.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