def image_coordinates(infile, outfile, make_coordinate_maps, make_distance_map,
overwrite):
"""Make maps that can be used to create profiles.
The following images can be created:
* LON -- Longitude coordinate
* LAT -- Latitude coordinate
* DIST -- Distance to mask
* SOLID_ANGLE -- Solid angle
"""
from astropy.io import fits
from gammapy.utils.fits import get_hdu
from gammapy.image import SkyMap, ExclusionMask
log.info('Reading {0}'.format(infile))
hdu = get_hdu(infile)
out_hdus = fits.HDUList()
if make_coordinate_maps:
skymap = SkyMap.empty_like(hdu)
log.info('Computing LON and LAT maps')
lon, lat = skymap.coordinates()
out_hdus.append(fits.ImageHDU(lon, hdu.header, 'LON'))
out_hdus.append(fits.ImageHDU(lat, hdu.header, 'LAT'))
if make_distance_map:
excl = ExclusionMask.from_image_hdu(hdu)
log.info('Computing DIST map')
dist = excl.exclusion_distance
out_hdus.append(fits.ImageHDU(dist, hdu.header, 'DIST'))
log.info('Writing {0}'.format(outfile))
out_hdus.writeto(outfile, clobber=overwrite)
def make_image_from_2d_bg():
center = SkyCoord(83.63, 22.01, unit='deg').galactic
energy_band = Energy([1, 10], 'TeV')
offset_band = Angle([0, 2.49], 'deg')
data_store = DataStore.from_dir(
'/Users/jouvin/Desktop/these/temp/bg_model_image/')
# TODO: fix `binarize` implementation
# exclusion_mask = exclusion_mask.binarize()
image = SkyMap.empty(nxpix=250,
nypix=250,
binsz=0.02,
xref=center.l.deg,
yref=center.b.deg,
proj='TAN',
coordsys='GAL')
refheader = image.to_image_hdu().header
exclusion_mask = ExclusionMask.read(
'$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
exclusion_mask = exclusion_mask.reproject(reference=refheader)
mosaic_images = MosaicImage(image,
energy_band=energy_band,
offset_band=offset_band,
data_store=data_store,
obs_table=data_store.obs_table,
exclusion_mask=exclusion_mask)
mosaic_images.make_images(make_background_image=True,
for_integral_flux=True,
radius=10.)
filename = 'fov_bg_maps_test.fits'
log.info('Writing {}'.format(filename))
mosaic_images.maps.write(filename, clobber=True)
def test_image_pipe(tmpdir):
tmpdir = str(tmpdir)
from subprocess import call
outdir = tmpdir
outdir2 = outdir + '/background'
cmd = 'mkdir -p {}'.format(outdir2)
print('Executing: {}'.format(cmd))
call(cmd, shell=True)
ds = DataStore.from_dir("$GAMMAPY_EXTRA/datasets/hess-crab4-hd-hap-prod2")
ds.copy_obs(ds.obs_table, tmpdir)
data_store = DataStore.from_dir(tmpdir)
bgmaker = OffDataBackgroundMaker(data_store, outdir=outdir2)
bgmaker.select_observations(selection='all')
bgmaker.group_observations()
bgmaker.make_model("2D")
bgmaker.save_models("2D")
fn = outdir2 + '/group-def.fits'
hdu_index_table = bgmaker.make_total_index_table(
data_store=data_store,
modeltype='2D',
out_dir_background_model=outdir2,
filename_obs_group_table=fn
)
fn = outdir + '/hdu-index.fits.gz'
hdu_index_table.write(fn, overwrite=True)
tmpdir = str(tmpdir)
center = SkyCoord(83.63, 22.01, unit='deg').galactic
energy_band = Energy([1, 10], 'TeV')
offset_band = Angle([0, 2.49], 'deg')
data_store = DataStore.from_dir(tmpdir)
# TODO: fix `binarize` implementation
# exclusion_mask = exclusion_mask.binarize()
image = SkyMap.empty(nxpix=250, nypix=250, binsz=0.02, xref=center.l.deg,
yref=center.b.deg, proj='TAN', coordsys='GAL')
refheader = image.to_image_hdu().header
exclusion_mask = ExclusionMask.read('$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
