def plot_mir_set(
ax,
starnames,
extra_off_val=0.0,
plam4=True,
norm_wave_range=[6.0, 10.0] * u.micron,
col_vals=["b", "g", "r", "m", "c", "y"],
ann_xvals=[35.0, 42.0] * u.micron,
ann_wave_range=[9.0, 15.0] * u.micron,
ann_rot=5.0,
ann_offset=0.2,
fontsize=12,
path="/home/kgordon/Python_git/extstar_data/",
subpath="DAT_files/",
):
"""
Plot a set of spectra
"""
n_col = len(col_vals)
for i in range(len(starnames)):
stardata = StarData(subpath + starnames[i] + ".dat", path=path, use_corfac=True)
stardata.plot(
ax,
mlam4=True,
norm_wave_range=norm_wave_range,
yoffset=extra_off_val + 0.5 * i,
yoffset_type="add",
pcolor=col_vals[i % n_col],
annotate_key="IRS",
annotate_wave_range=ann_wave_range,
annotate_text=starnames[i] + " " + stardata.sptype,
fontsize=fontsize,
annotate_rotation=ann_rot,
annotate_yoffset=ann_offset,
)
mpl.rc("lines", linewidth=1)
mpl.rc("axes", linewidth=2)
mpl.rc("xtick.major", width=2)
mpl.rc("xtick.minor", width=2)
mpl.rc("ytick.major", width=2)
mpl.rc("ytick.minor", width=2)
# setup the plot
fig, ax = plt.subplots(figsize=(13, 10))
# plot the bands and all spectra for this star
# plot all the spectra on the same plot
for k, cstarname in enumerate(starnames):
fstarname, file_path = get_full_starfile(cstarname)
starobs = StarData(fstarname, path=file_path)
starobs.plot(ax, norm_wave_range=[0.2, 0.3] * u.micron, yoffset=2**k)
# finish configuring the plot
ax.set_yscale("log")
ax.set_xscale("log")
ax.set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.3 * fontsize)
ax.set_ylabel(r"$F(\lambda)$ [$ergs\ cm^{-2}\ s\ \AA$]",
fontsize=1.3 * fontsize)
ax.tick_params("both", length=10, width=2, which="major")
ax.tick_params("both", length=5, width=1, which="minor")
# use the whitespace better
fig.tight_layout()
# plot or save to a file
save_str = "_spec"
half_num = len(starnames) // 2 + 1
col_vals = ["b", "g", "c"]
n_cols = len(col_vals)
for k, cstarname in enumerate(starnames):
fstarname, file_path = get_full_starfile(cstarname)
starobs = StarData(fstarname, path=file_path)
if k // half_num > 0:
yoff = 2.5**(k - half_num)
else:
yoff = 2.5**k
starobs.plot(
ax[k // half_num],
norm_wave_range=[0.2, 0.3] * u.micron,
yoffset=yoff,
pcolor=col_vals[k % n_cols],
annotate_key="IUE",
annotate_wave_range=[0.25, 0.27] * u.micron,
annotate_text=cstarname,
annotate_rotation=-10.,
annotate_yoffset=0.0,
fontsize=12,
)
print(cstarname)
# finish configuring the plot
for i in range(2):
ax[i].set_xlim(0.1, 0.325)
ylim = ax[i].get_ylim()
ax[i].set_ylim(1e-1, ylim[1])
ax[i].set_xscale("linear")
ax[i].set_yscale("log")
ax[i].set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.3 * fontsize)
def plot_multi_spectra(
starlist,
path,
mlam4=False,
HI_lines=False,
range=None,
norm_range=None,
spread=False,
exclude=[],
log=False,
class_offset=True,
text_offsets=[],
text_angles=[],
pdf=False,
outname="all_spec.pdf",
):
"""
Plot the observed band and spectral data of multiple stars in the same plot
Parameters
----------
starlist : list of strings
List of stars for which to plot the spectrum
path : string
Path to the data files
mlam4 : boolean [default=False]
Whether or not to multiply the flux F(lambda) by lambda^4 to remove the Rayleigh-Jeans slope
HI_lines : boolean [default=False]
Whether or not to indicate the HI-lines in the plot
range : list of 2 floats [default=None]
Wavelength range to be plotted (in micron) - [min,max]
norm_range : list of 2 floats [default=None]
Wavelength range to use to normalize the data (in micron)- [min,max]
spread : boolean [default=False]
Whether or not to spread the spectra out by adding a vertical offset to each spectrum
exclude : list of strings [default=[]]
List of data type(s) to exclude from the plot (e.g., IRS)
log : boolean [default=False]
