def _find_los(points_dset_source, camera, nbSample):
r"""
Find the line of sight axis which is along the angular momentum of the gas inside the camera box
Parameters
----------
points_dset_source : :ref:`PointDataSource`
fields "vel", "rho" and "size" needed
camera : pymses camera box definition restriction
nbSample : int (default=2000)
not working yet : may speed up if random sampling ?
"""
filtered_points_dset_source = RegionFilter(camera.get_bounding_box(),
points_dset_source)
filtered_points_dset = filtered_points_dset_source.flatten(
) # multiprocessing data reading and filtering
d = filtered_points_dset.fields["rho"] * (
filtered_points_dset.fields["size"]**3)
v = filtered_points_dset["vel"]
JJ = np.zeros_like(v)
p = d[:, np.newaxis] * v
JJ[:] = np.cross((filtered_points_dset.points[:] - camera.center), p[:])
J = np.sum(JJ, axis=0)
result_vect = J / sum(J**2)
result_vect = result_vect / np.linalg.norm(result_vect, 2)
return result_vect
def __init__(self,
source,
camera,
ext_size=0.0,
ext_3D=True,
keep_cache_dset=False,
use_camera_lvlmax=True):
"""
Filter build to fit the camera bounding box
Parameters
----------
source : pymses data source
camera : pymses camera
position (along w axis) of the fixed point in the right eye rotation
ext_size : float (default 0.0)
extension to the camera box (in box unit between 0 and 1), used only if ext_3D==True
ext_3D : boolean (default True)
if true, use an ExtendedCamera to extend the filtered region
keep_cache_dset : boolean (default False)
flag to keep the cache_dset dictonary of the source
during the filtering process
(used for PointsDataSet cache with the amrviewer GUI)
use_camera_lvlmax : ``boolean`` (default True)
Limit the transformation of the AMR grid to particles
to AMR cells under the camera octree levelmax (so that visible cells
are only the ones that have bigger size than the camera pixel size).
Set this to False when using directly particle data from ".part"
particles files (dark matter and stars particles), so as to get
the cache_dset working without the levelmax specification
"""
self.cam = camera
self.cam_box = camera.get_map_box()
self.ext_3D = ext_3D
if ext_3D:
# Extended camera
r = N.ones((2, 3)) * ext_size
r[0, :] = -r[0, :]
ecam = ExtendedCamera(camera, r)
else:
ecam = camera
# Init Filter with extended camera bounding box region
RegionFilter.__init__(self, ecam.get_bounding_box(), source)
# Max. read level setup
if use_camera_lvlmax:
lreq = min(camera.get_required_resolution(), source.read_lmax)
self.set_read_lmax(lreq)
if keep_cache_dset:
self.keep_cache_dset = keep_cache_dset
self.cache_dset = source.cache_dset
def amr2cell(ro=None,
list_var=None,
log_sfera=False,
camera_in={},
verbose=False):
"""
log_sfera: Boolean
True for sphere
"""
assert ro != None
assert list_var != None
from pymses.utils import regions
from pymses.filters import RegionFilter, CellsToPoints
amr = ro.amr_source(list_var)
center = camera_in['center']
radius = camera_in['region_size'][0]
if (log_sfera):
regione_sp = regions.Sphere(center, radius)
else:
sinistra = np.copy(center) - radius
destra = np.copy(center) + radius
regione_sp = regions.Box((sinistra, destra))
if (verbose):
print 'Extracting cells'
if (log_sfera):
print ' getting a sphere'
print ' center:', center
print ' radius:', radius
else:
print ' getting a box'
print ' center:', center
print ' size :', radius
print ' left :', sinistra
print ' right :', destra
# cut the region
amr = RegionFilter(regione_sp, amr)
amr = CellsToPoints(amr)
celle = amr.flatten()
amr = None
return celle
def load(self, *fields):
"""Loads a list of quantitys in the self.qtyDataFrame"""
print "-> Loading fields ...",
ro = self.ramsesOutput
df = self.qtyDataFrame
# Recherche les champs de *fields qui
# ne sont pas encore charges dans le dataframe
fields_to_load = []
for field in fields:
if field.name not in df.keys():
fields_to_load.append(field)
#
if fields_to_load:
amr_fields_to_read = Q.get_amrfields_to_read(*fields_to_load)
amrSource = ro.amr_source(amr_fields_to_read,
grav_compat=True,
verbose=self._verbose)
amrSource = RegionFilter(self.sphere, amrSource)
dset = CellsToPoints(amrSource).flatten()
for field in fields_to_load:
df[field.name] = pd.Series(field.process(ro, dset))
print " Fields loaded :",
for field in fields_to_load:
print field.name,
print ""
return fields_to_load
else:
print " No field to load"
return []
def particles2cell(ro=None,
star=True,
list_var=None,
log_sfera=False,
camera_in={},
verbose=False):
"""
log_sfera: Boolean
True for sphere
"""
assert ro is not None
assert list_var is not None
from pymses.utils import regions
from pymses.filters import RegionFilter
part = ro.particle_source(list_var)
# Filter all the particles which are initially present in the simulation
from pymses.filters import PointFunctionFilter
if star:
star_filter = lambda dset: dset["epoch"] != 0.0
part = PointFunctionFilter(star_filter, part)
else:
dm_filter = lambda dset: dset["epoch"] == 0.0
part = PointFunctionFilter(dm_filter, part)
center = camera_in['center']
radius = camera_in['region_size'][0]
if (log_sfera):
regione_sp = regions.Sphere(center, radius)
else:
sinistra = np.copy(center) - radius
destra = np.copy(center) + radius
regione_sp = regions.Box((sinistra, destra))
if (verbose):
print 'Extracting cells'
if (log_sfera):
print ' getting a sphere'
print ' center:', center
print ' radius:', radius
else:
print ' getting a box'
print ' center:', center
print ' size :', radius
print ' left :', sinistra
print ' right :', destra
# cut the region
part = RegionFilter(regione_sp, part)
celle = part.flatten()
return celle, part
def _find_galaxy_axis(points_dset_source, camera, nbSample):
'''
If a galaxy disk is centered in the camera box, this function should
return a galaxy disk othogonal axis.
from seren3.utils.camera_utils import find_galaxy_axis
Parameters
----------
points_dset_source : :ref:`PointDataSource`
fields "rho" and "size" needed
camera : pymses camera, the galaxy's center has to fit the camera's center
nbSample : int
number of max massive points to use to compute the axis through cross product
'''
filtered_points_dset_source = RegionFilter(camera.get_bounding_box(),
points_dset_source)
filtered_points_dset = filtered_points_dset_source.flatten(
) # multiprocessing data reading and filtering
region_filtered_mesh_mass = filtered_points_dset.fields["rho"] * (
filtered_points_dset.fields["size"]**3)
argsort = np.argsort(region_filtered_mesh_mass)
center = camera.center
nbSample = min(nbSample, argsort.size / 2 - 1)
result_vect = np.array([0., 0., 0.])
for i in range(nbSample):
index1 = argsort[-2 * i]
index2 = argsort[-2 * i - 1]
vect1 = filtered_points_dset.points[index1] - center
vect2 = filtered_points_dset.points[index2] - center
vect = np.cross(vect1, vect2)
sign = np.dot(vect, [0., 0., 1.])
if sign < 0:
vect = -vect
result_vect = result_vect + vect * (region_filtered_mesh_mass[index1] +
region_filtered_mesh_mass[index2]) * \
np.linalg.norm((vect1-vect2),2)
result_vect = result_vect / np.linalg.norm(result_vect, 2)
return result_vect
def test_sph_profile():
# Halo parameters
halo_center = [0.567811, 0.586055, 0.559156] # in box units
halo_radius = 0.00075 # in box units
# RamsesOutput
ro = RamsesOutput("/data/Aquarius/output", 193)
# Prepare to read the mass/epoch fields only
source = ro.particle_source(["mass", "epoch"])
# Sphere region
sph = Sphere(halo_center, halo_radius)
# Filtering particles
point_dset = RegionFilter(sph, source)
dm_filter = lambda dset: dset["epoch"] == 0.0
dm_parts = PointFunctionFilter(dm_filter, point_dset)
# Profile computation
m_weight_func = lambda dset: dset["mass"]
r_bins = numpy.linspace(0.0, halo_radius, 200)
