update readfos for addition and copy, query for fos
This commit is contained in:
@@ -51,15 +51,16 @@ class specpol(object):
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"""
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def __init__(self, other=None):
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if isinstance(other, specpol):
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if isinstance(other, __class__):
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# Copy constructor
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self.hd = deepcopy(other.hd)
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self.wav = deepcopy(other.wav)
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self.wav_err = deepcopy(other.wav_err)
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self.I = deepcopy(other.I)
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self.Q = deepcopy(other.Q)
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self.U = deepcopy(other.U)
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self.V = deepcopy(other.V)
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self.IQU_cov = deepcopy(other.IQU_cov)
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self.IQUV_cov = deepcopy(other.IQUV_cov)
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else:
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# Initialise to zero
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if isinstance(other, int):
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@@ -72,29 +73,52 @@ class specpol(object):
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"""
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Set all values to zero.
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"""
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self.hd = dict([])
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self.wav = np.zeros(n)
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self.wav_err = np.zeros((n, 2))
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self.I = np.zeros(n)
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self.Q = np.zeros(n)
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self.U = np.zeros(n)
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self.V = np.zeros(n)
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self.IQU_cov = np.zeros((4, 4, n))
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self.IQUV_cov = np.zeros((4, 4, n))
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@property
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def wav_rest(self, z=None):
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if z is None and "REDSHIFT" not in self.hd.keys():
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from astroquery.ipac.ned import Ned
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z = Ned.query_object(self.hd["TARGNAME"])["Redshift"][0]
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self.hd["REDSHIFT"] = z
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elif z is None:
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z = self.hd["REDSHIFT"]
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return self.wav / (z + 1)
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@property
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def wav_rest_err(self, z=None):
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if z is None and "REDSHIFT" not in self.hd.keys():
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from astroquery.ipac.ned import Ned
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z = Ned.query_object(self.hd["TARGNAME"])["Redshift"][0]
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self.hd["REDSHIFT"] = z
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elif z is None:
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z = self.hd["REDSHIFT"]
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return self.wav_err / (z + 1)
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@property
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def I_err(self):
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return np.sqrt(self.IQU_cov[0][0])
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return np.sqrt(self.IQUV_cov[0][0])
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@property
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def Q_err(self):
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return np.sqrt(self.IQU_cov[1][1])
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return np.sqrt(self.IQUV_cov[1][1])
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@property
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def U_err(self):
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return np.sqrt(self.IQU_cov[2][2])
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return np.sqrt(self.IQUV_cov[2][2])
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@property
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def V_err(self):
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return np.sqrt(self.IQU_cov[3][3])
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return np.sqrt(self.IQUV_cov[3][3])
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@property
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def QN(self):
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@@ -165,13 +189,12 @@ class specpol(object):
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]
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)
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self.I, self.Q, self.U, self.V = np.dot(mrot, np.array([self.I, self.Q, self.U, self.V]))
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self.IQU_cov = np.dot(mrot, np.dot(self.IQU_cov.T, mrot.T).T)
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self.IQUV_cov = np.dot(mrot, np.dot(self.IQUV_cov.T, mrot.T).T)
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def bin_size(self, size):
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def bin(self, bin_edges):
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"""
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Rebin spectra to selected bin size in Angstrom.
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Rebin spectra to given list of bin edges.
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"""
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bin_edges = np.arange(np.floor(self.wav.min()), np.ceil(self.wav.max()), size)
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in_bin = np.digitize(self.wav, bin_edges) - 1
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spec_b = specpol(bin_edges.shape[0] - 1)
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for i in range(bin_edges.shape[0] - 1):
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@@ -183,11 +206,22 @@ class specpol(object):
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spec_b.U[i] = np.sum(self.U[in_bin == i])
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spec_b.V[i] = np.sum(self.V[in_bin == i])
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for m in range(4):
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spec_b.IQU_cov[m][m][i] = np.sum(self.IQU_cov[m][m][in_bin == i])
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spec_b.IQUV_cov[m][m][i] = np.sum(self.IQUV_cov[m][m][in_bin == i])
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for n in [k for k in range(4) if k != m]:
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spec_b.IQU_cov[m][n][i] = np.sqrt(np.sum(self.IQU_cov[m][n][in_bin == i] ** 2))
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spec_b.IQUV_cov[m][n][i] = np.sqrt(np.sum(self.IQUV_cov[m][n][in_bin == i] ** 2))
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spec_b.hd = deepcopy(self.hd)
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spec_b.hd["NAXIS1"] = bin_edges.shape[0] - 1
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spec_b.hd["DATAMIN"], spec_b.hd["DATAMAX"] = spec_b.I.min(), spec_b.I.max()
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spec_b.hd["MINWAV"], spec_b.hd["MAXWAV"] = spec_b.wav.min(), spec_b.wav.max()
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return spec_b
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def bin_size(self, size):
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"""
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Rebin spectra to selected bin size in Angstrom.
