Difference between revisions of "mrcImageMultiCTFCompensation"

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Line 170: Line 170:
 
== Execution example ==
 
== Execution example ==
 
===-i  data===
 
===-i  data===
 +
<div>[[:Media:Input-B120.mrc|Original data]]'s image </div>
 +
<table>
 +
<tr>
 +
<td>[[File:Input-B120.png]]</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">0 (0, 0, 0)<br>
 +
255 (49, 32, 0)<br>
 +
21.0538<br>
 +
47.6709<br>
 +
0.595886<br></p>
 +
</td>
 +
</tr>
 +
</table>
 +
 +
Use simulation images that is multiplied each different CTF to above image, as input file.
 
<pre>
 
<pre>
−
/Eos/img/Input0.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF2.mrc 27000 2.1 200 0.1
−
/Eos/img/Input1.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF3.mrc 9000 2.1 200 0.1
−
/Eos/img/Input2.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF4.mrc 27000 2.1 400 0.1
−
/Eos/img/Input3.mrc 27000 2.1 200 0.1
+
/Eos/img/Input-B120-CTF5.mrc 27000 2.1 200 0.3
  
 
</pre>
 
</pre>
  
−
<div>Input0's image</div>
+
<div>[[:Media:Input-B120-CTF2.mrc|Input-B120-CTF2.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input0-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF2.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 188: Line 208:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-67.2449 (35, 36, 0)<br>
−
255 (30, 25, 0)<br>  
+
48.4524 (50, 51, 0)<br>
−
21.8076<br>  
+
-5.60279e-08<br>
−
47.9133<br>  
+
13.2796<br>
−
0.748645<br></p>  
+
0.165995<br></p>
 +
</td>
 +
<td>[[File:Input-B120-CTF2-Cnp.png]]<br>
 +
case: CTF Correction at single<br>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-49.3218 (28, 26, 0)<br>  
 +
133.566 (37, 38, 0)<br>  
 +
8.98254e-07<br>  
 +
26.7724<br>  
 +
0.334655<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>  
 
</table>  
  
−
<div>Input1's image</div>
+
<div>[[:Media:Input-B120-CTF3.mrc|Input-B120-CTF3.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input1-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF3.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 207: Line 242:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-57.5666 (25, 38, 0)<br>  
−
255 (30, 26, 0)<br>  
+
53.971 (44, 29, 0)<br>  
−
20.6895<br>  
+
-5.02996e-08<br>  
−
47.2143<br>  
+
9.30611<br>  
−
0.737723<br></p>  
+
0.116326<br></p>  
 
</td>  
 
</td>  
−
</tr>  
+
<td>[[File:Input-B120-CTF3-Cnp.png]]<br>
 +
case: CTF Correction at single<br>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-49.4192 (47, 51, 0)<br>
 +
137.108 (49, 32, 0)<br>
 +
5.49823e-07<br>
 +
19.7161<br>
 +
0.246452<br></p>
 +
</td> 
 +
</tr>
 
</table>  
 
</table>  
  
−
<div>Input2's image</div>
+
<div>[[:Media:Input-B120-CTF4.mrc|Input-B120-CTF4.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input2-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF4.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 226: Line 276:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-68.355 (24, 39, 0)<br>
−
255 (27, 32, 0)<br>  
+
42.4746 (44, 26, 0)<br>
−
19.0078<br>  
+
-3.45941e-08<br>
−
47.768<br>  
+
10.9018<br>
−
0.746374<br></p>  
+
0.136272<br></p>
 +
</td>
 +
<td>[[File:Input-B120-CTF4-Cnp.png]]<br>
 +
case: CTF Correction at single<br>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-43.0975 (26, 31, 0)<br>  
 +
117.683 (49, 32, 0)<br>  
 +
4.44953e-07<br>  
 +
22.9822<br>  
 +
0.287278<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>  
 
</table>  
  
−
<div>Input3's image</div>
+
<div>[[:Media:Input-B120-CTF5.mrc|Input-B120-CTF5.mrc]]'s image </div>
 
