def partial_wcs_flux_map():
energy_axis = MapAxis.from_energy_bounds(0.1, 10, 2, unit='TeV')
map_dict = {}
map_dict["norm"] = WcsNDMap.create(npix=10,
frame='galactic',
axes=[energy_axis],
unit='')
map_dict["norm"].data += 1.0
map_dict["norm_err"] = WcsNDMap.create(npix=10,
frame='galactic',
axes=[energy_axis],
unit='')
map_dict["norm_err"].data += 0.1
# Add another map
map_dict["sqrt_ts"] = WcsNDMap.create(npix=10,
frame='galactic',
axes=[energy_axis],
unit='')
map_dict["sqrt_ts"].data += 1.0
return map_dict
def test_asmooth_map_dataset_on_off():
kernel = Tophat2DKernel
scales = ASmoothMapEstimator.get_scales(3, factor=2,
kernel=kernel) * 0.1 * u.deg
asmooth = ASmoothMapEstimator(kernel=kernel,
scales=scales,
method="lima",
threshold=2.5)
counts = WcsNDMap.create(npix=(50, 50), binsz=0.02, unit="")
counts += 2
counts_off = WcsNDMap.create(npix=(50, 50), binsz=0.02, unit="")
counts_off += 3
acceptance = WcsNDMap.create(npix=(50, 50), binsz=0.02, unit="")
acceptance += 1
acceptance_off = WcsNDMap.create(npix=(50, 50), binsz=0.02, unit="")
acceptance_off += 3
dataset = MapDatasetOnOff(
counts=counts,
counts_off=counts_off,
acceptance=acceptance,
acceptance_off=acceptance_off,
)
smoothed = asmooth.run(dataset)
assert_allclose(smoothed["counts"].data[25, 25], 2)
assert_allclose(smoothed["background"].data[25, 25], 1)
assert_allclose(smoothed["significance"].data[25, 25], 4.391334)
def test_get_by_coord_bool_int():
mask = WcsNDMap.create(width=2, dtype="bool")
coords = {"lon": [0, 3], "lat": [0, 3]}
vals = mask.get_by_coord(coords)
assert_allclose(vals, [0, np.nan])
mask = WcsNDMap.create(width=2, dtype="int")
coords = {"lon": [0, 3], "lat": [0, 3]}
vals = mask.get_by_coord(coords)
assert_allclose(vals, [0, np.nan])
def test_stack_unit_handling():
m = WcsNDMap.create(npix=(3, 3), unit="m2 s")
m.data += 1
m_other = WcsNDMap.create(npix=(3, 3), unit="cm2 s")
m_other.data += 1
m.stack(m_other)
assert_allclose(m.data, 1.0001)
def setup(self):
self.images = {}
self.images["counts"] = WcsNDMap.create(binsz=0.02,
npix=101,
dtype=float)
self.images["counts"].data += 1.0
self.images["background"] = WcsNDMap.create(binsz=0.02,
npix=101,
dtype=float)
self.images["background"].data += 1e10
exclusion = WcsNDMap.create(binsz=0.02, npix=101, dtype=float)
exclusion.data += 1
exclusion.data[40:60, 40:60] = 0
self.images["exclusion"] = exclusion
def wcs_flux_map():
energy_axis = MapAxis.from_energy_bounds(0.1, 10, 2, unit="TeV")
map_dict = {}
map_dict["norm"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["norm"].data += 1.0
map_dict["norm_err"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["norm_err"].data += 0.1
map_dict["norm_errp"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["norm_errp"].data += 0.2
map_dict["norm_errn"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["norm_errn"].data += 0.2
map_dict["norm_ul"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["norm_ul"].data += 2.0
# Add another map
map_dict["sqrt_ts"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["sqrt_ts"].data += 1.0
# Add another map
map_dict["ts"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="")
map_dict["ts"].data[1] += 3.0
# Add another map
map_dict["success"] = WcsNDMap.create(npix=10,
frame="galactic",
axes=[energy_axis],
unit="",
dtype=np.dtype(bool))
map_dict["success"].data = True
map_dict["success"].data[0, 0, 1] = False
return map_dict
def plot_image(self):
"""Quick look counts map sky plot."""
