.DOCUMENT (WITH GROUP ASSIGNMENT): FALDOC
[Document file name produced by 'AP RA' or 'AP CA'.]
.Group number: 1
[Give 1 for output of AP RA or any of valid group
number coming from 'AP CA'.]
.CHECK 180 ROTATION (Y/N): N
[Answer 'Y' should be given only if the images to be processed
were on previous step aligned by 'AP RA' or 'AP CA 'with option
Half ring, which means that ACFs were aligned.
Answer 'N' results in the speed up of this procedure.]
.DOCUMENT FILE: SALDOC
[This is one of the the two outputs produced by this program.
It contains 6 columns:
1. File number. Real file number to deal with gaps in file series.2. Rotation angle. Image has to be rotated +angle to produce average. It is rewritten from the input doc. file with 180 deg. added if found to be needed by 'AP SA'.
3. Distance. Distance from the total rotational average. It is rewritten from the input.
4. X shift 5. Y shift After rotation image has to be shifted +X, +Y to produce the average.
6. Distance. Distance from the average found by 'AP RA'.]
.OUTPUT FILE: AVIMA001
[Output: Average image as found by whole procedure.]
NOTES
> > Example of the batch program implementing reference-free alignment > of the series of images using AP SA and AP RA commands. The program > uses following strategy: initially all the particles are centered > approximately using shift alignment (AP SA) with 180 degrees > rotation check. This is followed by a number (up to 9 in this version) > steps of shift and rotational alignment of the input data series. > After each such step the resulting average is centered using > phase approximation of the center of gravity command (CG PH). > This program works for consecutively numbered images only, but the > numbering does not have to start with one. > ; b02.sup - ALIGNMENT 01/09/98 ; ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ; ; Important notes: ; ; (1) To start the program one has to modify the input file names ; and specify input parameters: number of steps required, number ; of particles and ring numbers used by APRA (determined by the ; expected radius of the particle). ; ; (2) The shift alignment step does not enforce centering of the average ; by itself. The average produced by AP SA (AVS*** in the following ; program) has to be centered explicitly. In the program command ; CG PH (phase approximation of the center of gravity) is use for ; this purpose. It is not guaranteed to work for all the possible ; shapes and it is advisable to verify whether the average was ; shifted correctly. If not, the command can be easily replaced ; by the other mean of centration (for example croscorrelation ; with low-pass filtered disk). ; ; (3) Please note that CG PH will NOT work correctly for images ; with inverted contrast (dark particle on bright background). ; In such case either contrast of the particles has to be inverted, ; or the contrast of the average before application of CG PH. ; ; (4) VERY IMPORTANT: if you want to start the program again ; from the beginning you have to either delete previously produced ; document files or change the names of the existing file. ; ; (5) The program can be easily restarted to make additional steps ; of alignment. If initially program was ran for 5 steps of alignment ; than it is enough to change register X61 in the input block ; to the new iterations limit, remove part of the program between "End ; of the input parameters" block to the main do-loop LB9 and change ; in this line "2" to "6" (in this case, in general to the next step ; number). ; ; (6) The program makes it possible to calculate the current resolution ; of 2D average. The code has to be added by the user in the place marked. ; ; ; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ; ; DESCRIPTION OF THE FILE NAMES USED: ; ; The input data is the series of images ; data/PAR**** 1-1210 ; ; The output data is the separate series of images calculated after ; each step of alignment ; ali/PUR***** ; first digit stands for the number of alignment step, the remaining ; four digits are reserved for the particle number. ; ; Program uses the following document files: ; ; FALS - dummy file to initialize first shift alignment containing ; particle numbers ; ; APSA*** - ending with the number indicating the number of alignment ; step. This is the document file produced by the shift ; alignment (AP SA). Details are in the manual chapter APSA.MAN. ; ; APRA*** - ending with