mrcImageAutoRotationCorrelation3D

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mrcImageAutoRotationCorrelation3D is Eos's Command that calculates the correlation value of the three-dimensional data between mrcImage files. It decides the direction of the three-dimensional image that best fits with respect to the reference image. Thus, it is possible to output an image that is suited best for them.

Contents

Algorithm

Find the angle of rotation of rotating a three-dimensional image of reference, best fit on the basis of the correlation value. Correlation value with the function system some. It has been calculated that by seeking a correlation function from the calculation of the Fourier space basically to search the maximum value.

List of option

It is an argument of the following is required. -i/-r is an essential argument.

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage(Input file) NULL
-r Essential Input: mrcImage(Reference file) NULL
-o Optional Output: Parameter stdout(The standard output by default)
-cor Optional Output: Correlation map: mrcImage NULL
-fit Optional Output: RotatedImage at Maximum: mrcImage NULL
-EA Optional Input: mode of Euler Angle: 4 characters YOYS
-Rot1 Optional Input: range of Rot1(Euler Angle):min max delta 0.0 360.0 5.0
-Rot2 Optional Input: range of Rot2(Euler Angle):min max delta 0.0 180.0 5.0
-Rot3 Optional Input: range of Rot3(Euler Angle):min max delta 0.0 360.0 5.0
-Xrange Optional Input: x: min max: [pixel] 0 0 (The full range of the X-direction by default)
-Yrange Optional Input: y: min max: [pixel] 0 0 (The full range of the Y-direction by default)
-Zrange Optional Input: z: min max: [pixel] 0 0 (The full range of the Z-direction by default)
-M Optional Input: Selection mode of the correlation function 0
-MR Optional Input: Handling mode of image rotation 0
-m Optional Input: Interpolation mode of the image 0
-c Optional ConfigurationFile NULL
-h Optional Help 　

mode's details

-MR details

Value Description
0 padding 0
1 padding average
+0 within ellipsoidal area
+16 within square area
If it is considered around the medium as a single particle, it is recommended to 0.
16 is recommended otherwise.(For example, when there is an image to ambient.)


-M details

Value Description
0 Normal Correlation FxG*
1 Phase Correlation FxG*/ |FxG*|
2 Phase Correlation FxG*/sqrt(|FxG*|)
3 Normalized Normal Correlation FxG*/|F||G|)
16 (0,0) = 0


-m details

Setting of Interpolation Mode.

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


Execution example

The following is an example in which combined Reference image "test.ref" to Test image "test.in". Then the result of calculating correlation is stored in the "test.param", "test.cor" is output as Correlation map. The correlation is performed by rotating reference image at the ranges and deltas of Rot1, Rot2, Rot3. The following cases, Y-axis rotaion(Rot1), X-axis rotaion(Rot2), Z-axis rotaion(Rot3) are in the order of rotation for the Euler Angle is YOYS. When rotating, it is considered image is included in the whole rectangular, and the outer padding average. The correlation value is calculated from the correlation function (correlation map) by the inverse Fourier transform of the product of the Fourier space(F*G*).Then the movement distance is limited by -Xrange/-Yrange/-Zrange. 

$ mrcImageAutoRotationCorrelation3D -i test.in -r test.ref -o test.param -cor test.cor -fit test.fit -EA YOYS -Rot1 -20 20 10 -Rot2 -30 30 15 -Rot3 -10 10 5 -Xrange -1 1 -Yrange -2 2 -Zrange 0 0 -MR 17 -M 16 -m 2


Input file image

Input-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (1, 1, 0)

1 (19, 1, 0)
0.0111612
0.102481

0.00114578

Reference file image

Refer-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (1, 1, 0)