from gammapy.maps import WcsNDMap
m = WcsNDMap.create(npix=(360, 180), binsz=1.0, proj="AIT", frame="galactic")
m.fill_by_coord(self.radec)
m.plot(stretch="sqrt")
def test_flux_estimator_norm_range_template():
energy = MapAxis.from_energy_bounds(0.1,
10,
3.0,
unit="TeV",
name="energy_true")
template = WcsNDMap.create(npix=10,
axes=[energy],
unit="cm-2 s-1 sr-1 TeV-1")
spatial = TemplateSpatialModel(template, normalize=False)
spectral = PowerLawNormSpectralModel()
model = SkyModel(spectral_model=spectral,
spatial_model=spatial,
name="test")
model.spectral_model.norm.max = 10
model.spectral_model.norm.min = 0
estimator = FluxEstimator(source="test",
selection_optional=[],
reoptimize=True)
scale_model = estimator.get_scale_model(Models([model]))
assert_allclose(scale_model.norm.min, 0)
assert_allclose(scale_model.norm.max, 10)
assert scale_model.norm.interp == "log"
def test_convolve_pixel_scale_error():
m = WcsNDMap.create(binsz=0.05 * u.deg, width=5 * u.deg)
kgeom = WcsGeom.create(binsz=0.04 * u.deg, width=0.5 * u.deg)
kernel = PSFKernel.from_gauss(kgeom, sigma=0.1 * u.deg, max_radius=1.5 * u.deg)
with pytest.raises(ValueError):
m.convolve(kernel)
def test_asmooth_map_dataset_on_off():
kernel = Tophat2DKernel
scales = ASmoothMapEstimator.get_scales(3, factor=2,
kernel=kernel) * 0.1 * u.deg
asmooth = ASmoothMapEstimator(kernel=kernel,
scales=scales,
method="lima",
threshold=2.5)
axis = MapAxis.from_energy_bounds("1 TeV", "10 TeV", nbin=1)
counts = WcsNDMap.create(npix=(50, 50), binsz=0.02, unit="", axes=[axis])
counts += 2
counts_off = WcsNDMap.create(npix=(50, 50),
binsz=0.02,
unit="",
axes=[axis])
counts_off += 3
acceptance = WcsNDMap.create(npix=(50, 50),
binsz=0.02,
unit="",
axes=[axis])
acceptance += 1
acceptance_off = WcsNDMap.create(npix=(50, 50),
binsz=0.02,
unit="",
axes=[axis])
acceptance_off += 3
dataset = MapDatasetOnOff(
counts=counts,
counts_off=counts_off,
acceptance=acceptance,
acceptance_off=acceptance_off,
)
smoothed = asmooth.run(dataset)
assert_allclose(smoothed["counts"].data[25, 25], 2)
assert_allclose(smoothed["background"].data[25, 25], 1.25)
assert_allclose(smoothed["significance"].data[25, 25],
3.079799117645,
rtol=1e-2)
def test_map_interp_one_bin():
m = WcsNDMap.create(npix=(2, 1))
m.data = np.array([[1, 2]])
coords = {"lon": 0, "lat": [0, 0]}
data = m.interp_by_coord(coords)
assert data.shape == (2, )
assert_allclose(data, 1.5)
def test_wcs_nd_map_pad_axis():
axis = MapAxis.from_nodes([0, 1], unit="deg", name="axis")
m = WcsNDMap.create(npix=3, axes=[axis])
m.data += np.array([1, 2]).reshape((-1, 1, 1))
m_pad = m.pad(axis_name="axis", pad_width=1, mode="edge")
m_pad.data
assert_allclose(m_pad.data[:, 1, 1], [1, 1, 2, 2])
def test_convolve_pixel_scale_error():
m = WcsNDMap.create(binsz=0.05 * u.deg, width=5 * u.deg)
kgeom = WcsGeom.create(binsz=0.04 * u.deg, width=0.5 * u.deg)
kernel = PSFKernel.from_gauss(kgeom,
sigma=0.1 * u.deg,
