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OR 3DD - Orientation search - two volumes by cross correlation

(9/1/91 MR)

PURPOSE

Determines orientation and translation between two volumes.

USAGE

.OPERATION: OR 3DD X11,X12,X13,X14,X15,X16

[The optional output parameters X11,X12,X13,X14,X15,X16 specify register positions for the 3 euler rotation angles and the value shifts in x,y,and z. ]

.DEBUG=1: 0
[Enter 1 for some debug output, 2 for a lot of debug output. do not use 2 for files larger than 8X8X8]

.INPUT1 FILE: VOLUME001
[Enter first volume]

.INPUT2 FILE: VOLUME002
[Enter second volume]

.CCF-FILE: CCF001
[enter name of file that will receive the crosscorelation values for each calculated orientation and position]

.LINK ALPHA TO -GAMMA? (Y/N):

NUMBER OF ANGULAR STEPS (ODD)

.IN ALPHA,BETA: 3,3

.AND ALSO IN GAMMA: 3
[Enter the number of values to be used for each angle. The answers above (3,3,3) cause the program to try 27 (3**3) orientations in each position.]

AND NOW THE ANGULAR INCREMENTS

.IN ALPHA,BETA: 5.,5.

.AND ALSO IN GAMMA: 5.
[Enter the increments by which each angle should be varied]

AND THE ANGLES AROUND WHICH TO VARY
.FOR ALPHA,BETA: -10,15

.AND ALSO FOR GAMMA: -20
[Enter the values of the angles around which the volume orientation should be varied]

[With the answers given above, the program calculates (for each position) the (non-normalized) crosscorelation coefficients between volume 1 and volume 2 in 27 different orientations. alpha ranging from -15 to -5, beta from 10 to 20, and gamma from -25 to -15 ]

NUMBER OF POSITIONS (ODD)
.IN X,Y: 3,3

.AND ALSO IN Z: 3
[Enter number of positions at which the crosscorelation coefficient between the two volumes is to be determined for each orientation]

SHIFT INCREMENTS:
.IN X,Y: 1.,1.

.AND ALSO Z: 1.
[Enter increments by which to shift the volume]

AND THE SHIFT AROUND WHICH TO VARY
.IN X,Y: 3,-2

.AND ALSO Z: 0.
[Enter the position around which to vary the volume]

[In the above example the volume is positioned in x at 2,3,4, in y at -3,-2,-1 and in z at -1,0,1 for each orientation, and the (non-normalized) crosscorelation coefficient is calculated. Together with the 3X3X3 angles thus 27**2 crosscorelation coefficients are determined. The maximum of all coefficients determines the best orientation/position of the volume within the specified range. These values are used as the new values around which angles and positions can be varied in a next iteration.]

.MASK RADIUS: 25.
[Enter the radius of a spherical mask used in the calculation of the crosscorelation coefficients. This mask is applied to volume 2 only. The radius should be such, that radius + maximum shift is less than half the smallest volume dimension.]

.SAMPLING INTERVAL: 2
[Enter a factor for undersampling the voxels in the volume, which speeds up the computations]

.LINE LENGTH OF CCF-FILE: 121
[Enter NSAM for the CCF file. It is a good idea to have a line lenght that corresponds to a product between the number of variations]

.NUMBER OF ITERATIONS: 7
[Enter the number of iterations.]

NOTES

  1. Not distributed!!

SUBROUTINES

AL3DCALL, ALI3D

CALLER

UTIL3

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