def test_save_to_binary_file(self):
tmpfile = gf.generate_temp_file(extension='h5')
CP._save_to_bin_file(filename=tmpfile,
datasetname='d1',
mtx=np.array([0.1, 0.2]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
os.remove(tmpfile)
def test_add_to_log(self):
tmpfile = gf.generate_temp_file(extension='txt')
CP._add_to_log(filename=tmpfile, logstr='hello world')
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
with open(tmpfile, 'r') as file:
loadstr = file.read()
self.assertEqual(loadstr, 'hello world', msg='Message should match')
os.remove(tmpfile)
def test_save_to_text_file(self):
tmpfile = gf.generate_temp_file(extension='txt')
CP._save_to_txt_file(filename=tmpfile, mtx=np.array([0.1, 0.2]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
loadmtx = np.loadtxt(tmpfile)
self.assertTrue(np.array_equal(loadmtx, np.array([0.1, 0.2])),
msg=str('Arrays should match: {}'.format(loadmtx)))
os.remove(tmpfile)
def test_readingbinaryfile_array(self):
tmpfile = gf.generate_temp_file(extension='h5')
CP._save_to_bin_file(filename=tmpfile,
datasetname='d1',
mtx=np.array([[0.1, 0.2]]))
self.assertTrue(os.path.isfile(tmpfile), msg='File exists')
out = CP.read_in_bin_file(filename=tmpfile)
self.assertTrue(np.array_equal(out, np.array([[0.1, 0.2]])),
msg=str('Expected array match: {}'.format(out)))
os.remove(tmpfile)
def test_load_ser_sim_res_no_json(self):
tmpfolder = gf.generate_temp_folder()
os.makedirs(tmpfolder)
pres = CP.load_serial_simulation_results(tmpfolder)
shutil.rmtree(tmpfolder)
self.assertTrue(isinstance(pres['chain'], list))
self.assertTrue(isinstance(pres['s2chain'], list))
self.assertEqual(pres['chain'], [])
def test_read_in_parallel_unknown(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
out = CP.read_in_parallel_savedir_files(parallel_dir=parallel_dir,
extension='unknown')
self.assertEqual(out[0], None)
self.assertEqual(out[1], None)
self.assertEqual(out[2], None)
shutil.rmtree(parallel_dir)
def test_read_in_parallel_txt(self):
parallel_dir = gf.generate_temp_folder()
mcstat = setup_problem(parallel_dir, case='text')
out = CP.read_in_parallel_savedir_files(parallel_dir=parallel_dir,
extension='txt')
StandardCheck(out[0], mcstat)
StandardCheck(out[1], mcstat)
StandardCheck(out[2], mcstat)
shutil.rmtree(parallel_dir)
def test_generate_combined_chain(self):
pres = setup_pres()
combined_chain, index = CP.generate_combined_chain_with_index(
pres=pres)
self.assertEqual(combined_chain.shape, (100, 3),
msg='Default burnin should yield (100,3) array shape')
self.assertEqual(len(index), 100, msg='index should have length 100')
self.assertTrue(
np.array_equal(combined_chain[0:50, :], pres[0]['chain'][50:, :]))
self.assertTrue(
np.array_equal(combined_chain[50:, :], pres[1]['chain'][50:, :]))
def test_generate_combined_chain_non_default_burnin(self):
pres = setup_pres()
combined_chain, index = CP.generate_combined_chain_with_index(
pres=pres, burnin_percentage=0)
self.assertEqual(combined_chain.shape, (200, 3),
msg='Default burnin should yield (200,3) array shape')
self.assertEqual(len(index), 200, msg='index should have length 100')
self.assertTrue(
np.array_equal(combined_chain[0:100, :], pres[0]['chain']))
self.assertTrue(
np.array_equal(combined_chain[100:, :], pres[1]['chain']))
def test_print_log_files(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_bin = True
chains = mcstat._MCMC__chains
mcstat._MCMC__save_to_log_file(chains=chains, start=0, end=100)
capturedOutput = io.StringIO()
sys.stdout = capturedOutput
CP.print_log_files(savedir)
sys.stdout = sys.__stdout__
self.assertTrue(isinstance(capturedOutput.getvalue(), str),
msg='Should contain a string')
self.assertTrue('Display log file:' in capturedOutput.getvalue(),
msg='Expect string to contain these words')
shutil.rmtree(savedir)
def test_id_chain_no(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
chainfolders = os.listdir(parallel_dir)
chainfolders2 = CP.check_parallel_directory_contents(
parallel_dir, chainfolders)
self.assertEqual(
chainfolders2, ['chain_0', 'chain_1', 'chain_2'],
msg='List of strings do not match ({}): {} neq {}'.format(
parallel_dir, chainfolders2,
['chain_0', 'chain_1', 'chain_2']))
shutil.rmtree(parallel_dir)
def test_load_ser_sim_res(self):
tmpfolder = gf.generate_temp_folder()
tmpfolder0 = os.path.join(tmpfolder, 'chain_0')
os.makedirs(tmpfolder0)
tmpfile0 = 'chain_0.json'
tmpfile0 = os.path.join(tmpfolder0, tmpfile0)
results = dict(a=[0, 1], b='hello')
RS = ResultsStructure()
