Source code for yt.analysis_modules.sunrise_export.sunrise_exporter

Code to export from yt to Sunrise

from __future__ import print_function

# Copyright (c) 2013, yt Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file COPYING.txt, distributed with this software.

    import pyfits
except ImportError:

import os
import time
import numpy as np

import yt.utilities.lib.api as amr_utils

from yt import add_field
from yt.funcs import get_pbar, mylog
from yt.utilities.physical_ratios import \
    kpc_per_cm, \

[docs]def export_to_sunrise(ds, fn, star_particle_type, fc, fwidth, ncells_wide=None, debug=False,dd=None,**kwargs): r"""Convert the contents of a dataset to a FITS file format that Sunrise understands. This function will accept a dataset, and from that dataset construct a depth-first octree containing all of the data in the parameter file. This octree will be written to a FITS file. It will probably be quite big, so use this function with caution! Sunrise is a tool for generating synthetic spectra, available at . Parameters ---------- ds : `Dataset` The dataset to convert. fn : string The filename of the output FITS file. fc : array The center of the extraction region fwidth : array Ensure this radius around the center is enclosed Array format is (nx,ny,nz) where each element is floating point in unitary position units where 0 is leftmost edge and 1 the rightmost. Notes ----- Note that the process of generating simulated images from Sunrise will require substantial user input; see the Sunrise wiki at for more information. """ fc = np.array(fc) fwidth = np.array(fwidth) #we must round the dle,dre to the nearest root grid cells ile,ire,super_level,ncells_wide= \ round_ncells_wide(ds.domain_dimensions,fc-fwidth,fc+fwidth,nwide=ncells_wide) assert np.all((ile-ire)==(ile-ire)[0])"rounding specified region:")"from [%1.5f %1.5f %1.5f]-[%1.5f %1.5f %1.5f]"%(tuple(fc-fwidth)+tuple(fc+fwidth)))"to [%07i %07i %07i]-[%07i %07i %07i]"%(tuple(ile)+tuple(ire))) fle,fre = ile*1.0/ds.domain_dimensions, ire*1.0/ds.domain_dimensions"to [%1.5f %1.5f %1.5f]-[%1.5f %1.5f %1.5f]"%(tuple(fle)+tuple(fre))) #Create a list of the star particle properties in PARTICLE_DATA #Include ID, parent-ID, position, velocity, creation_mass, #formation_time, mass, age_m, age_l, metallicity, L_bol particle_data,nstars = prepare_star_particles(ds,star_particle_type,fle=fle,fre=fre, dd=dd,**kwargs) #Create the refinement hilbert octree in GRIDSTRUCTURE #For every leaf (not-refined) cell we have a column n GRIDDATA #Include mass_gas, mass_metals, gas_temp_m, gas_teff_m, cell_volume, SFR #since the octree always starts with one cell, an our 0-level mesh #may have many cells, we must create the octree region sitting #ontop of the first mesh by providing a negative level output, refinement,dd,nleaf = prepare_octree(ds,ile,start_level=super_level, debug=debug,dd=dd,center=fc) create_fits_file(ds,fn, refinement,output,particle_data,fle,fre) return fle,fre,ile,ire,dd,nleaf,nstars
