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Some improvements

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This commit is contained in:
Noe Brucy
2019-10-23 13:47:56 +02:00
parent 1211dbb7b8
commit 7311eb3329
2 changed files with 453 additions and 301 deletions
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disk_postprocess.py
+252 -115
View File
@@ -5,11 +5,10 @@ import os
import pymses
import numpy as np
import matplotlib as mpl
if os.environ.get("DISPLAY", "") == "":
print("No display found. Using non-interactive Agg backend")
mpl.use("Agg")
if os.environ.get('DISPLAY','') == '':
print('No display found. Using non-interactive Agg backend')
mpl.use('Agg')
from matplotlib.patches import Polygon
import pylab as P
import glob as glob
@@ -27,6 +26,9 @@ from pymses.analysis import Camera, raytracing, slicing, splatting
from pymses.filters import CellsToPoints
from pymses.analysis import ScalarOperator, FractionOperator, MaxLevelOperator
from scipy.stats import gaussian_kde
import matplotlib.patches as mpatches
from matplotlib.collections import PatchCollection
import module_extract as me
@@ -122,19 +124,9 @@ def compute_image_data(path, num, radius=0.5,
return
# Prepare saving data
if "T" in images and not "rho" in images:
images.append("rho")
if "Q" in images and not "coldens" in images:
images.append("coldens")
maps_disk = {
"time": time,
"im_extent": im_extent,
"center": center,
"radius": radius,
"lbox": lbox,
"images": images,
"axes_los": axes_los,
}
maps_disk = {'time' : time, 'im_extent' : im_extent,
'center' : center, 'radius' : radius, 'lbox' : lbox,
'images': images, 'axes_los': axes_los}
# Prepare raytracing
rho_op = ScalarOperator(lambda dset: dset["rho"], ro.info["unit_density"])
@@ -344,6 +336,11 @@ def plot_maps(path, num,
):
continue
if (image == 'jeans'):
maps_disk['jeans_' + ax_los] = np.sqrt(np.pi * maps_disk['T_' + ax_los] / maps_disk['rho_' + ax_los])
if (image == 'jeans_ratio'):
maps_disk['jeans_ratio_' + ax_los] = maps_disk['jeans_' + ax_los] * 2**(maps_disk['levels_' + ax_los])
map_disk = maps_disk[image + '_' + ax_los]
if image == 'Q' :
@@ -353,6 +350,13 @@ def plot_maps(path, num,
cmap='RdBu',
norm=mpl.colors.LogNorm(),
vmin=0.01, vmax=100.)
elif image == 'jeans_ratio' :
im = P.imshow(map_disk,
extent=im_extent,
origin='lower',
cmap='RdBu',
norm=mpl.colors.LogNorm(),
vmin=0.1, vmax=1000.)
else:
im = P.imshow(
map_disk,
@@ -396,7 +400,7 @@ def plot_maps(path, num,
cont.levels = cont.levels + 1
P.clabel(cont,
levels_ar[levels_ar < 11][1:],
cont.levels[cont.levels < 11],
inline=1, fontsize=8., fmt='%1d')
elif image == 'rho':
cbar.set_label(r'$\rho$ (code)')
@@ -421,6 +425,8 @@ def plot_maps(path, num,
cbar.set_label(r'$T (code)$')
elif image == 'Q':
cbar.set_label(r'$Q$')
elif image == 'jeans':
cbar.set_label(r'Jeans\'s lenght')
else:
cbar.set_label(image)
@@ -805,20 +811,67 @@ def plot_disk_prop(
P.close()
def disk_pdf(
path,
num,
maps_disk,
pos_star=[1.0, 1.0],
force=False,
interactive=False,
nb_bin_hist=50,
tag="",
rad_min=0.075,
rad_max=0.3,
put_title=True,
do_speed=True,
):
def sigma_pdf(fluct_maps, mask_flat, put_title=False, title='', nb_bin_hist=50, tag=''):
# Sigma-PDF
dcoldens = np.log10(fluct_maps['coldens']).flatten()
nb_cells = np.sum(mask_flat)
P.grid()
P.yscale('log')
P.ylim([0.5 / nb_cells, 1.])
