def test_dtopo_io():
r"""Test IO of dtopography class"""
test_data_path = os.path.join(testdir, "data", "alaska1964_test_data.tt3")
test_dtopo = dtopotools.DTopography(path=test_data_path)
temp_path = tempfile.mkdtemp()
try:
dtopo_paths = [os.path.join(temp_path, 'alaska1964.tt1'),
os.path.join(temp_path, 'alaska1964.tt3')]
# os.path.join(temp_path, 'alaska1964.tt2'),
for path in dtopo_paths:
test_dtopo.write(path)
dtopo = dtopotools.DTopography(path=path)
assert test_dtopo.dZ.shape == dtopo.dZ.shape, \
"Shape of dZ not equal for topo_type = %s." % dtopo.topo_type
assert numpy.allclose(test_dtopo.dZ, dtopo.dZ), \
"dZ not equal for %s" % path
except AssertionError as e:
test_dump_path = os.path.join(os.getcwd(), "test_dtopo_io")
shutil.mkdir(test_dump_path)
shutil.copy(temp_path, test_dump_path)
raise e
finally:
shutil.rmtree(temp_path)
def test_dtopo_io():
r"""Test IO of dtopography class"""
test_data_path = os.path.join(testdir, "data", "alaska1964_test_data.tt3")
test_dtopo = dtopotools.DTopography(path=test_data_path)
temp_path = tempfile.mkdtemp()
try:
dtopo_paths = [
os.path.join(temp_path, 'alaska1964.tt1'),
os.path.join(temp_path, 'alaska1964.tt3')
]
# os.path.join(temp_path, 'alaska1964.tt2'),
for path in dtopo_paths:
test_dtopo.write(path)
dtopo = dtopotools.DTopography(path=path)
assert test_dtopo.dZ.shape == dtopo.dZ.shape, \
"Shape of dZ not equal for topo_type = %s." % dtopo.topo_type
assert numpy.allclose(test_dtopo.dZ, dtopo.dZ), \
"dZ not equal for %s" % path
except AssertionError as e:
test_dump_path = os.path.join(os.getcwd(), "test_dtopo_io")
shutil.mkdir(test_dump_path)
shutil.copy(temp_path, test_dump_path)
raise e
finally:
shutil.rmtree(temp_path)
def __init__(self,THRESHOLD=10000,path="./"):
self.TABLE = skiplist.SkipList(isdup=False)
self.THRESHOLD = THRESHOLD
self.path = path
self.curr_active = max([int(f.replace('.sst', '').replace(self.path,'')) for f in glob(path+'*.sst')] or [1])
if os.path.exists(path) == False:
shutil.mkdir(path)
def __init__(self, THRESHOLD=10000, path="./"):
self.TABLE = {}
self.THRESHOLD = THRESHOLD
self.path = path
self.curr_active = max([int(f.replace(".sst", "").replace(self.path, "")) for f in glob(path + "*.sst")] or [1])
if os.path.exists(path) == False:
shutil.mkdir(path)
def load_data(self, path=None):
'''指定路径,加载该文件夹目录下所有数据文件'''
if path is not None:
self.path = path
if os.path.exists(path) == False:
shutil.mkdir(path)
for filename in glob(self.path + "*.sst"):
self.load_file(filename)
def load_data(self, path=None):
"""指定路径,加载该文件夹目录下所有数据文件"""
if path is not None:
self.path = path
if os.path.exists(path) == False:
shutil.mkdir(path)
for filename in glob(self.path + "*.sst"):
self.load_file(filename)
def cda(pagename, wiki='wecanfly', create=False):
pagename = unquote(pagename)
cfg = getattr(__import__('wiki_' + wiki), 'Config')
path = os.path.join(cfg.data_dir, 'pages', pagename, 'attachments')
if os.path.isdir(path):
os.chdir(path)
elif create:
shutil.mkdir(path)
os.chdir(path)
print path
def __init__(self, THRESHOLD=10000, path="./"):
self.TABLE = {}
self.THRESHOLD = THRESHOLD
self.path = path
self.curr_active = max([
int(f.replace('.sst', '').replace(self.path, ''))
for f in glob(path + '*.sst')
] or [1])
if os.path.exists(path) == False:
shutil.mkdir(path)
def main(xyz):
if not os.path.isfile(xyz):
raise IOError("%s is not a file." % (xyz))
sample_dir = 'sample'
if not os.path.isdir(sample_dir):
shutil.mkdir(sample_dir)
coordinates_fname = os.path.join(sample_dir, "r.txt")
atom_numbers_fname = os.path.join(sample_dir, "Z.txt")
Z = []
r = []
with open(xyz, 'r', newline='') as xyz_handle:
reader = csv.reader(xyz_handle, delimiter=' ')
for line in reader:
if len(line) < 4:
print("INFO: " + "".join(line))
continue
symbol = line[0]
element = getattr(elements, symbol)
Z.append(str(element.number))
coords = [float(x) for x in line[1:] if x != '']
r.append(coords)