[docs]def export_to_sunrise_from_halolist(ds,fni,star_particle_type, halo_list,domains_list=None,**kwargs): """ Using the center of mass and the virial radius for a halo, calculate the regions to extract for sunrise. The regions are defined on the root grid, and so individual octs may span a large range encompassing many halos and subhalos. Instead of repeating the oct extraction for each halo, arrange halos such that we only calculate what we need to. Parameters ---------- ds : `Dataset` The dataset to convert. We use the root grid to specify the domain. fni : string The filename of the output FITS file, but depends on the domain. The dle and dre are appended to the name. particle_type : int The particle index for stars halo_list : list of halo objects The halo list objects must have halo.CoM and halo.Rvir, both of which are assumed to be in unitary length units. frvir (optional) : float Ensure that CoM +/- frvir*Rvir is contained within each domain domains_list (optiona): dict of halos Organize halos into a dict of domains. Keys are DLE/DRE tuple values are a list of halos """ dn = ds.domain_dimensions if domains_list is None: domains_list = domains_from_halos(ds,halo_list,**kwargs) if fni.endswith('.fits'): fni = fni.replace('.fits','') for (num_halos, domain, halos) in domains_list: dle,dre = domain print('exporting: ') print("[%03i %03i %03i] -"%tuple(dle), end=' ') print("[%03i %03i %03i] "%tuple(dre), end=' ') print(" with %i halos"%num_halos) dle,dre = domain dle, dre = np.array(dle),np.array(dre) fn = fni fn += "%03i_%03i_%03i-"%tuple(dle) fn += "%03i_%03i_%03i"%tuple(dre) fnf = fn + '.fits' fnt = fn + '.halos' if os.path.exists(fnt): os.remove(fnt) fh = open(fnt,'w') for halo in halos: fh.write("%i "%halo.ID) fh.write("%6.6e "%(halo.CoM[0]*ds['kpc'])) fh.write("%6.6e "%(halo.CoM[1]*ds['kpc'])) fh.write("%6.6e "%(halo.CoM[2]*ds['kpc'])) fh.write("%6.6e "%(halo.Mvir)) fh.write("%6.6e \n"%(halo.Rvir*ds['kpc'])) fh.close() export_to_sunrise(ds, fnf, star_particle_type, dle*1.0/dn, dre*1.0/dn)
[docs]def domains_from_halos(ds,halo_list,frvir=0.15): domains = {} dn = ds.domain_dimensions for halo in halo_list: fle, fre = halo.CoM-frvir*halo.Rvir,halo.CoM+frvir*halo.Rvir dle,dre = np.floor(fle*dn), np.ceil(fre*dn) dle,dre = tuple(dle.astype('int')),tuple(dre.astype('int')) if (dle,dre) in domains.keys(): domains[(dle,dre)] += halo, else: domains[(dle,dre)] = [halo,] #for niceness, let's process the domains in order of #the one with the most halos domains_list = [(len(v),k,v) for k,v in domains.items()] domains_list.sort() domains_list.reverse() #we want the most populated domains first return domains_list
[docs]def prepare_octree(ds,ile,start_level=0,debug=True,dd=None,center=None): if dd is None: #we keep passing dd around to not regenerate the data all the time dd = ds.all_data() try: dd['MetalMass'] except KeyError: add_fields() #add the metal mass field that sunrise wants def _temp_times_mass(field, data): return data["Temperature"]*data["CellMassMsun"] add_field("TemperatureTimesCellMassMsun", function=_temp_times_mass) fields = ["CellMassMsun","TemperatureTimesCellMassMsun", "MetalMass","CellVolumeCode"] #gather the field data from octs pbar = get_pbar("Retrieving field data",len(fields)) field_data = [] for fi,f in enumerate(fields): field_data += dd[f], pbar.update(fi) pbar.finish() del field_data #first we cast every cell as an oct #ngrids = np.max([ for g in ds._grids]) grids = {} levels_all = {} levels_finest = {} for l in range(100): levels_finest[l]=0 levels_all[l]=0 pbar = get_pbar("Initializing octs ",len(ds.index.grids)) for gi,g in enumerate(ds.index.grids): ff = np.array([g[f] for f in fields]) og = amr_utils.OctreeGrid( g.child_index_mask.astype('int32'), ff.astype("float64"), g.LeftEdge.astype("float64"), g.ActiveDimensions.astype("int32"), np.ones(1,dtype="float64")*[0], g.Level, grids[] = og #how many refinement cells will we have? #measure the 'volume' of each mesh, but many #cells do not exist. an overstimate levels_all[g.Level] += #how many leaves do we have? #this overestimates. a child of -1 means no child, #but that cell may still be expanded on a submesh because #(at least in ART) the meshes are inefficient. g.clear_data() pbar.update(gi) pbar.finish() #create the octree grid list #oct_list = amr_utils.OctreeGridList(grids) #initialize arrays to be passed to the recursion algo o_length = np.sum(levels_all.values()) r_length = np.sum(levels_all.values()) output = np.zeros((o_length,len(fields)), dtype='float64') refined = np.zeros(r_length, dtype='int32') levels = np.zeros(r_length, dtype='int32') ids = np.zeros(r_length, dtype='int32') pos = position() hs = hilbert_state() start_time = time.time() if debug: printing = lambda x: print_oct(x) else: printing = None pbar = get_pbar("Building Hilbert DFO octree",len(refined)) RecurseOctreeDepthFirstHilbert( ile, pos, grids[0], #we always start on the root grid hs, output,refined,levels, grids, start_level, ids, debug=printing, tracker=pbar) pbar.finish() #by time we get it here the 'current' position is actually #for the next spot, so we're off by 1 print('took %1.2e seconds'%(time.time()-start_time)) print('refinement tree # of cells %i, # of leaves %i'%(pos.refined_pos,pos.output_pos)) print('first few entries :',refined[:12]) output = output[:pos.output_pos] refined = refined[:pos.refined_pos] levels = levels[:pos.refined_pos] return output,refined,dd,pos.refined_pos
[docs]def RecurseOctreeDepthFirstHilbert(cell_index, #integer (rep as a float) on the [grid_index] pos, #the output hydro data position and refinement position grid, #grid that this oct lives on (not its children) hilbert, #the hilbert state output, #holds the hydro data refined, #holds the refinement status of Octs, 0s and 1s levels, #For a given Oct, what is the level grids, #list of all patch grids available to us level, #starting level of the oct (not the children) ids, #record the oct ID debug=None,tracker=True): if tracker is not None: if pos.refined_pos%1000 == 500 : tracker.update(pos.refined_pos) if debug is not None: debug(vars()) child_grid_index = grid.child_indices[cell_index[0],cell_index[1],cell_index[2]] #record the refinement state levels[pos.refined_pos] = level is_leaf = (child_grid_index==-1) and (level>0) refined[pos.refined_pos] = not is_leaf #True is oct, False is leaf ids[pos.refined_pos] = child_grid_index #True is oct, False is leaf pos.refined_pos+= 1 if is_leaf: #never subdivide if we are on a superlevel #then we have hit a leaf cell; write it out for field_index in range(grid.fields.shape[0]): output[pos.output_pos,field_index] = \ grid.fields[field_index,cell_index[0],cell_index[1],cell_index[2]] pos.output_pos+= 1 else: assert child_grid_index>-1 #find the grid we descend into #then find the eight cells we break up into subgrid = grids[child_grid_index] #calculate the floating point LE of the children #then translate onto the subgrid integer index parent_fle = grid.left_edges + cell_index*grid.dx subgrid_ile = np.floor((parent_fle - subgrid.left_edges)/subgrid.dx) for (vertex, hilbert_child) in hilbert: #vertex is a combination of three 0s and 1s to #denote each of the 8 octs if level < 0: subgrid = grid #we don't actually descend if we're a superlevel #child_ile = cell_index + np.array(vertex)*2**(-level) child_ile = cell_index + np.array(vertex)*2**(-(level+1)) child_ile = child_ile.astype('int') else: child_ile = subgrid_ile+np.array(vertex) child_ile = child_ile.astype('int') RecurseOctreeDepthFirstHilbert(child_ile,pos, subgrid,hilbert_child,output,refined,levels,grids, level+1,ids = ids, debug=debug,tracker=tracker)