# Mass profile
# This triggers the actual reading of the particle data files from disk.
mass_profile = bin_spherical(dm_parts,
halo_center,
m_weight_func,
r_bins,
divide_by_counts=False)
# Density profile
sph_vol = 4.0 / 3.0 * numpy.pi * r_bins**3
shell_vol = numpy.diff(sph_vol)
rho_profile = mass_profile / shell_vol
# Plot
# Geometrical midpoint of the bins
length = ro.info["unit_length"].express(C.kpc)
bins_centers = (r_bins[1:] + r_bins[:-1]) / 2. * length
dens = ro.info["unit_density"].express(C.Msun / C.kpc**3)
#h5f = tables.openFile("./long_tests/sph_profile.h5", mode='w')
#h5f.createArray("/", "sph_profile", rho_profile)
#h5f.close()
h5f = tables.openFile("./long_tests/sph_profile.h5", mode='r')
rho_profileB = h5f.getNode("/sph_profile").read()
h5f.close()
#print rho_profile
assert (rho_profile - rho_profileB).all() < 10e-6
def __init__(self,
camera,
esize,
ramses_amr_source,
radius=None,
ngrid_max=2000000,
include_split_cells=False): #{{{
t0 = time()
self.ngrid_max = int(ngrid_max)
# Extended camera
r = numpy.ones((2, 3)) * esize
r[0, :] = -r[0, :]
from pymses.analysis.visualization.camera import ExtendedCamera
ecam = ExtendedCamera(camera, r)
bb = ecam.get_bounding_box()
if radius is None:
# Init Filter with extended camera bounding box region
reg = bb
else:
# Defined sphere region, checks the region includes the camera area
zmax = numpy.max([camera.far_cut_depth, camera.distance])
xmax = camera.region_size[0] / 2.
ymax = camera.region_size[1] / 2.
assert (radius**2 >= (xmax**2 + ymax**2 + zmax**2))
reg = Sphere(camera.center, radius + esize)
RegionFilter.__init__(self, reg, ramses_amr_source)
# Max. read level setup
lreq = camera.get_required_resolution()
self.set_read_lmax(lreq)
# Init. self.dset to None
self.dset = None
self.build_dset(ecam, radius, include_split_cells=include_split_cells)
print("CameraOctreeDatasource loaded up to level", lreq,\
"with ngrids =", self.dset.amr_struct["ngrids"],\
"(loading time = %.2fs"%(time() - t0), ")")
def _find_center_of_mass(points_dset_source, camera, nbSample):
r"""
Find the center of mass in the camera box
Parameters
----------
points_dset_source : :ref:`PointDataSource`
fields "rho" and "size" needed
camera : pymses camera box definition restriction
nbSample : int (default=2000)
not working yet : may speed up if random sampling ?
"""
filtered_points_dset_source = RegionFilter(camera.get_bounding_box(),
points_dset_source)
filtered_points_dset = filtered_points_dset_source.flatten(
) # multiprocessing data reading and filtering
d = filtered_points_dset.fields["rho"] * (
filtered_points_dset.fields["size"]**3)
mass = np.sum(d)
cm = np.sum(d[:, np.newaxis] * filtered_points_dset.points, axis=0) / mass
return cm
def filt_cube(self, cube, dset_type, fields):
'''
Return flattened dset of points contained by this cube
'''
if dset_type == Type.AMR:
source = self.amr_source(fields)
elif dset_type == Type.PART:
source = self.particle_source(fields)
else:
raise Exception("No such type: ", dset_type)
from pymses.filters import CellsToPoints
from pymses.filters import RegionFilter
filt_source = RegionFilter(cube, source)
return CellsToPoints(filt_source).flatten()
def sphere(self, halo, source):
'''
Return a pymses sphere centred on this halo
'''
pos = halo['pos'].in_units('code_length').value
r = halo['Rvir'].in_units('code_length').value
region = Sphere(pos, r)
filt_region = RegionFilter(region, source)
if filt_region is None:
raise Exception("Unable to create sphere: pos - ", pos + " r - ",
r)
#return filt_region
return Region(filt_region)
def __getitem__(self, fields):
"""
Data access via pymses for family specific tracked/derived fields
"""
from serensource import SerenSource
if not hasattr(fields, "__iter__"):
fields = [fields]
source, required_fields = self.get_source(fields, return_required_fields=True)
if self.family in ['amr', 'rt']:
from pymses.filters import CellsToPoints
source = CellsToPoints(source)
cpu_list = None
if hasattr(self.base, "region"):
from pymses.filters import RegionFilter
source = RegionFilter(self.base.region, source)
return SerenSource(self, source)
def amr2cube(source, var, xmin, xmax, cubelevel, out=None):
r"""
amr2cube tool.
