mrcImageAutoRotationCorrelation

mrcImageAutoRotationCorrelation is Eos's Command that calculates a correlation between images, including rotation.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage(2D)	NULL
-r	Essential	Reference: mrcImage(2D or 2DSet)	NULL
-o	Optional	Output: Parameter: mrcImage	NULL
-O	Optional	Output: Parameter: ASCII	stdout
-cor	Optional	Output: Correation Map at Maximum (Linear): mrcImage	NULL
-cor2	Optional	Output: Correation Map2 at Maximum (Set Mode Correlation): mrcImage	NULL
-corAll	Optional	Output: Correation Map with All Rotation: mrcImage	NULL
-fit	Optional	Output: RotatedImage at Maximum(Linear Correlation): mrcImage	NULL
-fit2	Optional	Output: RotatedImage at Maximum(Set Correlation mode): mrcImage	NULL
-nRot1	Optional	Rotation number: Rot1	1
-nRot2	Optional	Rotation number: Rot2	1
-nRot3	Optional	Rotation number: Rot3	1
-dRot1	Optional	Delta Angle: Rot1[Degree]; Def.: 360/nRot1	1.0
-dRot2	Optional	Delta Angle: Rot2[Degree]; Def.: 360/nRot2	1.0
-dRot3	Optional	Delta Angle: Rot3[Degree]; Def.: 360/nRot3	1.0
-startRot1	Optional	Start Angle: Rot1[Degree]	0.0
-startRot2	Optional	Start Angle: Rot2[Degree]	0.0
-startRot3	Optional	Start Angle: Rot3[Degree]	0.0
-n	Optional	入力: Rotation around the vertical axis against image plane: dRot = 360/n [degree]	36
-range	Optional	入力: SearchRange: Rotation around the vertical axis against image plane (minAngle, maxAngle)	(-5.0, 5.0)
-refStep1	Optional	SearchStep for Ref: Each Image along Rot1	1
-refStep2	Optional	SearchStep for Ref: Each Image along Rot2	1
-refStep3	Optional	SearchStep for Ref: Each Image along Rot3	1
-nRot1Area	Optional	number of Ref for Rot1 (nRot1AreaMin, nRot1AreaMax, nRot1AreaStep)	(-360, 360, 25)
-nRot2Area	Optional	number of Ref for Rot2 (nRot2AreaMin, nRot2AreaMax, nRot2AreaStep)	(-360, 360, 25)
-nRot3Area	Optional	number of Ref for Rot3 (nRot3AreaMin, nRot3AreaMax, nRot3AreaStep)	(-360, 360, 25)
-Iter	Optional	Iteration for Rotation around the vertical axis against image plane	1
-s	Optional	SearchRegion [pixel] (sminx, sminy, smaxx, smaxy): used in lmrcImageAutoRotationCorrelation	(0, 0, 0, 0)
-Shift	Optional	Image Shift, when in > ref
-RepeatX	Optional	RepeatX[A]	27.3
-RepeatXDelta	Optional	RepeatXDelta[A]	5
-RepeatY	Optional	RepeatY[A]	27.3
-RepeatYDelta	Optional	RepeatYDelta[A]	5
-Xshift	Optional	X-Shift Only
-NoShift	Optional	No-Shift
-Log	Optional	Output: Logfile	stdout
-pvm	Optional	Task Number	1
-pvmList	Optional	pvmList (ConfigurationFile)	NULL
-c	Optional	ConfigurationFile	NULL
-Method	Optional	0: Correlation, 1: SSDA	0
-StackOrder	Optional	Stack Order for Stacked 2D of references, refer to attention	0
-RefineMode	Optional	RefinementStep	0
-m	Optional	Mode	0
-h	Optional	Help

You should set -n or -range. (Used in rotation of the reference file)
Setting -nRot1, 2, 3、-dRot1, 2, 3、-startRot1, 2, 3 with reference to the reference file's Angular information.

e.g.）mrc3Dto2D -Rot1 89 91 1 -Rot2 0 359 2 -Rot3 3 12 3
           -nRot1 3     -dRot1 1 -startRot1 89 
           -nRot2 180 -dRot2 2 -startRot2  0 
           -nRot3 4     -dRot3 3 -startRot3  3

-m details

When Method=0

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

Refinement Correlation Map

Value	Description
0	sqrt(Sum \|Fi-Gi\|^2 / Sum \|Gi\|^2)
1	Sum \|Gi\|\|phaseFi - phaseGi\| / Sum \|Gi\|
2	sqrt(Sum \|Gi\|\|phaseFi - phaseGi\|^2 / Sum \|Gi\| )

You must not set bit 16: bit 16 is set in this program as default.

