noe/pipeline
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Remove depencency on Patrick's file, add wait option

Browse Source
This commit is contained in:
Noe Brucy
2019-04-14 11:52:39 +02:00
parent 260dcfc7a5
commit 9f53414ab1
2 changed files with 294 additions and 206 deletions
Download Patch File Download Diff File Expand all files Collapse all files
disk_postprocess.py
+231 -172
View File
@@ -3,38 +3,93 @@ import sys
import numpy as np
import os
import pymses
import matplotlib as mpl
if os.environ.get("DISPLAY", "") == "":
print("No display found. Using non-interactive Agg backend")
mpl.use("Agg")
import pylab as P
import glob as glob
import pickle as pickle
import module_extract as me
from pymses.filters import CellsToPoints
from pymses.sources.ramses import output
from pymses.analysis import Camera, raytracing, slicing
from pymses.filters import CellsToPoints
from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
P.rcParams["image.cmap"] = "plasma"
P.rcParams["savefig.dpi"] = 800
def make_image_temp(
def make_image_disk(
path,
num,
path_out=None,
order="<",
force=False,
tag="",
vel_red=20,
map_size=512,
put_title=True,
cpuamr=False,
):
"""
Make several useful image of an output of a simulation
Parameters
----------
path path of the Ramses output
num Ramses output number
path_out path of the pipeline output
order '<' or '>' TODO
force if set, erase any existing pipeline output files
tag string to add to the output name
vel_red number of point where velocity should be plot in the slices
map_size size of the map
cpuamr plot also levels and cpus at each step
"""
ro = pymses.RamsesOutput(path, num, order=order)
amr = ro.amr_source(["rho", "vel", "P", "Bl", "Br"])
rad = 0.5
center = [0.5, 0.5, 0.5]
make_image_aux(
amr,
ro,
center,
rad,
num,
path,
force=force,
path_out=path_out,
map_size=map_size,
vel_red=vel_red,
tag=tag,
cpuamr=cpuamr,
put_title=put_title,
)
def make_image_aux(
amr,
ro,
center,
radius,
num,
path,
i_im=0,
force=False,
path_out=None,
col_dens_only=False,
map_size=512,
vel_red=20,
im_pos=0.0,
tag="",
cpuamr=False,
put_title=True,
mass_norm=1.0,
AU_units=False,
):
"""
Make several useful image of an output of a simulation
Make several useful image of an output of a simulation, auxillary function
Parameters
----------
@@ -43,81 +98,66 @@ def make_image_temp(
center 3D array for coordinates center
num output number
path_out path of the pipeline output
force if set, erase any existing pipeline output files
tag string to add to the output name
vel_red number of point where velocity should be plot in the slices
map_size size of the map
cpuamr plot also levels and cpus at each step
"""
lbox = ro.info["boxlen"] # boxlen in codeunits (=>pc)
lbox = ro.info["boxlen"] # boxlen in codeunits
lbox_units = lbox
(
AU,
pc,
Ms,
Myr,
scale_n,
scale_d,
scale_t,
scale_l,
scale_v,
scale_T2,
scale_ener,
scale_mag,
microG,
km_s,
Cwnm,
scale_mass,
unit_col,
lbox_pc,
) = normalisation(ro)
G = 1.0 # Gravitational constant
ntick = 6
if AU_units:
units = pc / AU
lbox_units = lbox * units
titre_x = "x (AU)"
titre_y = "y (AU)"
titre_z = "z (AU)"
else:
units = 1.0
lbox_units = lbox
titre_x = "x (pc)"
titre_y = "y (pc)"
titre_z = "z (pc)"
lbox_cm = lbox * pc # lbox in cm
title_ax = {"x": "x (code)", "y": "y (code)", "z": "z (code)"}
time = ro.info["time"] # time in codeunits
time = time * scale_t / Myr
titre = "t=" + str(time)[0:5] + " (Myr)"
title = "t=" + str(time)[0:5] + " (code)"
if path_out is not None:
directory = path_out
else:
directory = path
rt = raytracing.RayTracer(amr, ro.info, rho_op)
