Source code for sherpa.astro.io.xstable

#
#  Copyright (C) 2023
#  Smithsonian Astrophysical Observatory
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"""Create XSPEC table models.

This module supports creating and writing out `XSPEC table models
<https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/general/ogip_92_009/ogip_92_009.html>`_,
which can then be read in by the
`sherpa.astro.xspec.read_xstable_model` and
`sherpa.astro.ui.load_xstable_model` routines.

These routines should be considered experimental, as it is not
obvious that the interface is as usable as it could be.

Example
-------

The following example creates an additive table model
that represents a gaussian model where the only parameters are
the line position and the normalization.

>>> import numpy as np
>>> from sherpa.astro.io import xstable
>>> from sherpa.astro.xspec import XSgaussian

We shall use the XSPEC gaussian model `sherpa.astro.xspec.XSgaussian`
to create the template models.

>>> mdl = XSgaussian()
>>> print(mdl)
gaussian
   Param        Type          Value          Min          Max      Units
   -----        ----          -----          ---          ---      -----
   gaussian.LineE thawed          6.5            0        1e+06        keV
   gaussian.Sigma thawed          0.1            0           20        keV
   gaussian.norm thawed            1            0        1e+24

The models will be evaluated over the 0.1 to 2 keV range, with
a bin spacing of 0.01 keV (note that the last bin ends at 1.99 and
not 2.0 keV thanks to the behavior of `numpy.arange`).

>>> egrid = np.arange(0.1, 2, 0.01)
>>> elo = egrid[:-1]
>>> ehi = egrid[1:]
>>> emid = (elo + ehi) / 2

The table model will interpolate over the line position over
the range of 0 to 2.4 inclusive, with a spacing of 0.1 keV:

>>> linepos = np.arange(0, 2.5, 0.1)
>>> minval = linepos[0]
>>> maxval = linepos[-1]

The model is evaluated over the grid defined by ``elo`` and ``ehi``
for each element of ``linepos``, which is used to set the
`sherpa.astro.xspec.XSgaussian.LineE` parameter:

>>> models = []
>>> for lp in linepos:
...     mdl.linee = lp
...     ymodel = mdl(elo, ehi)
...     models.append(ymodel)
...

This model has a single interpolated parameter which we call
``"pos"``.  Note that the delta parameter - here set to 0.01 - is only
used by Sherpa to decide if the parameter is frozen (value is
negative) or not, but is used by the optimiser in XSPEC. The values
field is set to those used to generate the spectral models.

>>> param = xstable.Param("pos", 1, 0.01, minval, maxval,
...                       values=linepos)

With this we can create the necessary information to create the
table model (`make_xstable_model`) and then write it out
as a FITS file (`write_xstable_model`):

>>> hdus = xstable.make_xstable_model("gaussy", elo, ehi, params=[param],
...                                   spectra=models)
>>> xstable.write_xstable_model("example.mod", hdus, clobber=True)

This file can then be used in Sherpa with either
`sherpa.astro.ui.load_xstable_model` or
`sherpa.astro.xspec.read_xstable_model`. For example:

>>> from sherpa.astro import ui
>>> ui.load_xstable_model("mygauss", "example.mod")
>>> print(mygauss)
xstablemodel.mygauss
   Param        Type          Value          Min          Max      Units
   -----        ----          -----          ---          ---      -----
   mygauss.pos  thawed            1            0          2.4
   mygauss.norm thawed            1            0        1e+24

Notes
-----

XSPEC models can be created without XSPEC support in Sherpa, but XSPEC
support is needed to read the files in.

For additive models it is assumed that the model values - that is,
each bin - have units of photon/cm^2/s. This is easy to accidentally
change - e.g.  in the example above if mdl.norm were changed to a
value other than 1 everything would work but Sherpa and XSPEC would
infer incorrect fluxes or luminosities.

