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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Gregory Bowman
# Contributors: Robert McGibbon
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import os
import tempfile
import unittest
import numpy as np
import tables
from mdtraj import io
from mdtraj.testing import eq
fd, temp = tempfile.mkstemp(suffix=".h5")
os.close(fd)
def teardown_module(module):
"""remove the temporary file created by tests in this file
this gets automatically called by pytest"""
os.unlink(temp)
def test_overwrite_1():
fid, fn = tempfile.mkstemp()
try:
a = np.arange(10)
b = a + 1
io.saveh(fn, a=a)
io.saveh(fn, b=b)
eq(io.loadh(fn, "a"), a)
eq(io.loadh(fn, "b"), b)
except:
raise
finally:
if os.path.exists(fn):
os.close(fid)
os.unlink(fn)
def test_overwrite_2():
fid, fn = tempfile.mkstemp()
try:
a = np.arange(10)
b = a + 1
io.saveh(fn, a=a)
io.saveh(fn, a=b)
eq(io.loadh(fn, "a"), b)
except:
raise
finally:
if os.path.exists(fn):
os.close(fid)
os.unlink(fn)
class test_io(unittest.TestCase):
def setUp(self):
# setup() is called before very test and just creates a
# temporary work space for reading/writing files.
fid, self.filename1 = tempfile.mkstemp()
fid, self.filename2 = tempfile.mkstemp()
self.data = np.arange(10000, dtype=np.float32)
# Write Data to an HDF5 file as a compressed CArray.
hdf_file = tables.open_file(self.filename1, "a")
hdf_file.create_carray(
"/",
"arr_0",
tables.Float32Atom(),
self.data.shape,
filters=io.COMPRESSION,
)
hdf_file.root.arr_0[:] = self.data[:]
hdf_file.flush()
hdf_file.close()
def test_load_1(self):
# Load by specifying array name
TestData = io.loadh(self.filename1, "arr_0")
eq(TestData, self.data)
def test_load_2(self):
# load using deferred=False
TestData = io.loadh(self.filename1, deferred=False)["arr_0"]
eq(TestData, self.data)
def test_load_3(self):
# load using deferred=True
deferred = io.loadh(self.filename1, deferred=True)
eq(deferred["arr_0"], self.data)
deferred.close()
def test_save(self):
# Save HDF5 to disk and load it back up
io.saveh(self.filename2, self.data)
TestData = io.loadh(self.filename2, "arr_0")
eq(TestData, self.data)
def teardown(self):
os.remove(self.filename1)
os.remove(self.filename2)
class test_io_int(test_io):
"Run the same test as the class above, but using int64 data"
def setUp(self):
# setup() is called before very test and just creates
# a temporary work space for reading/writing files.
fid, self.filename1 = tempfile.mkstemp()
fid, self.filename2 = tempfile.mkstemp()
self.data = np.arange(10000, dtype=np.int64)
# Write Data to an HDF5 file as a compressed CArray.
hdf_file = tables.open_file(self.filename1, "a")
hdf_file.create_carray(
"/",
"arr_0",
tables.Int64Atom(),
self.data.shape,
filters=io.COMPRESSION,
)
hdf_file.root.arr_0[:] = self.data[:]
hdf_file.flush()
hdf_file.close()
def test_groups():
# Test to ensure that files are loaded correctly even if they contain
# nested groups and stuff
x = np.random.randn(10)
y = np.random.randn(11)
f = tables.open_file(temp, "w")
f.create_group(where="/", name="mygroup")
f.create_array(where="/mygroup", name="myarray", obj=x)
f.create_array(where="/", name="mya2", obj=y)
f.close()
assert eq(io.loadh(temp)["mygroup/myarray"], x)
assert eq(io.loadh(temp)["mya2"], y)
assert eq(io.loadh(temp, deferred=False)["mygroup/myarray"], x)
assert eq(io.loadh(temp, deferred=False)["mya2"], y)
assert eq(io.loadh(temp, "mygroup/myarray"), x)
assert eq(io.loadh(temp, "mya2"), y)
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