=2

Smo.m2.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-41.8721

67.5276
4.82079
13.8056

0.17257

 Case: M=0

with -sx=9,-sy=9

　　－－－－－－＞		 Smo.m2M0x9y9.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-54.6403

54.0644
4.89358
13.5214

0.169018


Case: m=3

Smo.m3.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-41.8721

83.4967
4.85411
17.5032

0.21879

 Case: M=0

with -sx=9,-sy=9

　　－－－－－－＞		 Smo.m3M0x9y9.center-mrcImageSmoothing.png

Min

Max
Mean
SD

SE

-54.6403

56.99
4.87303
14.4517

0.180646


Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageSmoothing&oldid=4632"