[docs]def create_fits_file(ds,fn, refined,output,particle_data,fle,fre): #first create the grid structure structure = pyfits.Column("structure", format="B", array=refined.astype("bool")) cols = pyfits.ColDefs([structure]) st_table = pyfits.new_table(cols) = "GRIDSTRUCTURE" st_table.header.update("hierarch lengthunit", "kpc", comment="Length unit for grid") fdx = fre-fle for i,a in enumerate('xyz'): st_table.header.update("min%s" % a, fle[i] * ds['kpc']) st_table.header.update("max%s" % a, fre[i] * ds['kpc']) st_table.header.update("n%s" % a, fdx[i]) st_table.header.update("subdiv%s" % a, 2) st_table.header.update("subdivtp", "OCTREE", "Type of grid subdivision") #not the hydro grid data fields = ["CellMassMsun","TemperatureTimesCellMassMsun", "MetalMass","CellVolumeCode"] fd = {} for i,f in enumerate(fields): fd[f]=output[:,i] del output col_list = [] size = fd["CellMassMsun"].size tm = fd["CellMassMsun"].sum() col_list.append(pyfits.Column("mass_gas", format='D', array=fd['CellMassMsun'], unit="Msun")) col_list.append(pyfits.Column("mass_metals", format='D', array=fd['MetalMass'], unit="Msun")) # col_list.append(pyfits.Column("mass_stars", format='D', # array=np.zeros(size,dtype='D'),unit="Msun")) # col_list.append(pyfits.Column("mass_stellar_metals", format='D', # array=np.zeros(size,dtype='D'),unit="Msun")) # col_list.append(pyfits.Column("age_m", format='D', # array=np.zeros(size,dtype='D'),unit="yr*Msun")) # col_list.append(pyfits.Column("age_l", format='D', # array=np.zeros(size,dtype='D'),unit="yr*Msun")) # col_list.append(pyfits.Column("L_bol", format='D', # array=np.zeros(size,dtype='D'))) # col_list.append(pyfits.Column("L_lambda", format='D', # array=np.zeros(size,dtype='D'))) # The units for gas_temp are really K*Msun. For older Sunrise versions # you must set the unit to just K col_list.append(pyfits.Column("gas_temp_m", format='D', array=fd['TemperatureTimesCellMassMsun'], unit="K*Msun")) col_list.append(pyfits.Column("gas_teff_m", format='D', array=fd['TemperatureTimesCellMassMsun'], unit="K*Msun")) col_list.append(pyfits.Column("cell_volume", format='D', array=fd['CellVolumeCode'].astype('float64')*ds['kpc']**3.0, unit="kpc^3")) col_list.append(pyfits.Column("SFR", format='D', array=np.zeros(size, dtype='D'))) cols = pyfits.ColDefs(col_list) mg_table = pyfits.new_table(cols) mg_table.header.update("M_g_tot", tm) mg_table.header.update("timeunit", "yr") mg_table.header.update("tempunit", "K") = "GRIDDATA" # Add a dummy Primary; might be a better way to do this! col_list = [pyfits.Column("dummy", format="F", array=np.zeros(1, dtype='float32'))] cols = pyfits.ColDefs(col_list) md_table = pyfits.new_table(cols) md_table.header.update("snaptime", ds.current_time*ds['years']) = "YT" phdu = pyfits.PrimaryHDU() phdu.header.update('nbodycod','yt') hls = [phdu, st_table, mg_table,md_table] hls.append(particle_data) hdus = pyfits.HDUList(hls) hdus.writeto(fn, clobber=True)
[docs]def nearest_power(x): #round to the nearest power of 2 x-=1 x |= x >> 1 x |= x >> 2 x |= x >> 4 x |= x >> 8 x |= x >> 16 x+=1 return x
