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Add preliminary power spectrum integration

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This commit is contained in:
Noe Brucy
2020-05-14 15:55:01 +02:00
committed by Noe Brucy
parent bb6f1091eb
commit 1a07edb5b7
4 changed files with 175 additions and 40 deletions
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plotter.py
+21
View File
@@ -17,6 +17,7 @@ if os.environ.get("DISPLAY", "") == "":
mpl.use("Agg")
import pylab as P
from comparator import *
import pspec_read
P.rcParams["image.cmap"] = "plasma"
P.rcParams["savefig.dpi"] = 400
@@ -634,6 +635,8 @@ class Plotter(Aggregator, BaseProcessor):
colors=None,
nml_color=None,
legend=None,
subname_x=None,
subname_y=None,
**kwargs
):
@@ -643,6 +646,13 @@ class Plotter(Aggregator, BaseProcessor):
node_x = self.save.get_node(name_x)
node_y = self.save.get_node(name_y)
if subname_x:
hdf5_x = tables.open_file(node_x.read())
node_x = hdf5_x.get_node(subname_x)
if subname_y:
hdf5_y = tables.open_file(node_y.read())
node_y = hdf5_y.get_node(subname_y)
xlabel, xunit_old, xunit = self._ax_label_unit(
node_x, xlabel, xunit, xunit_coeff
)
@@ -772,6 +782,16 @@ class Plotter(Aggregator, BaseProcessor):
color=base_line.get_color(),
label=fitlabel,
)
if subname_x:
hdf5_x.close()
if subname_y:
hdf5_y.close()
def _pspec(self, name, **kwargs):
del kwargs["run"]
file_pspec = self.save.get_node("/hdf5/pspec").read()
num = self.save.root._v_attrs.num
getattr(pspec_read, "pspec_" + name)(file_pspec, ".", num, **kwargs)
def _overlay_fit(self, x, y, yerr=None, kind="linear", label=None, **kwargs):
if kind == "linear":
@@ -943,6 +963,7 @@ class Plotter(Aggregator, BaseProcessor):
partial(self._plot, "/profile/axis", "/profile/rho_prof"),
dependencies=["axis", "rho_prof"],
),
"pspec": PlotRule(self, self._pspec, dependencies={"pspec": None}),
}
averageables = ["coldens", "rho", "T", "Q"]
postprocessor.py
+7
View File
@@ -1,5 +1,6 @@
# coding: utf-8
import pandas as pd
import pspec_new
from baseprocessor import *
mass_func = lambda dset: dset["rho"] * dset["dx"] ** 3 # Mass function
@@ -584,6 +585,11 @@ class PostProcessor(HDF5Container):
return sinks_dict
def _pspec(self):
outfile = self.path_out + "/pspec.h5"
pspec_new.pspec(repo=self.path, iouts=[self.num], outfile=outfile)
return outfile
def def_rules(self):
self.rules = {
@@ -674,6 +680,7 @@ class PostProcessor(HDF5Container):
"Teff": cst.K,
},
),
"pspec": Rule(self, self._pspec, "Power spectrum", "/hdf5"),
# Helpers
"radial_bins": Rule(self, self._radial_bins, "Radial bins", "/radial"),
"rr": Rule(self, self._rr, "Coordinate map", "/maps"),
pspec_new.py
+75 -8
View File
@@ -15,7 +15,6 @@ from pymses.analysis import cube3d
import pymses.utils.misc
import tables as T
import bunch
from i_utils import args
from i_utils import tools
@@ -464,6 +463,45 @@ parser.add_argument("-s", "--size", help="cube size", type=float, default=1.0)
parser.add_argument(
"-l", "--level", help="cube level (default: levelMIN)", type=int, default=0
)
parser.add_argument(
"repo", help="RAMSES output repository", type=str, default=".", nargs="?"
)
parser.add_argument(
"iouts", help="output numbers", type=args.selection, default=":", nargs="?"
