# Licensed under a 3-clause BSD style license - see LICENSE.rst
import abc
import copy
import inspect
import logging
import numpy as np
import scipy.interpolate
from astropy import units as u
from astropy.coordinates import SkyCoord
from astropy.io import fits
from astropy.table import Column, QTable, Table
from astropy.utils import lazyproperty
from gammapy.utils.interpolation import interpolation_scale
from .utils import INVALID_INDEX, edges_from_lo_hi, find_bands_hdu, find_hdu
__all__ = ["MapCoord", "Geom", "MapAxis"]
log = logging.getLogger(__name__)
def make_axes(axes_in):
"""Make a sequence of `~MapAxis` objects."""
if axes_in is None:
return []
axes_out = []
for idx, ax in enumerate(axes_in):
if isinstance(ax, np.ndarray):
ax = MapAxis(ax)
if ax.name == "":
ax.name = "axis{}".format(idx)
axes_out += [ax]
return axes_out
def make_axes_cols(axes, axis_names=None):
"""Make FITS table columns for map axes.
Parameters
----------
axes : list
Python list of `MapAxis` objects
Returns
-------
cols : list
Python list of `~astropy.io.fits.Column`
"""
size = np.prod([ax.nbin for ax in axes])
chan = np.arange(0, size)
cols = [fits.Column("CHANNEL", "I", array=chan)]
if axis_names is None:
axis_names = [ax.name for ax in axes]
axis_names = [_.upper() for _ in axis_names]
axes_ctr = np.meshgrid(*[ax.center for ax in axes])
axes_min = np.meshgrid(*[ax.edges[:-1] for ax in axes])
axes_max = np.meshgrid(*[ax.edges[1:] for ax in axes])
for i, (ax, name) in enumerate(zip(axes, axis_names)):
if name == "ENERGY":
colnames = ["ENERGY", "E_MIN", "E_MAX"]
else:
s = "AXIS%i" % i if name == "" else name
colnames = [s, s + "_MIN", s + "_MAX"]
for colname, v in zip(colnames, [axes_ctr, axes_min, axes_max]):
array = np.ravel(v[i])
unit = ax.unit.to_string("fits")
cols.append(fits.Column(colname, "E", array=array, unit=unit))
return cols
def energy_axis_from_fgst_ccube(hdu):
bands = Table.read(hdu)
edges_min = bands["E_MIN"].quantity
edges_max = bands["E_MAX"].quantity
edges = edges_from_lo_hi(edges_min, edges_max)
return [MapAxis.from_edges(edges=edges, name="energy", interp="log")]
def energy_axis_from_fgst_template(hdu):
bands = Table.read(hdu)
allowed_names = ["Energy", "ENERGY", "energy"]
for colname in bands.colnames:
if colname in allowed_names:
tag = colname
break
nodes = bands[tag].data
return [MapAxis.from_nodes(nodes=nodes, name="energy", unit="MeV", interp="log")]
def axes_from_bands_hdu(hdu):
"""Read and returns the map axes from a BANDS table.
Parameters
----------
hdu : `~astropy.io.fits.BinTableHDU`
The BANDS table HDU.
Returns
-------
axes : list of `~MapAxis`
List of axis objects.
"""
axes = []
bands = Table.read(hdu)
for idx in range(5):
axcols = bands.meta.get("AXCOLS{}".format(idx + 1))
if axcols is None:
break
colnames = axcols.split(",")
node_type = "edges" if len(colnames) == 2 else "center"
# TODO: check why this extra case is needed
if colnames[0] == "E_MIN":
name = "energy"
else:
name = colnames[0].split("_")[0].lower()
interp = bands.meta.get("INTERP{}".format(idx + 1), "lin")
if node_type == "center":
nodes = np.unique(bands[colnames[0]].quantity)
else:
edges_min = np.unique(bands[colnames[0]].quantity)
edges_max = np.unique(bands[colnames[1]].quantity)
nodes = edges_from_lo_hi(edges_min, edges_max)
axis = MapAxis(nodes=nodes, node_type=node_type, interp=interp, name=name)
axes.append(axis)
return axes
def find_and_read_bands(hdu):
if hdu is None:
return []
if hdu.name == "ENERGIES":
axes = energy_axis_from_fgst_template(hdu)
elif hdu.name == "EBOUNDS":
axes = energy_axis_from_fgst_ccube(hdu)
else:
axes = axes_from_bands_hdu(hdu)
return axes
def get_shape(param):
if param is None:
return tuple()
if not isinstance(param, tuple):
param = [param]
return max([np.array(p, ndmin=1).shape for p in param])
def coordsys_to_frame(coordsys):
if coordsys in ["CEL", "C", "fk5", "fk4", "icrs"]:
return "icrs"
elif coordsys in ["GAL", "G", "galactic"]:
return "galactic"
else:
raise ValueError(f"Unrecognized coordinate system: {coordsys!r}")
def frame_to_coordsys(frame):
if frame in ["fk5", "fk4", "icrs"]:
return "CEL"
elif frame == "galactic":
return "GAL"
else:
raise ValueError(f"Unrecognized coordinate system: {frame!r}")
# TODO: remove (or improve)
def skycoord_to_lonlat(skycoord, coordsys=None):
"""Convert SkyCoord to lon, lat, frame.
