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NGC1068 overplot

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Thibault Barnouin
2024-10-03 17:12:30 +02:00
parent f84898a9b4
commit bd7cad46a1
4 changed files with 150 additions and 47 deletions
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7
package/FOC_reduction.py
View File

@@ -3,6 +3,7 @@
""" """
Main script where are progressively added the steps for the FOC pipeline reduction. Main script where are progressively added the steps for the FOC pipeline reduction.
""" """
from pathlib import Path from pathlib import Path
from sys import path as syspath from sys import path as syspath
@@ -58,7 +59,7 @@ def main(target=None, proposal_id=None, infiles=None, output_dir="./data", crop=
# Smoothing # Smoothing
smoothing_function = "combine" # gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine smoothing_function = "combine" # gaussian_after, weighted_gaussian_after, gaussian, weighted_gaussian or combine
smoothing_FWHM = 0.075 # If None, no smoothing is done smoothing_FWHM = 0.075 # If None, no smoothing is done
smoothing_scale = "arcsec" # pixel or arcsec smoothing_scale = "arcsec" # pixel or arcsec
# Rotation # Rotation
@@ -391,7 +392,7 @@ def main(target=None, proposal_id=None, infiles=None, output_dir="./data", crop=
proj_plots.polarization_map( proj_plots.polarization_map(
deepcopy(Stokes_hdul), deepcopy(Stokes_hdul),
data_mask, data_mask,
P_cut=P_cut if P_cut >= 1. else 3., P_cut=P_cut if P_cut >= 1.0 else 3.0,
SNRi_cut=SNRi_cut, SNRi_cut=SNRi_cut,
flux_lim=flux_lim, flux_lim=flux_lim,
step_vec=step_vec, step_vec=step_vec,
@@ -403,7 +404,7 @@ def main(target=None, proposal_id=None, infiles=None, output_dir="./data", crop=
proj_plots.polarization_map( proj_plots.polarization_map(
deepcopy(Stokes_hdul), deepcopy(Stokes_hdul),
data_mask, data_mask,
P_cut=P_cut if P_cut < 1. else 0.99, P_cut=P_cut if P_cut < 1.0 else 0.99,
SNRi_cut=SNRi_cut, SNRi_cut=SNRi_cut,
flux_lim=flux_lim, flux_lim=flux_lim,
step_vec=step_vec, step_vec=step_vec,

128
package/lib/plots.py
View File

@@ -225,6 +225,7 @@ def polarization_map(
display="default", display="default",
fig=None, fig=None,
ax=None, ax=None,
**kwargs,
): ):
""" """
Plots polarization map from Stokes HDUList. Plots polarization map from Stokes HDUList.
@@ -357,6 +358,47 @@ def polarization_map(
ax.coords[0].set_ticklabel_position("t") ax.coords[0].set_ticklabel_position("t")
ax.set_ylabel("Declination (J2000)", labelpad=-1) ax.set_ylabel("Declination (J2000)", labelpad=-1)
vmin, vmax = 0.0, stkI.max() * convert_flux
for key, value in [
["cmap", [["cmap", "inferno"]]],
["width", [["width", 0.5]]],
["linewidth", [["linewidth", 0.3]]],
]:
try:
_ = kwargs[key]
except KeyError:
for key_i, val_i in value:
kwargs[key_i] = val_i
if kwargs["cmap"] in [
"inferno",
"magma",
"Greys_r",
"binary_r",
"gist_yarg_r",
"gist_gray",
"gray",
"bone",
"pink",
"hot",
"afmhot",
"gist_heat",
"copper",
"gist_earth",
"gist_stern",
"gnuplot",
"gnuplot2",
"CMRmap",
"cubehelix",
"nipy_spectral",
"gist_ncar",
"viridis",
]:
ax.set_facecolor("black")
font_color = "white"
else:
ax.set_facecolor("white")
font_color = "black"
if display.lower() in ["intensity"]: if display.lower() in ["intensity"]:
# If no display selected, show intensity map # If no display selected, show intensity map
display = "i" display = "i"
@@ -367,7 +409,7 @@ def polarization_map(
