def test_surfshots():
fotos = fs.SurfaceSnapshots()
# Test underlying command
yield assert_equal, fotos.cmd, "tksurfer"
# Test mandatory args exception
yield assert_raises, ValueError, fotos.run
# Create testing files
files, cwd, oldwd = create_files_in_directory()
# Test input settins
fotos.inputs.subject_id = "fsaverage"
fotos.inputs.hemi = "lh"
fotos.inputs.surface = "pial"
# Test a basic command line
yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl snapshots.tcl"
# Test identity
schmotos = fs.SurfaceSnapshots(subject_id="mysubject",
hemi="rh",
surface="white")
yield assert_not_equal, fotos, schmotos
# Test that the tcl script gets written
fotos._write_tcl_script()
yield assert_equal, True, os.path.exists("snapshots.tcl")
# Test that we can use a different tcl script
foo = open("other.tcl", "w").close()
fotos.inputs.tcl_script = "other.tcl"
yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl other.tcl"
# Test that the interface crashes politely if graphics aren't enabled
try:
hold_display = os.environ["DISPLAY"]
del os.environ["DISPLAY"]
yield assert_raises, RuntimeError, fotos.run
os.environ["DISPLAY"] = hold_display
except KeyError:
pass
# Clean up our mess
clean_directory(cwd, oldwd)
def test_surfshots(create_files_in_directory_plus_dummy_file):
fotos = fs.SurfaceSnapshots()
# Test underlying command
assert fotos.cmd == "tksurfer"
# Test mandatory args exception
with pytest.raises(ValueError):
fotos.run()
# Create testing files
files, cwd = create_files_in_directory_plus_dummy_file
# Test input settins
fotos.inputs.subject_id = "fsaverage"
fotos.inputs.hemi = "lh"
fotos.inputs.surface = "pial"
# Test a basic command line
assert fotos.cmdline == "tksurfer fsaverage lh pial -tcl snapshots.tcl"
# Test identity
schmotos = fs.SurfaceSnapshots(subject_id="mysubject",
hemi="rh",
surface="white")
assert fotos != schmotos
# Test that the tcl script gets written
fotos._write_tcl_script()
assert os.path.exists("snapshots.tcl")
# Test that we can use a different tcl script
foo = open("other.tcl", "w").close()
fotos.inputs.tcl_script = "other.tcl"
assert fotos.cmdline == "tksurfer fsaverage lh pial -tcl other.tcl"
# Test that the interface crashes politely if graphics aren't enabled
try:
hold_display = os.environ["DISPLAY"]
del os.environ["DISPLAY"]
with pytest.raises(RuntimeError):
fotos.run()
os.environ["DISPLAY"] = hold_display
except KeyError:
pass
def makeBrainPic(freesurfer_dir):
for side in ['lh', 'rh']:
tcl_script = os.path.join(freesurfer_dir, 'tmp',
side + '_tksurfer.tcl')
#annotFile = os.path.join(freesurfer_dir,
#'mri/aparc+aseg.mgz')
#print os.path.dirname(freesurfer_dir)
shots = fs.SurfaceSnapshots(
subject_id=os.path.basename(freesurfer_dir),
subjects_dir=os.path.dirname(freesurfer_dir),
hemi=side,
tcl_script=tcl_script,
#annot_file = annotFile,
#overlay_range = (-4,4),
#screenshot_stem = freesurfer_dir+'_'+side,
six_images=True,
surface="inflated")
os.environ["SUBJECTS_DIR"] = os.path.dirname(freesurfer_dir)
#print shots.cmdline
#print "export SUBJECTS_DIR={0}".format(os.path.dirname(freesurfer_dir))
os.popen(shots.cmdline).read()
#print '*'*80
#try:
##res = shots.run()
#pass
#except:
#pass
createdList = [
side + '_' + x + '.tif' for x in ["inferior", "lateral", "medial"]
]
for img in createdList:
#print img
if 'baseline' in freesurfer_dir:
folderName = os.path.dirname(freesurfer_dir).split(
'/baseline')[0]
else:
folderName = os.path.dirname(freesurfer_dir)
shutil.move(
img.split('_')[1],
os.path.join(
'/ccnc/mri_team/',
os.path.basename(folderName) + '_' +
os.path.basename(img)))