Returns
-------
lon : `~numpy.ndarray`
Longitude in degrees.
lat : `~numpy.ndarray`
Latitude in degrees.
"""
if coordsys:
frame = coordsys_to_frame(coordsys)
skycoord = skycoord.transform_to(frame)
return skycoord.data.lon.deg, skycoord.data.lat.deg, skycoord.frame
def lonlat_to_skycoord(lon, lat, coordsys):
return SkyCoord(lon, lat, frame=coordsys_to_frame(coordsys), unit="deg")
def pix_tuple_to_idx(pix):
"""Convert a tuple of pixel coordinate arrays to a tuple of pixel indices.
Pixel coordinates are rounded to the closest integer value.
Parameters
----------
pix : tuple
Tuple of pixel coordinates with one element for each dimension
Returns
-------
idx : `~numpy.ndarray`
Array of pixel indices
"""
idx = []
for p in pix:
p = np.array(p, ndmin=1)
if np.issubdtype(p.dtype, np.integer):
idx += [p]
else:
p_idx = np.rint(p).astype(int)
p_idx[~np.isfinite(p)] = INVALID_INDEX.int
idx += [p_idx]
return tuple(idx)
def coord_to_idx(edges, x, clip=False):
"""Convert axis coordinates ``x`` to bin indices.
Returns -1 for values below/above the lower/upper edge.
"""
x = np.array(x, ndmin=1)
ibin = np.digitize(x, edges) - 1
if clip:
ibin[x < edges[0]] = 0
ibin[x > edges[-1]] = len(edges) - 1
else:
with np.errstate(invalid="ignore"):
ibin[x > edges[-1]] = INVALID_INDEX.int
ibin[~np.isfinite(x)] = INVALID_INDEX.int
return ibin
def coord_to_pix(edges, coord, interp="lin"):
"""Convert axis to pixel coordinates for given interpolation scheme."""
scale = interpolation_scale(interp)
interp_fn = scipy.interpolate.interp1d(
scale(edges), np.arange(len(edges), dtype=float), fill_value="extrapolate"
)
return interp_fn(scale(coord))
def pix_to_coord(edges, pix, interp="lin"):
"""Convert pixel to grid coordinates for given interpolation scheme."""
scale = interpolation_scale(interp)
interp_fn = scipy.interpolate.interp1d(
np.arange(len(edges), dtype=float), scale(edges), fill_value="extrapolate"
)
return scale.inverse(interp_fn(pix))
[docs]class MapAxis:
"""Class representing an axis of a map.
Provides methods for
transforming to/from axis and pixel coordinates. An axis is
defined by a sequence of node values that lie at the center of
each bin. The pixel coordinate at each node is equal to its index
in the node array (0, 1, ..). Bin edges are offset by 0.5 in
pixel coordinates from the nodes such that the lower/upper edge of
the first bin is (-0.5,0.5).
Parameters
----------
nodes : `~numpy.ndarray` or `~astropy.units.Quantity`
Array of node values. These will be interpreted as either bin
edges or centers according to ``node_type``.
interp : str
Interpolation method used to transform between axis and pixel
coordinates. Valid options are 'log', 'lin', and 'sqrt'.
name : str
Axis name
node_type : str
Flag indicating whether coordinate nodes correspond to pixel
edges (node_type = 'edge') or pixel centers (node_type =
'center'). 'center' should be used where the map values are
defined at a specific coordinate (e.g. differential
quantities). 'edge' should be used where map values are
defined by an integral over coordinate intervals (e.g. a
counts histogram).
unit : str
String specifying the data units.
"""
# TODO: Add methods to faciliate FITS I/O.
# TODO: Cache an interpolation object?
def __init__(self, nodes, interp="lin", name="", node_type="edges", unit=""):
self.name = name
if len(nodes) != len(np.unique(nodes)):
raise ValueError("MapAxis: node values must be unique")
if ~(np.all(nodes == np.sort(nodes)) or np.all(nodes[::-1] == np.sort(nodes))):
raise ValueError("MapAxis: node values must be sorted")
if len(nodes) == 1 and node_type == "center":
raise ValueError("Single bins can only be used with node-type 'edges'")
if isinstance(nodes, u.Quantity):
unit = nodes.unit if nodes.unit is not None else ""
nodes = nodes.value
else:
nodes = np.array(nodes)
self._unit = u.Unit(unit)
self._nodes = nodes
self._node_type = node_type
self._interp = interp
if (self._nodes < 0).any() and interp != "lin":
raise ValueError(
f"Interpolation scaling {interp!r} only support for positive node values."
)
# Set pixel coordinate of first node
if node_type == "edges":
self._pix_offset = -0.5
nbin = len(nodes) - 1
elif node_type == "center":
self._pix_offset = 0.0
nbin = len(nodes)
else:
raise ValueError(f"Invalid node type: {node_type!r}")
self._nbin = nbin
def __eq__(self, other):
if not isinstance(other, self.__class__):
return NotImplemented
# TODO: implement an allclose method for MapAxis and call it here
if self.edges.shape != other.edges.shape:
return False
if self.unit.is_equivalent(other.unit) is False:
return False
return (
np.allclose(
self.edges.to(other.unit).value, other.edges.value, atol=1e-6, rtol=1e-6
)
and self._node_type == other._node_type
and self._interp == other._interp
and self.name.upper() == other.name.upper()
)
def __ne__(self, other):
return not self.__eq__(other)
def __hash__(self):
return id(self)
@property
def interp(self):
"""Interpolation scale of the axis."""
