# Licensed under a 3-clause BSD style license - see LICENSE.rst
import abc
import copy
import inspect
import json
import numpy as np
from astropy import units as u
from astropy.io import fits
from gammapy.maps.hpx import HpxGeom
from gammapy.utils.scripts import make_path
from .geom import MapAxis, MapCoord, pix_tuple_to_idx
from .utils import INVALID_VALUE
__all__ = ["Map"]
[docs]class Map(abc.ABC):
"""Abstract map class.
This can represent WCS- or HEALPIX-based maps
with 2 spatial dimensions and N non-spatial dimensions.
Parameters
----------
geom : `~gammapy.maps.Geom`
Geometry
data : `~numpy.ndarray`
Data array
meta : `dict`
Dictionary to store meta data
unit : str or `~astropy.units.Unit`
Data unit
"""
tag = "map"
def __init__(self, geom, data, meta=None, unit=""):
self._geom = geom
self.data = data
self.unit = unit
if meta is None:
self.meta = {}
else:
self.meta = meta
def _init_copy(self, **kwargs):
"""Init map instance by copying missing init arguments from self.
"""
argnames = inspect.getfullargspec(self.__init__).args
argnames.remove("self")
argnames.remove("dtype")
for arg in argnames:
value = getattr(self, "_" + arg)
kwargs.setdefault(arg, copy.deepcopy(value))
return self.from_geom(**kwargs)
@property
def geom(self):
"""Map geometry (`~gammapy.maps.Geom`)"""
return self._geom
@property
def data(self):
"""Data array (`~numpy.ndarray`)"""
return self._data
@data.setter
def data(self, value):
if np.isscalar(value):
value = value * np.ones(self.geom.data_shape)
if isinstance(value, u.Quantity):
raise TypeError("Map data must be a Numpy array. Set unit separately")
if not value.shape == self.geom.data_shape:
value = value.reshape(self.geom.data_shape)
self._data = value
@property
def unit(self):
"""Map unit (`~astropy.units.Unit`)"""
return self._unit
@unit.setter
def unit(self, val):
self._unit = u.Unit(val)
@property
def meta(self):
"""Map meta (`dict`)"""
return self._meta
@meta.setter
def meta(self, val):
self._meta = val
@property
def quantity(self):
"""Map data times unit (`~astropy.units.Quantity`)"""
return u.Quantity(self.data, self.unit, copy=False)
@quantity.setter
def quantity(self, val):
val = u.Quantity(val, copy=False)
self.data = val.value
self.unit = val.unit
[docs] @staticmethod
def create(**kwargs):
"""Create an empty map object.
This method accepts generic options listed below, as well as options
for `HpxMap` and `WcsMap` objects. For WCS-specific options, see
`WcsMap.create` and for HPX-specific options, see `HpxMap.create`.
Parameters
----------
frame : str
Coordinate system, either Galactic ("galactic") or Equatorial
("icrs").
map_type : {'wcs', 'wcs-sparse', 'hpx', 'hpx-sparse', 'region'}
Map type. Selects the class that will be used to
instantiate the map.
binsz : float or `~numpy.ndarray`
Pixel size in degrees.
skydir : `~astropy.coordinates.SkyCoord`
Coordinate of map center.
axes : list
List of `~MapAxis` objects for each non-spatial dimension.
If None then the map will be a 2D image.
dtype : str
Data type, default is 'float32'
unit : str or `~astropy.units.Unit`
Data unit.
meta : `dict`
Dictionary to store meta data.
region : `~regions.SkyRegion`
Sky region used for the region map.
Returns
-------
map : `Map`
Empty map object.
"""
from .hpxmap import HpxMap
from .wcsmap import WcsMap
from .regionnd import RegionNDMap
map_type = kwargs.setdefault("map_type", "wcs")
if "wcs" in map_type.lower():
return WcsMap.create(**kwargs)
elif "hpx" in map_type.lower():
return HpxMap.create(**kwargs)
elif map_type == "region":
_ = kwargs.pop("map_type")
return RegionNDMap.create(**kwargs)
else:
raise ValueError(f"Unrecognized map type: {map_type!r}")
[docs] @staticmethod
def read(filename, hdu=None, hdu_bands=None, map_type="auto", format=None):
"""Read a map from a FITS file.
Parameters
----------
filename : str or `~pathlib.Path`
Name of the FITS file.
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.
map_type : {'wcs', 'wcs-sparse', 'hpx', 'hpx-sparse', 'auto'}
Map type. Selects the class that will be used to
instantiate the map. The map type should be consistent
with the format of the input file. If map_type is 'auto'
then an appropriate map type will be inferred from the
input file.
