def _get_model_from_roundtrip(model):
_roundtrip_stringstream = IOStreamHandle(StringIO())
_roundtrip_streamreader = ParametricModelYamlReader(
_roundtrip_stringstream)
_roundtrip_streamwriter = ParametricModelYamlWriter(
model, _roundtrip_stringstream)
_roundtrip_streamwriter.write()
_roundtrip_stringstream.seek(0) # return to beginning
return _roundtrip_streamreader.read()
def setUp(self):
_data = [1, 1, 4, 1, 1, 4, 2, 5, 5, 5, 2, 4, 2, 2, 18, 2, 8, 8, 9]
_nbins = 3
self._container = HistContainer(n_bins=_nbins,
bin_range=(0.0, 10.),
fill_data=_data)
self._container.add_error(err_val=0.1,
name='SC5A_1',
correlation=0.5,
relative=False)
self._container.add_error(
err_val=[i / 10. for i in range(1, _nbins + 1)],
name='SC5A_2',
correlation=0.5,
relative=False)
self._container.add_matrix_error(err_matrix=np.eye(_nbins) * 0.1,
name='MCov',
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(err_matrix=np.eye(_nbins),
name='MCor',
relative=False,
matrix_type='correlation',
err_val=0.03)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_DATASET_HIST))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_HIST_MSSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
self._ref_testfile_n_bins = 2
self._ref_testfile_bin_range = [1.0, 3.0]
self._ref_testfile_bin_edges = [1.0, 2.0, 3.0]
self._ref_testfile_data = [1, 1]
self._ref_testfile_err = [0.89442719, 1]
self._ref_testfile_cov_mat = np.array([[0.8, 0.3], [0.3, 1.0]])
self._ref_testfile_error_names = {
'ErrorOne', 'ErrorTwo', 'ErrorThree', 'ErrorFour'
}
def setUp(self):
self._test_n_bins = 5
self._test_bin_range = (0, 5)
self._test_bin_edges = np.arange(6)
self._test_model_parameters = np.array([0.0, 0.08])
self._test_x = np.linspace(start=0.0, stop=5.0, num=11, endpoint=True)
self._test_parametric_model = HistParametricModel(
n_bins=self._test_n_bins,
bin_range=self._test_bin_range,
model_density_func=HistModelFunction(
TestHistParametricModelYamlRepresenter.linear_model),
model_parameters=self._test_model_parameters)
self._test_parametric_model_with_errors = HistParametricModel(
n_bins=self._test_n_bins,
bin_range=self._test_bin_range,
model_density_func=HistModelFunction(
TestHistParametricModelYamlRepresenter.linear_model),
model_parameters=self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(err_val=0.1,
name='test_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def setUp(self):
self._model_function_formatter = IndexedModelFunctionFormatter(
name='quadratic_model',
latex_name='quadratic model',
index_name='x',
latex_index_name='X',
arg_formatters=[
ParameterFormatter(arg_name='a',
value=1.1,
error=0.1,
latex_name='A'),
ParameterFormatter(arg_name='b',
value=2.2,
error=0.1,
latex_name='B'),
ParameterFormatter(arg_name='c',
value=3.3,
error=0.1,
latex_name='C')
],
expression_string='{0} * {x} ** 2 + {1} * {x} + {2}',
latex_expression_string='{0}{x}^2 + {1}{x} + {2}')
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER_INDEXED))
self._roundtrip_streamreader = ModelFunctionFormatterYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ModelFunctionFormatterYamlWriter(
self._model_function_formatter, self._roundtrip_stringstream)
self._testfile_streamreader = ModelFunctionFormatterYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER_INDEXED_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER_INDEXED_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ModelFunctionFormatterYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ModelFunctionFormatterYamlReader(
self._testfile_stringstream_extra_keyword)
def setUp(self):
self._test_x = np.arange(10)
self._test_a = 2.0
self._test_b = -1.0
self._test_y = self.linear_model(self._test_x, self._test_a,
self._test_b)
self._model_function = HistModelFunction(self.linear_model)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST))
self._testfile_stringstream_with_formatter = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_WITH_FORMATTER))
self._roundtrip_streamreader = ModelFunctionYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ModelFunctionYamlWriter(
self._model_function, self._roundtrip_stringstream)
self._testfile_streamreader = ModelFunctionYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_formatter = ModelFunctionYamlReader(
self._testfile_stringstream_with_formatter)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ModelFunctionYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ModelFunctionYamlReader(
self._testfile_stringstream_extra_keyword)
def setUp(self):
self._test_x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self._test_model_parameters = np.array([1.1, -1.5])
self._test_parametric_model = XYParametricModel(
