def _read_particle_header(self):
if not self.ds.parameters["particles.write_in_plotfile"]:
self.pgrid_info = np.zeros((self.num_grids, 3), dtype='int64')
return
for fn in ['particle_position_%s' % ax for ax in 'xyz'] + \
['particle_mass'] + \
['particle_velocity_%s' % ax for ax in 'xyz']:
self.field_list.append(("io", fn))
header = open(os.path.join(self.ds.output_dir, "DM", "Header"))
version = header.readline()
ndim = header.readline()
nfields = header.readline()
ntotalpart = int(header.readline())
dummy = header.readline() # nextid
maxlevel = int(header.readline()) # max level
# Skip over how many grids on each level; this is degenerate
for i in range(maxlevel + 1): dummy = header.readline()
grid_info = np.fromiter((int(i) for line in header.readlines()
for i in line.split()),
dtype='int64',
count=3*self.num_grids).reshape((self.num_grids, 3))
# we need grid_info in `populate_grid_objects`, so save it to self
for g, pg in izip(self.grids, grid_info):
g.particle_filename = os.path.join(self.ds.output_dir, "DM",
"Level_%s" % (g.Level),
"DATA_%04i" % pg[0])
g.NumberOfParticles = pg[1]
g._particle_offset = pg[2]
self.grid_particle_count[:, 0] = grid_info[:, 1]
def _read_particle_header(self):
if not self.ds.parameters["particles"]:
self.pgrid_info = np.zeros((self.num_grids, 3), dtype='int64')
return
for fn in ['particle_position_%s' % ax for ax in 'xyz'] + \
['particle_mass'] + \
['particle_velocity_%s' % ax for ax in 'xyz']:
self.field_list.append(("io", fn))
header = open(os.path.join(self.ds.output_dir, "DM", "Header"))
version = header.readline() # NOQA
ndim = header.readline() # NOQA
nfields = header.readline() # NOQA
ntotalpart = int(header.readline()) # NOQA
nextid = header.readline() # NOQA
maxlevel = int(header.readline()) # NOQA
# Skip over how many grids on each level; this is degenerate
for i in range(maxlevel + 1):
header.readline()
grid_info = np.fromiter(
(int(i) for line in header.readlines() for i in line.split()),
dtype='int64',
count=3 * self.num_grids).reshape((self.num_grids, 3))
# we need grid_info in `populate_grid_objects`, so save it to self
for g, pg in izip(self.grids, grid_info):
g.particle_filename = os.path.join(self.ds.output_dir, "DM",
"Level_%s" % (g.Level),
"DATA_%04i" % pg[0])
g.NumberOfParticles = pg[1]
g._particle_offset = pg[2]
self.grid_particle_count[:, 0] = grid_info[:, 1]
def _populate_grid_objects(self):
for g,f in izip(self.grids, self.filenames):
g._prepare_grid()
g._setup_dx()
g.set_filename(f[0])
del self.filenames # No longer needed.
self.max_level = self.grid_levels.max()
def _populate_grid_objects(self):
reconstruct = ytcfg.getboolean("yt", "reconstruct_index")
for g, f in izip(self.grids, self.filenames):
g._prepare_grid()
g._setup_dx()
g.set_filename(f[0])
if reconstruct:
if g.Parent is not None: g._guess_properties_from_parent()
del self.filenames # No longer needed.
self.max_level = self.grid_levels.max()
def _populate_grid_objects(self):
reconstruct = ytcfg.getboolean("yt","reconstruct_index")
for g,f in izip(self.grids, self.filenames):
g._prepare_grid()
g._setup_dx()
g.set_filename(f[0])
if reconstruct:
if g.Parent is not None: g._guess_properties_from_parent()
del self.filenames # No longer needed.
self.max_level = self.grid_levels.max()
def save(self, name=None, suffix=None, mpl_kwargs=None):
r"""
Saves a 1d profile plot.
Parameters
----------
name : str
The output file keyword.
suffix : string
Specify the image type by its suffix. If not specified, the output
type will be inferred from the filename. Defaults to PNG.
mpl_kwargs : dict
A dict of keyword arguments to be passed to matplotlib.
