def main_style(args):
if args.ci:
# When the command is run in CI mode all the other parameters are ignored
selected_modules = automation_path.filter_user_selected_modules(None)
# Run pylint on all modules
return_code_sum = run_pylint(selected_modules)
# Run flake8 on modules
return_code_sum += run_pep8(selected_modules)
sys.exit(return_code_sum)
selected_modules = automation_path.filter_user_selected_modules(args.modules)
if not selected_modules:
sys.stderr('No module is selected.\n')
sys.exit(1)
if not args.suites:
return_code_sum = run_pylint(selected_modules) + run_pep8(selected_modules)
else:
return_code_sum = 0
if 'pep8' in args.suites:
return_code_sum += run_pep8(selected_modules)
if 'pylint' in args.suites:
return_code_sum += run_pylint(selected_modules)
sys.exit(return_code_sum)
def check_user_config(self):
if not os.path.isdir(self.user_config_dir):
try:
os.mkdir(self.user_config_dir, 0777)
except (IOError, os.error), value:
sys.stderr("Cannot write preferences into %s." % user_config_dir)
sys.exit(1)
def pepperoni(source, d, backup, write, rules):
"""
Pepperoni will read the python file SOURCE and modify it to match PEP008 standards
"""
if source:
with open(source, "rb") as fh:
data = fh.readlines()
if data:
corrected = utils.parse_file(data, rwd=rules)
if d:
dest = d
else:
if backup:
dest = utils.bak_file(source)
else:
dest = source
if write:
with open(source, "wb") as fh:
fh.writelines(data)
with open(dest, "wb") as fh:
fh.writelines(corrected)
else:
sys.stderr(corrected)
else:
print "Warning: No python file passed. Nothing was changed."
def makeNormalSequence ( bc, time=0, outfields=['*'], detfields=['*'], outhead=True, dethead=True ):
seq = []
params = bc['header'].get('chosen_param', None)
timestep = bc['header'].get('time_step', None)
if not params:
return seq
if ( timestep ):
timestep = float(timestep[0])
for row in bc['data']:
if len(row) != len(params):
print >> sys.stderr('Data row length does not match declared parameters')
seq.append({'type':'=', 'n':1, 'start':time, 'end':time + timestep,
'duration':timestep, 'setfields':params, 'setvalues':row,
'outfields':outfields, 'detfields':detfields,
'outhead':outhead, 'dethead':dethead})
time = time + timestep
outhead = False
dethead = False
else:
for row in bc['data']:
duration = float(row[0])
if len(row) != len(params) + 1:
print >> sys.stderr('Data row length does not match declared parameters')
seq.append({'type':'=', 'n':1, 'start':time, 'end':time + duration,
'duration':timestep, 'setfields':params, 'setvalues':row[1:],
'outfields':outfields, 'detfields':detfields,
'outhead':outhead, 'dethead':dethead})
time = time + duration
outhead = False
dethead = False
return seq
def make_cells(args):
if len(args) < 2:
print sys.stderr('expected 2 arguments')
sys.exit(1)
size = args[0]
seed_size = args[1]
#cell cell0 (clk, op, 0, rule, state[4:3], state[1:0], state[2]);
for i in xrange(size - 1, -1, -1):
r = ((i - 2 + size) % size, (i - 1 + size) % size)
l = ((i + 1) % size, (i + 2) % size)
if l[0] + 1 == l[1]:
left = 'state[%d:%d]' % (l[1], l[0])
else:
left = '{state[%d], state[%d]}' % (l[1], l[0])
if r[0] == r[1] - 1:
right = 'state[%d:%d]' % (r[1], r[0])
else:
right = '{state[%d], state[%d]}' % (r[1], r[0])
cell = 'state[%d]' % (i)
if i < seed_size:
seed = 'seed[%d]' % (i)
else:
seed = '1\'b0';
print 'cell_state cell' + repr(i) + '(clk, op, ' + seed + ', rule, ' + \
left + ', ' + cell + ', ' + right + ');'
def add_color(self, html_color, name):
"""Add color to used color, if there is no name for color, method will generate some name"""
self.add_package("color")
#hex->dec
if len(html_color) == 4: #triple color code
color = (int(html_color[1], 16), int(html_color[2], 16), int(html_color[3], 16))
else:
color = (int(html_color[1:3], 16), int(html_color[3:5], 16), int(html_color[5:7], 16))
#get name
if name:
if name in self._defined_colors and self._defined_colors[name] == color:
return name #we have already defined this color
if name in self._defined_colors and not self._defined_colors[name] == color:
#we have same name but different color codes, so we create new name by adding number to it
i = 1
while name + str(i) in self._defined_colors:
i += 1
self._defined_colors[name + str(i)] = color
self._other.append("\\definecolor{" + name + str(i) + "}{RGB}{" + ",".join((str(x) for x in color)) + "}")
return name + str(i)
#we have unique name so we just add it
self._defined_colors[name] = color
self._other.append("\\definecolor{" + name + "}{RGB}{" + ",".join((str(x) for x in color)) + "}")
return name
else:
sys.stderr("Invalid name for color")
def get_environ():
environ = {}
environ["KONIX_PLATFORM"] = sys.platform
logging.info("Installing for platform "+environ["KONIX_PLATFORM"])
KONIX_PWD = os.getcwd().replace("\\","/")
environ["KONIX_DEVEL_DIR"] = KONIX_PWD
environ["KONIX_BIN_DIR"] = environ["KONIX_DEVEL_DIR"]+"/"+"bin"
environ["KONIX_LIB_DIR"] = environ["KONIX_DEVEL_DIR"]+"/"+"lib"
environ["KONIX_SHARE_DIR"] = environ["KONIX_DEVEL_DIR"]+"/"+"share"
environ["KONIX_SRC_DIR"] = environ["KONIX_DEVEL_DIR"]+"/"+"src"
# add the lib dir to sys path in order to use the which lib so that I
# can find python executable. sys.executable won't work with cygwin
sys.path.insert(0, environ["KONIX_LIB_DIR"])
import which
python_bin = which.which("python").replace("\\", "/")
if python_bin == "":
sys.stderr("Python must be in the path for that install to work")
exit(1)
environ["PYTHON_BIN"] = python_bin
logging.info("Python bin is : "+python_bin)
environ["PYTHON_PATH"] = os.path.dirname(python_bin)
environ["KONIX_PWD"] = KONIX_PWD
environ["KONIX_CONFIG_DIR"] = KONIX_PWD+"/"+"config"
environ["KONIX_TUNING_DIR"] = KONIX_PWD+"/"+"tuning"
environ["HOME"] = os.path.expanduser("~").replace("\\","/")
environ["KONIX_PERSO_DIRS"] = os.path.join(environ["HOME"], "perso")
environ["KONIX_PERSO_DIR"] = os.path.join(environ["KONIX_PERSO_DIRS"], "perso")
environ["PATH_SEPARATOR"] = os.pathsep
environ["HOSTNAME"] = os.environ["HOSTNAME"]
environ["KONIX_SH_CUSTOM_FILE"] = environ["HOME"]+"/"+".shrc_custo"
environ["KONIX_EMACS_CUSTOM_FILE"] = environ["HOME"]+"/"+".emacs_custo"
return environ
def main():
if len(sys.argv) < 3:
print >> sys.stderr, ('Usage: %s <JSON files...> <output C++ file>' %
sys.argv[0])
print >> sys.stderr, sys.modules[__name__].__doc__
return 1
cpp_code = CC_HEADER
for json_file in sys.argv[1:-1]:
with open(json_file, 'r') as f:
json_text = f.read()
config = json.loads(json_text)
if 'monitored_domain' not in config:
print >> sys.stderr ('%s: no monitored_domain found' % json_file)
return 1
domain = config['monitored_domain']
if not domain_is_whitelisted(domain):
print >> sys.stderr ('%s: monitored_domain "%s" not in whitelist' %
(json_file, domain))
return 1
cpp_code += " // " + json_file + ":\n"
cpp_code += quote_and_wrap_text(json_text) + ",\n"
cpp_code += "\n"
cpp_code += CC_FOOTER
with open(sys.argv[-1], 'wb') as f:
f.write(cpp_code)
return 0
def select_from_x_pictures(num_to_get, subreddit):
try:
reddit = praw.Reddit(user_agent='wallpaper_grabber')
subs = reddit.get_subreddit(subreddit).get_hot(limit=num_to_get)
except praw.errors.InvalidSubreddit:
sys.stderr("Subreddit doesn't exist")
sys.exit()
filter_name = "^(.*[\\\/])" # This removes everything but after the last /
image = None
submissions = []
for img in subs:
if ".png" in img.url.lower() or ".jpg" in img.url.lower():
submissions.append(img.url)
attempts = 0
while attempts < num_to_get:
try:
check_file_exits()
image = random.choice(submissions)
filename = "wallpapers/" + re.sub(filter_name, '', image)
file = requests.get(image)
with open(filename, 'wb') as img:
img.write(file.content)
image = filename
except:
sys.stderr.write("Problem with downloading image")
attempts += 1
continue
return image
def eq_(a, b, msg=''):
'''
An assert with extra error messaging to make it easy to compare the objects
'''
if a != b:
sys.stderr("Assert Equality Error:\nA: %s\nB: %s\n%s" % (a, b, msg))
assert a == b, msg
def belongs_to_category(fasta_header, label_to_keep, seq_label ):
#Verify if label corresponds to the read header:
if fasta_header.find(seq_label[0]) > -1:
return label_to_keep == seq_label[1]
else:
sys.stderr("ERROR! Read label does not correspond to fasta line")
raise Exception("Fail :(")
def whoops(func, path, exc_info):
message = 'Could not remove %s' % path
if logger:
logger.error(message)
else:
sys.stderr(message)
sys.exit(1)
def get_emit_index(input_val, alphabet):
for i in range(0, len(alphabet)):
if alphabet[i] == input_val:
return i
sys.stderr("Could not find character " + input_val)
def communityMining(G, minCommSize=10):
"""
Find communities in the graph 'G' with more than 'minCommSize' nodes.
