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correct bugs

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This commit is contained in:
Noe Brucy
2020-04-21 10:39:24 +02:00
parent 9e5fc8b4ad
commit 8dfdf918a0
3 changed files with 100 additions and 52 deletions
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comparator.py
+31 -24
View File
@@ -137,19 +137,25 @@ class Comparator(Aggregator, HDF5Container):
return np.array(prop)
def _time_avg(self, name, start=None, end=None, span=None, group="/series"):
mean = np.zeros(len(self.runs))
median = np.zeros(len(self.runs))
std = np.zeros(len(self.runs))
v_min = np.zeros(len(self.runs))
v_max = np.zeros(len(self.runs))
q975 = np.zeros(len(self.runs))
q025 = np.zeros(len(self.runs))
q16 = np.zeros(len(self.runs))
q84 = np.zeros(len(self.runs))
serie0 = self.save.get_node(group + "/" + name + "/" + self.runs[0]).read()
if len(serie0.shape) > 1:
shape = [len(self.runs)] + list(serie0.shape[1:])
else:
shape = len(self.runs)
mean = np.zeros(shape)
median = np.zeros(shape)
std = np.zeros(shape)
v_min = np.zeros(shape)
v_max = np.zeros(shape)
q975 = np.zeros(shape)
q025 = np.zeros(shape)
q16 = np.zeros(shape)
q84 = np.zeros(shape)
for i, run in enumerate(self.runs):
serie = self.save.get_node(group + "/" + name + "/" + run).read()
time = self.save.get_node(group + "/time/" + run).read()
if len(serie.shape) <= 1:
mask = abs(serie) != np.inf
if not ((start, end, span) == (None, None, None)):
@@ -165,11 +171,13 @@ class Comparator(Aggregator, HDF5Container):
start_r = time[0]
else:
start_r = end_r - span
mask = (
mask & (time >= start_r) & (time <= end_r) & np.isfinite(serie)
)
serie = serie[mask]
mask = mask & (time >= start_r) & (time <= end_r) & np.isfinite(serie)
mean[i] = np.mean(serie[mask], axis=0)
std[i] = np.std(serie[mask], axis=0)
mean[i] = np.mean(serie, axis=0)
std[i] = np.std(serie, axis=0)
(
v_min[i],
q025[i],
@@ -178,7 +186,7 @@ class Comparator(Aggregator, HDF5Container):
q84[i],
q975[i],
v_max[i],
) = np.percentile(serie[mask], [0, 2.5, 16, 50, 84, 97.5, 100], axis=0)
) = np.percentile(serie, [0, 2.5, 16, 50, 84, 97.5, 100], axis=0)
return {
"runs": self.runs,
"mean": mean,
@@ -403,16 +411,6 @@ class Comparator(Aggregator, HDF5Container):
"q16": "16 percentile of {}".format(descr),
"q84": "84 percentile of {}".format(descr),
}
# units={
# "runs": cst.none,
# "mean": unit,
# "std": unit,
# "median": unit,
# "max": unit,
# "min": unit,
# "q025": unit,
# "q975": unit}
units = unit
if name is None:
@@ -528,6 +526,14 @@ class Comparator(Aggregator, HDF5Container):
group="/series",
dependencies={"time": None, "rho_prof": "__parent__"},
),
"time_coldens_pdf": Rule(
self,
partial(
self._time_series, partial(self.get_pp_value, "/hist/pdf_coldens")
),
group="/series",
dependencies={"time": None, "pdf_coldens": "__parent__"},
),
"time_pdf_slope_coldens": Rule(
self,
partial(
@@ -560,6 +566,7 @@ class Comparator(Aggregator, HDF5Container):
"time_pdf_slope_coldens",
"turb_power",
"time_rho_prof",
"time_coldens_pdf",
]:
self._gen_rule_avg(name)
plotter.py
+47 -6
View File
@@ -126,7 +126,7 @@ class Plotter(Aggregator, BaseProcessor):
name_full = name
if rule.is_valid(arg):
if rule.kind == "classic":
if rule.kind == "classic" or rule.kind == "runs":
try:
runs = kwargs.pop("runs")
if isinstance(runs, RunSelector):
@@ -136,9 +136,17 @@ class Plotter(Aggregator, BaseProcessor):
i = 0
for run in runs:
files = []
for num in self.nums[run]:
if rule.kind == "classic":
nums = self.nums[run]
else:
nums = [None]
for num in nums:
plot_filename = self._find_filename(name_full, run, num)
if rule.kind == "classic":
save = tables.open_file(self.pp[run][num].filename)
else:
save = tables.open_file(self.comp.filename, "r")
try:
self._plot_rule(
rule,
@@ -265,7 +273,10 @@ class Plotter(Aggregator, BaseProcessor):
return r"{} = {}".format(prop_label, prop_value_str)
if nml_key is None and label is None:
if "attrs" in self.save.root._v_attrs:
if (
"attrs" in self.save.root._v_attrs
and run in self.save.root._v_attrs.attrs
):
label_run = r"{}".format(self.save.root._v_attrs.attrs[run].label)
else:
label_run = run
@@ -479,8 +490,9 @@ class Plotter(Aggregator, BaseProcessor):
def _plot_hist(
self,
name,
ax_los=None,
run="",
ax_los,
run,
group="/hist/",
label=None,
unit=None,
unit_coeff=1.0,
@@ -495,13 +507,15 @@ class Plotter(Aggregator, BaseProcessor):
color=None,
colors=None,
nml_color=None,
fit=None,
fitlabel=None,
**kwargs
):
if not ax_los is None:
name = name + "_" + ax_los
node = self.save.get_node("/hist/" + name)
node = self.save.get_node(group + name)
if xlog is None:
try:
@@ -511,7 +525,12 @@ class Plotter(Aggregator, BaseProcessor):
label, unit_old, unit = self._ax_label_unit(node, label, unit, unit_coeff)
if "mean" in node:
index = node["runs"].read().index(run)
values, centers = node["mean"].read()[index]
else:
values, centers = node.read()
if xlog:
centers = centers + np.log10(unit_old.express(unit))
else:
@@ -570,6 +589,11 @@ class Plotter(Aggregator, BaseProcessor):
P.ylim([None, 1.0])
if not fit is None:
self._overlay_fit(
centers, values, kind=fit, ls="--", lw=1.5, label=fitlabel
)
def _plot(
self,
name_x,
@@ -582,6 +606,7 @@ class Plotter(Aggregator, BaseProcessor):
yunit=None,
xunit_coeff=1.0,
yunit_coeff=1.0,
ylog=False,
fit=None,
fitlabel=None,
smooth=0,
@@ -618,6 +643,9 @@ class Plotter(Aggregator, BaseProcessor):
if grid:
P.grid()
if ylog:
P.yscale("log")
if put_time:
time = self.save.root._v_attrs.time * self.comp.info["unit_time"]
time_str = self.pp_params.plot.time_fmt.format(
@@ -878,6 +906,19 @@ class Plotter(Aggregator, BaseProcessor):
"$\rho$-PDF",
dependencies=["rho_pdf"],
),
"avg_coldens_pdf": PlotRule(
self,
partial(
self._plot_hist,
"avg_time_coldens_pdf_z",
group="/comp/",
xlog=True,
put_time=False,
),
"PDF",
kind="runs",
dependencies={"avg_time_coldens_pdf": "z"},
),
"T_pdf": PlotRule(
self, partial(self._plot_hist, "T_pdf"), "T-PDF", dependencies=["T_pdf"]
),
postprocessor.py
+6 -6
View File
@@ -75,7 +75,7 @@ class PostProcessor(HDF5Container):
# Set the extend of the image
self._radius = 0.5 / self.pp_params.pymses.zoom
self._lbox = self.info["boxlen"]
self.lbox = self.info["boxlen"]
center = self.pp_params.pymses.center
im_extent = [
(-self._radius + center[0]),
@@ -91,7 +91,7 @@ class PostProcessor(HDF5Container):
self.save.root._v_attrs.dir = os.path.dirname(path)
self.save.root._v_attrs.run = os.path.basename(path)
self.save.root._v_attrs.num = num
self.save.root._v_attrs.lbox = self._lbox
self.save.root._v_attrs.lbox = self.lbox
self.save.root._v_attrs.unit_length = self.info["unit_length"]
self.save.root._v_attrs.time = time
@@ -361,7 +361,7 @@ class PostProcessor(HDF5Container):
# Operator to compute the angular speed times rho
def omega_rho_func(dset):
pos = dset.get_cell_centers()
pos = pos - (self.pp_params.disk.pos_star / self._lbox)
pos = pos - (self.pp_params.disk.pos_star / self.lbox)
xx = pos[:, :, 0]
yy = pos[:, :, 1]
rc = np.sqrt(xx ** 2 + yy ** 2) # cylindrical radius
@@ -401,7 +401,7 @@ class PostProcessor(HDF5Container):
dmap_cs = rt_cs.process(self._cam[ax_los])
dmap_col = self.save.root.maps.coldens_z.read()
map_Q = (
(self._lbox * dmap_cs.map.T)
(self.lbox * dmap_cs.map.T)
* dmap_omega.map.T
/ (np.pi * self.G * dmap_col)
)
@@ -412,7 +412,7 @@ class PostProcessor(HDF5Container):
Computes radial bins (for disk)
"""
pos_star = self.pp_params.disk.pos_star
im_extent = self.save.root.maps._v_attrs.im_extent
im_extent = np.array(self.save.root.maps._v_attrs.im_extent) * self.lbox
# radius of the corner of the box plus a margin
rad_of_box = (
@@ -442,7 +442,7 @@ class PostProcessor(HDF5Container):
"""
Computes the radius from the center
"""
im_extent = self.save.root.maps._v_attrs.im_extent
im_extent = np.array(self.save.root.maps._v_attrs.im_extent) * self.lbox
map_size = self.pp_params.pymses.map_size
pos_star = self.pp_params.disk.pos_star