def train_word2vec(self, input_file=None, size=128, augmentation=True):
self.size = size
save_emb_dir = os.path.join(self.save_dir, 'embedding')
if not check_path(save_emb_dir):
os.makedirs(save_emb_dir)
save_emb_file = os.path.join(save_emb_dir, 'node_w2v_%d' % size)
if check_path(save_emb_file):
print("pretrained embedding already exisits")
return
if input_file is None or not check_path(input_file):
input_file = os.path.join(self.save_dir, 'train_ast.pkl')
trees = pd.read_pickle(input_file)
print("Original sample number:", len(trees))
if augmentation:
cols = ['pre', 'post', 'level']
else:
cols = ['pre']
corpus = []
for c in cols:
corpus += trees[c].tolist()
print("Sample number to train Word2Vec model:", len(corpus))
from gensim.models.word2vec import Word2Vec
w2v = Word2Vec(corpus, size=size, workers=16, sg=1, min_count=3)
w2v.save(save_emb_file)
def run(experiment):
# Check whether all required paths exist
for key in experiment.config.keys():
if key.endswith("_dir"):
utils.check_path(experiment.config[key])
preprocess.preprocess(experiment)
results = process.train_and_evaluate(experiment)
def save_filter(self, remark: str) -> None:
filter_path = self.exp_path + 'filters/'
check_path(filter_path)
filter_params = np.array([
self.obs_filter.mean, self.obs_filter.square_sum,
self.obs_filter.count
])
np.save(filter_path + remark, filter_params)
print(f"-------Filter params saved to {filter_path}-------")
def check_squid_files(self):
"""Validates squid config, cache directory and ownership"""
print "Checking Squid Files......",
VAR_MAP = {'match_squid_conf': False,
'match_squid_cache': False,
'match_squid_ownership': False,
}
conf_err_msg = health_check_utils.check_path(
self.NAME,
"/etc/squid/squid.conf")
if not conf_err_msg == "":
self._set_status(0, conf_err_msg)
elif int(oct(os.stat('/etc/squid/squid.conf').st_mode)) < 644:
self._set_status(
0,
"[%s]Error: squid.conf has incorrect "
"file permissions" % self.NAME)
else:
VAR_MAP['match_squid_conf'] = True
squid_path_err_msg = health_check_utils.check_path(
self.NAME,
'/var/squid/')
if not squid_path_err_msg == "":
self.set_stauts(0, squid_path_err_msg)
elif health_check_utils.check_path(self.NAME,
'/var/squid/cache') != "":
self._set_status(
0,
health_check_utils.check_path(
self.NAME,
'/var/squid/cache'))
else:
VAR_MAP['match_squid_cache'] = True
uid = os.stat('/var/squid/').st_uid
gid = os.stat('/var/squid/').st_gid
if uid != gid or pwd.getpwuid(23).pw_name != 'squid':
self._set_status(
0,
"[%s]Error: /var/squid directory ownership "
"misconfigured" % self.NAME)
else:
VAR_MAP['match_squid_ownership'] = True
failed = []
for key in VAR_MAP.keys():
if VAR_MAP[key] is False:
failed.append(key)
if len(failed) != 0:
self.messages.append(
"[%s]Info: Failed components for squid config: %s"
% (self.NAME, ', '.join(item for item in failed)))
return True
def save_to_file(self):
"""Save options to settings file. """
check_path(self.config_path)
#print("cfg: %s", self.settings_file)
with open(self.settings_file, 'w', encoding="utf8") as settings_file:
options = self._get_options()
#print("options: %s" % options)
json.dump(options,
settings_file,
indent=4,
separators=(',', ': '))
def img_watermark(in_video, out_video):
check_path(out_video)
img_path = "./logo.png"
args = [
'ffmpeg', '-i', in_video, '-i', img_path, '-filter_complex',
'overlay=10:main_h-overlay_h-10', out_video
]
p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
raise Exception('ffprobe', out, err)
return out.decode('utf-8')
def trans_mapping(uniref90map, p_trans_map):
say("Loading transitive mapping file:\n ", p_trans_map)
check_path(p_trans_map)
overrides = {}
uniref90map_r = {}
for header, uniref90 in uniref90map.items():
uniref90map_r.setdefault(uniref90, set()).add(header)
with try_open(p_trans_map) as fh:
for row in csv.reader(fh, csv.excel_tab):