rho_op = ScalarOperator(lambda dset: dset["rho"], ro.info["unit_density"])
name = directory + "/coldens_z" + "_" + tag + "_" + format(num, "05") + ".jpeg"
if len(glob.glob(name)) == 1 and not force:
return
ax_names = ["x", "y", "z"]
up_axes = ["z", "z", "x"]
other_axes = ["z", "x", "y"]
rho_op = ScalarOperator(lambda dset: dset["rho"], ro.info["unit_density"])
rt = raytracing.RayTracer(amr, ro.info, rho_op)
axes_los = ["x", "y", "z"] # Line of sight axes
axes_h = ["y", "x", "x"] # Horizontal axes
axes_v = ["z", "z", "y"] # Vertical axes
ax_nb = {"x": 0, "y": 1, "z": 2}
image_names = ["coldens", "rho", "T"]
for i, ax_name in enumerate(ax_names):
for i, ax_los in enumerate(axes_los):
ax_h = axes_h[i]
ax_v = axes_v[i]
cam = Camera(
center=center,
line_of_sight_axis=ax_name,
line_of_sight_axis=ax_los,
region_size=[2.0 * radius, 2.0 * radius],
distance=radius,
far_cut_depth=radius,
up_vector=up_axes[i],
up_vector=ax_v,
map_max_size=map_size,
)
datamap = rt.process(cam, surf_qty=True)
map_col = np.log10(datamap.map.T * lbox_cm)
P.clf()
# Column density
dmap_col = datamap.map.T * lbox
map_col = np.log10(dmap_col)
P.close()
im = P.imshow(
map_col,
extent=[
@@ -129,38 +169,44 @@ def make_image_temp(
origin="lower",
)
P.locator_params(axis=other_axes[i], nbins=ntick)
P.locator_params(axis=up_axes[i], nbins=ntick)
P.locator_params(axis=ax_h, nbins=ntick)
P.locator_params(axis=ax_v, nbins=ntick)
if put_title:
P.title(titre)
P.title(title)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
P.xlabel(titre_x)
P.ylabel(titre_y)
cbar = P.colorbar(im)
cbar.set_label(r"$log(N) \, cm^{-2}$")
name = directory + "/coldens_" + ax_name + "_" + tag + +"_" + format(num, "05")
cbar.set_label(r"$log(N)$ (code)")
name = directory + "/coldens_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
# Rho slice
dmap_rho = slicing.SliceMap(amr, cam, rho_op, z=0.0)
map_rho = np.log10(dmap_rho.map)
map_rho = map_rho.T
vx_op = ScalarOperator(lambda dset: dset["vel"][:, 0], ro.info["unit_velocity"])
dmap_vx = slicing.SliceMap(amr, cam_z, vx_op, z=0.0)
map_vx_red = dmap_vx.map[::vel_red, ::vel_red]
vh_op = ScalarOperator(
lambda dset: dset["vel"][:, ax_nb[ax_h]], ro.info["unit_velocity"]
)
dmap_vh = slicing.SliceMap(amr, cam, vh_op, z=0.0)
map_vh_red = dmap_vh.map[
::vel_red, ::vel_red
] # take only a subset of velocities
map_vx_red = map_vx_red.T
map_vh_red = map_vh_red.T
vy_op = ScalarOperator(lambda dset: dset["vel"][:, 1], ro.info["unit_velocity"])
dmap_vy = slicing.SliceMap(amr, cam, vy_op, z=0.0)
map_vy_red = dmap_vy.map[::vel_red, ::vel_red]
vv_op = ScalarOperator(
lambda dset: dset["vel"][:, ax_nb[ax_v]], ro.info["unit_velocity"]
)
dmap_vv = slicing.SliceMap(amr, cam, vv_op, z=0.0)
map_vv_red = dmap_vv.map[::vel_red, ::vel_red]
map_vv_red = map_vv_red.T
map_vy_red = map_vy_red.T
P.clf()
P.close()
im = P.imshow(
map_rho,
extent=[
@@ -171,50 +217,45 @@ def make_image_temp(
],
origin="lower",
)
P.locator_params(axis=other_axes[i], nbins=ntick)
P.locator_params(axis=up_axes[i], nbins=ntick)
nx = map_vx_red.shape[0]
ny = map_vx_red.shape[1]
vec_x = (
np.arange(nx) * 2.0 / nx * radius - radius + center[0] + radius / nx
P.locator_params(axis=ax_h, nbins=ntick)
P.locator_params(axis=ax_v, nbins=ntick)
nh = map_vh_red.shape[0]
nv = map_vv_red.shape[1]
vec_h = (
np.arange(nh) * 2.0 / nh * radius - radius + center[0] + radius / nh
) * lbox_units
vec_y = (
np.arange(ny) * 2.0 / ny * radius - radius + center[1] + radius / nx
vec_v = (
np.arange(nv) * 2.0 / nv * radius - radius + center[1] + radius / nv