Returns
-------
map_out : `Map`
Map object
"""
with fits.open(str(make_path(filename)), memmap=False) as hdulist:
return Map.from_hdulist(hdulist, hdu, hdu_bands, map_type, format=format)
[docs] @staticmethod
def from_geom(geom, meta=None, data=None, unit="", dtype="float32"):
"""Generate an empty map from a `Geom` instance.
Parameters
----------
geom : `Geom`
Map geometry.
data : `numpy.ndarray`
data array
meta : `dict`
Dictionary to store meta data.
unit : str or `~astropy.units.Unit`
Data unit.
Returns
-------
map_out : `Map`
Map object
"""
from .hpx import HpxGeom
from .wcs import WcsGeom
from .region import RegionGeom
if isinstance(geom, HpxGeom):
map_type = "hpx"
elif isinstance(geom, WcsGeom):
map_type = "wcs"
elif isinstance(geom, RegionGeom):
map_type = "region"
else:
raise ValueError("Unrecognized geom type.")
cls_out = Map._get_map_cls(map_type)
return cls_out(geom, data=data, meta=meta, unit=unit, dtype=dtype)
[docs] @staticmethod
def from_hdulist(hdulist, hdu=None, hdu_bands=None, map_type="auto", format=None):
"""Create from `astropy.io.fits.HDUList`."""
if map_type == "auto":
map_type = Map._get_map_type(hdulist, hdu)
cls_out = Map._get_map_cls(map_type)
return cls_out.from_hdulist(
hdulist, hdu=hdu, hdu_bands=hdu_bands, format=format
)
@staticmethod
def _get_meta_from_header(header):
"""Load meta data from a FITS header."""
if "META" in header:
return json.loads(header["META"])
else:
return {}
@staticmethod
def _get_map_type(hdu_list, hdu_name):
"""Infer map type from a FITS HDU.
Only read header, never data, to have good performance.
"""
if hdu_name is None:
# Find the header of the first non-empty HDU
header = hdu_list[0].header
if header["NAXIS"] == 0:
header = hdu_list[1].header
else:
header = hdu_list[hdu_name].header
if ("PIXTYPE" in header) and (header["PIXTYPE"] == "HEALPIX"):
return "hpx"
else:
return "wcs"
@staticmethod
def _get_map_cls(map_type):
"""Get map class for given `map_type` string.
This should probably be a registry dict so that users
can add supported map types to the `gammapy.maps` I/O
(see e.g. the Astropy table format I/O registry),
but that's non-trivial to implement without avoiding circular imports.
"""
if map_type == "wcs":
from .wcsnd import WcsNDMap
return WcsNDMap
elif map_type == "wcs-sparse":
raise NotImplementedError()
elif map_type == "hpx":
from .hpxnd import HpxNDMap
return HpxNDMap
elif map_type == "hpx-sparse":
raise NotImplementedError()
elif map_type == "region":
from .regionnd import RegionNDMap
return RegionNDMap
else:
raise ValueError(f"Unrecognized map type: {map_type!r}")
[docs] def write(self, filename, overwrite=False, **kwargs):
"""Write to a FITS file.
Parameters
----------
filename : str
Output file name.
overwrite : bool
Overwrite existing file?
hdu : str
Set the name of the image extension. By default this will
be set to SKYMAP (for BINTABLE HDU) or PRIMARY (for IMAGE
HDU).
hdu_bands : str
Set the name of the bands table extension. By default this will
be set to BANDS.
format : str, optional
FITS format convention. By default files will be written
to the gamma-astro-data-formats (GADF) format. This
option can be used to write files that are compliant with
format conventions required by specific software (e.g. the
Fermi Science Tools). The following formats are supported:
- "gadf" (default)
- "fgst-ccube"
- "fgst-ltcube"
- "fgst-bexpcube"
- "fgst-srcmap"
- "fgst-template"
- "fgst-srcmap-sparse"
- "galprop"
- "galprop2"
sparse : bool
Sparsify the map by dropping pixels with zero amplitude.
This option is only compatible with the 'gadf' format.
"""
hdulist = self.to_hdulist(**kwargs)
hdulist.writeto(str(make_path(filename)), overwrite=overwrite)
[docs] def iter_by_image(self):
"""Iterate over image planes of the map.
This is a generator yielding ``(data, idx)`` tuples,
where ``data`` is a `numpy.ndarray` view of the image plane data,
and ``idx`` is a tuple of int, the index of the image plane.
The image plane index is in data order, so that the data array can be
indexed directly. See :ref:`mapiter` for further information.
"""
for idx in np.ndindex(self.geom.shape_axes):
yield self.data[idx[::-1]], idx[::-1]
[docs] def coadd(self, map_in, weights=None):
"""Add the contents of ``map_in`` to this map.
This method can be used to combine maps containing integral quantities (e.g. counts)
or differential quantities if the maps have the same binning.