Whether or not to plot the wavelengths on a log-scale
class_offset : boolean [default=True]
Whether or not to add an extra offset between main sequence and giant stars (only relevant when spread=True; this only works when the stars are sorted by spectral class, i.e. first the main sequence and then the giant stars)
text_offsets : list of floats [default=[]]
List of the same length as starlist with offsets for the annotated text
text_angles : list of integers [default=[]]
List of the same length as starlist with rotation angles for the annotated text
pdf : boolean [default=False]
Whether or not to save the figure as a pdf file
outname : string [default="all_spec.pdf"]
Name for the output pdf file
Returns
-------
Figure with band data points and spectra of multiple stars
"""
# plotting setup for easier to read plots
fontsize = 18
font = {"size": fontsize}
plt.rc("font", **font)
plt.rc("lines", linewidth=1)
plt.rc("axes", linewidth=2)
plt.rc("xtick.major", width=2)
plt.rc("xtick.minor", width=2)
plt.rc("ytick.major", width=2)
plt.rc("ytick.minor", width=2)
# create the plot
fig, ax = plt.subplots(figsize=(15, len(starlist) * 1.25))
colors = plt.get_cmap("tab10")
if norm_range is not None:
norm_range = norm_range * u.micron
# set default text offsets and angles
if text_offsets == []:
text_offsets = np.full(len(starlist), 0.2)
if text_angles == []:
text_angles = np.full(len(starlist), 10)
for i, star in enumerate(starlist):
# read in all bands and spectra for this star
starobs = StarData("%s.dat" % star.lower(), path=path, use_corfac=True)
# spread out the spectra if requested
# add extra whitespace when the luminosity class changes from main sequence to giant
if spread:
extra_off = 0
if "V" not in starobs.sptype and class_offset:
extra_off = 1
yoffset = extra_off + 0.5 * i
else:
yoffset = 0
# determine where to add the name of the star and its spectral type
# find the shortest plotted wavelength, and give preference to spectral data when available
exclude2 = []
if "BAND" in starobs.data.keys() and len(starobs.data.keys()) > 1:
exclude2 = ["BAND"]
(waves, fluxes,
flux_uncs) = starobs.get_flat_data_arrays(starobs.data.keys() -
(exclude + exclude2))
if range is not None:
waves = waves[waves >= range[0]]
min_wave = waves[0]
# find out which data type corresponds with this wavelength
for data_type in starobs.data.keys():
if data_type in exclude:
continue
used_waves = starobs.data[data_type].waves[
starobs.data[data_type].npts > 0]
if min_wave in used_waves.value:
ann_key = data_type
ann_range = [min_wave, min_wave] * u.micron
# plot the spectrum
starobs.plot(
ax,
pcolor=colors(i % 10),
norm_wave_range=norm_range,
mlam4=mlam4,
exclude=exclude,
yoffset=yoffset,
yoffset_type="add",
annotate_key=ann_key,
annotate_wave_range=ann_range,
annotate_text=star.upper() + " " + starobs.sptype,
annotate_yoffset=text_offsets[i],
annotate_rotation=text_angles[i],
annotate_color=colors(i % 10),
)
# plot HI-lines if requested
if HI_lines:
plot_HI(path, ax)
# zoom in on a specific region if requested
if range is not None:
zoom(ax, range)
outname = outname.replace(".pdf", "_zoom.pdf")
# finish configuring the plot
if not spread:
ax.set_yscale("log")
if log:
ax.set_xscale("log")
ax.set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.5 * fontsize)
ylabel = r"$F(\lambda)$"
if norm_range is not None:
if norm_range[0].unit == "micron":
units = r"$\mu m$"
else:
units = norm_range[0].unit
ylabel += "/$F$(" + str(int(np.mean(norm_range).value)) + units + ")"
else:
ylabel += r" [$ergs\ cm^{-2}\ s^{-1}\ \AA^{-1}$]"
if mlam4:
ylabel = r"$\lambda^4$" + ylabel.replace("]", r" $\mu m^4$]")
outname = outname.replace("spec", "spec_mlam4")
if spread:
ylabel += " + offset"
