def cc_check_features(self,kind='cc'):
v=self.env
test=Configure.check_data()
test.code='int main() {return 0;}\n'
test.env=v
test.execute=1
test.force_compiler=kind
ret=self.run_check(test)
self.check_message('compiler could create','programs',not(ret is False))
if not ret:self.fatal("no programs")
lib_obj=Configure.check_data()
lib_obj.code="int k = 3;\n"
lib_obj.env=v
lib_obj.build_type="shlib"
lib_obj.force_compiler=kind
ret=self.run_check(lib_obj)
self.check_message('compiler could create','shared libs',not(ret is False))
if not ret:self.fatal("no shared libs")
lib_obj=Configure.check_data()
lib_obj.code="int k = 3;\n"
lib_obj.env=v
lib_obj.build_type="staticlib"
lib_obj.force_compiler=kind
ret=self.run_check(lib_obj)
self.check_message('compiler could create','static libs',not(ret is False))
if not ret:self.fatal("no static libs")
def detect_tbb(conf):
env = conf.env
opt = Options.options
if Options.options.no_tbb:
print "TBB (multicore) is disabled"
return 0
if Options.options.tbb:
conf.env['CPPPATH_TBB'] = [Options.options.tbb + '/include']
conf.env['LIBPATH_TBB'] = [Options.options.tbb + '/lib']
else:
conf.env['CPPPATH_TBB'] = ['/opt/intel/include']
conf.env['LIBPATH_TBB'] = ['/opt/intel/lib']
res = Configure.find_file('tbb/parallel_for.h', conf.env['CPPPATH_TBB']+['/usr/include', '/usr/local/include'])
conf.check_message('header','tbb/parallel_for.h', (res != '') , res)
if (res == '') :
return 0
if Options.options.apple:
res = Configure.find_file('libtbb.dylib', conf.env['LIBPATH_TBB'] + ['/usr/lib', '/usr/local/lib'])
else:
res = Configure.find_file('libtbb.so', conf.env['LIBPATH_TBB'] + ['/usr/lib', '/usr/local/lib'])
conf.check_message('library','libtbb', (res != ''), res)
if (res == '') :
return 0
conf.env['LIB_TBB'] = ['tbb']
return 1
def detect_tbb(conf):
env = conf.env
opt = Options.options
if Options.options.no_tbb:
print "TBB (multicore) is disabled"
return 0
if Options.options.tbb:
conf.env['CPPPATH_TBB'] = [Options.options.tbb + '/include']
#conf.env['LIBPATH_TBB'] = [Options.options.tbb + '/lib']
conf.env['LIBPATH_TBB'] = [Options.options.tbb + '/lib/intel64/cc4.1.0_libc2.4_kernel2.6.16.21']
#print conf.env['LIBPATH_TBB']
else:
conf.env['CPPPATH_TBB'] = ['/opt/intel/include']
conf.env['LIBPATH_TBB'] = ['/opt/intel/lib']
res = Configure.find_file('tbb/parallel_for.h', conf.env['CPPPATH_TBB']+['/usr/include', '/usr/local/include'])
conf.check_message('header','tbb/parallel_for.h', (res != '') , res)
if (res == '') :
return 0
if Options.options.apple:
res = Configure.find_file('libtbb.dylib', conf.env['LIBPATH_TBB'] + ['/usr/lib', '/usr/local/lib'])
else:
res = Configure.find_file('libtbb.so', conf.env['LIBPATH_TBB'] + ['/usr/lib', '/usr/local/lib'])
conf.check_message('library','libtbb', (res != ''), res)
if (res == '') :
return 0
conf.env['LIB_TBB'] = ['tbb']
return 1
def detect(conf):
cython = conf.find_program('cython', var='CYTHON')
if not cython:
return False
# Register version checking method in configure class.
Configure.conf(check_cython_version)
conf.env['CYTHON_EXT'] = ['.pyx']
return True
def detect(conf):
cython = conf.find_program('cython', var='CYTHON')
if not cython:
return False
# Register version checking method in configure class.
Configure.conf(check_cython_version)
conf.env['CYTHON_EXT'] = ['.pyx']
return True
def test_missing_srcdir(self):
self._setup_options()
Utils.g_module = imp.new_module('main_wscript')
Utils.g_module.blddir = 'out'
# TODO: tests for WafError upon change
conf = Configure.ConfigurationContext()
self.failUnlessRaises(Utils.WscriptError, Scripting.configure, conf)
def detect(conf):
# xml2po
xml2po = conf.find_program('xml2po', var='XML2PO')
if not xml2po:
# xml2po: on win32 'xml2po' is not executable thus this hook
if conf.env['IS_WIN32']:
python = conf.find_program('python', var='PYTHON')
if not python:
conf.fatal(
'The program python (required by xml2po) could not be found'
)
xml2podir = Configure.find_file(
'xml2po', os.environ['PATH'].split(os.pathsep))
if not xml2podir:
conf.fatal('The program xml2po is mandatory!')