)
parser.add_argument(
"outfile",
help="output file format (see below for fields)",
type=str,
default=".",
nargs="?",
)
parser.add_argument(
"-n",
"--nodename",
help="node name format (see below for fields)",
type=str,
default="/out_%(iout)05d/d%(dim)d/%(varname)s",
)
parser.add_argument(
"-O",
"--order",
help="byte order (= for native)",
type=str,
default="=",
choices=["<", ">", "="],
)
parser.add_argument(
"-c",
"--center",
help="coordinates of the center",
type=args.center,
default=[0.5, 0.5, 0.5],
)
parser.add_argument("-s", "--size", help="cube size", type=float, default=1.0)
parser.add_argument(
"-l", "--level", help="cube level (default: levelMIN)", type=int, default=0
)
parser.add_argument(
"-k", "--kbins", help="number of wave number bins", type=int, default=100
)
@@ -504,7 +542,7 @@ def main(arg):
parser.error("Invalid slicing axis: %r" % arg.sliceaxis)
# Output numbers
iouts = tools.select_outputs(arg.repo, arg.iouts)
iouts = arg.iouts # tools.select_outputs(arg.repo, arg.iouts)
for iout in iouts:
print("Output %d" % iout)
@@ -547,7 +585,7 @@ def main(arg):
distance=arg.size / 2.0,
far_cut_depth=arg.size / 2.0,
up_vector="y",
map_max_size=256,
map_max_size=2 ** clvl,
)
cubes = {}
@@ -555,7 +593,7 @@ def main(arg):
operator = ScalarOperator(cube_vars[i], cube_units[i])
extractor = cube3d.CubeExtractor(amr, operator)
cubes[v] = extractor.process(
cam, cube_size=arg.size, resolution=256
cam, cube_size=arg.size, resolution=2 ** clvl
).data
else:
h5f = T.open_file("cube.hdf5", "r")
@@ -577,7 +615,6 @@ def main(arg):
% (clvl, read_lvl)
)
clvl = read_lvl
# Degrade cubes ----------------------------------------------------------------
if clvl < read_lvl:
print("Degrade cubes")
@@ -655,10 +692,23 @@ def main(arg):
pcubes["krs"] = pcube(fcubes["krsx"], fcubes["krsy"], fcubes["krsz"])
pcubes["B"] = pcube(fcubes["Bx"], fcubes["By"], fcubes["Bz"])
pcubes["cos_vB"] = pcube(fcubes["cos_vB"])
pcubes["vz"] = pcube(fcubes["vz"])
print("Compute 3D power spectra")
# 3D power spectra -------------------------------------------------------------
for v in ["rho", "logrho", "v", "kr", "vc", "vs", "krc", "krs", "B", "cos_vB"]:
for v in [
"rho",
"logrho",
"v",
"kr",
"vc",
"vs",
"krc",
"krs",
"B",
"cos_vB",
"vz",
]:
pspec, kbins, pspec2, fbins = pspectrum(
pcubes[v], cubes_k["k"], kbins, knorm, arg.fbins
)
@@ -751,6 +801,7 @@ def main(arg):
"By",
"Bz",
"cos_vB",
"vz",
]:
fcubes2[v] = ifft(fcubes[v], axis=saxis)
@@ -770,12 +821,25 @@ def main(arg):
pcubes2["krs"] = pcube(fcubes2["krsx"], fcubes2["krsy"], fcubes2["krsz"])
pcubes2["B"] = pcube(fcubes2["Bx"], fcubes2["By"], fcubes2["Bz"])
pcubes2["cos_vB"] = pcube(fcubes2["cos_vB"])
pcubes2["vz"] = pcube(fcubes2["vz"])
print("Compute 2D power spectra")
# 2D power spectra -------------------------------------------------------------
ns = 2 ** clvl
f = "_%%(i)0%dd" % (np.floor(np.log10(ns)) + 1)
for v in ["rho", "logrho", "v", "kr", "vc", "vs", "krc", "krs", "B", "cos_vB"]:
for v in [
"rho",
"logrho",
"v",
"kr",
"vc",
"vs",
"krc",
"krs",
"B",
"cos_vB",
"vz",
]:
for i in xrange(ns):
pspec, kbins, pspec2, fbins = pspectrum(
pcubes2[v][:, :, i], cubes_k["k"][:, :, i], kbins, knorm, arg.fbins
@@ -857,4 +921,7 @@ if __name__ == "__main__":
def pspec(**kwargs):
main(bunch.bunchify(kwargs))
arg = parser.parse_args("")
for kwarg in kwargs:
setattr(arg, kwarg, kwargs[kwarg])
main(arg)
pspec_read.py
+72 -32
View File
@@ -8,7 +8,7 @@ import matplotlib.pyplot as P
################################################################
def pspec_rho(file, path_out, num, color="r", save=False):
def pspec_rho(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/rho")
@@ -22,13 +22,13 @@ def pspec_rho(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^2 \mathcal{P}(\rho)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_rho_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_rho_" + format(num, "05") + ".jpeg")
def pspec_B(file, path_out, num, color="r", save=False):
def pspec_B(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/B")
@@ -42,13 +42,13 @@ def pspec_B(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^2 \mathcal{P}(B)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_B_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_B_" + format(num, "05") + ".jpeg")
def pspec_v(file, path_out, num, color="r", save=False):
def pspec_v(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/v")
@@ -62,13 +62,33 @@ def pspec_v(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^4 \mathcal{P}(v)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_v_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_v_" + format(num, "05") + ".jpeg")
def pspec_cos(file, path_out, num, color="r", save=False):
def pspec_vz(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/vz")
kbins = h5f.get_node(group, "kbins").read()
pspec = h5f.get_node(group, "pspec").read()
h5f.close()
k = np.sqrt(kbins[1:] * kbins[:-1])
pspec = k ** 4 * pspec
if save:
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^4 \mathcal{P}(vz)$", fontsize=12)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vz_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vz_" + format(num, "05") + ".jpeg")
def pspec_cos(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/cos_vB")
@@ -82,13 +102,13 @@ def pspec_cos(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^2 \mathcal{P}(\cos(\vec{v}.\vec{B}))$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_cos_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_cos_" + format(num, "05") + ".jpeg")
def pspec_logrho(file, path_out, num, color="r", save=False):
def pspec_logrho(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/logrho")