When Method=1

SSDA:Sequential Similarity Detection Algorithm

When Method=2

Rotational Cross-Correlation Function
-m NotSupported

-StackOrder details

Value	Description
0	mrcImage(2D)(for pdb2mrc2d) : default
1	mrcImage(2DSet)(for mrc3Dto2D)

-RefineMode details

Value	Description
0	for LinearCorrelation; default
1	for SetModeCorrelation

Relationship between -dRot and-nRotArea.

You should set -dRot in order to calculate nStep.

Search Area

-refStep[1|2|3]
Skip image number: Just skip ref-images
or
-nRot[1|2|3]Area
     Set the search area. You finally can refine parameters by each ref-image following -RefineMode.

Execution example

Input file's image

Input file (For StackOrder=0 (Default))

Min

Max
Mean
SD

SE

-10181.1 (29, 12, 0)

47629.2 (45, 47, 0)
6507.05
8180.03

102.25

Input file (For StackOrder=1)

Min

Max
Mean
SD

SE

-10181.1 (39, 22, 0)

47629.2 (55, 57, 0)
4567.29
7036.58

70.3658

Reference file's image

Reference file (For StackOrder=0(Default))

Size

Mode
Min
Max
Mean
SD

SE

( 80, 80, 1)

mrcFloatImage
0 (0, 0, 0)
49749.7 (27, 28, 0)
7212.9
8827.15

110.339

Reference file (For StackOrder=1)

z=0

z=72

z=341

Size

Mode
Min
Max
Mean
SD

SE

( 100, 100, 343)

mrcFloatImage
0 (0, 0, 0)
544.812 (37, 59, 341)
46.1383
74.5494

0.0402529

Example of options only essential

Output

in ref: numTailer 0 is different from ref.HeaderN.z 1
i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     6.57589e+09 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     6.74113e+09 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     6.82118e+09 at        8.000000        2.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:      6.8843e+09 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     6.89554e+09 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     6.92359e+09 at       13.000000        6.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     7.01844e+09 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:     7.04962e+09 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     7.07187e+09 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:     7.10135e+09 at        2.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 7.10135e+09 
1 0 1.5708 
2 0 2 
3 0 0 
4 0 0 
5 0 0 
6 0 0.579342

-O's data

0.000000        0.000000        0.000000 : 7101352448.000000 theta       89.999996 at        2.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input-1VOM-N-Rot3-2D Cor        0.579342

-cor 's image

Min

Max
Mean
SD

SE

1.40072e+09 (42, 52, 0)

7.10135e+09 (2, 8, 0)
3.75478e+09
1.49759e+09

1.87199e+07

-fit 's image

Min

Max
Mean
SD

SE

-10181.1 (4, 52, 0)

47629.2 (39, 36, 0)
6507.05
8180.03

102.25

Option -StackOrder

StackOrder=1

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.39447e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     5.44649e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     5.49704e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.49969e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     5.51818e+07 at       10.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.59496e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:       5.619e+07 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     5.65264e+07 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:       5.682e+07 at        2.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.682e+07 
1 0 0 1.5708 
2 0 0 2 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.645745 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 56820020.000000 theta       89.999996 at        2.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.645745

-cor 's image

Outdata-StackOrder1-mrcImageAutoRotationCorrelation.png

Min

Max
Mean
SD

SE

3.86164e+06 (37, 52, 0)

5.682e+07 (2, 8, 0)
2.10838e+07
1.3466e+07

134660

-fit 's image

Outdata1-StackOrder1-mrcImageAutoRotationCorrelation.png

Min

Max
Mean
SD

SE

-10181.1 (14, 62, 0)

47629.2 (49, 46, 0)
4567.29
7036.58

70.3658

In the following, Setting atStackOrder=1.

Option -nRot1, -nRot2, -nRot3, -dRot1, -dRot2, dRot3, -startRot1, -startRot2, -startRot3

Use the following settings.

