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Add rules to compute $\alpha$

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This commit is contained in:
Noe Brucy
2020-07-01 15:35:03 +02:00
parent cea59f78a3
commit 755831ce0b
4 changed files with 641 additions and 140 deletions
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plotter.py
+234 -66
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@@ -78,6 +78,9 @@ class Plotter(Aggregator, BaseProcessor):
"coldens0": "$\Sigma_0$",
"sfr_avg_window": "window",
"bx_bound": "$B_0$",
"levelmax": "$l_{\max}$",
"levelmin": "$l_{\min}$",
"comp_frac": "$1 - \\zeta$",
}
# Conversion table from namelist values (from amses config file) into LaTex strings
@@ -96,7 +99,7 @@ class Plotter(Aggregator, BaseProcessor):
pp_params=None,
selector=None,
tag=None,
**kwargs
**kwargs,
):
"""
@@ -147,7 +150,9 @@ class Plotter(Aggregator, BaseProcessor):
Check if the dependency belongs to the plotter object or to another one (comp, pp, ..)
"""
if dep in self.comp.rules:
done = self.comp.process(dep, dep_arg, overwrite, overwrite)
done = self.comp.process(
dep, dep_arg, overwrite, overwrite_dep=self.overwrite_dep
)
self.just_done.extend(done)
else:
super(Plotter, self)._not_self_dep(name, dep, dep_arg, overwrite, **kwargs)
@@ -171,10 +176,10 @@ class Plotter(Aggregator, BaseProcessor):
ax=None,
movie=False,
from_cells=False,
**kwargs
**kwargs,
):
"""
Generic method to process a rule, with its dependencies
Open storage and figure if needed before processing a rule
"""
if not arg is None:
name_full = name + "_" + str(arg)
@@ -217,7 +222,7 @@ class Plotter(Aggregator, BaseProcessor):
overwrite,
ax=ax[i],
run=run,
**kwargs
**kwargs,
)
except TypeError as e:
if str(e) in [
@@ -234,7 +239,7 @@ class Plotter(Aggregator, BaseProcessor):
overwrite,
ax=ax,
run=run,
**kwargs
**kwargs,
)
elif ax is None:
fig = P.figure()
@@ -246,7 +251,7 @@ class Plotter(Aggregator, BaseProcessor):
overwrite,
ax=P.gca(),
run=run,
**kwargs
**kwargs,
)
else:
raise
@@ -414,7 +419,7 @@ class Plotter(Aggregator, BaseProcessor):
norm="log",
put_cbar=True,
autoscale=True,
**kwargs
**kwargs,
):
"""
Plot data on a map
@@ -477,39 +482,81 @@ class Plotter(Aggregator, BaseProcessor):
P.title(title)
for i, plot_overlay in enumerate(overlays):
try:
plot_overlay(ax_los, **overlays_kwargs[i])
except:
plot_overlay(ax_los)
if plot_overlay in self.overlays:
plot_overlay = self.overlays[plot_overlay]
def _overlay_levels(self, ax_los):
try:
plot_overlay(ax_los, im_extent, **overlays_kwargs[i])
except:
plot_overlay(ax_los, im_extent)
def _overlay_contour(
self,
ax_los,
im_extent,
map_name,
log=False,
lvl_array=None,
lw=None,
lvl_th=None,
lvl_max_lbl=np.inf,
lbl_fmt="%g",
**kwargs,
):
"""
Add an overlay : contour of other map
"""
map_contour = self.save.get_node("/maps/{}_{}".format(map_name, ax_los)).read()
if log:
map_contour = np.log10(map_contour)
# Computing linewidths
mask_fin = np.isfinite(map_contour)
if lvl_array is None:
lvl_array = np.arange(
np.min(map_contour[mask_fin]), np.max(map_contour[mask_fin]) + 1
)
if lw is None:
lw = np.ones(lvl_array.size) * 2
if lvl_th:
lw[lvl_array >= lvl_th] = lw[lvl_array >= lvl_th] ** (
lvl_th - lvl_array[lvl_array >= lvl_th]
)
lw[lvl_array < lvl_th] = 1.0
cont = P.contour(
map_contour,
extent=im_extent,
origin="lower",
linewidths=lw,
levels=lvl_array,
**kwargs,
)
P.clabel(
cont,
lvl_array[lvl_array < lvl_max_lbl],
inline=1,
fontsize=8.0,
fmt=lbl_fmt,
)
def _overlay_levels(self, ax_los, im_extent, **kwargs):
"""
