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Box units conversion (#3)
* linting * fix long line * rename nb * rename import * add group catalog * move imports out of functions * add array_to_structured * add references * fix subsampling * fix coord bug * add 2M++ dists * save nb * fix comment * add snapshot path * add snapshot path * add read_info * Move transforms * add import radec * expand docs * Move flipcols * update nb * add flip_cols * create file * add blank line * Move units transfs * add blank line * add units import * rm imports * add import * add box_units * add comments
This commit is contained in:
Richard Stiskalek
GitHub
parent
c7665b8136
commit
942c36b142
18 changed files with 6730 additions and 1574 deletions
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@ -13,8 +13,8 @@
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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from .readsim import (get_csiborg_ids, get_sim_path, open_particle,
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open_unbinding, read_particle, read_clumpid, read_clumps,
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read_mmain,
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convert_mass_cols, convert_position_cols, flip_cols)
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from .readobs import (read_planck2015, read_2mpp)
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from .readsim import (get_csiborg_ids, get_sim_path, get_snapshot_path, # noqa
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read_info, # noqa
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open_particle, open_unbinding, read_particle, # noqa
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read_clumpid, read_clumps, read_mmain) # noqa
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from .readobs import (read_planck2015, read_2mpp) # noqa
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@ -69,7 +69,7 @@ def read_planck2015(fpath, dist_cosmo, max_comdist=None):
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return out
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def read_2mpp(fpath):
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def read_2mpp(fpath, dist_cosmo):
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"""
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Read in the 2M++ galaxy redshift catalogue [1], with the catalogue at [2].
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Removes fake galaxies used to fill the zone of avoidance.
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@ -83,16 +83,24 @@ def read_2mpp(fpath):
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-------
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out : structured array
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The catalogue.
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References
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----------
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[1] The 2M++ galaxy redshift catalogue; Lavaux, Guilhem, Hudson, Michael J.
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[2] https://cdsarc.cds.unistra.fr/viz-bin/cat/J/MNRAS/416/2840#/article
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"""
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from scipy.constants import c
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# Read the catalogue and select non-fake galaxies
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cat = numpy.genfromtxt(fpath, delimiter="|", )
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cat = cat[cat[:, 12] == 0, :]
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F64 = numpy.float64
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cols = [("RA", F64), ("DEC", F64), ("Ksmag", F64)]
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cols = [("RA", F64), ("DEC", F64), ("Ksmag", F64), ("ZCMB", F64),
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("CDIST_CMB", F64)]
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out = cols_to_structured(cat.shape[0], cols)
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out["RA"] = cat[:, 1] - 180
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out["RA"] = cat[:, 1]
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out["DEC"] = cat[:, 2]
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out["Ksmag"] = cat[:, 5]
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out["ZCMB"] = cat[:, 7] / (c * 1e-3)
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out["CDIST_CMB"] = dist_cosmo.comoving_distance(out["ZCMB"]).value
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return out
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@ -30,9 +30,6 @@ F32 = numpy.float32
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F64 = numpy.float64
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I32 = numpy.int32
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I64 = numpy.int64
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little_h = 0.705
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BOXSIZE = 677.7 / little_h # Mpc. Otherwise positions in [0, 1].
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BOXMASS = 3.749e19 # Msun
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def get_csiborg_ids(srcdir):
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@ -82,11 +79,62 @@ def get_sim_path(n, fname="ramses_out_{}", srcdir="/mnt/extraspace/hdesmond"):
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Returns
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-------
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path : str
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The complete path to the `n`th CSiBORG simulation.
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Path to the `n`th CSiBORG simulation.
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"""
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return join(srcdir, fname.format(n))
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def get_snapshot_path(Nsnap, simpath):
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"""
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Get a path to a CSiBORG IC realisation snapshot.
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Parameters
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----------
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Nsnap : int
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Snapshot index.
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simpath : str
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Path to the CSiBORG IC realisation.
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Returns
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-------
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snappath : str
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Path to the CSiBORG IC realisation snapshot.
