def depletion_degrees():
with app.app_context():
ree_data = sample_ree(normalized=True)
major_element_data = whole_rock_major_elements(dataframe=True)
mineral_data = xenolith_minerals("normalized_weight")
model = DepletionModel(argv[1])
_ = [get_spinel_data(s) for s in mineral_data]
spinel_data = DataFrame.from_dict(_).set_index('id')
ree_fit = model.fit_HREE(ree_data)
# Solid composition data is in %wt of solid component
Mg_fit = model.fit('Solid Composition', major_element_data, 'MgO')
Al_fit = model.fit('Solid Composition', major_element_data, 'Al2O3')
def series():
"""
Rename series for consistency
"""
fits = (ree_fit, Mg_fit, Al_fit)
names = ('ree', 'MgO', 'Al2O3')
for fit, name in zip(fits, names):
s = fit['mass']
s.name = name
yield s
masses = concat(list(series()), axis=1)
depletion = (100 - masses).reset_index()
return [r.to_dict() for i, r in depletion.iterrows()]
def create_data():
with app.app_context():
data = [
sample_temperatures(s, distinct=min, uncertainties=True)
for s in xenoliths()
]
with open(cache, "wb") as f:
dump(data, f)
return data
def ree_data(sample_id):
with app.app_context():
s = Sample.query.get(sample_id)
s.to_remove = for_removal[s.id]
# Index of elements to remove from regression
ix = N.in1d(rare_earths, s.to_remove)
s.X, s.Y = ree_pyroxene(s, 1.5) # Pressure in GPa
s.res = regress(s.X[~ix], s.Y[~ix])
s.temperature = temperature(s.res)
return s
def run_model():
fig, ax = plt.subplots(figsize=(4, 3.5))
with app.app_context():
data = sample_ree(normalized=True)
colors = sample_colors()
model = DepletionModel(argv[1])
ree_scatter(ax, model, data, colors)
ax.set_xlabel(r'HREE depletion degrees (%)')
ax.set_ylabel(r'Mass ratio: re-enriching fluid/sample')
ax.set_xlim([0, 20])
ax.set_ylim([0, 0.012])
fig.savefig('output/ree-trends.pdf', bbox_inches='tight')
import numpy as N
from uncertainties import ufloat
from figurator import tex_renderer, write_file
from xenoliths import app
from data import ree_data, summary_data
template = tex_renderer.get_template("temperature.tex")
with app.app_context():
text = template.render(samples=summary_data())
write_file("build/temperatures.tex", text)
def run_model(src, dst, clinopyroxene=False):
with app.app_context():
data = sample_ree(normalized=True, mode='whole_rock')
colors = sample_colors()
model = DepletionModel(src)
depleted = model.fit_HREE(data)
trace = model.tables['Solid Trace']
fig, ax = subplots(1, 1, figsize=(3.5, 3.5))
ax.plot(trace.Temperature, trace.Pressure / 1e4, 'k')
ax.set_ylabel(r'Pressure (GPa)')
ax.set_xlabel("Temperature (\u00b0C)")
df = concat([depleted, colors], axis=1)
ax.scatter(df.Temperature,
df.Pressure / 1e4,
color="white",
s=50,
zorder=8)
ax.scatter(df.Temperature,
df.Pressure / 1e4,
color=df.color,
s=20,
zorder=10)
for i, row in df.iterrows():
y = 0
x = 5
if i in ['CK-3', 'CK-7']:
x -= 28
y -= 5
ax.annotate(i,
xy=(row.Temperature, row.Pressure / 1e4),
color=row.color,
xytext=(x, y),
textcoords='offset points')
ax.set_ylim([2.5, 0])
ax.set_xlim([1230, 1350])
ax.annotate("garnet out",
xy=(1345, 2.05),
xytext=(-28, 2),
textcoords='offset points',
size=7,
style='italic')
ax.annotate("start: DMM at 3.0 GPa, 1350ºC",
xy=(1340, 2.5),
xytext=(-15, 2),
textcoords='offset points',
ha='right',
va='bottom',
size=7)
