Difference between revisions of "mrcImageTiltAxisSearch"

Latest revision as of 02:16, 4 August 2014

mrcImageTiltAxisSearch is Eos's Command that calculates the misalignment of tilt axis.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Optional	Input: mrcImage (If the search file is one)	NULL
-I	Optional	Input: ASCII (File List of search the axis)	NULL
-r	Essential	Reference: mrcImage (Untilted data)	NULL
-o	Essential	Output: mrcImage	NULL
-O	Optional	Output: ASCII (Estimate of misalignment of the tilt axis)	stdout
-range	Optional	start angle, end angle, delta	thetaMin=-90 thetaMax=+90 thetaDelta=1
-w	Optional	Projection Range around centre	0.5
-M	Optional	Mode (Setting of Interpolation method. No need to change.)	2
-CM	Optional		17
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-M details

Value	Description
0	Nearest neighbor method
1	Bi-linear interpolation method
2	Cubic convolution method
3	Polynomial interpolation method

-CM details

Value	Description
0	Normal correlation:FxG*
1	Phase correlation:FxG/\|FxG\|
2	Phase correlation:FxG/sqrt(\|FxG\|)
3	Standard Normal correlation:FxG*/(\|F\|\|G\|)
16	(0,0) = 0

Execution example

Input file's image

Option -I

Input file is as the following.

1vom-rot0.mrc (The tilt axis is misalignment for 2°)

Min

Max
Mean
SD

SE

-11367.8 (51, 62, 0)

51939.8 (29, 26, 0)
6580.18
9247.8

115.597

1vom-rot1.mrc (The tilt axis is misalignment for 10°)

Min

Max
Mean
SD

SE

-14918 (53, 17, 0)

58621.8 (30, 26, 0)
6579.96
9022.72

112.784

1vom-rot2.mrc (The tilt axis is misalignment for 45°)

Min

Max
Mean
SD

SE

-11517.4 (68, 34, 0)

41456.7 (51, 51, 0)
6543.11
8278.54

103.482

1vom-rot3.mrc (The tilt axis is misalignment for 60°)

Min

Max
Mean
SD

SE

-10181.1 (29, 12, 0)

47629.2 (45, 47, 0)
6507.05
8180.03

102.25

Reference file image

Min

Max
Mean
SD

SE

0 (0, 0, 0)

49749.7 (27, 28, 0)
7212.9
8827.15

110.339

※Input file、Reference fileは傾斜軸が10°ずれている

Option -range

Set the speculated misalignment of tilt axis.
Because it is 10° in this case, it is speculated and set-range 0 20 0.1 .

Option -i

Using 1vom-rot3.mrc (because the larger tilt angle can reduce the error.)

-o data's Output

Min

Max
Mean
SD

SE

1.66094 (178, 0, 0)

2.98337 (17, 0, 0)
2.28464
0.291971

0.0205941

By mrcImageMakeDump

0 0 2.11606 
1 0 2.27825 
2 0 2.39837 
3 0 2.48984 
4 0 2.56434 

...

15 0 2.84687 
16 0 2.89484 
17 0 2.98337 
18 0 2.92074 
19 0 2.83747 

...

176 0 1.8126 
177 0 1.75571 
178 0 1.66094 
179 0 1.77095 
180 0 1.86408 

...

196 0 1.96959 
197 0 1.92914 
198 0 1.90422 
199 0 1.89453 
200 0 1.89396

-O data's Output

   9.668

Option -I

-o data's Output

Min

Max
Mean
SD

SE

1.66094 (178, 3, 0)

5.97202 (199, 1, 0)
3.87448
1.57063

0.0553918

By mrcImageMakeDump

0 0 4.65631 
1 0 4.65526 
2 0 4.65832 
3 0 4.66586 
4 0 4.67802 

...

197 1 5.96871 
198 1 5.97113 
199 1 5.97202 
200 1 5.97128 
0 2 1.86252 

...

176 3 1.8126 
177 3 1.75571 
178 3 1.66094 
179 3 1.77095 
180 3 1.86408 

...