uniref90, uniref50 = row
headers = uniref90map_r.get(uniref90, set())
for h in headers:
overrides[h] = uniref50
return overrides
def parse_results(results):
say("Parsing results file:\n ", results)
check_path(results)
mapping = {}
mode = get_mode(results)
min_pident = float(mode.replace("uniref", ""))
with try_open(results) as fh:
for row in csv.reader(fh, csv.excel_tab):
h = Hit(row, config=c_output_format)
if h.qseqid not in mapping:
if h.pident >= min_pident and h.mcov >= c_min_coverage:
uniref = h.sseqid.split("|")[0]
mapping[h.qseqid] = uniref
return mapping
def split_by_time(in_video, out_video):
check_path(out_video)
start = '00:00:02'
l = '3'
# args = ['ffmpeg', '-i', in_video, '-c', 'copy', '-ss', start, out_video]
args = [
'ffmpeg', '-i', in_video, '-vcodec', 'copy', '-acodec', 'copy', '-ss',
start, '-t', l, '-sn', out_video
]
p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
raise Exception('ffmpeg', out, err)
print(out.decode('utf-8'))
def parse_spm5_preproc(work_dir, step):
doc = {}
if hasattr(step, 'spatial') and hasattr(step.spatial, 'realign'):
realign = step.spatial.realign.estwrite
motion = []
if len(realign.data[0].shape) == 0:
realign = [realign]
else:
realign = realign.data
for session in realign:
data_dir = find_data_dir(work_dir, check_path(session[0]))
motion.append(glob.glob(os.path.join(data_dir, 'rp_*.txt'))[0])
doc['motion'] = motion
if hasattr(step, 'spatial') and isinstance(step.spatial, np.ndarray):
doc['anatomy'] = makeup_path(work_dir,
check_path(step.spatial[0].preproc.data))
doc['wmanatomy'] = prefix_filename(
makeup_path(
work_dir,
check_path(step.spatial[1].normalise.write.subj.resample)),
'w')
if hasattr(step, 'temporal'):
doc['n_slices'] = int(step.temporal.st.nslices)
doc['ref_slice'] = int(step.temporal.st.refslice)
doc['slice_order'] = step.temporal.st.so.tolist()
doc['ta'] = float(step.temporal.st.ta)
doc['tr'] = float(step.temporal.st.tr)
doc['bold'] = []
doc['swabold'] = []
if len(step.temporal.st.scans[0].shape) == 0:
bold = [step.temporal.st.scans]
else:
bold = step.temporal.st.scans
for session in bold:
data_dir = find_data_dir(work_dir, str(session[0]))
doc['bold'].append(
check_paths([
os.path.join(data_dir,
os.path.split(str(x))[1]) for x in session
]))
doc['swabold'].append(
check_paths([
prefix_filename(
os.path.join(data_dir,
os.path.split(str(x))[1]), 'swa')
for x in session
]))
doc['n_scans'] = [len(s) for s in doc['bold']]
return doc
def check_snmp_mibs(self):
"""Checks if SNMP MIB files are properly placed"""
print "Checking SNMP MIBs......",
conf_err_msg = health_check_utils.check_path(self.NAME,
'/etc/snmp/snmp.conf')
if not conf_err_msg == "":
self._set_status(0, conf_err_msg)
mibs_err_msg = health_check_utils.check_path(
self.NAME,
'/usr/local/share/snmp/mibs')
if not mibs_err_msg == "":
self._set_status(0, mibs_err_msg)
return True
def build_seq_index(self, set_type, augmentation=True):
save_path = os.path.join(self.save_dir, 'embedding',
'%s.pkl' % set_type)
if check_path(save_path):
print("id sequence file already exists")
return
from gensim.models.word2vec import Word2Vec
word2vec = Word2Vec.load(
os.path.join(self.save_dir, 'embedding',
'node_w2v_%d' % self.size)).wv
vocab = word2vec.vocab
max_token = word2vec.vectors.shape[0]
def tree_to_index(seq_list):
result = [
vocab[w].index if w in vocab else max_token for w in seq_list
]
return result
if augmentation:
cols = ['pre', 'post', 'level']
else:
cols = ['pre']
fpath = os.path.join(self.save_dir, '%s_ast.pkl' % set_type)
trees = pd.read_pickle(fpath)
for c in cols:
trees[c] = trees[c].apply(tree_to_index)
cols = cols + ['label']
trees[cols].to_pickle(save_path)
seq_len = trees['pre'].apply(len)
print("min/max sequence lenght: ", seq_len.min(), seq_len.max())
def __init__(self, train_file, valid_file, test_file):
print("Beinging preprocess data...")