Parameters
----------
map_in : `Map`
Input map.
weights: `Map` or `~numpy.ndarray`
The weight factors while adding
"""
if not self.unit.is_equivalent(map_in.unit):
raise ValueError("Incompatible units")
# TODO: Check whether geometries are aligned and if so sum the
# data vectors directly
if weights is not None:
map_in = map_in * weights
idx = map_in.geom.get_idx()
coords = map_in.geom.get_coord()
vals = u.Quantity(map_in.get_by_idx(idx), map_in.unit)
self.fill_by_coord(coords, vals)
[docs] @abc.abstractmethod
def pad(self, pad_width, mode="constant", cval=0, order=1):
"""Pad the spatial dimensions of the map.
Parameters
----------
pad_width : {sequence, array_like, int}
Number of pixels padded to the edges of each axis.
mode : {'edge', 'constant', 'interp'}
Padding mode. 'edge' pads with the closest edge value.
'constant' pads with a constant value. 'interp' pads with
an extrapolated value.
cval : float
Padding value when mode='consant'.
order : int
Order of interpolation when mode='constant' (0 =
nearest-neighbor, 1 = linear, 2 = quadratic, 3 = cubic).
Returns
-------
map : `Map`
Padded map.
"""
pass
[docs] @abc.abstractmethod
def crop(self, crop_width):
"""Crop the spatial dimensions of the map.
Parameters
----------
crop_width : {sequence, array_like, int}
Number of pixels cropped from the edges of each axis.
Defined analogously to ``pad_with`` from `numpy.pad`.
Returns
-------
map : `Map`
Cropped map.
"""
pass
[docs] @abc.abstractmethod
def downsample(self, factor, preserve_counts=True, axis=None):
"""Downsample the spatial dimension by a given factor.
Parameters
----------
factor : int
Downsampling factor.
preserve_counts : bool
Preserve the integral over each bin. This should be true
if the map is an integral quantity (e.g. counts) and false if
the map is a differential quantity (e.g. intensity).
axis : str
Which axis to downsample. By default spatial axes are downsampled.
Returns
-------
map : `Map`
Downsampled map.
"""
pass
[docs] @abc.abstractmethod
def upsample(self, factor, order=0, preserve_counts=True, axis=None):
"""Upsample the spatial dimension by a given factor.
Parameters
----------
factor : int
Upsampling factor.
order : int
Order of the interpolation used for upsampling.
preserve_counts : bool
Preserve the integral over each bin. This should be true
if the map is an integral quantity (e.g. counts) and false if
the map is a differential quantity (e.g. intensity).
axis : str
Which axis to upsample. By default spatial axes are upsampled.
Returns
-------
map : `Map`
Upsampled map.
"""
pass
[docs] def resample_axis(self, axis, weights=None, ufunc=np.add):
"""Resample map to a new axis binning by grouping over smaller bins and apply ufunc to the bin contents.
By default, the map content are summed over the smaller bins. Other numpy ufunc can be used,
e.g. np.logical_and, np.logical_or
Parameters
----------
axis : `MapAxis`
New map axis.
weights : `Map`
Array to be used as weights. The spatial geometry must be equivalent
to `other` and additional axes must be broadcastable.
ufunc : `~numpy.ufunc`
ufunc to use to resample the axis. Default is numpy.add.
Returns
-------
map : `Map`
Map with resampled axis.
"""
geom = self.geom.resample_axis(axis)
axis_self = self.geom.axes[axis.name]
axis_resampled = geom.axes[axis.name]
# We don't use MapAxis.coord_to_idx because is does not behave as needed with boundaries
coord = axis_resampled.edges.value
edges = axis_self.edges.value
indices = np.digitize(coord, edges) - 1
idx = self.geom.axes.index_data(axis.name)
weights = 1 if weights is None else weights.data
if not isinstance(self.geom, HpxGeom):
shape = self.geom._shape[:2]
else:
shape = (self.geom.data_shape[-1],)
shape += tuple([ax.nbin if ax != axis else 1 for ax in self.geom.axes])
padded_array = np.append(self.data * weights, np.zeros(shape[::-1]), axis=idx)
slices = tuple([slice(0, _) for _ in geom.data_shape])
data = ufunc.reduceat(padded_array, indices=indices, axis=idx)[slices]
return self._init_copy(data=data, geom=geom)
[docs] def slice_by_idx(
self, slices,
):
"""Slice sub map from map object.
For usage examples, see :ref:`mapslicing`.
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
corresponding axes is dropped from the map. Axes not specified in the
dict are kept unchanged.
Returns
-------
map_out : `Map`
Sliced map object.
"""
geom = self.geom.slice_by_idx(slices)
slices = tuple([slices.get(ax.name, slice(None)) for ax in self.geom.axes])
data = self.data[slices[::-1]]
return self.__class__(geom=geom, data=data, unit=self.unit, meta=self.meta)
[docs] def get_image_by_coord(self, coords):
"""Return spatial map at the given axis coordinates.