196 3 1.96959 
197 3 1.92914 
198 3 1.90422 
199 3 1.89453 
200 3 1.89396

-O data's Output

  10.146

About accuracy, -I is better than -i. Thus, use -I usually.
In the following, Setting at -I

Option -w

Case: w=0.3

-o data's Output

Min

Max
Mean
SD

SE

1.23539 (185, 3, 0)

4.24526 (176, 0, 0)
2.68811
0.965312

0.0340439

By mrcImageMakeDump

0 0 3.68699 
1 0 3.65896 
2 0 3.63381 
3 0 3.61121 
4 0 3.59092 

...

174 0 4.22654 
175 0 4.23925 
176 0 4.24526 
177 0 4.24387 
178 0 4.2353 

...

183 3 1.25732 
184 3 1.24203 
185 3 1.23539 
186 3 1.25265 
187 3 1.26904 

...

196 3 1.38081 
197 3 1.3898 
198 3 1.39842 
199 3 1.40678 
200 3 1.41503

-O data's Output

   9.959

Option -M

Case: M=0

-o data's Output

Min

Max
Mean
SD

SE

1.49726 (123, 2, 0)

5.98241 (194, 1, 0)
3.78781
1.62837

0.0574282

By mrcImageMakeDump

0 0 5.09922 
1 0 5.09922 
2 0 5.09922 
3 0 5.09922 
4 0 5.09922 

...

192 1 5.96451 
193 1 5.9541 
194 1 5.98241 
195 1 5.94377 
196 1 5.84344 

...

121 2 2.04668 
122 2 1.64817 
123 2 1.49726 
124 2 2.02508 
125 2 1.96064 

...

196 3 2.36013 
197 3 2.18772 
198 3 2.17512 
199 3 2.05867 
200 3 1.86606

-O data's Output

  10.003

Case: M=1

-o data's Output

Min

Max
Mean
SD

SE

1.4577 (171, 3, 0)

6.07152 (198, 1, 0)
4.24402
1.70736

0.060214

By mrcImageMakeDump

0 0 5.62558 
1 0 5.64422 
2 0 5.66207 
3 0 5.67922 
4 0 5.6957 

...

196 1 6.06964 
197 1 6.07106 
198 1 6.07152 
199 1 6.07098 
200 1 6.06985 

...

169 3 1.55818 
170 3 1.48867 
171 3 1.4577 
172 3 1.49909 
173 3 1.62042 

...

196 3 1.7818 
197 3 1.79882 
198 3 1.79487 
199 3 1.77391 
200 3 1.86874

-O data's Output

  10.066

Case: M=3

-o data's Output

Min

Max
Mean
SD

SE

1.06309 (200, 2, 0)

5.74525 (196, 0, 0)
3.29668
1.45732

0.0513957

By mrcImageMakeDump

0 0 3.49023 
1 0 3.59306 
2 0 3.59611 
3 0 3.59923 
4 0 3.60242 

...

194 0 5.68631 
195 0 5.72896 
196 0 5.74525 
197 0 5.68198 
198 0 5.68832 

...

198 2 1.06931 
199 2 1.10243 
200 2 1.06309 
0 3 2.099 
1 3 2.39454 

...

196 3 1.40634 
197 3 1.27379 
198 3 1.43405 
199 3 1.32319 
200 3 1.31033

-O data's Output

  10.528

Option -CM

Case: CM=0

-oのOutput

Min

Max
Mean
SD

SE

2.22243e+12 (200, 3, 0)

2.76642e+12 (0, 0, 0)
2.44638e+12
2.12262e+11

7.48589e+09

By mrcImageMakeDump

0 0 2.76642e+12 
1 0 2.76593e+12 
2 0 2.7655e+12 
3 0 2.7651e+12 
4 0 2.76475e+12

...

196 3 2.22279e+12 
197 3 2.22268e+12 
198 3 2.2226e+12 
199 3 2.22252e+12 
200 3 2.22243e+12

-O data's Output

   9.973

Case: CM=16

-o data's Output

Min

Max
Mean
SD

SE

4.25548e+10 (34, 2, 0)

4.59601e+11 (40, 0, 0)
2.42289e+11
1.61268e+11

5.6875e+09

By mrcImageMakeDump

0 0 4.5856e+11 
1 0 4.58461e+11 
2 0 4.58368e+11 
3 0 4.58283e+11 
4 0 4.58207e+11 

...

