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Don't overwrite the cation fraction with the cation / neutral ratio
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@PAHdb
PAHdb committed Jan 13, 2025
1 parent edd3b1a commit 5a4f51a
Showing 1 changed file with 80 additions and 32 deletions.
112 changes: 80 additions & 32 deletions pypahdb/decomposer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,9 +43,11 @@ def _get_cation_neutral_ratio(self):
Calculate the cation neutral ratio if it is not already calculated and return it.
"""
if self._cation_neutral_ratio is None:
self._cation_neutral_ratio = self.charge_fractions['cation']
nonzero = np.nonzero(self.charge_fractions['neutral'])
self._cation_neutral_ratio[nonzero] /= self.charge_fractions['neutral'][nonzero]
self._cation_neutral_ratio = self.charge_fractions["cation"].copy()
nonzero = np.nonzero(self.charge_fractions["neutral"])
self._cation_neutral_ratio[nonzero] /= self.charge_fractions["neutral"][
nonzero
]

return self._cation_neutral_ratio

Expand All @@ -71,9 +73,7 @@ def save_pdf(self, filename, header="", domaps=True, doplots=True):
with PdfPages(filename) as pdf:
d = pdf.infodict()
d["Title"] = "pyPAHdb Results Summary"
d["Author"] = (
"Dr. C. Boersma, Dr. M.J. Shannon, and Dr. A. Maragkoudakis"
)
d["Author"] = "Dr. C. Boersma, Dr. M.J. Shannon, and Dr. A. Maragkoudakis"
d["Producer"] = "NASA Ames Research Center"
d["Creator"] = "pypahdb v{}(Python {}.{}.{})".format(
pypahdb.__version__,
Expand Down Expand Up @@ -120,34 +120,50 @@ def save_pdf(self, filename, header="", domaps=True, doplots=True):
else:
wcs = None

fig = self.plot_map(self.cation_neutral_ratio.value, "n$_{{cation}}$/n$_{{neutral}}$", wcs=wcs)
fig = self.plot_map(
self.cation_neutral_ratio.value,
"n$_{{cation}}$/n$_{{neutral}}$",
wcs=wcs,
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.nc, "average PAH size (N$_{{C}}$)", wcs=wcs)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.charge_fractions['neutral'], "PAH neutral fraction", wcs=wcs)
fig = self.plot_map(
self.charge_fractions["neutral"], "PAH neutral fraction", wcs=wcs
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.charge_fractions['cation'], "PAH cation fraction", wcs=wcs)
fig = self.plot_map(
self.charge_fractions["cation"], "PAH cation fraction", wcs=wcs
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.charge_fractions['anion'], "PAH anion fraction", wcs=wcs)
fig = self.plot_map(
self.charge_fractions["anion"], "PAH anion fraction", wcs=wcs
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.size_fractions['large'],
f"large PAH fraction (N$_{{C}}$ > {MEDIUM_SIZE})",
wcs=wcs)
fig = self.plot_map(
self.size_fractions["large"],
f"large PAH fraction (N$_{{C}}$ > {MEDIUM_SIZE})",
wcs=wcs,
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.size_fractions['medium'],
f"medium PAH fraction ({SMALL_SIZE} < N$_{{C}}$ ≤ {MEDIUM_SIZE})",
wcs=wcs)
fig = self.plot_map(
self.size_fractions["medium"],
f"medium PAH fraction ({SMALL_SIZE} < N$_{{C}}$ ≤ {MEDIUM_SIZE})",
wcs=wcs,
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.size_fractions['small'],
f"small PAH fraction (N$_{{C}}$ ≤ {SMALL_SIZE})",
wcs=wcs)
fig = self.plot_map(
self.size_fractions["small"],
f"small PAH fraction (N$_{{C}}$ ≤ {SMALL_SIZE})",
wcs=wcs,
)
pdf.savefig(fig)
plt.close(fig)
fig = self.plot_map(self.error, "error", wcs=wcs)
Expand Down Expand Up @@ -244,7 +260,11 @@ def _fits_to_disk(hdr, filename):
hdulist.append(fits.ImageHDU(data=value.value, name=key.upper()))
hdulist.append(fits.ImageHDU(data=self.error.value, name="ERROR"))
hdulist.append(fits.ImageHDU(data=self.nc.value, name="NC"))
hdulist.append(fits.ImageHDU(data=self.cation_neutral_ratio.value, name="CATION_NEUTRAL_RATIO"))
hdulist.append(
fits.ImageHDU(
data=self.cation_neutral_ratio.value, name="CATION_NEUTRAL_RATIO"
)
)

hdulist.writeto(filename, overwrite=True, output_verify="fix")