"""
if not self._plot_valid:
self._setup_plots()
unique = set(self.plots.values())
if len(unique) < len(self.plots):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.plots)
if not suffix:
suffix = "png"
suffix = ".%s" % suffix
fullname = False
if name is None:
if len(self.profiles) == 1:
prefix = self.profiles[0].ds
else:
prefix = "Multi-data"
name = "%s%s" % (prefix, suffix)
else:
sfx = get_image_suffix(name)
if sfx != '':
suffix = sfx
prefix = name[:name.rfind(suffix)]
fullname = True
else:
prefix = name
xfn = self.profiles[0].x_field
if isinstance(xfn, tuple):
xfn = xfn[1]
fns = []
for uid, plot in iters:
if isinstance(uid, tuple):
uid = uid[1]
if fullname:
fns.append("%s%s" % (prefix, suffix))
else:
fns.append("%s_1d-Profile_%s_%s%s" %
(prefix, xfn, uid, suffix))
mylog.info("Saving %s", fns[-1])
with matplotlib_style_context():
plot.save(fns[-1], mpl_kwargs=mpl_kwargs)
return fns
def save(self, name=None, suffix=None):
r"""
Saves a 1d profile plot.
Parameters
----------
name : str
The output file keyword.
suffix : string
Specify the image type by its suffix. If not specified, the output
type will be inferred from the filename. Defaults to PNG.
"""
if not self._plot_valid:
self._setup_plots()
unique = set(self.figures.values())
if len(unique) < len(self.figures):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.figures)
if not suffix:
suffix = "png"
suffix = ".%s" % suffix
if name is None:
if len(self.profiles) == 1:
prefix = self.profiles[0].ds
else:
prefix = "Multi-data"
name = "%s%s" % (prefix, suffix)
else:
sfx = get_image_suffix(name)
if sfx != '':
suffix = sfx
prefix = name[:name.rfind(suffix)]
else:
prefix = name
xfn = self.profiles[0].x_field
if isinstance(xfn, tuple):
xfn = xfn[1]
canvas_cls = get_canvas(name)
fns = []
for uid, fig in iters:
if isinstance(uid, tuple):
uid = uid[1]
canvas = canvas_cls(fig)
fns.append("%s_1d-Profile_%s_%s%s" % (prefix, xfn, uid, suffix))
mylog.info("Saving %s", fns[-1])
canvas.print_figure(fns[-1])
return fns
def save(self, name=None, suffix=None):
r"""
Saves a 1d profile plot.
Parameters
----------
name : str
The output file keyword.
suffix : string
Specify the image type by its suffix. If not specified, the output
type will be inferred from the filename. Defaults to PNG.
"""
if not self._plot_valid:
self._setup_plots()
unique = set(self.figures.values())
if len(unique) < len(self.figures):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.figures)
if not suffix:
suffix = "png"
suffix = ".%s" % suffix
if name is None:
if len(self.profiles) == 1:
prefix = self.profiles[0].ds
else:
prefix = "Multi-data"
name = "%s%s" % (prefix, suffix)
else:
sfx = get_image_suffix(name)
if sfx != '':
suffix = sfx
prefix = name[:name.rfind(suffix)]
else:
prefix = name
xfn = self.profiles[0].x_field
if isinstance(xfn, tuple):
xfn = xfn[1]
canvas_cls = get_canvas(name)
fns = []
for uid, fig in iters:
if isinstance(uid, tuple):
uid = uid[1]
canvas = canvas_cls(fig)
fns.append("%s_1d-Profile_%s_%s%s" % (prefix, xfn, uid, suffix))
mylog.info("Saving %s", fns[-1])
canvas.print_figure(fns[-1])
return fns
def _repr_html_(self):
"""Return an html representation of the plot object. Will display as a
png for each WindowPlotMPL instance in self.plots"""
ret = ''
unique = set(self.plots.values())
if len(unique) < len(self.plots):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.plots)
for uid, plot in iters:
with matplotlib_style_context():
img = plot._repr_png_()
img = base64.b64encode(img).decode()
ret += r'<img style="max-width:100%%;max-height:100%%;" ' \
r'src="data:image/png;base64,{0}"><br>'.format(img)
return ret
def _repr_html_(self):
"""Return an html representation of the plot object. Will display as a
png for each WindowPlotMPL instance in self.plots"""
ret = ''
unique = set(self.figures.values())
if len(unique) < len(self.figures):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.figures)
for uid, fig in iters:
canvas = mpl.FigureCanvasAgg(fig)
f = BytesIO()
canvas.print_figure(f)
f.seek(0)
img = base64.b64encode(f.read()).decode()
ret += r'<img style="max-width:100%%;max-height:100%%;" ' \
r'src="data:image/png;base64,{0}"><br>'.format(img)
return ret
def _repr_html_(self):
"""Return an html representation of the plot object. Will display as a
png for each WindowPlotMPL instance in self.plots"""
ret = ''
unique = set(self.figures.values())
if len(unique) < len(self.figures):
iters = izip(range(len(unique)), sorted(unique))
else:
iters = iteritems(self.figures)
for uid, fig in iters:
canvas = mpl.FigureCanvasAgg(fig)
f = BytesIO()
canvas.print_figure(f)
f.seek(0)
img = base64.b64encode(f.read()).decode()
ret += r'<img style="max-width:100%%;max-height:100%%;" ' \
r'src="data:image/png;base64,{0}"><br>'.format(img)
return ret
def compare_arbors(a1, a2, groups=None, fields=None):
"""
Compare all fields for all trees in two arbors.
"""
if groups is None:
groups = ["tree", "prog"]
if fields is None:
fields = a1.field_list
for field in fields:
assert (a1[field] == a2[field]).all()
i = 0
ntot = len(a1)
pbar = get_pbar("Comparing trees", ntot)
for t1, t2 in izip(a1, a2):
compare_trees(t1, t2, groups=groups, fields=fields)
i += 1
pbar.update(i)
pbar.finish()
def calculate_spectrum(self, data_source=None, star_mass=None,
star_creation_time=None,
star_metallicity_fraction=None,
star_metallicity_constant=None,
min_age=YTQuantity(0.0, 'yr')):
r"""For the set of stars, calculate the collective spectrum.
Attached to the output are several useful objects:
Attributes
----------
final_spec: array
The collective spectrum in units of flux binned in wavelength.
wavelength: array
The wavelength for the spectrum bins, in Angstroms.
total_mass: float
Total mass of all the stars.
avg_mass: float
Average mass of all the stars.
avg_metal: float
Average metallicity of all the stars.
Parameters
----------
data_source : AMRRegion object, optional
The region from which stars are extracted for analysis. If this is
not specified, the next three parameters must be supplied.
star_mass : Array or list of floats
An array of star masses in Msun units.
star_creation_time : Array or list of floats
An array of star creation times in code units.
star_metallicity_fraction : Array or list of floats
An array of star metallicity fractions, in code
units (which is not Z/Zsun, rather just Z).
star_metallicity_constant : Float
If desired, override the star
metallicity fraction of all the stars to the given value.
min_age : Float
Removes young stars younger than this number (in years)
from the spectrum. Default: 0 (all stars).
Examples
--------
>>> import yt
>>> from yt.analysis_modules.star_analysis.api import SpectrumBuilder
>>> ds = yt.load("Enzo_64/RD0006/RedshiftOutput0006")
>>> spec = SpectrumBuilder(ds, "bc", model="salpeter")
>>> sp = ds.sphere([0.5, 0.5, 0.5], 0.1)
>>> spec.calculate_spectrum(data_source=sp, min_age=1.e6)
"""
# Initialize values
self.final_spec = np.zeros(self.wavelength.size, dtype='float64')
self._data_source = data_source
if isinstance(star_mass, YTArray):
assert star_mass.units.same_dimensions_as(g.units)
elif star_mass is not None:
star_mass = YTArray(star_mass, 'Msun')
self.star_mass = star_mass
if isinstance(star_creation_time, YTArray):
assert star_creation_time.units.same_dimensions_as(s.units)
elif star_creation_time is not None:
star_creation_time = self._ds.arr(star_creation_time,
'code_time')
self.star_creation_time = star_creation_time
if isinstance(star_metallicity_fraction, YTArray):
assert \
star_metallicity_fraction.units.same_dimensions_as(Zsun.units)
elif star_metallicity_fraction is not None:
star_metallicity_fraction = self._ds.arr(
star_metallicity_fraction, 'code_metallicity'
)
self.star_metallicity_fraction = star_metallicity_fraction
if isinstance(min_age, YTQuantity):
assert min_age.units.same_dimensions_as(s.units)
elif min_age is not None:
min_age = YTQuantity(min_age, 'yr')