Parameters
----------
coords : tuple or dict
Tuple should be ordered as (x_0, ..., x_n) where x_i are coordinates
for non-spatial dimensions of the map. Dict should specify the axis
names of the non-spatial axes such as {'axes0': x_0, ..., 'axesn': x_n}.
Returns
-------
map_out : `Map`
Map with spatial dimensions only.
See Also
--------
get_image_by_idx, get_image_by_pix
Examples
--------
::
import numpy as np
from gammapy.maps import Map, MapAxis
from astropy.coordinates import SkyCoord
from astropy import units as u
# Define map axes
energy_axis = MapAxis.from_edges(
np.logspace(-1., 1., 4), unit='TeV', name='energy',
)
time_axis = MapAxis.from_edges(
np.linspace(0., 10, 20), unit='h', name='time',
)
# Define map center
skydir = SkyCoord(0, 0, frame='galactic', unit='deg')
# Create map
m_wcs = Map.create(
map_type='wcs',
binsz=0.02,
skydir=skydir,
width=10.0,
axes=[energy_axis, time_axis],
)
# Get image by coord tuple
image = m_wcs.get_image_by_coord(('500 GeV', '1 h'))
# Get image by coord dict with strings
image = m_wcs.get_image_by_coord({'energy': '500 GeV', 'time': '1 h'})
# Get image by coord dict with quantities
image = m_wcs.get_image_by_coord({'energy': 0.5 * u.TeV, 'time': 1 * u.h})
"""
if isinstance(coords, tuple):
coords = dict(zip(self.geom.axes.names, coords))
idx = self.geom.axes.coord_to_idx(coords)
return self.get_image_by_idx(idx)
[docs] def get_image_by_pix(self, pix):
"""Return spatial map at the given axis pixel coordinates
Parameters
----------
pix : tuple
Tuple of scalar pixel coordinates for each non-spatial dimension of
the map. Tuple should be ordered as (I_0, ..., I_n). Pixel coordinates
can be either float or integer type.
See Also
--------
get_image_by_coord, get_image_by_idx
Returns
-------
map_out : `Map`
Map with spatial dimensions only.
"""
idx = self.geom.pix_to_idx(pix)
return self.get_image_by_idx(idx)
[docs] def get_image_by_idx(self, idx):
"""Return spatial map at the given axis pixel indices.
Parameters
----------
idx : tuple
Tuple of scalar indices for each non spatial dimension of the map.
Tuple should be ordered as (I_0, ..., I_n).
See Also
--------
get_image_by_coord, get_image_by_pix
Returns
-------
map_out : `Map`
Map with spatial dimensions only.
"""
if len(idx) != len(self.geom.axes):
raise ValueError("Tuple length must equal number of non-spatial dimensions")
# Only support scalar indices per axis
idx = tuple([int(_) for _ in idx])
geom = self.geom.to_image()
data = self.data[idx[::-1]]
return self.__class__(geom=geom, data=data, unit=self.unit, meta=self.meta)
[docs] def get_by_coord(self, coords):
"""Return map values at the given map coordinates.
Parameters
----------
coords : tuple or `~gammapy.maps.MapCoord`
Coordinate arrays for each dimension of the map. Tuple
should be ordered as (lon, lat, x_0, ..., x_n) where x_i
are coordinates for non-spatial dimensions of the map.
Returns
-------
vals : `~numpy.ndarray`
Values of pixels in the map. np.nan used to flag coords
outside of map.
"""
coords = MapCoord.create(
coords, frame=self.geom.frame, axis_names=self.geom.axes.names
)
pix = self.geom.coord_to_pix(coords)
vals = self.get_by_pix(pix)
return vals
[docs] def get_by_pix(self, pix):
"""Return map values at the given pixel coordinates.
Parameters
----------
pix : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
Pixel indices can be either float or integer type.
Returns
-------
vals : `~numpy.ndarray`
Array of pixel values. np.nan used to flag coordinates
outside of map
"""
# FIXME: Support local indexing here?
# FIXME: Support slicing?
pix = np.broadcast_arrays(*pix)
idx = self.geom.pix_to_idx(pix)
vals = self.get_by_idx(idx)
mask = self.geom.contains_pix(pix)
if not mask.all():
invalid = INVALID_VALUE[self.data.dtype]
vals = vals.astype(type(invalid))
vals[~mask] = invalid
return vals
[docs] @abc.abstractmethod
def get_by_idx(self, idx):
"""Return map values at the given pixel indices.
Parameters
----------
idx : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
Returns
-------
vals : `~numpy.ndarray`
Array of pixel values.
np.nan used to flag coordinate outside of map
"""
pass
[docs] @abc.abstractmethod
def interp_by_coord(self, coords, interp=None, fill_value=None):
"""Interpolate map values at the given map coordinates.