max_radius=1.5 * u.deg)
with pytest.raises(ValueError) as excinfo:
m.convolve(kernel)
assert "Pixel size of kernel and map not compatible." == str(excinfo.value)
def test_map_spectrum_weight():
axis = MapAxis.from_edges([0.1, 10, 1000], unit="TeV", name="energy")
expo_map = WcsNDMap.create(npix=10, binsz=1, axes=[axis], unit="m2 s")
expo_map.data += 1
spectrum = ConstantSpectralModel(const="42 cm-2 s-1 TeV-1")
weighted_expo = _map_spectrum_weight(expo_map, spectrum)
assert weighted_expo.data.shape == (2, 10, 10)
assert weighted_expo.unit == "m2 s"
assert_allclose(weighted_expo.data.sum(), 100)
def test_convolve_kernel_size_error():
axis_1 = MapAxis.from_energy_bounds("1 TeV", "10 TeV", nbin=2)
axis_2 = MapAxis.from_energy_bounds("1 TeV", "10 TeV", nbin=3)
m = WcsNDMap.create(binsz=0.05 * u.deg, width=5 * u.deg, axes=[axis_1])
kgeom = WcsGeom.create(binsz=0.05 * u.deg, width=0.5 * u.deg, axes=[axis_2])
kernel = PSFKernel.from_gauss(kgeom, sigma=0.1 * u.deg, max_radius=1.5 * u.deg)
with pytest.raises(ValueError):
m.convolve(kernel)
def _counts_image(self):
opts = {
"width": (7, 7),
"binsz": 0.1,
"proj": "TAN",
"frame": "galactic",
"skydir": self.pointing_radec,
}
m = WcsNDMap.create(**opts)
m.fill_by_coord(self.radec)
m = m.smooth(width=1)
return m
def _scan_position(self, name, **kwargs):
saved_state = LikelihoodState(self.like)
skydir = kwargs.pop('skydir', self.roi[name].skydir)
scan_cdelt = kwargs.pop('scan_cdelt', 0.02)
nstep = kwargs.pop('nstep', 5)
use_cache = kwargs.get('use_cache', True)
use_pylike = kwargs.get('use_pylike', False)
optimizer = kwargs.get('optimizer', {})
# Fit without source
self.zero_source(name, loglevel=logging.DEBUG)
fit_output_nosrc = self._fit(loglevel=logging.DEBUG, **optimizer)
self.unzero_source(name, loglevel=logging.DEBUG)
saved_state.restore()
self.free_norm(name, loglevel=logging.DEBUG)
lnlmap = WcsNDMap.create(skydir=skydir,
binsz=scan_cdelt,
npix=(nstep, nstep),
frame=wcs_utils.coordsys_to_frame(
wcs_utils.get_coordsys(self.geom.wcs)))
src = self.roi.copy_source(name)
if use_cache and not use_pylike:
self._create_srcmap_cache(src.name, src)
coord = MapCoord.create(lnlmap.geom.get_coord(flat=True),
frame=lnlmap.geom.frame)
scan_skydir = coord.skycoord.icrs
for lon, lat, ra, dec in zip(coord.lon, coord.lat, scan_skydir.ra.deg,
scan_skydir.dec.deg):
spatial_pars = {'ra': ra, 'dec': dec}
self.set_source_morphology(name,
spatial_pars=spatial_pars,
use_pylike=use_pylike)
fit_output = self._fit(loglevel=logging.DEBUG, **optimizer)
lnlmap.set_by_coord((lon, lat), fit_output['loglike'])
self.set_source_morphology(name,
spatial_pars=src.spatial_pars,
use_pylike=use_pylike)
saved_state.restore()
lnlmap.data -= fit_output_nosrc['loglike']
tsmap = WcsNDMap(lnlmap.geom, 2.0 * lnlmap.data)
self._clear_srcmap_cache()
return tsmap, fit_output_nosrc['loglike']
def _counts_image(self):
width = self.galactic.b.max().deg - self.galactic.b.min().deg