# Convert to m.
r = numpy.array(r) * 1.0e-10
with open(coordinates_fname, 'w') as r_handle:
for coords in r:
r_handle.write("%.8e\t%.8e\t%.8e\n" %
(coords[0], coords[1], coords[2]))
with open(atom_numbers_fname, 'w') as Z_handle:
Z_handle.write(' '.join(Z))
import time
import shutil
import subprocess
experiment_name = time.time()
shutil.mkdir(experiment_name)
PROB_PUT = .1
N_ITER = 1000000
CACHE_SIZE = 100
SIZE_MEAN = 10000000
SIZE_VARIANCE = 1000000
KEY_VARINCE = 5
VERBOSE_GC_FLAG = "-verbose:gc"
BENCH_PROG = "com.scottandrewcarr.caching.BenchMark"
BASE_DIR="/home/carr27/caching"
def get_class_path():
cp = []
IDEA_OUTPUT = BASE_DIR + "/out"
COMMONS_LOGGING = BASE_DIR + "/libs/commons-logging-1.1.3.jar"
JCS = BASE_DIR + "/libs/jcs-1.3.jar"
cp.append(IDEA_OUTPUT)
cp.append(COMMONS_LOGGING)
cp.append(JCS)
cp_string = ""
for i in range(len(cp)):
if i == 0:
cp_string = cp[i]
else:
cp_string = cp_string + ":"+ cp[i]
return cp_string
def setup_package(install=False, build=False, clean=False):
"""setup_package()
Function to call distutils setup to install the package to the default location for third party modules.
Checks to see if required modules are installed and if not tries to install them (apart from Basemap)
"""
try:
from .__init__ import __author__, __version__, __email__, __doc__, __looseversion__, __build__
except:
from __init__ import __author__, __version__, __email__, __doc__, __looseversion__, __build__
kwargs = dict(
name='pyNLLoc',
version=str(__version__) + 'b' + str(__build__),
author=__author__,
author_email=__email__,
packages=['pyNLLoc'],
package_dir={'pyNLLoc': '.'},
requires=[],
install_requires=[],
provides=['pyNLLoc', 'Scat2Angle', 'XYZ2Angle'],
url='https://github.com/djpugh/pyNLLoc',
download_url='https://github.com/djpugh/pyNLLoc/tarball/v' +
__version__,
bugtrack_url='https://github.com/djpugh/pyNLLoc/issues',
scripts=['pyNLLoc.py', 'Scat2Angle.py', 'XYZ2Angle.py'],
description='pyNLLoc: Python functions for NonLinLoc and Scat2Angle',
long_description=__doc__ + '\n\n' + open('README.md').read() + '\n',
package_data={
'pyNLLoc': [
'README', 'make_angles.sh', 'GridLib.c', 'GetAngles.cpp',
'NLLoc_code/*/*', 'NLLoc_code/*.*'
]
},
classifiers=[
"Development Status :: 5 - Production/Stable",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
"Natural Language :: English", "Programming Language :: Python",
"Programming Language :: C++", "Topic :: Scientific/Engineering"
])
if _SETUPTOOLS:
kwargs['extras_require'] = {'Cluster': ['pyqsub>=1.0.0']}
kwargs['install_requires'].append('pyqsub>=1.0.0')
kwargs.pop('scripts')
kwargs['version'] = __looseversion__
kwargs['entry_points'] = {
'console_scripts': [
'pyNLLoc = pyNLLoc:pyNLLoc_run',
'Scat2Angle = pyNLLoc:Scat2Angle_run',
'XYZ2Angle = pyNLLoc:XYZ2Angle_run'
] #,'XYZ2Time = pyNLLoc:XYZ2Time_run']
}
if build or 'build_all' in sys.argv or 'build-all' in sys.argv:
#clean dist dir
try:
for fname in glob.glob('dist/*'):
try:
os.remove(fname)
except:
pass
except:
pass
print('------\nBUILDING DISTRIBUTIONS\n-----\n')
clean_package()