-nRot1	7
-nRot2	7
-nRot3	7
-dRot1	30
-dRot2	30
-dRot3	30
-startRot1	0
-startRot2	0
-startRot3	0

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.39447e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     5.44649e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     5.49704e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.49969e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     5.51818e+07 at       10.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.59496e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:       5.619e+07 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     5.65264e+07 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:       5.682e+07 at        2.000000        8.000000 :: CurrentMax :: Linear 

...

i1 6 i2 6 i3 6 total 342
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.39447e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     5.44649e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     5.49704e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.49969e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     5.51818e+07 at       10.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.59496e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:       5.619e+07 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     5.65264e+07 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:       5.682e+07 at        2.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.682e+07 
1 0 0 1.5708 
2 0 0 2 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.645745 
0 0 1 5.37979e+07 
1 0 1 3.83972 
2 0 1 90 
3 0 1 0 
4 0 1 0 
5 0 1 0 
6 0 1 0.651362 

...

0 0 341 6.27394e+07 
1 0 341 4.53786 
2 0 341 99 
3 0 341 0 
4 0 341 0.5 
5 0 341 0.5 
6 0 341 0.662522 
0 0 342 5.682e+07 
1 0 342 1.5708 
2 0 342 2 
3 0 342 0 
4 0 342 0.5 
5 0 342 0.5 
6 0 342 0.645745

-O's data

0:                        ZOYS        0.000000        0.000000        0.000000 : 56820020.000000 theta       89.999996 at        2.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.645745

1:                        ZOYS        0.000000        0.000000       30.000001 : 53797948.000000 theta      219.999970 at       90.000000        0.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.651362

2:                        ZOYS        0.000000        0.000000       60.000002 : 53766348.000000 theta      209.999972 at       91.000000        3.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.659182

3:                        ZOYS        0.000000        0.000000       90.000003 : 57648352.000000 theta      219.999970 at       90.000000       97.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.650031

4:                        ZOYS        0.000000        0.000000      120.000003 : 62450408.000000 theta      189.999976 at       93.000000       97.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.667284

5:                        ZOYS        0.000000        0.000000      149.999997 : 62085836.000000 theta      159.999982 at       92.000000        2.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.651323

...

338:                        ZOYS      180.000005      180.000005       60.000002 : 52729452.000000 theta       70.000000 at       99.000000       10.000000 onMap        0.500000        0.500000 /Eos/img/Input.mrc Cor        0.643224

339:                        ZOYS      180.000005      180.000005       90.000003 : 57608112.000000 theta       79.999998 at       99.000000        9.000000 onMap        0.500000        0.500000 /Eos/img/Input.mrc Cor        0.673268

340:                        ZOYS      180.000005      180.000005      120.000003 : 61187124.000000 theta      229.999981 at       93.000000       96.000000 onMap        0.500000        0.500000 /Eos/img/Input.mrc Cor        0.638519

341:                        ZOYS      180.000005      180.000005      149.999997 : 62739360.000000 theta      259.999975 at       99.000000       92.000000 onMap        0.500000        0.500000 /Eos/img/Input.mrc Cor        0.662522

342:                        ZOYS      180.000005      180.000005      180.000005 : 56820020.000000 theta       89.999996 at        2.000000        8.000000 onMap        0.500000        0.500000 /Eos/img/Input.mrc Cor        0.645745

-cor 's image

Min

Max
Mean
SD

SE

5.27267e+06 (34, 39, 0)

6.31155e+07 (0, 0, 0)
2.11017e+07
1.17079e+07

117079

-cor2 's image

Min

Max
Mean
SD

SE

4.09847e+06 (24, 43, 0)

6.34661e+07 (93, 98, 0)
2.12214e+07
1.56926e+07

156926

-fit 's image

Min

Max
Mean
SD

SE

-10751 (43, 30, 0)

46273 (57, 55, 0)
4567.43
7015.98

70.1598

-fit2 's image

Min

Max
Mean
SD

SE

-9665.14 (81, 55, 0)

47697.1 (65, 46, 0)
4629.43
7037.94

70.3794

Option -n

n=6

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.59496e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:      240.000007 Correlation:     5.61302e+07 at       91.000000       95.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.6182e+07 
1 0 0 4.18879 
2 0 0 91 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.630477 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 56182048.000000 theta      240.000007 at       91.000000       95.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.630477

-cor 's image

Min

Max
Mean
SD

SE

5.25627e+06 (55, 52, 0)

5.6182e+07 (91, 95, 0)
2.14062e+07
1.36225e+07

136225

-fit 's image

Min

Max
Mean
SD

SE

-9415.68 (64, 53, 0)