self.min_age = min_age
# Check to make sure we have the right set of data.
if data_source is None:
if self.star_mass is None or self.star_creation_time is None or \
(star_metallicity_fraction is None and
star_metallicity_constant is None):
mylog.error(
"""
If data_source is not provided, all of these paramters
need to be set:
star_mass (array, Msun),
star_creation_time (array, code units),
And one of:
star_metallicity_fraction (array, code units).
--OR--
star_metallicity_constant (float, code units).
""")
return None
if star_metallicity_fraction is not None:
self.star_metal = star_metallicity_fraction
else:
self.star_metal = \
self._ds.arr(np.ones_like(self.star_mass) *
star_metallicity_constant, 'Zsun')
else:
# Get the data we need.
if self.filter_provided:
ct = self._filter['creation_time']
# mass_stars = self._data_source[self._filter, "particle_mass"]
if star_metallicity_constant is None:
self.star_metal = self._data_source[
self._filter, "metallicity_fraction"].in_units('Zsun')
else:
self.star_metal = \
self._ds.arr(np.ones_like(
self._data_source[self._filter,
"metallicity_fraction"]) *
star_metallicity_constant, "Zsun")
else:
ct = self._data_source["creation_time"]
if ct is None:
errmsg = 'data source must have particle_age!'
mylog.error(errmsg)
raise RuntimeError(errmsg)
mask = ct > 0
if not any(mask):
errmsg = 'all particles have age < 0'
mylog.error(errmsg)
raise RuntimeError(errmsg)
# type = self._data_source['particle_type']
self.star_creation_time = ct[mask]
self.star_mass = self._data_source[
'particle_mass'][mask].in_units('Msun')
if star_metallicity_constant is not None:
self.star_metal = self._ds.arr(
np.ones_like(self.star_mass) *
star_metallicity_constant, 'Zsun')
else:
self.star_metal = self._data_source[
"metallicity_fraction"][mask].in_units('Zsun')
# Age of star in years.
dt = (self.time_now - self.star_creation_time).in_units('yr')
dt[dt < 0.0] = 0.0
# Remove young stars
sub = dt >= self.min_age
if len(sub) == 0:
return
self.star_metal = self.star_metal[sub]
dt = dt[sub]
self.star_creation_time = self.star_creation_time[sub]
# Figure out which METALS bin the star goes into.
Mindex = np.digitize(self.star_metal.in_units('Zsun'), METALS)
# Replace the indices with strings.
Mname = MtoD[Mindex]
# Figure out which age bin this star goes into.
Aindex = np.digitize(dt, self.age)
# Ratios used for the interpolation.
ratio1 = (dt - self.age[Aindex - 1]) / \
(self.age[Aindex] - self.age[Aindex - 1])
ratio2 = (self.age[Aindex] - dt) / \
(self.age[Aindex] - self.age[Aindex - 1])
# Sort the stars by metallicity and then by age, which should reduce
# memory access time by a little bit in the loop.
indexes = np.arange(self.star_metal.size)
sort = np.asarray([indexes[i]
for i in np.lexsort([indexes, Aindex, Mname])])
Mname = Mname[sort]
Aindex = Aindex[sort]
ratio1 = ratio1[sort]
ratio2 = ratio2[sort]
self.star_mass = self.star_mass[sort]
self.star_creation_time = self.star_creation_time[sort]
self.star_metal = self.star_metal[sort]
