def __init__(self):
# Parse config
settings.parse()
# Init database
self.session_factory = model.create_session_factory()
# Init
import routes
tornado.web.Application.__init__(self, routes.load(), **settings.get_app_settings())
def segment(settings_file):
version = '2016-7-12'
print "Loading settings from %s..." % settings_file
runs = settings.parse(settings_file)
for i, run in enumerate(runs):
print('Segment - running configuration %d of %d from %s' %
(i + 1, len(runs), settings_file))
# Get list of images in directory
image_list = images.list_files(run['directory'], run['input_ext'])
# Set up additonal run parameters
run['image_file_label'] = 'th=%05.4f_size=%04.0fu-%04.0fu' % (
run['threshold'], run['minimum_size'], run['maximum_size'])
run['image_label'] = contruct_image_label(run, version)
if not os.path.exists(run['full_output']):
os.makedirs(run['full_output'])
top_image_filename = image_list[-1]
objects, _ = setup_object_boxes(top_image_filename, run)
if run['mode'] == 'final':
# sanity check to avoid creating unnecessary file
if len(objects) > 10000:
sys.exit(
'Over 10,000 objects are identified in the image, are you sure you want to continue?'
)
print('Saving Settings into %s' % run['full_output'])
settings.save(run.copy())
# last plane in some image samples is not a true focus plane
if run['skip_last_plane']:
final_list = image_list[:-1]
else:
final_list = image_list
# Loop over the planes we're interested in, load an image, then process it
for plane_num, plane_image_filename in enumerate(final_list):
final(plane_image_filename, objects, run, plane_num)
def segment(settings_file):
version = '2016-7-12'
print "Loading settings from %s..." % settings_file
runs = settings.parse(settings_file)
for i, run in enumerate(runs):
print('Segment - running configuration %d of %d from %s'
% (i+1, len(runs), settings_file))
# Get list of images in directory
image_list = images.list_files(run['directory'], run['input_ext'])
# Set up additonal run parameters
run['image_file_label'] = 'th=%05.4f_size=%04.0fu-%04.0fu' % (run['threshold'],
run['minimum_size'],
run['maximum_size'])
run['image_label'] = contruct_image_label(run, version)
if not os.path.exists(run['full_output']):
os.makedirs(run['full_output'])
top_image_filename = image_list[-1]
objects, _ = setup_object_boxes(top_image_filename, run)
if run['mode'] == 'final':
# sanity check to avoid creating unnecessary file
if len(objects) > 10000:
sys.exit('Over 10,000 objects are identified in the image, are you sure you want to continue?')
print('Saving Settings into %s' % run['full_output'])
settings.save(run.copy())
# last plane in some image samples is not a true focus plane
if run['skip_last_plane']:
final_list = image_list[:-1]
else:
final_list = image_list
# Loop over the planes we're interested in, load an image, then process it
for plane_num, plane_image_filename in enumerate(final_list):
final(plane_image_filename, objects, run, plane_num)
def setUp(self):
self.conf1 = SomeSettings()
self.conf2 = MoreSettings()
self.conf2 = parse(MoreSettings(), StringIO('''
[settings]
item1=foo
integer=-23423
floatz=423.2
lines=23.3
32.3
42
keypair_of_lists=k:x,y,z
some_dict_thing={'foo': 1, 2: [1, 2, 3]}
a_long=12345678901234567890
[extra]
What Up=dog
[undeclared]
what=huh?
'''))
logger.setup()
with open(settings_filename, "r") as f:
lines = f.readlines()
# remove comments in json
lines = map(lambda line: re.sub("/\*.*\*/", "", line), lines)
settings_file_contents = "".join(lines)
settings_raw = json.loads(settings_file_contents)
#settings_log_text = None
# for line in log:
# if line['Activity'] in ['Create', 'Update']:
# settings_log_text = line['Data']
# settings_log_raw = json.loads(settings_log_text) if settings_log_text else settings_raw
# settings_in_log = settings.parse(settings_log_raw)
settings_in_file = settings.parse(settings_raw)
# settings_modified = (action is not "show status" and settings_in_log is not settings_in_file)
# TODO: bail if settings modified
settings = settings_in_file
## load hit metadata if it exists
hit_modes = dict()
hit = None
if os.path.isfile("hit_modes.json"):
hit_modes = json.load(open("hit_modes.json", "r"))
if mode in hit_modes:
hit = hit_modes[mode]
## connect to amazon
mtc = connection.MTurkConnection(aws_access_key_id=ACCESS_ID,
aws_secret_access_key=SECRET_KEY,
logger.setup()
with open(settings_filename, "r") as f:
lines = f.readlines()
# remove comments in json
lines = map(lambda line: re.sub("/\*.*\*/", "", line), lines)
settings_file_contents = "".join(lines)
settings_raw = json.loads(settings_file_contents)
#settings_log_text = None
# for line in log:
# if line['Activity'] in ['Create', 'Update']:
# settings_log_text = line['Data']
# settings_log_raw = json.loads(settings_log_text) if settings_log_text else settings_raw
# settings_in_log = settings.parse(settings_log_raw)
settings_in_file = settings.parse(settings_raw)
# settings_modified = (action is not "show status" and settings_in_log is not settings_in_file)
# TODO: bail if settings modified
settings = settings_in_file
## load hit metadata if it exists
hit_modes = dict()
hit = None
if os.path.isfile("hit_modes.json"):
hit_modes = json.load(open("hit_modes.json", "r"))
if mode in hit_modes:
hit = hit_modes[mode]
## connect to amazon
mtc = connection.MTurkConnection(aws_access_key_id=ACCESS_ID,
aws_secret_access_key=SECRET_KEY,