ax.annotate("↓",
xy=(1340, 2.5),
rotation=25,
xytext=(-7, 2),
textcoords='offset points',
ha='right',
va='bottom',
size=10)
update_axes(ax)
fig.savefig(dst, bbox_inches='tight')
def sample_colors():
with app.app_context():
samples = xenoliths()
return [s.color for s in samples]
def run_model(src, dst, clinopyroxene=False):
with app.app_context():
data = sample_ree(normalized=True,
mode='cpx' if clinopyroxene else 'whole_rock')
colors = sample_colors()
model = DepletionModel(src)
if clinopyroxene:
depleted = model.fit_HREE(data, table='clinopyroxene_0 trace')
else:
depleted = model.fit_HREE(data)
enrichment, multiplier = model.enrichment(data, depleted)
# Create primitive-mantle normalized dataset
Sun_PM = get_melts_data('literature/Sun_McDonough_PM.melts')
PM_trace = Sun_PM.trace.ix[:, 0]
# Add NMORB
NMORB = get_melts_data('literature/NMORB_trace.melts')
NMORB_trace = ree_only(NMORB.trace.transpose() / PM_trace)
# Alkali basalt
alkali = read_table('literature/Farmer_1995-Alkali-basalt.txt',
comment="#",
index_col=0)
alkali /= PM_trace
alkali_trace = ree_only(alkali)
vals = [element(i) for i in data.columns]
d = ree_only(depleted)
grid = dict(height_ratios=(4.5, 1), hspace=0.1, right=0.99, left=0.16)
fig, (ax1, ax2) = subplots(2, 1, figsize=(3.5, 6), gridspec_kw=grid)
def create_main_axis(ax):
for i, row in d.iterrows():
c = colors.ix[row.name][0]
# Plot real data
series = data.ix[row.name]
u = series.map(lambda x: x.n)
s = series.map(lambda x: x.s)
ax.fill_between(vals,
u - s,
u + s,
facecolor=c,
edgecolor='none',
alpha=0.2)
def plot(name, x, y, **kwargs):
if i == 'CK-3':
kwargs['label'] = name
else:
kwargs['label'] = ""
p = ax.plot(x, y, color=c, **kwargs)
if clinopyroxene:
s = 'clinopyroxene'
else:
s = 'whole-rock'
plot('Measured ' + s, vals, u)
# Plot calculated best fit
plot("Modeled depleted",
d.columns,
row,
linestyle='--',
linewidth=1)
v = enrichment.ix[row.name]
if i == 'CK-2':
# Don't include CK-2 because it isn't depleted, so results are spurious.
continue
plot("Enriching melt", d.columns, v, linestyle=':', linewidth=1)
# Plot NMORB
ax.fill_between(NMORB_trace.columns,
NMORB_trace.ix[0, :],
NMORB_trace.ix[0, :] - 0.5,
color='#bbbbbb',
linewidth=1.5,
zorder=-5,
label="")
ax.fill_between(alkali_trace.columns,
alkali_trace.min(),
alkali_trace.max(),
facecolor='#dddddd',
edgecolor='none',
zorder=-10,
label="")
ax.set_ylim(.01, 100)
ax.set_xlim(element('La') - 0.1, element('Lu'))
ax.yaxis.set_ticklabels(
["{:g}".format(v) for v in ax.yaxis.get_ticklocs()])
ax.set_ylabel("Rare-earth element abundance / Primitive Mantle")
ax.xaxis.set_ticks(vals)
ax.xaxis.set_ticklabels(data.columns)
ax.set_yscale('log')
ax.text(element('Ce') - 0.5,
40,
"Alkali basalt",
rotation=-28,
color='#888888')
ax.text(element('La'), 5, "NMORB", rotation=15, color='#888888')
legend = ax.legend(loc="upper right")
fr = legend.get_frame()
fr.set_lw(0.5)
create_main_axis(ax1)
update_axes(ax1)
fig.subplots_adjust(top=0.99, right=0.99)
ree_scatter(ax2, model, data, colors)
ax2.set_ylim([0, 1.2])
ax2.set_xlabel(r'HREE depletion degrees (%)')
ax2.set_ylabel("Enriching fluid\nassimilated (%)")
ax2.yaxis.set_label_coords(-0.1, 0.22)
update_axes(ax2)
axis_labels(ax1, ax2, pad=.16, fontsize=14)
fig.savefig(dst, bbox_inches='tight')