vmin, vmax = 1.0 / 2.0 * np.median(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux) vmin, vmax = 1.0 / 2.0 * np.median(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux)
else: else:
vmin, vmax = flux_lim vmin, vmax = flux_lim
im = ax.imshow(stkI * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(stkI * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=30, shrink=0.75, pad=0.025, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]") fig.colorbar(im, ax=ax, aspect=30, shrink=0.75, pad=0.025, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
levelsI = np.array([0.8, 2.0, 5.0, 10.0, 20.0, 50.0]) / 100.0 * vmax levelsI = np.array([0.8, 2.0, 5.0, 10.0, 20.0, 50.0]) / 100.0 * vmax
print("Total flux contour levels : ", levelsI) print("Total flux contour levels : ", levelsI)
@@ -382,7 +424,7 @@ def polarization_map(
vmin, vmax = 1.0 / 2.0 * np.median(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux) vmin, vmax = 1.0 / 2.0 * np.median(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux)
else: else:
vmin, vmax = flux_lim vmin, vmax = flux_lim
im = ax.imshow(stkI * convert_flux * pol, norm=LogNorm(vmin, vmax), aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(stkI * convert_flux * pol, norm=LogNorm(vmin, vmax), aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$F_{\lambda} \cdot P$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$F_{\lambda} \cdot P$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
levelsPf = np.linspace(vmax * 0.01, vmax * 0.99, 10) levelsPf = np.linspace(vmax * 0.01, vmax * 0.99, 10)
print("Polarized flux contour levels : ", levelsPf) print("Polarized flux contour levels : ", levelsPf)
@@ -391,13 +433,13 @@ def polarization_map(
# Display polarization degree map # Display polarization degree map
display = "p" display = "p"
vmin, vmax = 0.0, 100.0 vmin, vmax = 0.0, 100.0
im = ax.imshow(pol * 100.0, vmin=vmin, vmax=vmax, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(pol * 100.0, vmin=vmin, vmax=vmax, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$P$ [%]") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$P$ [%]")
elif display.lower() in ["pa", "pang", "pol_ang"]: elif display.lower() in ["pa", "pang", "pol_ang"]:
# Display polarization degree map # Display polarization degree map
display = "pa" display = "pa"
vmin, vmax = 0.0, 180.0 vmin, vmax = 0.0, 180.0
im = ax.imshow(princ_angle(pang), vmin=vmin, vmax=vmax, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(princ_angle(pang), vmin=vmin, vmax=vmax, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$\theta_P$ [°]") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$\theta_P$ [°]")
elif display.lower() in ["s_p", "pol_err", "pol_deg_err"]: elif display.lower() in ["s_p", "pol_err", "pol_deg_err"]:
# Display polarization degree error map # Display polarization degree error map
@@ -419,37 +461,37 @@ def polarization_map(
) )
im = ax.imshow(np.sqrt(stk_cov[0, 0]) * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap="inferno_r", alpha=1.0) im = ax.imshow(np.sqrt(stk_cov[0, 0]) * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap="inferno_r", alpha=1.0)
else: else:
im = ax.imshow(np.sqrt(stk_cov[0, 0]) * convert_flux, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(np.sqrt(stk_cov[0, 0]) * convert_flux, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$\sigma_I$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$\sigma_I$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA^{-1}$]")
