Difference between revisions of "mrcImageMultiCTFCompensation"
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(→Case: m=17) |
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=== Option -m=== | === Option -m=== | ||
− | ====Case: m=1, W= | + | ====Case: m=1, W=1==== |
=====Case: No other settings===== | =====Case: No other settings===== | ||
<div>-o 's image</div> | <div>-o 's image</div> | ||
Line 667: | Line 667: | ||
</pre> | </pre> | ||
− | ====Case: solventMode=1==== | + | =====Case: solventMode=1===== |
<div>-o 's image</div> | <div>-o 's image</div> | ||
<table> | <table> | ||
Line 678: | Line 678: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">- | + | <td><p align="left">-20.1029 (48, 51, 0)<br> |
− | + | 87.1488 (49, 32, 0)<br> | |
− | + | 2.38926<br> | |
− | + | 14.7396<br> | |
− | 0. | + | 0.184245<br></p> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 697: | Line 697: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">0. | + | <td><p align="left">0.00627302 (76, 14, 0<br> |
− | + | 222.088 (42, 0, 0)<br> | |
− | + | 4.12707<br> | |
− | + | 15.7098<br> | |
− | 0. | + | 0.196372<br></p> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 708: | Line 708: | ||
<div>-log 's data</div> | <div>-log 's data</div> | ||
<pre> | <pre> | ||
− | iter 0 : rms | + | iter 0 : rms 3.709238e+01 : min 1.000000e+06 |
+ | iter 1 : rms 3.539059e+00 : min 3.709238e+01 | ||
+ | iter 2 : rms 1.971014e+00 : min 3.539059e+00 | ||
+ | iter 3 : rms 1.314187e+00 : min 1.971014e+00 | ||
+ | iter 4 : rms 9.704149e-01 : min 1.314187e+00 | ||
+ | iter 5 : rms 7.649823e-01 : min 9.704149e-01 | ||
+ | iter 6 : rms 6.304888e-01 : min 7.649823e-01 | ||
+ | iter 7 : rms 5.362647e-01 : min 6.304888e-01 | ||
+ | iter 8 : rms 4.668152e-01 : min 5.362647e-01 | ||
+ | iter 9 : rms 4.135905e-01 : min 4.668152e-01 | ||
</pre> | </pre> | ||
− | + | =====Case: solventSTD=2.0, solventMode=1===== | |
− | ====Case: solventSTD=2.0, solventMode=1==== | + | |
<div>-o 's image</div> | <div>-o 's image</div> | ||
<table> | <table> | ||
Line 723: | Line 731: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left"> | + | <td><p align="left">85.3666 (27, 31, 0)<br> |
− | + | 146.065 (58, 33, 0)<br> | |
− | + | 101.654<br> | |
− | + | 5.9911<br> | |
− | 0. | + | 0.0748887<br></p> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 742: | Line 750: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">0. | + | <td><p align="left">0.00707058 (78, 44, 0)<br> |
− | + | 8132.32 (0, 0, 0)<br> | |
− | + | 4.62714<br> | |
− | + | 143.824<br> | |
− | + | 1.7978<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
Line 753: | Line 761: | ||
<div>-log 's data</div> | <div>-log 's data</div> | ||
<pre> | <pre> | ||
− | iter 0 : rms | + | iter 0 : rms 1.424218e+00 : min 1.000000e+06 |
− | iter 1 : rms | + | iter 1 : rms 2.156973e-01 : min 1.424218e+00 |
− | iter 2 : rms | + | iter 2 : rms 1.394271e-01 : min 2.156973e-01 |
− | iter 3 : rms 1. | + | iter 3 : rms 1.043566e-01 : min 1.394271e-01 |
− | iter 4 : rms | + | iter 4 : rms 8.473523e-02 : min 1.043566e-01 |
− | iter 5 : rms | + | iter 5 : rms 7.243526e-02 : min 8.473523e-02 |
− | iter 6 : rms | + | iter 6 : rms 6.412249e-02 : min 7.243526e-02 |
− | iter 7 : rms | + | iter 7 : rms 5.819677e-02 : min 6.412249e-02 |
− | iter 8 : rms | + | iter 8 : rms 5.380184e-02 : min 5.819677e-02 |
− | iter 9 : rms | + | iter 9 : rms 5.044070e-02 : min 5.380184e-02 |
</pre> | </pre> | ||
