def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Subtract from the first three columns of the input files the
three floats. If they are not provided they will be computed from the files
themselves. """
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument(
"ifname",
action="store",
nargs='+',
type=ap.FileType('r'),
help="Input file name(s), containing z in one of the columns")
p = apc.version_verbose(p, '1')
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p.add_argument("--rescale",
action="store",
type=float,
nargs=3,
help="""Values to subtract from the first three columns""")
p.add_argument("-o",
"--offset",
action="store",
type=float,
default=0,
help="""Extra offset to add to 'rescale'""")
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """ Rebin the power spectra for the input files.
The structure of the input files must be like the following:
# sum(w) sum(w^2n(z)) sum(w^2)
#data ### ### ###
#random ### ### ###
# k P(k) P(k)+noise n_modes
[...]
The output files will have the same structure
If the number of bins in the input file are not multiples of 'n_bins',
the last bins will be discarded
"""
p = ap.ArgumentParser(description=description,
formatter_class=apc.RawDescrArgDefHelpFormatter)
p.add_argument('merge_bins',
action='store',
type=int,
help="Number of bins to merge")
p.add_argument("ifname",
action=apc.file_exists(),
nargs='+',
help="""Input file name(s).""")
p = apc.version_verbose(p, '1')
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p.add_argument('-f',
'--from-bin',
type=int,
action='store',
help='Ignore the first %(dest)s bins')
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
description = """The weights w are preplaced by w/w_fpk, with w_fkp = 1/(1+ n(z) * pw )"""
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("pw",
action="store",
type=float,
help="Value of 'pw' to use for the FKP weight")
p.add_argument(
"ifname",
action="store",
nargs='+',
type=ap.FileType('r'),
help=
"Input file name(s), containing ra and dec in the first two columns")
p = apc.version_verbose(p, '0.1')
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p.add_argument("-n",
"--n-col",
type=int,
default=5,
help="""Column containin the number density""")
p.add_argument("-w",
"--w-col",
type=int,
default=3,
help="""Column containin the weights""")
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """ Read one or more files and extract a part of the file according to the constraints given.
Examples:
%(prog)s 'c3 < 4' filename
%(prog)s '(c3 < 4) | (c3 > 8)' filename
%(prog)s '(c4 > 8) & (c4 < 4)' filename
WARNING: The constraint is evaluated with 'eval' and no check is done upon local or global variables."""
p = ap.ArgumentParser(description=description,
formatter_class=ap.RawDescriptionHelpFormatter)
#p.add_argument("column", action="store", type=int, help="Column to check")
p.add_argument("constr",
action="store",
help="""Constraints to be applied to the desired column""")
p.add_argument("ifname",
nargs='+',
action=apc.file_exists(),
help="Input file name(s)")
p = apc.version_verbose(p, '1.0')
p, group = apc.insert_or_replace(p, print_def=True)
p, group = apc.overwrite_or_skip(p)
p, pandas = apc.pandas_group(p)
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files. (default: %(default)s)")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = "Move or swap some column in a (list of) file(s)."
p = ap.ArgumentParser(description=description, )
p.add_argument("from_cols", action="store", type=apc.int_or_list,
help="""Column(s) to copy. (if more than one, give them as a string
of integers separated by spaces)""")
p.add_argument("to_cols", action="store", type=apc.int_or_list,
help="""Where to copy the column(s). (if more than one, give them
as a string of integers separated by spaces)""")
p.add_argument("ifname", action=apc.file_exists(), nargs='+',
help="""Input file name(s)""")
p = apc.version_verbose(p, '0.1')
p.add_argument("-s", "--swap", action="store_true",
help="Swap 'from' with 'to'")
p.add_argument("--substitute", action="store", type=float,
help="""If given, substitutes the content of the columns
'from_cols' not contained in 'to_cols' with '%(dest)s'. This is
executed only if 'swap' is *False* and after moving""")
p, group = apc.insert_or_replace(p, print_def=True)
p, group = apc.overwrite_or_skip(p)
p, pandas = apc.pandas_group(p)
p.add_argument("--fmt", default="%7.6e", action=apc.StoreFmt, nargs='+',
help="Format of the output files. (default: %(default)s)")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group( p, description=description )
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
description = """Given a set of catalogues with x, y and z in the first three columns,
compute the redshift corresponding to the objects and write the output
in an extra column or in an existing one"""
p = ap.ArgumentParser(description=description, formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("ifname", action="store", nargs='+', type=ap.FileType('r'),
help="Input file name(s), containing ra and dec in the first two columns")
p = apc.version_verbose( p, '1' )
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p.add_argument("-z", "--z-col", type=int, help="""If given the redshifts are substituted in
'%(dest)s' column. Otherwise an extra column is appended in the output file""")
p.add_argument("-f", "--zdist-file", type=ap.FileType('r'),
help="""File containing a table with resdshift and comoving distance.