conf.env['XML2PO'] = Utils.to_list(
conf.env['PYTHON']) + [xml2podir + os.sep + 'xml2po']
conf.check_message('xml2po', '', True,
' '.join(conf.env['XML2PO']))
else:
conf.fatal('The program xml2po is mandatory!')
if conf.env['IS_WIN32']:
xsltproc = conf.find_program('xsltproc', var='XSLTPROC')
htmlhelpc = conf.find_program('hhc', var='HTMLHELPC')
def detect_mpi(conf):
env = conf.env
opt = Options.options
conf.env['LIB_MPI'] = ''
conf.env['MPI_FOUND'] = False
if Options.options.no_mpi:
return
if Options.options.mpi:
conf.env['CPPPATH_MPI'] = Options.options.mpi + '/include'
conf.env['LIBPATH_MPI'] = Options.options.mpi + '/lib'
else:
conf.env['CPPPATH_MPI'] = [
'/usr/include/mpi', '/usr/local/include/mpi', '/usr/include',
'/usr/local/include'
]
conf.env['LIBPATH_MPI'] = [
'/usr/lib', '/usr/local/lib', '/usr/lib/openmpi'
]
res = Configure.find_file('mpi.h', conf.env['CPPPATH_MPI'])
conf.check_message('header', 'mpi.h', (res != ''), res)
if (res == ''):
return 0
conf.env['MPI_FOUND'] = True
conf.env['LIB_MPI'] = ['mpi_cxx', 'mpi']
return 1
def pkg_check_modules(conf,uselib_name,expression,mandatory=True):
pkg_config=conf.env['PKG_CONFIG']
if not pkg_config:
if mandatory:
conf.fatal("pkg-config is not available")
else:
return False
argv=[pkg_config,'--cflags','--libs',expression]
cmd=subprocess.Popen(argv,stdout=subprocess.PIPE)
out,dummy=cmd.communicate()
retval=cmd.wait()
msg_checking=("pkg-config flags for %s"%(uselib_name,))
if Options.options.verbose:
if retval==0:
conf.check_message_custom(msg_checking,('(%s)'%expression),out)
else:
conf.check_message(msg_checking,('(%s)'%expression),False)
else:
conf.check_message(msg_checking,'',(retval==0),'')
conf.log.write('%r: %r (exit code %i)\n'%(argv,out,retval))
if retval==0:
config_c.parse_flags(out,uselib_name,conf.env)
conf.env[uselib_name]=True
return True
else:
conf.env[uselib_name]=False
if mandatory:
raise Configure.ConfigurationError('pkg-config check failed')
else:
return False
def main(): ''' 构造测试集，并用restore之前的模型来进行evaluate ''' # 读取配置文件 config = Configure() # 设置logger logger = get_logger(config['path_log']) # 读取词典 vocab_util = Vocab_Util() # dict[word] = idx vocab_words = vocab_util.load_vocab(config['word_vocab_file']) # dict[char] = idx vocab_chars = vocab_util.load_vocab(config['char_vocab_file']) # dict[tag] = idx vocab_tags = vocab_util.load_vocab(config['tag_vocab_file']) # 将词典封装给模型 vocabs = [vocab_words, vocab_chars, vocab_tags] embeddings = vocab_util.get_trimmed_glove_vectors(config['trimmed_file']) # 对数据进行处理 processing_word = get_processing_word(vocab_words = vocab_words, vocab_chars = vocab_chars, lowercase = True, chars = config['use_chars'], allow_unk = True) processing_tag = get_processing_word(vocab_words = vocab_tags, lowercase = False, allow_unk = False) # 得到训练数据 test_dataset = Dataset(filename = config['test_data'], max_iter = None, processing_word = processing_word, processing_tag = processing_tag) # 构造模型进行训练 model = ner_model(config,logger,vocabs,embeddings) model.build() model.restore_session() model.evaluate(test_dataset)
def CheckDuration():
""" CTFが開催中か確認する """
config = Configure.LoadConfig()
start = config['ctf']['duration']['start']
end = config['ctf']['duration']['end']
# 各種時刻を取得
tz = pytz.timezone(config['ctf']['duration']['timezone'])
dt_now = datetime.datetime.now(tz=tz)
dt_start = datetime.datetime(start['year'],
start['month'],
start['date'],
start['hour'],
start['minute'],
start['second'],
tzinfo=tz)
dt_end = datetime.datetime(end['year'],
end['month'],
end['date'],
end['hour'],
end['minute'],
end['second'],
tzinfo=tz)
# 開始前かの確認
if dt_now < dt_start:
return 1
# 終了後かの確認
if dt_now > dt_end:
return 2
return 0
def main():
logger = Logger.logger()
sources = Configure.servers(logger)
model = ModelStandard.ModelStandard()
view = ViewCurses.ViewCurses(model) if "TERM" in os.environ else ViewPrint.ViewPrint(model)
manifold = Manifold.Manifold(model, view)
body(manifold, sources, sources)
def load_input(__self__):
f = filedialog.askopenfilename(title="Open input file",
filetypes=[("Input file", "*.dat")])
if f is not "":
files, __self__.out = Configure.load_input(f)
__self__.temp = []
local_path = os.path.dirname(os.path.abspath(__file__))
##################################################
# Copies all relevant files to working directory #
##################################################
for fpath, fname in files:
destination = os.path.join(local_path, fname)
try:
shutil.copy(fpath, destination)
__self__.temp.append(destination)
files_in_root = 0
except:
files_in_root = 1
pass
#################################################################
#NOTE: If the input file selected is in the working directory, #
# there it no need to create a temporary input file #
#################################################################
if not files_in_root:
shutil.copy(f, os.path.join(local_path, "temp_input.dat"))
__self__.temp.append(os.path.join(local_path,
"temp_input.dat"))
__self__.launch(__input__="temp_input.dat")
else:
__self__.launch(__input__=f)
def detect(conf):
pocom=conf.find_program('msgfmt')
if not pocom:
conf.fatal('The program msgfmt (gettext) is mandatory!')