return self._interp
@property
def name(self):
"""Name of the axis."""
return self._name
@name.setter
def name(self, val):
self._name = val
@lazyproperty
def edges(self):
"""Return array of bin edges."""
pix = np.arange(self.nbin + 1, dtype=float) - 0.5
return u.Quantity(self.pix_to_coord(pix), self._unit, copy=False)
@lazyproperty
def center(self):
"""Return array of bin centers."""
pix = np.arange(self.nbin, dtype=float)
return u.Quantity(self.pix_to_coord(pix), self._unit, copy=False)
@lazyproperty
def bin_width(self):
"""Array of bin widths."""
return np.diff(self.edges)
@property
def nbin(self):
"""Return number of bins."""
return self._nbin
@property
def node_type(self):
"""Return node type ('center' or 'edge')."""
return self._node_type
@property
def unit(self):
"""Return coordinate axis unit."""
return self._unit
[docs] @classmethod
def from_bounds(cls, lo_bnd, hi_bnd, nbin, **kwargs):
"""Generate an axis object from a lower/upper bound and number of bins.
If node_type = 'edge' then bounds correspond to the
lower and upper bound of the first and last bin. If node_type
= 'center' then bounds correspond to the centers of the first
and last bin.
Parameters
----------
lo_bnd : float
Lower bound of first axis bin.
hi_bnd : float
Upper bound of last axis bin.
nbin : int
Number of bins.
interp : {'lin', 'log', 'sqrt'}
Interpolation method used to transform between axis and pixel
coordinates. Default: 'lin'.
"""
interp = kwargs.setdefault("interp", "lin")
node_type = kwargs.setdefault("node_type", "edges")
if node_type == "edges":
nnode = nbin + 1
elif node_type == "center":
nnode = nbin
else:
raise ValueError(f"Invalid node type: {node_type!r}")
if interp == "lin":
nodes = np.linspace(lo_bnd, hi_bnd, nnode)
elif interp == "log":
nodes = np.exp(np.linspace(np.log(lo_bnd), np.log(hi_bnd), nnode))
elif interp == "sqrt":
nodes = np.linspace(lo_bnd ** 0.5, hi_bnd ** 0.5, nnode) ** 2.0
else:
raise ValueError(f"Invalid interp: {interp}")
return cls(nodes, **kwargs)
[docs] @classmethod
def from_energy_bounds(cls, emin, emax, nbin, unit=None):
"""Make an energy axis.
Used frequently also to make energy grids, by making
the axis, and then using ``axis.center`` or ``axis.edges``.
Parameters
----------
emin, emax : `~astropy.units.Quantity`, float
Energy range
nbin : int
Number of bins
unit : `~astropy.units.Unit`
Energy unit
Returns
-------
axis : `MapAxis`
Axis with name "energy" and interp "log".
"""
if unit is None:
emin = u.Quantity(emin)
emax = u.Quantity(emax)
unit = emax.unit
emin = emin.to(unit)
else:
unit = u.Unit(unit)
emin = u.Quantity(emin, unit)
emax = u.Quantity(emax, unit)
return cls.from_bounds(
emin.value, emax.value, nbin=nbin, unit=unit, interp="log", name="energy"
)
[docs] @classmethod
def from_nodes(cls, nodes, **kwargs):
"""Generate an axis object from a sequence of nodes (bin centers).
This will create a sequence of bins with edges half-way
between the node values. This method should be used to
construct an axis where the bin center should lie at a
specific value (e.g. a map of a continuous function).
Parameters
----------
nodes : `~numpy.ndarray`
Axis nodes (bin center).
interp : {'lin', 'log', 'sqrt'}
Interpolation method used to transform between axis and pixel
coordinates. Default: 'lin'.
"""
if len(nodes) < 1:
raise ValueError("Nodes array must have at least one element.")
return cls(nodes, node_type="center", **kwargs)
[docs] @classmethod
def from_edges(cls, edges, **kwargs):
"""Generate an axis object from a sequence of bin edges.
This method should be used to construct an axis where the bin
edges should lie at specific values (e.g. a histogram). The
number of bins will be one less than the number of edges.
Parameters
----------
edges : `~numpy.ndarray`
Axis bin edges.
interp : {'lin', 'log', 'sqrt'}
Interpolation method used to transform between axis and pixel
coordinates. Default: 'lin'.
"""
if len(edges) < 2:
raise ValueError("Edges array must have at least two elements.")
return cls(edges, node_type="edges", **kwargs)
[docs] def pix_to_coord(self, pix):
"""Transform from pixel to axis coordinates.
Parameters
----------
pix : `~numpy.ndarray`
Array of pixel coordinate values.
Returns
-------
coord : `~numpy.ndarray`
Array of axis coordinate values.
"""
pix = pix - self._pix_offset
values = pix_to_coord(self._nodes, pix, interp=self._interp)
return u.Quantity(values, unit=self.unit, copy=False)
[docs] def coord_to_pix(self, coord):
"""Transform from axis to pixel coordinates.
Parameters
----------
coord : `~numpy.ndarray`
Array of axis coordinate values.
Returns
-------
pix : `~numpy.ndarray`
Array of pixel coordinate values.