<table>  
 
<table>  
 
<tr>  
 
<tr>  
−
<td>[[File:Input3-mrcImageMultiCTFCompensation.png]]</td>  
+
<td>[[File:Input-B120-CTF5.png]]</td>  
 
<td><p align="left">Min<br>  
 
<td><p align="left">Min<br>  
 
Max<br>  
 
Max<br>  
Line 245: Line 310:
 
SE<br></p>  
 
SE<br></p>  
 
</td>  
 
</td>  
−
<td><p align="left">0 (0, 0, 0)<br>  
+
<td><p align="left">-44.9091 (37, 36, 0)<br>  
−
255 (28, 33, 0)<br>  
+
26.5736 (28, 28, 0)<br>
−
18.3279<br>  
+
-2.71914e-08<br>
−
45.0774<br>  
+
8.97143<br>
−
0.704334<br></p>  
+
0.112143<br></p>
 +
</td>
 +
<td>[[File:Input-B120-CTF5-Cnp.png]]<br>
 +
case: CTF Correction at single<br>
 +
</td>
 +
<td><p align="left">Min<br>
 +
Max<br>
 +
Mean<br>
 +
SD<br>
 +
SE<br></p>
 +
</td>
 +
<td><p align="left">-33.0969 (49, 51, 0)<br>
 +
73.3827 (35, 37, 0)<br>  
 +
-1.68364e-08<br>  
 +
15.1195<br>  
 +
0.188993<br></p>  
 
</td>  
 
</td>  
 
</tr>  
 
</tr>  
 
</table>
 
</table>
−
 
+
<br>
  
 
=== Example of options only essential ===
 
=== Example of options only essential ===

Revision as of 05:51, 22 September 2014

mrcImageMultiCTFCompensation is Eos's Command that performs CTF Correction to multiple images that have each other same field and different CTF. It outputs the average image of each image after CTF Correction.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: ASCII(File List) stdin
-info2 Optional Input: ASCII(File List) stdin
-o Essential Output(average): mrcImage stdout
-f Optional Output(average): mrcImage(FFT) stdout
-W Optional WhiteNoise(Noise/Signal) 1.0
-WR Optional WhiteNoiseRaising 1.0
-SinWin Optional sin Windowing (R[/A]): (SinWinRmin, SinWinRmax) (0.1, 1.0)
-MaxIter Optional Max Iteration 10
-ctfMode Optional CTFMode 1
-solventMode Optional If solvent flatterning is used, NEED 0
-solventSTD Optional If solvent flatterning is used as mode=1, NEED -1.0
-Log Optional Log File Name stderr
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　

-ctfMode details

Value Description
0 Phase Only
1 Phase and Amplitude
+32 With Illumination Angle
+256 As Absolute Value

-m details

Value Description
0 CTF-weighted compensation, CTF/(SQR(CTF) + (NS)^2)
+1 Adding solvent-flattening process
+16 Without phase flipping, in case of images after phase only correction.

-i format

filename0 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
filename1 deltaF[A] Cs[mm] kV[kV] ratioOfAmpToPhase
     .                .            .           .                   .
     .                .            .           .                   .
     .                .            .           .                   .

-Info2 format

filename0.ctfinfo 
filename1.ctfinfo 
          .
          .
          .


Execution example

-i data

Original data's image
Input-B120.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

255 (49, 32, 0)
21.0538
47.6709

0.595886

Use simulation images that is multiplied each different CTF to above image, as input file. 

