Tibeuleu/FOC_Reduction
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Add rest wavelength to the top of the specpol.plot

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Thibault Barnouin
2025-01-10 16:52:16 +01:00
parent 88efd4dc60
commit a5d3607bb9
1 changed files with 33 additions and 47 deletions
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80
package/src/readfos.py
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@@ -66,8 +66,6 @@ class specpol(object):
self.I_r_err = deepcopy(other.I_r_err) self.I_r_err = deepcopy(other.I_r_err)
self.wav_r = deepcopy(other.wav_r) self.wav_r = deepcopy(other.wav_r)
self.wav_r_err = deepcopy(other.wav_r_err) self.wav_r_err = deepcopy(other.wav_r_err)
self.wav_r_rest = deepcopy(other.wav_r_rest)
self.wav_r_rest_err = deepcopy(other.wav_r_rest_err)
else: else:
# Initialise to zero # Initialise to zero
if isinstance(other, int): if isinstance(other, int):
@@ -89,8 +87,7 @@ class specpol(object):
self.V = np.zeros(n) self.V = np.zeros(n)
self.IQUV_cov = np.zeros((4, 4, n)) self.IQUV_cov = np.zeros((4, 4, n))
@property def rest(self, wav=None, z=None):
def wav_rest(self, z=None):
if z is None and "REDSHIFT" not in self.hd.keys(): if z is None and "REDSHIFT" not in self.hd.keys():
from astroquery.ipac.ned import Ned from astroquery.ipac.ned import Ned
@@ -98,10 +95,11 @@ class specpol(object):
self.hd["REDSHIFT"] = z self.hd["REDSHIFT"] = z
elif z is None: elif z is None:
z = self.hd["REDSHIFT"] z = self.hd["REDSHIFT"]
return self.wav / (z + 1) if wav is None:
wav = self.wav
return wav / (z + 1)
@property def unrest(self, wav=None, z=None):
def wav_rest_err(self, z=None):
if z is None and "REDSHIFT" not in self.hd.keys(): if z is None and "REDSHIFT" not in self.hd.keys():
from astroquery.ipac.ned import Ned from astroquery.ipac.ned import Ned
@@ -109,7 +107,9 @@ class specpol(object):
self.hd["REDSHIFT"] = z self.hd["REDSHIFT"] = z
elif z is None: elif z is None:
z = self.hd["REDSHIFT"] z = self.hd["REDSHIFT"]
return self.wav_err / (z + 1) if wav is None:
wav = self.wav
return wav * (z + 1)
@property @property
def I_err(self): def I_err(self):
@@ -209,15 +209,11 @@ class specpol(object):
spec_b.I_r_err = deepcopy(self.I_r_err) spec_b.I_r_err = deepcopy(self.I_r_err)
spec_b.wav_r = deepcopy(self.wav_r) spec_b.wav_r = deepcopy(self.wav_r)
spec_b.wav_r_err = deepcopy(self.wav_r_err) spec_b.wav_r_err = deepcopy(self.wav_r_err)
spec_b.wav_r_rest = deepcopy(self.wav_r_rest)
spec_b.wav_r_rest_err = deepcopy(self.wav_r_rest_err)
else: else:
spec_b.I_r = deepcopy(self.I) spec_b.I_r = deepcopy(self.I)
spec_b.I_r_err = deepcopy(self.I_err) spec_b.I_r_err = deepcopy(self.I_err)
spec_b.wav_r = deepcopy(self.wav) spec_b.wav_r = deepcopy(self.wav)
spec_b.wav_r_err = deepcopy(self.wav_err) spec_b.wav_r_err = deepcopy(self.wav_err)
spec_b.wav_r_rest = deepcopy(self.wav_rest)
spec_b.wav_r_rest_err = deepcopy(self.wav_rest_err)
for i in range(bin_edges.shape[0] - 1): for i in range(bin_edges.shape[0] - 1):
spec_b.wav[i] = np.mean(self.wav[in_bin == i]) spec_b.wav[i] = np.mean(self.wav[in_bin == i])
spec_b.wav_err[i] = (spec_b.wav[i] - bin_edges[i], bin_edges[i + 1] - spec_b.wav[i]) spec_b.wav_err[i] = (spec_b.wav[i] - bin_edges[i], bin_edges[i + 1] - spec_b.wav[i])
@@ -256,7 +252,7 @@ class specpol(object):
np.savetxt(join_path(output_dir, filename + ".txt"), data_dump) np.savetxt(join_path(output_dir, filename + ".txt"), data_dump)
return join_path(output_dir, filename) return join_path(output_dir, filename)
def plot(self, fig=None, ax=None, rest=False, savename=None, plots_folder=""): def plot(self, fig=None, ax=None, savename=None, plots_folder=""):
""" """
Display current spectra. Display current spectra.