"""
coord = u.Quantity(coord, self.unit, copy=False).value
pix = coord_to_pix(self._nodes, coord, interp=self._interp)
return np.array(pix + self._pix_offset, ndmin=1)
[docs] def coord_to_idx(self, coord, clip=False):
"""Transform from axis coordinate to bin index.
Parameters
----------
coord : `~numpy.ndarray`
Array of axis coordinate values.
clip : bool
Choose whether to clip the index to the valid range of the
axis. If false then indices for values outside the axis
range will be set -1.
Returns
-------
idx : `~numpy.ndarray`
Array of bin indices.
"""
coord = u.Quantity(coord, self.unit, copy=False).value
return coord_to_idx(self.edges.value, coord, clip)
[docs] def slice(self, idx):
"""Create a new axis object by extracting a slice from this axis.
Parameters
----------
idx : slice
Slice object selecting a subselection of the axis.
Returns
-------
axis : `~MapAxis`
Sliced axis object.
"""
center = self.center[idx].value
idx = self.coord_to_idx(center)
# For edge nodes we need to keep N+1 nodes
if self._node_type == "edges":
idx = tuple(list(idx) + [1 + idx[-1]])
nodes = self._nodes[(idx,)]
return MapAxis(
nodes,
interp=self._interp,
name=self._name,
node_type=self._node_type,
unit=self._unit,
)
[docs] def squash(self):
"""Create a new axis object by squashing the axis into one bin.
Returns
-------
axis : `~MapAxis`
Sliced axis object.
"""
# TODO: Decide on handling node_type=center
# See https://github.com/gammapy/gammapy/issues/1952
return MapAxis.from_bounds(
lo_bnd=self.edges[0].value,
hi_bnd=self.edges[-1].value,
nbin=1,
interp=self._interp,
name=self._name,
unit=self._unit,
)
def __repr__(self):
str_ = self.__class__.__name__
str_ += "\n\n"
fmt = "\t{:<10s} : {:<10s}\n"
str_ += fmt.format("name", self.name)
str_ += fmt.format("unit", "{!r}".format(str(self.unit)))
str_ += fmt.format("nbins", str(self.nbin))
str_ += fmt.format("node type", self.node_type)
vals = self.edges if self.node_type == "edges" else self.center
str_ += fmt.format(f"{self.node_type} min", "{:.1e}".format(vals.min()))
str_ += fmt.format(f"{self.node_type} max", "{:.1e}".format(vals.max()))
str_ += fmt.format("interp", self._interp)
return str_
def _init_copy(self, **kwargs):
"""Init map axis instance by copying missing init arguments from self.
"""
argnames = inspect.getfullargspec(self.__init__).args
argnames.remove("self")
for arg in argnames:
value = getattr(self, "_" + arg)
kwargs.setdefault(arg, copy.deepcopy(value))
return self.__class__(**kwargs)
[docs] def copy(self, **kwargs):
"""Copy `MapAxis` instance and overwrite given attributes.
Parameters
----------
**kwargs : dict
Keyword arguments to overwrite in the map axis constructor.
Returns
-------
copy : `MapAxis`
Copied map axis.
"""
return self._init_copy(**kwargs)
[docs] def group_table(self, edges):
"""Compute bin groups table for the map axis, given coarser bin edges.
Parameters
----------
edges : `~astropy.units.Quantity`
Group bin edges.
Returns
-------
groups : `~astropy.table.Table`
Map axis group table.
"""
# TODO: try to simplify this code
if not self.node_type == "edges":
raise ValueError("Only edge based map axis can be grouped")
edges_pix = self.coord_to_pix(edges)
edges_pix = np.clip(edges_pix, -0.5, self.nbin - 0.5)
edges_idx = np.round(edges_pix + 0.5) - 0.5
edges_idx = np.unique(edges_idx)
edges_ref = self.pix_to_coord(edges_idx)
groups = QTable()
groups[f"{self.name}_min"] = edges_ref[:-1]
groups[f"{self.name}_max"] = edges_ref[1:]
groups["idx_min"] = (edges_idx[:-1] + 0.5).astype(int)
groups["idx_max"] = (edges_idx[1:] - 0.5).astype(int)
if len(groups) == 0:
raise ValueError("No overlap between reference and target edges.")
groups["bin_type"] = "normal "
edge_idx_start, edge_ref_start = edges_idx[0], edges_ref[0]
if edge_idx_start > 0:
underflow = {
"bin_type": "underflow",
"idx_min": 0,
"idx_max": edge_idx_start,
f"{self.name}_min": self.pix_to_coord(-0.5),
f"{self.name}_max": edge_ref_start,
}
groups.insert_row(0, vals=underflow)
edge_idx_end, edge_ref_end = edges_idx[-1], edges_ref[-1]
if edge_idx_end < (self.nbin - 0.5):
overflow = {
"bin_type": "overflow",
"idx_min": edge_idx_end + 1,
"idx_max": self.nbin - 1,
f"{self.name}_min": edge_ref_end,
f"{self.name}_max": self.pix_to_coord(self.nbin - 0.5),
}
groups.add_row(vals=overflow)
group_idx = Column(np.arange(len(groups)))
groups.add_column(group_idx, name="group_idx", index=0)
return groups
def _up_down_sample(self, nbin):
if self.node_type == "edges":
nodes = self.edges
else:
nodes = self.center
lo_bnd, hi_bnd = nodes.min(), nodes.max()
return self.from_bounds(
lo_bnd=lo_bnd.value,
hi_bnd=hi_bnd.value,
nbin=nbin,
interp=self.interp,
node_type=self.node_type,
unit=self.unit,
name=self.name,
)
[docs] def upsample(self, factor):
"""Upsample map axis by a given factor.