opts = {
"width": (width, width),
"binsz": 0.05,
"proj": "TAN",
"frame": "galactic",
"skydir": self.pointing_radec,
}
m = WcsNDMap.create(**opts)
m.fill_by_coord(self.radec)
m = m.smooth(width=0.5)
return m
def map_flux_estimate():
axis = MapAxis.from_energy_edges((0.1, 1.0, 10.0), unit="TeV")
nmap = WcsNDMap.create(npix=5, axes=[axis])
cols = dict()
cols["norm"] = nmap.copy(data=1.0)
cols["norm_err"] = nmap.copy(data=0.1)
cols["norm_errn"] = nmap.copy(data=0.2)
cols["norm_errp"] = nmap.copy(data=0.15)
cols["norm_ul"] = nmap.copy(data=2.0)
return cols
def _scan_position(self, name, **kwargs):
saved_state = LikelihoodState(self.like)
skydir = kwargs.pop('skydir', self.roi[name].skydir)
scan_cdelt = kwargs.pop('scan_cdelt', 0.02)
nstep = kwargs.pop('nstep', 5)
use_cache = kwargs.get('use_cache', True)
use_pylike = kwargs.get('use_pylike', False)
optimizer = kwargs.get('optimizer', {})
# Fit without source
self.zero_source(name, loglevel=logging.DEBUG)
fit_output_nosrc = self._fit(loglevel=logging.DEBUG,
**optimizer)
self.unzero_source(name, loglevel=logging.DEBUG)
saved_state.restore()
self.free_norm(name, loglevel=logging.DEBUG)
lnlmap = WcsNDMap.create(skydir=skydir, binsz=scan_cdelt, npix=(nstep, nstep),
coordsys=wcs_utils.get_coordsys(self.geom.wcs))
src = self.roi.copy_source(name)
if use_cache and not use_pylike:
self._create_srcmap_cache(src.name, src)
coord = MapCoord.create(lnlmap.geom.get_coord(flat=True),
coordsys=lnlmap.geom.coordsys)
scan_skydir = coord.skycoord.icrs
for lon, lat, ra, dec in zip(coord.lon, coord.lat,
scan_skydir.ra.deg, scan_skydir.dec.deg):
spatial_pars = {'ra': ra, 'dec': dec}
self.set_source_morphology(name,
spatial_pars=spatial_pars,
use_pylike=use_pylike)
fit_output = self._fit(loglevel=logging.DEBUG,
**optimizer)
lnlmap.set_by_coord((lon, lat), fit_output['loglike'])
self.set_source_morphology(name, spatial_pars=src.spatial_pars,
use_pylike=use_pylike)
saved_state.restore()
lnlmap.data -= fit_output_nosrc['loglike']
tsmap = WcsNDMap(lnlmap.geom, 2.0 * lnlmap.data)
self._clear_srcmap_cache()
return tsmap, fit_output_nosrc['loglike']
def _counts_image(self):
from gammapy.maps import WcsNDMap
opts = {
"width": (7, 7),
"binsz": 0.1,
"proj": "TAN",
"coordsys": "GAL",
"skydir": self.pointing_radec,
}
m = WcsNDMap.create(**opts)
m.fill_by_coord(self.radec)
m = m.smooth(width=1)
return m
def make_reference_map(region,
center,
binsz="0.01 deg",
min_width="0.3 deg"):
"""Create empty reference map.
The size of the map is chosen such that all reflected regions are
contained on the image.
To do so, the reference map width is taken to be 4 times the distance between
the target region center and the rotation point. This distance is larger than
the typical dimension of the region itself (otherwise the rotation point would
lie inside the region). A minimal width value is added by default in case the
region center and the rotation center are too close.