− | + | =====Case: MaxIter=5, solventSTD=2.0, solventMode=1===== | |
− | ====Case: MaxIter=5, solventSTD=2.0, solventMode=1==== | + | |
<div>-o 's image</div> | <div>-o 's image</div> | ||
<table> | <table> | ||
Line 777: | Line 784: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left"> | + | <td><p align="left">35.7164 (27, 31, 0)<br> |
− | + | 94.8793 (58, 33, 0)<br> | |
− | + | 52.0534<br> | |
− | + | 5.94982<br> | |
− | 0. | + | 0.0743728<br></p> |
</td> | </td> | ||
</tr> | </tr> | ||
Line 796: | Line 803: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">0. | + | <td><p align="left">0.00307367 (71, 39, 0)<br> |
− | + | 4164.28 (0, 0, 0)<br> | |
− | + | 3.33262<br> | |
− | + | 73.8045<br> | |
− | + | 0.922556<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
Line 807: | Line 814: | ||
<div>-log 's data</div> | <div>-log 's data</div> | ||
<pre> | <pre> | ||
− | iter 0 : rms | + | iter 0 : rms 1.424218e+00 : min 1.000000e+06 |
− | iter 1 : rms | + | iter 1 : rms 2.156973e-01 : min 1.424218e+00 |
− | iter 2 : rms | + | iter 2 : rms 1.394271e-01 : min 2.156973e-01 |
− | iter 3 : rms 1. | + | iter 3 : rms 1.043566e-01 : min 1.394271e-01 |
− | iter 4 : rms | + | iter 4 : rms 8.473523e-02 : min 1.043566e-01 |
</pre> | </pre> | ||
− | |||
====Case: m=16==== | ====Case: m=16==== | ||
Line 826: | Line 832: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">- | + | <td><p align="left">-90.5402 (36, 37, 0)<br> |
− | + | 39.3153 (49, 51, 0)<br> | |
− | + | -1.13944e-07<br> | |
− | + | 18.1267<br> | |
− | + | 0.226584<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
Line 845: | Line 851: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left"> | + | <td><p align="left">1.17451e-06 (75, 37, 0)<br> |
− | + | 378.143 (42, 0, 0)<br> | |
− | + | 3.33762<br> | |
− | + | 19.4523<br> | |
− | + | 0.243154<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
− | |||
====Case: m=17==== | ====Case: m=17==== | ||
Line 866: | Line 871: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left"> | + | <td><p align="left">-363.432 (24, 39, 0)<br> |
− | + | 64206.9 (50, 53, 0)<br> | |
− | + | 12232.5<br> | |
− | + | 12224.9<br> | |
− | + | 152.812<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
Line 885: | Line 890: | ||
SE<br></p> | SE<br></p> | ||
</td> | </td> | ||
− | <td><p align="left">0. | + | <td><p align="left">0.000769818 (62, 30, 0)<br> |
− | + | 978599 (0, 0, 0)<br> | |
− | + | 2152.97<br> | |
− | + | 21751<br> | |
− | + | 271.888<br></p> | |
</td> | </td> | ||
</tr> | </tr> | ||
Line 896: | Line 901: | ||
<div>-log 's data</div> | <div>-log 's data</div> | ||
<pre> | <pre> | ||
− | iter 0 : rms | + | iter 0 : rms 2.228456e+00 : min 1.000000e+06 |
− | iter 1 : rms | + | iter 1 : rms 1.072463e+00 : min 2.228456e+00 |
− | iter 2 : rms | + | iter 2 : rms 8.595473e-01 : min 1.072463e+00 |
− | iter 3 : rms | + | iter 3 : rms 7.822678e-01 : min 8.595473e-01 |
− | iter 4 : rms | + | iter 4 : rms 7.485957e-01 : min 7.822678e-01 |
− | iter 5 : rms | + | iter 5 : rms 7.339871e-01 : min 7.485957e-01 |
− | iter 6 : rms | + | iter 6 : rms 7.188863e-01 : min 7.339871e-01 |
− | iter 7 : rms | + | iter 7 : rms 7.127621e-01 : min 7.188863e-01 |
− | iter 8 : rms | + | iter 8 : rms 7.096454e-01 : min 7.127621e-01 |
− | iter 9 : rms | + | iter 9 : rms 7.069848e-01 : min 7.096454e-01 |
</pre> | </pre> |
Latest revision as of 08:10, 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.
