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[Thermo] adopt review comments for SolutionBase.restore_data

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Ingmar Schoegl 2019-09-24 23:39:48 -05:00 • committed by Ray Speth
parent 2b61d3ad4a
commit 074fd2cd74
3 changed files with 42 additions and 50 deletions
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42
interfaces/cython/cantera/composite.py
View file

@ -616,13 +616,14 @@ class SolutionArray:
if not isinstance(data, np.ndarray) or data.ndim != 2:
raise TypeError("restore_data only works for 2D ndarrays")
elif len(labels) != data.shape[1]:
raise ValueError("inconsistent data and label dimensions")
raise ValueError("inconsistent data and label dimensions: "
"({} vs. {})".format(len(labels), data.shape[1]))
rows = data.shape[0]
if self._shape!=(0,) and self._shape!=(rows,):
if self._shape != (0,) and self._shape != (rows,):
raise ValueError('incompatible dimensions.')
# get full state information (may differ depending on type of ThermoPhase)
full_states = [fs for fs in self._phase._full_states.values()]
full_states = self._phase._full_states.values()
if isinstance(self._phase, PureFluid):
# make sure that potentially non-unique state definitions are checked last
last = ['TP', 'TX', 'PX']
@ -635,16 +636,22 @@ class SolutionArray:
has_species = False
for prefix in ['X_', 'Y_']:
spc = ['{}{}'.format(prefix, s) for s in self.species_names]
# solution species names also found in labels
valid_species = {s[2:]: labels.index(s) for s in spc
if s in labels}
# labels that start with prefix (indicating concentration)
all_species = [l for l in labels if l[:2] == prefix]
if len(valid_species):
if valid_species:
# save species mode and remaining full_state candidates
mode = prefix[0]
full_states = [v[:-1] for v in full_states if mode in v]
break
if len(valid_species) != len(all_species):
raise ValueError('incompatible species information.')
incompatible = list(set(valid_species) ^ set(all_species))
raise ValueError('incompatible species information for '
'{}'.format(incompatible))
if mode == '':
# concentration specifier ('X' or 'Y') is not used
full_states = {v[:2] for v in full_states}
# determine suitable thermo properties for reconstruction
@ -656,25 +663,19 @@ class SolutionArray:
'H': ('h', 'enthalpy_{}'.format(basis)),
'S': ('s', 'entropy_{}'.format(basis))}
for fs in full_states:
# identify property specifiers
state = [{fs[i]: labels.index(p) for p in prop[fs[i]] if p in labels}
for i in range(len(fs))]
found = [len(state[i]) for i in range(len(fs))]
if all(found):
if all(state):
# all property identifiers match
mode = fs + mode
break
if len(mode) == 1:
raise ValueError('invalid/incomplete state information.')
# raise warning if state is potentially not uniquely defined
if isinstance(self._phase, PureFluid) and mode in last:
warnings.warn('Using mode `{}` to restore data: may not '
'be sufficient to define unique state '
'for a PureFluid phase'.format(mode),
UserWarning)
# assemble and restore state information
state_data = tuple([data[:, state[i][mode[i]]] for i in range(len(state))])
if len(valid_species):
if valid_species:
state_data += (np.zeros((rows, self.n_species)),)
for i, s in enumerate(self.species_names):
if s in valid_species:
@ -818,8 +819,7 @@ class SolutionArray:
"""
# read data block and header separately
data = np.genfromtxt(filename, skip_header=1, delimiter=',')
labels = np.genfromtxt(filename,
max_rows=1, delimiter=',', dtype=str)
labels = np.genfromtxt(filename, max_rows=1, delimiter=',', dtype=str)
self.restore_data(data, list(labels))
@ -834,7 +834,7 @@ class SolutionArray:
"""
if isinstance(_pandas, ImportError):
raise ImportError(_pandas.msg)
raise _pandas
data, labels = self.collect_data(cols, *args, **kwargs)
return _pandas.DataFrame(data=data, columns=labels)
@ -849,9 +849,9 @@ class SolutionArray:
"""
data = df.to_numpy(dtype=float)
labels = [col for col in df.columns]
labels = list(df.columns)
self.restore_data(data, list(labels))
self.restore_data(data, labels)
def write_hdf(self, filename, cols=('extra', 'T', 'density', 'Y'),
key='df', mode=None, append=None, complevel=None,
@ -905,7 +905,7 @@ class SolutionArray:
"""
if isinstance(_pandas, ImportError):
raise ImportError(_pandas.msg)
raise _pandas
pd_kwargs = {'key': key} if key else {}
self.from_pandas(_pandas.read_hdf(filename, **pd_kwargs))