/Eos/img/Input-B120-CTF2.mrc 27000 2.1 200 0.1
/Eos/img/Input-B120-CTF3.mrc 9000 2.1 200 0.1
/Eos/img/Input-B120-CTF4.mrc 27000 2.1 400 0.1
/Eos/img/Input-B120-CTF5.mrc 27000 2.1 200 0.3
Input-B120-CTF2.mrc's image
Input-B120-CTF2.png

Min

Max
Mean
SD

SE

-67.2449 (35, 36, 0)

48.4524 (50, 51, 0)
-5.60279e-08
13.2796

0.165995

 Input-B120-CTF2-Cnp.png

case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.3218 (28, 26, 0)

133.566 (37, 38, 0)
8.98254e-07
26.7724

0.334655
Input-B120-CTF3.mrc's image
Input-B120-CTF3.png

Min

Max
Mean
SD

SE

-57.5666 (25, 38, 0)

53.971 (44, 29, 0)
-5.02996e-08
9.30611

0.116326

 Input-B120-CTF3-Cnp.png

case: CTF Correction at single

Min

Max
Mean
SD

SE

-49.4192 (47, 51, 0)

137.108 (49, 32, 0)
5.49823e-07
19.7161

0.246452
Input-B120-CTF4.mrc's image
Input-B120-CTF4.png

Min

Max
Mean
SD

SE

-68.355 (24, 39, 0)

42.4746 (44, 26, 0)
-3.45941e-08
10.9018

0.136272

 Input-B120-CTF4-Cnp.png

case: CTF Correction at single

Min

Max
Mean
SD

SE

-43.0975 (26, 31, 0)

117.683 (49, 32, 0)
4.44953e-07
22.9822

0.287278
Input-B120-CTF5.mrc's image
Input-B120-CTF5.png

Min

Max
Mean
SD

SE

-44.9091 (37, 36, 0)

26.5736 (28, 28, 0)
-2.71914e-08
8.97143

0.112143

 Input-B120-CTF5-Cnp.png

case: CTF Correction at single

Min

Max
Mean
SD

SE

-33.0969 (49, 51, 0)

73.3827 (35, 37, 0)
-1.68364e-08
15.1195

0.188993


Example of options only essential

-o 's image
Outdata-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-950.729 (30, 33, 0)

91.5373 (61, 58, 0)
-199.582
202.06

3.15719
-f 's image
Outdata2-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Option -W

Case: W=0.5

-o 's image
Outdata-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-178.794 (29, 32, 0)

31.7025 (15, 31, 0)
-7.67623
35.9686

0.562009
-f 's image
Outdata2-W-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000786083 (61, 50, 0)

656.031 (1, 0, 0)
5.93815
40.2896

0.629525


Option -WR

Case: WR=10.0, W=0.5

-o 's image
Outdata-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-153.883 (30, 32, 0)

23.7931 (15, 31, 0)
-7.67623
31.3292

0.489519
-f 's image
Outdata2-WR-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

9.05608e-06 (60, 32, 0)

587.065 (1, 0, 0)
4.29171
35.7021

0.557845


Option -SinWin

Case: SinWin=(0.05, 0.2)

-o 's image
Outdata-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-939.931 (30, 33, 0)

82.2886 (61, 59, 0)
-199.582
201.211

3.14392
-f 's image
Outdata2-SinWin-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (8, 0, 0)

12773.2 (0, 0, 0)
28.1205
365.158

5.70559


Option -ctfMode

Case: ctfMode=32

-o 's image
Outdata-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-1243.15 (30, 31, 0)

534.543 (1, 0, 0)
-7.92556e-07
404.255

6.31648
-f 's image
Outdata2-ctfMode32-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

12267.8 (1, 0, 0)
33.7224
477.688

7.46387


Case: ctfMode=256

-o 's image
Outdata-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-501.951 (1, 0, 0)

1288.01 (33, 32, 0)
-2.09152e-06
404.255

6.31648
-f 's image
Outdata2-ctfMode256-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

12267.8 (1, 0, 0)
33.7224
477.688

7.46387


Case: ctfMode=257

-o 's image
Outdata-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-50.4152 (5, 2, 0)

1009.22 (33, 32, 0)
199.582
202.06

3.15719
-f 's image
Outdata2-ctfMode257-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Option -m

Case: m=1, W=0.5

Case: No other settings
-o 's image
Outdata-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-175.249 (29, 32, 0)