argv = [sys.executable, "setup.py", "sdist"]
subprocess.call(argv)
clean_package()
argv = [sys.executable, "setup.py", "sdist", "--format=gztar"]
subprocess.call(argv)
if _SETUPTOOLS:
clean_package()
argv = [sys.executable, "setup.py", "bdist_egg"]
subprocess.call(argv)
clean_package()
argv = [sys.executable, "setup.py", "bdist_wheel"]
subprocess.call(argv)
clean_package()
argv = [sys.executable, "setup.py", "bdist_msi"]
subprocess.call(argv)
clean_package()
print('\n------\nBUILD COMPLETE\n------\n')
elif 'pypi_upload' in sys.argv:
argv = [sys.executable, "setup.py", "sdist", "upload", "-r", "pypi"]
subprocess.call(argv)
clean_package()
argv = [
sys.executable, "setup.py", "sdist", "--format=gztar", "upload",
"-r", "pypi"
]
subprocess.call(argv)
clean_package()
argv = [
sys.executable, "setup.py", "bdist_wininst", "upload", "-r", "pypi"
]
subprocess.call(argv)
clean_package()
argv = [
sys.executable, "setup.py", "bdist_wheel", "upload", "-r", "pypi"
]
subprocess.call(argv)
clean_package()
argv = [
sys.executable, "setup.py", "bdist_msi", "upload", "-r", "pypi"
]
subprocess.call(argv)
elif 'clean_all' in sys.argv or clean or 'clean-all' in sys.argv:
argv = [sys.executable, "setup.py", "clean", "--all"]
subprocess.call(argv)
try:
shutil.rmtree('build/')
except:
pass
try:
shutil.rmtree('pyNLLoc-' + __looseversion__ + '/')
shutil.mkdir('pyNLLoc-' + __looseversion__ + '/')
except:
try:
shutil.rmtree('pyNLLoc-' + __version__ + '/')
shutil.mkdir('pyNLLoc-' + __version__ + '/')
except:
pass
if _SETUPTOOLS:
try:
shutil.rmtree('pyNLLoc.egg-info/')
shutil.mkdir('pyNLLoc.egg-info/')
except:
pass
else:
if 'install' in sys.argv:
#Try to build GetNLLOCScatterAngles and add to scripts
ret = os.system('make all')
if ret != 0:
ret = os.system('./make_angles.sh')
if ret != 0:
print(
'\n\n*******************************\n\nC++ module not automatically compiled.\nPlease build manually.\n\n*******************************\n\n'
)
try:
setup(**kwargs)
except ValueError:
kwargs['version'] = __version__
setup(**kwargs)
def test_dynamic_tohoku(verbose=False, plot=False):
r"""Test dynamic faulting via a Tohoku example"""
shoreline_fname = os.path.join(testdir, 'data', 'tohoku_shoreline_1min.npy')
shoreline_xy = numpy.load(shoreline_fname)
subfault_fname = os.path.join(testdir, 'data', 'tohoku_ucsb.txt')
fault = dtopotools.UCSBFault()
fault.read(subfault_fname)
fault.rupture_type = 'dynamic'
if plot:
import matplotlib.pyplot as plt
fault.plot_subfaults(slip_color=True) # plot final slip
plt.show()
# seafloor deformation:
quick_test = True
if quick_test:
xlower = 140.
xupper = 146.
ylower = 35.
yupper = 41.
xylim = [xlower,xupper,ylower,yupper]
# dtopo parameters for 4 min resolution:
mx = int((xupper - xlower)*15 + 1)
my = int((yupper - ylower)*15 + 1)
else:
xlower = 135.
xupper = 150.
ylower = 30.
yupper = 45.
xylim = [xlower,xupper,ylower,yupper]
# dtopo parameters for 1 min resolution:
mx = int((xupper - xlower)*60 + 1)
my = int((yupper - ylower)*60 + 1)
x = numpy.linspace(xlower,xupper,mx)
y = numpy.linspace(ylower,yupper,my)
tmax = 0.
