def __init__(self, lower=-10, upper=5, n_bins=1500):
self.n_bins = n_bins
self.n_bin_edges = self.n_bins + 1
self.lower_bin_edge = lower
self.upper_bin_edge = upper
self.bin_range = self.upper_bin_edge - self.lower_bin_edge
# Size bins
self.size_bins = initialize_bins(self.lower_bin_edge,
self.upper_bin_edge, self.n_bin_edges)
self.size_bins_medians = calculate_bins_medians(self.size_bins)
# Volume bins
self.volume_bins = calculate_volume_sphere(self.size_bins)
self.volume_bins_medians = calculate_bins_medians(self.volume_bins)
# Search size bins
self.search_size_bins = \
initialize_bins(self.lower_bin_edge - self.bin_range,
self.upper_bin_edge,
self.n_bin_edges*2-1)
self.search_size_bins_medians = \
calculate_bins_medians(self.search_size_bins)
self.ratio_search_size_bins = \
calculate_ratio_bins(self.search_size_bins_medians)
# Search volume bins
self.search_volume_bins = \
calculate_volume_sphere(self.search_size_bins)
self.search_volume_bins_medians = \
calculate_bins_medians(self.search_volume_bins)
self.ratio_search_volume_bins = \
calculate_ratio_bins(self.search_volume_bins_medians)
def test_correct_outcome_of_radii(self, fixture_crystal_diameters):
radii = fixture_crystal_diameters / 2
actual = gen.calculate_volume_sphere(fixture_crystal_diameters,
diameter=False)
expected = \
np.array([4.18879020e-03, 4.18879020e+03, 6.54498469e-05]) * 8
assert actual == pytest.approx(expected)
def simulate_N_crystals(self, m):
"""Request crystals from CSD until accounted modal volume is
filled.
Idea: use pdf to speed up process --> This can only be done if
the CSD is converted to a 'crystal volume distribution'.
From this, the number of crystals per mineral class will be
known while also giving the total number of crystals (N) in 1 m³
of parent rock.
"""
total_volume_mineral = 0
requested_volume = self.pr_modal_volume[m]
crystals = []
crystals_append = crystals.append
crystals_total = 0
# crystals_total_append = crystals_total.append
rs = 0
while total_volume_mineral < requested_volume:
# volume that still needs to be filled with crystals
diff = requested_volume - total_volume_mineral
# ‘m’ represents the current mineral class
# +1 so that each time at least one crystal is requested
crystals_requested = \
int(diff / (self.pr_modal_mineralogy[m] * self.learning_rate)) + 1
# print(crystals_requested, end=", ")
crystals_total += crystals_requested
crystals_to_add = \
np.exp(self.pr_csds[m].rvs(size=crystals_requested,
random_state=rs))
crystals_append(gen.calculate_volume_sphere(crystals_to_add))
total_volume_mineral += np.sum(crystals[rs])
# print(requested_volume, total_volume_mineral)
rs += 1
try:
crystals_array = np.concatenate(crystals)
except ValueError:
crystals_array = np.array(crystals)
crystals_binned = \
(np.searchsorted(self.volume_bins,
crystals_array) - 1).astype(np.uint16)
# Capture and correct crystals that fall outside
# the leftmost bin as they end up as bin 0 but since 1 gets
# subtracted from all bins they end up as the highest value
# of np.uint16 as negative values are not possible
crystals_binned[crystals_binned > self.n_bins] = 0
return crystals_total, np.sum(crystals_total), \
total_volume_mineral, crystals_binned
def __init__(self):
# Create bin matrices to capture chemical weathering
self.size_bins_matrix = \
self.create_bins_matrix(self.size_bins)
self.volume_bins_matrix = \
calculate_volume_sphere(self.size_bins_matrix)
self.size_bins_medians_matrix = \
calculate_bins_medians(self.size_bins_matrix)
self.volume_bins_medians_matrix = \
calculate_bins_medians(self.volume_bins_matrix)
# Volume change matrix
self.volume_change_matrix = -np.diff(self.volume_bins_medians_matrix,
axis=0)
# Negative bin array thresholds
self.negative_volume_thresholds = \
np.argmax(self.size_bins_medians_matrix > 0, axis=2)
# Create search_bins_matrix
self.search_size_bins_matrix = \
self.create_bins_matrix(self.search_size_bins)
self.search_volume_bins_matrix = \
calculate_volume_sphere(self.search_size_bins_matrix)
# Create search_bins_medians_matrix
self.search_size_bins_medians_matrix = \
calculate_bins_medians(self.search_size_bins_matrix)
self.search_volume_bins_medians_matrix = \
calculate_bins_medians(self.search_volume_bins_matrix)
# Create ratio_search_bins_matrix
self.ratio_search_size_bins_matrix = calculate_ratio_bins(
self.search_size_bins_medians_matrix)
self.ratio_search_volume_bins_matrix = calculate_ratio_bins(
self.search_volume_bins_medians_matrix)
def test_correct_outcome_of_diameters(self, fixture_crystal_diameters):
actual = gen.calculate_volume_sphere(fixture_crystal_diameters)
expected = np.array([4.18879020e-03, 4.18879020e+03, 6.54498469e-05])
assert actual == pytest.approx(expected)