def from_hdulist(
cls,
hdulist,
psf_hdu="PSFMAP",
psf_hdubands="BANDSPSF",
exposure_hdu="EXPMAP",
exposure_hdubands="BANDSEXP",
):
"""Convert to `~astropy.io.fits.HDUList`.
Parameters
----------
psf_hdu : str
Name or index of the HDU with the psf_map data.
psf_hdubands : str
Name or index of the HDU with the psf_map BANDS table.
exposure_hdu : str
Name or index of the HDU with the exposure_map data.
exposure_hdubands : str
Name or index of the HDU with the exposure_map BANDS table.
"""
psf_map = Map.from_hdulist(hdulist, psf_hdu, psf_hdubands, "auto")
if exposure_hdu in hdulist:
exposure_map = Map.from_hdulist(
hdulist, exposure_hdu, exposure_hdubands, "auto"
)
else:
exposure_map = None
return cls(psf_map, exposure_map)
def from_hdulist(cls, hdulist, name=""):
"""Create map dataset from list of HDUs.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
Returns
-------
dataset : `MapDataset`
Map dataset.
"""
kwargs = {"name": name}
if "COUNTS" in hdulist:
kwargs["counts"] = Map.from_hdulist(hdulist, hdu="counts")
if "EXPOSURE" in hdulist:
kwargs["exposure"] = Map.from_hdulist(hdulist, hdu="exposure")
if "BACKGROUND" in hdulist:
background_map = Map.from_hdulist(hdulist, hdu="background")
kwargs["background_model"] = BackgroundModel(background_map)
if "EDISP_MATRIX" in hdulist:
kwargs["edisp"] = EnergyDispersion.from_hdulist(
hdulist, hdu1="EDISP_MATRIX", hdu2="EDISP_MATRIX_EBOUNDS"
)
if "EDISP" in hdulist:
edisp_map = Map.from_hdulist(hdulist, hdu="edisp")
exposure_map = Map.from_hdulist(hdulist, hdu="edisp_exposure")
kwargs["edisp"] = EDispMap(edisp_map, exposure_map)
if "PSF_KERNEL" in hdulist:
psf_map = Map.from_hdulist(hdulist, hdu="psf_kernel")
kwargs["psf"] = PSFKernel(psf_map)
if "PSF" in hdulist:
psf_map = Map.from_hdulist(hdulist, hdu="psf")
exposure_map = Map.from_hdulist(hdulist, hdu="psf_exposure")
kwargs["psf"] = PSFMap(psf_map, exposure_map)
if "MASK_SAFE" in hdulist:
mask_safe = Map.from_hdulist(hdulist, hdu="mask_safe")
mask_safe.data = mask_safe.data.astype(bool)
kwargs["mask_safe"] = mask_safe
if "MASK_FIT" in hdulist:
mask_fit = Map.from_hdulist(hdulist, hdu="mask_fit")
mask_fit.data = mask_fit.data.astype(bool)
kwargs["mask_fit"] = mask_fit
if "GTI" in hdulist:
gti = GTI(Table.read(hdulist, hdu="GTI"))
kwargs["gti"] = gti
return cls(**kwargs)
def from_hdulist(cls, hdulist, hdu_bands=None):
"""Create flux map dataset from list of HDUs.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
hdu_bands : str
Name of the HDU with the BANDS table. Default is 'BANDS'
If set to None, each map should have its own hdu_band
Returns
-------
flux_maps : `~gammapy.estimators.FluxMaps`
Flux maps object.
"""
try:
sed_type = hdulist[0].header["SED_TYPE"]
except KeyError:
raise ValueError(
f"Cannot determine SED type of flux map from primary header.")
maps = {}
for map_type in REQUIRED_MAPS[sed_type]:
maps[map_type] = Map.from_hdulist(hdulist,
hdu=map_type,
hdu_bands=hdu_bands)
for map_type in OPTIONAL_QUANTITIES[
sed_type] + OPTIONAL_QUANTITIES_COMMON:
if map_type.upper() in hdulist:
maps[map_type] = Map.from_hdulist(hdulist,
hdu=map_type,
hdu_bands=hdu_bands)
filename = hdulist[0].header.get("MODEL", None)
if filename:
reference_model = Models.read(filename)[0]
else:
reference_model = None
if "GTI" in hdulist:
gti = GTI(Table.read(hdulist["GTI"]))
else:
gti = None
return cls.from_dict(maps=maps,
sed_type=sed_type,
reference_model=reference_model,
gti=gti)
def test_map_time_axis_read_write(map_type):
time_axis = TimeMapAxis(
edges_min=[0, 2, 4] * u.d,
edges_max=[1, 3, 5] * u.d,
reference_time="2000-01-01",
)
energy_axis = MapAxis.from_energy_bounds("1 TeV", "10 TeV", nbin=5)
m = Map.create(
binsz=0.1,
width=10.0,
map_type=map_type,
skydir=SkyCoord(0.0, 30.0, unit="deg"),
axes=[energy_axis, time_axis],
)
hdulist = m.to_hdulist(hdu="COUNTS")
m2 = Map.from_hdulist(hdulist)
time_axis_new = m2.geom.axes["time"]
assert time_axis_new == time_axis
assert time_axis.reference_time.scale == "utc"
assert time_axis_new.reference_time.scale == "tt"
def from_hdulist(cls, hdulist, hdu_bands="BANDS"):
"""Create map dictionary from list of HDUs.