conf.env['POCOM']=pocom
intltool=conf.find_program('intltool-merge',var='INTLTOOL')
if not intltool:
if Options.platform=='win32':
perl=conf.find_program('perl',var='PERL')
if not perl:
conf.fatal('The program perl (required by intltool) could not be found')
intltooldir=Configure.find_file('intltool-merge',os.environ['PATH'].split(os.pathsep))
if not intltooldir:
conf.fatal('The program intltool-merge (intltool, gettext-devel) is mandatory!')
conf.env['INTLTOOL']=Utils.to_list(conf.env['PERL'])+[intltooldir+os.sep+'intltool-merge']
conf.check_message('intltool','',True,' '.join(conf.env['INTLTOOL']))
else:
conf.fatal('The program intltool-merge (intltool, gettext-devel) is mandatory!')
def getstr(varname):
return getattr(Options.options,varname,'')
prefix=conf.env['PREFIX']
datadir=getstr('datadir')
if not datadir:datadir=os.path.join(prefix,'share')
conf.define('LOCALEDIR',os.path.join(datadir,'locale'))
conf.define('DATADIR',datadir)
if conf.env['CC']or conf.env['CXX']:
conf.check(header_name='locale.h')
def GetInformation():
""" CTFの詳細情報を取得する """
config = Configure.LoadConfig()
ctf = {
'name': config['ctf']['name'],
'brand': config['ctf']['brand'],
'team': config['ctf']['team'],
'over-open': config['ctf']['over-open']
}
return ctf
def get_video(mol, molclass=None, traj=None, view=1):
if (molclass == None):
molclass = queue.getClass(mol)
if (traj == None):
traj = queue.get_latest_completed_trajectory(mol)
log("Showing video " + str([molclass, mol, traj, view]))
if (traj == 1):
traj = "INIT"
traj = str(traj)
trajvideo = Configure.molVideosPath(
molclass, mol) + mol + "_" + traj + "_view" + str(view) + ".gif"
log("Trajvideo is: " + trajvideo)
if not os.path.exists(trajvideo):
inputfile = Configure.molResultsPath(molclass, mol)
if (traj == "INIT"):
inputfile = inputfile + "data." + mol
else:
inputfile = inputfile + mol + "_" + traj + ".lammpstrj"
ovitoHandler.videoView(inputfile, view)
return trajvideo
def test_missing_configure(self): # white_box test: missing def configure() wscript_contents = """ blddir = 'build' srcdir = '.' """ self._write_wscript(wscript_contents, use_dic=False) self._setup_options() Utils.set_main_module(self._wscript_file_path) conf = Configure.ConfigurationContext() self.failUnlessRaises(Utils.WscriptError, Scripting.configure, conf)
def main():
# 读取配置文件
config = Configure()
# 设置logger
logger = get_logger(config['path_log'])
# 读取词典
vocab_util = Vocab_Util()
# dict[word] = idx
vocab_words = vocab_util.load_vocab(config['word_vocab_file'])
# dict[char] = idx
vocab_chars = vocab_util.load_vocab(config['char_vocab_file'])
# dict[tag] = idx
vocab_tags = vocab_util.load_vocab(config['tag_vocab_file'])
# 将词典封装给模型
vocabs = [vocab_words, vocab_chars, vocab_tags]
embeddings = vocab_util.get_trimmed_glove_vectors(config['trimmed_file'])
# 对数据进行处理
processing_word = get_processing_word(vocab_words=vocab_words,
vocab_chars=vocab_chars,
lowercase=True,
chars=config['use_chars'],
allow_unk=True)
processing_tag = get_processing_word(vocab_words=vocab_tags,
lowercase=False,
allow_unk=False)
# 得到训练数据
train_dataset = Dataset(filename=config['train_data'],
max_iter=None,
processing_word=processing_word,
processing_tag=processing_tag)
# 得到dev数据
dev_dataset = Dataset(filename=config['dev_data'],
max_iter=None,
processing_word=processing_word,
processing_tag=processing_tag)
# for data in train_dataset:
# print data
for x_batch, y_batch in train_dataset.get_minibatch(4):
print x_batch
print y_batch
# 构造模型进行训练
model = ner_model(config, logger, vocabs, embeddings)
# 构建模型图
model.build()
# 训练
model.train(train_dataset, dev_dataset)
def get_plot(molclass, mol, traj, plot):
log(("Showing plot ") + str([molclass, mol, traj, plot]))
if (traj == 1):
return
traj = str(traj)
trajplot = Configure.molGraphsPath(molclass,
mol) + mol + "_" + plot + ".png"
log("Trajplot is: " + trajplot)
if not os.path.exists(trajplot):
log("Creating plot...")