"""
count = 0
dendrogram = community.generate_dendrogram(G)
firstPartition = community.partition_at_level(dendrogram,0)
sys.stderr.write("Prune sparse clusters. ")
#remove early small communities
sparseComm = set([k for k,v in Counter(firstPartition.values()).iteritems() if v<minCommSize])
nodes = [node for node in G.nodes() if firstPartition[node] in sparseComm]
G.remove_nodes_from(nodes)
sys.stderr.write("Find communities. ")
# Partition again the graph and report big communities:
dendrogram = community.generate_dendrogram(G)
partition = community.partition_at_level(dendrogram,len(dendrogram)-2)
allfqdns = set(n for n,d in G.nodes(data=True) if d['bipartite']==1)
allHosts = set(n for n,d in G.nodes(data=True) if d['bipartite']==0)
size = float(len(set(partition.values())))
communities = []
bigComm = [k for k,v in Counter(partition.values()).iteritems() if v>minCommSize]
for com in bigComm :
comfqdns = [nodes for nodes in allfqdns if partition[nodes] == com]
comHosts = [nodes for nodes in allHosts if partition[nodes] == com]
comm = G.subgraph(comfqdns+comHosts)
if comm.order() < minCommSize :
sys.stderr("Remove small community (This shouldn't happen here?)\n")
continue
communities.append(comm)
return communities
def daemon(self):
try:
if os.fork():
sys.exit(0)
except OSError, e:
sys.stderr('%s, %d, %s' % ('Fork #1 failed', e.errno, e.strerror))
sys.exit(1)
def MakeConfig(opts):
"""
MakeConfigurationParameters
Create Configuration list from command options
"""
prof_list = []
cnt = 0
for opt, arg in opts:
if opt == ("--config"):
try:
# For C++ scope resolution operator
arg = re.sub("::", "@@", arg)
name, type, default = arg.split(":")
name = re.sub("@@", "::", name)
type = re.sub("@@", "::", type)
default = re.sub("@@", "::", default)
except:
sys.stderr("Invalid option: " \
+ opt \
+ "=" \
+ arg)
prof = Struct()
prof.name = name
prof.l_name = name.lower()
prof.u_name = name.upper()
prof.type = type
prof.default = default
prof_list.append(prof)
cnt += 1
return prof_list
def parse_GDS_columns(lines, subsets):
"""Parse list of line with columns description from SOFT file
of GDS (GEO Dataset)
:param lines: iterable -- iterator over lines
:returns: pandas.DataFrame -- columns description
"""
data = []
index = []
for line in lines:
line = line.rstrip()
if line.startswith("#"):
tmp = __parse_entry(line)
data.append(tmp[1])
index.append(tmp[0])
df = DataFrame(data, index=index, columns=['description'])
subset_ids = {"disease_state": {}, "individual": {}}
for subsetname, subset in subsets.iteritems():
for expid in subset.metadata["sample_id"][0].split(","):
if subset.get_type() == "disease state":
subset_ids["disease_state"][expid] = subset.metadata["description"][0]
elif subset.get_type() == "individual":
subset_ids["individual"][expid] = subset.metadata["description"][0]
else:
stderr("Unknown subset type: %s for subset %s\n" % (subset.get_type(), subsetname))
return df.join(DataFrame(subset_ids))
def build_file(infile, outfile):
try:
f = open(infile)
except IOError, msg:
sys.stderr("Could not open input file '%s' : %s\n", infile, msg)
sys.exit(1)
def make_h10giao(mol, dm0, with_gaunt=False, verbose=logger.WARN):
if isinstance(verbose, logger.Logger):
log = verbose
else:
log = logger.Logger(mol.stdout, verbose)
log.debug('first order Fock matrix / GIAOs')
n4c = dm0.shape[0]
n2c = n4c // 2
c = mol.light_speed
tg = mol.intor('cint1e_spgsp', 3)
vg = mol.intor('cint1e_gnuc', 3)
wg = mol.intor('cint1e_spgnucsp', 3)
vj, vk = _call_giao_vhf1(mol, dm0)
h1 = vj - vk
if with_gaunt:
sys.stderr('NMR gaunt part not implemented')
#TODO: import pyscf.lib.pycint as pycint
#TODO: vj, vk = scf.hf.get_vj_vk(pycint.rkb_giao_vhf_gaunt, mol, dm0)
#TODO: h1 += vj - vk
for i in range(3):
h1[i,:n2c,:n2c] += vg[i]
h1[i,n2c:,:n2c] += tg[i] * .5
h1[i,:n2c,n2c:] += tg[i].conj().T * .5
h1[i,n2c:,n2c:] += wg[i]*(.25/c**2) - tg[i]*.5
return h1
def writeFile(myQifData, fileName):
try:
saveData = open(fileName, "w")
saveData.write(myQifData)
print "File %s scritto correttamente!" % (fileName)
except:
sys.stderr("Errore: impossibile scrivere il file")
def getSample(readId, samples):
for i in samples:
s = readId.find(i)
if s == 0:
e = len(i)
return i[s:e]
sys.stderr("Read name does not contain a valid dataset name from config file\n")
exit(1)
def _get_manage_dot_py(host):
sys.stderr('{path}/virtualenv/bin/python {path}/source/manage.py'.format(
path = _get_base_folder(host)
)
)
return '{path}/virtualenv/bin/python {path}/source/manage.py'.format(
path = _get_base_folder(host)
)
def _ReadProcfs(procfs_entry_pathname):
try:
with open(procfs_entry_pathname, 'r') as procfs_entry:
val = procfs_entry.read().strip()
except IOError:
val = None
sys.stderr('procfs entry not found: %s' % procfs_entry_pathname)
return val
def main():
if len(sys.argv) < 4:
sys.stderr('concatfiles.py resulting_file file_name_1 file_name_2 (file_name_3) ... (file_name_n)\n')
sys.exit(1)
resulting_file_path = sys.argv[1]
files_to_concatenate = sys.argv[2:]
concatenate_files(files_to_concatenate, resulting_file_path)
def get_inner_product(list1, list2):
if len(list1) != len(list2):
sys.stderr('len(list1) != len(list2)')
sys.exit(-1)
_sum = 0.0
for _i in range(len(list1)):
_sum += list1[_i] * list2[_i]
return _sum
def mutate2(m2, m1_pdb, trash, filename, keep_files, obs):
"""
mutate residue 2
"""
print "mutate2: " + m2
file = open(filename, "r")
temp = open("temp.txt", "w")
for line in file:
if line[0:6:] == "<PDBS>":
temp.write(line[0:6:] + m1_pdb + ";\n")
elif line[0:14:] == "<PositionScan>":
temp.write(line[0:14:] + "to_delete.txt")
temp.write("," + m2)
temp.write(";\n")
else:
temp.write(line)
temp.close()
file.close()
os.rename("temp.txt", filename)
os.system(foldx + filename + " > /dev/null")
m2_mut_new_name = "".join((m1_pdb[:-4], "_", m2, ".pdb"))
nrg = "".join(("energies_", m2[2:-1], "_", m1_pdb[:-4], ".txt"))
nrg_new_name = "".join((m2_mut_new_name[:-4], ".txt"))
nrg_path = "".join((run_dir, "/", nrg))
if keep_files or obs:
nrg_copy = "".join((nrg_dir, "/", nrg_new_name))
shutil.copyfile(nrg_path, nrg_copy)
nrg_rename = "".join((run_dir, "/", nrg_new_name))
while True:
try:
os.rename(nrg_path, nrg_rename)
except OSError:
os.system(foldx + filename + " > /dev/null")
else:
break
trash.append(nrg_rename)
if os.path.isfile("to_delete.txt"):
os.remove("to_delete.txt")
if os.path.isfile("".join((run_dir, "/", aa_table()[m2[0]], m2[2:-1], "_", m1_pdb))):
os.remove("".join((run_dir, "/", aa_table()[m2[0]], m2[2:-1], "_", m1_pdb)))
m2_mut = "".join((aa_table()[m2[-1]], m2[2:-1], "_", m1_pdb))
m2_path = "".join((run_dir, "/", m2_mut))
if keep_files or obs:
m2_copy = "".join((pdb_dir, "/", m2_mut_new_name))
shutil.copyfile(m2_path, m2_copy)
m2_rename = "".join((run_dir, "/", m2_mut_new_name))
try:
os.rename(m2_path, m2_rename)
except OSError:
sys.stderr(m2_path + " not Found")
trash.append(m2_rename)
def node_insert_after (parent_node, old_node, new_node):
#this is not working:
#parent_node.insert (parent_node.getchildren().index(old_node) + 1, new_node)
for i, node in enumerate (parent_node.getchildren()):
if node.attrib[IDTAG] == old_node.attrib[IDTAG]:
break
else:
sys.stderr ("Error placing new tag - putting at the end of parent tag")
parent_node.insert (i + 1, new_node)
def raise_error(self, type="UnknownErrorType", message="No message"):
"""Raises an error
Logs an error using logging, and then exits
"""
logging.error(type + ": " + message)
sys.stderr(type + ": " + message)
exit(self.ERR_NO)
def get_map_template():
global map_template
if map_template is None:
with open("map-template.html", 'r') as infile:
map_template = infile.read()
if map_template is None:
stderr("ERROR: cannot find HTML template: map-template.html\n")
sysexit(1)
return map_template
def createDatabase(db_file, force = True):
"""Create BLAST db out of elements file"""
if force or not os.path.isfile(db_file + ".nhr"):
cmd = "makeblastdb -in %s -dbtype nucl" % (db_file)
p = subprocess.Popen(re.split("\s+", cmd), stderr=subprocess.PIPE, stdout=subprocess.PIPE)
output, err = p.communicate()
if err:
sys.stderr("madkeblastdb error:\n" + err.decode() + "\n")
sys.stderr('-------------------------')
def main():
"""Build and package Python2."""
parser = argparse.ArgumentParser(prog='Python setup',
description='This script will compile '
'Python 1.0.1+ and optionally create '
'a native macOS package.')
parser.add_argument('-b',
'--build',
action='store_true',
help='Compile the Python binary')
parser.add_argument('-s',
'--skip',
action='store_true',
help='Skip recompiling if possible. Only recommended '
'for development purposes.')
parser.add_argument('-p',
'--pkg',
action='store_true',
help='Package the Python output directory.')
parser.add_argument('-v',
'--verbose',
action='count',
default=1,
help="Increase verbosity level. Repeatable up to "
"2 times (-vv)")
parser.add_argument('--py',
default='2',
help='Python version to build. Accepts 2 or 3.')
if len(sys.argv) < 2:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
# set argument variables
log.verbose = args.verbose
skip = args.skip
root.root_check()
# Check for OpenSSL. If it isn't on disk in the proper location
# we can't link against it.
if not os.path.isdir(OPENSSL_INSTALL_PATH):
log.warn("OpenSSL must be installed to '{}' prior to compiling "
"Python.".format(OPENSSL_INSTALL_PATH))
sys.exit(1)
if str(args.py) == '2':
dist_url = CONFIG['python2_dist']
dist_hash = CONFIG['python2_dist_hash']
py_install_path = PYTHON2_INSTALL
py_version = PYTHON2_VERSION
elif str(args.py) == '3':
dist_url = CONFIG['python3_dist']
dist_hash = CONFIG['python3_dist_hash']
py_install_path = PYTHON3_INSTALL
py_version = PYTHON3_VERSION
else:
sys.stderr('Unsupported python version\n')
sys.exit(1)
if args.build:
log.info("Bulding Python...")
# When the skip option is passed and the build directory exists, skip
# download and compiling of Python. Note we still do linking.
if skip:
log.debug("Skip flag was provided. We will not compile Python "
"on this run.")
else:
dl_and_extract_python(dist_url, dist_hash)
# reset trigger flag as we needed to download Python
skip = False
build(py_version, py_install_path, skip=skip)
if args.pkg:
log.info("Building a package for Python...")