elif display.lower() in ["snri"]: elif display.lower() in ["snri"]:
# Display I_stokes signal-to-noise map # Display I_stokes signal-to-noise map
display = "snri" display = "snri"
vmin, vmax = 0.0, np.max(SNRi[np.isfinite(SNRi)]) vmin, vmax = 0.0, np.max(SNRi[np.isfinite(SNRi)])
if vmax * 0.99 > SNRi_cut: if vmax * 0.99 > SNRi_cut:
im = ax.imshow(SNRi, vmin=vmin, vmax=vmax, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(SNRi, vmin=vmin, vmax=vmax, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
levelsSNRi = np.linspace(SNRi_cut, vmax * 0.99, 5).astype(int) levelsSNRi = np.linspace(SNRi_cut, vmax * 0.99, 5).astype(int)
print("SNRi contour levels : ", levelsSNRi) print("SNRi contour levels : ", levelsSNRi)
ax.contour(SNRi, levels=levelsSNRi, colors="grey", linewidths=0.5) ax.contour(SNRi, levels=levelsSNRi, colors="grey", linewidths=0.5)
else: else:
im = ax.imshow(SNRi, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(SNRi, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$I_{Stokes}/\sigma_{I}$") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$I_{Stokes}/\sigma_{I}$")
elif display.lower() in ["snr", "snrp"]: elif display.lower() in ["snr", "snrp"]:
# Display polarization degree signal-to-noise map # Display polarization degree signal-to-noise map
display = "snrp" display = "snrp"
vmin, vmax = 0.0, np.max(SNRp[np.isfinite(SNRp)]) vmin, vmax = 0.0, np.max(SNRp[np.isfinite(SNRp)])
if vmax * 0.99 > P_cut: if vmax * 0.99 > P_cut:
im = ax.imshow(SNRp, vmin=vmin, vmax=vmax, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(SNRp, vmin=vmin, vmax=vmax, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
levelsSNRp = np.linspace(P_cut, vmax * 0.99, 5).astype(int) levelsSNRp = np.linspace(P_cut, vmax * 0.99, 5).astype(int)
print("SNRp contour levels : ", levelsSNRp) print("SNRp contour levels : ", levelsSNRp)
ax.contour(SNRp, levels=levelsSNRp, colors="grey", linewidths=0.5) ax.contour(SNRp, levels=levelsSNRp, colors="grey", linewidths=0.5)
else: else:
im = ax.imshow(SNRp, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(SNRp, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$P/\sigma_{P}$") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$P/\sigma_{P}$")
elif display.lower() in ["conf", "confp"]: elif display.lower() in ["conf", "confp"]:
# Display polarization degree signal-to-noise map # Display polarization degree signal-to-noise map
display = "confp" display = "confp"
vmin, vmax = 0.0, 1.0 vmin, vmax = 0.0, 1.0
im = ax.imshow(confP, vmin=vmin, vmax=vmax, aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(confP, vmin=vmin, vmax=vmax, aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
levelsconfp = np.array([0.500, 0.900, 0.990, 0.999]) levelsconfp = np.array([0.500, 0.900, 0.990, 0.999])
print("confp contour levels : ", levelsconfp) print("confp contour levels : ", levelsconfp)
ax.contour(confP, levels=levelsconfp, colors="grey", linewidths=0.5) ax.contour(confP, levels=levelsconfp, colors="grey", linewidths=0.5)
@@ -460,7 +502,7 @@ def polarization_map(
vmin, vmax = 1.0 * np.mean(np.sqrt(stk_cov[0, 0][mask]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux) vmin, vmax = 1.0 * np.mean(np.sqrt(stk_cov[0, 0][mask]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux)