os.system("python " + Configure.Aromodel_Path +
"/Analyze_SAM_Traj.py " + molclass + " " + mol + " " + traj)
return trajplot
def Query(query, param=None):
""" SQLクエリを発行する """
sqlite3.dbapi2.converters['DATETIME'] = sqlite3.dbapi2.converters['TIMESTAMP']
with closing(sqlite3.connect(Configure.GetDatabasePath())) as conn:
conn.row_factory = sqlite3.Row
cur = conn.cursor()
if param:
cur.execute(query, param)
else:
cur.execute(query)
result = cur.fetchall()
conn.commit()
return result
def get_print(mol, molclass=None, traj=None, view=1):
if (molclass == None):
molclass = queue.getClass(mol)
if (traj == None):
traj = queue.get_latest_completed_trajectory(mol)
log("Showing print " + str([molclass, mol, traj, view]))
traj = str(traj)
if (traj == "Last"):
return get_latest_print(molclass, mol, view)
if (traj == "1"):
traj = "INIT"
traj = str(traj)
trajprint = Configure.molPrintsPath(
molclass, mol) + mol + "_" + traj + "_view" + str(view) + ".png"
if not os.path.exists(trajprint):
inputfile = Configure.molResultsPath(molclass, mol)
if (traj == "INIT"):
inputfile = inputfile + "data." + mol
else:
inputfile = inputfile + mol + "_" + traj + ".lammpstrj"
ovitoHandler.printView(inputfile, view)
return trajprint
def test_attr_err_in_configure(self): # white_box test: configure raised AttributeError - don't raise WafError becasue of that wscript_contents = """ blddir = 'build' srcdir = '.' def configure(conf): raise AttributeError """ self._write_wscript(wscript_contents, use_dic=False) self._setup_options() Utils.set_main_module(self._wscript_file_path) conf = Configure.ConfigurationContext() self.failUnlessRaises(AttributeError, Scripting.configure, conf)
def detect(conf):
try:test_for_compiler=Options.options.check_cxx_compiler
except AttributeError:raise Configure.ConfigurationError("Add set_options(opt): opt.tool_options('compiler_cxx')")
for compiler in test_for_compiler.split():
try:
conf.check_tool(compiler)
except Configure.ConfigurationError,e:
debug('compiler_cxx: %r'%e)
else:
if conf.env['CXX']:
conf.check_message(compiler,'',True)
conf.env['COMPILER_CXX']=compiler
break
conf.check_message(compiler,'',False)
break
def closeEvent(self, event):
event.ignore()
close_state = Configure.read_config()
if close_state == '0':
self.hide_or_display()
elif close_state == '2':
QtGui.qApp.quit()
else:
self.close_dialog = CloseDialog(self)
self.close_dialog.setModal(False)
self.jiajia = self.close_dialog.exec_()
Configure.write_config(self.jiajia)
if self.jiajia == 0:
self.hide_or_display()
#self.ask_next_time = False
elif self.jiajia == 1:
self.hide_or_display()
#self.ask_next_time = True
elif self.jiajia == 2:
self.ask_next_time = False
QtGui.qApp.quit()
elif self.jiajia == 3:
self.ask_next_time = True
QtGui.qApp.quit()
def detect(conf):
pocom = conf.find_program('msgfmt')
if not pocom:
# if msgfmt should not be mandatory, catch the thrown exception in your wscript
conf.fatal('The program msgfmt (gettext) is mandatory!')
conf.env['POCOM'] = pocom
# NOTE: it is possible to set INTLTOOL in the environment, but it must not have spaces in it
intltool = conf.find_program('intltool-merge', var='INTLTOOL')
if not intltool:
# if intltool-merge should not be mandatory, catch the thrown exception in your wscript
if Options.platform == 'win32':
perl = conf.find_program('perl', var='PERL')
if not perl:
conf.fatal(
'The program perl (required by intltool) could not be found'
)
intltooldir = Configure.find_file(
'intltool-merge', os.environ['PATH'].split(os.pathsep))
if not intltooldir:
conf.fatal(
'The program intltool-merge (intltool, gettext-devel) is mandatory!'