exclusion_mask = exclusion_mask.reproject(reference=refheader)
images = ImageAnalysis(image, energy_band=energy_band, offset_band=offset_band, data_store=data_store,
obs_table=data_store.obs_table, exclusion_mask=exclusion_mask)
images.make_maps(radius=10., bkg_norm=True, spectral_index=2.3, for_integral_flux=True)
def plot_exclusion_mask(**kwargs):
"""Plot exclusion mask
The plot will be centered at the pointing position
Parameters
----------
size : `~astropy.coordinates.Angle`
Edge length of the plot
"""
from gammapy.image import ExclusionMask
from gammapy.spectrum import SpectrumExtraction
# Todo: plot exclusion mask as contours with skymap class
exclusion = ExclusionMask.from_fits(SpectrumExtraction.EXCLUDEDREGIONS_FILE)
ax = exclusion.plot(**kwargs)
return ax
def make_image_from_2d_bg():
center = SkyCoord(83.63, 22.01, unit='deg').galactic
energy_band = Energy([1, 10], 'TeV')
offset_band = Angle([0, 2.49], 'deg')
data_store = DataStore.from_dir('/Users/jouvin/Desktop/these/temp/bg_model_image/')
# TODO: fix `binarize` implementation
# exclusion_mask = exclusion_mask.binarize()
image = SkyMap.empty(nxpix=250, nypix=250, binsz=0.02, xref=center.l.deg,
yref=center.b.deg, proj='TAN', coordsys='GAL')
refheader = image.to_image_hdu().header
exclusion_mask = ExclusionMask.read('$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
exclusion_mask = exclusion_mask.reproject(reference=refheader)
images = ImageAnalysis(image, energy_band=energy_band, offset_band=offset_band, data_store=data_store,
obs_table=data_store.obs_table, exclusion_mask=exclusion_mask)
images.make_maps(radius=10., bkg_norm=True, spectral_index=2.3, for_integral_flux = True)
# images.make_total_exposure()
filename = 'fov_bg_maps.fits'
log.info('Writing {}'.format(filename))
images.maps.write(filename, clobber=True)
def image_coordinates(infile,
outfile,
make_coordinate_maps,
make_distance_map,
overwrite):
"""Make maps that can be used to create profiles.
The following images can be created:
* LON -- Longitude coordinate
* LAT -- Latitude coordinate
* DIST -- Distance to mask
* SOLID_ANGLE -- Solid angle
"""
from astropy.io import fits
from gammapy.utils.fits import get_hdu
from gammapy.image import SkyMap, ExclusionMask
log.info('Reading {0}'.format(infile))
hdu = get_hdu(infile)
out_hdus = fits.HDUList()
if make_coordinate_maps:
skymap = SkyMap.empty_like(hdu)
log.info('Computing LON and LAT maps')
lon, lat = skymap.coordinates()
out_hdus.append(fits.ImageHDU(lon, hdu.header, 'LON'))
out_hdus.append(fits.ImageHDU(lat, hdu.header, 'LAT'))
if make_distance_map:
excl = ExclusionMask.read(hdu)
log.info('Computing DIST map')
dist = excl.exclusion_distance
out_hdus.append(fits.ImageHDU(dist, hdu.header, 'DIST'))
log.info('Writing {0}'.format(outfile))
out_hdus.writeto(outfile, clobber=overwrite)
def test_image_pipe(tmpdir):
tmpdir = str(tmpdir)
from subprocess import call
outdir = tmpdir
outdir2 = outdir + '/background'
cmd = 'mkdir -p {}'.format(outdir2)
print('Executing: {}'.format(cmd))
call(cmd, shell=True)
ds = DataStore.from_dir("$GAMMAPY_EXTRA/datasets/hess-crab4-hd-hap-prod2")
ds.copy_obs(ds.obs_table, tmpdir)
data_store = DataStore.from_dir(tmpdir)
bgmaker = OffDataBackgroundMaker(data_store, outdir=outdir2)
bgmaker.select_observations(selection='all')
bgmaker.group_observations()
bgmaker.make_model("2D")
bgmaker.save_models("2D")
fn = outdir2 + '/group-def.fits'