self._test_x,
ModelFunctionBase(
TestXYParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors = XYParametricModel(
self._test_x,
ModelFunctionBase(
TestXYParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(axis='x',
err_val=0.1,
name='test_x_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def setUp(self):
self._model_parameter_formatter = ParameterFormatter(
'phi', name='ph', value=1.571, error=0.1, latex_name=r"\phi")
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER))
self._roundtrip_streamreader = ParameterFormatterYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ParameterFormatterYamlWriter(
self._model_parameter_formatter, self._roundtrip_stringstream)
self._testfile_streamreader = ParameterFormatterYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParameterFormatterYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParameterFormatterYamlReader(
self._testfile_stringstream_extra_keyword)
def setUp(self):
self._test_model_parameters = np.array([1.1, -1.5])
self._test_parametric_model = IndexedParametricModel(
IndexedModelFunction(
TestIndexedParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors = IndexedParametricModel(
IndexedModelFunction(
TestIndexedParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(err_val=0.1,
name='test_x_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def setup_streams(self):
self._testfile_stringstream = IOStreamHandle(StringIO(self.TEST_FIT))
self._testfile_stringstream_simple = IOStreamHandle(StringIO(self.TEST_FIT_SIMPLE))
self._testfile_streamreader = FitYamlReader(self._testfile_stringstream)
self._testfile_streamreader_simple = FitYamlReader(self._testfile_stringstream_simple)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_streamreader = FitYamlReader(self._roundtrip_stringstream)
self._roundtrip_streamwriter = FitYamlWriter(self._fit, self._roundtrip_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(StringIO(self.TEST_FIT_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(StringIO(self.TEST_FIT_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = FitYamlReader(self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = FitYamlReader(self._testfile_stringstream_extra_keyword)
def _get_model_from_string(input_string):
_testfile_stringstream = IOStreamHandle(StringIO(input_string))
return ParametricModelYamlReader(_testfile_stringstream).read()
class TestHistModelFunctionYamlRepresenter(unittest.TestCase):
@staticmethod
def linear_model(x, a, b):
return a * x + b
def setUp(self):
self._test_x = np.arange(10)
self._test_a = 2.0
self._test_b = -1.0
self._test_y = self.linear_model(self._test_x, self._test_a,
self._test_b)
self._model_function = HistModelFunction(self.linear_model)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST))
self._testfile_stringstream_with_formatter = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_WITH_FORMATTER))
self._roundtrip_streamreader = ModelFunctionYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ModelFunctionYamlWriter(
self._model_function, self._roundtrip_stringstream)
self._testfile_streamreader = ModelFunctionYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_formatter = ModelFunctionYamlReader(
self._testfile_stringstream_with_formatter)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ModelFunctionYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ModelFunctionYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_model_function = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_model_function, HistModelFunction))
self.assertTrue(
np.allclose(
_read_model_function.func(self._test_x, self._test_a,
self._test_b), self._test_y))
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_read_from_testfile_stream_with_formatter(self):
_read_model_function = self._testfile_streamreader_with_formatter.read(
)
self.assertTrue(isinstance(_read_model_function, HistModelFunction))
self.assertTrue(
np.allclose(
_read_model_function.func(self._test_x, self._test_a,
self._test_b), self._test_y))
_read_formatter = _read_model_function.formatter
self.assertTrue(isinstance(_read_formatter, ModelFunctionFormatter))
_read_arg_formatters = _read_formatter.arg_formatters
self.assertTrue(_read_formatter.name == 'linear_model')
self.assertTrue(_read_formatter.latex_name == 'linear model')
self.assertTrue(_read_arg_formatters[0].name == 'x')
self.assertTrue(_read_arg_formatters[0].latex_name == r'{r}')
self.assertTrue(_read_arg_formatters[1].name == 'alpha')
self.assertTrue(_read_arg_formatters[1].latex_name == r'{\alpha}')
self.assertTrue(_read_arg_formatters[2].name == 'beta')
self.assertTrue(_read_arg_formatters[2].latex_name == r'{\beta}')