else: else:
vmin, vmax = 1.0 * np.mean(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux) vmin, vmax = 1.0 * np.mean(np.sqrt(stk_cov[0, 0][stkI > 0.0]) * convert_flux), np.max(stkI[stkI > 0.0] * convert_flux)
im = ax.imshow(stkI * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap="inferno", alpha=1.0) im = ax.imshow(stkI * convert_flux, norm=LogNorm(vmin, vmax), aspect="equal", cmap=kwargs["cmap"], alpha=1.0)
fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA$]") fig.colorbar(im, ax=ax, aspect=50, shrink=0.75, pad=0.025, label=r"$F_{\lambda}$ [$ergs \cdot cm^{-2} \cdot s^{-1} \cdot \AA$]")
# Get integrated values from header # Get integrated values from header
@@ -474,7 +516,7 @@ def polarization_map(
plt.rcParams.update({"font.size": 10}) plt.rcParams.update({"font.size": 10})
px_size = wcs.wcs.get_cdelt()[0] * 3600.0 px_size = wcs.wcs.get_cdelt()[0] * 3600.0
px_sc = AnchoredSizeBar(ax.transData, 1.0 / px_size, "1 arcsec", 3, pad=0.25, sep=5, borderpad=0.25, frameon=False, size_vertical=0.005, color="w") px_sc = AnchoredSizeBar(ax.transData, 1.0 / px_size, "1 arcsec", 3, pad=0.25, sep=5, borderpad=0.25, frameon=False, size_vertical=0.005, color=font_color)
north_dir = AnchoredDirectionArrows( north_dir = AnchoredDirectionArrows(
ax.transAxes, ax.transAxes,
"E", "E",
@@ -489,8 +531,8 @@ def polarization_map(
head_length=10.0, head_length=10.0,
head_width=10.0, head_width=10.0,
angle=-Stokes[0].header["orientat"], angle=-Stokes[0].header["orientat"],
text_props={"ec": "k", "fc": "w", "alpha": 1, "lw": 0.4}, text_props={"ec": "k", "fc": font_color, "alpha": 1, "lw": 0.4},
arrow_props={"ec": "k", "fc": "w", "alpha": 1, "lw": 1}, arrow_props={"ec": "k", "fc": font_color, "alpha": 1, "lw": 1},
) )
if display.lower() in ["i", "s_i", "snri", "pf", "p", "pa", "s_p", "snrp", "confp"]: if display.lower() in ["i", "s_i", "snri", "pf", "p", "pa", "s_p", "snrp", "confp"]:
@@ -513,12 +555,14 @@ def polarization_map(
headwidth=0.0, headwidth=0.0,
headlength=0.0, headlength=0.0,
headaxislength=0.0, headaxislength=0.0,
width=0.5, width=kwargs["width"],
linewidth=0.75, linewidth=kwargs["linewidth"],
color="w", color="w",
edgecolor="k", edgecolor="k",
) )
pol_sc = AnchoredSizeBar(ax.transData, scale_vec, r"$P$= 100 %", 4, pad=0.25, sep=5, borderpad=0.25, frameon=False, size_vertical=0.005, color="w") pol_sc = AnchoredSizeBar(
ax.transData, scale_vec, r"$P$= 100 %", 4, pad=0.25, sep=5, borderpad=0.25, frameon=False, size_vertical=0.005, color=font_color
)
ax.add_artist(pol_sc) ax.add_artist(pol_sc)
ax.add_artist(px_sc) ax.add_artist(px_sc)
@@ -1302,7 +1346,7 @@ class overplot_pol(align_maps):
Inherit from class align_maps in order to get the same WCS on both maps. Inherit from class align_maps in order to get the same WCS on both maps.
""" """
def overplot(self, levels=None, P_cut=0.99, SNRi_cut=1.0, scale_vec=2.0, savename=None, **kwargs): def overplot(self, levels=None, P_cut=0.99, SNRi_cut=1.0, scale_vec=2.0, step_vec=1, savename=None, **kwargs):
self.Stokes_UV = self.map self.Stokes_UV = self.map
self.wcs_UV = self.map_wcs self.wcs_UV = self.map_wcs
# Get Data # Get Data
@@ -1339,8 +1383,8 @@ class overplot_pol(align_maps):
plt.rcParams.update({"font.size": 16}) plt.rcParams.update({"font.size": 16})
ratiox = max(int(stkI.shape[1] / stkI.shape[0]), 1) ratiox = max(int(stkI.shape[1] / stkI.shape[0]), 1)