Add an overlay : AMR levels
"""
map_level = self.save.get_node("/maps/{}_{}".format("levels", ax_los)).read()
# Computing linewidths
levels_ar = np.arange(np.min(map_level), np.max(map_level) + 1)
lw = np.ones(levels_ar.size) * 2
lvl_th = 8 # Level threeshold for reducing linewidths
lw[levels_ar >= lvl_th] = lw[levels_ar >= lvl_th] ** (
lvl_th - levels_ar[levels_ar >= lvl_th]
return self._overlay_contour(
ax_los,
im_extent,
"levels",
lbl_fmt="%1d",
lvl_th=8,
lvl_max_lbl=11,
**kwargs,
)
lw[levels_ar < lvl_th] = 1.0
cont = P.contour(
map_level,
extent=self.save.root.maps._v_attrs.im_extent,
origin="lower",
colors="grey",
linewidths=lw,
levels=levels_ar,
)
cont.levels = cont.levels + 1
P.clabel(cont, cont.levels[cont.levels < 11], inline=1, fontsize=8.0, fmt="%1d")
def _overlay_speed(
self, ax_los, unit=cst.km_s, unit_coeff=1.0, key_v=None, **kwargs
self, ax_los, im_extent, unit=cst.km_s, unit_coeff=1.0, key_v=None, **kwargs
):
"""
Add an overlay : velocity vector field
@@ -532,6 +579,8 @@ class Plotter(Aggregator, BaseProcessor):
) # take only a subset of velocities
map_vv_red = dmap_vv[::vel_red, ::vel_red] * unit_old.express(unit)
# TODO : redo this with im_extent
nh = map_vh_red.shape[0]
nv = map_vv_red.shape[1]
vec_h = (
@@ -559,7 +608,7 @@ class Plotter(Aggregator, BaseProcessor):
coordinates="figure",
)
def _overlay_B(self, ax_los, **kwargs):
def _overlay_B(self, ax_los, im_extent, **kwargs):
"""
Add an overlay : magnetic streamlines
"""
@@ -569,6 +618,8 @@ class Plotter(Aggregator, BaseProcessor):
dmap_Bh = dmap_Bh_node.read()
dmap_Bv = self.save.get_node("/maps/B_v_{}".format(ax_los)).read()
# TODO : redo this with im_extent
vel_red = self.pp_params.plot.vel_red
radius = self.save.root.maps._v_attrs.radius
center = self.save.root.maps._v_attrs.center
@@ -590,14 +641,33 @@ class Plotter(Aggregator, BaseProcessor):
P.streamplot(hh, vv, map_Bh_red, map_Bv_red)
def _plot_radial(self, name, ax_los, label=None, xlog=False, ylog=False):
def _plot_radial(
self,
name,
ax_los,
run,
ylabel=None,
xlog=False,
ylog=False,
ytransform=None,
title=None,
nml_key=None,
put_title=True,
put_time=True,
time_unit=cst.Myr,
**kwargs,
):
"""
Plot a radial profile (for disks, OUTDATED)
"""
radial_bins = self.save.get_node("/radial/radial_bins_" + ax_los).read()
bin_centers = 0.5 * (radial_bins[1:] + radial_bins[:-1])
mean_bin = self.save.get_node("/radial/{}_{}".format(name, ax_los)).read()
node = self.save.get_node("/radial/{}_{}".format(name, ax_los))
mean_bin = node.read()
if ytransform is not None:
mean_bin = ytransform(mean_bin)
P.grid()
P.xlabel(r"$r$")
@@ -606,20 +676,37 @@ class Plotter(Aggregator, BaseProcessor):
P.xscale("log")
if ylog:
P.yscale("log")
P.plot(bin_centers, mean_bin)
P.plot(bin_centers, mean_bin, **kwargs)
if not label is None:
P.ylabel(label)
if not ylabel is None:
P.ylabel(ylabel)
if put_title:
title = self._label_run(run, node, title, nml_key)
if put_time:
time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
time_str = self.pp_params.plot.time_fmt.format(
time.express(time_unit), time_unit.latex
)
if len(title) > 0:
title = title + " | " + time_str
else:
title = time_str
P.title(title)
def _plot_hist(
self,
name,
ax_los,
run,
ax_los=None,
run=None,
group="/hist/",
label=None,
xlabel=None,
unit=None,
unit_coeff=1.0,
ytransform=None,
label=None,
title=None,
nml_key=None,
put_time=True,
@@ -633,7 +720,7 @@ class Plotter(Aggregator, BaseProcessor):
nml_color=None,
fit=None,
fitlabel=None,
**kwargs
**kwargs,
):
"""
Plot an histogram (PDF, etc ...)
