def convert_dicoms(sid, dicom_dir_template, outputdir, queue=None, heuristic_func=None,
extension = None,embed=False,no_moco=False):
import os
from nipype.utils.filemanip import load_json,save_json
from glob import glob
sdir = dicom_dir_template%sid
tdir = os.path.join(outputdir, sid)
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
editfile = os.path.join(tdir,'%s.edit.txt' % sid)
if os.path.exists(editfile) and heuristic_func:
info = load_json(editfile)
elif not heuristic_func:
pass
else:
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
info = heuristic_func(sdir, os.path.join(tdir,'dicominfo.txt'))
save_json(infofile, info)
if heuristic_func:
for key in info:
if not os.path.exists(os.path.join(tdir,key)):
os.mkdir(os.path.join(tdir,key))
for idx, ext in enumerate(info[key]):
convertcmd = ['dcmstack', sdir,'--dest-dir', os.path.join(tdir,key),
'--file-ext', '*-%d-*'%ext, '--force-read', '-v', '--output-name', key+'%03d'%(idx+1)]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
if not no_moco:
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v']
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
import numpy as np
from bips.workflows.workflow19 import isMoco
foo = np.genfromtxt(os.path.join(tdir,'dicominfo.txt'),dtype=str)
for f in foo:
if not isMoco(glob(os.path.join(sdir,f[1]))[0]):
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v','--file-ext','*-%s-*'%f[2]]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
print "skipping moco run %s"%f[1]
return 1
def convert_dicoms(sid,
dicom_dir_template,
outputdir,
queue=None,
heuristic_func=None,
extension=None,
embed=False,
no_moco=False):
import os
from nipype.utils.filemanip import load_json, save_json
sdir = dicom_dir_template % sid
tdir = os.path.join(outputdir, sid)
infofile = os.path.join(tdir, '%s.auto.txt' % sid)
editfile = os.path.join(tdir, '%s.edit.txt' % sid)
if os.path.exists(editfile) and heuristic_func:
info = load_json(editfile)
elif not heuristic_func:
pass
else:
infofile = os.path.join(tdir, '%s.auto.txt' % sid)
info = heuristic_func(sdir, os.path.join(tdir, 'dicominfo.txt'))
save_json(infofile, info)
if heuristic_func:
for key in info:
if not os.path.exists(os.path.join(tdir, key)):
os.mkdir(os.path.join(tdir, key))
for idx, ext in enumerate(info[key]):
convertcmd = [
'dcmstack', sdir, '--dest-dir',
os.path.join(tdir, key), '--file-ext',
'*-%d-*' % ext, '--force-read', '-v', '--output-name',
key + '%03d' % (idx + 1)
]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
if not no_moco:
convertcmd = [
'dcmstack', sdir, '--dest-dir',
os.path.join(outputdir, sid), '--force-read', '-v'
]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
import numpy as np
from bips.workflows.workflow19 import isMoco
foo = np.genfromtxt(os.path.join(tdir, 'dicominfo.txt'), dtype=str)
for f in foo:
if not isMoco(os.path.join(sdir, f[1])):
convertcmd = [
'dcmstack', sdir, '--dest-dir',
os.path.join(outputdir, sid), '--force-read', '-v',
'--file-ext',
'*-%s-*' % f[2]
]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
return 1
def convert_dicoms(sid, dicom_dir_template, outputdir, queue=None, heuristic_func=None,
extension = None,embed=False,no_moco=False):
import os
from nipype.utils.filemanip import load_json,save_json
from glob import glob
sdir = dicom_dir_template%sid
tdir = os.path.join(outputdir, sid)
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
editfile = os.path.join(tdir,'%s.edit.txt' % sid)
if os.path.exists(editfile) and heuristic_func:
info = load_json(editfile)
elif not heuristic_func:
pass
else:
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
info = heuristic_func(sdir, os.path.join(tdir,'dicominfo.txt'))
save_json(infofile, info)
if heuristic_func:
import dicom
import dcmstack
for key in info:
if not os.path.exists(os.path.join(tdir,key)):
os.mkdir(os.path.join(tdir,key))
for idx, ext in enumerate(info[key]):
src = glob(os.path.join(sdir,'*-%d-*'%ext))
print key
dcm = dcmstack.DicomStack()
added_success = True
for f in src:
try:
dcm.add_dcm(dicom.read_file(f,force=True))
except:
added_success = False
print "error adding %s to stack"%f
if added_success:
a = dcm.to_nifti(embed_meta = embed)
a.to_filename(os.path.join(tdir,key,key+'%03d'%(idx+1)))
#convertcmd = ['dcmstack', sdir,'--dest-dir', os.path.join(tdir,key),
# '--file-ext', '*-%d-*'%ext, '--force-read', '-v', '--output-name', key+'%03d'%(idx+1)]
#if embed:
# convertcmd.append('--embed-meta')
#convertcmd = ' '.join(convertcmd)
#print convertcmd
#os.system(convertcmd)
else:
if not no_moco:
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v']
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
import numpy as np
from bips.workflows.workflow19 import isMoco
foo = np.genfromtxt(os.path.join(tdir,'dicominfo.txt'),dtype=str)
for f in foo:
if not isMoco(glob(os.path.join(sdir,f[1]))[0]):
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v','--file-ext','*-%s-*'%f[2]]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
print "skipping moco run %s"%f[1]
return 1
def convert_dicoms(sid, dicom_dir_template, outputdir, queue=None, heuristic_func=None,
extension = None,embed=False,no_moco=False):
import os
from nipype.utils.filemanip import load_json,save_json
from glob import glob
sdir = dicom_dir_template%sid
tdir = os.path.join(outputdir, sid)
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
editfile = os.path.join(tdir,'%s.edit.txt' % sid)
if os.path.exists(editfile) and heuristic_func:
info = load_json(editfile)
elif not heuristic_func:
pass
else:
infofile = os.path.join(tdir,'%s.auto.txt' % sid)
info = heuristic_func(sdir, os.path.join(tdir,'dicominfo.txt'))
save_json(infofile, info)
if heuristic_func:
import dicom
import dcmstack
for key in info:
if not os.path.exists(os.path.join(tdir,key)):
os.mkdir(os.path.join(tdir,key))
for idx, ext in enumerate(info[key]):
src = glob(os.path.join(sdir,'*-%d-*'%ext))
dcm = dcmstack.DicomStack()
for f in src:
dcm.add_dcm(dicom.read_file(f,force=True))
a = dcm.to_nifti(embed_meta = embed)
a.to_filename(os.path.join(tdir,key,key+'%03d'%(idx+1)))
#convertcmd = ['dcmstack', sdir,'--dest-dir', os.path.join(tdir,key),
# '--file-ext', '*-%d-*'%ext, '--force-read', '-v', '--output-name', key+'%03d'%(idx+1)]
#if embed:
# convertcmd.append('--embed-meta')
#convertcmd = ' '.join(convertcmd)
#print convertcmd
#os.system(convertcmd)
else:
if not no_moco:
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v']
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
import numpy as np
from bips.workflows.workflow19 import isMoco
foo = np.genfromtxt(os.path.join(tdir,'dicominfo.txt'),dtype=str)
for f in foo:
if not isMoco(glob(os.path.join(sdir,f[1]))[0]):
convertcmd = ['dcmstack', sdir, '--dest-dir', os.path.join(outputdir,sid),
'--force-read','-v','--file-ext','*-%s-*'%f[2]]
if embed:
convertcmd.append('--embed-meta')
convertcmd = ' '.join(convertcmd)
print convertcmd
os.system(convertcmd)
else:
print "skipping moco run %s"%f[1]
return 1