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"""
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bin_edges = np.arange(np.floor(self.wav.min()), np.ceil(self.wav.max()), size)
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return self.bin(bin_edges)
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def dump_txt(self, filename, output_dir=""):
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"""
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Dump current spectra to a text file.
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@@ -196,7 +230,7 @@ class specpol(object):
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np.savetxt(join_path(output_dir, filename + ".txt"), data_dump)
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return join_path(output_dir, filename)
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def plot(self, fig=None, ax=None, savename=None, plots_folder=""):
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def plot(self, fig=None, ax=None, rest=True, savename=None, plots_folder=""):
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"""
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Display current spectra.
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"""
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@@ -212,27 +246,33 @@ class specpol(object):
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else:
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self.fig = fig
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self.ax = ax
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if isinstance(ax, np.ndarray):
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if isinstance(self.ax, np.ndarray):
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ax1, ax2 = self.ax[:2]
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else:
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ax1 = self.ax
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if rest:
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wav, wav_err = self.wav_rest, self.wav_rest_err
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rest_str = "Rest "
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else:
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wav, wav_err = self.wav, self.wav_rest
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rest_str = ""
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# Display flux and polarized flux on first ax
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ax1.set_xlabel(r"Wavelength [$\AA$]")
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ax1.errorbar(self.wav, self.I, xerr=self.wav_err.T, yerr=self.I_err, color="k", fmt=".", label="I")
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ax1.errorbar(self.wav, self.PF, xerr=self.wav_err.T, yerr=self.PF_err, color="b", fmt=".", label="PF")
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ax1.set_xlabel(rest_str + r"Wavelength [$\AA$]")
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ax1.errorbar(wav, self.I, xerr=wav_err.T, yerr=self.I_err, color="k", fmt=".", label="I")
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ax1.errorbar(wav, self.PF, xerr=wav_err.T, yerr=self.PF_err, color="b", fmt=".", label="PF")
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ax1.set_ylabel(r"F$_\lambda$ [erg s$^{-1}$ cm$^{-2} \AA^{-1}$]")
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ax1.legend(ncols=2, loc=1)
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if isinstance(ax, np.ndarray):
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if isinstance(self.ax, np.ndarray):
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# When given 2 axes, display P and PA on second
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ax2.set_xlabel(r"Wavelength [$\AA$]")
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ax2.errorbar(self.wav, self.P, xerr=self.wav_err.T, yerr=self.P_err, color="b", fmt=".", label="P")
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ax2.set_xlabel(rest_str + r"Wavelength [$\AA$]")
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ax2.errorbar(wav, self.P, xerr=wav_err.T, yerr=self.P_err, color="b", fmt=".", label="P")
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ax2.set_ylim([0.0, 1.0])
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ax2.set_ylabel(r"P", color="b")
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ax2.tick_params(axis="y", color="b", labelcolor="b")
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ax22 = ax2.twinx()
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ax22.errorbar(self.wav, self.PA, xerr=self.wav_err.T, yerr=self.PA_err, color="r", fmt=".", label="PA [°]")
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ax22.errorbar(wav, self.PA, xerr=wav_err.T, yerr=self.PA_err, color="r", fmt=".", label="PA [°]")
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ax22.set_ylim([0.0, 180.0])
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ax22.set_ylabel(r"PA", color="r")
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ax22.tick_params(axis="y", color="r", labelcolor="r")
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@@ -248,6 +288,44 @@ class specpol(object):
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else:
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return self.ax
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def __add__(self, other):
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"""
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Spectra addition, if not same binning default to self bins.
