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RM OR - Orientational search between a 3d and 2d Radon transform.

(3/19/90)

PURPOSE

Calculates the angular crosscorelation function in three Euler angles between a 3d Radon transform and 2d Radon transform. Simultaneous translational alignment is possible. (This is the original program. It has been replaced by a set of more efficient programs: Combination of RM FT and RM ORF)

USAGE

.OPERATION: RM OR X11,X12,X13,X14,X15,X16

[The optional registers will return: Phi,Theta,Psi,Value of CCF maximum,x-shift,y-shift]

.DEBUG OUTPUT: 0
[Answer: 0 otherwise very large amounts of output are produced]

.TEMPLATE FOR 2D RADON OUTPUT: *
[If * is answered no output is produced. Otherwise every Radon transform (i.e. one for every combination of theta and phi) that is extracted from the 3D Radon transform is written to disk.]

.TEMPLATE FOR CCF OUTPUT: *
[If * is answered no ouptu is produced. Otherwise for each combination of theta and phi one cross-correlation function between the input and the extracted Radon transform is written to disk.]

If a file name was given for CCF output:

.PSI NUMBER OF CCF: 11
[Anwer the number of the angle psi for which the cross-corelation function is written. Ths angle psi depends on the start value for the psi-search and the psi increment.]

.3D RADON FILE: 3DRAD001
[Enter the name of the 3D Radon transform.]

.2D RADON FILE: RAD2D001
[Enter name of two-dimensional Radon transform.]

.SAMPLING RANGE AND INCREMENT IN EXTRACTED RADON TRANSFORM:

.ALPHA FROM,TO (DEF=2D): -90,88

.INCREMENT (DEF=2D: 2
[Enter parameter for the Radon transforms that are extracted from the 3D transform. The default is the same sampling as the 2D Radon transform.]

.PEAK FILE: peak001
[Enter name of file for the 3D angular cross-coraltion function.]

.(S)HIFTALIGN,(N)O SHIFTALIGN: S
[Enter S if a simultaneous translational alignment is desired.]

if "S" was answered:

.MAXIMUM SHIFT (IN INTEGER PIXELS): 5
[Enter radius for translational search.]

.(S)UBSEARCH OR (C)OMPLETE SEARCH?(=DEF): C
[Answer C. S has not been developed sufficiently.]

.THETA RANGE OF SEARCH (FROM,TO): -90,80

.INCREMENT: 10
[Enter search range and incement for theta (second Euler angle around y-axis.]

.PHI RANGE OF SEARCH (FROM,TO): -180,170

.INCRMENT: 10
[Enter search range and increment of first Euler Angle. (around z-axis.]

.PSI RANGE OF SEARCH (FROM,TO): -180,170

.INCREMENT: 10
[Enter search range of third Euler angle (around z'-axis, within the 2D projection plane.]

Remark: For refinement these angular ranges and increments should be chosen around the crude alignment values.

.(P)ASE CORRELATION: P
[Answer P if the cross-correlation is done with the Fourier coefficients normalized by their value. A Wiener style filter is applied. If NF is the new Fourier coefficient and OF is the old value the normalization formula is: NF = OF / (|OF| + epsilon).

if P was answered:

.EPSILON (0 TO 1): 0.001
[Enter value of epsilon for phase correlation.]

.FOURIER FILTER Y/N: Y
[Enter Y if you want to Fourier filter during the correlation.]

.# OF FILTRATIONS 1/2: 2
[Enter 2 if you want to combine two filters, 1 if only one filter is to be used.]

.(A)DDITIVE (=DEF),(M)ULTIPLICATIVE: M
[Combine the chosen filters either additive or multiplicative. For a band pass filter M is the ususal option.]

.(1)L.P./(2)H.P./(3)G.L.P./(4)G.H.P./(5)F.L.P./(6)F.H.P.,(7) R*: 5
[Enter desired filter. Similar to SPIDER opreation FF. 1: cutoff low pass filter, 2: cutoff high pass filter 3: Gaussian low pass filter, 4: Gaussian high pass filter. 5: Fermi low-pass filter, 6: Fermi high pass filter. 7: Multiplication with r* (the Fourier radius).

.FILTER RADIUS: 0.123
[Enter filter radius. also otion 7 currently asks for a radius, but the value is ignored.]

for Fermi filter:

.TEMPERATURE(0=CUTOFF): 0.03

NOTES

  1. Program needs power of 2 line dimensions. For more details see: M.Radermacher, Ultramicroscopy 53, 1994, 121-136

  2. Developed by M.Radermacher

  3. Not Distributed!

SUBROUTINES

PICRADCC, CC1GFILT, MRCCC5, FOUR2

CALLER

UTIL5

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