[docs]def round_ncells_wide(dds,fle,fre,nwide=None): fc = (fle+fre)/2.0 assert np.all(fle < fc) assert np.all(fre > fc) ic = np.rint(fc*dds) #nearest vertex to the center ile,ire = ic.astype('int'),ic.astype('int') cfle,cfre = fc.copy(),fc.copy() idx = np.array([0,0,0]) #just a random non-equal array width = 0.0 if nwide is None: #expand until borders are included and #we have an equaly-sized, non-zero box idxq,out=False,True while not out or not idxq: cfle,cfre = fc-width, fc+width ile = np.rint(cfle*dds).astype('int') ire = np.rint(cfre*dds).astype('int') idx = ire-ile width += 0.1/dds #quit if idxq is true: idxq = idx[0]>0 and np.all(idx==idx[0]) out = np.all(fle>cfle) and np.all(fre<cfre) out &= abs(np.log2(idx[0])-np.rint(np.log2(idx[0])))<1e-5 #nwide should be a power of 2 assert width[0] < 1.1 #can't go larger than the simulation volume nwide = idx[0] else: #expand until we are nwide cells span while not np.all(idx==nwide): assert np.any(idx<=nwide) cfle,cfre = fc-width, fc+width ile = np.rint(cfle*dds).astype('int') ire = np.rint(cfre*dds).astype('int') idx = ire-ile width += 1e-2*1.0/dds assert np.all(idx==nwide) assert idx[0]>0 maxlevel = -np.rint(np.log2(nwide)).astype('int') assert abs(np.log2(nwide)-np.rint(np.log2(nwide)))<1e-5 #nwide should be a power of 2 return ile,ire,maxlevel,nwide
[docs]def round_nearest_edge(ds,fle,fre): dds = ds.domain_dimensions ile = np.floor(fle*dds).astype('int') ire = np.ceil(fre*dds).astype('int') #this is the number of cells the super octree needs to expand to #must round to the nearest power of 2 width = np.max(ire-ile) width = nearest_power(width) maxlevel = -np.rint(np.log2(width)).astype('int') return ile,ire,maxlevel
[docs]def prepare_star_particles(ds,star_type,pos=None,vel=None, age=None, creation_time=None,initial_mass=None, current_mass=None,metallicity=None, radius = None, fle=[0.,0.,0.],fre=[1.,1.,1.], dd=None): if dd is None: dd = ds.all_data() idxst = dd["particle_type"] == star_type #make sure we select more than a single particle assert np.sum(idxst)>0 if pos is None: pos = np.array([dd["particle_position_%s" % ax] for ax in 'xyz']).transpose() idx = idxst & np.all(pos>fle,axis=1) & np.all(pos<fre,axis=1) assert np.sum(idx)>0 pos = pos[idx]*ds['kpc'] #unitary units -> kpc if age is None: age = dd["particle_age"][idx]*ds['years'] # seconds->years if vel is None: vel = np.array([dd["particle_velocity_%s" % ax][idx] for ax in 'xyz']).transpose() # Velocity is cm/s, we want it to be kpc/yr #vel *= (ds["kpc"]/ds["cm"]) / (365*24*3600.) vel *= kpc_per_cm * sec_per_year if initial_mass is None: #in solar masses initial_mass = dd["particle_mass_initial"][idx]*ds['Msun'] if current_mass is None: #in solar masses current_mass = dd["particle_mass"][idx]*ds['Msun'] if metallicity is None: #this should be in dimensionless units, metals mass / particle mass metallicity = dd["particle_metallicity"][idx] assert np.all(metallicity>0.0) if radius is None: radius = initial_mass*0.0+10.0/1000.0 #10pc radius formation_time = ds.current_time*ds['years']-age #create every column col_list = [] col_list.append(pyfits.Column("ID", format="J", array=np.arange(current_mass.size).astype('int32'))) col_list.append(pyfits.Column("parent_ID", format="J", array=np.arange(current_mass.size).astype('int32'))) col_list.append(pyfits.Column("position", format="3D", array=pos, unit="kpc")) col_list.append(pyfits.Column("velocity", format="3D", array=vel, unit="kpc/yr")) col_list.append(pyfits.Column("creation_mass", format="D", array=initial_mass, unit="Msun")) col_list.append(pyfits.Column("formation_time", format="D", array=formation_time, unit="yr")) col_list.append(pyfits.Column("radius", format="D", array=radius, unit="kpc")) col_list.append(pyfits.Column("mass", format="D", array=current_mass, unit="Msun")) col_list.append(pyfits.Column("age", format="D", array=age,unit='yr')) #For particles, Sunrise takes #the dimensionless metallicity, not the mass of the metals col_list.append(pyfits.Column("metallicity", format="D", array=metallicity,unit="Msun")) #make the table cols = pyfits.ColDefs(col_list) pd_table = pyfits.new_table(cols) = "PARTICLEDATA" #make sure we have nonzero particle number assert[0]>0 return pd_table,np.sum(idx)
[docs]def add_fields(): """Add three Eulerian fields Sunrise uses""" def _MetalMass(field, data): return data["Metallicity"] * data["CellMassMsun"] def _convMetalMass(data): return 1.0 add_field("MetalMass", function=_MetalMass, convert_function=_convMetalMass) def _initial_mass_cen_ostriker(field, data): # SFR in a cell. This assumes stars were created by the Cen & Ostriker algorithm # Check Grid_AddToDiskProfile.C and star_maker7.src star_mass_ejection_fraction = data.ds.get_parameter("StarMassEjectionFraction",float) xv1 = ((data.ds["InitialTime"] - data["creation_time"]) / data["dynamical_time"]) denom = (1.0 - star_mass_ejection_fraction * (1.0 - (1.0 + xv1)*np.exp(-xv1))) minitial = data["ParticleMassMsun"] / denom return minitial add_field("InitialMassCenOstriker", function=_initial_mass_cen_ostriker)
[docs]class position: def __init__(self): self.output_pos = 0 self.refined_pos = 0
[docs]class hilbert_state(): def __init__(self,dim=None,sgn=None,octant=None): if dim is None: dim = [0,1,2] if sgn is None: sgn = [1,1,1] if octant is None: octant = 5 self.dim = dim self.sgn = sgn self.octant = octant
[docs] def flip(self,i): self.sgn[i]*=-1
[docs] def swap(self,i,j): temp = self.dim[i] self.dim[i]=self.dim[j] self.dim[j]=temp axis = self.sgn[i] self.sgn[i] = self.sgn[j] self.sgn[j] = axis
[docs] def reorder(self,i,j,k): ndim = [self.dim[i],self.dim[j],self.dim[k]] nsgn = [self.sgn[i],self.sgn[j],self.sgn[k]] self.dim = ndim self.sgn = nsgn
[docs] def copy(self): return hilbert_state([self.dim[0],self.dim[1],self.dim[2]], [self.sgn[0],self.sgn[1],self.sgn[2]], self.octant)
[docs] def descend(self,o): child = self.copy() child.octant = o if o==0: child.swap(0,2) elif o==1: child.swap(1,2) elif o==2: pass elif o==3: child.flip(0) child.flip(2) child.reorder(2,0,1) elif o==4: child.flip(0) child.flip(1) child.reorder(2,0,1) elif o==5: pass elif o==6: child.flip(1) child.flip(2) child.swap(1,2) elif o==7: child.flip(0) child.flip(2) child.swap(0,2) return child
def __iter__(self): vertex = [0,0,0] j=0 for i in range(3): vertex[self.dim[i]] = 0 if self.sgn[i]>0 else 1 yield vertex, self.descend(j) vertex[self.dim[0]] += self.sgn[0] j+=1 yield vertex, self.descend(j) vertex[self.dim[1]] += self.sgn[1] j+=1 yield vertex, self.descend(j) vertex[self.dim[0]] -= self.sgn[0] j+=1 yield vertex, self.descend(j) vertex[self.dim[2]] += self.sgn[2] j+=1 yield vertex, self.descend(j) vertex[self.dim[0]] += self.sgn[0] j+=1 yield vertex, self.descend(j) vertex[self.dim[1]] -= self.sgn[1] j+=1 yield vertex, self.descend(j) vertex[self.dim[0]] -= self.sgn[0] j+=1 yield vertex, self.descend(j)