@@ -649,7 +736,7 @@ class Plotter(Aggregator, BaseProcessor):
except:
xlog = False
label, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
xlabel, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
if "mean" in node:
index = node["runs"].read().index(run)
@@ -662,6 +749,9 @@ class Plotter(Aggregator, BaseProcessor):
else:
centers = centers * unit_old.express(unit)
if ytransform is not None:
values = ytransform(values)
title = self._label_run(run, node, title, nml_key)
if put_time:
@@ -686,19 +776,22 @@ class Plotter(Aggregator, BaseProcessor):
except:
color = colors(nml)
if label == None:
label = title
if kind == "bar":
width = centers[1] - centers[0]
P.bar(centers, values, width, log=ylog, color=color, label=title, **kwargs)
P.bar(centers, values, width, log=ylog, color=color, label=label, **kwargs)
elif kind == "step":
if ylog:
P.yscale("log")
P.step(centers, values, where="mid", color=color, label=title, **kwargs)
P.step(centers, values, where="mid", color=color, label=label, **kwargs)
else:
raise ValueError("kind must be 'bar' or 'step'")
P.grid()
if not label is None:
P.xlabel(label)
P.xlabel(xlabel)
if not ylabel is None:
P.ylabel(ylabel)
@@ -749,7 +842,7 @@ class Plotter(Aggregator, BaseProcessor):
legend=None,
subname_x=None,
subname_y=None,
**kwargs
**kwargs,
):
"""
Generic plot routine, with name_x and name_y two path in the hdf5 file
@@ -991,7 +1084,7 @@ class Plotter(Aggregator, BaseProcessor):
def def_rules(self):
"""
That is where rules are defined
This is where rules are defined
"""
self.rules = {
# Generic rules
@@ -1000,13 +1093,69 @@ class Plotter(Aggregator, BaseProcessor):
),
"coldens": PlotRule(
self,
partial(self._plot_map, "coldens", label=r"$\Sigma$", unit=cst.coldens),
partial(
self._plot_map,
"coldens",
label=r"$\Sigma$",
# unit=cst.coldens
),
"Column density map",
dependencies=["coldens", "speed_h", "speed_v"],
dependencies=["coldens"],
),
"alpha_disk": PlotRule(
self,
partial(self._plot_map, "alpha_disk", label=r"$\alpha$"),
"Map of the Shakura&Sunaev alpha parameter for disks",
dependencies=["alpha_disk"],
),
"alpha_grav": PlotRule(
self,
partial(self._plot_map, "alpha_grav", label=r"$\alpha_g$"),
"Map of the grav Shakura&Sunaev alpha parameter for disks",
dependencies=["alpha_grav"],
),
"vphi": PlotRule(
self,
partial(
self._plot_map,
"vphi",
label=r"$v_\phi$",
# unit=cst.km_s
),
"Azimuthal speed",
dependencies=["vphi"],
),
"vr": PlotRule(
self,
partial(
self._plot_map,
"vr",
label=r"$v_r$",
# unit=cst.km_s
),
"Radial speed",
dependencies=["vr"],
),
"P_avg": PlotRule(
self,
partial(self._plot_map, "P_avg", label=r"$P$"),
"Pressure (average)",
dependencies=["P_avg"],
),
"rho_avg": PlotRule(
self,
partial(self._plot_map, "rho_avg", label=r"$\rho$"),
"Density (average)",
dependencies=["rho_avg"],
),
"rho": PlotRule(
self,
partial(self._plot_map, "rho", label=r"$\rho$", unit=cst.Msun_pc3),
partial(
self._plot_map,
"rho",
label=r"$\rho$",
# unit=cst.Msun_pc3
),
"Density slice at s = 0, with s = x, y or z.",
dependencies=["rho"],
),
@@ -1058,18 +1207,6 @@ class Plotter(Aggregator, BaseProcessor):
"Density slice with magnetic field and velocity overlay",
dependencies=["rho", "B_h", "B_v", "speed_h", "speed_v"],
),
"B_int_B_vel": PlotRule(
self,
partial(
self._plot_map,
"B_int",
label="B",
unit=cst.T,
overlays=[self._overlay_B, self._overlay_speed],
),
"Magnetic slice with magnetic field and velocity overlay",
dependencies=["B_int", "B_h", "B_v", "speed_h", "speed_v"],
),
"jeans_ratio": PlotRule(
self,
partial(
@@ -1303,7 +1440,19 @@ class Plotter(Aggregator, BaseProcessor):
),
}
averageables = ["coldens", "rho", "T", "Q"]
averageables = [
"coldens",
"rho",
"T",
"Q",
"vr",
"vphi",
"rho_avg",
"P_avg",
"T_avg",
"alpha_disk",
"alpha_grav",
]
for name in averageables:
self.rules["rad_" + name] = PlotRule(
self,
@@ -1331,6 +1480,7 @@ class Plotter(Aggregator, BaseProcessor):
"Fluctuation of {}".format(name),
dependencies=["fluct_" + name],
)
self.rules["pdf_" + name] = PlotRule(
self,
partial(
@@ -1343,4 +1493,22 @@ class Plotter(Aggregator, BaseProcessor):
dependencies=["fit_pdf_" + name],
)
for name_bin in averageables:
if name_bin is not name:
group = "mbb_{}_{}".format(name, name_bin)
self.rules["mbb_" + name + "_" + name_bin] = PlotRule(
self,
partial(self._plot_hist, group, ylabel=r"$\alpha$"),
"Mean of {} by bins of {}".format(name, name_bin),
dependencies=[group],
)
# Dict of overlays
self.overlays = {
"B": self._overlay_B,
"speed": self._overlay_speed,
"levels": self._overlay_levels,
"contour": self._overlay_contour,
}
super(Plotter, self).def_rules()