49.852 (15, 31, 0)
-1.99391
37.3853

0.584145
-f 's image
Outdata2-m1-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00642588 (59, 34, 0)

681.324 (34, 0, 0)
6.41058
40.1134

0.626771
-log 's data
iter          0 : rms   -1.965984e+01 : min    1.000000e+06

Case: solventMode=1

-o 's image
Outdata-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-220.728 (30, 32, 0)

42.9295 (15, 31, 0)
-9.08899
47.6864

0.7451
-f 's image
Outdata2-m1solventMode-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00745064 (63, 30, 0)

916.491 (1, 0, 0)
7.81324
53.2299

0.831717
-log 's data
iter          0 : rms   -3.997643e+00 : min    1.000000e+06


Case: solventSTD=2.0, solventMode=1

-o 's image
Outdata-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

342.42 (29, 32, 0)

552.916 (15, 31, 0)
513.538
35.9686

0.562009
-f 's image
Outdata2-m1solventSTD-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000751982 (61, 50, 0)

32866.4 (0, 0, 0)
21.7463
726.986

11.3592
-log 's data
iter          0 : rms    7.485705e-01 : min    1.000000e+06
iter          1 : rms    3.354889e-01 : min    7.485705e-01
iter          2 : rms    2.279355e-01 : min    3.354889e-01
iter          3 : rms    1.763709e-01 : min    2.279355e-01
iter          4 : rms    1.463149e-01 : min    1.763709e-01
iter          5 : rms    1.267555e-01 : min    1.463149e-01
iter          6 : rms    1.130881e-01 : min    1.267555e-01
iter          7 : rms    1.030489e-01 : min    1.130881e-01
iter          8 : rms    9.539606e-02 : min    1.030489e-01
iter          9 : rms    8.939259e-02 : min    9.539606e-02


Case: MaxIter=5, solventSTD=2.0, solventMode=1

-o 's image
Outdata-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

107.285 (29, 32, 0)

317.781 (15, 31, 0)
278.402
35.9686

0.562009
-f 's image
Outdata2-m1MaxIter-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.000789315 (61, 50, 0)

17817.7 (0, 0, 0)
14.3983
395.41

6.17827
-log 's data
iter          0 : rms    7.485705e-01 : min    1.000000e+06
iter          1 : rms    3.354889e-01 : min    7.485705e-01
iter          2 : rms    2.279355e-01 : min    3.354889e-01
iter          3 : rms    1.763709e-01 : min    2.279355e-01
iter          4 : rms    1.463149e-01 : min    1.763709e-01


Case: m=16

-o 's image
Outdata-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

-50.4152 (5, 2, 0)

1009.22 (33, 32, 0)
199.582
202.06

3.15719
-f 's image
Outdata2-m16-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.0117408 (32, 31, 0)

12773.2 (0, 0, 0)
30.7184
365.42

5.70969


Case: m=17

-o 's image
Outdata-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

161250 (60, 60, 0)

1.85064e+06 (29, 32, 0)
432887
388639

6072.49
-f 's image
Outdata2-m17-mrcImageMultiCTFCompensation.png

Min

Max
Mean
SD

SE

0.00899138 (31, 33, 0)

2.77048e+07 (0, 0, 0)
51930
757226

11831.7
-log 's data
iter          0 : rms    9.051428e-01 : min    1.000000e+06
iter          1 : rms    7.732108e-01 : min    9.051428e-01
iter          2 : rms    7.194946e-01 : min    7.732108e-01
iter          3 : rms    6.952064e-01 : min    7.194946e-01
iter          4 : rms    6.840820e-01 : min    6.952064e-01
iter          5 : rms    6.782160e-01 : min    6.840820e-01
iter          6 : rms    6.752780e-01 : min    6.782160e-01
iter          7 : rms    6.739355e-01 : min    6.752780e-01
iter          8 : rms    6.730211e-01 : min    6.739355e-01
iter          9 : rms    6.722654e-01 : min    6.730211e-01
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