) * lbox_units
xx, yy = np.meshgrid(vec_x, vec_y)
map_vx_red = map_vx_red * scale_v / km_s
map_vy_red = map_vy_red * scale_v / km_s
max_v = np.max(np.sqrt(map_vx_red ** 2 + map_vy_red ** 2))
Q = P.quiver(xx, yy, map_vx_red, map_vy_red, units="width")
hh, vv = np.meshgrid(vec_h, vec_v)
max_v = np.max(np.sqrt(map_vh_red ** 2 + map_vv_red ** 2))
Q = P.quiver(hh, vv, map_vh_red, map_vv_red, units="width")
P.quiverkey(
Q,
0.7,
0.95,
max_v,
r"$" + str(max_v)[0:4] + "\, km \, s^{-1}$",
r"$" + str(max_v)[0:4] + "$ (code)",
labelpos="E",
coordinates="figure",
)
if put_title:
P.title(titre)
P.xlabel(titre_x)
P.ylabel(titre_y)
P.title(title)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"$log(n) \, (cm^{-3})$")
cbar.set_label(r"$log(n)$ (code)")
name = directory + "/rho_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
name = directory + "/rho_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
P_op = ScalarOperator(lambda dset: dset["P"], ro.info["unit_pressure"])
dmap_P = slicing.SliceMap(amr, cam_z, P_op, z=0.0)
P.clf()
map_T = np.log10(dmap_P.map.T / dmap_rho.map.T * scale_T2)
dmap_P = slicing.SliceMap(amr, cam, P_op, z=0.0)
P.close()
dmap_T = dmap_P.map.T / dmap_rho.map.T
map_T = np.log10(dmap_T)
im = P.imshow(
map_T,
@@ -231,14 +272,45 @@ def make_image_temp(
P.locator_params(axis="y", nbins=ntick)
if put_title:
P.title(titre)
P.xlabel(titre_x)
P.ylabel(titre_y)
P.title(title)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"$log(T) \, (K)$")
name = directory + "/T_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
name = directory + "/T_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
# Toomre parameter
if False and ax_los == "z":
map_Q = np.log10(np.sqrt(dmap_P.map.T / dmap_rho.map.T)) / (
np.pi * map_col * G
)
im = P.imshow(
map_T,
extent=[
(-radius + center[0]) * lbox_units,
(radius + center[0]) * lbox_units,
(-radius + center[1]) * lbox_units,
(radius + center[1]) * lbox_units,
],
origin="lower",
)
P.locator_params(axis="x", nbins=ntick)
P.locator_params(axis="y", nbins=ntick)
if put_title:
P.title(title)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"$log(T) \, (K)$")
name = directory + "/Q_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
@@ -246,10 +318,10 @@ def make_image_temp(
level_op = MaxLevelOperator()
amr.set_read_levelmax(20)
rt = raytracing.RayTracer(amr, ro.info, level_op)
datamap = rt.process(cam_z, surf_qty=True)
datamap = rt.process(cam, surf_qty=True)
map_level = datamap.map.T
P.clf()
P.close()
im = P.imshow(
map_level,
extent=[
@@ -265,49 +337,25 @@ def make_image_temp(
P.locator_params(axis="y", nbins=ntick)
if put_title:
P.title(titre)
P.xlabel(titre_x)
P.ylabel(titre_y)
P.title(title)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"level")
name = (
directory + "/level_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
)
name = directory + "/level_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
if ps:
P.savefig(name + ".ps")
if descrip is not None:
dd = {}
dd.update(
{
"name": "mean AMR level in the z-direction"
+ " ("
+ tag
+ str(i_im)
+ ")"
}
)
dd.update({"type": "image"})
dd.update({"description": "Mean AMR level in the z-direction."})
dd.update({"display": 0})
dd.update({"item": i_im})
dd.update({"tag": tag})
data = {"jpeg": name_im}
dd.update({"data": data})
list_im.append(dd)
cpu_op = ScalarOperator(
lambda dset: dset.icpu * (np.ones(dset["P"].shape)),
ro.info["unit_pressure"],
)
rt = raytracing.RayTracer(amr, ro.info, cpu_op)
datamap = rt.process(cam_z, surf_qty=True)
datamap = rt.process(cam, surf_qty=True)