"""

from dataclasses import dataclass, field
import itertools
import time
from typing import Any, Optional, Union

import numpy as np

import sherpa


__all__ = ("BaseParam", "Param", "make_xstable_model",
           "write_xstable_model")


# In the typing support I have used Any to mean "ndarray".
#

[docs] @dataclass class BaseParam: """Represent a parameter. The absolute DELTA value is used by XSPEC but ignored by Sherpa. The sign of DELTA is used (by both Sherpa and XSPEC) to decide if the parameter should be frozen (DELTA is negative) or not by default. """ name: str """The parameter name. This must be unique and ideally a valid attribute name in Python, although the latter is not enforced. """ initial: float """The default value for the parameter.""" delta: float """The delta value for fitting. If negative then the parameter defaults to being frozen. Sherpa does not use this value (other than checking the sign) but XSPEC does. """ hardmin: float """The minimum value for the parameter.""" hardmax: float """The maximum value for the parameter.""" softmin: Optional[float] = None """The "soft" minimum. Defaults to hardmin if not given..""" softmax: Optional[float] = None """The "soft" maximum. Defaults to hardmax if not given.""" def __post_init__(self): """Validate the settings""" # Do we need to set up softmin/max? # if self.softmax is None: self.softmax = self.hardmax if self.softmin is None: self.softmin = self.hardmin # There should probably be a check that the name is not # an invalid Python attribute name. # if self.name.strip() == "": raise ValueError("name can not be empty") if self.softmin < self.hardmin: raise ValueError(f"Parameter {self.name} softmin={self.softmin} < hardmin={self.hardmin}") if self.softmax > self.hardmax: raise ValueError(f"Parameter {self.name} softmax={self.softmax} > hardmax={self.hardmax}") # We allow min == max if self.softmin > self.softmax: raise ValueError(f"Parameter {self.name} softmin={self.softmin} > softmax={self.softmax}") if self.initial < self.softmin or self.initial > self.softmax: raise ValueError(f"Parameter {self.name} initial={self.initial} outside softmin={self.softmin} to softmax={self.softmax}") if self.delta == 0: raise ValueError("delta can not be 0")
[docs] @dataclass class Param(BaseParam): """Represent an interpolated parameter.""" values: list[float] = field(default_factory=list) """The parameter values used to create the model spectra. Is is required that they range from hardmin to hardmax and are in monotonically increasing order (so it can not be an empty list). """ loginterp: bool = False """Are the values logarithmically interpolated (True) or linearly (False). Defaults to linear interpolation. """ def __post_init__(self): """Validate the settings""" super().__post_init__() if len(self.values) == 0: raise ValueError(f"Parameter {self.name} has no values") if self.values[0] != self.hardmin: raise ValueError(f"Parameter {self.name} hardmin={self.hardmin} != first value={self.values[0]}") if self.values[-1] != self.hardmax: raise ValueError(f"Parameter {self.name} hardmax={self.hardmax} != last value={self.values[-1]}") if np.any(np.diff(self.values) <= 0): raise ValueError(f"Parameter {self.name} values are not monotonically increasing")
# Perhaps the HeaderItem and Column types can be used in # sherpa.astro.io to pass information to and from the backends, rather # than the current system. However, that is for later work. # @dataclass class HeaderItem: """Represent a FITS header card. This does not support all FITS features. """ name: str """The keyword name (case insensitive)""" value: Union[str, bool, int, float] # will we need more? """The keyword value""" desc: Optional[str] """The description for the keyword""" unit: Optional[str] """The units of the value""" @dataclass class Column: """Represent a FITS column. This does not support all FITS features. """ name: str """The column name (case insensitive)""" values: Any # should be typed """The values for the column, as a ndarray. Variable-field arrays are represented as ndarrays with an object type. """ desc: Optional[str] """The column description""" unit: Optional[str] """The units of the column""" # To be generic this should probably be split into Primary, Table, and # Image HDUs. # @dataclass class TableHDU: """Represent a HDU: header and optional columns""" name: str """The name of the HDU""" header: list[HeaderItem] """The header values""" data: Optional[list[Column]] = None """The column data. This should be empty for a primary header, and have at least