Parameters
----------
coords : tuple or `~gammapy.maps.MapCoord`
Coordinate arrays for each dimension of the map. Tuple
should be ordered as (lon, lat, x_0, ..., x_n) where x_i
are coordinates for non-spatial dimensions of the map.
interp : {None, 'nearest', 'linear', 'cubic', 0, 1, 2, 3}
Method to interpolate data values. By default no
interpolation is performed and the return value will be
the amplitude of the pixel encompassing the given
coordinate. Integer values can be used in lieu of strings
to choose the interpolation method of the given order
(0='nearest', 1='linear', 2='quadratic', 3='cubic'). Note
that only 'nearest' and 'linear' methods are supported for
all map types.
fill_value : None or float value
The value to use for points outside of the interpolation domain.
If None, values outside the domain are extrapolated.
Returns
-------
vals : `~numpy.ndarray`
Interpolated pixel values.
"""
pass
[docs] @abc.abstractmethod
def interp_by_pix(self, pix, interp=None, fill_value=None):
"""Interpolate map values at the given pixel coordinates.
Parameters
----------
pix : tuple
Tuple of pixel coordinate arrays for each dimension of the
map. Tuple should be ordered as (p_lon, p_lat, p_0, ...,
p_n) where p_i are pixel coordinates for non-spatial
dimensions of the map.
interp : {None, 'nearest', 'linear', 'cubic', 0, 1, 2, 3}
Method to interpolate data values. By default no
interpolation is performed and the return value will be
the amplitude of the pixel encompassing the given
coordinate. Integer values can be used in lieu of strings
to choose the interpolation method of the given order
(0='nearest', 1='linear', 2='quadratic', 3='cubic'). Note
that only 'nearest' and 'linear' methods are supported for
all map types.
fill_value : None or float value
The value to use for points outside of the interpolation domain.
If None, values outside the domain are extrapolated.
Returns
-------
vals : `~numpy.ndarray`
Interpolated pixel values.
"""
pass
[docs] def interp_to_geom(self, geom, preserve_counts=False, **kwargs):
"""Interpolate map to input geometry.
Parameters
----------
geom : `~gammapy.maps.Geom`
Target Map geometry
preserve_counts : bool
Preserve the integral over each bin. This should be true
if the map is an integral quantity (e.g. counts) and false if
the map is a differential quantity (e.g. intensity)
**kwargs : dict
Keyword arguments passed to `Map.interp_by_coord`
Returns
-------
interp_map : `Map`
Interpolated Map
"""
coords = geom.get_coord()
# set nearest neighbour interpolation for mask as default
if self.data.dtype == bool:
kwargs.setdefault("interp", 0)
if preserve_counts:
if geom.ndim > 2:
assert self.geom.axes[0] == geom.axes[0] # Energy axis has to match
old_map_copy = self.copy()
old_map_copy.data /= self.geom.solid_angle().to_value("deg2")
data = old_map_copy.interp_by_coord(coords, **kwargs)
data *= geom.solid_angle().to_value("deg2")
else:
data = self.interp_by_coord(coords, **kwargs)
if self.data.dtype == bool:
data = data.astype(bool)
return Map.from_geom(geom, data=data, unit=self.unit)
[docs] def fill_events(self, events):
"""Fill event coordinates (`~gammapy.data.EventList`)."""
self.fill_by_coord(events.map_coord(self.geom))
[docs] def fill_by_coord(self, coords, weights=None):
"""Fill pixels at ``coords`` with given ``weights``.
Parameters
----------
coords : tuple or `~gammapy.maps.MapCoord`
Coordinate arrays for each dimension of the map. Tuple
should be ordered as (lon, lat, x_0, ..., x_n) where x_i
are coordinates for non-spatial dimensions of the map.
weights : `~numpy.ndarray`
Weights vector. Default is weight of one.
"""
idx = self.geom.coord_to_idx(coords)
self.fill_by_idx(idx, weights)
[docs] def fill_by_pix(self, pix, weights=None):
"""Fill pixels at ``pix`` with given ``weights``.
Parameters
----------
pix : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
Pixel indices can be either float or integer type. Float
indices will be rounded to the nearest integer.
weights : `~numpy.ndarray`
Weights vector. Default is weight of one.
"""
idx = pix_tuple_to_idx(pix)
return self.fill_by_idx(idx, weights=weights)
[docs] @abc.abstractmethod
def fill_by_idx(self, idx, weights=None):
"""Fill pixels at ``idx`` with given ``weights``.
Parameters
----------
idx : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
weights : `~numpy.ndarray`
Weights vector. Default is weight of one.
"""
pass
[docs] def set_by_coord(self, coords, vals):
"""Set pixels at ``coords`` with given ``vals``.
