print('Command not right. Exit!')
sys.exit()
for o, a in opts:
if o in ("-h", "--help"):
print(usage)
sys.exit()
if o in ("-l"):
projDir = a
if o in ("-p"):
plFilename = a
if o in ("-b"):
binning = int(a)
if o in ("-s"):
size = int(a)
if o in ("-f"):
offset = [int(i) for i in a.split(",")]
from pytom.basic.structures import ParticleList
pl = ParticleList('.')
pl.fromXMLFile(plFilename)
pl.setCenterInPickVolume(
-offset[0], -offset[1],
-offset[2]) # thomas has changed the sign of it!!!
from pytom.reconstruction.reconstructionStructures import ProjectionList
projs = ProjectionList()
projs.loadDirectory(projDir)
projs.generateVolumes(pl, size, binning, False, True, False)