# Change back into our local directory so we can output our package
# via relative paths
os.chdir(CURRENT_DIR)
rc = package.pkg(
root=py_install_path,
version=py_version,
identifier="{}.python".format(CONFIG['pkgid']),
install_location=py_install_path,
output='python-{}.pkg'.format(py_version),
)
if rc == 0:
log.info("Python packaged properly")
else:
log.error("Looks like package creation failed")
emu=False
clownr=False
for o,a in opts:
if o in ("-h", "--help"):
usage()
sys.exit(0)
elif o=="-r":
reduced=True
elif o=="--emu":
emu=True
elif o=="--clownr":
clownr=True
else:
assert False, "unhandled option"
if not args:
sys.stderr("Expecting ftbl file name\n")
usage()
fullsys=not reduced
C13_ftbl.clownr=clownr
fftbl=args[0]
if fftbl and fftbl[-5:] != ".ftbl":
fftbl+=".ftbl"
if fftbl and not os.path.exists(fftbl):
sys.stderr.write(me+": file '"+fftbl+"' does not exist.\n")
sys.exit(1)
# what kind of output we have?
mode=os.fstat(1).st_mode
f=sys.stdout if stat.S_ISFIFO(mode) or stat.S_ISREG(mode) else open(fftbl[:-4]+"sys", "w")
# parse ftbl
odargs, _ = odparser.parse_known_args()
jobmon_parser = construct_parser_jobmon()
jobmon_args, _ = jobmon_parser.parse_known_args()
sj = get_SGEJobInstance(odargs.out_dir, create_connection_config_from_args(jobmon_args))
sj.log_started()
parser = get_input_args.construct_parser_burdenator()
args = get_input_args.get_args_and_create_dirs(parser)
location_id = args.location_id
year_id = args.year_id
logger = logging.getLogger(__name__)
logger.info(
"Arguments passed to remote_run_pipeline_burdenator {}".format(args))
pipeline.run_pipeline_burdenator(args)
sj.log_completed()
except Exception as e:
# Add the exception to the log file, and also report it centrally to the job monitor.
# Do not send to stderr
message = "remote_run_pipeline_burdenator {l}, {y} failed with an uncaught exception: {ex}" \
.format(l=location_id, y=year_id, ex=e)
if logger:
logger.error(message)
else:
stderr(message)
sj.log_error(message)
sj.log_failed()
sys.exit(1)
q, numProcs, account, title, jobFile = pArgs
if q in qs:
queue, group = qs[q]
else:
if ':' in q:
queue, group = q.split(':', 1)
else:
queue, group = q, q
if queue == 'general':
print >>sys.stderr('''\
Keep in mind when submitting to queue "general" that jobs running on
this queue can be pre-empted. An effort is made to clean up, but it
would be wise to check for run-away processes if this submission does
not run to completion.''')
if group: group = '-W group_list=%s'%group
mppn = '4'
if '.' in numProcs:
numProcs, mppn = numProcs.split('.', 1)
# We assume that related script lives in the same directory as this script.
myDir = os.path.dirname(os.path.realpath(__file__))+os.path.sep
sqScript = myDir + 'SQDedDriver.py'
PBSScript = open(myDir + 'SQDedPBSScriptTemplate.py').read()%locals()
print PBSScript
import subprocess
import sys
HOST="localhost"
#ports are handled in ~/.ssh_config
COMMAND="uname -a"
ssh=subprocess.Popen(["ssh", "%s", % HOST, COMMAND],
shell=False,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,)
result=subprocess.stdout.readlines()
if result==[]:
error=ssh.stderr.readliens()
print (sys.stderr() "ERROR %s:" %error)
else:
print(result)
def main():
if len(sys.argv) != 3:
sys.stderr('makejson.py (input file name) [output js file]\n')
sys.exit(1)
makejsresource(sys.argv[1], sys.argv[2])
provided encoding to read and write.
"""
with io.open(fname, "r", encoding=encoding) as f, \
io.open(fname+".tmp", "w", encoding=encoding) as outf:
have_changed = update_version_in(f, outf, regex, versionline)
replace_on_change(fname, have_changed)
# Find out our version
with open("configure.ac") as f:
version = find_version(f)
# If we have no version, we can't proceed.
if version == None:
print("No version found in configure.ac", file=sys.stderr())
sys.exit(1)
print("The version is {}".format(version))
today = time.strftime("%Y-%m-%d", time.gmtime())
# In configure.ac, we replace the definition of APPROX_RELEASE_DATE
# with "{today} for {version}", but only if the version does not match
# what is already there.
def replace_fn(m):
if m.group(1) != version:
# The version changed -- we change the date.
return u'AC_DEFINE(APPROX_RELEASE_DATE, ["{}"], # for {}'.format(
today, version)
def main(argv=None):
CMD_CREATE_BASE = "create-base"
CMD_EXPORT_BASE = "export-base"
CMD_IMPORT_BASE = "import-base"
CMD_CREATE_OVERLAY = "create-overlay"
CMD_DOWNLOAD = "download"
CMD_SYNTHESIS = "synthesis"
CMD_HANDOFF = "handoff"
CMD_HANDOFF_RECV = "handoff-recv"
CMD_EXT_LIST = "ext-list"
commands = {
CMD_CREATE_BASE: "create base vm from the running instance",
CMD_CREATE_OVERLAY: "create VM overlay from the customizaed VM",
CMD_DOWNLOAD: "Download VM overlay",
CMD_SYNTHESIS: "VM Synthesis (Need downloadable URLs for VM overlay)",
CMD_HANDOFF: "Perform VM handoff to destination URL",
CMD_HANDOFF_RECV: "Send handoff recv message to the dest OpenStack",
CMD_EXT_LIST: "List available extensions",
CMD_EXPORT_BASE: "Export Base VM",
CMD_IMPORT_BASE: "Import Base VM",
}
settings, args = process_command_line(sys.argv[1:], commands)
token, endpoint, glance_endpoint = \
get_token(settings.server_address, settings.user_name,
settings.password, settings.tenant_name)
sys.stdout.write("Success to log in to %s for tenant %s..\n" % \
(settings.server_address, settings.tenant_name))
if len(args) < 1:
sys.stderr.write("Need command")
sys.exit(1)
if args[0] == CMD_CREATE_BASE:
if len(args) != 3:
msg = "Error: creating Base VM needs [VM UUID] and [new name]\n"
msg += " 1) VM UUID: UUID of a running instance that you want to use for base VM\n"
msg += " 2) new name: name for base VM\n"
sys.stderr.write(msg)
sys.exit(1)
instance_uuid = args[1]
snapshot_name = args[2]
request_cloudlet_base(settings.server_address, token,
urlparse(endpoint), instance_uuid, snapshot_name)
elif args[0] == CMD_CREATE_OVERLAY:
if len(args) != 3:
msg = "Error: creating VM overlay needs [VM UUID] and [new name]\n"
msg += " 1) VM UUID: UUID of a running instance that you want to create VM overlay\n"
msg += " 2) new name: name for VM overlay\n"
sys.stderr.write(msg)
sys.exit(1)
instance_uuid = args[1]
snapshot_name = args[2]
ret = request_create_overlay(settings.server_address, token,
urlparse(endpoint), instance_uuid,
snapshot_name)
pprint(ret)
elif args[0] == CMD_DOWNLOAD:
if len(args) != 2:
msg = "Error: downlading VM overlay needs [Image UUID]\n"
msg += " 1) Image UUID: UUID of a VM overlay\n"
sys.stderr.write(msg)
sys.exit(1)
image_name = args[1]
output_name = image_name + ".zip"
sys.stdout.write("Download %s to %s...\n" % (image_name, output_name))
overlay_download(settings.server_address, token,
urlparse(glance_endpoint), image_name, output_name)
elif args[0] == CMD_EXPORT_BASE:
if len(args) != 2:
msg = "Error: Exporting Base VM needs [Image UUID]\n"
msg += " 1) Image UUID: UUID of a Base VM (base disk)\n"
sys.stderr.write(msg)
sys.exit(1)
basedisk_uuid = args[1]
output_path = os.path.join(os.curdir, "base-%s.zip" % basedisk_uuid)
sys.stdout.write("Export %s to %s...\n" % (basedisk_uuid, output_path))
if os.path.exists(output_path):
is_overwrite = raw_input("%s exists. Overwirte it? (y/N) " %
output_path)
if is_overwrite != 'y':
sys.exit(1)
request_export_basevm(settings.server_address, token,
urlparse(endpoint), basedisk_uuid, output_path)
elif args[0] == CMD_IMPORT_BASE:
if len(args) != 3:
msg = "Error: Importing Base VM needs [Path to Base VM file] [Name for Base VM]\n"
msg += " 1) Path to Base VM file: Absolute path to base VM package\n"
msg += " 2) Name for Base VM: new name for Base VM\n"
sys.stderr.write(msg)
sys.exit(1)
import_filepath = args[1]
basevm_name = args[2]
if os.access(import_filepath, os.R_OK) == False:
sys.stderr("Cannot access the file at %s" % import_filepath)
sys.exit(1)
try:
request_import_basevm(settings.server_address, token,
urlparse(endpoint),
urlparse(glance_endpoint), import_filepath,
basevm_name)
sys.stdout.write("SUCCESS\n")
except CloudletClientError as e:
sys.stderr.write("Error: %s\n" % str(e))
elif args[0] == CMD_SYNTHESIS:
if len(args) != 3:
msg = "Error: synthesis cmd needs [overlay url] and [name of VM]\n"
sys.stderr.write(msg)
sys.exit(1)
overlay_url = str(args[1])
new_instance_name = str(args[2])
try:
ret = request_synthesis(settings.server_address,
token,
urlparse(endpoint),
key_name=None,
server_name=new_instance_name,
overlay_url=overlay_url)
pprint(ret)
except CloudletClientError as e:
sys.stderr.write("Error: %s\n" % str(e))
elif args[0] == CMD_HANDOFF:
if len(args) != 3:
msg = "Error: VM handoff needs [Instance UUID] []\n"
msg += " 1) Instance UUID: Absolute path to base VM package\n"
msg += " 2) Destination Credential : File path of a credential file for destination OpenStacknew\n"
sys.stderr.write(msg)
sys.exit(1)
instance_uuid = str(args[1])
handoff_dest_credential_file = str(args[2])
try:
# get token for the handoff destination
dest_cred = _parse_credential_file(handoff_dest_credential_file)
dest_account, dest_passwd, dest_tenant, dest_addr = dest_cred
dest_token, dest_endpoint, dest_glance_endpoint = \
get_token(dest_addr, dest_account, dest_passwd,
dest_tenant)
handoff_url = dest_endpoint
request_handoff(settings.server_address, token, urlparse(endpoint),
instance_uuid, handoff_url, dest_token)
except CloudletClientError as e:
sys.stderr.write(str(e))
sys.exit(1)
elif args[0] == CMD_HANDOFF_RECV:
if not len(args) == 3:
msg = "Need overlay_url and name of the instance"
raise CloudletClientError(msg)
overlay_url = str(args[1])
new_instance_name = str(args[2])
try:
_request_handoff_recv(settings.server_address,
token,
urlparse(endpoint),
server_name=new_instance_name,
overlay_url=overlay_url)
except CloudletClientError as e:
sys.stderr.write("Error: %s\n" % str(e))
elif args[0] == CMD_EXT_LIST:
filter_name = None
if len(args) == 2:
filter_name = args[1]
ext_info = get_extension(settings.server_address, token,
urlparse(endpoint), filter_name)
sys.stdout.write(json.dumps(ext_info, indent=2) + "\n")
else:
sys.stderr.write("No such command")
sys.exit(1)
return sources
def currentdir():
return os.path.dirname(__file__)
# configure, if not already done so
configname = os.path.join('include', 'config.h')
configname_in = os.path.join(currentdir(), 'src', 'include', 'config.h.in')
# run cmake if appropriate
if not os.path.exists(configname) or os.path.getmtime(
configname) < os.path.getmtime(configname_in):
if os.system('cmake %s' % currentdir()) or not os.path.exists(configname):
sys.stderr('Configuring with cmake failed\n')
sys.exit(1)
# inspect config.h, to find libraries to link to
def hasconfig(filename, symbol):
f = open(filename, 'r')
define = '#define HAVE_%s\n' % symbol
for line in f:
if line == define:
f.close()
return True
f.close()
return False
# calculate the window-sum for each element and associate the result with the rank of the element
ranks_with_window = partial_elements.map(
elements_summer(m, l, partition_weights)).flatMap(lambda x: x)
# output the result in the form: rank, window-sum
ranks_with_window = ranks_with_window.filter(lambda x: x[0] < n).map(
lambda x: str(x[0]) + ' ' + str(x[1]))
return ranks_with_window
def main(path_to_input, window_size, path_to_output, number_of_partitions):
spark.conf.set("spark.sql.shuffle.partitions", number_of_partitions)
spark.conf.set("spark.default.parallelism", number_of_partitions)
data = sc.textFile(path_to_input)
ranks_with_window = calculate_window_sum(data, window_size,
number_of_partitions)
ranks_with_window.saveAsTextFile(path_to_output)
if __name__ == '__main__':
if len(sys.argv) != 5:
sys.stderr("Incorrect number of arguments")
path_to_input = sys.argv[1]
window_size = int(sys.argv[2])
path_to_output = sys.argv[3]
number_of_partitions = int(sys.argv[4])
main(path_to_input, window_size, path_to_output, number_of_partitions)
def analyze(self, verbose=None, **kwargs):
sys.stderr('khf.analyze method not available')
def color_sketches_net(height,
width,
iterations,
batch_size,
content_weight,
tv_weight,
learning_rate,
generator_network='unet',
use_adversarial_net=False,
use_hint=False,
adv_net_weight=1.0,
weight_decay_lambda=1e-5,
sketch_reconstruct_weight=10.0 / 255.0,
print_iterations=None,
checkpoint_iterations=None,
save_dir="model/",
do_restore_and_generate=False,
do_restore_and_train=False,
restore_from_noadv_to_adv=False,
preprocessed_folder=None,
preprocessed_file_path_list=None,
content_preprocessed_folder=None,
color_rebalancing_folder=None,
from_screenshot=False,
from_webcam=False,
test_img_dir=None,
test_img_hint=None,
input_mode='sketch',
output_mode='rgb',
use_cpu=False):
"""
Stylize images.