@@ -102,13 +122,13 @@ def pspec_logrho(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^2 \mathcal{P}(\log(\rho))$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_logrho_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_logrho_" + format(num, "05") + ".jpeg")
def pspec_kr(file, path_out, num, color="r", save=False):
def pspec_kr(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/kr")
@@ -122,13 +142,13 @@ def pspec_kr(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^4 \mathcal{P}(\rho^{1/3}v)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_kr_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_kr_" + format(num, "05") + ".jpeg")
def pspec_vc(file, path_out, num, color="r", save=False):
def pspec_vc(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/vc")
@@ -142,13 +162,13 @@ def pspec_vc(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^4 \mathcal{P}(v_c)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vc_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vc_" + format(num, "05") + ".jpeg")
def pspec_vs(file, path_out, num, color="r", save=False):
def pspec_vs(file, path_out, num, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d3/vs")
@@ -162,7 +182,7 @@ def pspec_vs(file, path_out, num, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^4 \mathcal{P}(v_s)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vs_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vs_" + format(num, "05") + ".jpeg")
@@ -173,7 +193,7 @@ def pspec_vs(file, path_out, num, color="r", save=False):
###################################################################
def pspec_rho_2D(file, path_out, num, plan, color="r", save=False):
def pspec_rho_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/rho")
@@ -187,13 +207,13 @@ def pspec_rho_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k \mathcal{P}(\rho)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_rho_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_rho_2D_" + format(num, "05") + ".jpeg")
def pspec_B_2D(file, path_out, num, plan, color="r", save=False):
def pspec_B_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/B")
@@ -207,13 +227,13 @@ def pspec_B_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k \mathcal{P}(B)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_B_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_B_2D_" + format(num, "05") + ".jpeg")
def pspec_v_2D(file, path_out, num, plan, color="r", save=False):
def pspec_v_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/v")
@@ -227,13 +247,33 @@ def pspec_v_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^3 \mathcal{P}(v)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_v_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_v_2D_" + format(num, "05") + ".jpeg")
def pspec_cos_2D(file, path_out, num, plan, color="r", save=False):
def pspec_vz_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/vz")
kbins = h5f.get_node(group, "kbins_" + str(plan)).read()
pspec = h5f.get_node(group, "pspec_" + str(plan)).read()
h5f.close()
k = np.sqrt(kbins[1:] * kbins[:-1])
pspec = k ** 3 * pspec
if save:
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^3 \mathcal{P}(v_z)$", fontsize=12)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vz_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vz_2D_" + format(num, "05") + ".jpeg")
def pspec_cos_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/cos_vB")
@@ -247,13 +287,13 @@ def pspec_cos_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k \mathcal{P}(\cos(\vec{v}.\vec{B}))$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_cos_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_cos_2D_" + format(num, "05") + ".jpeg")
def pspec_logrho_2D(file, path_out, num, plan, color="r", save=False):
def pspec_logrho_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/logrho")
@@ -267,13 +307,13 @@ def pspec_logrho_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k \mathcal{P}(\log(\rho))$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_logrho_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_logrho_2D_" + format(num, "05") + ".jpeg")
def pspec_kr_2D(file, path_out, num, plan, color="r", save=False):
def pspec_kr_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/kr")
@@ -287,13 +327,13 @@ def pspec_kr_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^3 \mathcal{P}(\rho^{1/3}v)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_kr_2D_" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_kr_2D_" + format(num, "05") + ".jpeg")
def pspec_vc_2D(file, path_out, num, plan, color="r", save=False):
def pspec_vc_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/vc")
@@ -307,13 +347,13 @@ def pspec_vc_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^3 \mathcal{P}(v_c)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vc_2D" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vc_2D" + format(num, "05") + ".jpeg")
def pspec_vs_2D(file, path_out, num, plan, color="r", save=False):
def pspec_vs_2D(file, path_out, num, plan, color="r", save=False, **kwargs):
h5f = T.open_file(file, mode="r")
group = h5f.get_node("/out_" + format(num, "05") + "/d2/vs")
@@ -327,7 +367,7 @@ def pspec_vs_2D(file, path_out, num, plan, color="r", save=False):
P.figure(figsize=(8, 8))
P.xlabel(r"$k$", fontsize=12)
P.ylabel(r"$k^3 \mathcal{P}(v_s)$", fontsize=12)
P.loglog(k, pspec, "-", color=color)
P.loglog(k, pspec, "-", color=color, **kwargs)
if save:
P.savefig(path_out + "pspec_vs_2D" + format(num, "05") + ".ps")
P.savefig(path_out + "pspec_vs_2D" + format(num, "05") + ".jpeg")