P.xlabel(r'$\log(\Sigma / \bar{\Sigma})$')
P.ylabel(r'$\mathcal{P}_\Sigma$')
if put_title:
P.title(title)
values, edges, _ = P.hist(dcoldens[mask_flat],
nb_bin_hist, range=(-1, 3),
weights = np.ones(nb_cells) / nb_cells)
centers = 0.5 * (edges[1:] + edges[:-1])
# Variance
var = np.var(dcoldens[mask_flat])
# Compute the slope of the right part of the histogramm
mask_fit = (centers > 0.) & (centers < 1.25) & (values > 0)
if (np.sum(mask_fit > 0)):
(a, b, rho, _, stderr) = linregress(centers[mask_fit], np.log10(values[mask_fit]))
P.plot(centers, 10**(a*centers + b), '--', linewidth=2)
print("pdf a=%e, b=%e, rho=%e, var=%e"% (a, b, rho, var))
try :
beta = int(tag.split('_')[1][4:])
except ValueError :
beta = 0
fit = {'beta': beta,'slope': a, 'origin': b, 'correlation': rho, 'stderr':stderr, 'var':var}
return fit
def plot_dcsdrho(fluct_maps, mask_flat, put_title=False, title='', nb_bin_hist=50, tag=''):
drho = fluct_maps['rho'].flatten()
dcs = fluct_maps['cs'].flatten()
nb_points = np.sum(mask_flat)
size_hist = int(np.sqrt(nb_points))
P.hist2d(np.log10(drho[mask_flat]), np.log10(dcs[mask_flat]), (size_hist, size_hist), norm=mpl.colors.LogNorm())
P.xlabel(r'$\log(\rho / \bar{\rho})$')
P.ylabel(r'$\log(c_s / \bar{c_s})$')
P.ylim([-0.6, 0.6])
P.xlim([-1, 1.])
(a, b, rho, _, stderr) = linregress(np.log10(drho[mask_flat]), np.log10(dcs[mask_flat]))
P.plot(np.log10(drho[mask_flat]), a*np.log10(drho[mask_flat]) + b, '--', linewidth=2)
print("cs/rho a=%e, b=%e, rho=%e"% (a, b, rho))
try :
beta = int(tag.split('_')[1][4:])
except ValueError :
beta = 0
fit = {'beta': beta,'slope': a, 'origin': b, 'correlation': rho, 'stderr':stderr}
def disk_pdf(path, num, maps_disk,
pos_star=[1., 1.], force=False, interactive=False,
nb_bin_hist=50, tag='',
rad_min=0.075, rad_max=0.3, put_title=True,
do_speed=True):
# Load property file
name_prop = path + "/prop_disk_" + str(num).zfill(5) + ".save"
@@ -853,9 +906,11 @@ def disk_pdf(
print("maps file loaded")
# Properties
time = prop_disk["time"]
im_extent = maps_disk["im_extent"]
title = tag.split("_")[1] + " t=" + str(time)[0:5] + " (code)"
time = prop_disk['time']
im_extent = maps_disk['im_extent']
title = None
if (put_title):
title = tag.split('_')[1] + ' t='+ str(time)[0:5] +' (code)'
# Load coldens
coldens_map = maps_disk["coldens_z"]
@@ -883,16 +938,14 @@ def disk_pdf(
# Mask selecting the zone of interest
mask_map = (rr > rad_min) & (rr < rad_max)
mask_flat = mask_map.flatten()
# Additionnal maps
rho_map = maps_disk["rho_z"]
cs_map = np.sqrt(maps_disk["T_z"])
vx_map = maps_disk["vx_z"]
vy_map = maps_disk["vy_z"]
vx_map = maps_disk['vx_z']
vy_map = maps_disk['vy_z']
v_map = np.sqrt(vx_map**2 + vy_map**2)
v_kepl = np.sqrt(1.0 / rr)
xx_star = xx - pos_star[0]
yy_star = yy - pos_star[1]
vrad_map = (vx_map * xx_star + vy_map * yy_star) / rr
@@ -931,45 +984,29 @@ def disk_pdf(
avg_maps[cur_map] = np.reshape(avg_flat, rr.shape)
# Select zone of interest
avg_maps[cur_map][np.logical_not(mask_map)] = np.nan
# avg_maps[cur_map][np.logical_not(mask_map)] = np.nan
# Compute fluctuation
fluct_maps[cur_map] = map_arr / avg_maps[cur_map]
if not interactive:
plot_fluctuations_map(path, num, maps, fluct_maps, avg_maps, im_extent, mask_map, put_title, title,
nb_bin_hist, tag, prop_disk)
# Save on disk
f = open(name_prop,'w')
pickle.dump(prop_disk, f)
f.close()
return (xx, yy, fluct_maps)
def plot_fluctuations_map(path, num, maps, fluct_maps, avg_maps, im_extent, mask_map, put_title, title,
nb_bin_hist, tag, prop_disk, interactive=False):
mask_flat = mask_map.flatten()
# Sigma-PDF
dcoldens = np.log10(fluct_maps['coldens']).flatten()
nb_cells = np.sum(mask_flat)
P.grid()
P.yscale('log')
P.ylim([0.5 / nb_cells, 1.])
