def __init__(self,
sim_file,
groups_file,
group_ids_file,
n=1,
reverse=False,
bins=51,
reconstruct=True,
test=False,
basis_test=False,
n_test=51,
int_test=False,
x_max=1.0,
bases=[[0, 0, 0]]):
"""
Read in a sim-file for use with the shapelet analysis.
PARAMETERS:
sim_file: file containing the simulation snapshot
groups_file: file containing the location of groups
group_ids_file: file containing the ids of the group members
n: optional, default 1, number of groups to retain for further analysis (from largest to smallest)
reverse: optional, default False, whether to use the n SMALLEST groups rather than largest.
"""
self.n = n
self.int_test = int_test
if basis_test:
self.test_bases(n_test)
return
self.test = test
simops.readsim(sim_file)
simops.find_groups(groups_file, group_ids_file)
self.groups_pos = []
for i in range(n):
if not reverse:
self.groups_pos = self.groups_pos + [
np.asfortranarray(simops.pos[:,
simops.group_number == i + 1])
]
else:
self.groups_pos = self.groups_pos + [
np.asfortranarray(
simops.pos[:, simops.group_number ==
np.max(simops.group_number) - i])
]
simops.centre(self.groups_pos[i], mode=1)
simops.rotate(self.groups_pos[i], self.groups_pos[i],
[0.0, 0.0, 0.0], 0.0)
self.make_directories(sim_file)
if not self.test:
self.shapelets_main(bins, reconstruct)
else:
self.shapelets_test(x_max, bins, bases)
def __init__(self,sim_file,groups_file,group_ids_file, n=1,reverse=False,bins=51,reconstruct=True,
test=False,basis_test=False,n_test=51,int_test=False,x_max=1.0,bases=[[0,0,0]]):
"""
Read in a sim-file for use with the shapelet analysis.
PARAMETERS:
sim_file: file containing the simulation snapshot
groups_file: file containing the location of groups
group_ids_file: file containing the ids of the group members
n: optional, default 1, number of groups to retain for further analysis (from largest to smallest)
reverse: optional, default False, whether to use the n SMALLEST groups rather than largest.
"""
self.n = n
self.int_test = int_test
if basis_test:
self.test_bases(n_test)
return
self.test = test
simops.readsim(sim_file)
simops.find_groups(groups_file,group_ids_file)
self.groups_pos = []
for i in range(n):
if not reverse:
self.groups_pos = self.groups_pos + [np.asfortranarray(simops.pos[:,simops.group_number == i+1])]
else:
self.groups_pos = self.groups_pos + [np.asfortranarray(simops.pos[:,simops.group_number == np.max(simops.group_number)-i])]
simops.centre(self.groups_pos[i],mode=1)
simops.rotate(self.groups_pos[i],self.groups_pos[i],[0.0,0.0,0.0],0.0)
self.make_directories(sim_file)
if not self.test:
self.shapelets_main(bins, reconstruct)
else:
self.shapelets_test(x_max, bins, bases)
def __init__(self,filename,group_filename=None,ids_filename=None,n_groups=1,reverse=False,centring_mode=None,loud=False,subgroup_filename=None):
"""
Imports the simulation and detects groups and subgroups if specified.
"""
#Set the FORTRAN module parameter whether to write out extra information.
fsims.loud = loud
# readsim reads in the simulation and defines fsims.pos and fsims.vel amongst others.
fsims.readsim(filename)
# find_groups locates groups in the simulation and saves the array fsmims.group_number,
# which contains the number of the group for each particle.
if group_filename:
fsims.find_groups(group_filename,ids_filename)
# Modify the number of groups to work with in the stats part.
if n_groups is 'all':
self.n_groups = fsims.ngroups
else:
self.n_groups = n_groups
#If a subgroup filename was given, read in all the subgroups, saving a flagged subgroup number to each particle.
if subgroup_filename:
fsims.read_subgroupv(subgroup_filename)
self.subgroups_pos = []
#Initialize all variables for later use.