# Interpolate the flux for each star, adding to the total by weight.
pbar = get_pbar("Calculating fluxes", len(self.star_mass))
for i, star in enumerate(izip(Mname, Aindex, ratio1, ratio2,
self.star_mass)):
# Pick the right age bin for the right flux array.
flux = self.flux[star[0]][star[1], :]
# Get the one just before the one above.
flux_1 = self.flux[star[0]][star[1] - 1, :]
# interpolate in log(flux), linear in time.
int_flux = star[3] * np.log10(flux_1) + star[2] * np.log10(flux)
# Add this flux to the total, weighted by mass.
self.final_spec += np.power(10., int_flux) * star[4]
pbar.update(i)
pbar.finish()
# Normalize.
self.total_mass = self.star_mass.sum()
self.avg_mass = self.star_mass.mean()
tot_metal = (self.star_metal * self.star_mass).sum()
if tot_metal > 0:
self.avg_metal = math.log10(
(tot_metal / self.total_mass).in_units('Zsun'))
else:
self.avg_metal = -99
def calculate_spectrum(self,
data_source=None,
star_mass=None,
star_creation_time=None,
star_metallicity_fraction=None,
star_metallicity_constant=None,
min_age=YTQuantity(0.0, 'yr')):
r"""For the set of stars, calculate the collective spectrum.
Attached to the output are several useful objects:
Attributes
----------
final_spec: array
The collective spectrum in units of flux binned in wavelength.
wavelength: array
The wavelength for the spectrum bins, in Angstroms.
total_mass: float
Total mass of all the stars.
avg_mass: float
Average mass of all the stars.
avg_metal: float
Average metallicity of all the stars.
Parameters
----------
data_source : AMRRegion object, optional
The region from which stars are extracted for analysis. If this is
not specified, the next three parameters must be supplied.
star_mass : Array or list of floats
An array of star masses in Msun units.
star_creation_time : Array or list of floats
An array of star creation times in code units.
star_metallicity_fraction : Array or list of floats
An array of star metallicity fractions, in code
units (which is not Z/Zsun, rather just Z).
star_metallicity_constant : Float
If desired, override the star
metallicity fraction of all the stars to the given value.
min_age : Float
Removes young stars younger than this number (in years)
from the spectrum. Default: 0 (all stars).
Examples
--------
>>> import yt
>>> from yt.analysis_modules.star_analysis.api import SpectrumBuilder
>>> ds = yt.load("Enzo_64/RD0006/RedshiftOutput0006")
>>> spec = SpectrumBuilder(ds, "bc", model="salpeter")
>>> sp = ds.sphere([0.5, 0.5, 0.5], 0.1)
>>> spec.calculate_spectrum(data_source=sp, min_age=1.e6)
"""
# Initialize values
self.final_spec = np.zeros(self.wavelength.size, dtype='float64')
self._data_source = data_source
if isinstance(star_mass, YTArray):
assert star_mass.units.same_dimensions_as(g.units)
elif star_mass is not None:
star_mass = YTArray(star_mass, 'Msun')
self.star_mass = star_mass
if isinstance(star_creation_time, YTArray):
assert star_creation_time.units.same_dimensions_as(s.units)
elif star_creation_time is not None:
star_creation_time = self._ds.arr(star_creation_time, 'code_time')
self.star_creation_time = star_creation_time
if isinstance(star_metallicity_fraction, YTArray):
assert \
star_metallicity_fraction.units.same_dimensions_as(Zsun.units)
elif star_metallicity_fraction is not None:
star_metallicity_fraction = self._ds.arr(star_metallicity_fraction,
'code_metallicity')
self.star_metallicity_fraction = star_metallicity_fraction
if isinstance(min_age, YTQuantity):
assert min_age.units.same_dimensions_as(s.units)
elif min_age is not None:
min_age = YTQuantity(min_age, 'yr')
self.min_age = min_age
# Check to make sure we have the right set of data.
if data_source is None:
if self.star_mass is None or self.star_creation_time is None or \
(star_metallicity_fraction is None and
star_metallicity_constant is None):
mylog.error("""
If data_source is not provided, all of these paramters
need to be set:
star_mass (array, Msun),
star_creation_time (array, code units),
And one of:
star_metallicity_fraction (array, code units).