Parameters
----------
factor : int
Upsampling factor.
Returns
-------
axis : `MapAxis`
Usampled map axis.
"""
nbin = self.nbin * factor
return self._up_down_sample(nbin)
[docs] def downsample(self, factor):
"""Downsample map axis by a given factor.
Parameters
----------
factor : int
Downsampling factor.
Returns
-------
axis : `MapAxis`
Downsampled map axis.
"""
nbin = int(self.nbin / factor)
return self._up_down_sample(nbin)
[docs]class MapCoord:
"""Represents a sequence of n-dimensional map coordinates.
Contains coordinates for 2 spatial dimensions and an arbitrary
number of additional non-spatial dimensions.
For further information see :ref:`mapcoord`.
Parameters
----------
data : `dict` of `~numpy.ndarray`
Dictionary of coordinate arrays.
coordsys : {'CEL', 'GAL', None}
Spatial coordinate system. If None then the coordinate system
will be set to the native coordinate system of the geometry.
match_by_name : bool
Match coordinates to axes by name?
If false coordinates will be matched by index.
"""
def __init__(self, data, coordsys=None, match_by_name=True):
if "lon" not in data or "lat" not in data:
raise ValueError("data dictionary must contain axes named 'lon' and 'lat'.")
data = {k: np.atleast_1d(np.asanyarray(v)) for k, v in data.items()}
vals = np.broadcast_arrays(*data.values(), subok=True)
self._data = dict(zip(data.keys(), vals))
self._coordsys = coordsys
self._match_by_name = match_by_name
def __getitem__(self, key):
if isinstance(key, str):
return self._data[key]
else:
return list(self._data.values())[key]
def __iter__(self):
return iter(self._data.values())
@property
def ndim(self):
"""Number of dimensions."""
return len(self._data)
@property
def shape(self):
"""Coordinate array shape."""
return self[0].shape
@property
def size(self):
return self[0].size
@property
def lon(self):
"""Longitude coordinate in degrees."""
return self._data["lon"]
@property
def lat(self):
"""Latitude coordinate in degrees."""
return self._data["lat"]
@property
def theta(self):
"""Theta co-latitude angle in radians."""
theta = u.Quantity(self.lat, unit="deg", copy=False).to_value("rad")
return np.pi / 2.0 - theta
@property
def phi(self):
"""Phi longitude angle in radians."""
phi = u.Quantity(self.lon, unit="deg", copy=False).to_value("rad")
return phi
@property
def coordsys(self):
"""Coordinate system (str)."""
return self._coordsys
@property
def match_by_name(self):
"""Boolean flag: axis lookup by name (True) or index (False)."""
return self._match_by_name
@property
def skycoord(self):
return SkyCoord(
self.lon, self.lat, unit="deg", frame=coordsys_to_frame(self.coordsys)
)
@classmethod
def _from_lonlat(cls, coords, coordsys=None):
"""Create a `~MapCoord` from a tuple of coordinate vectors.
The first two elements of the tuple should be longitude and latitude in degrees.
Parameters
----------
coords : tuple
Tuple of `~numpy.ndarray`.
Returns
-------
coord : `~MapCoord`
A coordinates object.
"""
if isinstance(coords, (list, tuple)):
coords_dict = {"lon": coords[0], "lat": coords[1]}
for i, c in enumerate(coords[2:]):
coords_dict[f"axis{i}"] = c
else:
raise ValueError("Unrecognized input type.")
return cls(coords_dict, coordsys=coordsys, match_by_name=False)
@classmethod
def _from_skycoord(cls, coords, coordsys=None):
"""Create from vector of `~astropy.coordinates.SkyCoord`.
Parameters
----------
coords : tuple
Coordinate tuple with first element of type
`~astropy.coordinates.SkyCoord`.
coordsys : {'CEL', 'GAL', None}
Spatial coordinate system of output `~MapCoord` object.
If None the coordinate system will be set to the frame of
the `~astropy.coordinates.SkyCoord` object.
"""
skycoord = coords[0]
coordsys_skycoord = frame_to_coordsys(skycoord.frame.name)
coords = (skycoord.data.lon.deg, skycoord.data.lat.deg) + coords[1:]
coords = cls._from_lonlat(coords, coordsys=coordsys_skycoord)
if coordsys is None:
return coords
else:
return coords.to_coordsys(coordsys)
@classmethod
def _from_tuple(cls, coords, coordsys=None):
"""Create from tuple of coordinate vectors."""
if isinstance(coords[0], (list, np.ndarray)) or np.isscalar(coords[0]):
return cls._from_lonlat(coords, coordsys=coordsys)
elif isinstance(coords[0], SkyCoord):
return cls._from_skycoord(coords, coordsys=coordsys)
else:
raise TypeError(f"Type not supported: {type(coords)!r}")
@classmethod
def _from_dict(cls, coords, coordsys=None):
"""Create from a dictionary of coordinate vectors."""
if "lon" in coords and "lat" in coords:
return cls(coords, coordsys=coordsys)
elif "skycoord" in coords:
lon, lat, frame = skycoord_to_lonlat(coords["skycoord"], coordsys=coordsys)
coords_dict = {"lon": lon, "lat": lat}
for k, v in coords.items():
if k == "skycoord":
continue
coords_dict[k] = v
if coordsys is None:
coordsys = frame_to_coordsys(frame.name)
return cls(coords_dict, coordsys=coordsys)
else:
raise ValueError("coords dict must contain 'lon'/'lat' or 'skycoord'.")
