def constuct_req_file(args):
''' read the input requirements from user and create a new txt
file in the data_env that includes the requirements given by the user.
if a value wasn't provided by the user, use the defaults'''
print("Summarising the structural requirements...")
req_dict = {}
## 1. Load default params:
with open(os.path.join(args.sling_dir,"default.txt")) as f: ## get all the values from the req file
for line in f:
key, val = line.strip().split()
if key != "order":
val = int(val)
req_dict[key] = val
orders = ["upstream", "downstream", "either", "both"]
args_dict = vars(args)
for key in req_dict:
if args_dict[key] is not None:
if key == "order":
args_dict[key] = args_dict[key].lower()
req_dict[key] = args_dict[key]
utils.check_reqs(req_dict)
with open(os.path.join(args.sling_dir, args.name + ".txt"), "w") as out:
for key in req_dict:
out.write(key + "\t" + str(req_dict[key]) + "\n")
return
def get_requirements(args, data_env):
# path to the requirement document of each built in DB
reqs = utils.databases
if args["hmm_db"] in reqs: # built in collections
req_file = os.path.join(data_env, args["hmm_db"] + ".txt")
else: # not a built in collection, take the default values
req_file = os.path.join(data_env, "default.txt")
with open(req_file) as f: # get all the values from the req file
for line in f:
key, val = line.strip().split()
if key != "order":
val = int(val)
if args[key] is None: # otherwise, keep what the user gave
args[key] = val
utils.check_reqs(args)
return
#!/usr/bin/env python
from utils import check_reqs
check_reqs()
"""
Converts an image stack to an MRC file. Runs either as a command line program or as an importable function.
"""
def stack2mrc(stack, mrc, imfilter = lambda im: im):
"""
Converts an image stack to an MRC file. Returns the new MRC file object.
Arguments:
stack -- the images to read, an iterable of file names
mrc -- the MRC filename to save to
Optional Arguments:
imfilter -- a function/callable that takes and returns an image
"""
from mrc import MRC
from images import imread
stack = iter(stack)
try: img = imfilter(imread(stack.next()))
except StopIteration: raise ValueError("Must provide at least one image")
mrc = MRC(mrc, nx=img.shape[1], ny=img.shape[0], dtype=img.dtype)
mrc.append(img)
mrc.append_all(imfilter(imread(img)) for img in stack) # will skip the first one
mrc.write_header()
return mrc
manager.types[person].override_property('occupant_age', MockFn(PERSON.get_age))
manager.types[person].override_property('occupant_gender', MockFn(PERSON.get_sex))
manager.types[person].override_property('occupant_name', MockFn(PERSON.get_name))
for _ in range(SEED_ENTITIES):
manager.register(person)
for mocker in manager.types.values():
if mocker.killed:
manager.kill()
return
break
manager.kill()
if __name__ == '__main__':
check_reqs(reqs=['KERNEL_URL', 'KERNEL_USER', 'KERNEL_PASSWORD'])
NAMES = file_to_json(f'{RESOURCES_DIR}/sample-names.json')
POP_CENTERS = file_to_json(f'{RESOURCES_DIR}/sample-locations.json')
args = sys.argv
seed = 1000
try:
if len(args) > 1 and isinstance(int(args[1]), int):
seed = int(args[1])
except ValueError:
pass
main(seed_size=seed)
#!/usr/bin/env python
from utils import check_reqs
check_reqs()
"""
Converts an image file to a new format.
"""
def help_msg(err=0, msg=None):
from os.path import basename
from sys import stderr, argv, exit
from textwrap import fill, TextWrapper
from utils import get_terminal_width
import imfilter_util
w = max(get_terminal_width(), 20)
tw = TextWrapper(width=w, subsequent_indent=' ' * 18)
if msg != None: print >> stderr, fill(msg, w)
print "Usage:"
print tw.fill(" %s [args] input.xxx output.xxx" % basename(argv[0]))
print ""
print "Supports numerous file formats based on extension. The extension should be accurate to the filetype otherwise it may not work."
print ""
print "Optional arguments:"
print tw.fill(" -h --help Display this help")
for l in imfilter_util.usage:
print tw.fill(l) if len(l) > 20 and l[0] == ' ' else l
exit(err)
if __name__ == "__main__":
schema_decorators = schema_decorator(project_id, schema_ids)
LOGGER.debug(schema_decorators)
ps_ids = {ps.name: ps.id for ps in schema_decorators.values()}
ms = mappingset(project_id)
sub_id = mapping(project_id, ms.id, ps_ids)
LOGGER.debug(sub_id)
if __name__ == '__main__':
check_reqs(reqs=[
'KERNEL_URL',
'KERNEL_USER',
'KERNEL_PASSWORD',
'PROJECT_NAME',
'MAPPING_NAME',
])
try:
client = Client(KERNEL_URL,
KERNEL_USER,
KERNEL_PASSWORD,
log_level=CLIENT_LOGLEVEL,
realm=REALM,
keycloak_url=KEYCLOAK_URL)
except Exception as err:
LOGGER.error(f'Kernel is not ready. Please check '
f'''it's status or wait a moment and try again : {err}''')
sys.exit(1)