self.set_types = ['train', 'valid', 'test']
self.files = [train_file, valid_file, test_file]
for f in self.files:
assert check_path(f), "%s not exists" % f
self.save_dir = os.path.dirname(train_file)
def __init__(self, parameters):
if not isinstance(parameters, dict):
raise TypeError('"parameters" must be a dict type')
if 'path_data' not in parameters.keys():
raise KeyError(
'"path_data" is not in "parameters", "path_data" is a necessary parameter'
)
if not check_path(parameters['path_data']):
raise ValueError(f"'{parameters['path_data']}' does not exists")
if not parameters['target']:
raise KeyError(
'"target" is not in "parameters", "target" is a necessary parameter'
)
self.path = parameters['path_data']
self.sep = parameters['sep']
self.target = parameters['target']
self.id = parameters['id']
self.type = parameters['type']
self.num_features = parameters['num_features']
self.threshold = parameters['threshold']
self.n_jobs = parameters['n_jobs']
self.output_file_name = parameters['output_file_name']
self.df = None
logging.info(f"Object {self} is created")
def parse_spm8_preproc(work_dir, step):
doc = {}
if hasattr(step, 'spatial') and hasattr(step.spatial, 'preproc'):
doc['anatomy'] = makeup_path(
work_dir, check_path(step.spatial.preproc.data))
doc['wmanatomy'] = prefix_filename(doc['anatomy'], 'wm')
if hasattr(step, 'temporal'):
doc['n_slices'] = int(step.temporal.st.nslices)
doc['ref_slice'] = int(step.temporal.st.refslice)
doc['slice_order'] = step.temporal.st.so.tolist()
doc['ta'] = float(step.temporal.st.ta)
doc['tr'] = float(step.temporal.st.tr)
doc['bold'] = []
doc['swabold'] = []
if len(step.temporal.st.scans[0].shape) == 0:
bold = [step.temporal.st.scans]
else:
bold = step.temporal.st.scans
for session in bold:
data_dir = find_data_dir(work_dir, str(session[0]))
doc['bold'].append(check_paths(
[os.path.join(data_dir, os.path.split(str(x))[1])
for x in session]))
doc['swabold'].append(check_paths(
[prefix_filename(os.path.join(
data_dir, os.path.split(str(x))[1]), 'swa')
for x in session]))
doc['n_scans'] = [len(s) for s in doc['bold']]
return doc
def save_plot(self):
# add options to change file format, background color/transparency,
# resolution, padding, etc.
file_prefix = os.path.join('Plots', time.strftime('%Y-%m-%d'),
time.strftime('%Z.%H.%M.%S'))
plot_file = file_prefix + '.eps'
utils.check_path(plot_file)
try:
# bug in matplotlib 1.4.0 prevents this from working
# (https://github.com/matplotlib/matplotlib/pull/3434)
plt.savefig(plot_file, format='eps', bbox_inches='tight')
except:
plt.savefig(plot_file, format='eps')
print '\nPlot saved as ' + plot_file
plot_log_file = file_prefix + '.log'
self.save_log(filename=plot_log_file)
def __init__(self,
facenet_model_dir,
mtcnn_model_dir,
resize_factor=0.7,
match_thresh=0.7,
mtcnn_params=MTCNN_PARAMS_DEFAULT,
db_load_path=None,
database_verbose=False,
gpu_memory_fraction=0.4):
'''
Arguments:
facenet_model_dir: Directory containing the FaceNet model, with meta-file and ckpt-file
mtcnn_model_dir: Directory containing MTCNN model, det1.npy, det2.npy, det3.npy
resize_factor: input image will be resize to a smaller size before sent into MTCNN and FaceNet
match_thresh: the lower bound of a valid match (if distance between 2 embeddings is higher
than this threshold, then the corresponding 2 faces will be viewed as different)
mtcnn_params: Parameters of MTCNN, a dictionary with 3 keys, 'minsize', 'threshold', 'factor'
db_load_path: if set, load existed Face database
database_verbose: if True, print extra messages as database updates, and vice versa
gpu_memory_fraction: Fraction of GPU memory to be queried, in range [0,1]
Return:
an instance of FaceRecognizer object
'''
self._facenet_model_dir = os.path.abspath(
os.path.expanduser(facenet_model_dir))
self._mtcnn_model_dir = os.path.abspath(
os.path.expanduser(mtcnn_model_dir))
self._minsize = mtcnn_params['minsize']
self._threshold = mtcnn_params['threshold']
self._factor = mtcnn_params['factor']
self._match_thresh = match_thresh
self._resize_factor = resize_factor
# define graph to be built on
self._graph = tf.Graph()
# self._graph = tf.Graph()
# define session
sess_conf = tf.ConfigProto()
sess_conf.gpu_options.allow_growth = True
sess_conf.gpu_options.per_process_gpu_memory_fraction = gpu_memory_fraction
self._sess = tf.Session(graph=self._graph, config=sess_conf)
# I/O of Facenet
self._images_placeholder = []
self._embeddings = []
# database
if db_load_path is not None: # load existing Face database
db_load_path = utils.check_path(db_load_path)
with open(db_load_path, 'rb') as handle:
self._database = pickle.load(handle)
print('Load FaceDatabase from {}'.format(db_load_path))
self._database._verbose = database_verbose
else: # create new Face database
self._database = FaceDatabase(database_verbose)
# MTCNN
self._pnet = []
self._rnet = []
self._onet = []