self.assertTrue(
_read_formatter.expression_format_string == '{0} * {x} + {1}')
self.assertTrue(
_read_formatter.latex_expression_format_string == '{0}{x} + {1}')
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_model_function = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_model_function, HistModelFunction))
self.assertTrue(
np.allclose(
self._test_y,
_read_model_function.func(self._test_x, self._test_a,
self._test_b)))
_given_formatter = self._model_function.formatter
_read_formatter = _read_model_function.formatter
self.assertTrue(isinstance(_read_formatter, ModelFunctionFormatter))
_given_arg_formatters = _given_formatter.arg_formatters
_read_arg_formatters = _read_formatter.arg_formatters
self.assertTrue(_read_formatter.name == _given_formatter.name)
self.assertTrue(
_read_formatter.latex_name == _given_formatter.latex_name)
self.assertTrue(
_read_arg_formatters[0].name == _given_arg_formatters[0].name)
self.assertTrue(_read_arg_formatters[0].latex_name ==
_given_arg_formatters[0].latex_name)
self.assertTrue(
_read_arg_formatters[1].name == _given_arg_formatters[1].name)
self.assertTrue(_read_arg_formatters[1].latex_name ==
_given_arg_formatters[1].latex_name)
self.assertTrue(
_read_arg_formatters[2].name == _given_arg_formatters[2].name)
self.assertTrue(_read_arg_formatters[2].latex_name ==
_given_arg_formatters[2].latex_name)
self.assertTrue(_read_formatter.expression_format_string ==
_given_formatter.expression_format_string)
self.assertTrue(_read_formatter.latex_expression_format_string ==
_given_formatter.latex_expression_format_string)
class TestXYContainerYamlRepresentation(unittest.TestCase):
def setUp(self):
_data = [[0.0, .1, .3], [10, 24, 44]]
_ndat = len(_data[0])
self._container = XYContainer(x_data=_data[0], y_data=_data[1])
self._container.add_error(axis='y',
name="ySUA",
err_val=0.1,
correlation=0.0,
relative=False)
self._container.add_error(axis='y',
name="ySUR",
err_val=0.1,
correlation=0.0,
relative=True)
self._container.add_error(axis='y',
name="ySCA",
err_val=0.1,
correlation=1.0,
relative=False)
self._container.add_matrix_error(axis='y',
name="yMCov",
err_matrix=np.eye(_ndat) * 0.1,
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(axis='y',
name="yMCor",
err_matrix=np.eye(_ndat),
relative=False,
matrix_type='correlation',
err_val=0.1)
self._container.add_error(axis='x',
name="xSUA",
err_val=0.1,
correlation=0.0,
relative=False)
self._container.add_error(axis='x',
name="xSUR",
err_val=0.1,
correlation=0.0,
relative=True)
self._container.add_matrix_error(axis='x',
name="xMCov",
err_matrix=np.eye(_ndat) * 0.1,
relative=False,
matrix_type='covariance')
# self._container.add_simple_error(axis='x', err_val=0.1, correlation=0.0, relative=False)
# self._container.add_simple_error(axis='y', err_val=0.2, correlation=0.0, relative=False)
# self._container.add_matrix_error(axis='y', err_matrix=np.eye(8) * 0.1, relative=False, matrix_type='covariance')
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(StringIO(TEST_DATASET_XY))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_XY_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_XY_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
self._ref_testfile_x_data = [5, 17]
self._ref_testfile_y_data = [80.429, 80.339]
self._ref_testfile_x_err = [0.70710678, 0.70710678]
self._ref_testfile_y_err = [0.54772256, 0.54772256]
self._ref_testfile_y_cov_mat = np.array([[0.3, 0.1], [0.1, 0.3]])
self._ref_testfile_x_cov_mat = np.array([[0.5, 0.2], [0.2, 0.5]])
self._ref_testfile_error_names = {
'XErrorOne', 'XErrorTwo', 'YErrorOne', 'YErrorTwo'
}
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_container = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_container, XYContainer))
self.assertTrue(
np.allclose(_read_container.x, self._ref_testfile_x_data))
self.assertTrue(
np.allclose(_read_container.y, self._ref_testfile_y_data))
self.assertTrue(
np.allclose(_read_container.x_err, self._ref_testfile_x_err))
self.assertTrue(
np.allclose(_read_container.y_err, self._ref_testfile_y_err))
self.assertTrue(
np.allclose(
_read_container.x_cov_mat,
self._ref_testfile_x_cov_mat,
))
self.assertTrue(
np.allclose(
_read_container.y_cov_mat,
self._ref_testfile_y_cov_mat,
))
# check that the error names are the same
self.assertEqual(set(_read_container._error_dicts.keys()),
self._ref_testfile_error_names)
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_container = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_container, XYContainer))
# compare data members
self.assertTrue(np.allclose(self._container.x, _read_container.x))
self.assertTrue(np.allclose(self._container.y, _read_container.y))