If not given, this table is computed using the cosmological parameters
that can be set with the options.""")
description="""If the file with the table of z and D_c(z) is not given,
this is compute using the following parameters"""
p, cosmo = apc.cosmology_group( p, description=description )
cosmo.add_argument("--zrange", type=float, nargs=2, action="store", default=[0.4, 0.8],
help="Maximum and minimum redshift where to compute the comoving distance")
cosmo.add_argument("--nbins", action="store", type=int, default='500',
help='Number of bins in redshift.')
p.add_argument("--fmt", default="%7.6e", action=apc.StoreFmt, nargs='+',
help="Format of the output files")
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Execute operations between columns and save in a column.
Example:
c3+c6-1: add column 3 to column 6 and subtract 1.
"""
p = ap.ArgumentParser(
description=description,
#formatter_class=apc.RawDescrArgDefHelpFormatter)
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("operation",
action="store",
help="""Operation to execute between columns.""")
p.add_argument(
"to_col",
action="store",
type=int,
help="""Column where the operation is saved. If it is larger than
the number of columns, the result is appended""")
p.add_argument("ifname",
nargs='+',
action=apc.file_exists(),
help="""Input file name(s)""")
p = apc.version_verbose(p, '0.1')
p.add_argument(
"-s",
"--substitute",
action="store",
type=float,
help="""If given, substitutes the content of the columns used for
the operation with '%(dest)s'. This is executed before copying the
result of the operation to the desired column""")
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p, pandas = apc.pandas_group(p)
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files.")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Given a file with the fraction for downsample as function of redshift and
one or more catalogues, downsample them according to the given fractions"""
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument(
"downsample",
action=apc.file_exists(),
help="""File with the fraction to downsample as function of redshift."""
)
p.add_argument(
"ifname",
action=apc.file_exists(),
nargs='+',
help="Input file name(s), containing z in one of the columns")
p = apc.version_verbose(p, '0.1')
p.add_argument("-z",
"--z-column",
action="store",
type=int,
default=2,
help="Column containing the redshift")
p.add_argument(
"-k",
"--kind",
action="store",
type=select_interp,
default="linear",
help="""Specifies the kind of interpolation of the downsample file
as a string {} or as an integer specifying the order of the spline
interpolator to use. Default is ‘linear’.""".format(interp_type))
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p, pandas = apc.pandas_group(p)
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Given a table of 'z,n(z)', subsitute a column in the
catalogue(s) with the value of n(z), using the values of z from an other
column of the same file """
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("noz",
action="store",
type=ap.FileType('r'),
help="File containing a table of z, n(z)")
p.add_argument(
"ifname",
nargs='+',
action=apc.file_exists(),
help="""Input file name(s), containing z in one of the columns""")
p = apc.version_verbose(p, '1')
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p.add_argument("-z",
"--z-column",
action="store",
type=int,
default="-1",
help="Column in the catalogue with the redshift.")
p.add_argument("-n",
"--nz-column",
action="store",
type=int,
default="5",
help="Column in the catalogue in which n(z) is saved.")
p.add_argument("--zn-file-col",
action="store",
type=int,
nargs=2,
default=[0, 1],
help="""Columns in 'noz' containing z and n(z).""")
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """ Convert the file from ra, dec, redshift into cartesian coordinates assuming a cosmology.
The name of the output file name is derived from the input one and the modification
can be set with the options. ra, dec and redshift are by default assumed to be in the first three columns,
and all the following columns are by default copied after x, y and z. If the number of columns in
the input file (or in the ones read) is more than 8 the exceding ones are cut.
Redshift is copied in the last column.
The output file has the structure
x y z w bias n(x,y,z) n_b(z) M redshift
(The columns that are not present in the input file are filled with 1, except the redshift)"""
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("ifname", nargs='+', action=apc.file_exists(),
help="""Input file name(s), containing ra and dec in the first two
columns""")
p = apc.version_verbose( p, '1' )
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p, pandas = apc.pandas_group(p)
description="""Cosmology to use to convert ra, dec and z in distances. h0=1
is equivalent to have the distance in Mpc/h with any other value of h0"""
p, cosmo = apc.cosmology_group( p, description=description, h0_def=1. )
cosmo.add_argument("--zrange", action="store", nargs=2, type=float,
help="""Lower and upper limit for the redshift. If this option is
given the distance is computed only ones and then interpolated in
the values in the files""")
cosmo.add_argument("--nbins", action="store", type=int, default='500',
help='Number of bins in redshift.')
p.add_argument('--negative-z', action='store', choices=[None, 'skip', 'tozero'],
default=None, help="""If *None* no check on negative redshifts,
otherwise either skip the corresponding lines or set to 0""")
p.add_argument("--fmt", default="%7.6e", action=apc.StoreFmt, nargs='+',
help="Format of the output files")
p.add_argument("--usecols", action="store", nargs="+", type=int,
help="""Read the selected columns. By default read all the
columns.If thi option is used, make sure the the first three
columns read in are ra, dec and redshift.""")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group( p, description=description )
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """
Computes N(z) and n(z) from one column in a (set of) file(s) and save it
(them) for each file and/or computes the mean and save it. Weights can be
applied.
When the 'area' is not specified, a standard histogram is produced.