44745.6 (31, 56, 0)
4594.23
7038.51

70.3851

Option -range

range=(-60, 60)

Output

i1 0 i2 0 i3 0 total 0
Angle:      -60.000002 Correlation:      5.1279e+07 at       99.000000       90.000000 :: CurrentMax :: Linear 
Angle:       -6.666661 Correlation:     5.13026e+07 at        5.000000       98.000000 :: CurrentMax :: Linear 
Angle:       -3.333328 Correlation:      5.1938e+07 at        5.000000       99.000000 :: CurrentMax :: Linear 
Angle:        0.000006 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:        3.333339 Correlation:     5.29674e+07 at        4.000000        1.000000 :: CurrentMax :: Linear 
Angle:        6.666672 Correlation:     5.35356e+07 at        4.000000        1.000000 :: CurrentMax :: Linear 
Angle:       10.000006 Correlation:     5.39447e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       13.333339 Correlation:     5.42611e+07 at        8.000000        2.000000 :: CurrentMax :: Linear 
Angle:       16.666672 Correlation:     5.43412e+07 at        5.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000006 Correlation:     5.44649e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       23.333340 Correlation:     5.46866e+07 at        8.000000        2.000000 :: CurrentMax :: Linear 
Angle:       26.666674 Correlation:     5.48358e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       30.000008 Correlation:     5.49704e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000009 Correlation:     5.49969e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000010 Correlation:     5.51818e+07 at       10.000000        4.000000 :: CurrentMax :: Linear 
Angle:       53.333344 Correlation:     5.55007e+07 at        9.000000        6.000000 :: CurrentMax :: Linear 
Angle:       56.666678 Correlation:     5.56411e+07 at        8.000000        7.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.57754e+07 
1 0 0 0.98902 
2 0 0 10 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.600735 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 55775376.000000 theta       56.666678 at       10.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.600735

-cor 's image

Min

Max
Mean
SD

SE

4.64827e+06 (34, 49, 0)

5.57754e+07 (10, 8, 0)
2.15488e+07
1.35359e+07

135359

-fit 's image

Min

Max
Mean
SD

SE

-10396 (71, 3, 0)

44029.6 (47, 53, 0)
4790.58
7098.16

70.9816

Option -Iter

Iter=5

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.39447e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     5.44649e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     5.49704e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.49969e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     5.51818e+07 at       10.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.59496e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:       5.619e+07 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     5.65264e+07 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:       5.682e+07 at        2.000000        8.000000 :: CurrentMax :: Linear 
Angle:       90.000009 Correlation:       5.682e+07 at        2.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.000012 Correlation:     5.68742e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.000005 Correlation:     5.68742e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.010004 Correlation:     5.68742e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.020004 Correlation:     5.68743e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.030003 Correlation:     5.68743e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.040002 Correlation:     5.68744e+07 at        1.000000        8.000000 :: CurrentMax :: Linear 
Angle:       92.036983 Correlation:     5.68744e+07 at        1.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.70678e+07 
1 0 0 1.60635 
2 0 0 1 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.653006 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 57067756.000000 theta       92.036983 at        1.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.653006

-cor 's image

Min

Max
Mean
SD

SE

3.7826e+06 (36, 52, 0)

5.70678e+07 (1, 8, 0)
2.10833e+07
1.34285e+07

134285

-fit 's image

Min

Max
Mean
SD

SE

-10405.1 (67, 41, 0)

46806.6 (49, 45, 0)
4567.29
7006.63

70.0663

Option -s

Case: s=(10, 10, 90, 90)

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.17977e+07 at        0.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.25034e+07 at        0.000000        0.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.32351e+07 at       10.000000       10.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     5.48214e+07 at       11.000000       10.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     5.53809e+07 at       10.000000       10.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.53809e+07 
1 0 0 1.0472 
2 0 0 10 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.598098 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 55380888.000000 theta       60.000002 at       10.000000       10.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.598098

-cor 's image

Min

Max
Mean
SD

SE

4.22748e+06 (37, 46, 0)

5.59839e+07 (9, 8, 0)
2.14062e+07
1.36226e+07

136226

-fit 's image

Min

Max
Mean
SD

SE

-9242.14 (67, 1, 0)