# compare (total) errors and cov mats
# TODO: compare individual error components -> nontrivial because error ids change...
self.assertTrue(
np.allclose(self._container.x_err, _read_container.x_err))
self.assertTrue(
np.allclose(self._container.y_err, _read_container.y_err))
self.assertTrue(
np.allclose(self._container.x_cov_mat, _read_container.x_cov_mat))
self.assertTrue(
np.allclose(self._container.y_cov_mat, _read_container.y_cov_mat))
# check that the error names are the same
self.assertEqual(set(self._container._error_dicts.keys()),
set(_read_container._error_dicts.keys()))
class TestHistParametricModelYamlRepresenter(unittest.TestCase):
@staticmethod
def linear_model(x, a, b):
return a * x + b
def setUp(self):
self._test_n_bins = 5
self._test_bin_range = (0, 5)
self._test_bin_edges = np.arange(6)
self._test_model_parameters = np.array([0.0, 0.08])
self._test_x = np.linspace(start=0.0, stop=5.0, num=11, endpoint=True)
self._test_parametric_model = HistParametricModel(
n_bins=self._test_n_bins,
bin_range=self._test_bin_range,
model_density_func=HistModelFunction(
TestHistParametricModelYamlRepresenter.linear_model),
model_parameters=self._test_model_parameters)
self._test_parametric_model_with_errors = HistParametricModel(
n_bins=self._test_n_bins,
bin_range=self._test_bin_range,
model_density_func=HistModelFunction(
TestHistParametricModelYamlRepresenter.linear_model),
model_parameters=self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(err_val=0.1,
name='test_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_write_to_roundtrip_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
def test_read_from_testfile_stream(self):
_read_parametric_model = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_parametric_model,
HistParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(_read_parametric_model.n_bins == self._test_n_bins)
self.assertTrue(
np.allclose(_read_parametric_model.bin_range,
self._test_bin_range))
self.assertTrue(
np.allclose(_read_parametric_model.bin_edges,
self._test_bin_edges))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function_density(
self._test_x),
self._test_parametric_model.eval_model_function_density(
self._test_x)))
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_read_from_testfile_stream_with_errors(self):
_read_parametric_model = self._testfile_streamreader_with_errors.read()
self.assertTrue(isinstance(_read_parametric_model,
HistParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(_read_parametric_model.n_bins == self._test_n_bins)
self.assertTrue(
np.allclose(_read_parametric_model.bin_range,
self._test_bin_range))
self.assertTrue(
np.allclose(_read_parametric_model.bin_edges,
self._test_bin_edges))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function_density(
self._test_x),
self._test_parametric_model_with_errors.
eval_model_function_density(self._test_x)))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_error')
_read_error = _read_parametric_model.get_error('test_error')
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_parametric_model,
HistParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(_read_parametric_model.n_bins == self._test_n_bins)
self.assertTrue(
np.allclose(_read_parametric_model.bin_range,
self._test_bin_range))
self.assertTrue(
np.allclose(_read_parametric_model.bin_edges,
self._test_bin_edges))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function_density(
self._test_x),
self._test_parametric_model.eval_model_function_density(
self._test_x)))
def test_round_trip_with_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
self._roundtrip_stringstream_with_errors.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader_with_errors.read(
)
self.assertTrue(isinstance(_read_parametric_model,
HistParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(_read_parametric_model.n_bins == self._test_n_bins)
self.assertTrue(
np.allclose(_read_parametric_model.bin_range,
self._test_bin_range))
self.assertTrue(
np.allclose(_read_parametric_model.bin_edges,
self._test_bin_edges))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function_density(
self._test_x),
self._test_parametric_model_with_errors.
eval_model_function_density(self._test_x)))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_error')
_read_error = _read_parametric_model.get_error('test_error')
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
def setUp(self):
_data = [[0.0, .1, .3], [10, 24, 44]]
_ndat = len(_data[0])
self._container = XYContainer(x_data=_data[0], y_data=_data[1])
self._container.add_error(axis='y',
name="ySUA",
err_val=0.1,
correlation=0.0,
relative=False)
self._container.add_error(axis='y',
name="ySUR",
err_val=0.1,
correlation=0.0,
relative=True)
self._container.add_error(axis='y',
name="ySCA",
err_val=0.1,
correlation=1.0,
relative=False)
self._container.add_matrix_error(axis='y',
name="yMCov",
err_matrix=np.eye(_ndat) * 0.1,
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(axis='y',
name="yMCor",
err_matrix=np.eye(_ndat),
relative=False,
matrix_type='correlation',
err_val=0.1)
self._container.add_error(axis='x',
name="xSUA",
err_val=0.1,
correlation=0.0,
relative=False)
self._container.add_error(axis='x',
name="xSUR",
err_val=0.1,
correlation=0.0,
relative=True)
self._container.add_matrix_error(axis='x',
name="xMCov",
err_matrix=np.eye(_ndat) * 0.1,
relative=False,
matrix_type='covariance')
# self._container.add_simple_error(axis='x', err_val=0.1, correlation=0.0, relative=False)
# self._container.add_simple_error(axis='y', err_val=0.2, correlation=0.0, relative=False)
# self._container.add_matrix_error(axis='y', err_matrix=np.eye(8) * 0.1, relative=False, matrix_type='covariance')
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(StringIO(TEST_DATASET_XY))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_XY_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_XY_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
