def main(argv=None):
'''Run the driver script for this module. This code only runs if we're
being run as a script. Otherwise, it's silent and just exposes methods.'''
args = process_command_line(argv)
basename = os.path.basename(args.image)
sha = basename[:basename.rfind('.')]
# this only gets run the first time around, so if >1 image is
# specified, they will ALL be in the file named by the sha of the first
# one. But grepping around isn't too hard.
logging.basicConfig(filename=log_name_gen(sha, args.log),
level=logging.DEBUG,
format='%(asctime)s %(message)s')
logging.info("Beginning image %s", args.image)
try:
run_info = run_img(sitkstrats.read(args.image), sha, args.nseeds,
args.media_root, args.seed)
except Exception as exc: # pylint: disable=W0703
logging.critical("Encountered critical exception:\n%s", exc)
raise
write_info(run_info, filename=os.path.join(args.log, sha + "-seg.json"))
return 0
def main(argv=None):
'''Run the driver script for this module. This code only runs if we're
being run as a script. Otherwise, it's silent and just exposes methods.'''
args = process_command_line(argv)
basename = os.path.basename(args.image)
sha = basename[:basename.rfind('.')]
# this only gets run the first time around, so if >1 image is
# specified, they will ALL be in the file named by the sha of the first
# one. But grepping around isn't too hard.
logging.basicConfig(filename=log_name_gen(sha, args.log),
level=logging.DEBUG,
format='%(asctime)s %(message)s')
logging.info("Beginning image %s", args.image)
try:
run_info = run_img(sitkstrats.read(args.image), sha,
args.nseeds, args.media_root, args.seed)
except Exception as exc: # pylint: disable=W0703
logging.critical("Encountered critical exception:\n%s", exc)
raise
write_info(run_info, filename=os.path.join(args.log, sha+"-seg.json"))
return 0
def run_img(img, sha, nseeds, root_dir, addl_seed): # pylint: disable=C0111
'''Run the entire protocol on a particular image starting with sha hash'''
img_info = {}
lung_img, lung_info = debug_log(sitkstrats.segment_lung, (img, {
'probe_size': 7
}), root_dir, sha)
img_info['lungseg'] = lung_info
# (img, tmp_info) = debug_log(sitkstrats.crop_to_segmentation,
# (img_in, lung_img),
# root_dir, sha, subdir="crop")
# lung_img = sitkstrats.crop_to_segmentation(lung_img, lung_img)[0]
# img_info['crop'] = tmp_info
segstrats = configure_strats()
seed_indep_imgs = {}
seed_indep_info = {}
seeds = []
for (sname, strat) in [(strnam, segstrats[strnam]['seed-independent'])
for strnam in segstrats]:
try:
optha = opthash(strat['opts'])
fname = os.path.join(root_dir, strat['strategy'].__name__,
sha + "-" + optha + ".nii")
tmp_img = sitkstrats.read(fname)
tmp_info = strat['opts']
tmp_info['file'] = os.path.join(fname)
logging.info(
"Loaded seed-independent image for '%s', '%s' from file",
sname, fname)
except RuntimeError:
logging.debug("Building seed-independent image '%s', '%s'.", sname,
fname)
(tmp_img, tmp_info) = debug_log(strat['strategy'],
(img, strat['opts']), root_dir,
sha)
logging.info("Built seed-independent image '%s', '%s' in %s",
sname, fname, tmp_info['time'])
seed_indep_imgs[sname] = tmp_img
seed_indep_info[sname] = tmp_info
# compute seeds, first by taking the centers of mass of a bunch of the
# watershed segemented regions, then by adding a bunch of random ones that
# are inside the lung field.
if nseeds > 1 or addl_seed is None:
(seeds,
tmp_info) = sitkstrats.com_calc(img=seed_indep_imgs['watershed'],
max_size=0.05,
min_size=1e-5,
lung_img=lung_img)
img_info['deterministic-seeds'] = tmp_info
seeds.extend(sitkstrats.distribute_seeds(lung_img,
nseeds - len(seeds)))
else:
print("Provided seed only.")