Contents
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
![]() |
Min Max |
0 (0, 0, 0) 255 (49, 32, 0) |
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
![]() |
Min Max |
-67.2449 (35, 36, 0) 48.4524 (50, 51, 0) |
Min Max |
-49.3218 (28, 26, 0) 133.566 (37, 38, 0) |
![]() |
Min Max |
-57.5666 (25, 38, 0) 53.971 (44, 29, 0) |
Min Max |
-49.4192 (47, 51, 0) 137.108 (49, 32, 0) |
![]() |
Min Max |
-68.355 (24, 39, 0) 42.4746 (44, 26, 0) |
Min Max |
-43.0975 (26, 31, 0) 117.683 (49, 32, 0) |
![]() |
Min Max |
-44.9091 (37, 36, 0) 26.5736 (28, 28, 0) |
Min Max |
-33.0969 (49, 51, 0) 73.3827 (35, 37, 0) |
Case: Options only essential
![]() |
Min Max |
-40.2801 (48, 52, 0) 104.151 (36, 38, 0) |
![]() |
Min Max |
7.30857e-06 (75, 37, 0) 378.143 (42, 0, 0) |
Option -W
Case: W=1
![]() |
Min Max |
-17.0714 (27, 31, 0) 23.2441 (40, 52, 0) |
![]() |
Min Max |
3.22907e-07 (0, 0, 0) 62.9461 (46, 78, 0) |
Option -WR
Case: WR=10.0, W=0.5
![]() |
Min Max |
-11.5567 (27, 31, 0) 15.7516 (24, 39, 0) |
![]() |
Min Max |
2.72506e-08 (75, 37, 0) 45.7637 (46, 78, 0) |
Option -SinWin
Case: SinWin=(0.05, 0.2)
![]() |
Min Max |
-39.9332 (48, 52, 0) 102.315 (36, 38, 0) |
![]() |
Min Max |
0 (40, 1, 0) 378.143 (42, 0, 0) |
Option -ctfMode
Case: ctfMode=32
![]() |
Min Max |
-24.2681 (68, 48, 0) 207.103 (36, 38, 0) |
![]() |
Min Max |
0 (0, 0, 0) 1280.12 (41, 0, 0) |
Case: ctfMode=256
![]() |
Min Max |
-191.228 (36, 38, 0) 26.7763 (67, 30, 0) |
![]() |
Min Max |
0 (0, 0, 0) 1280.12 (41, 0, 0) |
Case: ctfMode=257
![]() |
Min Max |
-90.5402 (36, 37, 0) 39.3153 (49, 51, 0) |
![]() |
Min Max |
1.17451e-06 (75, 37, 0) 378.143 (42, 0, 0) |
Option -m
Case: m=1, W=1
Case: No other settings
![]() |
Min Max |
-9.82557 (48, 51, 0) 92.1757 (49, 32, 0) |
![]() |
Min Max |
0.00108315 (40, 41, 0) 491.438 (0, 0, 0) |
iter 0 : rms 1.013455e+01 : min 1.000000e+06 iter 1 : rms 1.355871e+00 : min 1.013455e+01 iter 2 : rms 8.647722e-01 : min 1.355871e+00 iter 3 : rms 6.229646e-01 : min 8.647722e-01 iter 4 : rms 4.844930e-01 : min 6.229646e-01 iter 5 : rms 3.971868e-01 : min 4.844930e-01 iter 6 : rms 3.377429e-01 : min 3.971868e-01 iter 7 : rms 2.951728e-01 : min 3.377429e-01 iter 8 : rms 2.629044e-01 : min 2.951728e-01 iter 9 : rms 2.370113e-01 : min 2.629044e-01
Case: solventMode=1