self._ref_testfile_x_data = [5, 17]
self._ref_testfile_y_data = [80.429, 80.339]
self._ref_testfile_x_err = [0.70710678, 0.70710678]
self._ref_testfile_y_err = [0.54772256, 0.54772256]
self._ref_testfile_y_cov_mat = np.array([[0.3, 0.1], [0.1, 0.3]])
self._ref_testfile_x_cov_mat = np.array([[0.5, 0.2], [0.2, 0.5]])
self._ref_testfile_error_names = {
'XErrorOne', 'XErrorTwo', 'YErrorOne', 'YErrorTwo'
}
class TestXYParametricModelYamlRepresenter(unittest.TestCase):
@staticmethod
def linear_model(x, a, b):
return a * x + b
def setUp(self):
self._test_x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self._test_model_parameters = np.array([1.1, -1.5])
self._test_parametric_model = XYParametricModel(
self._test_x,
ModelFunctionBase(
TestXYParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors = XYParametricModel(
self._test_x,
ModelFunctionBase(
TestXYParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(axis='x',
err_val=0.1,
name='test_x_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_XY_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_write_to_roundtrip_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
def test_read_from_testfile_stream(self):
_read_parametric_model = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_parametric_model, XYParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
_read_parametric_model.x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self.assertTrue(
np.allclose(_read_parametric_model.y,
self._test_parametric_model.y))
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_read_from_testfile_stream_with_errors(self):
_read_parametric_model = self._testfile_streamreader_with_errors.read()
self.assertTrue(isinstance(_read_parametric_model, XYParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
_read_parametric_model.x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self.assertTrue(
np.allclose(_read_parametric_model.y,
self._test_parametric_model_with_errors.y))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_x_error')
_read_error = _read_parametric_model.get_error('test_x_error')
self.assertTrue(_given_error['axis'] == _read_error['axis'])
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_parametric_model, XYParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
_read_parametric_model.x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self.assertTrue(
np.allclose(_read_parametric_model.y,
self._test_parametric_model.y))
def test_round_trip_with_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
self._roundtrip_stringstream_with_errors.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader_with_errors.read(
)
self.assertTrue(isinstance(_read_parametric_model, XYParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
_read_parametric_model.x = np.array([0.0, 1.0, 2.0, 3.0, 4.0, 5.0])
self.assertTrue(
np.allclose(_read_parametric_model.y,
self._test_parametric_model_with_errors.y))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_x_error')
_read_error = _read_parametric_model.get_error('test_x_error')
self.assertTrue(_given_error['axis'] == _read_error['axis'])
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
class TestHistContainerYamlRepresentation(unittest.TestCase):
def setUp(self):
_data = [1, 1, 4, 1, 1, 4, 2, 5, 5, 5, 2, 4, 2, 2, 18, 2, 8, 8, 9]
_nbins = 3
self._container = HistContainer(n_bins=_nbins,
bin_range=(0.0, 10.),
fill_data=_data)
self._container.add_error(err_val=0.1,
name='SC5A_1',
correlation=0.5,
relative=False)
self._container.add_error(
err_val=[i / 10. for i in range(1, _nbins + 1)],
name='SC5A_2',
correlation=0.5,
relative=False)
self._container.add_matrix_error(err_matrix=np.eye(_nbins) * 0.1,
name='MCov',
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(err_matrix=np.eye(_nbins),
name='MCor',
relative=False,
matrix_type='correlation',
err_val=0.03)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_DATASET_HIST))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_HIST_MSSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_HIST_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
self._ref_testfile_n_bins = 2
self._ref_testfile_bin_range = [1.0, 3.0]
self._ref_testfile_bin_edges = [1.0, 2.0, 3.0]
self._ref_testfile_data = [1, 1]
self._ref_testfile_err = [0.89442719, 1]
self._ref_testfile_cov_mat = np.array([[0.8, 0.3], [0.3, 1.0]])
self._ref_testfile_error_names = {
'ErrorOne', 'ErrorTwo', 'ErrorThree', 'ErrorFour'
}
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_container = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_container, HistContainer))
self.assertTrue(_read_container.n_bins == self._ref_testfile_n_bins)
self.assertTrue(
np.allclose(_read_container.bin_range,
self._ref_testfile_bin_range))
self.assertTrue(
np.allclose(_read_container.bin_edges,
self._ref_testfile_bin_edges))
self.assertTrue(
np.allclose(_read_container.data, self._ref_testfile_data))
self.assertTrue(
np.allclose(_read_container.err, self._ref_testfile_err))
self.assertTrue(
np.allclose(
_read_container.cov_mat,
self._ref_testfile_cov_mat,
))
# check that the error names are the same
self.assertEqual(set(_read_container._error_dicts.keys()),
self._ref_testfile_error_names)
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_container = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_container, HistContainer))
self.assertTrue(self._container.n_bins == _read_container.n_bins)
self.assertTrue(
np.allclose(self._container.bin_range, _read_container.bin_range))
self.assertTrue(
np.allclose(self._container.bin_edges, _read_container.bin_edges))
# compare data members
self.assertTrue(np.allclose(self._container.data,
_read_container.data))