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"""
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spec_a = specpol(self)
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if np.all(self.wav == other.wav):
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spec_b = other
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else:
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bin_edges = np.zeros(spec_a.wav.shape[0] + 1)
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bin_edges[:-1], bin_edges[-1] = spec_a.wav - spec_a.wav_err[:, 0], spec_a.wav[-1] + spec_a.wav_err[-1:1]
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spec_b = other.bin(bin_edges=bin_edges)
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spec_a.I += deepcopy(spec_b.I)
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spec_a.Q += deepcopy(spec_b.Q)
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spec_a.U += deepcopy(spec_b.U)
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spec_a.V += deepcopy(spec_b.V)
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spec_a.IQUV_cov += deepcopy(spec_b.IQUV_cov)
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spec_a.hd["DATAMIN"], spec_a.hd["DATAMAX"] = spec_a.I.min(), spec_a.I.max()
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spec_a.hd["EXPTIME"] += spec_b.hd["EXPTIME"]
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spec_a.hd["ROOTNAME"] += "+" + spec_b.hd["ROOTNAME"]
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return spec_a
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def __deepcopy__(self, memo={}):
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spec = specpol(self.wav.shape[0])
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spec.__dict__.update(self.__dict__)
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spec.hd = deepcopy(self.hd, memo)
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spec.wav = deepcopy(self.wav, memo)
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spec.wav_err = deepcopy(self.wav_err, memo)
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spec.I = deepcopy(self.I, memo)
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spec.Q = deepcopy(self.Q, memo)
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spec.U = deepcopy(self.U, memo)
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spec.V = deepcopy(self.V, memo)
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spec.IQUV_cov = deepcopy(self.IQUV_cov, memo)
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return spec
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class FOSspecpol(specpol):
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"""
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@@ -256,41 +334,99 @@ class FOSspecpol(specpol):
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def __init__(self, stokes, data_folder=""):
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"""
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Initialise object from fits filename or hdulist.
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Initialise object from fits filename, fits hdulist or copy.
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"""
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if isinstance(stokes, __class__):
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# Copy constructor
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self.rootname = deepcopy(stokes.rootname)
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self.hd = deepcopy(stokes.hd)
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self.wav = deepcopy(stokes.wav)
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self.wav_err = deepcopy(stokes.wav_err)
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self.I = deepcopy(stokes.I)
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self.Q = deepcopy(stokes.Q)
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self.U = deepcopy(stokes.U)
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self.V = deepcopy(stokes.V)
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self.IQUV_cov = deepcopy(stokes.IQUV_cov)
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self.P_fos = deepcopy(stokes.P_fos)
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self.P_fos_err = deepcopy(stokes.P_fos_err)
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self.PC_fos = deepcopy(stokes.PC_fos)
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self.PC_fos_err = deepcopy(stokes.PC_fos_err)
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self.PA_fos = deepcopy(stokes.PA_fos)
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self.PA_fos_err = deepcopy(stokes.PA_fos_err)
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self.subspec = {}
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for name in ["PASS1", "PASS2", "PASS12", "PASS12corr"]:
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spec = deepcopy(stokes.subspec[name])
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self.subspec[name] = spec
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elif stokes is None or isinstance(stokes, int):
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self.zero(n=stokes)
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else:
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self.from_file(stokes, data_folder=data_folder)
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@classmethod
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def zero(self, n=1):
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"""
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Set all values to zero.
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"""
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self.rootname = ""
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self.hd = dict([])
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self.wav = np.zeros((4, n))
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self.wav_err = np.zeros((4, n, 2))
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self.I = np.zeros((4, n))
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self.Q = np.zeros((4, n))
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self.U = np.zeros((4, n))
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self.V = np.zeros((4, n))
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self.IQUV_cov = np.zeros((4, 4, 4, n))
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self.subspec = {}
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for i, name in enumerate(["PASS1", "PASS2", "PASS12", "PASS12corr"]):
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spec = specpol(n)
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spec.hd, spec.wav, spec.wav_err, spec.I, spec.Q, spec.U, spec.V = self.hd, self.wav[i], self.wav_err[i], self.I[i], self.Q[i], self.U[i], self.V[i]
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spec.IQUV_cov = self.IQUV_cov[:, :, i, :]
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self.subspec[name] = spec
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self.P_fos = np.zeros(self.I.shape)
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self.P_fos_err = np.zeros(self.I.shape)
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self.PC_fos = np.zeros(self.I.shape)
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self.PC_fos_err = np.zeros(self.I.shape)
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self.PA_fos = np.zeros(self.I.shape)
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self.PA_fos_err = np.zeros(self.I.shape)
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def from_file(self, stokes, data_folder=""):
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"""
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Initialise object from fits file or hdulist.
