; BATCH CONVERTS EMAN2 COORDINATES FILE TO SPIDER FORMAT
;
; NOTE: REQUIRES emancoords2spiderdoc.py

; ------- Inputs -------
fr l
[filenums]../sel_micrograph                         ; micrograph list
fr l
[eman_coords]../Micrographs/mic{****[mic-num]}.box  ; EMAN coordinates

; ------ Output ------
fr l
[spider_coords]coords/sndc{****[mic-num]}           ; SPIDER coordinates doc
fr l
[summary_doc]summary-eman2spi                       ; summary doc

; -- END BATCH HEADER --

; prepare summary doc
de
[summary_doc]
SD /       MICNUM    NUMPARTICLES
[summary_doc]

[particle-counter] = 0

; get #micrographs
ud n [num-mics]
[filenums]

; loop through micrographs
do [mic-key] = 1, [num-mics]
    ; get micrograph#
    ud ic [mic-key], [mic-num]
    [filenums]

    ; run Python script
    vm
    emancoords2spiderdoc.py [eman_coords] [spider_coords].$DATEXT

    ; get #particles
    ud n [mic-parts]
    [spider_coords]

    ; write to summary
    sd [mic-key], [mic-num], [mic-parts]
    [summary_doc]

    ; update cumulative counter
    [particle-counter] = [particle-counter] + [mic-parts]
enddo
; end micrograph-loop

VM
echo ; echo "Converted coordinates for {*******[particle-counter]} particles in {*****[num-mics]} micrographs"

; close doc
ud ice
[filenums]
SD /           NUM_MICS   NUMPARTICLES
[summary_doc]
sd -1, [num-mics],[particle-counter]
[summary_doc]
sd e
[summary_doc]

en d

; Modified 2010-09-08