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"""
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return join(simpath, "output_{}".format(str(Nsnap).zfill(5)))
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def read_info(Nsnap, simpath):
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"""
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Read CSiBORG simulation snapshot info.
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Parameters
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----------
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Nsnap : int
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Snapshot index.
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simpath : str
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Path to the CSiBORG IC realisation.
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Returns
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-------
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info : dict
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Dictionary of info paramaters. Note that both keys and values are
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strings.
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"""
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# Open the info file
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snappath = get_snapshot_path(Nsnap, simpath)
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filename = join(snappath, "info_{}.txt".format(str(Nsnap).zfill(5)))
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with open(filename, "r") as f:
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info = f.read().split()
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# Throw anything below ordering line out
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info = numpy.asarray(info[:info.index("ordering")])
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# Get indexes of lines with `=`. Indxs before/after be keys/vals
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eqindxs = numpy.asarray([i for i in range(info.size) if info[i] == '='])
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keys = info[eqindxs - 1]
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vals = info[eqindxs + 1]
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return {key: val for key, val in zip(keys, vals)}
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def open_particle(n, simpath, verbose=True):
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"""
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Open particle files to a given CSiBORG simulation.
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@ -109,11 +157,9 @@ def open_particle(n, simpath, verbose=True):
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"""
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# Zeros filled snapshot number and the snapshot path
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nout = str(n).zfill(5)
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snappath = join(simpath, "output_{}".format(nout))
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infopath = join(snappath, "info_{}.txt".format(nout))
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snappath = get_snapshot_path(n, simpath)
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ncpu = int(read_info(n, simpath)["ncpu"])
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with open(infopath, "r") as f:
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ncpu = int(f.readline().split()[-1])
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if verbose:
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print("Reading in output `{}` with ncpu = `{}`.".format(nout, ncpu))
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@ -136,6 +182,7 @@ def open_particle(n, simpath, verbose=True):
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# Read in this order
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ncpuloc = f.read_ints()
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if ncpuloc != ncpu:
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infopath = join(snappath, "info_{}.txt".format(nout))
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raise ValueError("`ncpu = {}` of `{}` disagrees with `ncpu = {}` "
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"of `{}`.".format(ncpu, infopath, ncpuloc, fpath))
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ndim = f.read_ints()
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@ -382,74 +429,3 @@ def read_mmain(n, srcdir, fname="Mmain_{}.npy"):
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out[name] = arr[:, i]
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return out
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def convert_mass_cols(arr, cols):
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r"""
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Convert mass columns from box units to :math:`M_{\odot}`. `arr` is passed
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by reference and is not explicitly returned back.
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Parameters
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----------
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arr : structured array
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The array whose columns are to be converted.
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cols : str or list of str
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The mass columns to be converted.
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Returns
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-------
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None
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"""
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cols = [cols] if isinstance(cols, str) else cols
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for col in cols:
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arr[col] *= BOXMASS
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def convert_position_cols(arr, cols, zero_centered=True):
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r"""
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Convert position columns from box units to :math:`\mathrm{Mpc}`. `arr` is
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passed by reference and is not explicitly returned back.
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Parameters
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----------
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arr : structured array
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The array whose columns are to be converted.
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cols : str or list of str
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The mass columns to be converted.
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zero_centered : bool, optional
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Whether to translate the well-resolved origin in the centre of the
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simulation to the :math:`(0, 0 , 0)` point. By default `True`.
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Returns
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-------
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None
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"""
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cols = [cols] if isinstance(cols, str) else cols
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for col in cols:
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arr[col] *= BOXSIZE
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if zero_centered:
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arr[col] -= BOXSIZE / 2
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def flip_cols(arr, col1, col2):
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"""
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Flip values in columns `col1` and `col2`. `arr` is passed by reference and
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is not explicitly returned back.
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Parameters
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----------
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arr : structured array
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The array whose columns are to be converted.
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col1 : str
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The first column name.
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col2 : str
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The second column name.
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Returns
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-------
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nothing
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"""
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dum = numpy.copy(arr[col1])
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arr[col1] = arr[col2]
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arr[col2] = dum
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