Expand Down Expand Up @@ -470,8 +490,12 @@ def plot_fit(self, i=0, j=0):
)
ax0.plot(abscissa, model, label="fit", color="tab:red", lw=1.5)
error_str = "$error$=%-4.2f" % (self.error[i][j])
ax0.text(0.025, 0.88, error_str, ha="left", va="center", transform=ax0.transAxes)
ax0.set_ylabel(f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]')
ax0.text(
0.025, 0.88, error_str, ha="left", va="center", transform=ax0.transAxes
)
ax0.set_ylabel(
f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]'
)

# ax1: Residual.
ax1.plot(abscissa, data - model, lw=1, label="residual", color="gray")
Expand All @@ -493,17 +517,27 @@ def plot_fit(self, i=0, j=0):
)
ax2.plot(abscissa, model, color="tab:red", lw=1.5)
ax2.plot(
abscissa, self.size["large"][:, i, j], label="large", lw=1, color="tab:orange"
abscissa,
self.size["large"][:, i, j],
label="large",
lw=1,
color="tab:orange",
)
ax2.plot(
abscissa, self.size["medium"][:, i, j], label="medium", lw=1, color="tab:green"
abscissa,
self.size["medium"][:, i, j],
label="medium",
lw=1,
color="tab:green",
)
ax2.plot(
abscissa, self.size["small"][:, i, j], label="small", lw=1, color="tab:blue"
)
size_str = "$f_{large}$=%3.1f" % (self.size_fractions['large'][i][j])
size_str = "$f_{large}$=%3.1f" % (self.size_fractions["large"][i][j])
ax2.text(0.025, 0.88, size_str, ha="left", va="center", transform=ax2.transAxes)
ax2.set_ylabel(f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]')
ax2.set_ylabel(
f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]'
)

# ax3: Charge breakdown.
ax3.errorbar(
Expand All @@ -524,16 +558,30 @@ def plot_fit(self, i=0, j=0):
abscissa, charge["anion"][:, i, j], label="anion", lw=1, color="tab:orange"
)
ax3.plot(
abscissa, charge["neutral"][:, i, j], label="neutral", lw=1, color="tab:cyan"
abscissa,
charge["neutral"][:, i, j],
label="neutral",
lw=1,
color="tab:cyan",
)
ax3.plot(
abscissa, charge["cation"][:, i, j], label="cation", lw=1, color="tab:purple"
abscissa,
charge["cation"][:, i, j],
label="cation",
lw=1,
color="tab:purple",
)
cnr_str = "$n_{cation}/n_{neutral}$=%3.1f" % (
self.charge_fractions["cation"][i][j]
/ self.charge_fractions["neutral"][i][j]
)
cnr_str = ("$n_{cation}/n_{neutral}$=%3.1f" %
(self.charge_fractions['cation'][i][j]/self.charge_fractions['neutral'][i][j]))
ax3.text(0.025, 0.88, cnr_str, ha="left", va="center", transform=ax3.transAxes)
ax3.set_xlabel(f'{self.spectrum.meta["colnames"][0]} [{self.spectrum.spectral_axis.unit}]')
ax3.set_ylabel(f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]')
ax3.set_xlabel(
f'{self.spectrum.meta["colnames"][0]} [{self.spectrum.spectral_axis.unit}]'
)
ax3.set_ylabel(
f'{self.spectrum.meta["colnames"][1]} [{self.spectrum.flux.unit}]'
)

# Set tick parameters and add legends to axes.
for ax in (ax0, ax1, ax2, ax3):
Expand Down

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