[docs] @classmethod
def create(cls, data, coordsys=None):
"""Create a new `~MapCoord` object.
This method can be used to create either unnamed (with tuple input)
or named (via dict input) axes.
Parameters
----------
data : tuple, dict, `MapCoord` or `~astropy.coordinates.SkyCoord`
Object containing coordinate arrays.
coordsys : {'CEL', 'GAL', None}, optional
Set the coordinate system for longitude and latitude. If
None longitude and latitude will be assumed to be in
the coordinate system native to a given map geometry.
Examples
--------
>>> from astropy.coordinates import SkyCoord
>>> from gammapy.maps import MapCoord
>>> lon, lat = [1, 2], [2, 3]
>>> skycoord = SkyCoord(lon, lat, unit='deg')
>>> energy = [1000]
>>> c = MapCoord.create((lon,lat))
>>> c = MapCoord.create((skycoord,))
>>> c = MapCoord.create((lon,lat,energy))
>>> c = MapCoord.create(dict(lon=lon,lat=lat))
>>> c = MapCoord.create(dict(lon=lon,lat=lat,energy=energy))
>>> c = MapCoord.create(dict(skycoord=skycoord,energy=energy))
"""
if isinstance(data, cls):
if data.coordsys is None or coordsys == data.coordsys:
return data
else:
return data.to_coordsys(coordsys)
elif isinstance(data, dict):
return cls._from_dict(data, coordsys=coordsys)
elif isinstance(data, (list, tuple)):
return cls._from_tuple(data, coordsys=coordsys)
elif isinstance(data, SkyCoord):
return cls._from_skycoord((data,), coordsys=coordsys)
else:
raise TypeError(f"Unsupported input type: {type(data)!r}")
[docs] def to_coordsys(self, coordsys):
"""Convert to a different coordinate frame.
Parameters
----------
coordsys : {'CEL', 'GAL'}
Coordinate system, either Galactic ('GAL') or Equatorial ('CEL').
Returns
-------
coords : `~MapCoord`
A coordinates object.
"""
if coordsys == self.coordsys:
return copy.deepcopy(self)
else:
skycoord = lonlat_to_skycoord(self.lon, self.lat, self.coordsys)
lon, lat, frame = skycoord_to_lonlat(skycoord, coordsys=coordsys)
data = copy.deepcopy(self._data)
if isinstance(self.lon, u.Quantity):
lon = u.Quantity(lon, unit="deg", copy=False)
if isinstance(self.lon, u.Quantity):
lat = u.Quantity(lat, unit="deg", copy=False)
data["lon"] = lon
data["lat"] = lat
return self.__class__(data, coordsys, self._match_by_name)
[docs] def apply_mask(self, mask):
"""Return a masked copy of this coordinate object.
Parameters
----------
mask : `~numpy.ndarray`
Boolean mask.
Returns
-------
coords : `~MapCoord`
A coordinates object.
"""
data = {k: v[mask] for k, v in self._data.items()}
return self.__class__(data, self.coordsys, self._match_by_name)
[docs] def copy(self):
"""Copy `MapCoord` object."""
return copy.deepcopy(self)
def __repr__(self):
return (
f"{self.__class__.__name__}\n\n"
f"\taxes : {list(self._data.keys())}\n"
f"\tshape : {self.shape[::-1]}\n"
f"\tndim : {self.ndim}\n"
f"\tcoordsys : {self.coordsys}\n"
)
[docs]class Geom(abc.ABC):
"""Map geometry base class.
See also: `~gammapy.maps.WcsGeom` and `~gammapy.maps.HpxGeom`
"""
@property
@abc.abstractmethod
def data_shape(self):
"""Shape of the Numpy data array matching this geometry."""
pass
@property
@abc.abstractmethod
def is_allsky(self):
pass
@property
@abc.abstractmethod
def center_coord(self):
pass
@property
@abc.abstractmethod
def center_pix(self):
pass
@property
@abc.abstractmethod
def center_skydir(self):
pass
[docs] @classmethod
def from_hdulist(cls, hdulist, hdu=None, hdu_bands=None):
"""Load a geometry object from a FITS HDUList.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
HDU list containing HDUs for map data and bands.
hdu : str
Name or index of the HDU with the map data.
hdu_bands : str
Name or index of the HDU with the BANDS table. If not
defined this will be inferred from the FITS header of the
map HDU.
Returns
-------
geom : `~Geom`
Geometry object.