ratioy = max(int(stkI.shape[0] / stkI.shape[1]), 1) ratioy = max(int(stkI.shape[0] / stkI.shape[1]), 1)
px_scale = self.wcs_UV.wcs.get_cdelt()[0] / self.other_wcs.wcs.get_cdelt()[0] self.px_scale = self.wcs_UV.wcs.get_cdelt()[0] / self.other_wcs.wcs.get_cdelt()[0]
self.fig_overplot, self.ax_overplot = plt.subplots(figsize=(10 * ratiox, 10 * ratioy), subplot_kw=dict(projection=self.other_wcs)) self.fig_overplot, self.ax_overplot = plt.subplots(figsize=(10 * ratiox, 12 * ratioy), subplot_kw=dict(projection=self.other_wcs))
self.fig_overplot.subplots_adjust(hspace=0, wspace=0, bottom=0.1, left=0.1, top=0.80, right=1.02) self.fig_overplot.subplots_adjust(hspace=0, wspace=0, bottom=0.1, left=0.1, top=0.80, right=1.02)
self.ax_overplot.set_xlabel(label="Right Ascension (J2000)") self.ax_overplot.set_xlabel(label="Right Ascension (J2000)")
@@ -1357,8 +1401,8 @@ class overplot_pol(align_maps):
for key, value in [ for key, value in [
["cmap", [["cmap", "inferno"]]], ["cmap", [["cmap", "inferno"]]],
["norm", [["vmin", vmin], ["vmax", vmax]]], ["norm", [["vmin", vmin], ["vmax", vmax]]],
["width", [["width", 0.5 * px_scale]]], ["width", [["width", 0.5 * self.px_scale]]],
["linewidth", [["linewidth", 0.3 * px_scale]]], ["linewidth", [["linewidth", 0.3 * self.px_scale]]],
]: ]:
try: try:
_ = kwargs[key] _ = kwargs[key]
@@ -1403,11 +1447,10 @@ class overplot_pol(align_maps):
# Display full size polarization vectors # Display full size polarization vectors
if scale_vec is None: if scale_vec is None:
self.scale_vec = 2.0 * px_scale self.scale_vec = 2.0 * self.px_scale
pol[np.isfinite(pol)] = 1.0 / 2.0 pol[np.isfinite(pol)] = 1.0 / 2.0
else: else:
self.scale_vec = scale_vec * px_scale self.scale_vec = scale_vec * self.px_scale
step_vec = 1
self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0])) self.X, self.Y = np.meshgrid(np.arange(stkI.shape[1]), np.arange(stkI.shape[0]))
self.U, self.V = pol * np.cos(np.pi / 2.0 + pang * np.pi / 180.0), pol * np.sin(np.pi / 2.0 + pang * np.pi / 180.0) self.U, self.V = pol * np.cos(np.pi / 2.0 + pang * np.pi / 180.0), pol * np.sin(np.pi / 2.0 + pang * np.pi / 180.0)
self.Q = self.ax_overplot.quiver( self.Q = self.ax_overplot.quiver(
@@ -1518,18 +1561,18 @@ class overplot_pol(align_maps):
while not self.aligned: while not self.aligned:
self.align() self.align()
self.overplot(levels=levels, P_cut=P_cut, SNRi_cut=SNRi_cut, scale_vec=scale_vec, savename=savename, **kwargs) self.overplot(levels=levels, P_cut=P_cut, SNRi_cut=SNRi_cut, scale_vec=scale_vec, savename=savename, **kwargs)
plt.show(block=True)
def add_vector(self, position="center", pol_deg=1.0, pol_ang=0.0, **kwargs): def add_vector(self, position="center", pol_deg=1.0, pol_ang=0.0, **kwargs):
if position == "center": if isinstance(position, str) and position == "center":
position = np.array(self.X.shape) / 2.0 position = np.array(self.X.shape) / 2.0
if isinstance(position, SkyCoord): if isinstance(position, SkyCoord):
position = self.other_wcs.world_to_pixel(position) position = self.other_wcs.world_to_pixel(position)
u, v = pol_deg * np.cos(np.radians(pol_ang) + np.pi / 2.0), pol_deg * np.sin(np.radians(pol_ang) + np.pi / 2.0) u, v = pol_deg * np.cos(np.radians(pol_ang) + np.pi / 2.0), pol_deg * np.sin(np.radians(pol_ang) + np.pi / 2.0)
for key, value in [ for key, value in [
["scale", [["scale", self.scale_vec]]], ["scale", [["scale", 1.0 / self.scale_vec]]],