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"""
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if isinstance(stokes, str):
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self.file_root = stokes.split("_")[0]
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self.hd = getheader(join_path(data_folder, self.file_root + "_c0f.fits"))
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wav = getdata(join_path(data_folder, self.file_root + "_c0f.fits"))
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stokes = getdata(join_path(data_folder, self.file_root + "_c3f.fits"))
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self.rootname = stokes.split("_")[0]
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self.hd = dict(getheader(join_path(data_folder, self.rootname + "_c0f.fits")))
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wav = getdata(join_path(data_folder, self.rootname + "_c0f.fits"))
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stokes = getdata(join_path(data_folder, self.rootname + "_c3f.fits"))
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elif isinstance(stokes, hdu.hdulist.HDUList):
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self.hd = stokes.header
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self.file_root = self.hd["FILENAME"].split("_")[0]
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wav = getdata(join_path(data_folder, self.file_root + "_c0f"))
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self.hd = dict(stokes.header)
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self.rootname = self.hd["FILENAME"].split("_")[0]
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wav = getdata(join_path(data_folder, self.rootname + "_c0f"))
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stokes = stokes.data
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else:
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raise ValueError("Input must be a path to a fits file or an HDUlist")
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self.wav = np.concat((wav[0:2, :], wav[0].reshape(1, wav.shape[1]), wav[0].reshape(1, wav.shape[1])), axis=0)
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self.wav_err = np.zeros((self.wav.shape[0], self.wav.shape[1], 2))
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self.IQU_cov = np.zeros((4, 4, self.wav.shape[0], self.wav.shape[1]))
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self.IQUV_cov = np.zeros((4, 4, self.wav.shape[0], self.wav.shape[1]))
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self.I = stokes[0::14]
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self.IQU_cov[0, 0] = stokes[4::14] ** 2
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self.IQUV_cov[0, 0] = stokes[4::14] ** 2
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self.Q = stokes[1::14]
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self.IQU_cov[1, 1] = stokes[5::14] ** 2
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self.IQUV_cov[1, 1] = stokes[5::14] ** 2
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self.U = stokes[2::14]
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self.IQU_cov[2, 2] = stokes[6::14] ** 2
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self.IQUV_cov[2, 2] = stokes[6::14] ** 2
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self.V = stokes[3::14]
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self.IQU_cov[3, 3] = stokes[7::14] ** 2
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self.IQUV_cov[3, 3] = stokes[7::14] ** 2
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self.subspec = {}
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for i, name in enumerate(["PASS1", "PASS2", "PASS12", "PASS12corr"]):
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spec = specpol(self.wav[i].shape[0])
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spec.wav, spec.wav_err, spec.I, spec.Q, spec.U, spec.V = self.wav[i], self.wav_err[i], self.I[i], self.Q[i], self.U[i], self.V[i]
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spec.IQU_cov = self.IQU_cov[:, :, i, :]
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spec.rotate((i != 3) * self.hd["PA_APER"])
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spec.hd, spec.wav, spec.wav_err, spec.I, spec.Q, spec.U, spec.V = self.hd, self.wav[i], self.wav_err[i], self.I[i], self.Q[i], self.U[i], self.V[i]
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spec.IQUV_cov = self.IQUV_cov[:, :, i, :]
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spec.rotate(-(name[-4:] != "corr") * spec.hd["PA_APER"])
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self.subspec[name] = spec
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self.P_fos = stokes[8::14]
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@@ -302,12 +438,6 @@ class FOSspecpol(specpol):
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)
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self.PA_fos_err = princ_angle(np.degrees(stokes[13::14]))
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def __del__(self):
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if hasattr(self, "ax"):
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del self.ax
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if hasattr(self, "fig"):
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del self.fig
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def dump_txt(self, filename, spec_list=None, output_dir=""):
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"""
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Dump current spectra to a text file.