48125.4 (45, 52, 0)
4752.22
7093.69

70.9369

Option -Xshift

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.26071e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.37368e+07 at        8.000000        0.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     5.41667e+07 at        9.000000        0.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     5.43115e+07 at       12.000000        0.000000 :: CurrentMax :: Linear 
Angle:      209.999972 Correlation:     5.54661e+07 at       90.000000        0.000000 :: CurrentMax :: Linear 
Angle:      219.999970 Correlation:     5.63017e+07 at       87.000000        0.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.64479e+07 
1 0 0 3.83972 
2 0 0 87 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.616989 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 56447876.000000 theta      219.999970 at       87.000000        0.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.616989

-cor 's image

Min

Max
Mean
SD

SE

4.49334e+06 (32, 43, 0)

5.64679e+07 (87, 99, 0)
2.11472e+07
1.35414e+07

135414

-fit 's image

Min

Max
Mean
SD

SE

-9377.36 (69, 32, 0)

46398.6 (30, 56, 0)
4767.8
7093.8

70.938

Option -NoShift

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     5.17977e+07 at        0.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     5.25034e+07 at        0.000000        0.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.25187e+07 
1 0 0 0.174533 
2 0 0 0 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.569916 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 52518672.000000 theta       10.000001 at        0.000000        0.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.569916

-cor 's image

Min

Max
Mean
SD

SE

4.84809e+06 (59, 62, 0)

5.40394e+07 (8, 1, 0)
2.10808e+07
1.29171e+07

129171

-fit 's image

Min

Max
Mean
SD

SE

-10751 (43, 30, 0)

46273 (57, 55, 0)
4567.43
7015.98

70.1598

Option -Method

Case: Method=1

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     1.98836e-08 at        1.000000        1.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     1.98864e-08 at        2.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     1.98869e-08 at        4.000000        2.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     1.98872e-08 at        4.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     1.98885e-08 at        5.000000        7.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:     1.98918e-08 at       10.000000        7.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:     1.98924e-08 at       10.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     1.98924e-08 at       10.000000        8.000000 :: CurrentMax :: Linear 
Angle:      139.999986 Correlation:     1.98924e-08 at       10.000000        8.000000 :: CurrentMax :: Linear 
Angle:      179.999978 Correlation:     1.98925e-08 at       10.000000        8.000000 :: CurrentMax :: Linear 
Angle:      199.999974 Correlation:     1.98925e-08 at       10.000000        8.000000 :: CurrentMax :: Linear 
Angle:      219.999970 Correlation:     1.98954e-08 at       88.000000        0.000000 :: CurrentMax :: Linear 
Angle:      229.999981 Correlation:     1.98993e-08 at       84.000000        2.000000 :: CurrentMax :: Linear 
Angle:      239.999979 Correlation:     1.98996e-08 at       84.000000        2.000000 :: CurrentMax :: Linear 
Angle:      269.999973 Correlation:     1.98996e-08 at       84.000000        2.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.50836e+07 
1 0 0 4.71239 
2 0 0 97 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.614368 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 55083556.000000 theta      269.999973 at       97.000000       93.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.614368

-cor 's image

Min

Max
Mean
SD

SE

3.87269e+06 (61, 49, 0)

5.50836e+07 (97, 93, 0)
2.10838e+07
1.3466e+07

134660

-fit 's image

Min

Max
Mean
SD

SE

-10181.1 (70, 42, 0)

47629.2 (35, 58, 0)
4567.29
7036.58

70.3658

Option -m

Case: m=1

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:           4.647 at       27.000000       65.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:          4.9051 at        4.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:         4.99076 at       25.000000        0.000000 :: CurrentMax :: Linear 
Angle:       50.000004 Correlation:         5.33912 at        2.000000        1.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:         5.38227 at       14.000000        4.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 5.11028 
1 0 0 1.39626 
2 0 0 14 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.527721 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 :        5.110277 theta       79.999998 at       14.000000        4.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.527721

-cor 's image

Min

Max
Mean
SD

SE

-4.62855 (13, 13, 0)

5.11028 (14, 4, 0)
0.01
0.99995

0.0099995

-fit 's image

Min

Max
Mean
SD

SE

-9468.38 (54, 3, 0)

47984.9 (51, 58, 0)
4586.89
7013.6

70.136

Case: m=2

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:         3116.99 at       96.000000        1.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:         3549.18 at        4.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:         3689.18 at       25.000000        0.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:         4100.32 at        2.000000        7.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 4100.32 
1 0 0 1.5708 
2 0 0 2 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.643534 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 :     4100.317383 theta       89.999996 at        2.000000        7.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.643534

