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TF DDF - Transfer Function - Determine DeFocus and amplitude contrast

(10/29/96)

PURPOSE

Calculate the defocus and amplitude contrast ratio from minima of 1D profile of contrast transfer function. Input can be single image or a series of images.

SEE ALSO

TF [Transfer Function - defocus dependent]
TF C [Transfer Function - complex]
TF C3 [Transfer Function - complex 3D]
TF CT [Transfer Function - phase flipping, complex, ternary]
TF CT3 [Transfer Function - complex, ternary 3D]
TF CTF [Transfer Function - CTF correction]
TF D [Transfer Function - display]
TF DEV [Transfer Function - determine envelope function]
TF DNS [Transfer Function - determine and delete noise background]
TF FL [Transfer Function - flip sign of Fourier transform]
TF MFL [Transfer Function - make filter file for 'TF FL']

USAGE

.OPERATION: TF DDF

.HOW MANY IMAGES IN THE SERIES: 1
[Enter the number of images. If you want to process a series images, input images in either increasing or decreasing sequence.]

.IMAGE FILE: ro008
[Enter file name of 1D profile of power spectrum.]

.MAXIMUM SP. FREQ [A-1]: 0.105
[Enter the spatial frequency limit in 1/Angstroem units. The maximum spatial frequency is 1/(2*pixel).]

.SEARCH NEIGHBOUR AREA [POINT]: 5
[Enter the local distance for defining minima.]

.CHANGE SEARCHING NEIGHBOUR (Y/N): n
[Normally the number of minima can be judged by eye, so you can change the SEARCH NEIGHBOUR AREA value to get the number of minima that you expect. If you answer "Y" here, the last question will be asked again; if you answer "N", the program will go to the next question.]

.HOW MANY POINTS DO YOU WANT?: 3
[Enter the number of minima you want to include in the calculation.]

POINT # 1
.SP. FREQ. POINTS/ ABERRATION (PI): 22.0,0
[Enter the grid point of the minimum, which is found in the second column in the list of minima found by the program, and its corresponding aberration value in units of pi. For overfocus, the first minimum is zero, the second is 1, the next is 2, and so on. For underfocus, the first minimum is -1, the second is -2, the next is -3, and so on.]

POINT # 2
.SP. FREQ. POINTS/ ABERRATION (PI): 93,1

POINT # 3
.SP. FREQ. POINTS/ ABERRATION (PI): 130,2

If a defocus series is used, the following question will be asked:

.CONSTRAINTS: (1), (2) or (3): 1
[Enter the choice of constraints, as follows:
(1) same amplitude,
(2) same amplitude and define defocus interval,
(3) same defocus. ]

.WAVELENGTH LAMBDA [A]: 0.037
[Enter the electron wavelength, in Angstroems.]

.SPHERICAL ABERRATION CS [MM]: 2.0
[Enter the spherical aberration coefficient, in mm.]

.DO YOU WANT TO GENERATE A FILTER? (Y/N) : y
[This option can generate a 1D filter file which is used by TF FL to correct the CTF.]

If you answer "Y", the program asks:

.OUTPUT FILE: fil008
[Enter the name for the filter file. The filter files are generated in the same sequence as the input files if you process a series.]

NOTES

  1. The outline of the theory is as for TF.

  2. The amplitude contrast ratio is calculated by a grid search method, and low spatial frequecy minima are treated with a special weighting for amplitude contrast.

  3. The method to prepare a 1D profile is described in J. Zhu and J. Frank (1994) In, Electron Microscopy 1994 (Proceedings of the 13th Intl. Congr. on Electr. Microsc. (Paris)), pp.465-6. The procedure is given below:
     
            fr 
            ?image file ?                 ;input image <p1> 
            fr 
            ?power spectrum file ?        ;output power spectrum <p2> 
            x21=0 
            x42=200 
            do lb1 i=1,12                 ;number of pieces horizontal direction 
            x41=120 
            do lb2 j=1,12		      ;number of pieces in vertical direction 
            wi			      ;get small pieces of the input image 
            p1 
            _1 
            (512,512)                     ;size of small pieces 
            x41,x42 
            ra			      ;correct ramp effects 
            _1 
            _2 
            x21=x21+1 
            pw			      ;calc power spectrum of each small piece 
            _2			      ;calc square root of power spectrum 
            _3 
            sq			      ;calculate real power spectrum 
            _3			       
            pwax21 
            wi			      ;window central section of quick checking 
            pwax21 
            pwbx21 
            (80,80) 
            (217,217) 
            x41=x41+256		      ;50% overlapping with its neighbours 
            lb2 
            x42=x42+256 
            lb1 
            as r			      ;average over power spectra of small 
            pwa***                        ;pieces 
            1-144 
            A 
            _1 
            _2 
            wu			      ;calculate the square root of power  
            _1			      ;spectrum so it agrees with SPIDER 
            p2                            ;convention 
            re 
    

SUBROUTINES

DEFOCUS, DEFO001, DEFO003

CALLER

UTIL1

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