TODO: modify the description.
This function yields tuples (iteration, image); `iteration` is None
if this is the final image (the last iteration). Other tuples are yielded
every `checkpoint_iterations` iterations.
:param: lr_decay_steps: learning rate decays by lr_decay_rate after lr_decay steps.
Default per https://arxiv.org/abs/1603.03417
:param: min_lr: The minimum learning rate. Default per https://arxiv.org/abs/1603.03417
:param: lr_decay_rate: learning rate decays by lr_decay_rate after lr_decay steps.
Default per https://arxiv.org/abs/1603.03417
:param: use_semantic_masks: If it is true, the input to the generator network will be the semantic masks instead
of the content image. The content image will serve as ground truth for loss (I haven't decided whether to use content
or style loss).
:rtype: iterator[tuple[int|None,image]]
"""
# Before training, make sure everything is set correctly.
if use_hint:
assert test_img_hint is not None
height, width = get_compatible_shape(height, width)
input_shape = (1, height, width, 3)
print(
'The input shape is: %s. Input mode is: %s. Output mode is: %s. Using %s generator network'
% (str(input_shape), input_mode, output_mode, generator_network))
content_img_preprocessed = None
sketches_preprocessed = None
prev_content_preprocessed_file_i = 0
# Define tensorflow placeholders and variables.
with tf.Graph().as_default():
input_images = tf.placeholder(
tf.float32,
shape=[
batch_size, input_shape[1], input_shape[2],
1 if generator_network != 'lnet' else 3
],
name='input_sketches' if input_mode == 'sketch' else 'input_bw')
if use_hint:
input_hint = tf.placeholder(
tf.float32,
shape=[batch_size, input_shape[1], input_shape[2], 3],
name='input_hint')
input_concatenated = tf.concat(3, (input_images, input_hint))
if generator_network == 'unet_color':
assert input_mode == 'sketch' or (input_mode == 'raw_sketch'
and do_restore_and_generate)
color_output = unet_color_util.net(input_concatenated)
sketch_output = lnet_util.net(
(color_output - 128) / 128
) * 255 # This is the reconstructed sketch from the color output.
elif generator_network == 'lnet':
assert input_mode == 'color' and not use_adversarial_net and not use_hint
# This step is not necessary but kept to be in sync with chainer repo.
input_concatenated = (input_concatenated - 128) / 128
color_output = lnet_util.net(input_concatenated,
trainable=True) * 255
elif generator_network == 'backprop':
assert input_mode == 'sketch'
color_output = tf.get_variable(
'backprop_input_var',
shape=[batch_size, input_shape[1], input_shape[2], 3],
initializer=tf.random_normal_initializer(
mean=128, stddev=10.0)) + 0 * input_images
sketch_output = lnet_util.net(
(color_output - 128) / 128
) * 255 # This is the reconstructed sketch from the color output.
else:
# TODO: change the error message.
raise AssertionError(
"Please input a valid generator network name. Possible options are: TODO. Got: %s"
% (generator_network))
else:
if generator_network == 'unet_color':
assert input_mode == 'sketch' or (input_mode == 'raw_sketch'
and do_restore_and_generate)
color_output = unet_color_util.net(input_images)
sketch_output = lnet_util.net(
(color_output - 128) / 128
) * 255 # This is the reconstructed sketch from the color output.
elif generator_network == 'lnet':
assert input_mode == 'color' and not use_adversarial_net and not use_hint
# This step is not necessary but kept to be in sync with chainer repo.
input_images = (input_images - 128) / 128
color_output = lnet_util.net(input_images,
trainable=True) * 255
elif generator_network == 'backprop':
assert input_mode == 'sketch'
color_output = tf.get_variable(
'backprop_input_var',
shape=[batch_size, input_shape[1], input_shape[2], 3],
initializer=tf.random_normal_initializer(
)) + 0 * input_images
sketch_output = lnet_util.net(
(color_output - 128) / 128
) * 255 # This is the reconstructed sketch from the color output.
else:
raise AssertionError(
"Please input a valid generator network name. Possible options are: TODO. Got: %s"
% (generator_network))
generator_all_var = unet_util.get_net_all_variables()
sketch_reconstruct_all_var = lnet_util.get_net_all_variables()
if not do_restore_and_generate:
assert preprocessed_folder is not None and preprocessed_file_path_list is not None and \
preprocessed_folder[-1] == '/'
learning_rate_init = tf.constant(learning_rate)
learning_rate_var = tf.get_variable(name='learning_rate_var',
trainable=False,
initializer=learning_rate_init)
color_expected_output = tf.placeholder(
tf.float32,
shape=[
batch_size, input_shape[1], input_shape[2],
3 if generator_network != 'lnet' else 1
],
name='color_expected_output')
# Use the mean difference loss. Used to use tf.nn.l2_loss. Don't know how big of a difference that makes.
# color_loss_non_adv =tf.nn.l2_loss(color_output - color_expected_output) / batch_size
color_loss_non_adv = tf.reduce_mean(
tf.abs(color_output - color_expected_output))
weight_decay_loss_non_adv = conv_util.weight_decay_loss(
scope='unet') * weight_decay_lambda
# This is only for unet_color, not for training the lnet,
sketch_expected_output = lnet_util.net(
(color_expected_output - 128) / 128, reuse=True) * 255
sketch_reconstruct_loss_non_adv = tf.reduce_mean(
tf.abs(sketch_output -
sketch_expected_output)) * sketch_reconstruct_weight
generator_loss_non_adv = color_loss_non_adv + weight_decay_loss_non_adv + sketch_reconstruct_loss_non_adv
# tv_loss = tv_weight * total_variation(image)
if use_adversarial_net:
adv_net_input = tf.placeholder(
tf.float32,
shape=[batch_size, input_shape[1], input_shape[2], 3],
name='adv_net_input')
adv_net_prediction_image_input = adv_net_util.net(
adv_net_input)
adv_net_prediction_generator_input = adv_net_util.net(
color_output, reuse=True)
adv_net_all_var = adv_net_util.get_net_all_variables()
weight_decay_loss_adv = conv_util.weight_decay_loss(
scope='adv_net') * weight_decay_lambda
logits_from_i = adv_net_prediction_image_input
logits_from_g = adv_net_prediction_generator_input
# One represent labeling the image as coming from real image. Zero represent labeling it as generated.
adv_loss_from_i = tf.reduce_mean(
tf.nn.sparse_softmax_cross_entropy_with_logits(
logits_from_i, tf.ones(
[batch_size], dtype=tf.int64))) * adv_net_weight
adv_loss_from_g = tf.reduce_mean(
tf.nn.sparse_softmax_cross_entropy_with_logits(
logits_from_g, tf.zeros(
[batch_size], dtype=tf.int64))) * adv_net_weight
adv_loss = adv_loss_from_i + adv_loss_from_g + weight_decay_loss_adv
generator_loss_through_adv = tf.reduce_mean(
tf.nn.sparse_softmax_cross_entropy_with_logits(
logits_from_g, tf.ones(
[batch_size], dtype=tf.int64))) * adv_net_weight
# Beta1 = 0.5 according to dcgan paper
adv_train_step = tf.train.AdamOptimizer(
learning_rate_var, beta1=0.5,
beta2=0.999).minimize(adv_loss, var_list=adv_net_all_var)
# adv_train_step_i = tf.train.AdamOptimizer(learning_rate_var, beta1=0.5,
# beta2=0.999).minimize(adv_loss_from_i, var_list=adv_net_all_var)
# adv_train_step_g = tf.train.AdamOptimizer(learning_rate_var, beta1=0.5,
# beta2=0.999).minimize(adv_loss_from_g, var_list=adv_net_all_var)
generator_train_step_through_adv = tf.train.AdamOptimizer(
learning_rate_var, beta1=0.5,
beta2=0.999).minimize(generator_loss_through_adv,
var_list=generator_all_var)
generator_train_step = tf.train.AdamOptimizer(
learning_rate_var, beta1=0.9,
beta2=0.999).minimize(generator_loss_non_adv)
with tf.control_dependencies(
[generator_train_step_through_adv, generator_train_step]):
generator_both_train = tf.no_op(
name='generator_both_train')
adv_loss_real_sum = scalar_summary("adv_loss_real",
adv_loss_from_i)
adv_loss_fake_sum = scalar_summary("adv_loss_fake",
adv_loss_from_g)
adv_loss_weight_decay_sum = scalar_summary(
"adv_loss_weight_decay", weight_decay_loss_adv)
generator_loss_through_adv_sum = scalar_summary(
"g_loss_through_adv", generator_loss_through_adv)
adv_loss_sum = scalar_summary("adv_loss", adv_loss)
generator_loss_l2_sum = scalar_summary(
"generator_loss_non_adv", generator_loss_non_adv)
generator_loss_weight_decay_sum = scalar_summary(
"generator_loss_weight_decay", weight_decay_loss_non_adv)
sketch_reconstruct_loss_non_adv_sum = scalar_summary(
"sketch_reconstruct_loss_non_adv",
sketch_reconstruct_loss_non_adv)
g_sum = merge_summary([
generator_loss_through_adv_sum, generator_loss_l2_sum,
generator_loss_weight_decay_sum,
sketch_reconstruct_loss_non_adv_sum
])
adv_sum = merge_summary([
adv_loss_fake_sum, adv_loss_real_sum,
adv_loss_weight_decay_sum, adv_loss_sum
])
else:
# optimizer setup
# Training using adam optimizer. Setting comes from https://arxiv.org/abs/1610.07629.
generator_train_step = tf.train.AdamOptimizer(
learning_rate_var, beta1=0.9,
beta2=0.999).minimize(generator_loss_non_adv)
generator_loss_l2_sum = scalar_summary("color_loss_non_adv",
generator_loss_non_adv)
generator_loss_weight_decay_sum = scalar_summary(
"generator_loss_weight_decay", weight_decay_loss_non_adv)
sketch_reconstruct_loss_non_adv_sum = scalar_summary(
"sketch_reconstruct_loss_non_adv",
sketch_reconstruct_loss_non_adv)
g_sum = merge_summary([
generator_loss_l2_sum, generator_loss_weight_decay_sum,
sketch_reconstruct_loss_non_adv_sum
])
def print_progress(i,
feed_dict,
adv_feed_dict,
start_time,
total_iterations,
last=False):
stderr.write('Iteration %d/%d\n' % (i + 1, iterations))
if last or (print_iterations and i % print_iterations == 0):
current_time = time.time()
if i > 0:
seconds_passed = current_time - start_time
seconds_remaining = float(total_iterations -
i) / i * seconds_passed
m, s = divmod(seconds_remaining, 60)
h, m = divmod(m, 60)
stderr.write(
'Estimated time remaining: "%d:%02d:%02d"' %
(h, m, s))
stderr.write('Learning rate %f\n' %
(learning_rate_var.eval()))
# TODO: change this
stderr.write(
' generator l2 loss: %g\n' %
generator_loss_non_adv.eval(feed_dict=feed_dict))
stderr.write(' sketch loss: %g\n' %
sketch_reconstruct_loss_non_adv.eval(
feed_dict=feed_dict))
if not generator_network == 'backprop':
stderr.write(' w decay gen loss: %g\n' %
weight_decay_loss_non_adv.eval(
feed_dict=feed_dict))
# if generator_network == 'unet_both' or generator_network == 'colorful_img_both':
# stderr.write(' bw loss: %g\n' % color_loss_non_adv.eval(feed_dict=feed_dict))
# stderr.write(' ab loss: %g\n' % ab_loss_non_adv.eval(feed_dict=feed_dict))
if use_adversarial_net:
stderr.write(
' adv_from_i loss: %g\n' %
adv_loss_from_i.eval(feed_dict=adv_feed_dict))
stderr.write(
' adv_from_g loss: %g\n' %
adv_loss_from_g.eval(feed_dict=adv_feed_dict))
stderr.write('generator adv loss: %g\n' %
generator_loss_through_adv.eval(
feed_dict=adv_feed_dict))
stderr.write(' w decay adv loss: %g\n' %
weight_decay_loss_adv.eval(
feed_dict=adv_feed_dict))
# Optimization
# It used to track and record only the best one with lowest loss. This is no longer necessary and I think
# just recording the one generated at each round will make it easier to debug.
best_image = None
start_time = time.time()
if restore_from_noadv_to_adv and use_adversarial_net:
saver = tf.train.Saver(generator_all_var + [learning_rate_var])
else:
saver = tf.train.Saver()
if use_cpu:
config = tf.ConfigProto(device_count={'GPU': 0})
else:
config = None
with tf.Session(config=config) as sess:
if do_restore_and_generate:
assert batch_size == 1
ckpt = tf.train.get_checkpoint_state(save_dir)
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_checkpoint_path)
else:
stderr("No checkpoint found. Exiting program")
return
if from_screenshot:
# This is the x and y offset, the coordinate where we start capturing screen shot.
kScreenX = 300
kScreenY = 300
elif from_webcam:
cap = cv2.VideoCapture(0)
# Set width and height.
ret = cap.set(3, 1280)
ret = cap.set(4, 960)
ret, frame = cap.read()
print('The dimension of this camera is : %d x %d' %
(frame.shape[1], frame.shape[0]))
else:
assert test_img_dir is not None
iterator = 0
while from_screenshot or from_webcam or (iterator == 0):
if from_screenshot:
pass
# w = gtk.gdk.get_default_root_window()
# sz = w.get_size()
# print "The size of the window is %d x %d" % sz
# pb = gtk.gdk.Pixbuf(gtk.gdk.COLORSPACE_RGB, False, 8, input_shape[1], input_shape[2])
# pb = pb.get_from_drawable(w, w.get_colormap(), kScreenX, kScreenY, 0, 0, input_shape[1],
# input_shape[2])
# content_image = pb.pixel_array
elif from_webcam:
ret, frame = cap.read()
content_image = scipy.misc.imresize(
frame, (input_shape[1], input_shape[2]))
else:
content_image = imread(
test_img_dir, (input_shape[1], input_shape[2]))
content_image = np.array([content_image])
if input_mode == 'sketch':
color_expected_output = tf.placeholder(
tf.float32,
shape=[
batch_size, input_shape[1], input_shape[2],
3 if generator_network != 'lnet' else 1
],
name='color_expected_output')
sketch_expected_output = lnet_util.net(
(color_expected_output - 128) / 128,
reuse=True) * 255
content_image_yuv = cv2.cvtColor(
np.asarray(content_image[0, ...], dtype=np.uint8),
cv2.COLOR_RGB2YUV)
image_sketches = sketch_expected_output.eval(
feed_dict={
color_expected_output:
np.array([content_image_yuv])
})
# image_sketches = sketches_util.image_to_sketch(content_image)
# image_sketches = np.expand_dims(image_sketches, axis=3)
elif input_mode == 'bw':
content_image_lab = colorful_img_network_util.rgb_to_lab(
content_image)
image_sketches = content_image_lab[..., 0:1]
# image_sketches = np.expand_dims(rgb2gray(content_image), axis=3)
elif input_mode == 'color':
image_sketches = np.zeros(content_image.shape)
# image_sketches = np.expand_dims(rgb2gray(content_image), axis=3)
elif input_mode == 'raw_sketch':
image_sketches = rgb2gray(content_image, keep_dim=True)
else:
raise AssertionError('Input mode error.')
# Do some processing...
image_sketches, content_image = sketches_util.generate_training_batch(
image_sketches, content_image, train=False)
# Now generate an image using the style_blend_weights given.
if input_mode == 'color':
feed_dict = {input_images: content_image}
else:
feed_dict = {input_images: image_sketches[..., :1]}
if use_hint:
image_hint = hint_imread(
test_img_hint, (input_shape[1], input_shape[2]))
feed_dict[input_hint] = np.array([image_hint])
generated_bw = color_output.eval(feed_dict=feed_dict)
iterator += 1
if generator_network != 'lnet':
# Whenever using cv2.cvtColor, be careful not to use float values... It gives out wierd answers.
print(generated_bw[0, 0, 0:5, :])
print(content_image[0, 0, 0:5, :])
generated_image = np.array([
cv2.cvtColor(
np.asarray(generated_bw[0, ...],
dtype=np.uint8), cv2.COLOR_YUV2RGB)
])
# generated_image = image_sketches[...,:1]
else:
generated_image = generated_bw
yield (iterator, generated_image)
else:
# Initialize log writer
summary_writer = SummaryWriter("./logs", sess.graph)
# initialize pre-processsed numpy array
if content_preprocessed_folder is not None:
if not os.path.isfile(content_preprocessed_folder +
'record.txt'):
raise AssertionError(
'No preprocessed content images found in %s. To use this feature, first use some '
'other file to call read_resize_and_save_all_imgs_in_dir.'
% (content_preprocessed_folder))
content_preprocessed_record = sketches_util.read_preprocessed_sketches_npy_record(
content_preprocessed_folder)
if content_preprocessed_record[0][
3] != height or content_preprocessed_record[0][
4] != width:
raise AssertionError(
'The height and/or width of the preprocessed numpy files does not '
'match those of the current setting.')
# Read the first file
print('Reading preprocessed content images.')
content_img_preprocessed = np.load(
content_preprocessed_record[
prev_content_preprocessed_file_i][0])
sketches_preprocessed = np.load(
content_preprocessed_record[
prev_content_preprocessed_file_i][1])
# Do Training.
iter_start = 0
if do_restore_and_train:
ckpt = tf.train.get_checkpoint_state(save_dir)
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_checkpoint_path)
iter_start = get_global_step_from_save_dir(
ckpt.model_checkpoint_path)
else:
raise AssertionError(
"No checkpoint found. Exiting program")
return
if restore_from_noadv_to_adv and use_adversarial_net:
# Simply running this doesn;t seem to work.
# sess.run(tf.initialize_variables(adv_net_all_var))
# Get all variables except the generator net and the learning rate
if '0.12.0' in tf.__version__:
all_vars = tf.get_collection(
tf.GraphKeys.GLOBAL_VARIABLES)
else:
all_vars = tf.get_collection(
tf.GraphKeys.VARIABLES)
var_not_saved = [
item for item in all_vars
if item not in (generator_all_var +
[learning_rate_var])
]
sess.run(tf.initialize_variables(var_not_saved))
# Now change the saver back to normal
saver = tf.train.Saver()
raise NotImplementedError
else:
# # In the past I ran this. Now I have lnet which is a pretrained network.
# sess.run(tf.initialize_all_variables())
saver = tf.train.Saver(sketch_reconstruct_all_var)
ckpt = tf.train.get_checkpoint_state(
'model/chainer_converted/')
saver.restore(sess, ckpt.model_checkpoint_path)
# Get variables not in lnet and initialize them
# Get all variables except the generator net and the learning rate
if '0.12.0' in tf.__version__:
all_vars = tf.get_collection(
tf.GraphKeys.GLOBAL_VARIABLES)
else:
all_vars = tf.get_collection(tf.GraphKeys.VARIABLES)
var_not_saved = [
item for item in all_vars
if item not in sketch_reconstruct_all_var
]
sess.run(tf.initialize_variables(var_not_saved))
# Now change the saver back to normal
saver = tf.train.Saver()
# Get path to all content images.
image_subpaths = read_preprocessed_file_path_list(
preprocessed_file_path_list)
# Ignore the ones at the end.
if batch_size != 1 and len(image_subpaths) % batch_size != 0:
image_subpaths = image_subpaths[:-(len(image_subpaths) %
batch_size)]
print('The size of training dataset is %d images.' %
len(image_subpaths))
preprocessed_colored_folder = preprocessed_folder + 'color/'
preprocessed_sketch_folder = preprocessed_folder + 'line/'
content_dirs = map(lambda p: preprocessed_colored_folder + p,
image_subpaths)
sketch_dirs = map(lambda p: preprocessed_sketch_folder + p,
image_subpaths)
# # Test training GAN differently***
# generators_turn = True
# # END TEST***
current_lr = learning_rate_var.eval()
if abs(current_lr - learning_rate) > 0.00000001:
print(
"Given learning rate is different from the learning rate stored. Changing lr %f -> %f"
% (current_lr, learning_rate))
sess.run(learning_rate_var.assign(learning_rate))
for i in range(iter_start, iterations):
if content_preprocessed_folder is not None:
current_content_preprocessed_file_i, index_within_preprocessed = \
sketches_util.find_corresponding_sketches_npy_from_record(
content_preprocessed_record, i * batch_size, batch_size)
if prev_content_preprocessed_file_i != current_content_preprocessed_file_i:
prev_content_preprocessed_file_i = current_content_preprocessed_file_i
content_img_preprocessed = np.load(
content_preprocessed_record[
current_content_preprocessed_file_i][0])
sketches_preprocessed = np.load(
content_preprocessed_record[
current_content_preprocessed_file_i][1])
content_pre_list = content_img_preprocessed[
index_within_preprocessed:
index_within_preprocessed + batch_size,
...].astype(np.float32)
if input_mode == 'sketch':
image_sketches = sketches_preprocessed[
index_within_preprocessed:
index_within_preprocessed + batch_size,
...].astype(np.float32)
image_sketches = np.expand_dims(image_sketches,
axis=3)
elif input_mode == 'bw':
content_image_lab = colorful_img_network_util.rgb_to_lab(
content_pre_list)
image_sketches = content_image_lab[..., 0:1]
# image_sketches = np.expand_dims(rgb2gray(content_pre_list), axis=3)
elif input_mode == 'color':
image_sketches = content_pre_list
elif input_mode == 'raw_sketch':
raise AssertionError(
'Input mode raw_sketch should not be trained.')