"""
if hdu is None:
hdu = find_hdu(hdulist)
else:
hdu = hdulist[hdu]
if hdu_bands is None:
hdu_bands = find_bands_hdu(hdulist, hdu)
if hdu_bands is not None:
hdu_bands = hdulist[hdu_bands]
return cls.from_header(hdu.header, hdu_bands)
[docs] def make_bands_hdu(self, hdu=None, hdu_skymap=None, conv=None):
header = fits.Header()
self._fill_header_from_axes(header)
axis_names = None
# FIXME: Check whether convention is compatible with
# dimensionality of geometry
if conv == "fgst-ccube":
hdu = "EBOUNDS"
axis_names = ["energy"]
elif conv == "fgst-template":
hdu = "ENERGIES"
axis_names = ["energy"]
elif conv == "gadf" and hdu is None:
if hdu_skymap:
hdu = f"{hdu_skymap}_BANDS"
else:
hdu = "BANDS"
# else:
# raise ValueError('Unknown conv: {}'.format(conv))
cols = make_axes_cols(self.axes, axis_names)
cols += self._make_bands_cols()
return fits.BinTableHDU.from_columns(cols, header, name=hdu)
@abc.abstractmethod
def _make_bands_cols(self):
pass
[docs] @abc.abstractmethod
def get_idx(self, idx=None, local=False, flat=False):
"""Get tuple of pixel indices for this geometry.
Returns all pixels in the geometry by default. Pixel indices
for a single image plane can be accessed by setting ``idx``
to the index tuple of a plane.
Parameters
----------
idx : tuple, optional
A tuple of indices with one index for each non-spatial
dimension. If defined only pixels for the image plane with
this index will be returned. If none then all pixels
will be returned.
local : bool
Flag to return local or global pixel indices. Local
indices run from 0 to the number of pixels in a given
image plane.
flat : bool, optional
Return a flattened array containing only indices for
pixels contained in the geometry.
Returns
-------
idx : tuple
Tuple of pixel index vectors with one vector for each
dimension.
"""
pass
[docs] @abc.abstractmethod
def get_coord(self, idx=None, flat=False):
"""Get the coordinate array for this geometry.
Returns a coordinate array with the same shape as the data
array. Pixels outside the geometry are set to NaN.
Coordinates for a single image plane can be accessed by
setting ``idx`` to the index tuple of a plane.
Parameters
----------
idx : tuple, optional
A tuple of indices with one index for each non-spatial
dimension. If defined only coordinates for the image
plane with this index will be returned. If none then
coordinates for all pixels will be returned.
flat : bool, optional
Return a flattened array containing only coordinates for
pixels contained in the geometry.
Returns
-------
coords : tuple
Tuple of coordinate vectors with one vector for each
dimension.
"""
pass
[docs] @abc.abstractmethod
def coord_to_pix(self, coords):
"""Convert map coordinates to pixel coordinates.
Parameters
----------
coords : tuple
Coordinate values in each dimension of the map. This can
either be a tuple of numpy arrays or a MapCoord object.
If passed as a tuple then the ordering should be
(longitude, latitude, c_0, ..., c_N) where c_i is the
coordinate vector for axis i.
Returns
-------
pix : tuple
Tuple of pixel coordinates in image and band dimensions.
"""
pass
[docs] def coord_to_idx(self, coords, clip=False):
"""Convert map coordinates to pixel indices.
Parameters
----------
coords : tuple or `~MapCoord`
Coordinate values in each dimension of the map. This can
either be a tuple of numpy arrays or a MapCoord object.
If passed as a tuple then the ordering should be
(longitude, latitude, c_0, ..., c_N) where c_i is the
coordinate vector for axis i.
clip : bool
Choose whether to clip indices to the valid range of the
geometry. If false then indices for coordinates outside
the geometry range will be set -1.
Returns
-------
pix : tuple
Tuple of pixel indices in image and band dimensions.
Elements set to -1 correspond to coordinates outside the
map.
"""
pix = self.coord_to_pix(coords)
return self.pix_to_idx(pix, clip=clip)
[docs] @abc.abstractmethod
def pix_to_coord(self, pix):
"""Convert pixel coordinates to map coordinates.
Parameters
----------
pix : tuple
Tuple of pixel coordinates.
Returns
-------
coords : tuple
Tuple of map coordinates.
"""
pass
[docs] @abc.abstractmethod
def pix_to_idx(self, pix, clip=False):
"""Convert pixel coordinates to pixel indices.
Returns -1 for pixel coordinates that lie outside of the map.
Parameters
----------
pix : tuple
Tuple of pixel coordinates.
clip : bool
Choose whether to clip indices to the valid range of the
geometry. If false then indices for coordinates outside
the geometry range will be set -1.
Returns
-------
idx : tuple
Tuple of pixel indices.
"""
pass
[docs] @abc.abstractmethod
def contains(self, coords):
"""Check if a given map coordinate is contained in the geometry.
Parameters
----------
coords : tuple or `~gammapy.maps.MapCoord`
Tuple of map coordinates.
Returns
-------
containment : `~numpy.ndarray`
Bool array.
"""
pass
[docs] def contains_pix(self, pix):
"""Check if a given pixel coordinate is contained in the geometry.
Parameters
----------
pix : tuple
Tuple of pixel coordinates.
Returns
-------
containment : `~numpy.ndarray`
Bool array.
"""
idx = self.pix_to_idx(pix)
return np.all(np.stack([t != INVALID_INDEX.int for t in idx]), axis=0)
[docs] def slice_by_idx(self, slices):
"""Create a new geometry by slicing the non-spatial axes.
Parameters
----------
slices : dict
Dict of axes names and integers or `slice` object pairs. Contains one
element for each non-spatial dimension. For integer indexing the
correspoding axes is dropped from the map. Axes not specified in the
dict are kept unchanged.