# embeddings and corresponding names obtained from current inference
self._cur_embs = []
self._cur_embs_name = []
def getEdgeFeatureCSV(years,resource):
gs={}
global countries
cList =[]
As=[]
for y in years:
gs[y]=get_graph(y, resource)
e = get_graph(y,'essex')
cList.append(set(gs[y].nodes()))
cList.append(set(e.nodes()))
#print 'For the year'
#pprint(gs[y].nodes())
#pprint(e.nodes())
#pprint(cList)
countries = list(set.intersection(*cList))
print 'Countries included so far:'
print countries
edgefeatureYears=years[:-1]
nodefeatureYear=years[-2]
nodefeatureYears=[nodefeatureYear]
nodefeatures=node_feature_extraction(nodefeatureYears,nodefeatureDict,resource)
edgefeatures=edge_feature_extraction(edgefeatureYears, countries, edgefeatureDict,resource)
nodeToEdgeFeatures=convertNodalFeaturesToEdgeFeatures(countries, nodefeatureYears, nodefeatures)
edgefeatures.update(nodeToEdgeFeatures)
features=edgefeatures.keys()
check_path('data/raw/features/'+resource[0]+'/edgedata/')
filename=open('data/raw/features/'+resource[0]+'/edgedata/'+str(years[-1])+'.csv', 'wb')
writer = csv.writer(filename)
fnames=copy.deepcopy(features)
fnames.append("t")
fnames.insert(0, "edge")
writer.writerow(fnames)
for c1 in countries:
for c2 in countries:
row=[c1+"_"+c2, ]
for f in features:
row.append(edgefeatures[f][(c1, c2)])
try:
t=gs[years[-1]][c1][c2]["weight"]
except:
t=0
row.append(t)
writer.writerow(row)
def __init__(self, parameters):
if not isinstance(parameters, dict):
raise TypeError('"parameters" must be a dict type')
if 'path_data' not in parameters.keys():
raise KeyError(
'"path_data" is not in "parameters", "path_data" is a necessary parameter'
)
if not check_path(parameters['path_data']) or not check_dir(
parameters['path_data']):
raise ValueError(
f"'{parameters['path_data']}' does not exists or is not folder"
)
if not check_csv(parameters['path_data']):
raise ValueError(
f"'{parameters['path_data']}' must contain only csv files")
all_file_founded, list_not_founded_files = check_csv_files(
parameters['path_data'], parameters['tables'])
if not all_file_founded:
raise ValueError(
f"{list_not_founded_files} is not founded in {parameters['path_data']}"
)
self.path = parameters['path_data']
self.tables = parameters['tables']
self.main_table = parameters['main_table']
self.depth = parameters['depth']
self.relations = parameters['relations']
self.sep = parameters['sep']
self.n_jobs = min(os.cpu_count(), parameters['n_jobs'])
self.chunk_size = parameters['chunk_size']
self.max_features = parameters['max_features']
self.target = parameters['target']
self.paths_files = [
os.path.join(self.path, table) for table, _ in self.tables.items()
]
self.drop_contains = [col for _, col in self.tables.items() if col
] + [self.target + ')']
self.dict_dataframes = dict()
self.entities = None
self.agg_primitives = parameters['agg_primitives']
self.trans_primitives = parameters['trans_primitives']
self.feature_matrix = None
self.feature_names = None
self.output_file_name = parameters['output_file_name']
self.time_indecies = parameters['time_indecies']
self.time_variables = parameters[
'time_variables'] # TODO заменить на обработку из файла Ани
self.feature_names_file = parameters['file_name_for_features']
self.generate_selected_features = parameters[
'generate_selected_features']
self.file_name_with_selected_features = parameters[
'file_with_selected_features']
self.selected_features = list()
logging.info(f"Object {self} is created")
def proc_func(csv_path):
start_time = time.time()
print(csv_path + ' has began ...')
ckpt_path = ckpt_folder + csv_path + '.ckpt'
check_path(ckpt_path, binary=True)
ckpt_index = read_ckpt(ckpt_path)
csv_file = csv.reader(open(csv_folder + csv_path + '.csv'))
_ = next(csv_file)
rows = [row for row in csv_file]
print('start from checkpoint ' + str(ckpt_index + 1) + ' in ' +
str(csv_path))
for i in tqdm(range(ckpt_index + 1, len(rows))):
process(rows[i][0], rows[i][1])
save_ckpt(i, ckpt_path)
print(csv_path + ' has been done in ' + str(time.time() - start_time))
def init_log(args):
import time
current_time = time.strftime("%Y-%m-%d_%H:%M:%S", time.localtime())
# Creating log file
save_path = './mnist/'
check_path(save_path)
file = save_path + 'q_' + args.hiddens + '_n_' + str(args.num_masks) + \
'_lr_' + str(args.learning_rate) + '_wd_' + str(args.weight_decay) + \
'_b_' + str(args.batch_size) + '_' + current_time
logging.basicConfig(
filename=file + '.log',
filemode='w',
level=logging.INFO,
format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
logger = logging.getLogger(__name__)
return logger, file
def parse_spm5_preproc(work_dir, step):
doc = {}
if hasattr(step, 'spatial') and hasattr(step.spatial, 'realign'):
realign = step.spatial.realign.estwrite
motion = []
if len(realign.data[0].shape) == 0:
realign = [realign]
else:
realign = realign.data
for session in realign:
