ax.plot(1.0 / x, p92_comps(x), "k--", alpha=0.5)
ax2.plot(1.0 / x, p92_comps(x), "k--", alpha=0.5)
p92_comps = p92_fit.copy()
p92_comps.FUV_amp_0 = 0.0
p92_comps.NUV_amp_0 = 0.0
p92_comps.SIL1_amp_0 = 0.0
p92_comps.SIL2_amp_0 = 0.0
ax.plot(1.0 / x, p92_comps(x), "k--", alpha=0.5)
ax2.plot(1.0 / x, p92_comps(x), "k--", alpha=0.5)
# finish configuring the plot
ax.set_yscale("linear")
ax.set_xscale("log")
ax.set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.3 * fontsize)
ax.set_ylabel(extdata._get_ext_ytitle(extdata.type),
fontsize=1.3 * fontsize)
ax.tick_params("both", length=10, width=2, which="major")
ax.tick_params("both", length=5, width=1, which="minor")
ax.legend()
# finish configuring the subplot
sp_xlim = [2.0, 35.0]
ax2.set_xlim(sp_xlim)
# ax2.set_ylim(-best_fit_Av-0.1, -best_fit_Av+0.5)
(indxs, ) = np.where((x.value > 1.0 / sp_xlim[1])
& (x.value < 1.0 / sp_xlim[0]))
if extdata.type == "elx":
ax2.set_ylim(
min([min(p92_fit(x)[indxs]), -best_fit_Av]) - 0.1,
max(p92_fit(x)[indxs]) + 0.1)
def plot_extinction(
starpair,
path,
alax=False,
extmodels=False,
fitmodel=False,
HI_lines=False,
range=None,
exclude=[],
log=False,
pdf=False,
):
"""
Plot the extinction curve of a star
Parameters
----------
starpair : string
Name of the star pair for which to plot the extinction curve, in the format "reddenedstarname_comparisonstarname" (no spaces)
path : string
Path to the data files
alax : boolean [default=False]
Whether or not to plot A(lambda)/A(X) instead of E(lambda-X)
extmodels: boolean [default=False]
Whether or not to overplot Milky Way extinction curve models
fitmodel: boolean [default=False]
Whether or not to overplot a fitted model
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]
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
pdf : boolean [default=False]
Whether or not to save the figure as a pdf file
Returns
-------
Figure with extinction curve
"""
# 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, size=10)
plt.rc("xtick.minor", width=1, size=5)
plt.rc("ytick.major", width=2, size=10)
plt.rc("ytick.minor", width=1, size=5)
plt.rc("axes.formatter", min_exponent=2)
# create the plot
fig, ax = plt.subplots(figsize=(13, 10))
# read in and plot the extinction curve data for this star
extdata = ExtData("%s%s_ext.fits" % (path, starpair.lower()))
extdata.plot(ax, alax=alax, exclude=exclude, color="k")
# define the output name
outname = "%s_ext_%s.pdf" % (starpair.lower(), extdata.type)
# plot Milky Way extinction models if requested
if extmodels:
plot_extmodels(extdata, alax)
# overplot a fitted model if requested
if fitmodel:
plot_fitmodel(extdata, res=True)
# 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
ax.set_title(starpair.split("_")[0], fontsize=50)
ax.text(
0.99,
0.95,
"comparison: " + starpair.split("_")[1],
fontsize=25,
horizontalalignment="right",
transform=ax.transAxes,
)
if log:
ax.set_xscale("log")
plt.xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.5 * fontsize)
ax.set_ylabel(extdata._get_ext_ytitle(ytype=extdata.type),
fontsize=1.5 * fontsize)
# show the figure or save it to a pdf file
if pdf:
fig.savefig(path + outname, bbox_inches="tight")
plt.close()
else:
plt.show()
def plot_average(
path,
filename="average_ext.fits",
ax=None,
extmodels=False,
fitmodel=False,
HI_lines=False,
range=None,
exclude=[],
log=False,
spread=False,
annotate_key=None,
annotate_wave_range=None,
pdf=False,
):
"""
Plot the average extinction curve
Parameters
----------
path : string
Path to the average extinction curve fits file
filename : string [default="average_ext.fits"]
Name of the average extinction curve fits file
ax : AxesSubplot [default=None]
Axes of plot on which to add the average extinction curve if pdf=False
extmodels: boolean [default=False]
Whether or not to overplot Milky Way extinction curve models
fitmodel: boolean [default=False]
