WcsNDMap

class gammapy.maps.WcsNDMap(geom, data=None, dtype='float32', meta=None, unit='')

Bases: gammapy.maps.WcsMap

HEALPix map with any number of non-spatial dimensions.

This class uses an ND numpy array to store map values. For maps with non-spatial dimensions and variable pixel size it will allocate an array with dimensions commensurate with the largest image plane.

Parameters

geomWcsGeom

WCS geometry object.

datandarray

Data array. If none then an empty array will be allocated.

dtypestr, optional

Data type, default is float32

metadict

Dictionary to store meta data.

unitstr or Unit

The map unit

Attributes Summary

data	Data array (ndarray)
geom	Map geometry (Geom)
meta	Map meta (dict)
quantity	Map data times unit (Quantity)
unit	Map unit (Unit)

Methods Summary

apply_edisp(self, edisp)	Apply energy dispersion to map.
coadd(self, map_in[, weights])	Add the contents of map_in to this map.
convolve(self, kernel[, use_fft])	Convolve map with a kernel.
copy(self, \*\*kwargs)	Copy map instance and overwrite given attributes, except for geometry.
create([map_type, npix, binsz, width, proj, …])	Factory method to create an empty WCS map.
crop(self, crop_width)	Crop the spatial dimensions of the map.
cutout(self, position, width[, mode])	Create a cutout around a given position.
downsample(self, factor[, preserve_counts, axis])	Downsample the spatial dimension by a given factor.
fill_by_coord(self, coords[, weights])	Fill pixels at coords with given weights.
fill_by_idx(self, idx[, weights])	Fill pixels at idx with given weights.
fill_by_pix(self, pix[, weights])	Fill pixels at pix with given weights.
fill_events(self, events)	Fill event coordinates (EventList).
from_geom(geom[, meta, data, map_type, …])	Generate an empty map from a Geom instance.
from_hdu(hdu[, hdu_bands])	Make a WcsNDMap object from a FITS HDU.
from_hdulist(hdu_list[, hdu, hdu_bands])	Make a WcsMap object from a FITS HDUList.
get_by_coord(self, coords)	Return map values at the given map coordinates.
get_by_idx(self, idx)	Return map values at the given pixel indices.
get_by_pix(self, pix)	Return map values at the given pixel coordinates.
get_image_by_coord(self, coords)	Return spatial map at the given axis coordinates.
get_image_by_idx(self, idx)	Return spatial map at the given axis pixel indices.
get_image_by_pix(self, pix)	Return spatial map at the given axis pixel coordinates
get_spectrum(self[, region, func])	Extract spectrum in a given region.
interp_by_coord(self, coords[, interp, …])	Interpolate map values at the given map coordinates.
interp_by_pix(self, pix[, interp, fill_value])	Interpolate map values at the given pixel coordinates.
iter_by_image(self)	Iterate over image planes of the map.
make_hdu(self[, hdu, hdu_bands, sparse, conv])	Make a FITS HDU from this map.
pad(self, pad_width[, mode, cval, order])	Pad the spatial dimensions of the map.
plot(self[, ax, fig, add_cbar, stretch])	Plot image on matplotlib WCS axes.
plot_interactive(self[, rc_params])	Plot map with interactive widgets to explore the non spatial axes.
read(filename[, hdu, hdu_bands, map_type])	Read a map from a FITS file.
reduce_over_axes(self, func[, keepdims])	Reduce map over all non spatial axes
sample_coord(self, n_events[, random_state])	Sample position and energy of events.
set_by_coord(self, coords, vals)	Set pixels at coords with given vals.
set_by_idx(self, idx, vals)	Set pixels at idx with given vals.
set_by_pix(self, pix, vals)	Set pixels at pix with given vals.
slice_by_idx(self, slices)	Slice sub map from map object.
smooth(self, width[, kernel])	Smooth the map.
stack(self, other[, weights])	Stack cutout into map.
sum_over_axes(self[, keepdims])	To sum map values over all non-spatial axes.
to_hdulist(self[, hdu, hdu_bands, sparse, conv])	Convert to HDUList.
upsample(self, factor[, order, …])	Upsample the spatial dimension by a given factor.
write(self, filename[, overwrite])	Write to a FITS file.

Attributes Documentation

data

Data array (ndarray)

geom

Map geometry (Geom)

meta

Map meta (dict)

quantity

Map data times unit (Quantity)

unit

Map unit (Unit)

Methods Documentation

apply_edisp(self, edisp)

Apply energy dispersion to map. Requires energy axis.