38 0 4.5955e+11 
39 0 4.59586e+11 
40 0 4.59601e+11 
41 0 4.59589e+11 
42 0 4.59553e+11 

...

32 2 4.33837e+10 
33 2 4.2829e+10 
34 2 4.25548e+10 
35 2 4.29276e+10 
36 2 4.33223e+10 

...

196 3 1.00736e+11 
197 3 1.00591e+11 
198 3 1.00438e+11 
199 3 1.0027e+11 
200 3 1.00082e+11

-O data's Output

   9.979

Case: CM=18

-o data's Output

Min

Max
Mean
SD

SE

182002 (115, 2, 0)

921359 (119, 0, 0)
574178
296936

10472.1

By mrcImageMakeDump

0 0 854840 
1 0 855240 
2 0 855704 
3 0 856251 
4 0 856892 

...

117 0 921121 
118 0 921303 
119 0 921359 
120 0 921286 
121 0 921070 

...

113 2 184920 
114 2 182180 
115 2 182002 
116 2 182423 
117 2 183137 

...

196 3 266598 
197 3 267662 
198 3 268966 
199 3 270519 
200 3 272332

-O data's Output

  10.020

Case: CM=19

-o data's Output

Min

Max
Mean
SD

SE

0.00308662 (34, 2, 0)

0.0317806 (42, 0, 0)
0.0171323
0.0111276

0.000392441

By mrcImageMakeDump

0 0 0.0314164 
1 0 0.0314149 
2 0 0.0314133 
3 0 0.0314116 
4 0 0.0314101

...

40 0 0.0317746 
41 0 0.0317788 
42 0 0.0317806 
43 0 0.0317806 
44 0 0.0317788 

...

32 2 0.00314582 
33 2 0.0031061 
34 2 0.00308662 
35 2 0.00311397 
36 2 0.0031428 

...

196 3 0.00750586 
197 3 0.00749485 
198 3 0.00748321 
199 3 0.00747043 
200 3 0.00745608