--OR--
star_metallicity_constant (float, code units).
""")
return None
if star_metallicity_fraction is not None:
self.star_metal = star_metallicity_fraction
else:
self.star_metal = \
self._ds.arr(np.ones_like(self.star_mass) *
star_metallicity_constant, 'Zsun')
else:
# Get the data we need.
if self.filter_provided:
ct = self._filter['creation_time']
# mass_stars = self._data_source[self._filter, "particle_mass"]
if star_metallicity_constant is None:
self.star_metal = self._data_source[
self._filter, "metallicity_fraction"].in_units('Zsun')
else:
self.star_metal = \
self._ds.arr(np.ones_like(
self._data_source[self._filter,
"metallicity_fraction"]) *
star_metallicity_constant, "Zsun")
else:
ct = self._data_source["creation_time"]
if ct is None:
errmsg = 'data source must have particle_age!'
mylog.error(errmsg)
raise RuntimeError(errmsg)
mask = ct > 0
if not any(mask):
errmsg = 'all particles have age < 0'
mylog.error(errmsg)
raise RuntimeError(errmsg)
# type = self._data_source['particle_type']
self.star_creation_time = ct[mask]
self.star_mass = self._data_source['particle_mass'][
mask].in_units('Msun')
if star_metallicity_constant is not None:
self.star_metal = self._ds.arr(
np.ones_like(self.star_mass) *
star_metallicity_constant, 'Zsun')
else:
self.star_metal = self._data_source[
"metallicity_fraction"][mask].in_units('Zsun')
# Age of star in years.
dt = (self.time_now - self.star_creation_time).in_units('yr')
dt[dt < 0.0] = 0.0
# Remove young stars
sub = dt >= self.min_age
if len(sub) == 0:
return
self.star_metal = self.star_metal[sub]
dt = dt[sub]
self.star_creation_time = self.star_creation_time[sub]
# Figure out which METALS bin the star goes into.
Mindex = np.digitize(self.star_metal.in_units('Zsun'), METALS)
# Replace the indices with strings.
Mname = MtoD[Mindex]
# Figure out which age bin this star goes into.
Aindex = np.digitize(dt, self.age)
# Ratios used for the interpolation.
ratio1 = (dt - self.age[Aindex - 1]) / \
(self.age[Aindex] - self.age[Aindex - 1])
ratio2 = (self.age[Aindex] - dt) / \
(self.age[Aindex] - self.age[Aindex - 1])
# Sort the stars by metallicity and then by age, which should reduce
# memory access time by a little bit in the loop.
indexes = np.arange(self.star_metal.size)
sort = np.asarray(
[indexes[i] for i in np.lexsort([indexes, Aindex, Mname])])
Mname = Mname[sort]
Aindex = Aindex[sort]
ratio1 = ratio1[sort]
ratio2 = ratio2[sort]
self.star_mass = self.star_mass[sort]
self.star_creation_time = self.star_creation_time[sort]
self.star_metal = self.star_metal[sort]
# Interpolate the flux for each star, adding to the total by weight.
pbar = get_pbar("Calculating fluxes", len(self.star_mass))
for i, star in enumerate(
izip(Mname, Aindex, ratio1, ratio2, self.star_mass)):
# Pick the right age bin for the right flux array.
flux = self.flux[star[0]][star[1], :]
# Get the one just before the one above.
flux_1 = self.flux[star[0]][star[1] - 1, :]
# interpolate in log(flux), linear in time.
int_flux = star[3] * np.log10(flux_1) + star[2] * np.log10(flux)
# Add this flux to the total, weighted by mass.
self.final_spec += np.power(10., int_flux) * star[4]
pbar.update(i)
pbar.finish()
# Normalize.
self.total_mass = self.star_mass.sum()
self.avg_mass = self.star_mass.mean()
tot_metal = (self.star_metal * self.star_mass).sum()
if tot_metal > 0:
self.avg_metal = math.log10(
(tot_metal / self.total_mass).in_units('Zsun'))
else:
self.avg_metal = -99