Parameters

edispgammapy.irf.EnergyDispersion

Energy dispersion matrix

Returns

mapWcsNDMap

Map with energy dispersion applied.

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_inMap

Input map.

weights: `Map` or `~numpy.ndarray`

The weight factors while adding

convolve(self, kernel, use_fft=True, **kwargs)

Convolve map with a kernel.

If the kernel is two dimensional, it is applied to all image planes likewise. If the kernel is higher dimensional it must match the map in the number of dimensions and the corresponding kernel is selected for every image plane.

Parameters

kernelPSFKernel or numpy.ndarray

Convolution kernel.

use_fftbool

Use scipy.signal.fftconvolve or scipy.ndimage.convolve.

kwargsdict

Keyword arguments passed to scipy.signal.fftconvolve or scipy.ndimage.convolve.

Returns

mapWcsNDMap

Convolved map.

copy(self, **kwargs)

Copy map instance and overwrite given attributes, except for geometry.

Parameters

**kwargsdict

Keyword arguments to overwrite in the map constructor.

Returns

copyMap

Copied Map.

classmethod create(map_type='wcs', npix=None, binsz=0.1, width=None, proj='CAR', coordsys='CEL', refpix=None, axes=None, skydir=None, dtype='float32', meta=None, unit='')

Factory method to create an empty WCS map.

Parameters

map_type{‘wcs’, ‘wcs-sparse’}

Map type. Selects the class that will be used to instantiate the map.

npixint or tuple or list

Width of the map in pixels. A tuple will be interpreted as parameters for longitude and latitude axes. For maps with non-spatial dimensions, list input can be used to define a different map width in each image plane. This option supersedes width.

widthfloat or tuple or list

Width of the map in degrees. A tuple will be interpreted as parameters for longitude and latitude axes. For maps with non-spatial dimensions, list input can be used to define a different map width in each image plane.

binszfloat or tuple or list

Map pixel size in degrees. A tuple will be interpreted as parameters for longitude and latitude axes. For maps with non-spatial dimensions, list input can be used to define a different bin size in each image plane.

skydirtuple or SkyCoord

Sky position of map center. Can be either a SkyCoord object or a tuple of longitude and latitude in deg in the coordinate system of the map.

coordsys{‘CEL’, ‘GAL’}, optional

Coordinate system, either Galactic (‘GAL’) or Equatorial (‘CEL’).

axeslist

List of non-spatial axes.

projstring, optional

Any valid WCS projection type. Default is ‘CAR’ (cartesian).

refpixtuple

Reference pixel of the projection. If None then this will be chosen to be center of the map.

dtypestr, optional

Data type, default is float32

conv{‘fgst-ccube’,’fgst-template’,’gadf’}, optional

FITS format convention. Default is ‘gadf’.

metadict

Dictionary to store meta data.

unitstr or Unit

The unit of the map

Returns

mapWcsMap

A WCS map object.

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

mapMap

Cropped map.

cutout(self, position, width, mode='trim')

Create a cutout around a given position.

Parameters

positionSkyCoord

Center position of the cutout region.

widthtuple of Angle

Angular sizes of the region in (lon, lat) in that specific order. If only one value is passed, a square region is extracted.

mode{‘trim’, ‘partial’, ‘strict’}

Mode option for Cutout2D, for details see Cutout2D.

Returns

cutoutWcsNDMap

Cutout map

downsample(self, factor, preserve_counts=True, axis=None)

Downsample the spatial dimension by a given factor.

Parameters

factorint

Downsampling factor.

preserve_countsbool

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).

axisstr

Which axis to downsample. By default spatial axes are downsampled.

Returns

mapMap

Downsampled map.

fill_by_coord(self, coords, weights=None)

Fill pixels at coords with given weights.

Parameters

coordstuple or 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.

weightsndarray

Weights vector. Default is weight of one.

fill_by_idx(self, idx, weights=None)

Fill pixels at idx with given weights.

Parameters

idxtuple

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.

weightsndarray

Weights vector. Default is weight of one.

fill_by_pix(self, pix, weights=None)

Fill pixels at pix with given weights.

Parameters

pixtuple

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.

weightsndarray

Weights vector. Default is weight of one.

fill_events(self, events)

Fill event coordinates (EventList).

static from_geom(geom, meta=None, data=None, map_type='auto', unit='', dtype='float32')

Generate an empty map from a Geom instance.