)
conf.env['INTLTOOL'] = Utils.to_list(
conf.env['PERL']) + [intltooldir + os.sep + 'intltool-merge']
conf.check_message('intltool', '', True,
' '.join(conf.env['INTLTOOL']))
else:
conf.fatal(
'The program intltool-merge (intltool, gettext-devel) is mandatory!'
)
def getstr(varname):
return getattr(Options.options, varname, '')
prefix = conf.env['PREFIX']
datadir = getstr('datadir')
if not datadir: datadir = os.path.join(prefix, 'share')
conf.define('LOCALEDIR', os.path.join(datadir, 'locale'))
conf.define('DATADIR', datadir)
if conf.env['CC'] or conf.env['CXX']:
# Define to 1 if <locale.h> is present
conf.check(header_name='locale.h')
def test_cxx_is_missing(self):
# white_box test: 'compiler_cxx' options are essential for its configuration
wscript_contents = """
blddir = 'build'
srcdir = '.'
def configure(conf):
conf.check_tool('compiler_cxx')
"""
self._write_wscript(wscript_contents, use_dic=False)
opt_obj = Options.Handler()
opt_obj.parse_args()
Options.options.prefix = Options.default_prefix
Utils.set_main_module(self._wscript_file_path)
conf = Configure.ConfigurationContext()
self.failUnlessRaises(Utils.WscriptError, Scripting.configure, conf)
def pkg_check_module_variable(conf,module,variable):
pkg_config=conf.env['PKG_CONFIG']
if not pkg_config:
conf.fatal("pkg-config is not available")
argv=[pkg_config,'--variable',variable,module]
cmd=subprocess.Popen(argv,stdout=subprocess.PIPE)
out,dummy=cmd.communicate()
retval=cmd.wait()
out=out.rstrip()
msg_checking=("pkg-config variable %r in %s"%(variable,module,))
conf.check_message_custom(msg_checking,'',out)
conf.log.write('%r: %r (exit code %i)\n'%(argv,out,retval))
if retval==0:
return out
else:
raise Configure.ConfigurationError('pkg-config check failed')
def test_invalid_tool(self):
# white_box test: tool not exists
wscript_contents = """
blddir = 'build'
srcdir = '.'
def configure(conf):
conf.check_tool('no_way_such_a_tool_exists_gwerghergjekrhgker')
"""
self._write_wscript(wscript_contents, use_dic=False)
opt_obj = Options.Handler()
opt_obj.parse_args()
Options.options.prefix = Options.default_prefix
Utils.set_main_module(self._wscript_file_path)
conf = Configure.ConfigurationContext()
self.failUnlessRaises(Utils.WscriptError, Scripting.configure, conf)
def GetStartTime(utc=False):
""" CTFの開始時刻を文字列で返す """
config = Configure.LoadConfig()
start = config['ctf']['duration']['start']
time_format = config['ctf']['duration']['format']
tz = pytz.timezone(config['ctf']['duration']['timezone'])
dt_start = datetime.datetime(start['year'],
start['month'],
start['date'],
start['hour'],
start['minute'],
start['second'],
tzinfo=tz)
if utc:
return dt_start.astimezone(pytz.timezone('UTC'))
else:
return dt_start.strftime(time_format)
def GetEndTime(utc=False):
""" CTFの修了時刻を文字列で返す """
config = Configure.LoadConfig()
end = config['ctf']['duration']['end']
time_format = config['ctf']['duration']['format']
tz = pytz.timezone(config['ctf']['duration']['timezone'])
dt_end = datetime.datetime(end['year'],
end['month'],
end['date'],
end['hour'],
end['minute'],
end['second'],
tzinfo=tz)
if utc:
return dt_end.astimezone(pytz.timezone('UTC'))
else:
return dt_end.strftime(time_format)
def _setup_configure(self, blddir='', srcdir=''):
if not blddir:
blddir = self._blddir
if not blddir:
raise ValueError('no blddir argument, no self._blddir !')
if not srcdir:
blddir = self._test_dir_root
if not blddir:
raise ValueError(
'no srcdir argument, no self._test_dir_root !')