# compare (total) errors and cov mats
# TODO: compare individual error components -> nontrivial because error ids change...
self.assertTrue(np.allclose(self._container.err, _read_container.err))
self.assertTrue(
np.allclose(self._container.cov_mat, _read_container.cov_mat))
# check that the error names are the same
self.assertEqual(set(self._container._error_dicts.keys()),
set(_read_container._error_dicts.keys()))
class TestIndexedContainerYamlRepresentation(unittest.TestCase):
def setUp(self):
_data = [4, 5, 6, 2, 4, 5., 3.01e-5, 4.4e+45]
_ndat = len(_data)
self._container = IndexedContainer(data=_data)
self._container.add_error(err_val=0.1,
name="SUA",
correlation=0.0,
relative=False)
self._container.add_error(err_val=0.1,
name="SUR",
correlation=0.0,
relative=True)
self._container.add_error(err_val=0.1,
name="SCA",
correlation=1.0,
relative=False)
self._container.add_matrix_error(err_matrix=np.eye(_ndat) * 0.1,
name="MCov",
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(err_matrix=np.eye(_ndat),
name="MCor",
relative=False,
matrix_type='correlation',
err_val=0.1)
# # xy
# self._container.add_simple_error(axis='x', err_val=0.1, correlation=0.0, relative=False)
# self._container.add_simple_error(axis='y', err_val=0.2, correlation=0.0, relative=False)
# self._container.add_matrix_error(axis='y', err_matrix=np.eye(8) * 0.1, relative=False, matrix_type='covariance')
# # hist
# self._container.add_simple_error(err_val=2, correlation=0.5, relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._ref_testfile_data = [80.429, 80.339]
self._ref_testfile_err = [0.89442719, 0.89442719]
self._ref_testfile_cov_mat = np.array([[0.8, 0.3], [0.3, 0.8]])
self._ref_testfile_error_names = {
'ErrorOne', 'ErrorTwo', 'ErrorThree', 'ErrorFour'
}
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_container = self._testfile_streamreader.read()
self.assertTrue(isinstance(_read_container, IndexedContainer))
self.assertTrue(
np.allclose(_read_container.data, self._ref_testfile_data))
self.assertTrue(
np.allclose(_read_container.err, self._ref_testfile_err))
self.assertTrue(
np.allclose(
_read_container.cov_mat,
self._ref_testfile_cov_mat,
))
# check that the error names are the same
self.assertEqual(set(_read_container._error_dicts.keys()),
self._ref_testfile_error_names)
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_container = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_container, IndexedContainer))
# compare data members
self.assertTrue(np.allclose(self._container.data,
_read_container.data))
# compare (total) errors and cov mats
# TODO: compare individual error components -> nontrivial because error ids change...
self.assertTrue(np.allclose(self._container.err, _read_container.err))
self.assertTrue(
np.allclose(self._container.cov_mat, _read_container.cov_mat))
# check that the error names are the same
self.assertEqual(set(self._container._error_dicts.keys()),
set(_read_container._error_dicts.keys()))
def setUp(self):
_data = [4, 5, 6, 2, 4, 5., 3.01e-5, 4.4e+45]
_ndat = len(_data)
self._container = IndexedContainer(data=_data)
self._container.add_error(err_val=0.1,
name="SUA",
correlation=0.0,
relative=False)
self._container.add_error(err_val=0.1,
name="SUR",
correlation=0.0,
relative=True)
self._container.add_error(err_val=0.1,
name="SCA",
correlation=1.0,
relative=False)
self._container.add_matrix_error(err_matrix=np.eye(_ndat) * 0.1,
name="MCov",
relative=False,
matrix_type='covariance')
self._container.add_matrix_error(err_matrix=np.eye(_ndat),
name="MCor",
relative=False,
matrix_type='correlation',
err_val=0.1)
# # xy
# self._container.add_simple_error(axis='x', err_val=0.1, correlation=0.0, relative=False)
# self._container.add_simple_error(axis='y', err_val=0.2, correlation=0.0, relative=False)
# self._container.add_matrix_error(axis='y', err_matrix=np.eye(8) * 0.1, relative=False, matrix_type='covariance')
# # hist
# self._container.add_simple_error(err_val=2, correlation=0.5, relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED))
self._roundtrip_streamreader = DataContainerYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = DataContainerYamlWriter(
self._container, self._roundtrip_stringstream)
self._testfile_streamreader = DataContainerYamlReader(
self._testfile_stringstream)
self._ref_testfile_data = [80.429, 80.339]
self._ref_testfile_err = [0.89442719, 0.89442719]
self._ref_testfile_cov_mat = np.array([[0.8, 0.3], [0.3, 0.8]])
self._ref_testfile_error_names = {
'ErrorOne', 'ErrorTwo', 'ErrorThree', 'ErrorFour'
}
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_DATASET_INDEXED_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = DataContainerYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = DataContainerYamlReader(
self._testfile_stringstream_extra_keyword)
class TestModelParameterFormatterYamlRepresenter(unittest.TestCase):
def setUp(self):
self._model_parameter_formatter = ParameterFormatter(
'phi', name='ph', value=1.571, error=0.1, latex_name=r"\phi")
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER))