data_dir = find_data_dir(work_dir, check_path(session[0]))
motion.append(glob.glob(os.path.join(data_dir, 'rp_*.txt'))[0])
doc['motion'] = motion
if hasattr(step, 'spatial') and isinstance(step.spatial, np.ndarray):
doc['anatomy'] = makeup_path(
work_dir, check_path(step.spatial[0].preproc.data))
doc['wmanatomy'] = prefix_filename(makeup_path(
work_dir,
check_path(step.spatial[1].normalise.write.subj.resample)),
'w')
if hasattr(step, 'temporal'):
doc['n_slices'] = int(step.temporal.st.nslices)
doc['ref_slice'] = int(step.temporal.st.refslice)
doc['slice_order'] = step.temporal.st.so.tolist()
doc['ta'] = float(step.temporal.st.ta)
doc['tr'] = float(step.temporal.st.tr)
doc['bold'] = []
doc['swabold'] = []
if len(step.temporal.st.scans[0].shape) == 0:
bold = [step.temporal.st.scans]
else:
bold = step.temporal.st.scans
for session in bold:
data_dir = find_data_dir(work_dir, str(session[0]))
doc['bold'].append(check_paths(
[os.path.join(data_dir, os.path.split(str(x))[1])
for x in session]))
doc['swabold'].append(check_paths(
[prefix_filename(os.path.join(
data_dir, os.path.split(str(x))[1]), 'swa')
for x in session]))
doc['n_scans'] = [len(s) for s in doc['bold']]
return doc
def run(self):
source_file = self.LATEST_YOUTUBE_DL + YOUTUBEDL_BIN
destination_file = os.path.join(self.download_path, YOUTUBEDL_BIN)
self._talk_to_gui('download', destination_file)
check_path(self.download_path)
try:
stream = request.urlopen(source_file,
timeout=self.DOWNLOAD_TIMEOUT)
with open(destination_file, 'wb') as dest_file:
dest_file.write(stream.read())
self._talk_to_gui('correct')
except (HTTPError, URLError, IOError) as error:
self._talk_to_gui('error', error)
if not self.quiet:
self._talk_to_gui('finish')
def text_watermark(in_video, out_video):
check_path(out_video)
text = "测试中文水印"
x = 10
y = 10
fontf = "./hysjsJ.ttf"
fontsize = 12
fcolor = "white"
sc = 'black'
shadow_x = 5
shadow_y = 5
custom = "drawtext=text={text}:x=100:y=H-th-100:fontfile={fontf}:fontsize=38:fontcolor=red:shadowcolor=black:shadowx=5:shadowy=5 "
custom = custom.format(text=text, fontf=fontf)
args = ['ffmpeg', '-i', in_video, '-vf', custom, out_video]
p = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
out, err = p.communicate()
if p.returncode != 0:
raise Exception('ffprobe', out, err)
return out.decode('utf-8')
def _write(self, data, mode):
"""Write data to the log file.
That's the main method for writing to the log file.
Args:
data (string): String to write on the log file.
mode (string): Can be any IO mode supported by python.
"""
check_path(self.config_path)
with open(self.log_file, mode) as log:
if mode == 'a' and self.add_time:
msg = self.TIME_TEMPLATE.format(time=strftime('%c'),
error_msg=data)
else:
msg = data
log.write(msg)
def check_rsyslogd(self):
"""Validates rsyslogd configuration and service"""
print "Checking rsyslog......",
conf_err_msg = health_check_utils.check_path(self.NAME,
'/etc/rsyslog.conf')
if not conf_err_msg == "":
self._set_status(0, conf_err_msg)
dir_err_msg = health_check_utils.check_path(self.NAME,
'/etc/rsyslog.d/')
if not dir_err_msg == "":
self._set_status(0, dir_err_msg)
serv_err_msg = health_check_utils.check_service_running(self.NAME,
'rsyslogd')
if not serv_err_msg == "":
self._set_status(0, serv_err_msg)
return True
def uniref_search(diamond=None,
database=None,
query=None,
seqtype=None,
temp=None,
diamond_options=None,
force_search=False):
if which(diamond) is None:
die("<diamond> is not executable as: {}".format(diamond))
for path in [database, query, temp]:
check_path(path)
binary = {"nuc": "blastx", "prot": "blastp"}[seqtype]
mode = get_mode(database)
results = os.path.split(query)[1]
results = os.path.join(temp, results)
results = ".".join([results, mode, "hits"])
command = [
diamond,
binary,
"--db",
database,
"--query",
query,
"--outfmt",
c_output_format,
"--tmpdir",
temp,
"--out",
results,
"--id",
get_mode(results).replace("uniref", ""),
c_diamond_filters,
]
command = " ".join([str(k) for k in command])
command += (" " + diamond_options) if diamond_options is not None else ""
if force_search or not os.path.exists(results):
say("Executing:\n ", command)
os.system(command)
else:
say("Using existing results file:\n ", results)
return results
def get_intra_images(mat_file, work_dir, memory=Memory(None)):
mat = memory.cache(load_matfile)(mat_file)['SPM']
images = {}
images['beta_maps'] = []
images['c_maps'] = {}
images['t_maps'] = {}
images['contrasts'] = {}
for c in mat.xCon:
name = safe_name(str(c.name))
try:
images['c_maps'][name] = check_path(
os.path.join(work_dir, str(c.Vcon.fname)))
images['t_maps'][name] = check_path(
os.path.join(work_dir, str(c.Vspm.fname)))
images['contrasts'][name] = c.c.tolist()
except:
pass # sometimes c.Vcon is an empty array
for i, b in enumerate(mat.Vbeta):
images['beta_maps'].append(
check_path(os.path.join(work_dir, str(b.fname))))
return images