hdu_index_table = bgmaker.make_total_index_table(
data_store=data_store,
modeltype='2D',
out_dir_background_model=outdir2,
filename_obs_group_table=fn)
fn = outdir + '/hdu-index.fits.gz'
hdu_index_table.write(fn, overwrite=True)
tmpdir = str(tmpdir)
center = SkyCoord(83.63, 22.01, unit='deg').galactic
energy_band = Energy([1, 10], 'TeV')
offset_band = Angle([0, 2.49], 'deg')
data_store = DataStore.from_dir(tmpdir)
# TODO: fix `binarize` implementation
# exclusion_mask = exclusion_mask.binarize()
image = SkyMap.empty(nxpix=250,
nypix=250,
binsz=0.02,
xref=center.l.deg,
yref=center.b.deg,
proj='TAN',
coordsys='GAL')
refheader = image.to_image_hdu().header
exclusion_mask = ExclusionMask.read(
'$GAMMAPY_EXTRA/datasets/exclusion_masks/tevcat_exclusion.fits')
exclusion_mask = exclusion_mask.reproject(reference=refheader)
images = ImageAnalysis(image,
energy_band=energy_band,
offset_band=offset_band,
data_store=data_store,
obs_table=data_store.obs_table,
exclusion_mask=exclusion_mask)
images.make_maps(radius=10.,
bkg_norm=True,
spectral_index=2.3,
for_integral_flux=True)
"""
from astropy.coordinates import SkyCoord, Angle
from gammapy.datasets import gammapy_extra
from gammapy.image import ExclusionMask
from gammapy.data import DataStore
from gammapy.region import SkyCircleRegion
from gammapy.spectrum import SpectrumAnalysis
from gammapy.utils.energy import EnergyBounds
center = SkyCoord(83.63, 22.01, unit='deg', frame='icrs')
radius = Angle('0.3 deg')
on_region = SkyCircleRegion(pos=center, radius=radius)
bkg_method = dict(type='reflected', n_min=3)
exclusion_file = gammapy_extra.filename("datasets/exclusion_masks/"
"tevcat_exclusion.fits")
excl = ExclusionMask.from_fits(exclusion_file)
bounds = EnergyBounds.equal_log_spacing(1, 10, 40, unit='TeV')
store = gammapy_extra.filename("datasets/hess-crab4")
ds = DataStore.from_dir(store)
obs = [23523, 23559]
ana = SpectrumAnalysis(datastore=ds, obs=obs, on_region=on_region,
bkg_method=bkg_method, exclusion=excl, ebounds=bounds)
ana.write_ogip_data(outdir='ogip_data')
def run_spectrum_analysis_using_config(config):
"""Wrapper function to run a 1D spectral analysis using a config dict
Parameters
----------
config : dict
config
Returns
-------
analysis : `~gammapy.spectrum.SpectrumAnalysis`
Spectrum analysis instance
"""
# Observations
obs = config['general']['runlist']
store = config['general']['datastore']
nobs = config['general']['nruns']
# Binning
sec = config['binning']
if sec['equal_log_spacing']:
emin = Energy(sec['emin'])
emax = Energy(sec['emax'])
nbins = sec['nbins']
ebounds = EnergyBounds.equal_log_spacing(
emin, emax, nbins)
else:
if sec['binning'] is None:
raise ValueError("No binning specified")
log.debug('Binning: {}'.format(ebounds))
# ON region
radius = Angle(config['on_region']['radius'])
x = config['on_region']['center_x']
y = config['on_region']['center_y']
frame = config['on_region']['system']
center = SkyCoord(x, y, frame=frame)
on_region = SkyCircleRegion(center, radius)
# OFF region
off_type = config['off_region']['type']
if off_type == 'ring':
irad = Angle(config['off_region']['inner_radius'])
orad = Angle(config['off_region']['outer_radius'])
bkg_method = dict(type='ring', inner_radius=irad,
outer_radius=orad)
elif off_type == 'reflected':
bkg_method = dict(type='reflected')
# Exclusion
excl_file = config['excluded_regions']['file']
exclusion = ExclusionMask.from_fits(excl_file)