Parameters
----------
coords : tuple or `~gammapy.maps.MapCoord`
Coordinate arrays for each dimension of the map. Tuple
should be ordered as (lon, lat, x_0, ..., x_n) where x_i
are coordinates for non-spatial dimensions of the map.
vals : `~numpy.ndarray`
Values vector.
"""
idx = self.geom.coord_to_pix(coords)
self.set_by_pix(idx, vals)
[docs] def set_by_pix(self, pix, vals):
"""Set pixels at ``pix`` with given ``vals``.
Parameters
----------
pix : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
Pixel indices can be either float or integer type. Float
indices will be rounded to the nearest integer.
vals : `~numpy.ndarray`
Values vector.
"""
idx = pix_tuple_to_idx(pix)
return self.set_by_idx(idx, vals)
[docs] @abc.abstractmethod
def set_by_idx(self, idx, vals):
"""Set pixels at ``idx`` with given ``vals``.
Parameters
----------
idx : tuple
Tuple of pixel index arrays for each dimension of the map.
Tuple should be ordered as (I_lon, I_lat, I_0, ..., I_n)
for WCS maps and (I_hpx, I_0, ..., I_n) for HEALPix maps.
vals : `~numpy.ndarray`
Values vector.
"""
pass
[docs] def plot_grid(self, figsize=None, ncols=3, **kwargs):
"""Plot map as a grid of subplots for non-spatial axes
Parameters
----------
figsize : tuple of int
Figsize to plot on
ncols : int
Number of columns to plot
**kwargs : dict
Keyword arguments passed to `Map.plot`.
Returns
-------
axes : `~numpy.ndarray` of `~matplotlib.pyplot.Axes`
Axes grid
"""
import matplotlib.pyplot as plt
if len(self.geom.axes) > 1:
raise ValueError("Grid plotting is only supported for one non spatial axis")
axis = self.geom.axes[0]
cols = min(ncols, axis.nbin)
rows = 1 + (axis.nbin - 1) // cols
if figsize is None:
width = 12
figsize = (width, width * rows / cols)
if self.geom.is_hpx:
wcs = self.geom.to_wcs_geom().wcs
else:
wcs = self.geom.wcs
fig, axes = plt.subplots(
ncols=cols,
nrows=rows,
subplot_kw={"projection": wcs},
figsize=figsize,
gridspec_kw={"hspace": 0.1, "wspace": 0.1},
)
for idx in range(cols * rows):
ax = axes.flat[idx]
try:
image = self.get_image_by_idx((idx,))
except IndexError:
ax.set_visible(False)
continue
if image.geom.is_hpx:
image_wcs = (image.to_wcs(normalize=False, proj="AIT", oversample=2,),)
else:
image_wcs = image
image_wcs.plot(ax=ax, **kwargs)
if axis.node_type == "center":
info = f"{axis.center[idx]:.1f}"
else:
info = f"{axis.edges[idx]:.1f} - {axis.edges[idx + 1]:.1f} "
ax.set_title(f"{axis.name.capitalize()} " + info)
lon, lat = ax.coords[0], ax.coords[1]
lon.set_ticks_position("b")
lat.set_ticks_position("l")
row, col = np.unravel_index(idx, shape=(rows, cols))
if col > 0:
lat.set_ticklabel_visible(False)
lat.set_axislabel("")
if row < (rows - 1):
lon.set_ticklabel_visible(False)
lon.set_axislabel("")
return axes
[docs] def plot_interactive(self, rc_params=None, **kwargs):
"""
Plot map with interactive widgets to explore the non spatial axes.
Parameters
----------
rc_params : dict
Passed to ``matplotlib.rc_context(rc=rc_params)`` to style the plot.
**kwargs : dict
Keyword arguments passed to `WcsNDMap.plot`.