Because FITS keywords are case insensitive, all key names will return as lower-case.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
hdu_bands : str
Name of the HDU with the BANDS table. Default is 'BANDS'
If set to None, each map should have its own hdu_band
Returns
-------
maps : `~gammapy.maps.Maps`
Maps object.
"""
maps = cls()
for hdu in hdulist:
if hdu.is_image and hdu.data is not None:
map_name = hdu.name.lower()
maps[map_name] = Map.from_hdulist(hdulist,
hdu=map_name,
hdu_bands=hdu_bands)
return maps
def from_hdulist(
cls,
hdulist,
hdu=None,
hdu_bands=None,
exposure_hdu=None,
exposure_hdu_bands=None,
):
"""Create from `~astropy.io.fits.HDUList`.
Parameters
----------
hdulist : `~astropy.fits.HDUList`
HDU list.
hdu : str
Name or index of the HDU with the IRF map.
hdu_bands : str
Name or index of the HDU with the IRF map BANDS table.
exposure_hdu : str
Name or index of the HDU with the exposure map data.
exposure_hdu_bands : str
Name or index of the HDU with the exposure map BANDS table.
Returns
-------
irf_map : `IRFMap`
IRF map.
"""
if hdu is None:
hdu = cls._hdu_name
irf_map = Map.from_hdulist(hdulist, hdu=hdu, hdu_bands=hdu_bands)
if exposure_hdu is None:
exposure_hdu = cls._hdu_name + "_exposure"
if exposure_hdu in hdulist:
exposure_map = Map.from_hdulist(hdulist,
hdu=exposure_hdu,
hdu_bands=exposure_hdu_bands)
else:
exposure_map = None
return cls(irf_map, exposure_map)
def test_map_unit_read_write(map_type, unit):
m = Map.create(binsz=0.1, width=10.0, map_type=map_type, unit=unit)
hdu_list = m.to_hdulist(hdu="COUNTS")
header = hdu_list["COUNTS"].header
assert Unit(header["BUNIT"]) == Unit(unit)
m2 = Map.from_hdulist(hdu_list)
assert m2.unit == unit
def from_hdulist(cls, hdulist, name=""):
"""Create map dataset from list of HDUs.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
Returns
-------
dataset : `MapDataset`
Map dataset.
"""
init_kwargs = {}
init_kwargs["name"] = name
if "COUNTS" in hdulist:
init_kwargs["counts"] = Map.from_hdulist(hdulist, hdu="counts")
if "COUNTS_OFF" in hdulist:
init_kwargs["counts_off"] = Map.from_hdulist(hdulist, hdu="counts_off")
if "ACCEPTANCE" in hdulist:
init_kwargs["acceptance"] = Map.from_hdulist(hdulist, hdu="acceptance")
if "ACCEPTANCE_OFF" in hdulist:
init_kwargs["acceptance_off"] = Map.from_hdulist(
hdulist, hdu="acceptance_off"
)
if "EXPOSURE" in hdulist:
init_kwargs["exposure"] = Map.from_hdulist(hdulist, hdu="exposure")
if "EDISP_MATRIX" in hdulist:
init_kwargs["edisp"] = EnergyDispersion.from_hdulist(
hdulist, hdu1="EDISP_MATRIX", hdu2="EDISP_MATRIX_EBOUNDS"
)
if "PSF_KERNEL" in hdulist:
psf_map = Map.from_hdulist(hdulist, hdu="psf_kernel")
init_kwargs["psf"] = PSFKernel(psf_map)
if "MASK_SAFE" in hdulist:
mask_safe_map = Map.from_hdulist(hdulist, hdu="mask_safe")
init_kwargs["mask_safe"] = mask_safe_map.data.astype(bool)
if "MASK_FIT" in hdulist:
mask_fit_map = Map.from_hdulist(hdulist, hdu="mask_fit")
init_kwargs["mask_fit"] = mask_fit_map.data.astype(bool)
if "GTI" in hdulist:
gti = GTI(Table.read(hdulist, hdu="GTI"))
init_kwargs["gti"] = gti
return cls(**init_kwargs)
def test_map_meta_read_write(map_type):
meta = {"user": "******"}
m = Map.create(
binsz=0.1,
width=10.0,
map_type=map_type,
skydir=SkyCoord(0.0, 30.0, unit="deg"),
meta=meta,
)
hdulist = m.to_hdulist(hdu="COUNTS")
header = hdulist["COUNTS"].header
assert header["META"] == '{"user": "******"}'
m2 = Map.from_hdulist(hdulist)
assert m2.meta == meta
def from_hdulist(cls, hdulist):
"""Create map dataset from list of HDUs.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
Returns
-------
dataset : `MapDataset`
Map dataset.