1 (19, 1, 0)
0.00852714
0.0897409

0.00100333


Option -Rot1, -Rot2, -Rot3

Case: Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.140128 -0.006095
Max: YOYS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.157113 -0.005784
Max: YOYS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.178878 -0.006212
Max: YOYS 0.000000 0.000000 149.999997 at -14.000000 -17.000000 -20.000000 Cor 6348069965383335936.000000 -0.005416
Max: YOYS 0.000000 0.000000 210.000013 at -14.000000 -17.000000 -20.000000 Cor 6354297599243059200.000000 -0.005659
Max: YOYS 0.000000 0.000000 270.000001 at -14.000000 -17.000000 -20.000000 Cor 6356619767800922112.000000 -0.006271
Max: YOYS 0.000000 0.000000 330.000016 at -14.000000 -17.000000 -20.000000 Cor 6358941936358785024.000000 0.017826
Max: YOYS 0.000000 30.000001 0.000000 at -14.000000 -17.000000 -20.000000 Cor 6361264104916647936.000000 -0.005977
Max: YOYS 0.000000 30.000001 60.000002 at -14.000000 -17.000000 -20.000000 Cor 6363586273474510848.000000 -0.005946
Max: YOYS 0.000000 30.000001 120.000003 at -14.000000 -17.000000 -20.000000 Cor 6365908442032373760.000000 -0.005885
Max: YOYS 0.000000 30.000001 180.000005 at -13.000000 -17.000000 -20.000000 Cor 36902486550580822016.000000 -0.006037
-cor image
Outdata-Rot1Rot2Rot3-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0804175 (0, 0, 6)

3.69025e+19 (0, 1, 6)
6.32628e+18
1.10996e+18

3.22712e+16
-fit image
Outdata2-Rot1Rot2Rot3-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (15, 13, 1)
0.00425752
0.0650531

0.000727315


Option -EA

Case: EA=ZENS, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: ZENS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.140128 -0.006095
Max: ZENS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.157113 -0.005784
Max: ZENS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.178878 -0.006212
-cor image
Outdata-EA-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0336148 (1, 4, 0)

0.178878 (0, 0, 3)
0.0440549
0.0119811

0.00034834
-fit image
Outdata2--mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (1, 17, 1)
0.0045
0.0669309

0.000748311


Option -Xrange, -Yrange, Zrange

Case: Xrange=(10, 15), Yrange=(10, 15), Zrange=(10, 15), Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at 0.000000 0.000000 0.000000 Cor 0.033541 0.056044
Max: YOYS 0.000000 0.000000 120.000003 at 14.000000 12.000000 10.000000 Cor 0.033731 0.016596
Max: YOYS 0.000000 0.000000 210.000013 at 14.000000 13.000000 11.000000 Cor 0.033857 -0.005534
Max: YOYS 0.000000 30.000001 299.999995 at 10.000000 14.000000 10.000000 Cor 0.044848 -0.005701
Max: YOYS 0.000000 90.000003 120.000003 at 10.000000 14.000000 10.000000 Cor 0.045006 -0.006493
Max: YOYS 30.000001 149.999997 180.000005 at 13.000000 10.000000 13.000000 Cor 0.045016 0.015388
Max: YOYS 60.000002 0.000000 90.000003 at 12.000000 12.000000 10.000000 Cor 0.045173 -0.006438
Max: YOYS 120.000003 120.000003 30.000001 at 14.000000 12.000000 13.000000 Cor 0.055965 -0.006359
-cor image
Outdata-range-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0114748 (1, 4, 1)

0.0559651 (4, 4, 1)
0.0270246
0.00637686

0.000185402
-fit image
Outdata2-range-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (5, 1, 0)
0.00500987
0.0705332

0.000788586


Option -MR

Case: MR=1, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.141222 -0.006563
Max: YOYS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.157193 -0.005707
Max: YOYS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.177568 -0.006511
-cor image
Outdata-MR1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0385571 (7, 1, 4)

0.177568 (0, 0, 3)
0.0485775
0.0100862

0.000293248
-fit image
Outdata2-MR1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 1)

1 (1, 17, 1)
0.0107168
0.0667423

0.000746202


Case: MR=16, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -31.000000 -20.000000 -20.000000 Cor 0.212045 0.003815
-cor image
Outdata-MR16-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0454467 (9, 5, 3)

0.212045 (0, 0, 0)
0.0594773
0.0110256

0.000320561
-fit image
Outdata2-MR16-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 1, 0)