Parameters

geomGeom

Map geometry.

datanumpy.ndarray

data array

metadict

Dictionary to store meta data.

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 geometry. If map_type is ‘auto’ then an appropriate map type will be inferred from type of geom.

unitstr or Unit

Data unit.

Returns

map_outMap

Map object

classmethod from_hdu(hdu, hdu_bands=None)

Make a WcsNDMap object from a FITS HDU.

Parameters

hduBinTableHDU or ImageHDU

The map FITS HDU.

hdu_bandsBinTableHDU

The BANDS table HDU.

classmethod from_hdulist(hdu_list, hdu=None, hdu_bands=None)

Make a WcsMap object from a FITS HDUList.

Parameters

hdu_listHDUList

HDU list containing HDUs for map data and bands.

hdustr

Name or index of the HDU with the map data.

hdu_bandsstr

Name or index of the HDU with the BANDS table.

Returns

wcs_mapWcsMap

Map object

get_by_coord(self, coords)

Return map values at the given map coordinates.

Parameters

coordstuple or 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

valsndarray

Values of pixels in the map. np.nan used to flag coords outside of map.

get_by_idx(self, idx)

Return map values at the given pixel indices.

Parameters

idxtuple

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

valsndarray

Array of pixel values. np.nan used to flag coordinate outside of map

get_by_pix(self, pix)

Return map values at the given pixel coordinates.

Parameters

pixtuple

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

valsndarray

Array of pixel values. np.nan used to flag coordinates outside of map

get_image_by_coord(self, coords)

Return spatial map at the given axis coordinates.

Parameters

coordstuple 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_outMap

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})

get_image_by_idx(self, idx)

Return spatial map at the given axis pixel indices.

Parameters

idxtuple

Tuple of scalar indices for each non spatial dimension of the map. Tuple should be ordered as (I_0, …, I_n).

Returns

map_outMap

Map with spatial dimensions only.

See also

get_image_by_coord, get_image_by_pix

get_image_by_pix(self, pix)

Return spatial map at the given axis pixel coordinates

Parameters

pixtuple

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.

Returns

map_outMap

Map with spatial dimensions only.

See also

get_image_by_coord, get_image_by_idx

get_spectrum(self, region=None, func=<function nansum at 0x10ac0be18>)

Extract spectrum in a given region.

The spectrum can be computed by summing (or, more generally, applying func) along the spatial axes in each energy bin. This occurs only inside the region, which by default is assumed to be the whole spatial extension of the map.

Parameters

region: `~regions.Region`

Region (pixel or sky regions accepted).

funcnumpy.ufunc

Function to reduce the data.

Returns

spectrumCountsSpectrum

Spectrum in the given region.

interp_by_coord(self, coords, interp=None, fill_value=None)

Interpolate map values at the given map coordinates.

Parameters

coordstuple or 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_valueNone or float value

The value to use for points outside of the interpolation domain. If None, values outside the domain are extrapolated.

Returns

valsndarray

Interpolated pixel values.

interp_by_pix(self, pix, interp=None, fill_value=None)

Interpolate map values at the given pixel coordinates.

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 Iterating by image for further information.

make_hdu(self, hdu='SKYMAP', hdu_bands=None, sparse=False, conv=None)

Make a FITS HDU from this map.

Parameters

hdustr

The HDU extension name.

hdu_bandsstr

The HDU extension name for BANDS table.

sparsebool

Set INDXSCHM to SPARSE and sparsify the map by only writing pixels with non-zero amplitude.

Returns

hduBinTableHDU or ImageHDU

HDU containing the map data.

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.

cvalfloat

Padding value when mode=’consant’.

orderint

Order of interpolation when mode=’constant’ (0 = nearest-neighbor, 1 = linear, 2 = quadratic, 3 = cubic).

Returns

mapMap

Padded map.

plot(self, ax=None, fig=None, add_cbar=False, stretch='linear', **kwargs)

Plot image on matplotlib WCS axes.

Parameters

axWCSAxes, optional

WCS axis object to plot on.

figFigure

Figure object.

add_cbarbool

Add color bar?

stretchstr

Passed to astropy.visualization.simple_norm.

**kwargsdict

Keyword arguments passed to imshow.

Returns

figFigure

Figure object.

axWCSAxes

WCS axis object

cbarColorbar or None

Colorbar object.

plot_interactive(self, rc_params=None, **kwargs)

Plot map with interactive widgets to explore the non spatial axes.

Parameters

rc_paramsdict

Passed to matplotlib.rc_context(rc=rc_params) to style the plot.

