#!/bin/tcsh -f

#######################################################################
## Usage: Frop_dm4Stk.sc > log &
##
##Converts projections of K2 data from dm4 to bin2-mrc format (stack) 
##and further to motion corrected mrc projections 
##(using motioncorr by Yifan Cheng Lab). 
##The script also uses raw2mrc from EMAN.
##
##This script and Frop_dm4Stk.cpp is written by Teru Nakagawa (Aug 5th 2014)
#### Variables ########################################################
set INPUT_FILE_ROOT = VacA665_apol_grid37_1_
set first = 101 # assumes that odd numbered images are dm4 stacks
set last = 463
set slices = 30 #total number of slices in stack
#######################################################################
set Frop_dm4stk_DIR = /home/ohimd/test/Frop_dm4Stk
set raw2mrc_DIR = /programs/x86_64-linux/eman/1.9/bin/raw2mrc
set motioncorr_DIR = /home/ohimd/test/motioncorr
while ($first <= ${last})
set imnum =  `echo $first | awk '{printf("%04d",$1)}'`

#run Frop_dm4Stk
${Frop_dm4stk_DIR} ${INPUT_FILE_ROOT}${imnum}.dm4 ${slices} ${INPUT_FILE_ROOT}${imnum}.raw

#run raw2mrc (EMAN)
${raw2mrc_DIR} ${INPUT_FILE_ROOT}${imnum}.raw ${INPUT_FILE_ROOT}${imnum}.mrc size=3710,3710,${slices} type=float

rm -f ${INPUT_FILE_ROOT}${imnum}.raw

#run motioncorr
${motioncorr_DIR} ${INPUT_FILE_ROOT}${imnum}.mrc -fod 4

printf "\n Frop_dm4stk -> raw2mrc -> motioncorr: converted image ${INPUT_FILE_ROOT}${imnum}.dm4\n"
@ first++
@ first++
end