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@@ -319,7 +449,7 @@ class FOSspecpol(specpol):
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outfiles.append(spec_list[name].dump_txt(filename="_".join([filename, name]), output_dir=output_dir))
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return outfiles
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def plot(self, spec_list=None, savename=None, plots_folder="", fos=False):
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def plot(self, spec_list=None, rest=True, savename=None, plots_folder="", fos=False):
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"""
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Display current spectra in single figure.
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"""
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@@ -336,14 +466,20 @@ class FOSspecpol(specpol):
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):
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self.ax[i][0].set_title(title)
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if fos:
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self.ax[i][0] = spec_list[name].plot(ax=self.ax[i][0])
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self.ax[i][1].set_xlabel(r"Wavelength [$\AA$]")
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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")
|
||||
if rest:
|
||||
wav, wav_err = self.wav_rest, self.wav_rest_err
|
||||
rest_str = "Rest "
|
||||
else:
|
||||
wav, wav_err = self.wav, self.wav_rest
|
||||
rest_str = ""
|
||||
self.ax[i][0] = spec_list[name].plot(ax=self.ax[i][0], rest=rest)
|
||||
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_ylabel(r"P", color="b")
|
||||
self.ax[i][1].tick_params(axis="y", color="b", labelcolor="b")
|
||||
ax22 = self.ax[i][1].twinx()
|
||||
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.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.set_ylim([0.0, 180.0])
|
||||
ax22.set_ylabel(r"PA", color="r")
|
||||
ax22.tick_params(axis="y", color="r", labelcolor="r")
|
||||
@@ -354,7 +490,7 @@ class FOSspecpol(specpol):
|
||||
self.ax[i] = spec_list[name].plot(ax=self.ax[i])
|
||||
self.ax[0][0].set_ylim(ymin=0.0)
|
||||
|
||||
self.fig.suptitle("_".join([self.hd["TARGNAME"], str(self.hd["PROPOSID"]), self.hd["FILENAME"], self.hd["APER_ID"]]))
|
||||
self.fig.suptitle("_".join([self.hd["TARGNAME"], str(self.hd["PROPOSID"]), self.hd["ROOTNAME"], self.hd["APER_ID"]]))
|
||||
if savename is not None:
|
||||
self.fig.savefig(join_path(plots_folder, savename + ".pdf"), dpi=300, bbox_inches="tight")
|
||||
outfiles.append(join_path(plots_folder, savename + ".pdf"))
|
||||
@@ -371,6 +507,49 @@ class FOSspecpol(specpol):
|
||||
self.subspec[key][name] = self.subspec[name].bin_size(size)
|
||||
return self.subspec[key]
|
||||
|
||||
def __add__(self, other):
|
||||
"""
|
||||
Spectra addition, if not same binning default to self bins.
|
||||
"""
|
||||
spec_a = FOSspecpol(self)
|
||||
if np.all(self.wav == other.wav):
|
||||
spec_b = other
|
||||
else:
|
||||
bin_edges = np.zeros(spec_a.wav.shape[0] + 1)
|
||||
bin_edges[:-1], bin_edges[-1] = spec_a.wav - spec_a.wav_err[:, 0], spec_a.wav[-1] + spec_a.wav_err[-1:1]
|
||||
spec_b = other.bin(bin_edges=bin_edges)
|
||||
|
||||
spec_a.I += deepcopy(spec_b.I)
|
||||
spec_a.Q += deepcopy(spec_b.Q)