else:
raise AssertionError('Input mode error.')
else:
current_content_dirs = get_batch_paths(
content_dirs, i * batch_size, batch_size)
current_sketch_dirs = get_batch_paths(
sketch_dirs, i * batch_size, batch_size)
content_pre_list = read_and_resize_batch_images(
current_content_dirs, None, None)
image_sketches = read_and_resize_bw_mask_images(
current_sketch_dirs, None, None,
len(current_sketch_dirs), 1)
# if input_mode == 'sketch':
# image_sketches = sketches_util.image_to_sketch(content_pre_list)
# image_sketches = np.expand_dims(image_sketches, axis=3)
# elif input_mode == 'bw':
# content_image_lab = colorful_img_network_util.rgb_to_lab(content_pre_list)
# image_sketches = content_image_lab[...,0:1]
# # image_sketches = np.expand_dims(rgb2gray(content_pre_list), axis=3)
# else:
# raise AssertionError('Input mode error.')
# Do some processing...
image_sketches, content_pre_list = sketches_util.generate_training_batch(
image_sketches, content_pre_list, train=True)
if generator_network == 'lnet':
feed_dict = {
color_expected_output: image_sketches[..., :1]
}
else:
feed_dict = {color_expected_output: content_pre_list}
if use_hint:
# image_hint = sketches_util.generate_hint_from_image(content_pre_list)
# feed_dict[input_hint] = image_hint
image_hint = image_sketches[..., 1:]
feed_dict[input_hint] = image_hint
image_sketches = image_sketches[..., :1]
if input_mode == 'color':
feed_dict[input_images] = content_pre_list
else:
feed_dict[input_images] = image_sketches
last_step = (i == iterations - 1)
if use_adversarial_net:
# adv_feed_dict = {input_images:image_sketches, adv_net_input: content_pre_list}
# if use_hint:
# adv_feed_dict[input_hint] = image_hint
adv_feed_dict = copy.copy(feed_dict)
adv_feed_dict[adv_net_input] = content_pre_list
# TEST printing before training
print_progress(i,
feed_dict=feed_dict,
adv_feed_dict=adv_feed_dict,
start_time=start_time,
total_iterations=iterations,
last=last_step)
# Update D network
_, summary_str = sess.run([adv_train_step, adv_sum],
feed_dict=adv_feed_dict)
summary_writer.add_summary(summary_str, i)
# Update G network
_, summary_str = sess.run(
[generator_both_train, g_sum],
feed_dict=adv_feed_dict)
summary_writer.add_summary(summary_str, i)
else:
adv_feed_dict = None
print_progress(i,
feed_dict=feed_dict,
adv_feed_dict=adv_feed_dict,
start_time=start_time,
total_iterations=iterations,
last=last_step)
_, summary_str = sess.run(
[generator_train_step, g_sum], feed_dict=feed_dict)
summary_writer.add_summary(summary_str, i)
# TEST printing after training
print_progress(i,
feed_dict=feed_dict,
adv_feed_dict=adv_feed_dict,
start_time=start_time,
total_iterations=iterations,
last=last_step)
if (checkpoint_iterations
and i % checkpoint_iterations == 0) or last_step:
saver.save(sess,
save_dir + 'model.ckpt',
global_step=i)
print('Checkpoint saved.')
if test_img_dir is not None:
test_image = imread(test_img_dir)
test_image_shape = test_image.shape
# The for loop will run once and terminate. Can't use return and yield in the same function so this is a hacky way to do it.
# Set use_cpu = true to save graphical memory
for _, generated_image in color_sketches_net(
test_image_shape[0],
test_image_shape[1],
iterations,
1,
content_weight,
tv_weight,
learning_rate,
generator_network=generator_network,
use_adversarial_net=
False, # use_adversarial_net=use_adversarial_net,
use_hint=use_hint,
save_dir=save_dir,
do_restore_and_generate=True,
do_restore_and_train=False,
from_screenshot=False,
from_webcam=False,
test_img_dir=test_img_dir,
test_img_hint=test_img_hint,
input_mode=input_mode,
output_mode=output_mode,
use_cpu=use_cpu):
pass
best_image = generated_image
# Because we now have batch, choose the first one in the batch as our sample image.
yield ((None if last_step else i),
None if test_img_dir is None else best_image)
postsurvey_filename = sys.argv[4]
postsurvey2_filename = sys.argv[5]
###
#Start with only files from the Aug pilot (other files will not match
#in columns because of different survey questions)
######
#make a list of the filenames in the folder
file_language_tuples = []
for current_root, dirnames_d, filenames_d in os.walk(folderpath):
csv_filenames = fnmatch.filter(filenames_d, "*.csv")
if current_root == folderpath:
if len(csv_filenames) > 0:
print >> sys.stderr(""), \
"ERROR: need at least one level of nesting " \
+ "in data folder '" + folderpath + "'"
sys.exit()
continue
full_pathnames = [os.path.join(current_root, f) \
for f in csv_filenames]
subfolder = folderpath.join(current_root.split(folderpath)[1:])
first_subfolder = None
for folder in subfolder.split('/'):
if len(folder) > 0:
first_subfolder = folder
break
curr_tuples = [(f, first_subfolder) for f in full_pathnames]
file_language_tuples += curr_tuples
import sys
WIDTH = 80
URBAN_URL = 'http://api.urbandictionary.com/v0/define?term=%s'
if len(sys.argv) < 2:
sys.stderr.write("usage: urban <term>\n")
sys.exit(1)
term = '+'.join(sys.argv[1:])
try:
resp = urllib2.urlopen(URBAN_URL % (term,))
data = json.loads(resp.read())
except Exception:
sys.stderr("error contacting urban dictionary.\n")
sys.exit(1)
if data['result_type'] != 'exact':
sys.stderr("no definitions.\n")
sys.exit(1)
definitions = data['list']
definitions.sort(key=lambda x: -1.0 * x['thumbs_up']/x['thumbs_down'])
definitions = definitions[:3]
def render_def(n, d):
res = ''
line = "%d)" % (n + 1,)
for word in d.split():
if len(line) + 1 + len(word) > WIDTH:
from src import BayesNet
import sys
if __name__ == '__main__':
if len(sys.argv) != 4:
sys.stderr('trainFile testFile learningMethod')
sys.exit()
trainFilename, testFilename, method = sys.argv[1:]
model = BayesNet.BayesNet()
model.loadTrain(trainFilename)
model.loadTest(testFilename)
if method == 'n':
model.buildNaiveBayes()
if method == 't':
model.buildTAN()
model.printResults()
def _sigHandler(self, signum, frame):
"signal handler to stop logging and terminate process"
self.finishUp()
sys.stderr("Warning: profiler exiting on signal\n")
sys.exit(1)
def eprint(msg):
sys.stderr(msg)
argparser = ArgumentParser(usage=usage)
argparser.add_argument('-j',
'--json',
type=str,
default='-',
help='input json file')
args = argparser.parse_args()
return args
if __name__ == "__main__":
argresult = parser()
filename = argresult.json
if filename is None:
filename = "-"
if filename == "-":
dat = sys.stdin.read()
else:
if not os.path.exists(filename):
sys.stderr("No such file [%s]" % filename)
sys.exit(1)
with open(argresult.json, "r") as f:
dat = f.read()
try:
print(digest(dat))
except Exception as e:
print(e)
print("Invalid input", file=sys.stderr)
def getRttDataAthena(configFile=None):
print("Find RTT differentiel for each traceroute")
if configFile is None:
configFile = "conf/getRttDataAthena.conf"
if os.path.exists(configFile):
expParam = json.load(open(configFile, "r"), object_hook=json_util.object_hook)
else:
sys.stderr("No config file found!\nPlease copy conf/%s.default to conf/%s\n" % (configFile, configFile))
pool = Pool(expParam["nbProcesses"], initializer=rttAnalysis.processInit) # , maxtasksperchild=binMult)
if not expParam["prefixes"] is None:
expParam["prefixes"] = re.compile(expParam["prefixes"])
client = pymongo.MongoClient("mongodb-iijlab")
db = client.atlas
detectionExperiments = db.rttExperiments
alarmsCollection = db.rttChanges
# expId = detectionExperiments.insert_one(expParam).inserted_id
sampleMediandiff = {}
ip2asn = {}
gi = pygeoip.GeoIP("../lib/GeoIPASNum.dat")
start = int(calendar.timegm(expParam["start"].timetuple()))
end = int(calendar.timegm(expParam["end"].timetuple()))
rawDiffRtt = defaultdict(list)
rawNbProbes = defaultdict(list)
rawDates = defaultdict(list)
for currDate in range(start, end, expParam["timeWindow"]):
sys.stderr.write("Rtt analysis %s" % datetime.datetime.utcfromtimestamp(currDate))
tsS = time.time()
diffRtt = defaultdict(dict)
nbRow = 0
currDatetime= datetime.datetime.utcfromtimestamp(int(currDate))
endDatetime= datetime.datetime.utcfromtimestamp(int(currDate+int(expParam["timeWindow"])))
msmIds= expParam["msmIds"]
msmType= expParam["msmType"]
# Prepare the SQL request for the given period
sqlRequest = generateSQLAthenaRequest(currDatetime, endDatetime, currDate, currDate+expParam["timeWindow"], msmIds)
print ("The created SQL request is : \n %s"%sqlRequest)
# Find Results
result = get_traceroutes_by_sql_request(sqlRequest)
if len(result)>0 :
IRtt, row= computeRtt_athena(result)
diffRtt, nbRow = mergeRttResults_athena(IRtt, row)
for k, v in diffRtt.iteritems():
rawDiffRtt[k].extend(v["rtt"])
rawDates[k].extend([currDatetime] * len(v["rtt"]))
timeSpent = (time.time() - tsS)
sys.stderr.write(", %s sec/bin, %s row/sec\r" % (timeSpent, float(nbRow) / timeSpent))
pool.close()
pool.join()
return (rawDiffRtt, rawNbProbes, rawDates)
hangulcode = jamotosyllable(choseong, jungseong, jongseong)
return hangulcode
# start main procedure
data_file_name = "Unihan.txt"
if len(sys.argv) == 2:
data_file_name = sys.argv[1]
try:
data_file = open(data_file_name, 'r')
except:
sys.stderr("Cant open file: %s\n" % data_file_name)
help()
sys.exit(1)
gather_copyright = 0
table = {}
for line in data_file.readlines():
# check for comment, jump over comments
if line[0] == '#':
if gather_copyright == 0:
if string.find(line, "Format information:") != -1:
gather_copyright = 1
continue
copyright += ' * ' + string.strip(line[1:]) + '\n'
continue
else:
def color_sketches_net(height, width, iterations, batch_size, content_weight, tv_weight,
learning_rate,
lr_decay_steps=50000,
min_lr=0.00001, lr_decay_rate=0.7, print_iterations=None,
checkpoint_iterations=None, save_dir="model/", do_restore_and_generate=False,
do_restore_and_train=False, real_folder=None, fake_folder=None):
"""
Stylize images.
This function yields tuples (iteration, image); `iteration` is None
if this is the final image (the last iteration). Other tuples are yielded
every `checkpoint_iterations` iterations.
:param: lr_decay_steps: learning rate decays by lr_decay_rate after lr_decay steps.
Default per https://arxiv.org/abs/1603.03417
:param: min_lr: The minimum learning rate. Default per https://arxiv.org/abs/1603.03417
:param: lr_decay_rate: learning rate decays by lr_decay_rate after lr_decay steps.