img_info['deterministic-seeds'] = None
if addl_seed is not None:
# additional seed is given in terms of the input image, and must
# be corrected for cropping.
if 'crop' in img_info:
origin = img_info['crop']['origin']
assert len(addl_seed) == len(origin)
addl_seed = [
addl_seed[i] - origin[i] for i in range(len(addl_seed))
]
seeds.insert(0, addl_seed)
if len(seeds) > nseeds:
logging.warning(
"The number of seeds generated in the deterministic " +
"phase (%s) is greater than the allowed number of " +
"seeds (%s). The list of seeds is being truncated.", len(seeds),
nseeds)
# with many deterministic seeds, this list can be longer than nseeds.
seeds = seeds[0:nseeds]
seg_info = seeddep(seed_indep_imgs, seeds, root_dir, sha, segstrats,
img_info['lungseg']['size'], img)
img_info['noduleseg'] = {}
for seed in seg_info:
for segstrat in seg_info[seed]:
combined_info = {'seed-dependent': seg_info[seed][segstrat]}
if segstrat in seed_indep_info:
combined_info['seed-independent'] = seed_indep_info[segstrat]
img_info['noduleseg'].setdefault(seed,
{})[segstrat] = combined_info
return img_info
def run_img(img, sha, nseeds, root_dir, addl_seed): # pylint: disable=C0111
'''Run the entire protocol on a particular image starting with sha hash'''
img_info = {}
lung_img, lung_info = debug_log(sitkstrats.segment_lung,
(img, {'probe_size': 7}),
root_dir, sha)
img_info['lungseg'] = lung_info
# (img, tmp_info) = debug_log(sitkstrats.crop_to_segmentation,
# (img_in, lung_img),
# root_dir, sha, subdir="crop")
# lung_img = sitkstrats.crop_to_segmentation(lung_img, lung_img)[0]
# img_info['crop'] = tmp_info
segstrats = configure_strats()
seed_indep_imgs = {}
seed_indep_info = {}
for (sname, strat) in [(strnam, segstrats[strnam]['seed-independent'])
for strnam in segstrats]:
try:
optha = opthash(strat['opts'])
fname = os.path.join(root_dir, strat['strategy'].__name__,
sha + "-" + optha + ".nii")
tmp_img = sitkstrats.read(fname)
tmp_info = strat['opts']
tmp_info['file'] = os.path.join(fname)
logging.info(
"Loaded seed-independent image for '%s', '%s' from file",
sname, fname)
except RuntimeError:
logging.debug(
"Building seed-independent image '%s', '%s'.", sname, fname)
(tmp_img, tmp_info) = debug_log(strat['strategy'],
(img, strat['opts']),
root_dir,
sha)
logging.info(
"Built seed-independent image '%s', '%s' in %s",
sname, fname, tmp_info['time'])
seed_indep_imgs[sname] = tmp_img
seed_indep_info[sname] = tmp_info
# compute seeds, first by taking the centers of mass of a bunch of the
# watershed segemented regions, then by adding a bunch of random ones that
# are inside the lung field.
(seeds, tmp_info) = sitkstrats.com_calc(img=seed_indep_imgs['watershed'],
max_size=0.05, min_size=1e-5,
lung_img=lung_img)
img_info['deterministic-seeds'] = tmp_info
seeds.extend(sitkstrats.distribute_seeds(lung_img, nseeds-len(seeds)))
if addl_seed is not None:
# additional seed is given in terms of the input image, and must
# be corrected for cropping.
origin = img_info['crop']['origin']
assert len(addl_seed) == len(origin)
addl_seed = [addl_seed[i] - origin[i]
for i in range(len(addl_seed))]
seeds.insert(0, addl_seed)
if len(seeds) > nseeds:
logging.warning("The number of seeds generated in the deterministic " +
"phase (%s) is greater than the allowed number of " +
"seeds (%s). The list of seeds is being truncated.",
len(seeds), nseeds)
# with many deterministic seeds, this list can be longer than nseeds.
seeds = seeds[0:nseeds]
seg_info = seeddep(seed_indep_imgs, seeds,
root_dir, sha, segstrats, img_info['lungseg']['size'],
img)
img_info['noduleseg'] = {}
for seed in seg_info:
for segstrat in seg_info[seed]:
combined_info = {'seed-dependent': seg_info[seed][segstrat]}
if segstrat in seed_indep_info:
combined_info['seed-independent'] = seed_indep_info[segstrat]
img_info['noduleseg'].setdefault(
seed, {})[segstrat] = combined_info
return img_info