P.xlabel(r'$\log(\Sigma / \bar{\Sigma})$')
P.ylabel(r'$\mathcal{P}_\Sigma$')
if put_title:
P.title(title)
values, edges, _ = P.hist(
dcoldens[mask_flat],
nb_bin_hist,
range=(-1, 3),
weights=np.ones(nb_cells) / nb_cells,
)
centers = 0.5 * (edges[1:] + edges[:-1])
# Variance
var = np.var(dcoldens[mask_flat])
# Compute the slope of the right part of the histogramm
mask_fit = (centers > 0.) & (centers < 1.25) & (values > 0)
if (np.sum(mask_fit > 0)):
(a, b, rho, _, stderr) = linregress(centers[mask_fit], np.log10(values[mask_fit]))
P.plot(centers, 10**(a*centers + b), '--', linewidth=2)
print("a=%e, b=%e, rho=%e, var=%e"% (a, b, rho, var))
try :
beta = int(tag.split('_')[1][4:])
except ValueError :
beta = 0
fit = {'beta': beta,'slope': a, 'origin': b, 'correlation': rho, 'stderr':stderr, 'var':var}
prop_disk['fit'] = fit
fit = sigma_pdf(fluct_maps, mask_flat, put_title, title, nb_bin_hist, tag)
if interactive:
P.figure()
else:
@@ -999,13 +1036,10 @@ def disk_pdf(
P.savefig(path + '/drho_hist_' + tag + '_' + str(num).zfill(5) + out_ext)
P.close()
# Derived quantities
dcoldens = np.log10(fluct_maps['coldens']).flatten()
dcs = fluct_maps['cs'].flatten()
dv = fluct_maps['v'].flatten()
dvaz_kepl = abs(maps['vaz'] - v_kepl) / v_kepl
fluct_maps['vaz_kepl'] = dvaz_kepl
dmach = abs(maps['v'] - avg_maps['v']) / maps['cs']
dmach[dmach > 10.] = 10.
fluct_maps['mach'] = dmach
@@ -1017,31 +1051,10 @@ def disk_pdf(
prop_disk['dmach_mean'] = dmach_mean
print("dmach_mean = {}".format(dmach_mean))
# Fluctuations plots
# dcs = f(drho)
P.hist2d(
np.log10(drho[mask_flat]),
np.log10(dcs[mask_flat]),
(1000, 1000),
norm=mpl.colors.LogNorm(),
)
P.xlabel(r"$\log(\rho / \bar{\rho})$")
P.ylabel(r"$\log(c_s / \bar{c_s})$")
P.ylim([-0.6, 0.6])
P.xlim([-1, 1.])
(a, b, rho, _, stderr) = linregress(np.log10(drho[mask_flat]), np.log10(dcs[mask_flat]))
P.plot(np.log10(drho[mask_flat]), a*np.log10(drho[mask_flat]) + b, '--', linewidth=2)
print("cs/rho a=%e, b=%e, rho=%e"% (a, b, rho))
try :
beta = int(tag.split('_')[1][4:])
except ValueError :
beta = 0
fit = {'beta': beta,'slope': a, 'origin': b, 'correlation': rho, 'stderr':stderr}
prop_disk['fit_cs'] = fit
prop_disk['fit_cs'] = plot_dcsdrho(fluct_maps, mask_flat, put_title, title, nb_bin_hist, tag)
P.colorbar()
if interactive:
@@ -1096,15 +1109,6 @@ def disk_pdf(
vmin=-2.,
vmax=2.)