""" """
@@ -278,36 +274,32 @@ class specpol(object):
else: else:
ax1 = self.ax ax1 = self.ax
if rest:
wav, wav_err = self.wav_rest, self.wav_rest_err
if hasattr(self, "I_r"):
wav_r, wav_r_err = self.wav_r_rest, self.wav_r_rest_err
rest_str = "Rest "
else:
wav, wav_err = self.wav, self.wav_err
if hasattr(self, "I_r"):
wav_r, wav_r_err = self.wav_r, self.wav_r_err
rest_str = ""
# Display flux and polarized flux on first ax # Display flux and polarized flux on first ax
ax1.set_xlabel(rest_str + r"Wavelength [$\AA$]") ax1.set_xlabel(r"Wavelength [$\AA$]")
secax1 = ax1.secondary_xaxis("top", functions=(self.rest, self.unrest))
secax1.set_xlabel(r"Rest wavelength [$\AA$]")
if hasattr(self, "I_r"): if hasattr(self, "I_r"):
ax1.errorbar(wav_r, self.I_r, xerr=wav_r_err.T, yerr=self.I_r_err, color="k", fmt=".", label="I") ax1.errorbar(self.wav_r, self.I_r, xerr=self.wav_r_err.T, yerr=self.I_r_err, color="k", fmt=".", label="I")
ymax = np.max(self.I_r + self.I_r_err * 1.5)
else: else:
ax1.errorbar(wav, self.I, xerr=wav_err.T, yerr=self.I_err, color="k", fmt=".", label="I") ax1.errorbar(self.wav, self.I, xerr=self.wav_err.T, yerr=self.I_err, color="k", fmt=".", label="I")
ax1.errorbar(wav, self.PF, xerr=wav_err.T, yerr=self.PF_err, color="b", fmt=".", label="PF") ymax = np.max(self.I + self.I_err * 3.0)
ax1.errorbar(self.wav, self.PF, xerr=self.wav_err.T, yerr=self.PF_err, color="b", fmt=".", label="PF")
ax1.set_ylabel(r"F$_\lambda$ [erg s$^{-1}$ cm$^{-2} \AA^{-1}$]") ax1.set_ylabel(r"F$_\lambda$ [erg s$^{-1}$ cm$^{-2} \AA^{-1}$]")
ax1.set_ylim(ymin=0.0) ax1.set_ylim([0.0, ymax])
ax1.legend(ncols=2, loc=1) ax1.legend(ncols=2, loc=1)
if isinstance(self.ax, np.ndarray): if isinstance(self.ax, np.ndarray):
# When given 2 axes, display P and PA on second # When given 2 axes, display P and PA on second
ax2.set_xlabel(rest_str + r"Wavelength [$\AA$]") ax2.set_xlabel(r"Wavelength [$\AA$]")
ax2.errorbar(wav, self.P, xerr=wav_err.T, yerr=self.P_err, color="b", fmt=".", label="P") secax2 = ax2.secondary_xaxis("top", functions=(self.rest, self.unrest))
secax2.set_xlabel(r"Rest wavelength [$\AA$]")
ax2.errorbar(self.wav, self.P, xerr=self.wav_err.T, yerr=self.P_err, color="b", fmt=".", label="P")
ax2.set_ylim([0.0, 1.0]) ax2.set_ylim([0.0, 1.0])
ax2.set_ylabel(r"P", color="b") ax2.set_ylabel(r"P", color="b")
ax2.tick_params(axis="y", color="b", labelcolor="b") ax2.tick_params(axis="y", color="b", labelcolor="b")
ax22 = ax2.twinx() ax22 = ax2.twinx()
ax22.errorbar(wav, self.PA, xerr=wav_err.T, yerr=self.PA_err, color="r", fmt=".", label="PA [°]") ax22.errorbar(self.wav, self.PA, xerr=self.wav_err.T, yerr=self.PA_err, color="r", fmt=".", label="PA [°]")
ax22.set_ylim([0.0, 180.0]) ax22.set_ylim([0.0, 180.0])
ax22.set_ylabel(r"PA", color="r") ax22.set_ylabel(r"PA", color="r")
ax22.tick_params(axis="y", color="r", labelcolor="r") ax22.tick_params(axis="y", color="r", labelcolor="r")
@@ -340,8 +332,6 @@ class specpol(object):
spec_a.I_r_err = deepcopy(self.I_r_err + spec_b.I_r_err) spec_a.I_r_err = deepcopy(self.I_r_err + spec_b.I_r_err)
spec_a.wav_r = deepcopy(self.wav_r) spec_a.wav_r = deepcopy(self.wav_r)
spec_a.wav_r_err = deepcopy(self.wav_r_err) spec_a.wav_r_err = deepcopy(self.wav_r_err)
spec_a.wav_r_rest = deepcopy(self.wav_r_rest)
spec_a.wav_r_rest_err = deepcopy(self.wav_r_rest_err)
spec_a.I += deepcopy(spec_b.I) spec_a.I += deepcopy(spec_b.I)
spec_a.Q += deepcopy(spec_b.Q) spec_a.Q += deepcopy(spec_b.Q)
spec_a.U += deepcopy(spec_b.U) spec_a.U += deepcopy(spec_b.U)
@@ -365,8 +355,6 @@ class specpol(object):
