/usr/bin/pysurfer is in python-surfer 0.7-2.1~deb9u1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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"""
This is the top-level command-line interface script for PySurfer.
It accepts all of the relevant arguments, then turns around and calls
IPython on itself to then drop the user into an IPython environment.
"""
import os
import sys
from surfer._commandline import parser
from distutils.version import LooseVersion
import importlib
if __name__ == '__main__':
is_ipython = False
try:
get_ipython
is_ipython = True
except NameError:
try: # for old iPython versions
_ip
is_ipython = True
except NameError:
pass
# Make sure this is going to work before we have to
# boot up mlab/IPython
if len(sys.argv) > 3:
subjects_dir = os.environ['SUBJECTS_DIR']
if sys.argv[2] in ['both', 'split']:
hemi_checks = ['lh', 'rh']
else:
hemi_checks = [sys.argv[2]]
for h in hemi_checks:
surf_file = os.path.join(subjects_dir,
"%s/surf/%s.%s" % (sys.argv[1], h,
sys.argv[3]))
if not os.path.exists(surf_file):
sys.exit("ERROR: Could not find %s" % surf_file)
if not is_ipython:
# Parse the args so that --help exits back to the shell
# instead of into IPython (this would be cleaner if I
# could figure out whether that is possible to do
# from with a script IPython is executing on startup
if len(sys.argv) < 4:
parser.parse_args(["--help"])
else:
args = parser.parse_args()
# Start IPython and execute the load script
path = os.path.split(__file__)[0]
load_file = __file__
import IPython
if LooseVersion(IPython.__version__) < '0.11':
flag = '-nobanner '
flag += '-wthread '
else:
flag = '--no-banner '
try:
gui = 'wx'
importlib.import_module(gui)
except ImportError:
pass
gui = 'qt'
flag += '--gui={gui} -i '.format(gui=gui)
cmd = 'ipython %s ' % (flag + __file__ +
' "%s"' % ' '.join(sys.argv[1:]))
os.system(cmd)
else:
args = parser.parse_args(sys.argv[1].split())
from surfer import Brain
# Load up the figure and underlying brain object
b = Brain(args.subject_id, args.hemi, args.surf, title=args.title,
cortex=args.cortex, alpha=args.alpha, size=args.size,
background=args.background, foreground=args.foreground,
views=args.views)
# Maybe load some morphometry
if args.morphometry is not None:
b.add_morphometry(args.morphometry)
# Maybe load an overlay
if args.overlay is not None:
if args.range is not None:
args.min, args.max = args.range
b.add_overlay(args.overlay, args.min, args.max, args.sign)
# Maybe load an annot
if args.annotation is not None:
if not args.borders:
args.borders = any([args.overlay, args.morphometry])
b.add_annotation(args.annotation, borders=args.borders)
# Maybe load a label
if args.label is not None:
if not args.borders:
args.borders = any([args.overlay, args.morphometry])
b.add_label(args.label, borders=args.borders)
# Also point brain at the Brain() object
brain = b
# It's nice to have mlab in the namespace, but we'll import it
# after the other stuff so getting usage is not interminable
from mayavi import mlab
assert mlab # make pyflakes happy
# Now clean up the namespace a bit
del parser, args
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