Whether or not to overplot a fitted model
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]
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
spread : boolean [default=False]
Whether or not to offset the average extinction curve from the other curves (only relevant when pdf=False and ax=None)
annotate_key : string [default=None]
type of data for which to annotate text (e.g., SpeX_LXD) (only relevant when pdf=False and ax=None)
annotate_wave_range : list of 2 floats [default=None]
min/max wavelength range for the annotation of the text (only relevant when pdf=False and ax=None)
pdf : boolean [default=False]
- If False, the average extinction curve will be overplotted on the current plot (defined by ax)
- If True, the average extinction curve will be plotted in a separate plot and saved as a pdf
Returns
-------
Plots the average extinction curve
"""
# read in the average extinction curve (if it exists)
if os.path.isfile(path + filename):
average = ExtData(path + filename)
else:
warnings.warn(
"An average extinction curve with the name " + filename +
" could not be found in " + path +
". Please calculate the average extinction curve first with the calc_ave_ext function in measure_extinction/utils/calc_ext.py.",
UserWarning,
)
# make a new plot if requested
if pdf:
# 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, size=10)
plt.rc("xtick.minor", width=1, size=5)
plt.rc("ytick.major", width=2, size=10)
plt.rc("ytick.minor", width=1, size=5)
plt.rc("axes.formatter", min_exponent=2)
# create the plot
fig, ax = plt.subplots(figsize=(13, 10))
average.plot(ax, exclude=exclude, color="k")
# plot Milky Way extinction models if requested
if extmodels:
plot_extmodels(average, alax=True)
# overplot a fitted model if requested
if fitmodel:
plot_fitmodel(average, res=True)
# 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)
# finish configuring the plot
if log:
ax.set_xscale("log")
plt.xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.5 * fontsize)
ax.set_ylabel(average._get_ext_ytitle(ytype=average.type),
fontsize=1.5 * fontsize)
fig.savefig(path + "average_ext.pdf", bbox_inches="tight")
# return the figure and axes for additional manipulations
return fig, ax
else:
if spread:
yoffset = -0.3
else:
yoffset = 0
average.plot(
ax,
color="k",
alpha=0.6,
yoffset=yoffset,
annotate_key=annotate_key,
annotate_wave_range=annotate_wave_range,
annotate_text="average",
annotate_yoffset=0.05,
)
# overplot a fitted model if requested
if fitmodel:
plot_fitmodel(average, yoffset=yoffset)
def plot_multi_extinction(
starpair_list,
path,
alax=False,
average=False,
extmodels=False,
fitmodel=False,
HI_lines=False,
range=None,
spread=False,
exclude=[],
log=False,
text_offsets=[],
text_angles=[],
pdf=False,
):
"""
Plot the extinction curves of multiple stars in the same plot
Parameters
----------
starpair_list : list of strings
List of star pairs for which to plot the extinction curve, in the format "reddenedstarname_comparisonstarname" (no spaces)
path : string
Path to the data files
alax : boolean [default=False]
Whether or not to plot A(lambda)/A(X) instead of E(lambda-X)
average : boolean [default=False]
Whether or not to plot the average extinction curve
extmodels: boolean [default=False]
Whether or not to overplot Milky Way extinction curve models
fitmodel: boolean [default=False]
Whether or not to overplot a fitted model
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]
spread : boolean [default=False]
Whether or not to spread the extinction curves out by adding a vertical offset to each curve
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
text_offsets : list of floats [default=[]]
List of the same length as starpair_list with offsets for the annotated text
text_angles : list of integers [default=[]]
List of the same length as starpair_list with rotation angles for the annotated text