the number indicating the number of alignment ; step. This is the document file produced by the rotational ; alignment (AP RA). Details are in the manual chapter APRA.MAN. ; ; PRM*** - ending with the number indicating the number of alignment ; step. This is the document file containing the combined alignment ; parameters for each particle after all alignment steps made ; up to this one. When applied to the initial (input) data ; they will produce the aligned and centered series of particles. ; The angles (after reversing the sing) can be used in 3D ; reconstruction. ; This file contains four columns: ; 1 2 3 4 ; particle number angle X shift Y shift ; ; SHIFTS - contains X,Y shifts needed to center the average calculated ; after each shift alignment. ; ; ; The program requires specification of the following input: ; X61 - number of alignment steps ; First is the initialization step - shift only (APSA) ; Next X61-1 double steps are made - (rotation + shift) ; ; X62 - number of particles ; X63 - first particle number ; X41 - first ring number (required by AP RA) ; X42 - last ring number (required by AP RA) ; ; ; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ; ; ; Beginning of the program. ; -------------------------; ; ; Specify input parameters: ;-------------------------------------------------------------------; ; X61 - number of alignment steps ; First is the initialization step - shift only (APSA) ; Next X61-1 double steps are made - (rotation + shift) X61=5 ; X62 - number of particles X62=2530 ; X63 - first particle number X63=1 ; ; X41,X42 - specification of first and last ring numbers X41=5 X42=29 ; ; End of the input parameters block. ;-------------------------------------------------------------------; ; ; X71 - current step number X71=1 ; FALS is a dummy document file containing particle numbers in the first ; column. In general they do not have to be in consecutive order ; neither begin from one. X31=0.0 X32=1.0 DO LB1 I=1,X62 SD X0,X0,X31,X31,X32 RESULTs/FALS LB1 SD E RESULTs/FALS ; ; First shift alignment with 180 degs check to center all the particles. AP SA data/PAR001 RESULTs/FALS 1 Y RESULTs/APSAX71 RESULTs/AVSX71 ; ; ; Calculate center of gravity using CG PH to center the average. ; CG PH,X21,X22 RESULTs/AVSX71 SD X71,X21,X22 SHIFTS ; ; X21 and X22 contain integer shift values which will be used to ; center all the images. ; ; ; Shift and rotate all the input data (using center correction ; shifts found by CG PH). The resulting file series will be used ; in the next alignment step. ; DO LB2 I=1,X62 ; For short image series use UD IC instead on remove ";" signs ; from UD ICE lines in the program. UD S,X0,X31,X32,X33,X34,X35,X36 RESULTs/APSAX71 X34=X34-X21 X35=X35-X22 X91=X71*10000+X31 RT SQ data/PARX31 ali/PUR00X91 X32 X34,X35 SD X0,X31,X32,X34,X35 RESULTs/PRMX71 LB2 SD E RESULTs/PRMX71 ; ;UD ICE ;RESULTs/APSAX71 ; ; ; Main loop LB9 - make X61-1 steps of alignment. ; ---------------------------------------------; ; DO LB9 I=2,X61 ; X71=X0 X70=X71-1 X93=X70*10000+X63 X92=X70*10000+X62 ; ; Rotational alignment AP RA ali/PUR***** X93-X92 X41,X42 (1) F RESULTs/APRAX71 ; ; Shift alignment AP SA ali/PUR00X93 RESULTs/APRAX71 (1) N RESULTs/APSAX71 RESULTs/AVSX71 ; ; Calculate center of gravity using CG PH to center the average. ; CG PH,X82,X84,X21,X22 RESULTs/AVSX71 SD X71,X21,X22 SHIFTS ; ; At this stage it is advisable to remove the aligned image series ; aligned during the provious step for the sake of the disk space. ; ;DE A ;ali/PUR00X93 ; ; ; Rewrite the whole image series combining alignment parameters ; and applying them to the input series PAR****. A new, aligned ; and centered series PUR***** is produced. ; DO LB8 I=1,X62 ; For short image series use UD IC instead on remove ";" signs ; from UD ICE lines in the program. UD S,X0,X81,X82,X84,X85 RESULTs/PRMX70 UD S,X0,X31,X32,X33,X34,X35,X36 RESULTs/APSAX71 SA P,X82,X84,X85,X32,X34,X35,X52,X54,X55 X54=X54-X21 X55=X55-X22 X91=X71*10000+X81 RT SQ data/PARX81 ali/PUR00X91 X52 X54,X55 SD X0,X81,X52,X54,X55 RESULTs/PRMX71 LB8 ;UD ICE ;RESULTs/PRMX70 ; ; ; The following block can be used to calculate current averages ; and estimate the resolution. ;X93=X71*10000+X63 ;X92=X71*10000+X62 ;AS R ;ali/PUR00X93 ;X93-X92 ;E ;AASX71 ;AAVX71 ;ABSX71 ;ABVX71 ; ; Calculate the resolution using AASX71 and ABSX71. ; Use your own procedure ..... ; LB9 EN ; ; End of the program. ; -------------------;