-O data's Output

  10.015

@@ Line 1: / Line 1: @@
-'''mrcImageTiltAxisSearch''' is傾斜軸のずれを計算する [[Eos]]'s [[Command]].
+'''mrcImageTiltAxisSearch''' is [[Eos]]'s [[Command]] that calculates the misalignment of tilt axis.
 == List of option ==
@@ Line 14: / Line 14: @@
 				<td>-i</td>
 				<td>Optional</td>
-				<td>Input設定: [[mrcImage]]（ファイルが１つの時に設定）</td>
+				<td>Input: [[mrcImage]] (If the search file is one)</td>
 				<td>NULL</td>
 			</tr>
@@ Line 20: / Line 20: @@
 				<td>-I</td>
 				<td>Optional</td>
-				<td>Input設定: [[ASCII]]（軸を探すファイルのリストを設定）</td>
+				<td>Input: [[ASCII]] (File List of search the axis)</td>
 				<td>NULL</td>
 			</tr>
@@ Line 26: / Line 26: @@
 				<td>-r</td>
 				<td>Essential</td>
-				<td>Referenceを設定: [[mrcImage]]（傾斜角度０度のデータを設定）</td>
+				<td>Reference: [[mrcImage]] (Untilted data)</td>
 				<td>NULL</td>
 			</tr>
@@ Line 32: / Line 32: @@
 				<td>-o</td>
 				<td>Essential</td>
-				<td>Output設定: [[mrcImage]]</td>
+				<td>Output: [[mrcImage]]</td>
 				<td>NULL</td>
 			</tr>
@@ Line 38: / Line 38: @@
 				<td>-O</td>
 				<td>Optional</td>
-				<td>Output設定: [[ASCII]]（傾斜軸のずれを予測した値が入る）</td>
+				<td>Output: [[ASCII]] (Estimate of misalignment of the tilt axis)</td>
 				<td>stdout</td>
 			</tr>
@@ Line 44: / Line 44: @@
 				<td>-range</td>
 				<td>Optional</td>
-				<td>開始角度、終了角度、刻み幅の設定</td>
+				<td>start angle, end angle, delta</td>
 				<td>thetaMin=-90 thetaMax=+90 thetaDelta=1</td>
 			</tr>
@@ Line 50: / Line 50: @@
 				<td>-w</td>
 				<td>Optional</td>
-				<td>相関を取る領域を設定</td>
+				<td>Projection Range around centre</td>
 				<td>0.5</td>
 			</tr>
@@ Line 57: / Line 57: @@
 				<td>Optional</td>
 				<td>Mode<br>
-				（インターポレーションの値の計算方法を選択。現段階では変更の必要なし）</td>
+				(Setting of Interpolation method. No need to change.)</td>
 				<td>2</td>
 			</tr>
@@ Line 108: / Line 108: @@
 				<tr>
 					<td>3</td>
-					<td>多項式法</td>
+					<td>Polynomial interpolation method</td>
 				</tr>
 			</div>
 		</table>
 ===-CM  details===
 		<table border="1">
@@ Line 122: / Line 122: @@
 				<tr>
 					<td>0</td>
-					<td>正規相関:FxG*</td>
+					<td>Normal correlation:FxG*</td>
 				</tr>
 				<tr>
 					<td>1</td>
-					<td>位相相関:FxG*/|FxG*|</td>
+					<td>Phase correlation:FxG*/|FxG*|</td>
 				</tr>
 				<tr>
 					<td>2</td>
-					<td>位相相関:FxG*/sqrt(|FxG*|)</td>
+					<td>Phase correlation:FxG*/sqrt(|FxG*|)</td>
 				</tr>
 				<tr>
 					<td>3</td>
-					<td>標準化された正規相関:FxG*/(|F||G|)</td>
+					<td>Standard Normal correlation:FxG*/(|F||G|)</td>
 				</tr>
 				<tr>
@@ Line 142: / Line 142: @@
 			</div>
 		</table>
 == Execution example ==
 === Input file's image ===
-<div>オプション　-Iで使用するリスト</div>
+<div>Option -I</div>
-<div>以下のようなリスト内容をファイルデータとする</div>
+<div>Input file is as the following.</div>
 	[[File:List-mrcImageTiltAxisSearch.png]]
 <br>
-<div>[[Media:Input-1VOM-N-Rot-2D.mrc | 1vom-rot0.mrc]]（傾斜角度が2°ずれている）</div>
+<div>[[Media:Input-1VOM-N-Rot-2D.mrc | 1vom-rot0.mrc]] (The tilt axis is misalignment for 2°)</div>
 	<table>
 		<tr>
@@ Line 170: / Line 169: @@
 	</table>
-<div>[[:Media:Input-1VOM-N-Rot1-2D.mrc | 1vom-rot1.mrc]]（傾斜角度が10°ずれている）</div>
+<div>[[:Media:Input-1VOM-N-Rot1-2D.mrc | 1vom-rot1.mrc]] (The tilt axis is misalignment for 10°)</div>
 	<table>
 		<tr>
@@ Line 189: / Line 188: @@
 	</table>
-<div>[[:Media:Input-1VOM-N-Rot2-2D.mrc | 1vom-rot2.mrc]]（傾斜角度が45°ずれている）</div>
+<div>[[:Media:Input-1VOM-N-Rot2-2D.mrc | 1vom-rot2.mrc]] (The tilt axis is misalignment for 45°)</div>
 	<table>
 		<tr>
@@ Line 208: / Line 207: @@
 	</table>
-<div>[[:Media:Input-1VOM-N-Rot3-2D.mrc | 1vom-rot3.mrc]]（傾斜角度が60°ずれている）</div>
+<div>[[:Media:Input-1VOM-N-Rot3-2D.mrc | 1vom-rot3.mrc]] (The tilt axis is misalignment for 60°)</div>
 	<table>
 		<tr>
@@ Line 227: / Line 226: @@
 	</table>
 <br>
 ===[[:Media:Input-1VOM-2D.mrc | Reference file]] image===
 	<table>

Difference between revisions of "mrcImageTiltAxisSearch"

Latest revision as of 02:16, 4 August 2014

Contents

List of option

Main option

-M details

-CM details

Execution example

Input file's image

Reference file image

Option -range

Option -i

Option -I

Option -w

Case: w=0.3

Option -M

Case: M=0

Case: M=1

Case: M=3

Option -CM

Case: CM=0

Case: CM=16

Case: CM=18

Case: CM=19

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