RS.save_json_object(results, tmpfile0)
pres = CP.load_serial_simulation_results(tmpfolder0)
shutil.rmtree(tmpfolder)
self.assertTrue(isinstance(pres['a'], np.ndarray))
self.assertTrue(isinstance(pres['b'], str))
self.assertEqual(pres['b'], 'hello')
def test_cpwe_creation_with_txt(self):
mcstat = gf.setup_mcmc_case_cp()
mcstat.simulation_options.savedir = 'test'
chainfile, s2chainfile, sschainfile, covchainfile = CP._create_path_with_extension_for_all_logs(
options=mcstat.simulation_options, extension='txt')
self.assertEqual(chainfile,
'test/chainfile.txt',
msg='Expect matching string')
self.assertEqual(s2chainfile,
'test/s2chainfile.txt',
msg='Expect matching string')
self.assertEqual(sschainfile,
'test/sschainfile.txt',
msg='Expect matching string')
self.assertEqual(covchainfile,
'test/covchainfile.txt',
msg='Expect matching string')
def test_id_chain_no_with_bad_items(self):
parallel_dir = gf.generate_temp_folder()
setup_problem(parallel_dir, case='binary')
tmpfile = gf.generate_temp_file()
os.mkdir(parallel_dir + os.sep + 'chain')
if not os.path.exists(parallel_dir + os.sep + tmpfile):
with open(parallel_dir + os.sep + tmpfile, 'w'):
pass
chainfolders = os.listdir(parallel_dir)
chainfolders2 = CP.check_parallel_directory_contents(
parallel_dir, chainfolders)
self.assertEqual(
chainfolders2, ['chain_0', 'chain_1', 'chain_2'],
msg='List of strings do not match ({}): {} neq {}'.format(
parallel_dir, chainfolders2,
['chain_0', 'chain_1', 'chain_2']))
shutil.rmtree(parallel_dir)
def test_read_in_savedir_files_txt(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_txt = True
mcstat._MCMC__save_to_log_file(chains=mcstat._MCMC__chains,
start=0,
end=100)
mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
out = CP.read_in_savedir_files(savedir, extension='txt')
StandardCheck(out, mcstat)
shutil.rmtree(savedir)
def test_read_in_savedir_files_unknown(self):
mcstat = gf.setup_case()
savedir = gf.generate_temp_folder()
mcstat.simulation_options.savedir = savedir
mcstat.simulation_options.save_to_txt = True
mcstat._MCMC__save_to_log_file(chains=mcstat._MCMC__chains,
start=0,
end=100)
mcstat._MCMC__save_to_log_file(chains=[
dict(mtx=np.dot(mcstat._covariance._R.transpose(),
mcstat._covariance._R))
],
start=0,
end=100,
covmtx=True)
out = CP.read_in_savedir_files(savedir, extension='unknown')
self.assertEqual(out, None, msg='Expect None')
shutil.rmtree(savedir)
from pymcmcstat.chain import ChainProcessing as CP
from pymcmcstat.chain.ChainStatistics import chainstats
from pymcmcstat.plotting.MCMCPlotting import Plot
# Initialize classes
MCP = Plot()
# define directory where log files are saved
savedir = 'serial_chain'
# compare reading in binary versus text data
ns = 1
# -------
start = time.time()
for ii in range(ns):
results = CP.read_in_savedir_files(savedir, extension='h5')
end = time.time()
binary_time = end - start
# -------
start = time.time()
for ii in range(ns):
results = CP.read_in_savedir_files(savedir, extension='txt')
end = time.time()
text_time = end - start
# -------
print('Binary: {} sec\n'.format(binary_time / ns))
print('Text: {} sec\n'.format(text_time / ns))
def test_readinbinaryfile_warning(self):
out = CP.read_in_bin_file(filename='abcdedf0123')
self.assertEqual(out, [], msg='expect empty list')
def test_cpwe_basic(self):
file = CP._create_path_without_extension(savedir='test', file='file')
self.assertEqual(file, 'test/file', msg='Expect matching string')
def test_check_directory(self):
tmpfolder = gf.generate_temp_folder()
CP._check_directory(tmpfolder)
self.assertTrue(os.path.isdir(tmpfolder), msg='Directory exists')
os.removedirs(tmpfolder)
def test_generate_chain_list_with_non_default_burnin(self):
pres = setup_pres()
chains = CP.generate_chain_list(pres=pres, burnin_percentage=0)
self.assertEqual(len(chains), 2, msg='expect length of 2')
self.assertTrue(np.array_equal(chains[0], pres[0]['chain']))
self.assertTrue(np.array_equal(chains[1], pres[1]['chain']))
def test_generate_chain_list(self):
pres = setup_pres()
chains = CP.generate_chain_list(pres=pres)
self.assertEqual(len(chains), 2, msg='expect length of 2')
self.assertTrue(np.array_equal(chains[0], pres[0]['chain'][50:, :]))
self.assertTrue(np.array_equal(chains[1], pres[1]['chain'][50:, :]))
def test_readingtextfile_array(self, mock_load):
out = CP.read_in_txt_file(filename='abcdedf0123')
self.assertTrue(np.array_equal(out, np.array([0.1, 0.2])),
msg=str('Expected array match: {}'.format(out)))