def make_fresh_dir(path):
"""Make a fresh directory. Delete first if exists"""
path = Path(path)
if path.is_dir():
shutil.rmtree(str(path))
path.mkdir()
return path
def write_ogip(self, phafile=None, bkgfile=None, rmffile=None, arffile=None,
outdir=None, clobber=True):
"""Write OGIP files
Only those objects are written have been created with the appropriate
functions before
Parameters
----------
phafile : str
PHA filename
bkgfile : str
BKG filename
arffile : str
ARF filename
rmffile : str
RMF : filename
outdir : None
directory to write the files to
clobber : bool
Overwrite
"""
if outdir is None:
outdir = "ogip_data"
basedir = Path(outdir)
basedir.mkdir(exist_ok=True)
if arffile is None:
arffile = basedir / "arf_run{}.fits".format(self.obs)
if rmffile is None:
rmffile = basedir / "rmf_run{}.fits".format(self.obs)
if phafile is None:
phafile = basedir / "pha_run{}.pha".format(self.obs)
if bkgfile is None:
bkgfile = basedir / "bkg_run{}.pha".format(self.obs)
self.phafile = phafile
if self.pha is not None:
self.pha.write(str(phafile), bkg=str(bkgfile), arf=str(arffile),
rmf=str(rmffile), clobber=clobber)
if self.bkg is not None:
self.bkg.write(str(bkgfile), clobber=clobber)
if self.arf is not None:
self.arf.write(str(arffile), energy_unit='keV', effarea_unit='cm2',
clobber=clobber)
if self.rmf is not None:
self.rmf.write(str(rmffile), energy_unit='keV', clobber=clobber)
def build_notebooks(args):
if "GAMMAPY_DATA" not in os.environ:
logging.info("GAMMAPY_DATA environment variable not set.")
logging.info(
"Running notebook tests requires this environment variable.")
logging.info("Exiting now.")
sys.exit()
# prepare folder structure
pathsrc = Path(args.src)
path_temp = Path("temp")
path_empty_nbs = Path("tutorials")
path_filled_nbs = Path("docs") / "notebooks"
path_static_nbs = Path("docs") / "_static" / "notebooks"
rmtree(str(path_temp), ignore_errors=True)
path_temp.mkdir(parents=True, exist_ok=True)
path_filled_nbs.mkdir(parents=True, exist_ok=True)
path_static_nbs.mkdir(parents=True, exist_ok=True)
if pathsrc == path_empty_nbs:
rmtree(str(path_temp), ignore_errors=True)
rmtree(str(path_static_nbs), ignore_errors=True)
rmtree(str(path_filled_nbs), ignore_errors=True)
copytree(str(path_empty_nbs), str(path_temp), ignore=ignorefiles)
elif pathsrc.exists():
notebookname = pathsrc.name
pathdest = path_temp / notebookname
copyfile(str(pathsrc), str(pathdest))
else:
logging.info("Notebook file does not exist.")
sys.exit()
# strip and blackformat
subprocess.call("gammapy jupyter --src temp black", shell=True)
subprocess.call("gammapy jupyter --src temp strip", shell=True)
# test /run
passed = True
for path in path_temp.glob("*.ipynb"):
if not notebook_test(path):
passed = False
# convert into scripts
# copy generated filled notebooks to doc
# if passed:
if pathsrc == path_empty_nbs:
# copytree is needed to copy subfolder images
copytree(str(path_empty_nbs), str(path_static_nbs), ignore=ignoreall)
for path in path_static_nbs.glob("*.ipynb"):
subprocess.call("jupyter nbconvert --to script '{}'".format(
str(path)),
shell=True)
copytree(str(path_temp), str(path_filled_nbs), ignore=ignorefiles)
else:
pathsrc = path_temp / notebookname
pathdest = path_static_nbs / notebookname
copyfile(str(pathsrc), str(pathdest))
subprocess.call("jupyter nbconvert --to script '{}'".format(
str(pathdest)),
shell=True)
pathdest = path_filled_nbs / notebookname
copyfile(str(pathsrc), str(pathdest))
# else:
# logging.info("Tests have not passed.")
# logging.info("Tutorials not ready for documentation building process.")
# rmtree(str(path_static_nbs), ignore_errors=True)
# tear down
rmtree(str(path_temp), ignore_errors=True)
# In[ ]:
def hgps_data_download():
base_url = "https://www.mpi-hd.mpg.de/hfm/HESS/hgps/data/"
for filename in hgps_filenames:
url = base_url + filename
path = hgps_data_path / filename
if path.exists():
print("Already downloaded: {}".format(path))
else:
print("Downloading {} to {}".format(url, path))
urlretrieve(url, str(path))
hgps_data_path.mkdir(parents=True, exist_ok=True)
hgps_data_download()
print("\n\nFiles at {} :\n".format(hgps_data_path.absolute()))
for path in hgps_data_path.iterdir():
print(path)
# ## Catalog with Astropy
#
# ### FITS file content
#
# Let's start by just opening up `hgps_catalog_v1.fits.gz` and looking at the content.
#
# Note that ``astropy.io.fits.open`` doesn't work with `Path` objects yet,
# so you have to call `str(path)` and pass a string.
# define energy grid
energy = energy_axis.edges * energy_axis.unit
# mean edisp
edisp = obs_list.make_mean_edisp(position=src_pos,
e_true=energy,
e_reco=energy)
# ### Save maps and IRFs to disk
#
# It is common to run the preparation step independent of the likelihood fit, because often the preparation of maps, PSF and energy dispersion is slow if you have a lot of data. We first create a folder:
# In[ ]:
path = Path("analysis_3d")
path.mkdir(exist_ok=True)
# And the write the maps and IRFs to disk by calling the dedicated `.write()` methods:
# In[ ]:
# write maps
maps["counts"].write(str(path / "counts.fits"), overwrite=True)
maps["background"].write(str(path / "background.fits"), overwrite=True)
maps["exposure"].write(str(path / "exposure.fits"), overwrite=True)
# write IRFs
psf_kernel.write(str(path / "psf.fits"), overwrite=True)
edisp.write(str(path / "edisp.fits"), overwrite=True)
# ## Likelihood fit