ax.set_ylabel(ylabel, fontsize=1.5 * fontsize)
ax.tick_params("both", length=10, width=2, which="major")
ax.tick_params("both", length=5, width=1, which="minor")
# show the figure or save it to a pdf file
if pdf:
fig.savefig(path + outname, bbox_inches="tight")
else:
plt.show()
# return the figure and axes for additional manipulations
return fig, ax
def plot_spectrum(
star,
path,
mlam4=False,
HI_lines=False,
range=None,
norm_range=None,
exclude=[],
pdf=False,
):
"""
Plot the observed band and spectral data of a star
Parameters
----------
star : string
Name of the star for which to plot the spectrum
path : string
Path to the data files
mlam4 : boolean [default=False]
Whether or not to multiply the flux F(lambda) by lambda^4 to remove the Rayleigh-Jeans slope
HI_lines : boolean [default=False]
Whether or not to indicate the HI-lines in the plot
range : list of 2 floats [default=None]
Wavelength range to be plotted (in micron) - [min,max]
norm_range : list of 2 floats [default=None]
Wavelength range to use to normalize the data (in micron)- [min,max]
exclude : list of strings [default=[]]
List of data type(s) to exclude from the plot (e.g., IRS)
pdf : boolean [default=False]
Whether or not to save the figure as a pdf file
Returns
-------
Figure with band data points and spectrum
"""
# plotting setup for easier to read plots
fontsize = 18
font = {"size": fontsize}
plt.rc("font", **font)
plt.rc("lines", linewidth=1)
plt.rc("axes", linewidth=2)
plt.rc("xtick.major", width=2)
plt.rc("xtick.minor", width=2)
plt.rc("ytick.major", width=2)
plt.rc("ytick.minor", width=2)
# create the plot
fig, ax = plt.subplots(figsize=(13, 10))
# read in and plot all bands and spectra for this star
starobs = StarData("%s.dat" % star.lower(), path=path, use_corfac=True)
if norm_range is not None:
norm_range = norm_range * u.micron
starobs.plot(ax, norm_wave_range=norm_range, mlam4=mlam4, exclude=exclude)
# plot HI-lines if requested
if HI_lines:
plot_HI(path, ax)
# define the output name
outname = star.lower() + "_spec.pdf"
# zoom in on a specific region if requested
if range is not None:
zoom(ax, range)
outname = outname.replace(".pdf", "_zoom.pdf")
# finish configuring the plot
ax.set_xscale("log")
ax.set_yscale("log")
ax.set_title(star.upper(), fontsize=50)
ax.set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.5 * fontsize)
if mlam4:
ax.set_ylabel(
r"$F(\lambda)\ \lambda^4$ [$ergs\ cm^{-2}\ s^{-1}\ \AA^{-1}\ \mu m^4$]",
fontsize=1.5 * fontsize,
)
outname = outname.replace("spec", "spec_mlam4")
else:
ax.set_ylabel(
r"$F(\lambda)$ [$ergs\ cm^{-2}\ s^{-1}\ \AA^{-1}$]",
fontsize=1.5 * fontsize,
)
ax.tick_params("both", length=10, width=2, which="major")
ax.tick_params("both", length=5, width=1, which="minor")
# show the figure or save it to a pdf file
if pdf:
fig.savefig(path + outname, bbox_inches="tight")
plt.close()
else:
plt.show()
fontsize = 18
font = {'size': fontsize}
mpl.rc('font', **font)
mpl.rc('lines', linewidth=1)
mpl.rc('axes', linewidth=2)
mpl.rc('xtick.major', width=2)
mpl.rc('xtick.minor', width=2)
mpl.rc('ytick.major', width=2)
mpl.rc('ytick.minor', width=2)
# setup the plot
fig, ax = plt.subplots(figsize=(13, 10))
# plot the bands and all spectra for this star
import astropy.units as u
starobs.plot(ax, mlam4=True, norm_wave_range=[10., 20.] * u.micron)
# finish configuring the plot
ax.set_yscale('log')
ax.set_xscale('log')
ax.set_xlabel('$\lambda$ [$\mu m$]', fontsize=1.3 * fontsize)
ax.set_ylabel('$F(\lambda)$ [$ergs\ cm^{-2}\ s\ \AA$]',
fontsize=1.3 * fontsize)
ax.tick_params('both', length=10, width=2, which='major')
ax.tick_params('both', length=5, width=1, which='minor')
# use the whitespace better
fig.tight_layout()
# plot or save to a file
save_str = '_spec'