def get_intra_images(mat_file, work_dir, memory=Memory(None)):
mat = memory.cache(load_matfile)(mat_file)['SPM']
images = {}
images['beta_maps'] = []
images['c_maps'] = {}
images['t_maps'] = {}
images['contrasts'] = {}
for c in mat.xCon:
name = safe_name(str(c.name))
try:
images['c_maps'][name] = check_path(
os.path.join(work_dir, str(c.Vcon.fname)))
images['t_maps'][name] = check_path(
os.path.join(work_dir, str(c.Vspm.fname)))
images['contrasts'][name] = c.c.tolist()
except:
pass # sometimes c.Vcon is an empty array
for i, b in enumerate(mat.Vbeta):
images['beta_maps'].append(
check_path(os.path.join(work_dir, str(b.fname))))
return images
def test_windows_target(args):
utils.check_path(os.path.join(os.environ["QTKITS"], "msvc2017_64"))
msvc_env = R"C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvars64.bat"
utils.check_path(msvc_env)
qmake_path = os.path.join(os.environ["QTKITS"], "msvc2017_64", "bin",
"qmake.exe")
utils.check_path(qmake_path)
def plot_tsne(embeddings,
vocab,
output_path,
format='png',
random_state=0,
normalize=False):
"""
embeddings: numpy.array of shape (num_concepts, emb_dim)
vocab: list[str]
output_path: str
format: str (optional, default 'png')
random_state: str (optional, default 0)
"""
assert len(embeddings) == len(vocab)
concept2id = {w: i for i, w in enumerate(vocab)}
all_ids = []
offsets = [0]
for cate in ['animals', 'vehicles', 'grammar', 'verb']:
cate_ids = [concept2id[s] for s in categories[cate] if s in concept2id]
all_ids += cate_ids
offsets.append(offsets[-1] + len(cate_ids))
oov_rate = 1 - len(cate_ids) / len(categories[cate])
print('[tsne] {} oov rate = {}'.format(cate, oov_rate))
original_x = embeddings[np.array(all_ids)]
if normalize:
original_x = original_x / np.sqrt(
(original_x**2).sum(1))[:, np.newaxis]
reduced_x = TSNE(2, random_state=random_state).fit_transform(original_x)
fig = plt.figure()
ax = fig.add_subplot(111)
for i, cate in enumerate(['animals', 'vehicles', 'grammar', 'verb']):
cate_x = reduced_x[offsets[i]:offsets[i + 1]]
ax.scatter(cate_x[:, 0], cate_x[:, 1], label=cate, color=colors[i])
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.legend(fancybox=True, shadow=True)
check_path(output_path)
fig.savefig(output_path, format=format, bbox_inches='tight')
def get_intra_preproc(mat_file, work_dir, n_scans, memory=Memory(None)):
mat = memory.cache(load_matfile)(mat_file)['SPM']
preproc = {}
get_motion_file = False
if len(n_scans) > 1:
preproc['motion'] = []
for session in mat.Sess:
preproc['motion'].append(session.C.C.tolist())
if session.C.C.size == 0:
get_motion_file = True
else:
preproc['motion'] = [mat.Sess.C.C.tolist()]
if mat.Sess.C.C.size == 0:
get_motion_file = True
swabold = check_paths(mat.xY.P)
if len(nb.load(makeup_path(work_dir, swabold[0])).shape) == 4:
swabold = np.unique(swabold)
else:
swabold = np.split(swabold, np.cumsum(n_scans)[:-1])
if get_motion_file:
preproc['motion'] = []
for session in swabold:
session_dir = find_data_dir(work_dir, check_path(session[0]))
if get_motion_file:
motion_file = glob.glob(os.path.join(session_dir, 'rp_*.txt'))[0]
motion = np.fromfile(motion_file, sep=' ')
motion = motion.reshape(motion.shape[0] / 6, 6)
preproc['motion'].append(motion)
if isinstance(session, (list, np.ndarray)):
scans = [
os.path.join(session_dir,
os.path.split(scan)[1].strip())
for scan in session
]
preproc.setdefault('swabold', []).append(scans)
preproc.setdefault('abold', []).append(
[strip_prefix_filename(scan, 2) for scan in scans])
preproc.setdefault('bold', []).append(
[strip_prefix_filename(scan, 3) for scan in scans])
else:
preproc.setdefault('swabold', []).append(session)
preproc.setdefault('abold',
[]).append(strip_prefix_filename(session, 2))
preproc.setdefault('bold',
[]).append(strip_prefix_filename(session, 3))
return preproc
def f_to_csv(featureData,filepath,year):
"""
Takes featureData as returned by feature_extraction and a featureDict
and formats rows = country codes, columns = feature values
with a header by featureData keys
"""
fkeys = ['country code']
for f in featureData:
fkeys.append(f)
formatted = feature_reformat(featureData)
formattedAgain = [] #Turn it from a dictionary into a list
for c in formatted:
boo = [c]
boo.extend(formatted[c])
formattedAgain.append(boo)
check_path(filepath)
with open(filepath+year+'.csv', 'wb') as f:
writer = csv.writer(f)
writer.writerow(fkeys)
writer.writerows(formattedAgain)
return True
def _get_toolchain(tree, root, keep_archive=False, clean=False): archive = _create_name(tree, suffix=".tar.bz2") tree.insert(0, root) dir = path.join(_create_path(tree)) archive_dir = path.join(dir, archive) if not check_path(dir, clean): if download(TOOLCHAIN_FORGE + archive, archive_dir): extract(archive_dir, dir) if not keep_archive: remove(archive_dir) else: print "! %s already exists" % dir
def check_apache_conf(self, apache_service):
"""
Validates if Apache settings.