["width", [["width", 0.1]]], ["width", [["width", 0.5 * self.px_scale]]],
["linewidth", [["linewidth", 0.3 * self.px_scale]]],
["color", [["color", "k"]]], ["color", [["color", "k"]]],
["edgecolor", [["edgecolor", "w"]]], ["edgecolor", [["edgecolor", "w"]]],
]: ]:
@@ -1540,7 +1583,17 @@ class overplot_pol(align_maps):
kwargs[key_i] = val_i kwargs[key_i] = val_i
handles, labels = self.legend.legend_handles, [l.get_text() for l in self.legend.texts] handles, labels = self.legend.legend_handles, [l.get_text() for l in self.legend.texts]
new_vec = self.ax_overplot.quiver( new_vec = self.ax_overplot.quiver(
*position, u, v, units="xy", angles="uv", scale_units="xy", pivot="mid", headwidth=0.0, headlength=0.0, headaxislength=0.0, **kwargs *position,
u,
v,
units="xy",
angles="uv",
scale_units="xy",
pivot="mid",
headwidth=0.0,
headlength=0.0,
headaxislength=0.0,
**kwargs,
) )
handles.append(FancyArrowPatch((0, 0), (0, 1), arrowstyle="-", fc=new_vec.get_fc(), ec=new_vec.get_ec())) handles.append(FancyArrowPatch((0, 0), (0, 1), arrowstyle="-", fc=new_vec.get_fc(), ec=new_vec.get_ec()))
labels.append(new_vec.get_label()) labels.append(new_vec.get_label())
@@ -3355,9 +3408,7 @@ if __name__ == "__main__":
parser.add_argument( parser.add_argument(
"-pdf", "--static-pdf", metavar="static_pdf", required=False, help="Whether the analysis tool or the static pdfs should be outputed", default=None "-pdf", "--static-pdf", metavar="static_pdf", required=False, help="Whether the analysis tool or the static pdfs should be outputed", default=None
) )
parser.add_argument( parser.add_argument("-t", "--type", metavar="type", required=False, help="Type of plot to be be outputed", default=None)
"-t", "--type", metavar="type", required=False, help="Type of plot to be be outputed", default=None
)
args = parser.parse_args() args = parser.parse_args()
if args.file is not None: if args.file is not None:
@@ -3497,7 +3548,16 @@ if __name__ == "__main__":
display="confp", display="confp",
) )
else: else:
pol_map(Stokes_UV, P_cut=args.pcut, SNRi_cut=args.snri, step_vec=args.step_vec, scale_vec=args.scale_vec, flux_lim=args.lim, pa_err=args.pang_err, selection=args.type) pol_map(
Stokes_UV,
P_cut=args.pcut,
SNRi_cut=args.snri,
step_vec=args.step_vec,
scale_vec=args.scale_vec,
flux_lim=args.lim,
pa_err=args.pang_err,
selection=args.type,
)
else: else:
print( print(
"python3 plots.py -f <path_to_reduced_fits> -p <P_cut> -i <SNRi_cut> -st <step_vec> -sc <scale_vec> -l <flux_lim> -pa <pa_err> --pdf <static_pdf>" "python3 plots.py -f <path_to_reduced_fits> -p <P_cut> -i <SNRi_cut> -st <step_vec> -sc <scale_vec> -l <flux_lim> -pa <pa_err> --pdf <static_pdf>"

20
package/src/emission_center.py
View File

@@ -40,23 +40,23 @@ def main(infile, target=None, output_dir=None):
if target is None: if target is None:
target = Stokes[0].header["TARGNAME"] target = Stokes[0].header["TARGNAME"]
fig = figure(figsize=(8,8),layout="constrained") fig = figure(figsize=(8, 8.5), layout="constrained")
fig, ax = polarization_map(Stokes, P_cut=0.99, step_vec=2, scale_vec=5, display="i", fig=fig) fig, ax = polarization_map(Stokes, P_cut=0.99, step_vec=1, scale_vec=3, display="i", fig=fig, width=0.33, linewidth=0.5)
ax.plot(*Stokescenter, marker="+", color="gray", label="Best confidence for center: {0}".format(Stokespos.to_string("hmsdms"))) ax.plot(*Stokescenter, marker="+", color="gray", label="Best confidence for center: {0}".format(Stokespos.to_string("hmsdms")))