1 (8, 1, 0)
0.0111612
0.102481

0.00114578


Case: MR=17, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -31.000000 -20.000000 -20.000000 Cor 0.212045 0.003815
-cor image
Outdata-MR17-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0454467 (9, 5, 3)

0.212045 (0, 0, 0)
0.0594773
0.0110256

0.000320561
-fit image
Outdata2-MR17-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 1, 0)

1 (8, 1, 0)
0.0111612
0.102481

0.00114578


Option -M

Case: M=1, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -20.000000 -21.000000 -25.000000 Cor 7.951506 -0.006330
Max: YOYS 0.000000 180.000005 0.000000 at -20.000000 -22.000000 -28.000000 Cor 12.379415 -0.006212
-cor image
Outdata-M1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

4.31499 (2, 2, 1)

12.3794 (0, 6, 0)
5.69666
0.775057

0.0225341
-fit image
Outdata2-M1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (8, 1, 0)
0.0045
0.0669309

0.000748311


Case: M=2, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -20.000000 -21.000000 -25.000000 Cor 0.669592 -0.006330
Max: YOYS 0.000000 180.000005 0.000000 at -20.000000 -22.000000 -28.000000 Cor 1.027818 -0.006212
-cor image
Outdata-M2-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.350646 (0, 2, 1)

1.02782 (0, 6, 0)
0.963981
0.136232

0.00396083
-fit image
Outdata2-M2-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (8, 1, 0)
0.0045
0.0669309

0.000748311


Case: M=3, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -20.000000 -21.000000 -28.000000 Cor 0.218833 -0.006388
Max: YOYS 0.000000 180.000005 0.000000 at -20.000000 -22.000000 -28.000000 Cor 0.328095 -0.006212
Max: YOYS 0.000000 180.000005 60.000002 at -25.000000 -30.000000 -20.000000 Cor 1.000000 -0.006033
-cor image
Outdata-M3-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0938449 (7, 0, 0)

1 (0, 6, 2)
0.143836
0.0360716

0.00104875
-fit image
Outdata2-M3-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (8, 19, 1)
0.00400752
0.0631187

0.000705688


Case: M=16, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.140128 -0.006095
Max: YOYS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.157113 -0.005784
Max: YOYS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.178878 -0.006212
-cor image
Outdata-M16-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0298141 (7, 0, 0)

0.178878 (0, 0, 3)
0.040371
0.0105544

0.000306859
-fit image
Outdata2-M16-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (1, 17, 1)
0.0045
0.0669309

0.000748311


Option -m

Case: m=1, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.140128 -0.006095
Max: YOYS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.158153 -0.008176
Max: YOYS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.178878 -0.006212
-cor image
Outdata-m1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0176277 (1, 5, 4)

0.178878 (0, 0, 3)
0.0280273
0.0115913

0.000337007
-fit image
Outdata2-m1-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

1 (1, 17, 1)
0.0045
0.0669309

0.000748311


Case: m=2, Rot1=(0, 360, 30), Rot2=(0, 180, 30), Rot3=(0, 360, 30)

-o data
Max: YOYS 0.000000 0.000000 0.000000 at -23.000000 -28.000000 -20.000000 Cor 0.140128 -0.006095
Max: YOYS 0.000000 0.000000 30.000001 at -18.000000 -32.000000 -20.000000 Cor 0.151922 -0.006019
Max: YOYS 0.000000 0.000000 90.000003 at -26.000000 -30.000000 -20.000000 Cor 0.178878 -0.006212
-cor image
Outdata-m2-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

0.0256789 (8, 5, 7)

0.178878 (0, 0, 3)
0.0361763
0.0103279

0.000300277
-fit image
Outdata2-m2-mrcImageAutoRotationCorrelation3D.png

Min

Max
Mean
SD

SE

-4.76837e-07 (10, 14, 9)

1 (1, 17, 1)
0.0045
0.0669309

0.000748311

References

Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageAutoRotationCorrelation3D&oldid=2205"