"""
# allow amr2cube to work with a vector
op = var
if isinstance(var, str):
op = lambda dset: dset[var]
# TODO : add cache_dset reuse possibility
# Region CPU-filtering
b = Box([xmin, xmax])
rsource = RegionFilter(b, source)
rsource.set_read_lmax(cubelevel)
try:
from multiprocessing import Process, Queue, cpu_count
if cpu_count() == 1:
raise (Exception
) # don't use multiprocessing if there is only one cpu
dsets = []
from pymses.utils import misc
NUMBER_OF_PROCESSES = min(len(rsource._data_list), cpu_count(),
misc.NUMBER_OF_PROCESSES_LIMIT)
# define long computing process method to do in parallel
def read_dsets_to_cartesian(cpu_task_queue, dsets_queue, rsource):
"""Utility method for amr2cube multiprocessing method.
It reads the given list of data file and concatenate resulting dsets
Parameters
----------
cpu_task_queue : ``list`` of ``int``
queue of data file number corresponding to data files that have to be read by a process
dsets_queue : multiprocessing queue
to send the result to parent process
"""
len_dsets = 0
out = None
for icpu in iter(cpu_task_queue.get, 'STOP'):
dset = rsource.get_domain_dset(icpu)
active_mask = dset.get_active_mask()
g_levels = dset.get_grid_levels()
# We do the processing only if needed, i.e. only if the
# amr level cubelevel of active cells in the dset is >0
if len(g_levels[active_mask] == cubelevel) > 0:
if out is None:
out = dset.to_cartesian(var, xmin, xmax, cubelevel)
else:
dset.to_cartesian(var, xmin, xmax, cubelevel, dest=out)
len_dsets += 1
if len_dsets == 0:
dsets_queue.put("NoDset")
else:
dsets_queue.put(out)
# Create queues
cpu_task_queue = Queue()
dsets_queue = Queue()
# Submit tasks
for task in rsource._data_list:
cpu_task_queue.put(task)
# Start worker processes
for i in range(NUMBER_OF_PROCESSES):
Process(target=read_dsets_to_cartesian,
args=(cpu_task_queue, dsets_queue, rsource)).start()
# Tell child processes to stop when they have finished
for i in range(NUMBER_OF_PROCESSES):
cpu_task_queue.put('STOP')
# Get results
for i in range(NUMBER_OF_PROCESSES):
outP = dsets_queue.get()
if outP != "NoDset":
if out is None:
out = outP
else:
out += outP
except Exception:
print('WARNING: multiprocessing unavailable')
for dset in rsource.iter_dsets():
active_mask = dset.get_active_mask()
g_levels = dset.get_grid_levels()
# We do the processing only if needed, i.e. only if the
# amr level cubelevel of active cells in the dset is >0
if len(g_levels[active_mask] == cubelevel) > 0:
if out is None:
out = dset.to_cartesian(var, xmin, xmax, cubelevel)
else:
dset.to_cartesian(var, xmin, xmax, cubelevel, dest=out)
return out
def get_domain_dset(self, idomain): #{{{
if self.dset is None:
return RegionFilter.get_domain_dset(self, idomain)
else:
return self.dset
def mstar_halomass_tree(self, tree, ds):
snapshot = self._snapshot
ro = snapshot.raw_snapshot()
parts = ro.particle_source(["mass", "epoch"])
amr = ro.amr_source(['rho'])
#Figure out the smallest possible cell size in code units
boxlen = ro.info['boxlen']
lmax = ro.info['levelmax']
min_dx = boxlen/float(2**(lmax))
offset = tree.get_offset()
snap_num = self._snapshot.output_number() - offset
halos = tree.sub_catalogue('snap_num', snap_num)
#idx = np.where(tree._tree[:]['snap_num'] == self._snapshot.output_number()-30)[0]
#halos = tree[idx] # Is this right?
print 'Loaded halos have snap_num:', halos[1]['snap_num']
mstar = []
mhalo = []
i = 1
for halo in halos:
#Check if distinct halo
if not halo['pid'].value == -1:
print 'Halo %d skipped: PID = %d'%(halo['id'].value, halo['pid'].value)
continue
#Unit conversion
cen = halo['pos']
cen = ds.arr(cen.value, cen.unit)
r = halo['Rvir']
r = ds.arr(r.value, r.unit)
#Create the sphere
cen = cen.in_units('code_length').value
r = r.in_units('code_length').value
r_amr = float(r)
#If the halo radius is smaller than the min cell size,
#we need to try and approximate the masses enclosed.