![]() |
Min Max |
-20.1029 (48, 51, 0) 87.1488 (49, 32, 0) |
![]() |
Min Max |
0.00627302 (76, 14, 0 222.088 (42, 0, 0) |
iter 0 : rms 3.709238e+01 : min 1.000000e+06 iter 1 : rms 3.539059e+00 : min 3.709238e+01 iter 2 : rms 1.971014e+00 : min 3.539059e+00 iter 3 : rms 1.314187e+00 : min 1.971014e+00 iter 4 : rms 9.704149e-01 : min 1.314187e+00 iter 5 : rms 7.649823e-01 : min 9.704149e-01 iter 6 : rms 6.304888e-01 : min 7.649823e-01 iter 7 : rms 5.362647e-01 : min 6.304888e-01 iter 8 : rms 4.668152e-01 : min 5.362647e-01 iter 9 : rms 4.135905e-01 : min 4.668152e-01
Case: solventSTD=2.0, solventMode=1
![]() |
Min Max |
85.3666 (27, 31, 0) 146.065 (58, 33, 0) |
![]() |
Min Max |
0.00707058 (78, 44, 0) 8132.32 (0, 0, 0) |
iter 0 : rms 1.424218e+00 : min 1.000000e+06 iter 1 : rms 2.156973e-01 : min 1.424218e+00 iter 2 : rms 1.394271e-01 : min 2.156973e-01 iter 3 : rms 1.043566e-01 : min 1.394271e-01 iter 4 : rms 8.473523e-02 : min 1.043566e-01 iter 5 : rms 7.243526e-02 : min 8.473523e-02 iter 6 : rms 6.412249e-02 : min 7.243526e-02 iter 7 : rms 5.819677e-02 : min 6.412249e-02 iter 8 : rms 5.380184e-02 : min 5.819677e-02 iter 9 : rms 5.044070e-02 : min 5.380184e-02
Case: MaxIter=5, solventSTD=2.0, solventMode=1
![]() |
Min Max |
35.7164 (27, 31, 0) 94.8793 (58, 33, 0) |
![]() |
Min Max |
0.00307367 (71, 39, 0) 4164.28 (0, 0, 0) |
iter 0 : rms 1.424218e+00 : min 1.000000e+06 iter 1 : rms 2.156973e-01 : min 1.424218e+00 iter 2 : rms 1.394271e-01 : min 2.156973e-01 iter 3 : rms 1.043566e-01 : min 1.394271e-01 iter 4 : rms 8.473523e-02 : min 1.043566e-01
Case: m=16
![]() |
Min Max |
-90.5402 (36, 37, 0) 39.3153 (49, 51, 0) |
![]() |
Min Max |
1.17451e-06 (75, 37, 0) 378.143 (42, 0, 0) |
Case: m=17
![]() |
Min Max |
-363.432 (24, 39, 0) 64206.9 (50, 53, 0) |
![]() |
Min Max |
0.000769818 (62, 30, 0) 978599 (0, 0, 0) |
iter 0 : rms 2.228456e+00 : min 1.000000e+06 iter 1 : rms 1.072463e+00 : min 2.228456e+00 iter 2 : rms 8.595473e-01 : min 1.072463e+00 iter 3 : rms 7.822678e-01 : min 8.595473e-01 iter 4 : rms 7.485957e-01 : min 7.822678e-01 iter 5 : rms 7.339871e-01 : min 7.485957e-01 iter 6 : rms 7.188863e-01 : min 7.339871e-01 iter 7 : rms 7.127621e-01 : min 7.188863e-01 iter 8 : rms 7.096454e-01 : min 7.127621e-01 iter 9 : rms 7.069848e-01 : min 7.096454e-01