analysis = SpectrumAnalysis(datastore=store, obs=obs, on_region=on_region,
bkg_method=bkg_method, exclusion=exclusion,
nobs=nobs, ebounds=ebounds)
if config['general']['create_ogip']:
outdir = config['general']['outdir']
analysis.write_ogip_data(outdir)
if config['general']['run_fit']:
model = config['model']['type']
thres_low = Energy(config['model']['threshold_low'])
thres_high = Energy(config['model']['threshold_high'])
fit = analysis.run_hspec_fit(model, thres_low, thres_high)
return analysis
from astropy.coordinates import SkyCoord, Angle
from astropy.wcs import WCS
from gammapy.region import find_reflected_regions
from gammapy.extern.regions.shapes import CircleSkyRegion
from gammapy.image import ExclusionMask
from gammapy.utils.testing import requires_data
mask = ExclusionMask.empty(name='Exclusion Mask', nxpix=801, nypix=701, binsz=0.01,
coordsys='CEL', xref=83.2, yref=22.7)
mask.fill_random_circles(n=8, min_rad=30, max_rad=80)
pos = SkyCoord(80.2, 23.5, unit='deg', frame='icrs')
radius = Angle(0.4, 'deg')
test_region = CircleSkyRegion(pos, radius)
center = SkyCoord(82.8, 22.5, unit='deg', frame='icrs')
regions = find_reflected_regions(test_region, center, mask)
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(8, 5), dpi=80)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], projection=mask.wcs)
mask.plot(ax, fig)
for reg in regions:
reg.plot(ax, facecolor='red')
test_region.plot(ax, facecolor='blue')
plt.show()
from astropy.coordinates import SkyCoord, Angle
from astropy.wcs import WCS
from gammapy.region import find_reflected_regions
from gammapy.extern.regions.shapes import CircleSkyRegion
from gammapy.image import ExclusionMask
from gammapy.utils.testing import requires_data
mask = ExclusionMask.empty(name='Exclusion Mask',
nxpix=801,
nypix=701,
binsz=0.01,
coordsys='CEL',
xref=83.2,
yref=22.7)
mask.fill_random_circles(n=8, min_rad=30, max_rad=80)
pos = SkyCoord(80.2, 23.5, unit='deg', frame='icrs')
radius = Angle(0.4, 'deg')
test_region = CircleSkyRegion(pos, radius)
center = SkyCoord(82.8, 22.5, unit='deg', frame='icrs')
regions = find_reflected_regions(test_region, center, mask)
import matplotlib.pyplot as plt
fig = plt.figure(figsize=(8, 5), dpi=80)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], projection=mask.wcs)
mask.plot(ax, fig)
for reg in regions:
reg.plot(ax, facecolor='red')
test_region.plot(ax, facecolor='blue')
from astropy.coordinates import SkyCoord, Angle
from astropy.wcs import WCS
from gammapy.region import find_reflected_regions, SkyCircleRegion
from gammapy.image import ExclusionMask, make_empty_image
from gammapy.utils.testing import requires_data
hdu = make_empty_image(nxpix=801, nypix=701, binsz=0.01,
coordsys='CEL', xref=83.2, yref=22.7)
mask = ExclusionMask.create_random(hdu, n=8, min_rad=30, max_rad=80)
pos = SkyCoord(80.2, 23.5, unit='deg', frame='icrs')
radius = Angle(0.4, 'deg')
test_region = SkyCircleRegion(pos=pos, radius=radius)
center = SkyCoord(82.8, 22.5, unit='deg', frame='icrs')
regions = find_reflected_regions(test_region, center, mask)
import matplotlib.pyplot as plt
wcs = WCS(hdu.header)
fig = plt.figure(figsize=(8, 5), dpi=80)
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8], projection=wcs)
mask.plot(ax)
for reg in regions:
patch = reg.plot(ax, facecolor='red')
ax.add_patch(patch)
patch2 = test_region.plot(ax, facecolor='blue')
ax.add_patch(patch2)
plt.show()