"""
init_kwargs = {}
init_kwargs["counts"] = Map.from_hdulist(hdulist, hdu="counts")
init_kwargs["exposure"] = Map.from_hdulist(hdulist, hdu="exposure")
background_map = Map.from_hdulist(hdulist, hdu="background")
init_kwargs["background_model"] = BackgroundModel(background_map)
if "EDISP_MATRIX" in hdulist:
init_kwargs["edisp"] = EnergyDispersion.from_hdulist(
hdulist, hdu1="EDISP_MATRIX", hdu2="EDISP_MATRIX_EBOUNDS")
if "PSF_KERNEL" in hdulist:
psf_map = Map.from_hdulist(hdulist, hdu="psf_kernel")
init_kwargs["psf"] = PSFKernel(psf_map)
if "MASK_SAFE" in hdulist:
mask_safe_map = Map.from_hdulist(hdulist, hdu="mask_safe")
init_kwargs["mask_safe"] = mask_safe_map.data.astype(bool)
if "MASK_FIT" in hdulist:
mask_fit_map = Map.from_hdulist(hdulist, hdu="mask_fit")
init_kwargs["mask_fit"] = mask_fit_map.data.astype(bool)
return cls(**init_kwargs)
# In rare cases e.g. when the FITS file is not valid or meta data is missing from the header it can be necessary to modify the header of a certain HDU before creating the `Map` object. In this case we can use `astropy.io.fits` directly to read the FITS file:
# In[ ]:
filename = (os.environ["GAMMAPY_DATA"] +
"/fermi-3fhl-gc/fermi-3fhl-gc-exposure.fits.gz")
hdulist = fits.open(filename)
hdulist.info()
# And then modify the header keyword and use `Map.from_hdulist()` to create the `Map` object after:
# In[ ]:
hdulist["PRIMARY"].header["BUNIT"] = "cm2 s"
Map.from_hdulist(hdulist=hdulist)
# ### Writing Maps
#
# Writing FITS files is mainoy exposure via the `Map.write()` method. Here is a first example:
# In[ ]:
m_cube.write("example_cube.fits", overwrite=True)
# By default Gammapy does not overwrite files. In this example we set `overwrite=True` in case the cell gets executed multiple times. Now we can read back the cube from disk using `Map.read()`:
# In[ ]:
m_cube = Map.read("example_cube.fits")
print(m_cube)
print(m_2fhl_gc)
# In rare cases e.g. when the FITS file is not valid or meta data is missing from the header it can be necessary to modify the header of a certain HDU before creating the `Map` object. In this case we can use `astropy.io.fits` directly to read the FITS file:
# In[ ]:
filename = os.environ["GAMMAPY_DATA"] + "/fermi_survey/all.fits.gz"
hdulist = fits.open(filename)
hdulist.info()
# And then modify the header keyword and use `Map.from_hdulist()` to create the `Map` object after:
# In[ ]:
hdulist["exposure"].header["BUNIT"] = "cm2 s"
Map.from_hdulist(hdulist=hdulist, hdu="exposure")
# ### 3.2 Writing Maps
#
# Writing FITS files is mainoy exposure via the `Map.write()` method. Here is a first example:
# In[ ]:
m_cube.write("example_cube.fits", overwrite=True)
# By default Gammapy does not overwrite files. In this example we set `overwrite=True` in case the cell gets executed multiple times. Now we can read back the cube from disk using `Map.read()`:
# In[ ]:
m_cube = Map.read("example_cube.fits")
print(m_cube)
def from_hdulist(
cls,
hdulist,
hdu=None,
hdu_bands=None,
exposure_hdu=None,
exposure_hdu_bands=None,
format="gadf",
):
"""Create from `~astropy.io.fits.HDUList`.