Examples
--------
You can try this out e.g. using a Fermi-LAT diffuse model cube with an energy axis::
from gammapy.maps import Map
m = Map.read("$GAMMAPY_DATA/fermi_3fhl/gll_iem_v06_cutout.fits")
m.plot_interactive(add_cbar=True, stretch="sqrt")
If you would like to adjust the figure size you can use the ``rc_params`` argument::
rc_params = {'figure.figsize': (12, 6), 'font.size': 12}
m.plot_interactive(rc_params=rc_params)
"""
import matplotlib as mpl
import matplotlib.pyplot as plt
from ipywidgets.widgets.interaction import interact, fixed
from ipywidgets import SelectionSlider, RadioButtons
if self.geom.is_image:
raise TypeError("Use .plot() for 2D Maps")
kwargs.setdefault("interpolation", "nearest")
kwargs.setdefault("origin", "lower")
kwargs.setdefault("cmap", "afmhot")
rc_params = rc_params or {}
stretch = kwargs.pop("stretch", "sqrt")
interact_kwargs = {}
for axis in self.geom.axes:
if axis.node_type == "edges":
options = [
f"{val_min:.2e} - {val_max:.2e} {axis.unit}"
for val_min, val_max in zip(axis.edges[:-1], axis.edges[1:])
]
else:
options = [f"{val:.2e} {axis.unit}" for val in axis.center]
interact_kwargs[axis.name] = SelectionSlider(
options=options,
description=f"Select {axis.name}:",
continuous_update=False,
style={"description_width": "initial"},
layout={"width": "50%"},
)
interact_kwargs[axis.name + "_options"] = fixed(options)
interact_kwargs["stretch"] = RadioButtons(
options=["linear", "sqrt", "log"],
value=stretch,
description="Select stretch:",
style={"description_width": "initial"},
)
@interact(**interact_kwargs)
def _plot_interactive(**ikwargs):
idx = [
ikwargs[ax.name + "_options"].index(ikwargs[ax.name])
for ax in self.geom.axes
]
img = self.get_image_by_idx(idx)
stretch = ikwargs["stretch"]
with mpl.rc_context(rc=rc_params):
fig, ax, cbar = img.plot(stretch=stretch, **kwargs)
plt.show()
[docs] def copy(self, **kwargs):
"""Copy map instance and overwrite given attributes, except for geometry.
Parameters
----------
**kwargs : dict
Keyword arguments to overwrite in the map constructor.
Returns
-------
copy : `Map`
Copied Map.
"""
if "geom" in kwargs:
raise ValueError("Can't copy and change geometry of the map.")
return self._init_copy(**kwargs)
[docs] def apply_edisp(self, edisp):
"""Apply energy dispersion to map. Requires energy axis.
Parameters
----------
edisp : `gammapy.irf.EDispKernel`
Energy dispersion matrix
Returns
-------
map : `WcsNDMap`
Map with energy dispersion applied.
"""
# TODO: either use sparse matrix mutiplication or something like edisp.is_diagonal
if edisp is not None:
loc = self.geom.axes.index("energy_true")
data = np.rollaxis(self.data, loc, len(self.data.shape))
data = np.dot(data, edisp.pdf_matrix)
data = np.rollaxis(data, -1, loc)
energy_axis = edisp.energy_axis.copy(name="energy")
else:
data = self.data
energy_axis = self.geom.axes["energy_true"].copy(name="energy")
geom = self.geom.to_image().to_cube(axes=[energy_axis])
return self._init_copy(geom=geom, data=data)
[docs] def sum_over_axes(self, axes_names=None, keepdims=True, weights=None):
"""To sum map values over all non-spatial axes.
Parameters
----------
keepdims : bool, optional
If this is set to true, the axes which are summed over are left in
the map with a single bin
axes_names: list of str
Names of MapAxis to reduce over. If None, all will summed over
weights : `Map`
Weights to be applied. The Map should have the same geometry.
Returns
-------
map_out : `~Map`
Map with non-spatial axes summed over
"""
return self.reduce_over_axes(
func=np.add, axes_names=axes_names, keepdims=keepdims, weights=weights
)
[docs] def reduce_over_axes(
self, func=np.add, keepdims=False, axes_names=None, weights=None
):
"""Reduce map over non-spatial axes
Parameters
----------
func : `~numpy.ufunc`
Function to use for reducing the data.
keepdims : bool, optional
If this is set to true, the axes which are summed over are left in
the map with a single bin
axes_names: list
Names of MapAxis to reduce over
If None, all will reduced
weights : `Map`
Weights to be applied.
Returns
-------
map_out : `~Map`
Map with non-spatial axes reduced
"""
if axes_names is None:
axes_names = self.geom.axes.names
map_out = self.copy()
for axis_name in axes_names:
map_out = map_out.reduce(
axis_name, func=func, keepdims=keepdims, weights=weights
)
return map_out
[docs] def reduce(self, axis_name, func=np.add, keepdims=False, weights=None):
"""Reduce map over a single non-spatial axis
Parameters
----------
axis_name: str
The name of the axis to reduce over
func : `~numpy.ufunc`
Function to use for reducing the data.
keepdims : bool, optional
If this is set to true, the axes which are summed over are left in
the map with a single bin
weights : `Map`
Weights to be applied.
Returns
-------
map_out : `~Map`
Map with the given non-spatial axes reduced
"""
if keepdims:
geom = self.geom.squash(axis_name=axis_name)
else:
geom = self.geom.drop(axis_name=axis_name)
idx = self.geom.axes.index_data(axis_name)
data = self.data
if weights is not None:
data = data * weights
data = func.reduce(data, axis=idx, keepdims=keepdims, where=~np.isnan(data))
return self._init_copy(geom=geom, data=data)
[docs] @classmethod
def from_images(cls, images, axis=None):
"""Create Map from list of images and a non-spatial axis.