self._roundtrip_streamreader = ParameterFormatterYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ParameterFormatterYamlWriter(
self._model_parameter_formatter, self._roundtrip_stringstream)
self._testfile_streamreader = ParameterFormatterYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_PARAMETER_FORMATTER_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParameterFormatterYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParameterFormatterYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_model_parameter_formatter = self._testfile_streamreader.read()
self.assertTrue(
isinstance(_read_model_parameter_formatter, ParameterFormatter))
self.assertTrue(_read_model_parameter_formatter.name ==
self._model_parameter_formatter.name)
self.assertTrue(_read_model_parameter_formatter.value is None)
self.assertTrue(_read_model_parameter_formatter.error is None)
self.assertTrue(_read_model_parameter_formatter.latex_name ==
self._model_parameter_formatter.latex_name)
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_parameter_formatter = self._roundtrip_streamreader.read()
self.assertTrue(
isinstance(_read_parameter_formatter, ParameterFormatter))
self.assertTrue(_read_parameter_formatter.name ==
self._model_parameter_formatter.name)
self.assertTrue(_read_parameter_formatter.value is None)
self.assertTrue(_read_parameter_formatter.error is None)
self.assertTrue(_read_parameter_formatter.latex_name ==
self._model_parameter_formatter.latex_name)
class TestIndexedParametricModelYamlRepresenter(unittest.TestCase):
TEST_X = np.arange(6)
@staticmethod
def linear_model(a, b):
return a * np.arange(6) + b
def setUp(self):
self._test_model_parameters = np.array([1.1, -1.5])
self._test_parametric_model = IndexedParametricModel(
IndexedModelFunction(
TestIndexedParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors = IndexedParametricModel(
IndexedModelFunction(
TestIndexedParametricModelYamlRepresenter.linear_model),
self._test_model_parameters)
self._test_parametric_model_with_errors.add_error(err_val=0.1,
name='test_x_error',
correlation=0,
relative=False)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_stringstream_with_errors = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED))
self._testfile_stringstream_with_errors = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_WITH_ERRORS))
self._roundtrip_streamreader = ParametricModelYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamreader_with_errors = ParametricModelYamlReader(
self._roundtrip_stringstream_with_errors)
self._roundtrip_streamwriter = ParametricModelYamlWriter(
self._test_parametric_model, self._roundtrip_stringstream)
self._roundtrip_streamwriter_with_errors = ParametricModelYamlWriter(
self._test_parametric_model_with_errors,
self._roundtrip_stringstream_with_errors)
self._testfile_streamreader = ParametricModelYamlReader(
self._testfile_stringstream)
self._testfile_streamreader_with_errors = ParametricModelYamlReader(
self._testfile_stringstream_with_errors)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_PARAMETRIC_MODEL_INDEXED_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ParametricModelYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ParametricModelYamlReader(
self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_write_to_roundtrip_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
def test_read_from_testfile_stream(self):
_read_parametric_model = self._testfile_streamreader.read()
self.assertTrue(
isinstance(_read_parametric_model, IndexedParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(
np.allclose(_read_parametric_model.eval_model_function(),
self._test_parametric_model.eval_model_function()))
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_read_from_testfile_stream_with_errors(self):
_read_parametric_model = self._testfile_streamreader_with_errors.read()
self.assertTrue(
isinstance(_read_parametric_model, IndexedParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function(),
self._test_parametric_model_with_errors.eval_model_function()))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_x_error')
_read_error = _read_parametric_model.get_error('test_error')
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader.read()
self.assertTrue(
isinstance(_read_parametric_model, IndexedParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(
np.allclose(_read_parametric_model.eval_model_function(),
self._test_parametric_model.eval_model_function()))
def test_round_trip_with_stringstream_with_errors(self):
self._roundtrip_streamwriter_with_errors.write()
self._roundtrip_stringstream_with_errors.seek(0) # return to beginning
_read_parametric_model = self._roundtrip_streamreader_with_errors.read(
)
self.assertTrue(
isinstance(_read_parametric_model, IndexedParametricModel))
self.assertTrue(
np.allclose(_read_parametric_model.parameters,
self._test_model_parameters))
self.assertTrue(
np.allclose(
_read_parametric_model.eval_model_function(),
self._test_parametric_model_with_errors.eval_model_function()))
_given_error = self._test_parametric_model_with_errors.get_error(
'test_x_error')