43
interfaces/cython/cantera/test/test_thermo.py
View file

@ -1571,20 +1571,18 @@ class TestSolutionArray(utilities.CanteraTest):
except ImportError as err:
# pandas is not installed and correct exception is raised
pass
except Exception as err:
raise(err)
def test_restore(self):
def check(a, b, atol=None):
if atol is None:
fcn = lambda c, d: np.allclose(c, d)
self.assertArrayNear(a.T, b.T)
self.assertArrayNear(a.P, b.P)
self.assertArrayNear(a.X, b.X)
else:
fcn = lambda c, d: np.allclose(c, d, atol=atol)
check = fcn(a.T, b.T)
check &= fcn(a.P, b.P)
check &= fcn(a.X, b.X)
return check
self.assertArrayNear(a.T, b.T, atol=atol)
self.assertArrayNear(a.P, b.P, atol=atol)
self.assertArrayNear(a.X, b.X, atol=atol)
# test ThermoPhase
a = ct.SolutionArray(self.gas)
@ -1601,7 +1599,7 @@ class TestSolutionArray(utilities.CanteraTest):
# basic restore
b = ct.SolutionArray(self.gas)
b.restore_data(data, labels)
self.assertTrue(check(a, b))
check(a, b)
# skip concentrations
b = ct.SolutionArray(self.gas)
@ -1636,12 +1634,12 @@ class TestSolutionArray(utilities.CanteraTest):
# auto-detection of extra
b = ct.SolutionArray(self.gas)
b.restore_data(np.hstack([t, data]), ['time'] + labels)
self.assertTrue(check(a, b))
check(a, b)
# explicit extra
b = ct.SolutionArray(self.gas, extra=('time',))
b.restore_data(np.hstack([t, data]), ['time'] + labels)
self.assertTrue(check(a, b))
check(a, b)
self.assertTrue((b.time == t.ravel()).all())
# wrong extra
@ -1666,7 +1664,7 @@ class TestSolutionArray(utilities.CanteraTest):
# basic restore
b = ct.SolutionArray(self.gas)
b.restore_data(data, labels)
self.assertTrue(check(a, b, atol=1e-6))
check(a, b, atol=1e-6)
# skip calculated properties
cols = ('T', 'P', 'X', 'gibbs_mass', 'forward_rates_of_progress')
@ -1674,7 +1672,7 @@ class TestSolutionArray(utilities.CanteraTest):
b = ct.SolutionArray(self.gas)
b.restore_data(data, labels)
self.assertTrue(check(a, b))
check(a, b)
self.assertTrue(len(b._extra_arrays) == 0)
# test PureFluid
@ -1688,22 +1686,11 @@ class TestSolutionArray(utilities.CanteraTest):
b = ct.SolutionArray(w)
b.restore_data(data, labels)
self.assertTrue(check(a, b))
check(a, b)
# partial data
cols = ('T', 'X')
data, labels = a.collect_data(cols=cols)
with warnings.catch_warnings(record=True) as warn:
# cause all warnings to always be triggered.
warnings.simplefilter("always")
b = ct.SolutionArray(w)
b.restore_data(data, labels)
self.assertTrue(check(a, b))
self.assertTrue(len(warn) == 1)
self.assertTrue(issubclass(warn[-1].category, UserWarning))
self.assertTrue("may not be sufficient to define unique state"
in str(warn[-1].message))
b = ct.SolutionArray(w)
b.restore_data(data, labels)
check(a, b)

7
interfaces/cython/cantera/thermo.pyx
View file

@ -1581,7 +1581,12 @@ cdef class PureFluid(ThermoPhase):
elif np.isclose(X, 0.) or np.isclose(X, 1.):
self.TP = T, P
else:
raise ValueError('invalid thermodynamic state')
raise ValueError(
'invalid thermodynamic state: the TPX setter '
'received a combination of property values that '
'do not represent a valid state. As an alternative, '
'specify the state using two fully independent '
'properties (e.g. TD)')
property UVX:
"""