map_cpu = datamap.map.T
P.clf()
P.close()
im = P.imshow(
map_cpu,
extent=[
@@ -322,16 +370,14 @@ def make_image_temp(
P.locator_params(axis="y", nbins=ntick)
if put_title:
P.title(titre)
P.title(title)
P.xlabel(titre_x)
P.ylabel(titre_y)
P.xlabel(title_ax[ax_h])
P.ylabel(title_ax[ax_v])
cbar = P.colorbar(im)
cbar.set_label(r"level")
cbar.set_label(r"cpu")
name = (
directory + "/cpu_z" + "_" + tag + str(i_im) + "_" + format(num, "05")
)
name = directory + "/cpu_" + ax_los + "_" + tag + "_" + format(num, "05")
name_im = name + ".jpeg"
P.savefig(name_im)
@@ -409,8 +455,7 @@ def disk_prop(
v_az = (pos[:, 0] * vel[:, 1] - pos[:, 1] * vel[:, 0]) / norm_pos
# Select cells that are actually in the disk, ie within the scale height
# TODO Check units
G = 1.0 # G=6.8e-8
G = 1.0
cs = np.sqrt(cells["P"] / cells["rho"]) # sound velocity
height = cs * np.sqrt(rc ** 3 / (G * mass_star))
mask_pos = np.abs(pos[:, 2]) < height # condition on position
@@ -439,6 +484,7 @@ def disk_prop(
v_kepl_rad = np.zeros(nb_bin - 1)
v_rad_rad = np.zeros(nb_bin - 1)
alpha_rey_rad = np.zeros(nb_bin - 1)
Q_kepl_rad = np.zeros(nb_bin - 1)
for i in range(nb_bin - 1):
mask_bin = (rc_disk > rad[i]) & (rc_disk < rad[i + 1])
@@ -502,9 +548,11 @@ def disk_prop(
v_rad_rad = v_rad_rad # * scale_v / km_s
v_kepl_rad = v_kepl_rad
Q_kepl_rad = cs_rad * v_az_rad / (np.pi * G * coldens_rad * rad[0 : nb_bin - 1])
prop_disk = {
"time": time,
"rad_AU": rad[0 : nb_bin - 1],
"rad": rad[0 : nb_bin - 1],
"center": pos_star,
"alpha_rey": alpha_rey_rad,
"v_rad": v_rad_rad,
@@ -515,6 +563,7 @@ def disk_prop(
"press": press_rad,
"temp": temp_rad,
"cs": cs_rad,
"Q_kepl": Q_kepl_rad,
}
# store the results
@@ -545,12 +594,14 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
prop_disk = pickle.load(f)
f.close()
P.clf()
# Check if the output file exists, and exit if it is the case
name_save = path + "/rho_disk_r_" + str(num).zfill(5) + ".jpeg"
if not force and len(glob.glob(name_save)) != 0:
return
P.close()
P.plot(
np.log10(prop_disk["rad_AU"]),
np.log10(prop_disk["rho"]),
color="k",
linewidth=2,
np.log10(prop_disk["rad"]), np.log10(prop_disk["rho"]), color="k", linewidth=2
)
P.ylabel(r"$\log(n) \, (cm^{-3})$")
P.xlabel("disk radius")
@@ -559,12 +610,9 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/rho_disk_r_" + str(num).zfill(5) + ".jpeg")
P.clf()
P.close()
P.plot(
np.log10(prop_disk["rad_AU"]),
np.log10(prop_disk["temp"]),
color="k",
linewidth=2,
np.log10(prop_disk["rad"]), np.log10(prop_disk["temp"]), color="k", linewidth=2
)
P.ylabel(r"$\log(T) \, (K)$")
P.xlabel("disk radius")
@@ -573,15 +621,15 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/T_disk_r_" + str(num).zfill(5) + ".jpeg")
P.clf()
P.close()
P.xscale("log")
P.yscale("symlog", linthreshy=0.01)
P.plot((prop_disk["rad_AU"]), ((prop_disk["v_rad"])), color="k", linewidth=2)
P.plot((prop_disk["rad_AU"]), ((prop_disk["v_kepl"])), color="b", linewidth=2)
P.plot((prop_disk["rad_AU"]), (abs(prop_disk["v_az"])), color="r", linewidth=2)
P.plot((prop_disk["rad_AU"]), ((prop_disk["cs"])), color="c", linewidth=2)
P.plot((prop_disk["rad"]), ((prop_disk["v_rad"])), color="k", linewidth=2)
P.plot((prop_disk["rad"]), ((prop_disk["v_kepl"])), color="b", linewidth=2)
P.plot((prop_disk["rad"]), (abs(prop_disk["v_az"])), color="r", linewidth=2)
P.plot((prop_disk["rad"]), ((prop_disk["cs"])), color="c", linewidth=2)
P.legend((r"$v_r$", r"$v_{kepl}$", r"$v_\phi$", r"$c_s$"), loc="upper right")
@@ -592,9 +640,9 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/V_disk_r_" + str(num).zfill(5) + ".jpeg")