label = r'$log(\rho/\bar{\rho})$'
elif cur_map == 'vaz_kepl':
im = P.imshow(fluct_map,
extent=im_extent,
origin='lower',
cmap='RdBu_r',
norm=mpl.colors.LogNorm(),
vmax=1.,
vmin=0.01)
label = r'$|v_\varphi - v_{kepl}|/v_{kepl}$'
elif cur_map == 'vaz':
im = P.imshow(fluct_map,
extent=im_extent,
@@ -1135,12 +1139,6 @@ def disk_pdf(
P.savefig(name_im)
P.close()
# Save on disk
f = open(name_prop,'w')
pickle.dump(prop_disk, f)
f.close()
@@ -1541,3 +1539,142 @@ def clump_study(path, num, path_out, tag, force=False, rho_thres=1e3, lvl_thres=
# P.imshow(np.log10(m['coldens_z']), extent=m['im_extent'], cmap='plasma')
# P.savefig(path_out + '/clumps_size_' + tag + '_' + str(num).zfill(5) + out_ext)
class interactive_plots:
def onbuttonrelease(self, event):
"""Deal with click events"""
button = ['left','middle','right']
toolbar = P.get_current_fig_manager().toolbar
if toolbar.mode=='zoom rect' and event.inaxes == self.ax_col:
print("zooming ")
xlim = self.ax_col.get_xlim()
ylim = self.ax_col.get_ylim()
self.reset_mask()
elif self.add_mask and event.inaxes == self.ax_col:
self.plot_side()
P.draw()
def onbuttonpress(self, event):
"""Deal with click events"""
button = ['left','middle','right']
toolbar = P.get_current_fig_manager().toolbar
if toolbar.mode!='':
print("You clicked on something, but toolbar is in mode {:s}.".format(toolbar.mode))
print(self.add_mask)
if self.add_mask and toolbar.mode=='' and event.inaxes == self.ax_col:
ix, iy = event.xdata, event.ydata
print("Add patch {}, {}".format(ix, iy))
xlim = self.ax_col.get_xlim()
ylim = self.ax_col.get_ylim()
radius = 0.05 * min(abs(xlim[1] - xlim[0]), abs(ylim[1] - ylim[0]))
circle = mpatches.Circle([ix, iy], radius, color='black', alpha=0.1, ec="none")
self.circles.append(circle)
self.ax_col.add_artist(circle)
self.ax_col.draw_artist(circle)
self.patch_mask = self.patch_mask | ((self.xx - ix)**2 + (self.yy -iy)**2 < radius**2)
#self.plot_side()
def onkeypress(self, event):
"""whenever a key is pressed"""
if not event.inaxes:
return
if event.key == 't':
self.add_mask = not self.add_mask
print("Add mode is {}".format(self.add_mask))
elif event.key == 'r':
self.reset_mask()
def plot_side(self):
if (self.add_mask):
mask = (self.patch_mask & self.mask).flatten()
else:
mask = self.mask.flatten()
self.ax_gamma.clear()
P.sca(self.ax_gamma)
plot_dcsdrho(self.fluct_maps, mask, tag=self.tag)
self.ax_pdf.clear()
P.sca(self.ax_pdf)
sigma_pdf(self.fluct_maps, mask, tag=self.tag, nb_bin_hist=self.args.pdf_nb_bin)
def reset_mask(self):
xlim = self.ax_col.get_xlim()
ylim = self.ax_col.get_ylim()
self.mask = (self.xx >= xlim[0]) & (self.xx <= xlim[1]) & (self.yy >= ylim[0]) & (self.yy <= ylim[1])
self.patch_mask = np.full(self.mask.shape, False)
for circle in self.circles:
circle.remove()
self.circles = []
self.plot_side()
P.draw()
def __init__(self, args, path, num,
maps_disk=None,
tag='',
set_lim=True) :
"""
Interactive plotting
Parameters
----------
num output number
path path of the pipeline output
"""
self.args = args
self.add_mask = False
self.circles = []
self.tag = tag
path_out = path
# Load maps file
print("load maps file")
name_maps = path + '/maps_disk' + '_' + tag + '_' + format(num,'05') + '.save'
if maps_disk is None:
if (len(glob.glob(name_maps)) == 0):
raise IOError('no pickle file for disk maps {}. Run make_image_disk() first'.format(name_maps))
f = open(name_maps,'r')
maps_disk = pickle.load(f)
f.close()
print("maps file loaded")
im_extent = maps_disk['im_extent']
fig = P.figure();
self.ax_col = P.subplot(1, 2, 1)
coldens = maps_disk['coldens_z']
im = self.ax_col.imshow(coldens,
extent=im_extent,
origin='lower',
norm=mpl.colors.LogNorm())
if set_lim:
im.set_clim(0.01, 100)
self.ax_col.set_xlabel(r'$x$')
self.ax_col.set_ylabel(r'$y$')
self.xx, self.yy, self.fluct_maps = disk_pdf(path, num, maps_disk, tag=self.tag, force=True, put_title=False, interactive=True)
coord_flat = zip(self.xx.flatten(), self.yy.flatten())
self.ax_gamma = P.subplot(2, 2, 2)