pdf : boolean [default=False]
Whether or not to save the figure as a pdf file
Returns
-------
Figure with extinction curves 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, size=10)
plt.rc("xtick.minor", width=1, size=5)
plt.rc("ytick.major", width=2, size=10)
plt.rc("ytick.minor", width=1, size=5)
plt.rc("axes.formatter", min_exponent=2)
# create the plot
fig, ax = plt.subplots(figsize=(15, len(starpair_list) * 1.25))
colors = plt.get_cmap("tab10")
# set default text offsets and angles
if text_offsets == []:
text_offsets = np.full(len(starpair_list), 0.2)
if text_angles == []:
text_angles = np.full(len(starpair_list), 10)
for i, starpair in enumerate(starpair_list):
# read in the extinction curve data
extdata = ExtData("%s%s_ext.fits" % (path, starpair.lower()))
# spread out the curves if requested
if spread:
yoffset = 0.25 * i
else:
yoffset = 0.0
# determine where to add the name of the star
# find the shortest plotted wavelength
(waves, exts,
ext_uncs) = extdata.get_fitdata(extdata.waves.keys() - exclude)
if range is not None:
waves = waves[waves.value >= range[0]]
min_wave = waves[-1]
# find out which data type corresponds with this wavelength
for data_type in extdata.waves.keys():
if data_type in exclude:
continue
used_waves = extdata.waves[data_type][extdata.npts[data_type] > 0]
if min_wave in used_waves:
ann_key = data_type
ann_range = [min_wave, min_wave] * u.micron
# plot the extinction curve
extdata.plot(
ax,
color=colors(i % 10),
alpha=0.7,
alax=alax,
exclude=exclude,
yoffset=yoffset,
annotate_key=ann_key,
annotate_wave_range=ann_range,
annotate_text=extdata.red_file.split(".")[0].upper(),
annotate_yoffset=text_offsets[i],
annotate_rotation=text_angles[i],
annotate_color=colors(i % 10),
)
# overplot a fitted model if requested
if fitmodel:
plot_fitmodel(extdata, yoffset=yoffset)
# overplot Milky Way extinction curve models if requested
if extmodels:
if alax:
plot_extmodels(extdata, alax)
else:
warnings.warn(
"Overplotting Milky Way extinction curve models on a figure with multiple observed extinction curves in E(lambda-V) units is disabled, because the model curves in these units are different for every star, and would overload the plot. Please, do one of the following if you want to overplot Milky Way extinction curve models: 1) Use the flag --alax to plot ALL curves in A(lambda)/A(V) units, OR 2) Plot all curves separately by removing the flag --onefig.",
stacklevel=2,
)
# plot the average extinction curve if requested
if average:
plot_average(
path,
ax=ax,
extmodels=extmodels,
fitmodel=fitmodel,
exclude=exclude,
spread=spread,
annotate_key=ann_key,
annotate_wave_range=ann_range,
)
# define the output name
outname = "all_ext_%s.pdf" % (extdata.type)
# 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 log:
ax.set_xscale("log")
ax.set_xlabel(r"$\lambda$ [$\mu m$]", fontsize=1.5 * fontsize)
ylabel = extdata._get_ext_ytitle(ytype=extdata.type)
if spread:
ylabel += " + offset"
ax.set_ylabel(ylabel, fontsize=1.5 * fontsize)
# 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
extdata.plot_ext(ax, alav=args.alav)
# fix the x,y plot limits
# ax.set_xlim(ax.get_xlim())
# ax.set_xlim(0.1, 2.5)
ax.set_ylim(ax.get_ylim())
# finish configuring the plot
ax.set_yscale('linear')
ax.set_xscale('log')
ax.set_xlabel('$\lambda$ [$\mu m$]', fontsize=1.3 * fontsize)
if args.alav:
ytype = 'alav'
else:
ytype = 'elv'
ax.set_ylabel(extdata._get_ext_ytitle(ytype), fontsize=1.3 * fontsize)
ax.tick_params('both', length=10, width=2, which='major')
ax.tick_params('both', length=5, width=1, which='minor')
ax.set_title(args.extfile)
# plot extinctionm models
if args.extmodels:
x = np.arange(0.12, 3.0, 0.01) * u.micron
Rvs = [2.0, 3.1, 4.0, 5.0]
for cRv in Rvs:
t = CCM89(Rv=cRv)
ax.plot(x,
t(x),
'k--',
linewidth=2,
label='R(V) = {:4.2f}'.format(cRv))