-cor 's image

Min

Max
Mean
SD

SE

-988.559 (43, 30, 0)

4100.32 (2, 7, 0)
459.171
691.654

6.91654

-fit 's image

Min

Max
Mean
SD

SE

-10181.1 (15, 62, 0)

47629.2 (50, 46, 0)
4567.29
7036.58

70.3658

Case: m=3

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:       0.0249515 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:        0.025585 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:       0.0258299 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:       0.0260054 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:        0.026012 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:       0.0261232 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:       0.0266464 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:       0.0268115 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:       0.0269496 at        2.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 0.0269496 
1 0 0 1.5708 
2 0 0 2 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.645745 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 :        0.026950 theta       89.999996 at        2.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.645745

-cor 's image

Min

Max
Mean
SD

SE

0.00183157 (37, 52, 0)

0.0269496 (2, 8, 0)
0.01
0.00638688

6.38688e-05

-fit 's image

Min

Max
Mean
SD

SE

-10181.1 (14, 62, 0)

47629.2 (49, 46, 0)
4567.29
7036.58

70.3658

Case: m=16

Output

i1 0 i2 0 i3 0 total 0
Angle:        0.000000 Correlation:     3.15233e+07 at        4.000000        0.000000 :: CurrentMax :: Linear 
Angle:       10.000001 Correlation:     3.28602e+07 at        7.000000        1.000000 :: CurrentMax :: Linear 
Angle:       20.000001 Correlation:     3.33789e+07 at        8.000000        1.000000 :: CurrentMax :: Linear 
Angle:       30.000001 Correlation:     3.38323e+07 at        9.000000        2.000000 :: CurrentMax :: Linear 
Angle:       40.000002 Correlation:     3.38539e+07 at       11.000000        4.000000 :: CurrentMax :: Linear 
Angle:       60.000002 Correlation:      3.4532e+07 at        9.000000        8.000000 :: CurrentMax :: Linear 
Angle:       70.000000 Correlation:     3.51027e+07 at        8.000000        8.000000 :: CurrentMax :: Linear 
Angle:       79.999998 Correlation:     3.54435e+07 at        4.000000        7.000000 :: CurrentMax :: Linear 
Angle:       89.999996 Correlation:     3.57362e+07 at        2.000000        8.000000 :: CurrentMax :: Linear

-o's data (By mrcImageMakeDump)

0 0 0 3.57362e+07 
1 0 0 1.5708 
2 0 0 2 
3 0 0 0 
4 0 0 0 
5 0 0 0 
6 0 0 0.645745 
0 0 1 0 
1 0 1 0 

...

4 0 342 0 
5 0 342 0 
6 0 342 0

-O's data

ZOYS        0.000000        0.000000        0.000000 : 35736232.000000 theta       89.999996 at        2.000000        8.000000 onMap        0.000000        0.000000 /Eos/img/Input.mrc Cor        0.645745

-cor 's image

Min

Max
Mean
SD

SE

-1.72221e+07 (37, 52, 0)

3.57362e+07 (2, 8, 0)
0.0612706
1.3466e+07

134660

-fit 's image

Min

Max
Mean
SD

SE

-10181.1 (14, 62, 0)

47629.2 (49, 46, 0)
4567.29
7036.58

70.3658

Value	Description
0	sqrt(Sum \|Fi-Gi\|^2 / Sum \|Gi\|^2)
1	Sum \|Gi\|\|phaseFi - phaseGi\| / Sum \|Gi\|
2	sqrt(Sum \|Gi\|\|phaseFi - phaseGi\|^2 / Sum \|Gi\| )

mrcImageAutoRotationCorrelation

Contents

List of option

Main option

-m details

When Method=0

When Method=1

When Method=2

-StackOrder details

-RefineMode details

Relationship between -dRot and-nRotArea.

Search Area

Execution example

Input file's image

Reference file's image

Example of options only essential

Option -StackOrder

StackOrder=1

Option -nRot1, -nRot2, -nRot3, -dRot1, -dRot2, dRot3, -startRot1, -startRot2, -startRot3

Option -n

n=6

Option -range

range=(-60, 60)

Option -Iter

Iter=5

Option -s

Case: s=(10, 10, 90, 90)

Option -Xshift

Option -NoShift

Option -Method

Case: Method=1

Option -m

Case: m=1

Case: m=2

Case: m=3

Case: m=16

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