for s in fault.subfaults:
tmax = max(tmax, s.rupture_time + s.rise_time + s.rise_time_ending)
if verbose:
print("rupture ends at time ",tmax)
times = numpy.linspace(0,tmax,10)
dtopo = fault.create_dtopography(x,y,times,verbose=True)
dz_final = dtopo.dZ[-1]
dz_max = dz_final.max()
if plot:
# Incorporate this function in dtopotools to replace animate_dz_colors?
def plot_subfaults_dz(t, fig=None):
if fig is None:
fig = plt.figure(figsize=(12,5))
else:
fig.clf()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
fault.plot_subfaults(axes=ax1, slip_color=True, slip_time=t, xylim=xylim)
dtopo.plot_dz_colors(axes=ax2, t=t, cmax_dz=dz_max)
ax1.plot(shoreline_xy[:,0],shoreline_xy[:,1],'g')
ax2.plot(shoreline_xy[:,0],shoreline_xy[:,1],'g')
plt.axis(xylim)
fig.show()
return fig
dtopo.plot_dz_colors(t=tmax)
plt.show()
fig = plt.figure(figsize=(12,5))
for t in list(numpy.linspace(0,150,16)) + [170,200]:
plot_subfaults_dz(t,fig)
plt.draw()
plt.show()
time.sleep(1)
temp_path = tempfile.mkdtemp()
try:
fname = os.path.join(temp_path, 'tohoku_ucsb_dynamic.tt3')
dtopo.write(fname, 3)
except Exception as e:
test_name = inspect.stack()[1][-2][0][:-3]
test_dump_path = os.path.join(os.getcwd(), test_name)
shutil.mkdir(test_dump_path)
shutil.copy(temp_path, test_dump_path)
raise e
finally:
shutil.rmtree(temp_path)
if verbose:
print('Created ',fname)
def test_dynamic_tohoku(verbose=False, plot=False):
r"""Test dynamic faulting via a Tohoku example"""
shoreline_fname = os.path.join(testdir, 'data',
'tohoku_shoreline_1min.npy')
shoreline_xy = numpy.load(shoreline_fname)
subfault_fname = os.path.join(testdir, 'data', 'tohoku_ucsb.txt')
fault = dtopotools.UCSBFault()
fault.read(subfault_fname)
fault.rupture_type = 'dynamic'
if plot:
import matplotlib.pyplot as plt
fault.plot_subfaults(slip_color=True) # plot final slip
plt.show()
# seafloor deformation:
quick_test = True
if quick_test:
xlower = 140.
xupper = 146.
ylower = 35.
yupper = 41.
xylim = [xlower, xupper, ylower, yupper]
# dtopo parameters for 4 min resolution:
mx = int((xupper - xlower) * 15 + 1)
my = int((yupper - ylower) * 15 + 1)
else:
xlower = 135.
xupper = 150.
ylower = 30.
yupper = 45.
xylim = [xlower, xupper, ylower, yupper]
# dtopo parameters for 1 min resolution:
mx = int((xupper - xlower) * 60 + 1)
my = int((yupper - ylower) * 60 + 1)
x = numpy.linspace(xlower, xupper, mx)
y = numpy.linspace(ylower, yupper, my)
tmax = 0.
for s in fault.subfaults:
tmax = max(tmax, s.rupture_time + s.rise_time + s.rise_time_ending)
if verbose:
print("rupture ends at time ", tmax)
times = numpy.linspace(0, tmax, 10)
dtopo = fault.create_dtopography(x, y, times, verbose=True)
dz_final = dtopo.dZ[-1]
dz_max = dz_final.max()
if plot:
# Incorporate this function in dtopotools to replace animate_dz_colors?
def plot_subfaults_dz(t, fig=None):
if fig is None:
fig = plt.figure(figsize=(12, 5))
else:
fig.clf()
ax1 = fig.add_subplot(121)
ax2 = fig.add_subplot(122)
fault.plot_subfaults(axes=ax1,
slip_color=True,
slip_time=t,
xylim=xylim)
dtopo.plot_dz_colors(axes=ax2, t=t, cmax_dz=dz_max)
ax1.plot(shoreline_xy[:, 0], shoreline_xy[:, 1], 'g')
ax2.plot(shoreline_xy[:, 0], shoreline_xy[:, 1], 'g')
plt.axis(xylim)
fig.show()
return fig
dtopo.plot_dz_colors(t=tmax)
plt.show()
fig = plt.figure(figsize=(12, 5))
for t in list(numpy.linspace(0, 150, 16)) + [170, 200]:
plot_subfaults_dz(t, fig)
plt.draw()
plt.show()
time.sleep(1)
temp_path = tempfile.mkdtemp()
try:
fname = os.path.join(temp_path, 'tohoku_ucsb_dynamic.tt3')
dtopo.write(fname, 3)
except Exception as e:
test_name = inspect.stack()[1][-2][0][:-3]
test_dump_path = os.path.join(os.getcwd(), test_name)
shutil.mkdir(test_dump_path)
shutil.copy(temp_path, test_dump_path)
raise e
finally:
shutil.rmtree(temp_path)
if verbose:
print('Created ', fname)