self.ax_pdf = P.subplot(2,2,4)
xlim = self.ax_col.get_xlim()
ylim = self.ax_col.get_ylim()
self.mask = (self.xx >= xlim[0]) & (self.xx <= xlim[1]) & (self.yy >= ylim[0]) & (self.yy <= ylim[1])
self.patch_mask = np.full(self.mask.shape, False)
self.plot_side()
fig.canvas.mpl_connect('button_release_event', self.onbuttonrelease)
fig.canvas.mpl_connect('button_press_event', self.onbuttonpress)
fig.canvas.mpl_connect('key_press_event', self.onkeypress)
P.tight_layout()
P.show()
pipeline_disk.py
+40 -25
View File
@@ -109,26 +109,23 @@ parser.add_argument("--print_outputs",
help="print names of outputs",
action='store_true')
parser.add_argument(
"--fft", help="use quick and dirty fft rendering", action="store_true"
)
parser.add_argument(
"--images",
nargs="*",
default=["coldens", "rho", "speed", "Q", "T"],
choices=["coldens", "rho", "speed", "Q", "T", "levels", "cpu"],
)
parser.add_argument(
"--axes", nargs="*", default=["x", "y", "z"], choices=["x", "y", "z"]
)
parser.add_argument("--zoom", help="zoom", type=float, default=2.0)
parser.add_argument(
"-ms",
"--mapsize",
parser.add_argument("--fft",
help="use quick and dirty fft rendering",
action='store_true')
parser.add_argument("--images", nargs='*',
default=['coldens', 'rho', 'speed', 'Q', 'T'],
choices=['coldens', 'rho', 'speed', 'Q', 'T', 'levels', 'cpu', 'jeans', 'jeans_ratio'])
parser.add_argument("--axes", nargs='*',
default=['x', 'y', 'z'],
choices=['x', 'y', 'z'])
parser.add_argument("--zoom",
help="zoom",
type=float,
default=2.)
parser.add_argument("-ms", "--mapsize",
help="size of the maps created in he map mode (in pixel)",
type=int,
default=1024,
)
default=1024)
parser.add_argument("--nb_bin",
@@ -221,8 +218,23 @@ me.P = dp.P
# List of id that were successfully computed
run_succeded = {}
# Care for dependencies
images = args.images
if 'jeans_ratio' in images and not 'jeans' in images :
images = ['jeans'] + images
if 'jeans_ratio' in images and not 'levels' in images :
images.append('levels')
if 'jeans' in images and not 'T' in images :
images.append('T')
if ('T' in images or 'jeans' in images) and not 'rho' in images :
images.append('rho')
if 'Q' in images and not 'coldens' in images :
images.append('coldens')
# Go through all runs
for run in runs:
path_suffix = project + "/" + run
path_suffix = project + '/' + run
path_in = storage_in + path_suffix
path_out = storage_out + path_suffix
@@ -234,8 +246,8 @@ for run in runs:
if not os.path.exists(path_out):
os.makedirs(path_out)
try:
copy(path_in + "/disk.nml", path_out)
copy(path_in + "/output_00001/compilation.txt", path_out)
copy(path_in + '/disk.nml', path_out)
copy(path_in + '/output_00001/compilation.txt', path_out)
except:
pass
@@ -271,7 +283,7 @@ for run in runs:
map_size=args.mapsize,
force=args.force_redo,
axes_los=args.axes,
images=args.images,
images=images,
pos_star=np.array([args.x, args.y, args.z]),
fft=args.fft)
print("[{}, {}] maps computed".format(run, num))
@@ -280,7 +292,7 @@ for run in runs:
maps_disk = dp.plot_maps(path_out, num,
maps_disk=maps_disk,
axes_los=args.axes,
images=args.images,
images=images,
tag=tag_run,
force=args.force_redo,
interactive=args.interactive,
@@ -322,12 +334,15 @@ for run in runs:
print("[{}, {}] computing clumps".format(run, num))
dp.clump_study(path_in, num, path_out, tag_run)
print("[{}, {}] clumps computed".format(run, num))
if args.interactive:
print("[{}, {}] Interactive session".format(run, num))
maps_disk = dp.interactive_plots(args, path_out, num, tag=tag_run)
# If we are here, success !
success = True
run_succeded[run].append(num)
except (ValueError, IOError, KeyError) as e:
print(e)
if args.watch and failures < args.allowed_failures:
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, num, args.waiting_time, args.allowed_failures - failures))
time.sleep(args.waiting_time)
@@ -372,7 +387,7 @@ if args.compare:
pdf=args.pdf or args.cpdf)
except (KeyError, IOError) as e:
print(e)
if args.skip:
if (args.skip):
pass
else:
raise