:param apache_service : service type of apache, os dependent.
e.g. httpd or apache2
:type apache_service : string
"""
print "Checking Apache Config......",
conf_err_msg = health_check_utils.check_path(
self.NAME,
"/etc/%s/conf.d/ods-server.conf" % apache_service)
if not conf_err_msg == "":
self._set_status(0, conf_err_msg)
wsgi_err_msg = health_check_utils.check_path(
self.NAME,
'/var/www/compass/compass.wsgi')
if not wsgi_err_msg == "":
self._set_status(0, wsgi_err_msg)
return True
def __init__(self, args, verbose=True):
self.verbose = verbose
# define social LSTM model
print('Building social LSTM model')
with open(utils.check_path(args.social_conf_path), 'rb') as f:
self._social_conf = pickle.load(f)
self._model = SocialModel(self._social_conf, True)
# define session
self._sess = tf.InteractiveSession()
# restore model parameters
restorer = tf.train.Saver()
ckpt = tf.train.get_checkpoint_state(
os.path.abspath(os.path.expanduser(args.ckpt_dir)))
print('loading model: {}'.format(ckpt.model_checkpoint_path))
restorer.restore(self._sess, ckpt.model_checkpoint_path)
# probability of a new pedestrian pops up if self._cur_num_peds doesn't reach self._max_num_peds
self._new_peds_prob = args.new_peds_prob
# maximum number of pedestrian in a frame
self._max_num_peds = self._social_conf.maxNumPeds
# number of pedestrian in the current frame
self._cur_num_peds = 0
# a list to indicate which pedestrians among all max_num_peds pedestrian exist
self._peds_exist = [False] * self.max_num_peds
# internal data for social LSTM model
self._data = np.zeros((1, self._max_num_peds, 3)) # shape=(1,MNP,3)
self._grid_data = np.zeros(
(1, self._max_num_peds, self._max_num_peds,
self._social_conf.grid_size**2)) # shape=(1,MNP,MNP,grid_size**2)
self._init_data = np.zeros((args.init_num_step, self._max_num_peds,
3)) # shape=(init_num_step,MNP,3)
self._init_grid_data = np.zeros(
(args.init_num_step, self._max_num_peds, self._max_num_peds,
self._social_conf.grid_size**2
)) # shape=(init_num_step,MNP,MNP,grid_size**2)
# shape of background, a 2-element list [width, height]
self._bg_shape = args.bg_shape
# number of step for initialization of a pedestrian
self._init_num_step = args.init_num_step
# for interpolation
self._n_interp = args.n_interp
self._interp_count = 0
self._prev_data = np.zeros(self._data.shape)
self._output_data = np.zeros(self._data.shape)
def get_intra_preproc(mat_file, work_dir, n_scans, memory=Memory(None)):
mat = memory.cache(load_matfile)(mat_file)['SPM']
preproc = {}
get_motion_file = False
if len(n_scans) > 1:
preproc['motion'] = []
for session in mat.Sess:
preproc['motion'].append(session.C.C.tolist())
if session.C.C.size == 0:
get_motion_file = True
else:
preproc['motion'] = [mat.Sess.C.C.tolist()]
if mat.Sess.C.C.size == 0:
get_motion_file = True
swabold = check_paths(mat.xY.P)
if len(nb.load(makeup_path(work_dir, swabold[0])).shape) == 4:
swabold = np.unique(swabold)
else:
swabold = np.split(swabold, np.cumsum(n_scans)[:-1])
if get_motion_file:
preproc['motion'] = []
for session in swabold:
session_dir = find_data_dir(work_dir, check_path(session[0]))
if get_motion_file:
motion_file = glob.glob(os.path.join(session_dir, 'rp_*.txt'))[0]
motion = np.fromfile(motion_file, sep=' ')
motion = motion.reshape(motion.shape[0] / 6, 6)
preproc['motion'].append(motion)
if isinstance(session, (list, np.ndarray)):
scans = [os.path.join(session_dir, os.path.split(scan)[1].strip())
for scan in session]
preproc.setdefault('swabold', []).append(scans)
preproc.setdefault('abold', []).append(
[strip_prefix_filename(scan, 2) for scan in scans])
preproc.setdefault('bold', []).append(
[strip_prefix_filename(scan, 3) for scan in scans])
