#!/usr/bin/env python2

import subprocess
import re
import os
from slurm import send_sbatch

defacer = '/nas/usr/local/bin/mri_deface_linux'
def_dir = '/nas/usr/local/share/mri_deface/'
tal_gca = def_dir+'talairach_mixed_with_skull.gca'
face_gca = def_dir+'face.gca'
finder = 'find /nas/data/facehbi/bids/sub-* -name "*.nii.gz"'
outdir = '/nas/data/facehbi/defaced/'
time = '2:0:0'
cpus = 4
wdir = os.environ.get('PWD')

if not os.path.isdir(outdir): os.mkdir(outdir)
ifiles = subprocess.check_output('find /nas/data/facehbi/bids/sub-* -name "*.nii.gz"', shell=True).split('\n')
for ifile in ifiles:
  if os.path.exists(ifile):
    cdata = {'time':time, 'cpus':4, 'job_name':'deface'}
    ofile = re.sub('bids','defaced/bids',ifile)
    dst_dir = os.path.dirname(ofile)
    if not os.path.isdir(dst_dir): os.makedirs(dst_dir)
    order1 = defacer+' '+ifile+' '+tal_gca+' '+face_gca+' '+ofile
    jfile = re.sub('\.nii\.gz','.json',ifile)
    ojfile = re.sub('\.nii\.gz','.json',ofile)
    order2 = 'cp '+jfile+' '+ojfile
    name = os.path.basename(ifile).split('.')[0]
    cdata['filename'] = wdir+'/deface_'+name+'.sh'
    cdata['output'] = wdir+'/deface_'+name+'.out'
    cdata['command'] = order1+'\n'+order2+'\n'
    send_sbatch(cdata)
mdata = {'job_name':'deface', 'filename':wdir+'/deface_end.sh', 'output':wdir+'/deface_end.log', 'dependency':'singleton'}
send_sbatch(mdata)