; pick.bat
                                           
; parameters : 
; x91 - the number of the first particle (CHANGE THIS WITH EACH RUN!)
; x87 - overview number for ZI file
;
; The following are obtained/derived from the parameter doc file:
; x39 - pixel size
; x92 - window size of particles
; x27 - actual size of particles 
;
; Inputs
;   Micrographs/raw{***x11}.tif - scanned micrograph files
;   noise - used to normalize the statistics of the particle backgrounds.
; Outputs
;   ser****** - the output serial files for automaticly selected particles
;   ndc{***x55} - the output document files from peak search
;   sndc{***x55} -  upperleft corner coordinates for particles
;
                                                                 
MD 
SET MP
0      ; use all processors available
                                                                
x91 = 0  ; the first particle number (= 0 or last picked before) 

; x87 = decimation factor for DC S command
;  0 = get value from param file
;  1 = full sized image
;  2 = 1/2 size
;  4 = 1/4 size

x87 = 0  ; decimation factor (0 = get value from  param file)

; ----------- Input files --------------
FR G
[params]../params      ; parameter file 
FR G
[FILENUMS]../filenums     ; file numbers
FR G
[mic]../Micrographs/mic{****x12};            ;   ;micrographs
FR G
[noise]noise             ; noise file

; ----------- Output files --------------
FR G
[ser]win/ser******       ; template for particle images
FR G
[ndc]coords/ndc{****x12}    ; template for peak search doc file
FR G
[sndc]coords/sndc{****x12}  ; template for doc file with coordinates

; -------------- END BATCH HEADER --------------------------

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
;  DO NOT CHANGE BELOW (unless you have to)
;

FR G
[out]out{****x12}       ; temporary spider file template

; get pixelsize 
UD 5,x39
[params]

; get window size and actual size from parameter file
; if they are zero, then compute them
UD 17,x92
[params]
UD 18,x27
[params]

; actual size = 250 A
; window = 368 A
; pixelsize = x39

IF (x92.LT.1) x92 = INT(368/X39)
IF (x27.LT.1) x27 = INT(250/X39)

x31= 0.075*(x39/4.78)                                                        
; low pass filter radius                                                   
; frequency=2*pixel size/filt.rad.=const: x31=0.075*(x39/4.78)
; approxim.(particle size/2)+1)/interpolated x dimension                         ; or ((x92/2)+1)/x71 - corrected for better res.                                

x44=4       ; compression of the mic for peak search       

x79=INT(x27/x44)  ;actual size of a particle divided by x44=width of peaks

x27=int(x27/4)+1  		; Range of CCC in center step.
     
; noise will be in _7                                                           
cp                                                                              
[noise]                                                                         
_7 
                                                                             
; mask will be in _8                                                            
X55=INT(X92/2)-2
mo
mask
x92,x92
C
X55

ar                                                                              
mask                                                                            
_8                                                                              
(p1-1)*(-1)                                                                     
x93 = 1                        

; get the filenumbers
ud n,x20
[FILENUMS]

DO LB2 x11=1,x20
ud x11,x12
[FILENUMS]
; x12 is now the micrograph number

@convert_p[x12,x87]
[params]        ; parameter file
[mic]  ; input Micrograph
[out]  ; template for output spider file

                                                                     
; if the output doc files already exist, delete them
    IQ FI x88
    [ndc]
    IF (x88.EQ.1) THEN
        DE
        [ndc]
    ENDIF
    IQ FI x88
    [sndc]
    IF (x88.EQ.1) THEN
        DE
        [sndc]
    ENDIF

@pick_p[x91,x31,x44,x92,x79,x27]
[out]
[ndc]
[ser]
[sndc]

;delete the temporary spider file
DE
[out]

LB4

LB2

EN D