If the images have a non-spatial axis of length 1 a new axes is generated
from by merging the individual axes. The image geometries must be aligned.
Parameters
----------
images : list of `Map` objects
Images
axis : `MapAxis`
Map axis
Returns
-------
map : `Map`
Map with additional non-spatial axis.
"""
geom_ref = images[0].geom.to_image()
data = []
for image in images:
if not image.geom.to_image() == geom_ref:
raise ValueError("Image geometries not aligned")
data.append(image.data)
if axis is None:
try:
axis = MapAxis.from_stack(axes=[image.geom.axes[0] for image in images])
except IndexError:
ValueError(
"Images don't have a non-spatial axis. Please provide"
" the axis separately"
)
return cls.from_geom(
data=np.stack(data), geom=geom_ref.to_cube(axes=[axis]), unit=images[0].unit
)
[docs] def to_cube(self, axes):
"""Append non-spatial axes to create a higher-dimensional Map.
This will result in a Map with 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. The data is reshaped onto the
new geometry
Parameters
----------
axes : list
Axes that will be appended to this Map.
The axes should have only one bin
Returns
-------
map : `~gammapy.maps.WcsNDMap`
new map
"""
for ax in axes:
if ax.nbin > 1:
raise ValueError(ax.name, "should have only one bin")
geom = self.geom.to_cube(axes)
data = self.data.reshape((1,) * len(axes) + self.data.shape)
return self.from_geom(data=data, geom=geom, unit=self.unit)
def __repr__(self):
geom = self.geom.__class__.__name__
axes = ["skycoord"] if self.geom.is_hpx else ["lon", "lat"]
axes = axes + [_.name for _ in self.geom.axes]
return (
f"{self.__class__.__name__}\n\n"
f"\tgeom : {geom} \n "
f"\taxes : {axes}\n"
f"\tshape : {self.geom.data_shape[::-1]}\n"
f"\tndim : {self.geom.ndim}\n"
f"\tunit : {self.unit}\n"
f"\tdtype : {self.data.dtype}\n"
)
def _arithmetics(self, operator, other, copy):
"""Perform arithmetics on maps after checking geometry consistency."""
if isinstance(other, Map):
if self.geom == other.geom:
q = other.quantity
else:
raise ValueError("Map Arithmetics: Inconsistent geometries.")
else:
q = u.Quantity(other, copy=False)
out = self.copy() if copy else self
out.quantity = operator(out.quantity, q)
return out
def _boolean_arithmetics(self, operator, other, copy):
"""Perform arithmetics on maps after checking geometry consistency."""
if operator == np.logical_not:
out = self.copy()
out.data = operator(out.data)
return out
if isinstance(other, Map):
if self.geom == other.geom:
other = other.data
else:
raise ValueError("Map Arithmetics: Inconsistent geometries.")
out = self.copy() if copy else self
out.data = operator(out.data, other)
return out
def __add__(self, other):
return self._arithmetics(np.add, other, copy=True)
def __iadd__(self, other):
return self._arithmetics(np.add, other, copy=False)
def __sub__(self, other):
return self._arithmetics(np.subtract, other, copy=True)
def __isub__(self, other):
return self._arithmetics(np.subtract, other, copy=False)
def __mul__(self, other):
return self._arithmetics(np.multiply, other, copy=True)
def __imul__(self, other):
return self._arithmetics(np.multiply, other, copy=False)
def __truediv__(self, other):
return self._arithmetics(np.true_divide, other, copy=True)
def __itruediv__(self, other):
return self._arithmetics(np.true_divide, other, copy=False)
def __le__(self, other):
return self._arithmetics(np.less_equal, other, copy=True)
def __lt__(self, other):
return self._arithmetics(np.less, other, copy=True)
def __ge__(self, other):
return self._arithmetics(np.greater_equal, other, copy=True)
def __gt__(self, other):
return self._arithmetics(np.greater, other, copy=True)
def __eq__(self, other):
return self._arithmetics(np.equal, other, copy=True)
def __ne__(self, other):
return self._arithmetics(np.not_equal, other, copy=True)
def __and__(self, other):
return self._boolean_arithmetics(np.logical_and, other, copy=True)
def __or__(self, other):
return self._boolean_arithmetics(np.logical_or, other, copy=True)
def __invert__(self):
return self._boolean_arithmetics(np.logical_not, None, copy=True)
def __xor__(self, other):
return self._boolean_arithmetics(np.logical_xor, other, copy=True)
def __iand__(self, other):
return self._boolean_arithmetics(np.logical_and, other, copy=False)
def __ior__(self, other):
return self._boolean_arithmetics(np.logical_or, other, copy=False)
def __ixor__(self, other):
return self._boolean_arithmetics(np.logical_xor, other, copy=False)
def __array__(self):
return self.data