P.clf()
P.close()
P.plot(
np.log10(prop_disk["rad_AU"]),
np.log10(prop_disk["rad"]),
np.log10(prop_disk["coldens"]),
color="k",
linewidth=2,
@@ -606,13 +654,13 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/coldens_disk_r_" + str(num).zfill(5) + ".jpeg")
P.clf()
# Alpha
P.close()
P.xscale("log")
P.yscale("symlog", linthreshy=0.001)
P.yscale("log")
P.ylim([1e-5, 1.0])
P.plot(prop_disk["rad_AU"], abs(prop_disk["alpha_rey"]), color="b", linewidth=2)
# P.legend(r'$\alpha_{Rey}$', loc='upper right')
P.plot(prop_disk["rad"], abs(prop_disk["alpha_rey"]), color="b", linewidth=2)
P.ylabel(r"$\alpha$")
P.xlabel("disk radius ")
@@ -621,6 +669,17 @@ def plot_disk_prop(path, num, force=False, pdf=False, tag=""):
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/alpha_disk_r_" + str(num).zfill(5) + ".jpeg")
# Q
P.close()
P.xscale("log")
P.yscale("log", linthreshy=0.001)
P.plot(prop_disk["rad"], abs(prop_disk["Q_kepl"]), color="b", linewidth=2)
P.ylabel(r"$Q$")
P.xlabel("disk radius ")
if pdf:
P.savefig(path + "alpha_disk_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "alpha_disk_r_" + str(num).zfill(5) + ".jpeg")
P.savefig(path + "/Q_r_" + str(num).zfill(5) + ".pdf")
P.savefig(path + "/Q_r_" + str(num).zfill(5) + ".jpeg")
pipeline_disk.py
+46 -17
View File
@@ -1,11 +1,11 @@
# coding: utf-8
import sys
import numpy as np
import module_extract as me
import extract_disk as d
import pymses
import os
from shutil import copy
import argparse
import time
import disk_postprocess as dp
@@ -24,19 +24,39 @@ parser.add_argument("-s", "--step", help="step between two output", type=int, de
parser.add_argument(
"-d", "--disk", help="do specific disk radial analysis", action="store_true"
)
parser.add_argument("-p", "--project", help="specify project name", default="disk")
parser.add_argument(
"-w", "--watch", help="wait and watch for missing outputs", action="store_true"
)
parser.add_argument(
"-wt",
"--waiting_time",
help="time between to successive try when watching new outputs (in second)",
type=int,
default=120,
)
parser.add_argument(
"-af",
"--allowed_failures",
help="number of allowed failures when waiting",
default=30,
)
args = parser.parse_args()
user = "nbrucy"
folder = "simus"
project = "disk"
project = args.project
runs = args.runs
first = args.first_output
last = args.last_output
step = args.step
for run in runs:
path_suffix = user + "/" + folder + "/" + project + "/" + run
path_in = storage_in + path_suffix
@@ -44,23 +64,32 @@ for run in runs:
if not os.path.exists(path_out):
os.makedirs(path_out)
copy(path_in + "/disk.nml", path_out)
copy(path_in + "/output_00001/compilation.txt", path_out)
for i in range(first, last + 1, step):
me.make_image_zoom(
path_in,
i,
[0.5],
sinks=False,
force=False,
path_out=path_out,
tag=run + "_",
cpuamr=False,
mag_im=False,
AU_units=False,
failures = 0
success = False
while not success:
try:
dp.make_image_disk(
path_in, i, path_out=path_out, tag=run, map_size=1024
)
# me.look(path_in, i)
if args.disk:
dp.disk_prop(
path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=True
path_in, i, path_out=path_out, rad_ext=1, nb_bin=50, force=False
)
dp.plot_disk_prop(path_out, i, tag=run + "_")
dp.plot_disk_prop(path_out, i, tag=run)
success = True
except ValueError:
if args.watch and failures < args.allowed_failures:
failures = failures + 1
print(
"Unable to proceed for run {} output {}. Trying again in {} s ({} tries remaining)".format(
run, i, args.waiting_time, args.allowed_failures - failures
)
)
time.sleep(args.waiting_time)
else:
raise