Default per https://arxiv.org/abs/1603.03417
:param: use_semantic_masks: If it is true, the input to the generator network will be the semantic masks instead
of the content image. The content image will serve as ground truth for loss (I haven't decided whether to use content
or style loss).
:rtype: iterator[tuple[int|None,image]]
"""
# Before training, make sure everything is set correctly.
input_shape = (1, height, width, 3)
print('The input shape is: %s' % (str(input_shape)))
# Define tensorflow placeholders and variables.
with tf.Graph().as_default():
learning_rate_decayed_init = tf.constant(learning_rate)
learning_rate_decayed = tf.get_variable(name='learning_rate_decayed', trainable=False,
initializer=learning_rate_decayed_init)
adv_net_input_real = tf.placeholder(tf.float32,
shape=[batch_size, input_shape[1], input_shape[2], 3], name='adv_net_input_real')
adv_net_prediction_image_input = adv_net_util.net(adv_net_input_real)
adv_net_input_fake = tf.placeholder(tf.float32,
shape=[batch_size, input_shape[1], input_shape[2], 3], name='adv_net_input_fake')
adv_net_prediction_generator_input = adv_net_util.net(adv_net_input_fake, reuse=True)
adv_net_all_var = adv_net_util.get_net_all_variables()
logits_from_i = adv_net_prediction_image_input
logits_from_g = adv_net_prediction_generator_input
# One represent labeling the image as coming from real image. Zero represent labeling it as generated.
adv_loss_from_i = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(logits_from_i, tf.ones([batch_size], dtype=tf.int64)))
adv_loss_from_g = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(logits_from_g, tf.zeros([batch_size], dtype=tf.int64)))
adv_loss = adv_loss_from_i + adv_loss_from_g
adv_train_step = tf.train.AdamOptimizer(learning_rate_decayed, beta1=0.5,
beta2=0.999).minimize(adv_loss, var_list=adv_net_all_var)
adv_train_step_i = tf.train.AdamOptimizer(learning_rate_decayed, beta1=0.5,
beta2=0.999).minimize(adv_loss_from_i, var_list=adv_net_all_var)
adv_train_step_g = tf.train.AdamOptimizer(learning_rate_decayed, beta1=0.5,
beta2=0.999).minimize(adv_loss_from_g, var_list=adv_net_all_var)
# with tf.control_dependencies([generator_train_step_through_adv, adv_train_step]):
with tf.control_dependencies([adv_train_step_i, adv_train_step_g]):
adv_generator_both_train = tf.no_op(name='adv_generator_both_train')
def print_progress(i, adv_feed_dict, last=False):
stderr.write(
'Iteration %d/%d\n' % (i + 1, iterations))
if last or (print_iterations and i % print_iterations == 0):
stderr.write('Learning rate %f\n' % (learning_rate_decayed.eval()))
stderr.write(' adv_from_i loss: %g\n' % adv_loss_from_i.eval(feed_dict=adv_feed_dict))
stderr.write(' adv_from_g loss: %g\n' % adv_loss_from_g.eval(feed_dict=adv_feed_dict))
# Optimization
# It used to track and record only the best one with lowest loss. This is no longer necessary and I think
# just recording the one generated at each round will make it easier to debug.
best_real_image = None
best_fake_image = None
best_real_loss = 100.0
best_fake_loss = 100.0
saver = tf.train.Saver()
with tf.Session() as sess:
with open(save_dir + 'adv_loss.tsv', 'w') as loss_record_file:
loss_record_file.write('i\tcurrent_generator_l2_loss\tcurrent_adv_loss_i\tcurrent_adv_loss_g\tcurrent_gen_loss_through_adv\n')
# Do Training.
iter_start = 0
if do_restore_and_train:
ckpt = tf.train.get_checkpoint_state(save_dir)
if ckpt and ckpt.model_checkpoint_path:
saver.restore(sess, ckpt.model_checkpoint_path)
iter_start = get_global_step_from_save_dir(ckpt.model_checkpoint_path)
else:
stderr("No checkpoint found. Exiting program")
return
else:
sess.run(tf.initialize_all_variables())
# Get path to all content images.
real_dirs = get_all_image_paths_in_dir(real_folder)
# Ignore the ones at the end.
if batch_size != 1 and len(real_dirs) % batch_size != 0:
real_dirs = real_dirs[:-(len(real_dirs) % batch_size)]
print('The size of real dataset is %d images.' % len(real_dirs))
fake_dirs = get_all_image_paths_in_dir(fake_folder)
# Ignore the ones at the end.
if batch_size != 1 and len(fake_dirs) % batch_size != 0:
fake_dirs = fake_dirs[:-(len(fake_dirs) % batch_size)]
print('The size of fake dataset is %d images.' % len(fake_dirs))
# # Test training GAN differently***
# generators_turn = True
# # END TEST***
for i in range(iter_start, iterations):
# First decay the learning rate if we need to
if (i % lr_decay_steps == 0 and i!= iter_start):
current_lr = learning_rate_decayed.eval()
sess.run(learning_rate_decayed.assign(max(min_lr, current_lr * lr_decay_rate)))
current_content_dirs = get_batch_paths(real_dirs, i * batch_size, batch_size)
content_pre_list = read_and_resize_batch_images(current_content_dirs, input_shape[1],
input_shape[2])
current_fake_dirs = get_batch_paths(fake_dirs, i * batch_size, batch_size)
fake_pre_list = read_and_resize_batch_images(current_fake_dirs, input_shape[1],
input_shape[2])
last_step = (i == iterations - 1)
adv_feed_dict = {adv_net_input_real: content_pre_list, adv_net_input_fake: fake_pre_list}
# TEST printing before training
print_progress(i, adv_feed_dict=adv_feed_dict, last=last_step)
# if generators_turn:
# # generator_train_step.run(feed_dict=feed_dict)
# generator_train_step_through_adv.run(feed_dict=adv_feed_dict)
# adv_train_step.run(feed_dict=adv_feed_dict)
# generator_train_step_through_adv.run(feed_dict=adv_feed_dict)
# adv_train_step.run(feed_dict=adv_feed_dict)
adv_generator_both_train.run(feed_dict=adv_feed_dict)
# if i < 10000:
# generator_train_step.run(feed_dict=feed_dict)
print_progress(i, adv_feed_dict= adv_feed_dict, last=last_step)
# TODO:
if i%10==0:
with open(save_dir + 'adv_loss.tsv', 'a') as loss_record_file:
current_adv_loss_i = adv_loss_from_i.eval(feed_dict=adv_feed_dict)
current_adv_loss_g = adv_loss_from_g.eval(feed_dict=adv_feed_dict)
loss_record_file.write('%d\t%g\t%g\n' % (i, current_adv_loss_i, current_adv_loss_g))
if current_adv_loss_i < best_real_loss:
best_real_loss = current_adv_loss_i
best_real_image = content_pre_list
if current_adv_loss_g < best_fake_loss:
best_fake_loss = current_adv_loss_g
best_fake_image = fake_pre_list
if (checkpoint_iterations and i % checkpoint_iterations == 0) or last_step:
# saver.save(sess, save_dir + 'model.ckpt', global_step=i)
# Because we now have batch, choose the first one in the batch as our sample image.
yield (
(None if last_step else i),
best_real_image, best_fake_image
)
def distance_query_generator(filename):
"""
Creates the following dicts with the values of distances:
- query_intra_distances: values from the distances same chain same dom.
- query_inter_distances: values between different chains diff domains.
"""
# Creation of variables to work with new dicts
trans_dom_query = {}
query_inter_distances = {}
query_intra_distances = {}
file_id = (filename.split('/')[-1])[:-3]
if '.pdb' in filename:
try:
trans_dom_query = phobius_runner(filename[:-3] + 'fasta')
except:
sys.stderr('***It is recomendable add the fasta seq as \
a separated file in the current directory ***\n ')
fasta_fil = open('fasta_to_generate.fasta', 'w')
seq_fasta = get_seq_PDB_CIF(filename)
fasta_fil.write(seq_fasta)
fasta_fil.close()
trans_dom_query = phobius_runner('fasta_to_generate.fasta')
entity = PDBParser()
elif '.cif' in filename:
try:
trans_dom_query = phobius_runner(filename[:-3] + 'fasta')
except:
raise ValueError(
'To use .cif files introduce a fasta with the following name: '
+ filename[:-3] + 'fasta')
entity = MMCIFParser()
structure = entity.get_structure('X', filename)
model = structure[0]
for key, value in trans_dom_query.items():
logging.info('Chain processed: {}\n Transdom: {}'.format(key, value))
if '.pdb' in filename:
for chain in model:
chain1 = chain
else:
chain1 = model[key]
for val in value:
beg_helix1, end_helix1 = int(val[0]), int(val[1])
# ################INTRA DISTANCES ####################################
select_and_save_distances_query(beg_helix1, end_helix1, beg_helix1,
end_helix1, chain1, chain1,
query_intra_distances)
# ################INTER DISTANCES SAME CHAIN ##############################
for val2 in value:
if val == val2:
continue
beg_helix2, end_helix2 = int(val2[0]), int(val2[1])
select_and_save_distances_query(beg_helix1, end_helix1,
beg_helix2, end_helix2, chain1,
chain1, query_inter_distances)
# ################INTER DISTANCES BTWN CHAIN ########################
for key, value in trans_dom_query.items():
if '.pdb' in filename:
for chain in model:
chain2 = chain
else:
chain2 = model[key]
if chain1 == chain2:
continue
for val3 in value:
beg_helix3, end_helix3 = int(val3[0]), int(val3[1])
select_and_save_distances_query(beg_helix1, end_helix1,
beg_helix3, end_helix3,
chain1, chain2,
query_inter_distances)
return (query_intra_distances, query_inter_distances)
"""
from pymodbus.compat import IS_PYTHON3, PYTHON_VERSION
if IS_PYTHON3 and PYTHON_VERSION >= (3, 4):
import asyncio
import logging
# ----------------------------------------------------------------------- #
# Import the required asynchronous client
# ----------------------------------------------------------------------- #
from pymodbus.client.asynchronous.tcp import AsyncModbusTCPClient as ModbusClient
from pymodbus.client.asynchronous.udp import (AsyncModbusUDPClient as
ModbusClient)
from pymodbus.client.asynchronous import schedulers
else:
import sys
sys.stderr("This example needs to be run only on python 3.4 and above")
sys.exit(1)
from threading import Thread
import time
# --------------------------------------------------------------------------- #
# configure the client logging
# --------------------------------------------------------------------------- #
logging.basicConfig()
log = logging.getLogger()
log.setLevel(logging.DEBUG)
# --------------------------------------------------------------------------- #
# specify slave to query
# --------------------------------------------------------------------------- #
import sys
sys.path.append("./helpers/")
from producers import MyKafkaProducer
### main method that produces messages into Kafka topic ###
if __name__ == "__main__":
if len(sys.argv) != 4:
sys.stderr("Usage: main_produce.py <kafkaconfigfile> <schemafile> <s3configfile> \n")
sys.exit(-1)
kafka_configfile, schema_file, s3_configfile = sys.argv[1:4]
prod = MyKafkaProducer(kafka_configfile, schema_file, s3_configfile)
prod.produce_msgs()
def generate_scripts(args):
# supported languages
langId = {
'portuguese': 'pt',
'french': 'fr',
'serbo-croatian': 'sh',
'polish': 'pl',
'czech': 'cs',
'modern-greek': 'el',
'catalan': 'ca',
'bulgarian': 'bg',
'danish': 'da',
'estonian': 'et',
'quechua': 'qu',
'swedish': 'sv',
'armenian': 'hy',
'macedonian': 'mk',
'arabic': 'ar',
'dutch': 'nl',
'hungarian': 'hu',
'italian': 'it',
'romanian': 'ro',
'ukranian': 'uk',
'german': 'de',
'finnish': 'fi',
'russian': 'ru',
'turkish': 'tr',
'spanish': 'es'
}
mode = args.mode
embeddings = args.embedding_types.split(',')
data_dir = args.data_dir
# NOTE:
# embeddings dir should have the following directory structure
# embeddings_dir/language_id/embedding_type/final_embeds.vec
# example: embeddings/de/word2vec/final_embeds.vec
embedding_dir = args.embedding_dir
# directory of output files
json_config_dir = args.json_config_dir
bash_dir = args.bash_dir
model_dir = args.model_dir
languages = {}
if args.languages != 'all':
language_set = args.languages.split(',')
else:
language_set = langId.keys()
for lang in language_set:
languages[lang] = langId[lang]
# load feature template
json_template = os.path.join("scripts", "subword" + mode + ".json")
# this file lists number of possible values for each feature
feature_set = os.path.join("scripts", mode + "_features.txt")
# load feature dicts, currently only supported for five languages
# German, Turkish, Finnish, Spanish, Russian
# see feature_set file for examples
feat_dict = defaultdict(lambda: defaultdict(int))
with open(feature_set) as f:
for line in f:
line = line.strip()
feature, lang, count, _ = line.split('\t')
if lang in languages:
feature = feature.replace(' ', '_')
feat_dict[feature][lang] = count
# generate JSON config files
for emb_type in embeddings:
for task in feat_dict.keys():
for lang in feat_dict[task]:
output_file = os.path.join(json_config_dir, emb_type,
task + '-' + lang + '.json')
os.makedirs(os.path.dirname(output_file), exist_ok=True)
fout = open(output_file, 'w')
embedding_file = os.path.join(embedding_dir, langId[lang],
emb_type, 'final_embeds.vec')
if not os.path.isfile(embedding_file):
print(embedding_file)
sys.stderr("Embedding is not available for ", lang,
". This language will be skipped.")