#Not sure how correct this is...
factor = 1
if r < min_dx:
r_amr += min_dx
vol_halo = (4./3.)*np.pi*r**3
vol_cell = (4./3.)*np.pi*r_amr**3
factor = vol_halo/vol_cell
#Define the regions
region_part = Sphere(cen, r)
region_amr = Sphere(cen, r_amr)
#Filter the particles
filt_parts = RegionFilter(region_part, parts)
part_source = filt_parts.flatten()
dm = np.where(part_source['epoch'] == 0)[0]
stars = np.where(part_source['epoch'] != 0)[0]
part_mass = part_source['mass']*ro.info['unit_mass'].express(C.Msun)
if len(part_mass[dm]) < 50:
print 'Discarding halo with less than 200 particles. Mvir=%e'%halo['Mvir'].value
continue
#Filter the AMR data
filt_amr = RegionFilter(region_amr, amr)
cell_source = CellsToPoints(filt_amr)
cells = cell_source.flatten()
rho = cells['rho']*ro.info['unit_density'].express(C.Msun/C.kpc**3)
vol = (cells.get_sizes()*ro.info['unit_length'].express(C.kpc))**3
cell_mass = rho*vol
#Compute the total mass enclosed
gas_mass = np.sum(cell_mass)*factor # Multiply by factor incase we had to inflate the sphere
stellar_mass = np.sum(part_mass[stars])
particle_mass = np.sum(part_mass)
total_mass = gas_mass + particle_mass
mstar.append(stellar_mass)
mhalo.append(total_mass)
i+=1
print i
#print i
if(config.verbose and (i%100)==0): print 'Processed %d halos...'%i
return np.array(mstar), np.array(mhalo)
def fgas_halomass(self, halos=None):
snapshot = self._snapshot
ro = snapshot.raw_snapshot()
amr = ro.amr_source(['rho'])
parts = ro.particle_source(["mass"])
#Figure out the smallest possible cell size in code units
boxlen = ro.info['boxlen']
lmax = ro.info['levelmax']
min_dx = boxlen/float(2**(lmax))
if config.verbose: print 'min_dx=', min_dx
if (halos == None):
halos = snapshot.halos()
if config.verbose: print 'Processing %d halos'%len(halos)
fgas = []
mhalo = []
#z = self._snapshot.current_redshift()
#a = 1./(1.+z)
i = 0
for halo in halos:
if halo['num_p'] < 150:
break
#if tree:
#Find this halo and count number of progenitors.
#If too high, skip (frequent mergers -> tidal stripping)
#idx_tree_halo = (tree._tree[:]['orig_halo_id'] == halo['id'].value) &\
# (tree._tree[:]['snap_num'] == snapshot.rockstar_output_number())
#print idx_tree_halo
#tree_halo = tree._tree[idx_tree_halo]
#assert(len(tree_halo)==1)
#all_halos = []
#tree.find_progs(np.array([tree_halo]), all_halos)
#num_progs = len(all_halos)
#print 'Halo %d has %d progenitors'%(halo['id'], num_progs)
#if num_progs > 150: continue
#Create the sphere
cen = halo['pos'].in_units('code_length').value
r = halo['Rvir'].in_units('code_length').value
r_amr = float(r)
#If the halo radius is smaller than the min cell size,
#we need to try and approximate the masses enclosed.
#Not sure how correct this is...
factor = 1
if r < min_dx:
r_amr += min_dx
vol_halo = (4./3.)*np.pi*r**3
vol_cell = (4./3.)*np.pi*r_amr**3
factor = vol_halo/vol_cell
#Define the regions
region_part = Sphere(cen, r)
region_amr = Sphere(cen, r_amr)
#Filter the particles
filt_parts = RegionFilter(region_part, parts)
part_source = filt_parts.flatten()
part_mass = part_source['mass']*ro.info['unit_mass'].express(C.Msun)
#Filter the AMR data
filt_amr = RegionFilter(region_amr, amr)
cell_source = CellsToPoints(filt_amr)
cells = cell_source.flatten()
rho = cells['rho']*ro.info['unit_density'].express(C.Msun/C.kpc**3)
vol = (cells.get_sizes()*ro.info['unit_length'].express(C.kpc))**3
cell_mass = rho*vol
#Compute the total mass enclosed
gas_mass = np.sum(cell_mass)*factor # Multiply by factor incase we had to inflate the sphere
particle_mass = np.sum(part_mass)
total_mass = gas_mass + particle_mass
fgas.append(gas_mass/total_mass)
mhalo.append(total_mass)
i+=1
#print i
if(config.verbose and (i%100)==0): print 'Processes %d halos...'%i
return np.array(fgas), np.array(mhalo)