The output files have the following structure:
bin_center bin_lower bin_upper hist (std)
std is added only if the mean is required
"""
p = ap.ArgumentParser(description=description,
formatter_class=apc.RawDescrArgDefHelpFormatter)
int_or_oper = """If integer, the given column is considered. Operations
between columns can be performed preceding the column number with a c: e.g.
c3+c6-1 add columns 3 and 6 and subtract 1 from the result. only after the
histogram is created"""
p.add_argument("column",
action="store",
type=apc.int_or_str,
help="""Columns
containing the redshift (or whatever variable for the histogram).
""" + int_or_oper)
p.add_argument("ifname",
nargs='+',
action=apc.file_exists(),
help="""Input file name(s)""")
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
p = apc.version_verbose(p, '0.1')
p.add_argument(
"-w",
"--weight",
action="store",
type=apc.int_or_str,
help="""Weight for the histogram. Operation permitted as for 'column'
If boolean expressions like '(c3==1)&(c6==0)', the weight is interpreted
as 1 if *True*, as 0 if *False*""")
p.add_argument("-n",
"--nbins",
action="store",
type=int,
default='50',
help="Number of bins per histogram.")
p.add_argument(
"--range",
action="store",
nargs=2,
type=float,
help="""Lower and upper range of the bins. Computed from the first
file if any of the following are required:
i) the mean;
ii) n(z) [so the area needs to be computed];
iii) pandas and chunks
""")
p.add_argument("--mean",
action="store",
type=apc.outfile,
help="""Save the mean in file '%(dest)s'""")
p.add_argument("--mean-only",
action="store_true",
help="Only the mean of the histograms is saved")
p, pandas = apc.pandas_group(p)
description = """
If the area of the survey is given, the effective volume per bin is
computed and the histogram of n(z) is returned. 'h0=1' is equivalent to
requiring the volume to be in (Mpc/h)^3. For performance reasons, if the
range is not given it will be computed as for when the mean is requested"""
p, cosmo = apc.cosmology_group(p, description=description, h0_def=1)
cosmo.add_argument("-a",
"--area",
type=float,
action="store",
help="Area of the survey in steradians")
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Read two columns c1, c2 from 'replacement' file, then
replace in 'column' of the input file(s) c1 -> c2."""
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument("column",
action="store",
type=int,
help="Column to substitute")
p.add_argument("replacement",
action=apc.file_exists(),
help="""File containing the substitution to do.""")
p.add_argument("ifname",
nargs='+',
action=apc.file_exists(),
help="Input file name(s)")
p = apc.version_verbose(p, '1.0')
p, group = apc.insert_or_replace(p, print_def=True)
p, group = apc.overwrite_or_skip(p)
p.add_argument("-c",
"--repl-columns",
nargs='+',
action=apc.required_length(1, 2),
type=int,
default=[0, 1],
help="""Columns to read from 'replacement'
file. If only one column is read, the content of 'column' in
'ifname' is casted to int.""")
p, pandas = apc.pandas_group(p)
p.add_argument("--fmt",
default="%7.6e",
action=apc.StoreFmt,
nargs='+',
help="Format of the output files. (default: %(default)s)")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)
def parse(argv):
"""
This function accept a list of strings, create and fill a parser istance
and return a populated namespace
Parameters
----------
argv: list of strings
list to be parsed
output: namespace
---------
"""
import argparse as ap
import argparse_custom as apc
description = """Give a list of fits files, read some of the
columns into a numpy array and then save them into ascii files. Operations
between colums permitted but numbers are interpreted as such and not
columns. Permitted operations: {0}
""".format(permitted_operations)
p = ap.ArgumentParser(description=description,
formatter_class=ap.ArgumentDefaultsHelpFormatter)
p.add_argument(
"ifname",
nargs='+',
action=apc.file_exists(),
help="Input file name(s), containing z in one of the columns")
p = apc.version_verbose(p, '1')
p, group = apc.insert_or_replace(p)
p, group = apc.overwrite_or_skip(p)
finfo = p.add_argument_group(title="file information",
description="""Get
information from the fits files""")
finfo.add_argument("--show-columns",
action="store_true",
help="""Print on
screen the info for the first file in 'ifname'""")
finfo.add_argument("--all-files",
action="store_true",
help="""Show the info of all
the files. Ignored if '--show-columns' not used.""")
finfo.add_argument(
"--tofile",
action="store",
type=ap.FileType("w"),
help="""Write the output to file '%(dest)s' instead than to
stdout. Ignored if '--show-columns' not used.""")
p.add_argument(
"-c",
"--columns",
nargs='+',
default=["RA", "DEC", "Z"],
help="""Read the given column(s). Can be: integer, string and lists.
Operations permitted for string entry like 'a+b-1': 'a' and 'b' are column
name and '1' a number.""")
p.add_argument("--fmt",
action=apc.StoreFmt,
nargs='+',
default="%7.6e",
help="Format of the output files.")
description = """Parameters related to the parallel computation"""
p, parallel = apc.parallel_group(p, description=description)
return p.parse_args(args=argv)