Returns
-------
geom : `~Geom`
Sliced geometry.
"""
axes = []
for ax in self.axes:
ax_slice = slices.get(ax.name, slice(None))
if isinstance(ax_slice, slice):
ax_sliced = ax.slice(ax_slice)
axes.append(ax_sliced)
# in the case where isinstance(ax_slice, int) the axes is dropped
return self._init_copy(axes=axes)
[docs] @abc.abstractmethod
def to_image(self):
"""Create 2D image geometry (drop non-spatial dimensions).
Returns
-------
geom : `~Geom`
Image geometry.
"""
pass
[docs] @abc.abstractmethod
def to_cube(self, axes):
"""Append non-spatial axes to create a higher-dimensional geometry.
This will result in a new geometry with
N+M dimensions where N is the number of current dimensions and
M is the number of axes in the list.
Parameters
----------
axes : list
Axes that will be appended to this geometry.
Returns
-------
geom : `~Geom`
Map geometry.
"""
pass
[docs] def coord_to_tuple(self, coord):
"""Generate a coordinate tuple compatible with this geometry.
Parameters
----------
coord : `~MapCoord`
"""
if self.ndim != coord.ndim:
raise ValueError("ndim mismatch")
if not coord.match_by_name:
return tuple(coord._data.values())
coord_tuple = [coord.lon, coord.lat]
for ax in self.axes:
coord_tuple += [coord[ax.name]]
return coord_tuple
[docs] @abc.abstractmethod
def pad(self, pad_width):
"""
Pad the geometry at the edges.
Parameters
----------
pad_width : {sequence, array_like, int}
Number of values padded to the edges of each axis.
Returns
-------
geom : `~Geom`
Padded geometry.
"""
pass
[docs] @abc.abstractmethod
def crop(self, crop_width):
"""
Crop the geometry at the edges.
Parameters
----------
crop_width : {sequence, array_like, int}
Number of values cropped from the edges of each axis.
Returns
-------
geom : `~Geom`
Cropped geometry.
"""
pass
[docs] @abc.abstractmethod
def downsample(self, factor, axis):
"""Downsample the spatial dimension of the geometry by a given factor.
Parameters
----------
factor : int
Downsampling factor.
axis : str
Axis to downsample.
Returns
-------
geom : `~Geom`
Downsampled geometry.
"""
pass
[docs] @abc.abstractmethod
def upsample(self, factor, axis):
"""Upsample the spatial dimension of the geometry by a given factor.
Parameters
----------
factor : int
Upsampling factor.
axis : str
Axis to upsample.
Returns
-------
geom : `~Geom`
Upsampled geometry.
"""
pass
[docs] @abc.abstractmethod
def solid_angle(self):
"""Solid angle (`~astropy.units.Quantity` in ``sr``)."""
pass
def _fill_header_from_axes(self, header):
for idx, ax in enumerate(self.axes, start=1):
key = "AXCOLS%i" % idx
name = ax.name.upper()
if ax.name == "energy" and ax.node_type == "edges":
header[key] = "E_MIN,E_MAX"
elif ax.name == "energy" and ax.node_type == "center":
header[key] = "ENERGY"
elif ax.node_type == "edges":
header[key] = f"{name}_MIN,{name}_MAX"
elif ax.node_type == "center":
header[key] = name
else:
raise ValueError(f"Invalid node type {ax.node_type!r}")
key_interp = "INTERP%i" % idx
header[key_interp] = ax._interp
@property
def is_image(self):
"""Whether the geom is equivalent to an image without extra dimensions."""
if self.axes is None:
return True
return len(self.axes) == 0
[docs] def get_axis_by_name(self, name):
"""Get an axis by name (case in-sensitive).
Parameters
----------
name : str
Name of the requested axis
Returns
-------
axis : `~gammapy.maps.MapAxis`
Axis
"""
axes = {axis.name.upper(): axis for axis in self.axes}
return axes[name.upper()]
[docs] def get_axis_index_by_name(self, name):
"""Get an axis index by name (case in-sensitive).
Parameters
----------
name : str
Axis name
Returns
-------
index : int
Axis index
"""
names = [axis.name.upper() for axis in self.axes]
return names.index(name.upper())
def _init_copy(self, **kwargs):
"""Init map geom instance by copying missing init arguments from self.
"""
argnames = inspect.getfullargspec(self.__init__).args
argnames.remove("self")
for arg in argnames:
value = getattr(self, "_" + arg)
kwargs.setdefault(arg, copy.deepcopy(value))
return self.__class__(**kwargs)
[docs] def copy(self, **kwargs):
"""Copy and overwrite given attributes.
Parameters
----------
**kwargs : dict
Keyword arguments to overwrite in the map geometry constructor.
Returns
-------
copy : `Geom`
Copied map geometry.
"""
return self._init_copy(**kwargs)
[docs] def energy_mask(self, emin=None, emax=None):
"""Create a mask for a given energy range.
Parameters
----------
emin, emax : `~astropy.units.Quantity`
Energy range
"""
# get energy axes and values
energy_axis = self.get_axis_by_name("energy")
edges = energy_axis.edges
# set default values
emin = emin if emin is not None else edges[0]
emax = emax if emax is not None else edges[-1]
# create mask
coords = self.get_coord()
mask = coords["energy"] > emin
mask &= coords["energy"] < emax
return mask