def get_jenni(config_path):
config_files = []
config = configs.Configs([config_path])
config.load_modules(config_files)
try:
Watcher()
except Exception, e:
print >> sys.stderr, 'Warning:', e, '(in __init__.py)'
def generate_vocab(data_path):
train_files = glob.glob(data_path + 'train/*')
valid_files = glob.glob(data_path + 'valid/*')
cfgs = configs.Configs()
all_dic = {}
files = train_files + valid_files
i = 0
for file in tqdm.tqdm(files):
with open(file, 'r', encoding='utf-8') as f:
new = f.read()
for w in new:
all_dic[w] = all_dic.get(w, 0) + 1
i += 1
# if i == 2000:
# break
all_dic = {i: j for i, j in all_dic.items() if j >= 100}
dic = {}
w2i = {}
i2w = {}
w2w = {}
for w in [cfgs.W_PAD, cfgs.W_UNK, cfgs.W_EOS]:
w2i[w] = len(dic)
i2w[w2i[w]] = w
dic[w] = 10000
w2w[w] = w
for w, tf in all_dic.items():
if w in dic:
continue
w2i[w] = len(dic)
i2w[w2i[w]] = w
dic[w] = tf
w2w[w] = w
hfw = []
sorted_x = sorted(dic.items(), key=operator.itemgetter(1), reverse=True)
# print(sorted_x)
for w in sorted_x:
hfw.append(w[0])
assert len(hfw) == len(dic)
assert len(w2i) == len(dic)
print("dump dict...")
print(len(w2i))
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Handle connections to WMS API"""
import ssl
import urllib2
import urlparse
import logging
import configs
CONFIG_FILE = "/opt/google/gehttpd/wsgi-bin/wms/ogc/wms.cfg"
CONFIGS = configs.Configs(CONFIG_FILE)
logger = logging.getLogger("wms_maps")
def HandleConnection(url):
logger.debug("Opening url: [%s]", url)
if CONFIGS.GetStr("DATABASE_HOST") != "":
url = CONFIGS.GetStr("DATABASE_HOST") + urlparse.urlsplit(url)[2:]
fp = None
try:
# Set the context based on cert requirements
if CONFIGS.GetBool("VALIDATE_CERTIFICATE"):
cert_file = CONFIGS.GetStr("CERTIFICATE_CHAIN_PATH")
self.pp_dir_sa, npz_dir),
shell=True)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-n',
'--number',
type=int,
default=None,
help='How many patients to maximally process.')
args = parser.parse_args()
total_stime = time.time()
import configs
cf = configs.Configs()
# analysis finding: the following patients have unclear annotations. some raters gave more than one judgement
# on the same roi.
patients_to_exclude = [
"0137a", "0404a", "0204a", "0252a", "0366a", "0863a", "0815a", "0060a",
"0249a", "0436a", "0865a"
]
# further finding: the following patients contain nodules with segmentation-label inconsistencies
# running Preprocessor.verify_seg_label_pairings() produces a data frame with detailed findings.
patients_to_exclude += ["0305a", "0447a"]
exclude_paths = [
os.path.join(cf.raw_data_dir, pid) for pid in patients_to_exclude
]
# These pids are automatically found and excluded, when setting exclude_inconsistents=True at Preprocessor
# initialization instead of passing the pre-compiled list.
rel_dir = os.path.relpath(out_dir,
self.cf.pp_rootdir).split(os.sep)
npz_out_dir = os.path.join(self.cf.pp_npz_dir,
str(os.sep).join(rel_dir))
print("npz out dir: ", npz_out_dir)
os.makedirs(npz_out_dir, exist_ok=True)
group_df.to_pickle(os.path.join(npz_out_dir, 'info_df.pickle'))
dmanager.pack_dataset(out_dir,
npz_out_dir,
recursive=True,
verbose=False)
else:
print(
"Did not convert .npy-files to .npz because npz directory not set in configs."
)
if __name__ == '__main__':
import configs as cf
cf = cf.Configs()
total_stime = time.time()
toy_gen = ToyGenerator(cf)
toy_gen.create_sets()
toy_gen.convert_copy_npz()
mins, secs = divmod((time.time() - total_stime), 60)
h, mins = divmod(mins, 60)
t = "{:d}h:{:02d}m:{:02d}s".format(int(h), int(mins), int(secs))
print("{} total runtime: {}".format(os.path.split(__file__)[1], t))