continue
with open(json_template) as f:
for line in f:
if '_data_path' in line:
path = data_dir + '/' + task + '/' + lang
newline = line.replace('[data_dir]/[feat]/[lang]',
path)
fout.write(newline)
elif emb_type == 'elmo' and 'embedding_dim' in line:
newline = line.replace('300', '1024')
fout.write(newline)
elif emb_type == 'elmo' and 'input_dim' in line:
if mode == 'classification':
newline = line.replace('300', '1024')
elif mode == 'contrastive':
newline = line.replace('600', '2048')
fout.write(newline)
elif 'hidden_dims' in line:
newline = line.replace('x',
str(feat_dict[task][lang]))
fout.write(newline)
elif 'pretrained_embedding_file' in line:
newline = line.replace('pretrained_embedding_file',
embedding_file)
fout.write(newline)
else:
fout.write(line)
fout.close()
# generate bash scripts
for emb_type in embeddings:
# train scripts
bash_file = os.path.join(bash_dir,
'run_' + mode + '_' + emb_type + '.sh')
os.makedirs(os.path.dirname(bash_file), exist_ok=True)
with open(bash_file, 'w', encoding='utf-8') as f:
# write headings
f.write('#!/bin/bash\n\n')
f.write(
'export PYTHON_PATH=$PATH\nexport PYTHONIOENCODING=utf-8\n\n')
for task in feat_dict.keys():
for lang in feat_dict[task]:
json_file = os.path.join(json_config_dir, emb_type,
task + '-' + lang + '.json')
model_path = os.path.join(model_dir, lang, emb_type, task)
f.write('allennlp train ' + json_file + ' -s ' +
model_path + ' --include-package classifiers\n')
make_executable(bash_file)
def win_ipconfig():
"""
Calls the windows command line tool ipconfig with the "/all" argument. Parses the printed output into a sequence of dictionaries like:
[ { "name": "entry_name", "properties": {"entry_property": "...", ...,}}, ...]
Discovered entry properties include:
subnet_mask,
primary_dns_suffix,
media_state,
description,
link_local_ipv6_address,
ipv6_address,
dhcpv6_iaid,
autocnofiguration_enabled,
host_name,
ipv4_address,
node_type,
wins_proxy_enabled,
dhcpv6_client_duid,
connection_specific_dns_suffix,
dhcp_enabled,
dns_suffix_search_list,
dns_servers,
default_gateway,
lease_obtained,
lease_expires,
netbios_over_tcpip,
ip_routing_enabled,
physical_address,
dhcp_server
"""
ipconfig_output = ""
entries = []
property_key_set = set()
# call ipconfig
try:
result = subprocess.run(
#["ipconfig", "/all"],
"ipconfig /all",
check=True,
shell=True,
stdout=subprocess.PIPE)
ipconfig_output = result.stdout.decode("utf-8")
except subprocess.CalledProcessError as cpe:
sys.stderr("call to ipconfig failed")
return entries
# process the ipconfig output
lines = ipconfig_output.split("\r\n")
a = ipconfig_output.replace('\r\n', '\t')
a = a.strip('\t')
a = re.sub(r' ?(\. )+', '', a)
a = re.sub(r' :', ':', a)
a = re.sub(r'\t\t(?=[A-Za-z])', '\r\n', a)
a = re.sub(r': \t', ': EMPTY\t', a)
a = re.sub(r'\t {4,}', ',', a)
a = re.sub(r'\t +', '\t', a)
a = re.sub(r'(?<=[A-Za-z])\t\t', ':\t\t', a)
b = a.split('\r\n')
# convert the ipconfig output into a dict
for c in b:
name, properties = c.split('\t\t')
properties = properties.split('\t')
props_dict = {}
for p in properties:
if ':' in p:
key, value = re.split(':', p, maxsplit=1)
key = key.strip().lower()
key = re.sub(r'[^a-zA-Z0-9]', '_', key)
property_key_set.add(key)
v = value.strip()
if "," in v:
v = v.split(',')
props_dict[key] = v
entry = dict(name=name.strip(':'), properties=props_dict)
entries.append(entry)
g_logger.debug("unique properties: {}".format(", ".join(property_key_set)))
return entries
chip_x += [float(base1_x)]
chip_y += [float(base1_y)]
elif 'base2' in chip_name:
chip_x += [float(base2_x)]
chip_y += [float(base2_y)]
elif 'base3' in chip_name:
chip_x += [float(base2_x)]
chip_y += [float(base2_y)]
elif 'spreader' in chip_name:
chip_x += [float(spreader_x)]
chip_y += [float(spreader_y)]
elif 'null' == chip_name:
chip_x += [0.00001]
chip_y += [0.00001]
else:
sys.stderr('invalid chip name in input file ' + input_file)
sys.exit()
lay += [int(data[1])]
x += [float(data[2])]
y += [float(data[3])]
if int(data[1]) == layer_tmp:
count_tmp += 1
layer_tmp = int(data[1])
else:
count_tmp = 1
layer_tmp = int(data[1])
count += [count_tmp]
num = len(rotate)
system_size = -10.0
def main():
train_test = sys.argv[1]
if train_test not in ["train", "predict"]:
sys.stderr("train or predict")
exit(1)
config_name = sys.argv[2]
forced_decode_data = "data/brae.train.data"
phrase_data_path = "data/phrase.list"
src_count_path = "data/src.trans.data"
tar_count_path = "data/tar.trans.data"
brae_config = BRAEISOMAPConfig(config_name)
train_name = "dim%d_lrec%f_lsem%f_ll2%f_alpha%f_beta%f_num%d_seed%d_batch%d_lr%f" % (brae_config.dim,
brae_config.weight_rec,
brae_config.weight_sem,
brae_config.weight_l2,
brae_config.alpha,
brae_config.beta,
brae_config.trans_num,
brae_config.random_seed,
brae_config.batch_size,
brae_config.optimizer.param["lr"])
model_name = "model/%s" % train_name
temp_model = model_name + ".temp"
if train_test == "train":
start_iter = int(sys.argv[3]) if len(sys.argv) > 3 else 0
end_iter = int(sys.argv[4]) if len(sys.argv) > 4 else 25
pre_logger("braeisomap_" + train_name)
np.random.seed(brae_config.random_seed)
if start_iter == 0:
src_word_dict, tar_word_dict = read_phrase_pair_vocab(forced_decode_data)
src_word_dict, tar_word_dict = add_trans_word_vocab(src_count_path, src_word_dict, tar_word_dict)
tar_word_dict, src_word_dict = add_trans_word_vocab(tar_count_path, src_word_dict, tar_word_dict)
src_word_dict = filter_vocab(src_word_dict, min_count=0)
tar_word_dict = filter_vocab(tar_word_dict, min_count=0)
src_phrases, tar_phrases, src_tar_pair = read_phrase_list(forced_decode_data, src_word_dict, tar_word_dict)
src_phrases, tar_phrases = read_trans_list(src_count_path, src_phrases, tar_phrases,
src_word_dict, tar_word_dict)
tar_phrases, src_phrases = read_trans_list(tar_count_path, tar_phrases, src_phrases,
tar_word_dict, src_word_dict)
src_phrases = clean_text(src_phrases)
tar_phrases = clean_text(tar_phrases)
brae = pre_model(src_word_dict, tar_word_dict, brae_config, verbose=True)
with open(temp_model, 'wb') as fout:
pickle.dump(src_phrases, fout)
pickle.dump(tar_phrases, fout)
pickle.dump(src_tar_pair, fout)
pickle.dump(brae, fout)
pickle.dump(np.random.get_state(), fout)
if end_iter == 1:
exit(1)
else:
with open(temp_model, 'rb') as fin:
src_phrases = pickle.load(fin)
tar_phrases = pickle.load(fin)
src_tar_pair = pickle.load(fin)
brae = pickle.load(fin)
np.random.set_state(pickle.load(fin))
brae.train(src_phrases, tar_phrases, src_tar_pair, brae_config, model_name, start_iter, end_iter)
brae.save_model("%s.model" % model_name)
elif train_test == "predict":
num_process = int(sys.argv[3]) if len(sys.argv) > 3 else 0
brae_predict(phrase_data_path, train_name + ".pred", model_file="%s.model" % model_name,
bilinear=True, num_process=num_process)
else:
sys.stderr("train or predict")
exit(1)
def get_emit_index(input_val, alphabet):
for i in range(len(alphabet)):
if alphabet[i] == input_val:
return i
sys.stderr("Could not find character " + input_val)
resulting_plist_path = os.path.join(build_dir, SAFARI_MANIFEST)
plistlib.writePlist(plist, resulting_plist_path)
background_dom = parseString('<html><head></head></html>')
head = background_dom.getElementsByTagName('head')[0]
for script in scripts['background_scripts']:
script_element = background_dom.createElement('script')
script_element.attributes['src'] = script
# This is a hack to avoid generating self closing script tag
script_element.appendChild(background_dom.createTextNode(''))
head.appendChild(script_element)
# Another hack to remove xml starting tag
xml = '\n'.join(
node.toxml('utf-8') for node in background_dom.childNodes)
background.write(xml)
if __name__ == '__main__':
if not len(sys.argv) == 4:
sys.stderr('assign_scripts.py browser_name manifest_path build_dir \n')
sys.exit(1)
[browser_name, manifest_path, build_dir] = sys.argv[1:]
if browser_name == 'chrome':
chrome(manifest_path, build_dir)
elif browser_name == 'safari':
safari(manifest_path, build_dir)