_read_error = _read_parametric_model.get_error('test_x_error')
self.assertTrue(_given_error['enabled'] == _read_error['enabled'])
self.assertTrue(
np.allclose(_given_error['err'].error, _read_error['err'].error))
self.assertTrue(
_given_error['err'].corr_coeff == _read_error['err'].corr_coeff)
class TestModelFunctionFormatterYamlRepresenter(unittest.TestCase):
def setUp(self):
self._model_function_formatter = ModelFunctionFormatter(
name='quadratic_model',
latex_name='quadratic model',
arg_formatters=[
ParameterFormatter(arg_name='x', latex_name='X'),
ParameterFormatter(arg_name='a',
value=1.1,
error=0.1,
latex_name='A'),
ParameterFormatter(arg_name='b',
value=2.2,
error=0.1,
latex_name='B'),
ParameterFormatter(arg_name='c',
value=3.3,
error=0.1,
latex_name='C')
],
expression_string='{0} * {x} ** 2 + {1} * {x} + {2}',
latex_expression_string='{0}{x}^2 + {1}{x} + {2}')
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._testfile_stringstream = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER))
self._roundtrip_streamreader = ModelFunctionFormatterYamlReader(
self._roundtrip_stringstream)
self._roundtrip_streamwriter = ModelFunctionFormatterYamlWriter(
self._model_function_formatter, self._roundtrip_stringstream)
self._testfile_streamreader = ModelFunctionFormatterYamlReader(
self._testfile_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(
StringIO(TEST_MODEL_FUNCTION_FORMATTER_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = ModelFunctionFormatterYamlReader(
self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = ModelFunctionFormatterYamlReader(
self._testfile_stringstream_extra_keyword)
def _assert_model_function_formatters_equal(self, formatter1, formatter2):
self.assertTrue(formatter1.name == formatter2.name)
self.assertTrue(formatter1.latex_name == formatter2.latex_name)
for _arg_formatter_1, _arg_formatter_2 in zip(
formatter1._arg_formatters, formatter2._arg_formatters):
self.assertTrue(_arg_formatter_1.name == _arg_formatter_2.name)
self.assertTrue(
_arg_formatter_1.latex_name == _arg_formatter_2.latex_name)
self.assertTrue(formatter1.expression_format_string ==
formatter2.expression_format_string)
self.assertTrue(formatter1.latex_expression_format_string ==
formatter2.latex_expression_format_string)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream(self):
_read_model_function_formatter = self._testfile_streamreader.read()
self.assertTrue(
isinstance(_read_model_function_formatter, ModelFunctionFormatter))
self._assert_model_function_formatters_equal(
_read_model_function_formatter, self._model_function_formatter)
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_with_stringstream(self):
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_model_function_formatter = self._roundtrip_streamreader.read()
self.assertTrue(
isinstance(_read_model_function_formatter, ModelFunctionFormatter))
self._assert_model_function_formatters_equal(
_read_model_function_formatter, self._model_function_formatter)
class AbstractTestFitRepresenter(object):
FIT_CLASS = None
TEST_FIT = None
TEST_FIT_SIMPLE = None
TEST_FIT_MISSING_KEYWORD = None
TEST_FIT_EXTRA_KEYWORD = None
@abc.abstractmethod
def setUp(self):
pass
def setup_streams(self):
self._testfile_stringstream = IOStreamHandle(StringIO(self.TEST_FIT))
self._testfile_stringstream_simple = IOStreamHandle(StringIO(self.TEST_FIT_SIMPLE))
self._testfile_streamreader = FitYamlReader(self._testfile_stringstream)
self._testfile_streamreader_simple = FitYamlReader(self._testfile_stringstream_simple)
self._roundtrip_stringstream = IOStreamHandle(StringIO())
self._roundtrip_streamreader = FitYamlReader(self._roundtrip_stringstream)
self._roundtrip_streamwriter = FitYamlWriter(self._fit, self._roundtrip_stringstream)
self._testfile_stringstream_missing_keyword = IOStreamHandle(StringIO(self.TEST_FIT_MISSING_KEYWORD))
self._testfile_stringstream_extra_keyword = IOStreamHandle(StringIO(self.TEST_FIT_EXTRA_KEYWORD))
self._testfile_streamreader_missing_keyword = FitYamlReader(self._testfile_stringstream_missing_keyword)
self._testfile_streamreader_extra_keyword = FitYamlReader(self._testfile_stringstream_extra_keyword)
def test_write_to_roundtrip_stringstream(self):
self._roundtrip_streamwriter.write()
def test_read_from_testfile_stream_missing_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_missing_keyword.read()
def test_read_from_testfile_stream_extra_keyword(self):
with self.assertRaises(YamlReaderException):
self._testfile_streamreader_extra_keyword.read()
def test_round_trip_save_results(self):
self._fit.do_fit()
self._roundtrip_streamwriter.write()
self._roundtrip_stringstream.seek(0) # return to beginning
_read_fit = self._roundtrip_streamreader.read()
self.assertTrue(isinstance(_read_fit, self.FIT_CLASS))
self.assertTrue(self._fit.did_fit == _read_fit.did_fit)
self.assertTrue(
np.allclose(
self._fit.parameter_cov_mat,
_read_fit.parameter_cov_mat
)
)
self.assertTrue(
np.allclose(
self._fit.parameter_errors,
_read_fit.parameter_errors
)
)
self.assertTrue(
np.allclose(
self._fit.parameter_cor_mat,
_read_fit.parameter_cor_mat
)
)