Parameters
----------
hdulist : `~astropy.fits.HDUList`
HDU list.
hdu : str
Name or index of the HDU with the IRF map.
hdu_bands : str
Name or index of the HDU with the IRF map BANDS table.
exposure_hdu : str
Name or index of the HDU with the exposure map data.
exposure_hdu_bands : str
Name or index of the HDU with the exposure map BANDS table.
format : {"gadf", "gtpsf"}
File format
Returns
-------
irf_map : `IRFMap`
IRF map.
"""
if format == "gadf":
if hdu is None:
hdu = IRF_MAP_HDU_SPECIFICATION[cls.tag]
irf_map = Map.from_hdulist(hdulist,
hdu=hdu,
hdu_bands=hdu_bands,
format=format)
if exposure_hdu is None:
exposure_hdu = IRF_MAP_HDU_SPECIFICATION[cls.tag] + "_exposure"
if exposure_hdu in hdulist:
exposure_map = Map.from_hdulist(hdulist,
hdu=exposure_hdu,
hdu_bands=exposure_hdu_bands,
format=format)
else:
exposure_map = None
elif format == "gtpsf":
rad_axis = MapAxis.from_table_hdu(hdulist["THETA"], format=format)
table = Table.read(hdulist["PSF"])
energy_axis_true = MapAxis.from_table(table, format=format)
geom_psf = RegionGeom.create(region=None,
axes=[rad_axis, energy_axis_true])
psf_map = Map.from_geom(geom=geom_psf,
data=table["Psf"].data,
unit="sr-1")
geom_exposure = geom_psf.squash("rad")
exposure_map = Map.from_geom(geom=geom_exposure,
data=table["Exposure"].data,
unit="cm2 s")
return cls(psf_map=psf_map, exposure_map=exposure_map)
else:
raise ValueError(f"Format {format} not supported")
return cls(irf_map, exposure_map)
def from_hdulist(cls, hdulist, hdu_bands=None):
"""Create flux map dataset from list of HDUs.
Parameters
----------
hdulist : `~astropy.io.fits.HDUList`
List of HDUs.
hdu_bands : str
Name of the HDU with the BANDS table. Default is 'BANDS'
If set to None, each map should have its own hdu_band
Returns
-------
fluxmaps : `~gammapy.estimators.FluxMaps`
the flux map.
"""
try:
sed_type = hdulist[0].header["SED_TYPE"]
except KeyError:
raise ValueError(
f"Cannot determine SED type of flux map from primary header.")
result = {}
for map_type in REQUIRED_MAPS[sed_type]:
if map_type.upper() in hdulist:
result[map_type] = Map.from_hdulist(hdulist,
hdu=map_type,
hdu_bands=hdu_bands)
else:
raise ValueError(
f"Cannot find required map {map_type} for SED type {sed_type}."
)
for map_type in OPTIONAL_MAPS[sed_type]:
if map_type.upper() in hdulist:
result[map_type] = Map.from_hdulist(hdulist,
hdu=map_type,
hdu_bands=hdu_bands)
# Read additional image hdus
for hdu in hdulist[1:]:
if hdu.is_image:
if hdu.name.lower() not in (REQUIRED_MAPS[sed_type] +
OPTIONAL_MAPS[sed_type]):
result[hdu.name.lower()] = Map.from_hdulist(
hdulist, hdu=hdu.name, hdu_bands=hdu_bands)
model_filename = hdulist[0].header.get("MODEL", None)
reference_model = None
if model_filename:
try:
reference_model = Models.read(model_filename)[0]
except FileNotFoundError:
raise FileNotFoundError(
f"Cannot find {model_filename} model file. Check MODEL keyword."
)
if "GTI" in hdulist:
gti = GTI(Table.read(hdulist["GTI"]))
else:
gti = None
return cls.from_dict(result, sed_type, reference_model, gti)
from astropy.io import fits
import argparse
if __name__ == '__main__':
usage = "usage: %(prog)s -f path/to/fits/file.fits"
description = "plot a fits template"
parser = argparse.ArgumentParser(usage=usage, description=description)
parser.add_argument('-f', '--file', required=True)
args = parser.parse_args()
filepath = PosixPath(args.file)
try:
m = Map.read(fits_file)
except:
fits_file = fits.open(filepath)
# get meta data, gives problems with JSON encoder
meta = fits_file[0].header.pop("META", None)
# read in map
m = Map.from_hdulist(fits_file)
# plot the map
fig, ax, _ = m.sum_over_axes(['energy_true']).plot(stretch="log",
add_cbar=True)
ax.tick_params(direction="out")
ax.grid(ls=":", color="0.5", lw=0.5)
plt.savefig("template_map.png")