else:
preproc.setdefault('swabold', []).append(session)
preproc.setdefault('abold', []).append(
strip_prefix_filename(session, 2))
preproc.setdefault('bold', []).append(
strip_prefix_filename(session, 3))
return preproc
def start(self):
check_path(PATH['test_data'], create=True)
with open(pjoin(PATH['test_data'], 'test.in'), 'w') as fw, \
open(pjoin(PATH['data'], 'testing_data.txt')) as f, \
open(pjoin(PATH['data'], 'correct', 'MSR_Sentence_Completion_Challenge_V1',
'Data', 'Holmes.machine_format.answers.txt')) as fans:
#regex = re.compile(r'^(.*)\[([^]])\](.*)$')
regex = re.compile(r'^(\d+[a-e]\)) +(.*)\[([^]]*)\](.*)$')
while True:
s = f.readline().strip('\n')
if not s: return
fin_s = regex.sub(r'\2[]\4', s)
match = regex.match(s)
opt = [match.group(3)]
for i in range(4):
s = f.readline()
match = regex.match(s)
opt.append(match.group(3))
sans = fans.readline().strip('\n')
ans = regex.match(sans).group(3)
fw.write('{}\n{}\n{} {}\n'.format(
fin_s, ' '.join(opt), ans, opt.index(ans)
))
def _c2ast(self, fpath, set_name):
save_path = os.path.join(self.save_dir, "%s_ast.pkl" % set_name)
if check_path(save_path):
return
from pycparser import c_parser
from parsetree import TreeTraverse
cparser = c_parser.CParser()
tparser = TreeTraverse()
df = pd.read_pickle(fpath)
df['ast'] = df['code'].apply(cparser.parse)
df['pre'] = df['ast'].apply(tparser.preorder)
df['post'] = df['ast'].apply(tparser.postorder)
df['level'] = df['ast'].apply(tparser.levelorder)
df.to_pickle(save_path)
def check_ntp(self):
"""Validates ntp configuration and service"""
print "Checking NTP......",
conf_err_msg = health_check_utils.check_path(self.NAME,
'/etc/ntp.conf')
if not conf_err_msg == "":
self._set_status(0, conf_err_msg)
serv_err_msg = health_check_utils.check_service_running(self.NAME,
'ntpd')
if not serv_err_msg == "":
self._set_status(0, serv_err_msg)
return True
def load_intra(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
mat = mat_file['SPM']
doc.update(get_intra_infos(mat_file, memory))
doc['mask'] = check_path(os.path.join(work_dir, str(mat.VM.fname)))
doc['onsets'], doc['conditions'] = get_intra_onsets(mat_file, memory)
doc.update(get_intra_preproc(mat_file, work_dir, doc['n_scans'], memory))
doc.update(get_intra_images(mat_file, work_dir, memory))
doc.update(
get_intra_design(mat_file, doc['n_scans'], doc['contrasts'], memory))
return doc
def load_intra(mat_file, memory=Memory(None), **kwargs):
doc = {}
mat_file = os.path.realpath(mat_file)
doc.update(parse_path(mat_file, **kwargs))
work_dir = os.path.split(mat_file)[0]
mat_file = memory.cache(load_matfile)(mat_file)
mat = mat_file['SPM']
doc.update(get_intra_infos(mat_file, memory))
doc['mask'] = check_path(os.path.join(work_dir, str(mat.VM.fname)))
doc['onsets'], doc['conditions'] = get_intra_onsets(mat_file, memory)
doc.update(get_intra_preproc(mat_file, work_dir, doc['n_scans'], memory))
doc.update(get_intra_images(mat_file, work_dir, memory))
doc.update(get_intra_design(
mat_file, doc['n_scans'], doc['contrasts'], memory))
return doc
def main():
project_dir = get_project_dir()
flatc_path = os.path.join(project_dir, ".vendor", "installed",
"msvc-2017-x64-windows-release", "bin",
"flatc.exe")
msg_fbs = os.path.join(project_dir, "app", "messages", "messages.fbs")
udp_hdr_fbs = os.path.join(project_dir, "app", "messages", "udpheader.fbs")
utils.check_path(flatc_path)
utils.check_path(msg_fbs)
utils.check_path(udp_hdr_fbs)
gen_msgs = f"{flatc_path} --cpp {msg_fbs}"
gen_udp_hdr = f"{flatc_path} --cpp {udp_hdr_fbs}"
with utils.pushd(os.path.join(project_dir, "app", "messages")):
utils.execute(gen_msgs.split())
utils.execute(gen_udp_hdr.split())