one entry for a table HDU. """ def key(name: str, value: Union[str, bool, int, float], desc: Optional[str] = None, unit: Optional[str] = None) -> HeaderItem: "Easily make a HeaderItem" return HeaderItem(name=name, value=value, desc=desc, unit=unit) def col(name: str, values: Any, desc: Optional[str] = None, unit: Optional[str] = None) -> Column: "Easily make a column" return Column(name=name, values=values, desc=desc, unit=unit) def xstable_primary(name: str, unit: str, addmodel: bool, redshift: bool, escale: bool, lolim: float, hilim: float, xfxp: Optional[list[str]] = None) -> TableHDU: """The PRIMARY block for an xspec table model.""" header = [ key("HDUCLASS", "OGIP", "format conforms to OGIP standard"), key("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC"), key("HDUVERS", "1.2.0", "version of format"), key("MODlNAME", name, "Model name"), key("MODLUNIT", unit, "Model units"), key("ADDMODEL", addmodel, "If T then this is an additive table model"), key("REDSHIFT", redshift, "If T then redshift will be a parameter"), key("ESCALE", escale, "If T then escale will be a parameter"), key("LOELIMIT", lolim, "Model value for energies below ENERGIES block"), key("HIELIMIT", hilim, "Model value for energies above ENERGIES block") ] if xfxp: header.append(key("NXFLTEXP", len(xfxp), "Number of model spectra per grid point")) for idx, val in enumerate(xfxp, 1): header.append(key(f"XFXP{idx:04d}", val, f"The expression for model {idx}")) # Let users know who created the file and when. # header.append(key("CREATOR", f"sherpa {sherpa.__version__}", "Code that created the file")) header.append(key("DATE", time.strftime("%Y-%m-%dT%H:%M:%S"), "Date file created")) return TableHDU(name="PRIMARY", header=header) def xstable_parameters(params: list[Param], addparams: Optional[list[BaseParam]]) -> TableHDU: """The PARAMETERS block for an xspec table model.""" nint = len(params) nadd = 0 if addparams is None else len(addparams) ntotal = nint + nadd header = [ key("HDUCLASS", "OGIP", "format conforms to OGIP standard"), key("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC"), key("HDUCLAS2", "PARAMETERS", "extension containing parameter info"), key("HDUVERS", "1.0.0", "version of format"), key("NINTPARM", nint, "Number of interpolation parameters"), key("NADDPARM", nadd, "Number of additional parameters") ] # Provide the parameters and then the additional parameters. # def get(field): f1 = [getattr(p, field) for p in params] if addparams is None: return f1 return f1 + [getattr(p, field) for p in addparams] methods = [1 if p.loginterp else 0 for p in params] + [0] * nadd nvalues = [len(p.values) for p in params] + [0] * nadd # Should the VALUE field use a variable-length field or not? # max_nvalues = max(nvalues) if nint > 1 and max_nvalues > 3: # The main array stores objects as each row can have different # lengths. # values = np.zeros(ntotal, dtype=object) for idx, p in enumerate(params): values[idx] = np.asarray(p.values, dtype=np.float32) # Empty arrays for the additional arrays for idx in range(nint, ntotal): values[idx] = np.asarray([], dtype=np.float32) else: values = np.zeros((ntotal, max_nvalues), dtype=np.float32) for idx, p in enumerate(params): values[idx, :len(p.values)] = p.values data = [ col("NAME", np.asarray(get("name"), dtype="U12"), "name of the parameter"), col("METHOD", np.asarray(methods, dtype=np.int32), "0 if linear, 1 if logarithmic"), col("INITIAL", np.asarray(get("initial"), dtype=np.float32), "Starting point"), col("DELTA", np.asarray(get("delta"), dtype=np.float32), "If negative frozen by default"), col("MINIMUM", np.asarray(get("hardmin"), dtype=np.float32), "hard lower limit"), col("BOTTOM", np.asarray(get("softmin"), dtype=np.float32), "soft lower limit"), col("TOP", np.asarray(get("softmax"), dtype=np.float32), "soft upper limit"), col("MAXIMUM", np.asarray(get("hardmax"), dtype=np.float32), "hard upper limit"), col("NUMBVALS", np.asarray(nvalues, dtype=np.int32), "number of tabulated parameter values"), col("VALUE", values, "tabulated parameter values") ] return TableHDU(name="PARAMETERS", header=header, data=data) def xstable_energies(energ_lo: Any, energ_hi: Any) -> TableHDU: """The ENERGIES block for an xspec table model.""" header = [ key("HDUCLASS", "OGIP", "format conforms to OGIP standard"), key("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC"), key("HDUCLAS2", "ENERGIES", "extension containing energy bin info"), key("HDUVERS", "1.0.0", "version of format") ] data = [ col("ENERG_LO", np.asarray(energ_lo, dtype=np.float32), "Minimum energy