The WCS of the map is the TAN projection at the `center` in the coordinate
system used by the `region` center.
Parameters
----------
region : `~regions.SkyRegion`
Region to rotate
center : `~astropy.coordinates.SkyCoord`
Rotation point
binsz : `~astropy.coordinates.Angle`
Reference map bin size. Default : 0.01 deg
min_width : `~astropy.coordinates.Angle`
Minimal map width. Default : 0.3 deg
Returns
-------
reference_map : `~gammapy.maps.WcsNDMap`
Map containing the region
"""
try:
if "ra" in region.center.representation_component_names:
coordsys = "CEL"
else:
coordsys = "GAL"
except:
raise TypeError("Algorithm not yet adapted to this Region shape")
# width is the full width of an image (not the radius)
width = 4 * region.center.separation(center) + Angle(min_width)
return WcsNDMap.create(skydir=center,
binsz=binsz,
width=width,
coordsys=coordsys,
proj="TAN")
def test_convolve_vs_smooth():
axes = [
MapAxis(np.logspace(0.0, 3.0, 3), interp="log"),
MapAxis(np.logspace(1.0, 3.0, 4), interp="lin"),
]
binsz = 0.05 * u.deg
m = WcsNDMap.create(binsz=binsz, width=1.05 * u.deg, axes=axes)
m.data[:, :, 10, 10] = 1.0
desired = m.smooth(kernel="gauss", width=0.5 * u.deg, mode="constant")
gauss = Gaussian2DKernel(10).array
actual = m.convolve(kernel=gauss)
assert_allclose(actual.data, desired.data, rtol=1e-3)
def make_reference_map(region,
center,
binsz="0.01 deg",
min_width="0.3 deg"):
"""Create empty reference map.
The size of the map is chosen such that all reflected regions are
contained on the image.
To do so, the reference map width is taken to be 4 times the distance between
the target region center and the rotation point. This distance is larger than
the typical dimension of the region itself (otherwise the rotation point would
lie inside the region). A minimal width value is added by default in case the
region center and the rotation center are too close.
The WCS of the map is the TAN projection at the `center` in the coordinate
system used by the `region` center.
Parameters
----------
region : `~regions.SkyRegion`
Region to rotate
center : `~astropy.coordinates.SkyCoord`
Rotation point
binsz : `~astropy.coordinates.Angle`
Reference map bin size.
min_width : `~astropy.coordinates.Angle`
Minimal map width.
Returns
-------
reference_map : `~gammapy.maps.WcsNDMap`
Map containing the region
"""
frame = region.center.frame.name
# width is the full width of an image (not the radius)
width = 4 * region.center.separation(center) + Angle(min_width)
return WcsNDMap.create(skydir=center,
binsz=binsz,
width=width,
frame=frame,
proj="TAN")
def images():
fov = 2.5 * u.deg
m_ref = WcsNDMap.create(binsz=0.05, npix=201, dtype=float)
m_ref.data += 1.0
coords = m_ref.geom.get_coord().skycoord
center = m_ref.geom.center_skydir
mask = coords.separation(center) < fov
images = dict()
images["counts"] = m_ref.copy(data=np.zeros_like(m_ref.data) + 2.0)
images["counts"].data *= mask
images["background"] = m_ref.copy(data=np.zeros_like(m_ref.data) + 1.0)
images["background"].data *= mask
exclusion = m_ref.copy(data=np.zeros_like(m_ref.data) + 1.0)
exclusion.data[90:110, 90:110] = 0
images["exclusion"] = exclusion
return images
def _counts_image(self, allsky):
if allsky:
opts = {
"npix": (360, 180),
"binsz": 1.0,
"proj": "AIT",
"frame": "galactic"
}
else:
opts = {
"width": self._plot_width,
"binsz": 0.05,
"proj": "TAN",
"frame": "galactic",
"skydir": self._plot_center,
}
m = WcsNDMap.create(**opts)
m.fill_by_coord(self.radec)
m = m.smooth(width=0.5)
return m
"""Example how to compute and plot reflected regions."""