spec_a.I_r_err = deepcopy(self.I_r_err) * other spec_a.I_r_err = deepcopy(self.I_r_err) * other
spec_a.wav_r = deepcopy(self.wav_r) spec_a.wav_r = deepcopy(self.wav_r)
spec_a.wav_r_err = deepcopy(self.wav_r_err) spec_a.wav_r_err = deepcopy(self.wav_r_err)
spec_a.wav_r_rest = deepcopy(self.wav_r_rest)
spec_a.wav_r_rest_err = deepcopy(self.wav_r_rest_err)
spec_a.I *= other spec_a.I *= other
spec_a.Q *= other spec_a.Q *= other
spec_a.U *= other spec_a.U *= other
@@ -479,7 +467,7 @@ class FOSspecpol(specpol):
self.wav_err = np.zeros((self.wav.shape[0], self.wav.shape[1], 2)) self.wav_err = np.zeros((self.wav.shape[0], self.wav.shape[1], 2))
wav_err = [np.mean((self.wav[j, 1:] - self.wav[j, :-1]) / 2) for j in range(self.wav.shape[0])] wav_err = [np.mean((self.wav[j, 1:] - self.wav[j, :-1]) / 2) for j in range(self.wav.shape[0])]
for i in range(self.wav.shape[1]): for i in range(self.wav.shape[1]):
self.wav_err[:, i] = np.array([(wav_err[j], wav_err[j]) for j in range(self.wav.shape[0])]) self.wav_err[:, i] = np.abs(np.array([(wav_err[j], wav_err[j]) for j in range(self.wav.shape[0])]))
self.IQUV_cov = np.zeros((4, 4, self.wav.shape[0], self.wav.shape[1])) self.IQUV_cov = np.zeros((4, 4, self.wav.shape[0], self.wav.shape[1]))
@@ -520,7 +508,7 @@ class FOSspecpol(specpol):
outfiles.append(spec_list[name].dump_txt(filename="_".join([filename, name]), output_dir=output_dir)) outfiles.append(spec_list[name].dump_txt(filename="_".join([filename, name]), output_dir=output_dir))
return outfiles return outfiles
def plot(self, spec_list=None, rest=True, savename=None, plots_folder="", fos=False): def plot(self, spec_list=None, savename=None, plots_folder="", fos=False):
""" """
Display current spectra in single figure. Display current spectra in single figure.
""" """
@@ -537,20 +525,18 @@ class FOSspecpol(specpol):
): ):
self.ax[i][0].set_title(title) self.ax[i][0].set_title(title)
if fos: if fos:
if rest: self.ax[i][0] = spec_list[name].plot(ax=self.ax[i][0])
wav, wav_err = self.wav_rest, self.wav_rest_err self.ax[i][1].set_xlabel(r"Wavelength [$\AA$]")
rest_str = "Rest " secax1 = self.ax[i][0].secondary_xaxis("top", functions=(self.rest, self.unrest))
else: secax1.set_xlabel(r"Rest wavelength [$\AA$]")
wav, wav_err = self.wav, self.wav_rest secax2 = self.ax[i][1].secondary_xaxis("top", functions=(self.rest, self.unrest))
rest_str = "" secax2.set_xlabel(r"Rest wavelength [$\AA$]")
self.ax[i][0] = spec_list[name].plot(ax=self.ax[i][0], rest=rest) self.ax[i][1].errorbar(self.wav[i], self.P_fos[i], xerr=self.wav_err[i].T, yerr=self.P_fos_err[i], color="b", fmt=".", label="P_fos")
self.ax[i][1].set_xlabel(rest_str + r"Wavelength [$\AA$]")
self.ax[i][1].errorbar(wav[i], self.P_fos[i], xerr=wav_err[i].T, yerr=self.P_fos_err[i], color="b", fmt=".", label="P_fos")
self.ax[i][1].set_ylim([0.0, 1.0]) self.ax[i][1].set_ylim([0.0, 1.0])
self.ax[i][1].set_ylabel(r"P", color="b") self.ax[i][1].set_ylabel(r"P", color="b")
self.ax[i][1].tick_params(axis="y", color="b", labelcolor="b") self.ax[i][1].tick_params(axis="y", color="b", labelcolor="b")
ax22 = self.ax[i][1].twinx() ax22 = self.ax[i][1].twinx()
ax22.errorbar(wav[i], self.PA_fos[i], xerr=wav_err[i].T, yerr=self.PA_fos_err[i], color="r", fmt=".", label="PA_fos [°]") ax22.errorbar(self.wav[i], self.PA_fos[i], xerr=self.wav_err[i].T, yerr=self.PA_fos_err[i], color="r", fmt=".", label="PA_fos [°]")
ax22.set_ylim([0.0, 180.0]) ax22.set_ylim([0.0, 180.0])
ax22.set_ylabel(r"PA", color="r") ax22.set_ylabel(r"PA", color="r")
ax22.tick_params(axis="y", color="r", labelcolor="r") ax22.tick_params(axis="y", color="r", labelcolor="r")