**kwargsdict

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)

static read(filename, hdu=None, hdu_bands=None, map_type='auto')

Read a map from a FITS file.

Parameters

filenamestr or Path

Name of the FITS file.

hdustr

Name or index of the HDU with the map data.

hdu_bandsstr

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_outMap

Map object

reduce_over_axes(self, func, keepdims=False)

Reduce map over all non spatial axes

Parameters

func~numpy.ufunc

Function to use for reducing the data.

keepdimsbool, optional

If this is set to true, the axes which are summed over are left in the map with a single bin

Returns

map_outWcsNDMap

Map with non-spatial axes reduced

sample_coord(self, n_events, random_state=0)

Sample position and energy of events.

Parameters

n_eventsint

Number of events to sample.

random_state{int, ‘random-seed’, ‘global-rng’, RandomState}

Defines random number generator initialisation. Passed to get_random_state.

Returns

coordsMapCoord object.

Sequence of coordinates and energies of the sampled events.

set_by_coord(self, coords, vals)

Set pixels at coords with given vals.

Parameters

coordstuple or 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.

valsndarray

Values vector.

set_by_idx(self, idx, vals)

Set pixels at idx with given vals.

Parameters

idxtuple

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.

valsndarray

Values vector.

set_by_pix(self, pix, vals)

Set pixels at pix with given vals.

Parameters

pixtuple

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.

valsndarray

Values vector.

slice_by_idx(self, slices)

Slice sub map from map object.

For usage examples, see Indexing and Slicing.

Parameters

slicesdict

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_outMap

Sliced map object.

smooth(self, width, kernel='gauss', **kwargs)

Smooth the map.

Iterates over 2D image planes, processing one at a time.

Parameters

widthQuantity, str or float

Smoothing width given as quantity or float. If a float is given it interpreted as smoothing width in pixels. If an (angular) quantity is given it converted to pixels using geom.wcs.wcs.cdelt. It corresponds to the standard deviation in case of a Gaussian kernel, the radius in case of a disk kernel, and the side length in case of a box kernel.

kernel{‘gauss’, ‘disk’, ‘box’}

Kernel shape

kwargsdict

Keyword arguments passed to uniform_filter (‘box’), gaussian_filter (‘gauss’) or convolve (‘disk’).

Returns

imageWcsNDMap

Smoothed image (a copy, the original object is unchanged).

stack(self, other, weights=None)

Stack cutout into map.

Parameters

otherWcsNDMap

Other map to stack

weightsWcsNDMap

Array to be used as weights.

sum_over_axes(self, keepdims=False)

To sum map values over all non-spatial axes.

Parameters

keepdimsbool, optional

If this is set to true, the axes which are summed over are left in the map with a single bin

Returns

map_outWcsNDMap

Map with non-spatial axes summed over

to_hdulist(self, hdu=None, hdu_bands=None, sparse=False, conv='gadf')

Convert to HDUList.

Parameters

hdustr

Name or index of the HDU with the map data.

hdu_bandsstr

Name or index of the HDU with the BANDS table.

sparsebool

Sparsify the map by only writing pixels with non-zero amplitude.

conv{‘gadf’, ‘fgst-ccube’,’fgst-template’}

FITS format convention.

Returns

hdu_listHDUList

upsample(self, factor, order=0, preserve_counts=True, axis=None)

Upsample the spatial dimension by a given factor.

Parameters

factorint

Upsampling factor.

orderint

Order of the interpolation used for upsampling.

preserve_countsbool

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).

axisstr

Which axis to upsample. By default spatial axes are upsampled.

Returns

mapMap

Upsampled map.

write(self, filename, overwrite=False, **kwargs)

Write to a FITS file.

Parameters

filenamestr

Output file name.

overwritebool

Overwrite existing file?

hdustr

Set the name of the image extension. By default this will be set to SKYMAP (for BINTABLE HDU) or PRIMARY (for IMAGE HDU).

hdu_bandsstr

Set the name of the bands table extension. By default this will be set to BANDS.

convstr

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). Supported conventions are ‘gadf’, ‘fgst-ccube’, ‘fgst-ltcube’, ‘fgst-bexpcube’, ‘fgst-template’, ‘fgst-srcmap’, ‘fgst-srcmap-sparse’, ‘galprop’, and ‘galprop2’.

sparsebool

Sparsify the map by dropping pixels with zero amplitude. This option is only compatible with the ‘gadf’ format.