confcentcont = ax.contour(Stokescentconf, [0.001], colors="gray") confcentcont = ax.contour(Stokescentconf, [0.01], colors="gray")
confcont = ax.contour(Stokesconf, [0.9905], colors="r") confcont = ax.contour(Stokesconf, [0.9905], colors="r")
snr3cont = ax.contour(Stokessnr, [3.0], colors="b", linestyles="dashed") # snr3cont = ax.contour(Stokessnr, [3.0], colors="b", linestyles="dashed")
snr4cont = ax.contour(Stokessnr, [4.0], colors="b") # snr4cont = ax.contour(Stokessnr, [4.0], colors="b")
handles, labels = ax.get_legend_handles_labels() handles, labels = ax.get_legend_handles_labels()
labels.append(r"Center $Conf_{99.9\%}$ contour") labels.append(r"Center $Conf_{99\%}$ contour")
handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcentcont.get_edgecolor()[0])) handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcentcont.get_edgecolor()[0]))
labels.append(r"Polarization $Conf_{99\%}$ contour") labels.append(r"Polarization $Conf_{99\%}$ contour")
handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcont.get_edgecolor()[0])) handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=confcont.get_edgecolor()[0]))
labels.append(r"$SNR_P \geq$ 3 contour") # labels.append(r"$SNR_P \geq$ 3 contour")
handles.append(Rectangle((0, 0), 1, 1, fill=False, ls="--", ec=snr3cont.get_edgecolor()[0])) # handles.append(Rectangle((0, 0), 1, 1, fill=False, ls="--", ec=snr3cont.get_edgecolor()[0]))
labels.append(r"$SNR_P \geq$ 4 contour") # labels.append(r"$SNR_P \geq$ 4 contour")
handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=snr4cont.get_edgecolor()[0])) # handles.append(Rectangle((0, 0), 1, 1, fill=False, ec=snr4cont.get_edgecolor()[0]))
ax.legend(handles=handles, labels=labels, bbox_to_anchor=(0.0, -0.02, 1.0, 0.01), loc="upper left", mode="expand", borderaxespad=0.0) ax.legend(handles=handles, labels=labels, bbox_to_anchor=(0.0, -0.02, 1.0, 0.01), loc="upper left", mode="expand", borderaxespad=0.0)
if output_dir is not None: if output_dir is not None:

42
package/src/overplot_NGC1068.py Executable file
View File

@@ -0,0 +1,42 @@
#!/usr/bin/python3
# -*- coding:utf-8 -*-
from pathlib import Path
from sys import path as syspath
syspath.append(str(Path(__file__).parent.parent))
import numpy as np
from astropy.io import fits
from lib.plots import overplot_pol, plt
from matplotlib.colors import LogNorm
Stokes_UV = fits.open("./data/NGC1068/5144/NGC1068_FOC_b0.05arcsec_c0.07arcsec_crop.fits")
Radio = fits.open("./data/NGC1068/MERLIN-VLA/Combined_crop.fits")
levels = np.logspace(-0.5, 1.99, 7) / 100.0 * Stokes_UV[0].data.max() * Stokes_UV[0].header["photflam"]
A = overplot_pol(Stokes_UV, Radio, norm=LogNorm())
A.plot(
levels=levels,
P_cut=0.99,
SNRi_cut=1.0,
scale_vec=3,
step_vec=1,
norm=LogNorm(5e-5, 1e-1),
cmap="inferno_r",
width=0.8,
linewidth=1.2,
)
A.add_vector(
A.other_wcs.celestial.wcs.crpix - (1.0, 1.0),
pol_deg=0.124,
pol_ang=100.7,
width=2,
linewidth=2,
scale=1.0 / (A.px_scale * 6.0),
edgecolor="b",
color="b",
label=r"IXPE torus: P = $12.4 (\pm 3.6)$%, PA = $100.7 (\pm 8.3)$°",
)
A.fig_overplot.savefig("./plots/NGC1068/NGC1068_radio_overplot_full.pdf", dpi=300, bbox_inches="tight")
plt.show()
A.write_to(path1="./data/NGC1068/FOC_Radio.fits", path2="./data/NGC1068/Radio_FOC.fits", suffix="aligned")