# Configure uses arguments defined by Options
opt_obj = Options.Handler()
opt_obj.parse_args()
Options.options.prefix = Options.default_prefix
return Configure.ConfigurationContext(srcdir=srcdir, blddir=blddir)
def pkg_check_modules(conf, uselib_name, expression, mandatory=True):
pkg_config = conf.env['PKG_CONFIG']
if not pkg_config:
if mandatory:
conf.fatal("pkg-config is not available")
else:
return False
if Options.options.verbose:
extra_msg = ' (%s)' % expression
else:
extra_msg = ''
conf.start_msg('Checking for pkg-config flags for %s%s' %
(uselib_name, extra_msg))
argv = [pkg_config, '--cflags', '--libs', expression]
cmd = subprocess.Popen(argv,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, err = cmd.communicate()
retval = cmd.wait()
conf.to_log('%r: %r (exit code %i)\n%s' % (argv, out, retval, err))
if retval != 0:
conf.end_msg(False)
sys.stderr.write(err)
else:
if Options.options.verbose:
conf.end_msg(out)
else:
conf.end_msg(True)
if retval == 0:
conf.parse_flags(out, uselib_name, conf.env)
conf.env[uselib_name] = True
return True
else:
conf.env[uselib_name] = False
if mandatory:
raise Configure.ConfigurationError('pkg-config check failed')
else:
return False
def __init__(self, File_Name, molclass, molName, label=None):
# label defaults to molName if not otherwise specified
self.label = label
if label == None:
self.label = molName
self.mol_class = molclass
self.mol = molName
self.SnapShotList = self.readSnapshots(File_Name)
self.Num_Snaps = len(self.SnapShotList)
self.graphsPath = Configure.molGraphsPath(molclass, molName)
if not os.path.exists(self.graphsPath):
os.mkdir(self.graphsPath)
# TODO: Check numCarbons
self.numCarbon = 5670
return
def detect_sdl(conf):
env = conf.env
opt = Options.options
conf.env['LIB_SDL'] = ''
conf.env['LIB_SDL_gfx'] = ''
conf.env['SDL_FOUND'] = False
libPath = '-Wl,-rpath,'
if Options.options.sdl:
conf.env['CPPPATH_SDL'] = Options.options.sdl + '/include/SDL'
conf.env['CPPPATH_SDL_gfx'] = Options.options.sdl + '/include/SDL'
conf.env['LIBPATH_SDL'] = Options.options.sdl + '/lib'
conf.env['LIBPATH_SDL_gfx'] = Options.options.sdl + '/lib'
libPath += (Options.options.sdl + '/lib')
else:
conf.env['CPPPATH_SDL'] = [
'/usr/include/SDL', '/usr/local/include/SDL', '/usr/include'
]
conf.env['CPPPATH_SDL_gfx'] = [
'/usr/include/SDL', '/usr/local/include/SDL', '/usr/include'
]
conf.env['LIBPATH_SDL'] = [
'/usr/lib', '/usr/local/lib', '/usr/lib/SDL'
]
conf.env['LIBPATH_SDL_gfx'] = [
'/usr/lib', '/usr/local/lib', '/usr/lib/SDL'
]
libPath += '/usr/local/lib'
res = Configure.find_file('SDL.h', conf.env['CPPPATH_SDL_gfx'])
conf.check_message('header', 'SDL.h', (res != ''), res)
if (res == ''):
return 0
conf.env['CCDEFINES_SDL'] = ['_GNU_SOURCE=1', '_REENTRANT']
conf.env['CCDEFINES_SDL_gfx'] = ['_GNU_SOURCE=1', '_REENTRANT']
conf.env['CXXDEFINES_SDL'] = ['_GNU_SOURCE=1', '_REENTRANT']
conf.env['CXXDEFINES_SDL_gfx'] = ['_GNU_SOURCE=1', '_REENTRANT']
conf.env['SDL_FOUND'] = True
conf.env['HAVE_SDL'] = 1
conf.env['HAVE_SDL_gfx'] = 1
conf.env['LIB_SDL'] = ['SDL', 'pthread']
conf.env['LIB_SDL_gfx'] = ['SDL_gfx']
conf.env['LINKFLAGS_SDL'] = [libPath]
return 1
def main():
'''
完成数据的预处理
'''
configure = Configure('./config.cfg')
processing_word = get_processing_word(lowercase=True)
# 构造dataset
train_dataset = Dataset(configure['train_data'],
processing_word=processing_word)
dev_dataset = Dataset(configure['train_data'],
processing_word=processing_word)
test_dataset = Dataset(configure['train_data'],
processing_word=processing_word)
# 构造word和tag的vocab
vocab_util = Vocab_Util()
vocab_words, vocab_tags = vocab_util.get_vocabs_from_datasets(
[train_dataset, dev_dataset, test_dataset])