self.groups_pos = []
self.groups_vel = []
self.groups_pos_f = []
self.groups_vel_f = []
self.axis_b = []
self.axis_c = []
self.axis_d = []
self.original_group_centres = []
for i in range(self.n_groups):
#Save the particles to their respective groups
group_pos, group_vel = fsims.specify_groups(i+1,fsims.grouplen[i])
self.groups_vel = self.groups_vel + [np.asfortranarray(group_vel)]
self.groups_pos = self.groups_pos + [np.asfortranarray(group_pos)]
#Save the original group centre (the first particle position of each group)
self.original_group_centres = self.original_group_centres + [np.array(group_pos[:,0])]
# Recentre each group around its first particle
fsims.centre(self.groups_pos[i],centring_mode)
#Rotate each group so its longest axis is the x-axis.
fsims.rotate(self.groups_pos[i],np.asfortranarray(self.groups_vel[i]),[0.0,0.0,0.0],0.0)
#Save axis ratios for further use.
self.axis_b.append(float(fsims.axis_ratio_b))
self.axis_c.append(float(fsims.axis_ratio_c))
self.axis_d.append(float(fsims.axis_ratio_d))
#Locate subgroups.Particles are in no particular order though!
self.subgroups_pos = self.subgroups_pos + [[]]
#Arrange the subgroup numbers contained in each group in descending order so that non-grouped particles are last.
indices = list(set(fsims.subgroup_number[fsims.group_number == i+1]))
indices.sort(reverse=True)
for index in indices:
self.subgroups_pos[i] = self.subgroups_pos[i] + [np.array(self.groups_pos[i])[:,fsims.subgroup_number[fsims.group_number == i+1]== index]]
#Make the directory structure that files will be saved to.
self.make_directories(filename)
def __init__(self,
filename,
group_filename=None,
ids_filename=None,
n_groups=1,
reverse=False,
centring_mode=None,
loud=False,
subgroup_filename=None):
"""
Imports the simulation and detects groups and subgroups if specified.
"""
#Set the FORTRAN module parameter whether to write out extra information.
fsims.loud = loud
# readsim reads in the simulation and defines fsims.pos and fsims.vel amongst others.
fsims.readsim(filename)
# find_groups locates groups in the simulation and saves the array fsmims.group_number,
# which contains the number of the group for each particle.
if group_filename:
fsims.find_groups(group_filename, ids_filename)
# Modify the number of groups to work with in the stats part.
if n_groups is 'all':
self.n_groups = fsims.ngroups
else:
self.n_groups = n_groups
#If a subgroup filename was given, read in all the subgroups, saving a flagged subgroup number to each particle.
if subgroup_filename:
fsims.read_subgroupv(subgroup_filename)
self.subgroups_pos = []
#Initialize all variables for later use.
self.groups_pos = []
self.groups_vel = []
self.groups_pos_f = []
self.groups_vel_f = []
self.axis_b = []
self.axis_c = []
self.axis_d = []
self.original_group_centres = []
for i in range(self.n_groups):
#Save the particles to their respective groups
group_pos, group_vel = fsims.specify_groups(
i + 1, fsims.grouplen[i])
self.groups_vel = self.groups_vel + [
np.asfortranarray(group_vel)
]
self.groups_pos = self.groups_pos + [
np.asfortranarray(group_pos)
]
#Save the original group centre (the first particle position of each group)
self.original_group_centres = self.original_group_centres + [
np.array(group_pos[:, 0])
]
# Recentre each group around its first particle
fsims.centre(self.groups_pos[i], centring_mode)
#Rotate each group so its longest axis is the x-axis.
fsims.rotate(self.groups_pos[i],
np.asfortranarray(self.groups_vel[i]),
[0.0, 0.0, 0.0], 0.0)
#Save axis ratios for further use.
self.axis_b.append(float(fsims.axis_ratio_b))
self.axis_c.append(float(fsims.axis_ratio_c))
self.axis_d.append(float(fsims.axis_ratio_d))
#Locate subgroups.Particles are in no particular order though!
self.subgroups_pos = self.subgroups_pos + [[]]
#Arrange the subgroup numbers contained in each group in descending order so that non-grouped particles are last.
indices = list(
set(fsims.subgroup_number[fsims.group_number == i + 1]))
indices.sort(reverse=True)
for index in indices:
self.subgroups_pos[i] = self.subgroups_pos[i] + [
np.array(self.groups_pos[i])[:, fsims.subgroup_number[
fsims.group_number == i + 1] == index]
]
#Make the directory structure that files will be saved to.
self.make_directories(filename)