of the bin", unit="keV"), col("ENERG_HI", np.asarray(energ_hi, dtype=np.float32), "Maximum energy of the bin", unit="keV"), ] return TableHDU(name="ENERGIES", header=header, data=data) def xstable_spectra(paramvals: list[tuple[float, ...]], spectra: list[Any], addparam: Optional[list[BaseParam]], addspectra: Optional[list[list[Any]]], units: Optional[str]) -> TableHDU: """The SPECTRA block for an xspec table model.""" header = [ key("HDUCLASS", "OGIP", "format conforms to OGIP standard"), key("HDUCLAS1", "XSPEC TABLE MODEL", "model spectra for XSPEC"), key("HDUCLAS2", "MODEL SPECTRA", "extension containing model spectra"), key("HDUVERS", "1.0.0", "version of format") ] # The sizes have already been checked. # unit_opt = None if units == "" else units pvals = np.asarray(paramvals, dtype=np.float32) data = [ col("PARAMVAL", np.asarray(paramvals, dtype=np.float32), "Parameter values for spectrum"), col("INTPSPEC", np.asarray(spectra, dtype=np.float32), "Spectrum for interpolated parameters", unit=unit_opt) ] # Do we have any additional parameters? # if addparam is not None and addspectra is not None: zipped = zip(addparam, addspectra) for idx, (param, aspec) in enumerate(zipped, 1): data.append(col(f"ADDSP{idx:03d}", np.asarray(aspec, dtype=np.float32), desc=f"Additional spectrum {idx:03d}: {param.name}", unit=unit_opt)) return TableHDU(name="SPECTRA", header=header, data=data) # We could either send in the parameter values broken up by parameter, # or as a list of those used to create spectra (either way, we need to # deconstruct/reconstruct the other form). For now we send them in # per-parameter, but it could be changed if this approach is found to # be more awkward for users. #
[docs] def make_xstable_model(name: str, egrid_lo: Any, egrid_hi: Any, params: list[Param], spectra: list[Any], addparams: Optional[list[BaseParam]] = None, addspectra: Optional[list[list[Any]]] = None, addmodel: bool = True, redshift: bool = False, escale: bool = False, lolim: float = 0, hilim: float = 0, units: Optional[str] = None, xfxp: Optional[list[str]] = None ) -> list[TableHDU]: """Create the blocks for a XSPEC table model. An XSPEC table model can be either additive or multiplicative, contain 1 or more interpolated parameters, 0 or more additional parameters, and support additional parameters (redshift and escale), as well as setting the value to use outside the tabulated energy range. The table defines the energy grid the models are defined on, and the models used (one per set of parameters unless the xfxp argument is set). Parameters ---------- name : str The model name (stored in the table). Any spaces are removed. egrid_lo, egrid_hi : sequence of float The energy grid (in keV) used to define the spectra. It is required that len(egrid_lo) == len(egrid_hi), the arrays are in increasing order, that they are consecutive so that egrid_hi[i] == egrid_lo[i + 1], and that egrid_lo[0] > 0. params : sequence of Param The definitions of the parameters used to interpolate the models. It must have at least one element. spectra : sequence of sequence of float The spectra for each set of parameters in paramvals. It is a 2D array of shape(nrows, len(egrid_lo)), and each row matches the corresponding parameter grouping: paramvals[0].values[i], paramvals[1].values[j], .. where the first parameter loops the slowest. The number of rows is the multiplication of the number of parameter values. addparams : sequence of BaseParam or None, optional The definitions of the additional parameters; that is those that are not interpolated over. addspectra : sequence of sequence of sequence of float or None, optional The spectra for the additional parameters. It must is a 3D array of shape (nrows, len(addparams), len(egrid_lo)). addmodel : bool, optional Is this an additive model (True) or a multiplicative one (False). The default is True (additive). redshift : bool, optional Should the redshift parameter be added? The default is False. escale : bool, optional Should the escale parameter be added? The default is False. lolim, hilim : bool, optional The value to be used when energies are below or above the values in egrid_lo or egrid_hi respectively. units : str or None, optional The model units. For additive models the default is "photons/cm^2/s" and for multiplicative models it is "". xfxp : sequence of str or None If there are multiple spectra per parameter grid point, these values give the expression to use (the number of elements is the number of spectra per grid point). It is expected this is None or has a length more than 