# 构造词向量中的词
vocab_glove = vocab_util.get_vocabs_from_glove(configure['glove_file'])
# 取交集，同时出现在词向量词典和数据集中的词
vocab_words = vocab_words & vocab_glove
# 加入UNK和数字NUM
vocab_words.add(UNK)
vocab_words.add(NUM)
# 保存单词和tag的vocab文件
vocab_util.write_vocab(vocab_words, configure['word_vocab_file'])
vocab_util.write_vocab(vocab_tags, configure['tag_vocab_file'])
# 获取Trim Glove Vectors，并存储
vocab = vocab_util.load_vocab(configure['word_vocab_file'])
vocab_util.export_trimmed_glove_vectors(vocab, configure['glove_file'],
configure['trimmed_file'],
configure['word_embedding_dim'])
# 构造char vocab, 并且进行存储
train_dataset = Dataset(configure['train_data'])
vocab_chars = vocab_util.get_char_vocab_from_datasets(train_dataset)
vocab_util.write_vocab(vocab_chars, configure['char_vocab_file'])
def detect(conf):
try:
test_for_compiler = Options.options.check_fortran_compiler
except AttributeError:
raise Configure.ConfigurationError(
"Add set_options(opt): opt.tool_options('compiler_fortran')")
for compiler in test_for_compiler.split():
try:
conf.check_tool(compiler)
except Configure.ConfigurationError:
pass
else:
if conf.env['FC']:
conf.check_message("%s" % compiler, '', True)
conf.env["COMPILER_FC"] = "%s" % compiler
return
conf.check_message("%s" % fortran_compiler, '', False)
break
conf.env["COMPILER_FC"] = None
def detect_eigen(conf):
env = conf.env
opt = Options.options
conf.env['LIB_EIGEN'] = ''
conf.env['EIGEN_FOUND'] = False
if Options.options.no_eigen:
return 0
if Options.options.eigen:
conf.env['CPPPATH_EIGEN'] = Options.options.eigen
conf.env['LIBPATH_EIGEN'] = Options.options.eigen
else:
conf.env['CPPPATH_EIGEN'] = ['/usr/include/eigen3', '/usr/local/include/eigen3', '/usr/include', '/usr/local/include']
res = Configure.find_file('Eigen/Core', conf.env['CPPPATH_EIGEN'])
conf.check_message('header','Eigen/Core', (res != '') , res)
if (res == '') :
return 0
conf.env['EIGEN_FOUND'] = True
return 1
def detect_mpi(conf):
env = conf.env
opt = Options.options
conf.env['LIB_MPI'] = 'mpi'
conf.env['MPI_FOUND'] = False
if Options.options.no_mpi :
return
if Options.options.mpi:
conf.env['CPPPATH_MPI'] = Options.options.mpi + '/include'
conf.env['LIBPATH_MPI'] = [Options.options.mpi + '/lib', Options.options.mpi + '/lib64']
else:
conf.env['CPPPATH_MPI'] = ['/usr/include/mpi', '/usr/local/include/mpi', '/usr/include', '/usr/local/include']
conf.env['LIBPATH_MPI'] = ['/usr/lib', '/usr/local/lib']
res = Configure.find_file('mpi.h', conf.env['CPPPATH_MPI'] )
conf.check_message('header','mpi.h', (res != '') , res)
if (res == '') :
return 0
conf.env['MPI_FOUND'] = True
return 1
def detect(conf):
pocom = conf.find_program("msgfmt")
if not pocom:
# if msgfmt should not be mandatory, catch the thrown exception in your wscript
conf.fatal("The program msgfmt (gettext) is mandatory!")
conf.env["POCOM"] = pocom
# NOTE: it is possible to set INTLTOOL in the environment, but it must not have spaces in it
intltool = conf.find_program("intltool-merge", var="INTLTOOL")
if not intltool:
# if intltool-merge should not be mandatory, catch the thrown exception in your wscript
if Options.platform == "win32":
perl = conf.find_program("perl", var="PERL")
if not perl:
conf.fatal("The program perl (required by intltool) could not be found")
intltooldir = Configure.find_file("intltool-merge", os.environ["PATH"].split(os.pathsep))
if not intltooldir:
conf.fatal("The program intltool-merge (intltool, gettext-devel) is mandatory!")
conf.env["INTLTOOL"] = Utils.to_list(conf.env["PERL"]) + [intltooldir + os.sep + "intltool-merge"]
conf.check_message("intltool", "", True, " ".join(conf.env["INTLTOOL"]))
else:
conf.fatal("The program intltool-merge (intltool, gettext-devel) is mandatory!")