import matplotlib.pyplot as plt
import numpy as np
from astropy.coordinates import SkyCoord, Angle
from regions import CircleSkyRegion
from gammapy.maps import WcsNDMap
from gammapy.background import ReflectedRegionsFinder
# Exclude a rectangular region
exclusion_mask = WcsNDMap.create(npix=(801, 701), binsz=0.01, skydir=(83.6, 23.0))
coords = exclusion_mask.geom.get_coord().skycoord
mask = (Angle("23d") < coords.dec) & (coords.dec < Angle("24d"))
exclusion_mask.data = np.invert(mask)
pos = SkyCoord(83.633, 22.014, unit="deg")
radius = Angle(0.3, "deg")
on_region = CircleSkyRegion(pos, radius)
center = SkyCoord(83.633, 24, unit="deg")
# One can impose a minimal distance between ON region and first reflected regions
finder = ReflectedRegionsFinder(
region=on_region,
center=center,
exclusion_mask=exclusion_mask,
min_distance_input="0.2 rad",
)
finder.run()
fig1 = plt.figure(1)
finder.plot(fig=fig1)
import matplotlib.pyplot as plt
from astropy.coordinates import Angle, SkyCoord
from regions import CircleSkyRegion
from gammapy.makers import ReflectedRegionsFinder
from gammapy.maps import WcsNDMap, RegionGeom
# Exclude a rectangular region
exclusion_mask = WcsNDMap.create(npix=(801, 701),
binsz=0.01,
skydir=(83.6, 23.0))
coords = exclusion_mask.geom.get_coord().skycoord
data = (Angle("23 deg") < coords.dec) & (coords.dec < Angle("24 deg"))
exclusion_mask.data = ~data
pos = SkyCoord(83.633, 22.014, unit="deg")
radius = Angle(0.3, "deg")
on_region = CircleSkyRegion(pos, radius)
center = SkyCoord(83.633, 24, unit="deg")
# One can impose a minimal distance between ON region and first reflected regions
finder = ReflectedRegionsFinder(
region=on_region,
center=center,
exclusion_mask=exclusion_mask,
min_distance_input="0.2 rad",
)
regions = finder.run()
fig, axes = plt.subplots(
ncols=3,
def test_plot_allsky():
m = WcsNDMap.create(binsz=10 * u.deg)
with mpl_plot_check():
m.plot()
def test_plot_grid():
axis = MapAxis([0, 1, 2], node_type="edges")
m = WcsNDMap.create(binsz=0.1 * u.deg, width=1 * u.deg, axes=[axis])
with mpl_plot_check():
m.plot_grid()
on_ellipse_annulus = EllipseAnnulusSkyRegion(
center=position,
inner_width=1.5 * u.deg,
outer_width=2.5 * u.deg,
inner_height=3 * u.deg,
outer_height=4 * u.deg,
angle=130 * u.deg,
)
another_position = SkyCoord(80.3, 22.0, unit="deg")
on_rectangle = RectangleSkyRegion(center=another_position,
width=2.0 * u.deg,
height=4.0 * u.deg,
angle=50 * u.deg)
# Now we plot those regions. We first create an empty map
empty_map = WcsNDMap.create(skydir=position,
width=10 * u.deg,
binsz=0.1 * u.deg,
proj="TAN")
empty_map.data += 1.0
empty_map.plot(cmap="gray", vmin=0, vmax=1)
# To plot the regions, we convert them to PixelRegion with the map wcs
on_circle.to_pixel(empty_map.geom.wcs).plot()
on_rectangle.to_pixel(empty_map.geom.wcs).plot()
on_ellipse_annulus.to_pixel(empty_map.geom.wcs).plot()
plt.show()
def test_plot_allsky():
axis = MapAxis([0, 1], node_type="edges")
m = WcsNDMap.create(binsz=10 * u.deg, axes=[axis])
with mpl_plot_check():
m.plot()