1. Returns ------- hdus : list of TableHDU The header and column data needed to create a FITS file. See Also -------- write_xstable_model Notes ----- This supports version 1.2.0 of the `XSPEC table model specification <https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/general/ogip_92_009/ogip_92_009.html>`_, although this code should be considered experimental. It is not designed to be memory efficient, so for models that use a large number of spectra, other tools may make more sense. """ nxfxp = 1 if xfxp is None else len(xfxp) # Not sure what the restrictions are, so just remove any spaces. # name_str = name.translate({32: None}) if units is None: unit_str = "photons/cm^2/s" if addmodel else "" else: unit_str = units # Check the parameter ranges make sense. # if len(params) == 0: raise ValueError("params can not be empty") # Check the parameter names are unique. We do a case-insensitive # comparison, but we write out the user-specified name. # names = [p.name.lower() for p in params] if addparams is not None: names += [p.name.lower() for p in addparams] snames = set(names) if len(names) != len(snames): raise ValueError(f"Parameter names are not unique") # Check the additional parameters # nadd = 0 if addparams is None else len(addparams) naddspec = 0 if addspectra is None else len(addspectra) if nadd != naddspec: raise ValueError(f"Mismatch between addparams and addspectra sizes: {nadd} {naddspec}") # What are the parameter combinations? The last parameter # loops fastest. If XFXP keyword are given then we have to # replicate each set of parameters nxfxp times. # pvals_indiv = [p.values for p in params] if nxfxp > 1: pvals_indiv.append([0] * nxfxp) pvalues = list(itertools.product(*pvals_indiv)) if nxfxp > 1: # remove the fake parameter used to duplicate each row pvalues = [pv[:-1] for pv in pvalues] # Does pvalues match the expected number of spectra? # npvs = len(pvalues) nspectra = len(spectra) if npvs != nspectra: raise ValueError(f"Expected {npvs} spectra, found {nspectra}") if addspectra is not None: for idx, aspec in enumerate(addspectra): naspec = len(aspec) if npvs != naspec: # We should use a type that combines # addparams/spectra but for now make mypy happy. # assert addparams is not None raise ValueError(f"Expected {npvs} spectra for additional parameter {addparams[idx].name}, found {naspec}") # Check the energy grid makes sense nlo = len(egrid_lo) nhi = len(egrid_hi) if nlo != nhi: raise ValueError(f"egrid_lo/hi do not match: {nlo} vs {nhi}") if nlo == 0: raise ValueError("egrid_lo/hi can not be empty") if np.any(np.diff(egrid_lo) <= 0): raise ValueError("egrid_lo is not monotonically increasing") if np.any(np.diff(egrid_hi) <= 0): raise ValueError("egrid_hi is not monotonically increasing") # Technically we should do a Knuth-like numerical comparison here, # but the assumption is that we created them so that they are # consecutive, so it's okay for this check (and to try and stop # yet-more-Xray-files-from-being-not-quite-valid(TM)). # if np.any(egrid_lo[1:] != egrid_hi[:-1]): raise ValueError("egrid_lo/hi are not consecutive") # Check we have the correct number of values in each spectrum. # for sp in spectra: nsp = len(sp) if nsp != nlo: raise ValueError(f"Spectrum should have {nlo} elements " f"but has {nsp}") if addspectra is not None: for idx, aspecs in enumerate(addspectra): for asp in aspecs: nsp = len(asp) if nsp != nlo: # We should use a type that combines # addparams/spectra but for now make mypy happy. # assert addparams is not None raise ValueError(f"Spectrum for parameter " f"{addparams[idx].name} should " f"have {nlo} elements but has {nsp}") # Create the separate blocks. # out = [] out.append(xstable_primary(name_str, unit_str, bool(addmodel), bool(redshift), bool(escale), float(lolim), float(hilim), xfxp=xfxp)) out.append(xstable_parameters(params, addparams)) out.append(xstable_energies(egrid_lo, egrid_hi)) out.append(xstable_spectra(pvalues, spectra, addparams, addspectra, units=unit_str)) return out
[docs] def write_xstable_model(filename: str, hdus: list[TableHDU], clobber: bool = False) -> None: """Write a XSPEC table model to disk. Parameters ---------- filename : str The filename to create. hdus : list of TableHDU The output of make_xstable_model. clobber : bool, optional If `True` then the output file will be over-written if it already exists, otherwise an error is raised. See Also -------- make_xstable_model """ from sherpa.astro import io assert io.backend is not None # for mypy io.backend.set_hdus(filename, hdus, clobber=clobber)