|
||||
spec_a.U += deepcopy(spec_b.U)
|
||||
spec_a.V += deepcopy(spec_b.V)
|
||||
spec_a.IQUV_cov += deepcopy(spec_b.IQUV_cov)
|
||||
for name in ["PASS1", "PASS2", "PASS12", "PASS12corr"]:
|
||||
spec_a.subspec[name] += deepcopy(spec_b.subspec[name])
|
||||
spec_a.subspec[name].hd["DATAMIN"], spec_a.subspec[name].hd["DATAMAX"] = spec_a.subspec[name].I.min(), spec_a.subspec[name].I.max()
|
||||
spec_a.subspec[name].hd["EXPTIME"] += spec_b.subspec[name].hd["EXPTIME"]
|
||||
spec_a.subspec[name].hd["ROOTNAME"] += "+" + spec_b.subspec[name].hd["ROOTNAME"]
|
||||
|
||||
spec_a.hd["DATAMIN"], spec_a.hd["DATAMAX"] = spec_a.I.min(), spec_a.I.max()
|
||||
spec_a.hd["EXPTIME"] += spec_b.hd["EXPTIME"]
|
||||
spec_a.hd["ROOTNAME"] += "+" + spec_b.hd["ROOTNAME"]
|
||||
return spec_a
|
||||
|
||||
def __deepcopy__(self, memo):
|
||||
spec = FOSspecpol(self.wav.shape[0])
|
||||
spec.__dict__.update(self.__dict__)
|
||||
|
||||
for key in self.subspec.keys():
|
||||
spec.subspec[key] = deepcopy(self.subspec[key])
|
||||
|
||||
return spec
|
||||
|
||||
def __del__(self):
|
||||
if hasattr(self, "ax"):
|
||||
del self.ax
|
||||
if hasattr(self, "fig"):
|
||||
del self.fig
|
||||
|
||||
|
||||
def main(infiles, bin_size=None, output_dir=None):
|
||||
outfiles = []
|
||||
@@ -394,19 +573,35 @@ def main(infiles, bin_size=None, output_dir=None):
|
||||
infiles = [p[1] for p in prod]
|
||||
|
||||
roots = np.unique([file.split("_")[0] for file in infiles])
|
||||
for file_root in roots:
|
||||
print(file_root)
|
||||
spec = FOSspecpol(file_root, data_folder)
|
||||
filename = "_".join([spec.hd["TARGNAME"], "FOS", str(spec.hd["PROPOSID"]), spec.file_root, spec.hd["APER_ID"]])
|
||||
aper = dict([])
|
||||
for rootname in roots:
|
||||
print(rootname)
|
||||
spec = FOSspecpol(rootname, data_folder)
|
||||
filename = "_".join([spec.hd["TARGNAME"], "FOS", str(spec.hd["PROPOSID"]), spec.rootname, spec.hd["APER_ID"]])
|
||||
if bin_size is not None:
|
||||
key = "{0:.2f}bin".format(bin_size)
|
||||
spec.bin_size(bin_size)
|
||||
outfiles += spec.dump_txt("_".join([filename, key]), spec_list=spec.subspec[key], output_dir=output_dir)
|
||||
outfiles += spec.plot(savename="_".join([filename, key]), spec_list=spec.subspec[key], plots_folder=plots_folder)
|
||||
if hasattr(aper, spec.hd["APER_ID"]):
|
||||
aper[spec.hd["APER_ID"]].append(spec.subspec[key]["PASS12corr"])
|
||||
else:
|
||||
aper[spec.hd["APER_ID"]] = [spec.subspec[key]["PASS12corr"]]
|
||||
else:
|
||||
outfiles += spec.dump_txt(filename, output_dir=output_dir)
|
||||
outfiles += spec.plot(savename=filename, plots_folder=plots_folder)
|
||||
del spec
|
||||
if hasattr(aper, spec.hd["APER_ID"]):
|
||||
aper[spec.hd["APER_ID"]].append(spec.subspec["PASS12corr"])
|
||||
else:
|
||||
aper[spec.hd["APER_ID"]] = [spec.subspec["PASS12corr"]]
|
||||
plt.close("all")
|
||||
for key in aper.keys():
|
||||
filename = "_".join([spec.hd["TARGNAME"], "FOS", str(spec.hd["PROPOSID"]), "SUM"])
|
||||
if bin_size is not None:
|
||||
filename += "_{0:.2f}bin".format(bin_size)
|
||||
spec = np.sum(aper[key])
|
||||
outfiles.append(spec.dump_txt("_".join([filename, key]), output_dir=output_dir))
|
||||
outfiles.append(spec.plot(savename="_".join([filename, key]), plots_folder=plots_folder)[2])
|
||||
plt.show()
|
||||
|
||||
return outfiles
|
||||
|
||||
Reference in New Issue
Block a user