def getstr(varname):
return getattr(Options.options, varname, "")
prefix = conf.env["PREFIX"]
datadir = getstr("datadir")
if not datadir:
datadir = os.path.join(prefix, "share")
conf.define("LOCALEDIR", os.path.join(datadir, "locale"))
conf.define("DATADIR", datadir)
if conf.env["CC"] or conf.env["CXX"]:
# Define to 1 if <locale.h> is present
conf.check(header_name="locale.h")
def detect(conf):
pocom = conf.find_program('msgfmt')
if not pocom:
# if msgfmt should not be mandatory, catch the thrown exception in your wscript
conf.fatal('The program msgfmt (gettext) is mandatory!')
conf.env['POCOM'] = pocom
# NOTE: it is possible to set INTLTOOL in the environment, but it must not have spaces in it
intltool = conf.find_program('intltool-merge', var='INTLTOOL')
if not intltool:
# if intltool-merge should not be mandatory, catch the thrown exception in your wscript
if Options.platform == 'win32':
perl = conf.find_program('perl', var='PERL')
if not perl:
conf.fatal('The program perl (required by intltool) could not be found')
intltooldir = Configure.find_file('intltool-merge', os.environ['PATH'].split(os.pathsep))
if not intltooldir:
conf.fatal('The program intltool-merge (intltool, gettext-devel) is mandatory!')
conf.env['INTLTOOL'] = Utils.to_list(conf.env['PERL']) + [intltooldir + os.sep + 'intltool-merge']
conf.check_message('intltool', '', True, ' '.join(conf.env['INTLTOOL']))
else:
conf.fatal('The program intltool-merge (intltool, gettext-devel) is mandatory!')
def getstr(varname):
return getattr(Options.options, varname, '')
prefix = conf.env['PREFIX']
datadir = getstr('datadir')
if not datadir: datadir = os.path.join(prefix,'share')
conf.define('LOCALEDIR', os.path.join(datadir, 'locale'))
conf.define('DATADIR', datadir)
if conf.env['CC'] or conf.env['CXX']:
# Define to 1 if <locale.h> is present
conf.check(header_name='locale.h')
def detect(conf):
# xml2po
xml2po = conf.find_program('xml2po', var='XML2PO')
if not xml2po:
# xml2po: on win32 'xml2po' is not executable thus this hook
if conf.env['IS_WIN32']:
python = conf.find_program('python', var='PYTHON')
if not python:
conf.fatal('The program python (required by xml2po) could not be found')
xml2podir = Configure.find_file('xml2po', os.environ['PATH'].split(os.pathsep))
if not xml2podir:
conf.fatal('The program xml2po is mandatory!')
conf.env['XML2PO'] = Utils.to_list(conf.env['PYTHON']) + [xml2podir + os.sep + 'xml2po']
conf.check_message('xml2po', '', True, ' '.join(conf.env['XML2PO']))
else:
conf.fatal('The program xml2po is mandatory!')
if conf.env['IS_WIN32']:
xsltproc = conf.find_program('xsltproc', var='XSLTPROC')
htmlhelpc = conf.find_program('hhc', var='HTMLHELPC')
from __future__ import print_function
from SensorsResponse import *
from PlotUtil import *
import Configure as CF
from Nh5 import *
from cities import dorotea
from LogConfig import *
"""
Code
"""
if __name__ == '__main__':
INFO, CFP = CF.configure(sys.argv[0],sys.argv[1:])
if INFO:
print(dorotea)
wait()
print("""
DOROTEA:
1. Reads an MCRD file produced by NEXUS, which stores TWF1ns waveforms
for the PMTs and SiPMs as well as data on geometry, sensors and MC.
2. Simulates the response of the energy plane in the PMTs and
outputs PMT TWF25ns e.g., waveforms in bins of 25 ns (and in adc counts)
which correspond to the output of the EP FEE.
def run_configure(opts, args):
Configure.opts = opts
Configure.args = args
Configure.main(opts.configfile)
conf.log.write('%r: %r (exit code %i)\n'%(argv,out,retval))
if retval==0:
config_c.parse_flags(out,uselib_name,conf.env)
conf.env[uselib_name]=True
return True
else:
conf.env[uselib_name]=False
if mandatory:
raise Configure.ConfigurationError('pkg-config check failed')
else:
return False
def pkg_check_module_variable(conf,module,variable):
pkg_config=conf.env['PKG_CONFIG']
if not pkg_config:
conf.fatal("pkg-config is not available")
argv=[pkg_config,'--variable',variable,module]
cmd=subprocess.Popen(argv,stdout=subprocess.PIPE)
out,dummy=cmd.communicate()
retval=cmd.wait()
out=out.rstrip()
msg_checking=("pkg-config variable %r in %s"%(variable,module,))
conf.check_message_custom(msg_checking,'',out)
conf.log.write('%r: %r (exit code %i)\n'%(argv,out,retval))
if retval==0:
return out
else:
raise Configure.ConfigurationError('pkg-config check failed')
Configure.conf(pkg_check_modules)
Configure.conf(pkg_check_module_variable)
