def test_append_3d():
from fact.io import initialize_h5py, append_to_h5py
array = np.zeros(100, dtype=[('x', 'float64', (3, 3))])
with tempfile.NamedTemporaryFile(suffix='.hdf5') as f:
with h5py.File(f.name, 'w') as h5file:
initialize_h5py(h5file, array, key='events')
append_to_h5py(h5file, array, key='events')
append_to_h5py(h5file, array, key='events')
def test_initialize_h5py():
from fact.io import initialize_h5py
df = pd.DataFrame({
'x': [1, 2, 3],
'name': ['Crab', 'Mrk 501', 'Test'],
't': ['2017-10-01 21:22', '2017-10-01 21:23', '2017-10-01 21:24'],
's': [[0, 1], [0, 2], [0, 3]],
})
df['t'] = pd.to_datetime(df['t'])
with tempfile.NamedTemporaryFile(suffix='.hdf5') as f:
with h5py.File(f.name, 'w') as h5file:
initialize_h5py(h5file, df.to_records(index=False), key='events')
with h5py.File(f.name, 'r') as h5file:
assert h5file['events']['name'].dtype == np.dtype('O')
assert h5file['events']['x'].dtype == np.dtype('int64')
assert h5file['events']['t'].dtype == np.dtype('S48')
assert h5file['events']['s'].shape == (0, 2)
def write_to_hdf(recarray, filename, key='events'):
with h5py.File(filename, mode='a') as f:
if key not in f:
initialize_h5py(f, recarray, key=key)
append_to_h5py(f, recarray, key=key)
def write_fits_to_hdf5(outputfile,
inputfiles,
mode='a',
compression='gzip',
progress=True,
key='events'):
initialized = False
version = None
with h5py.File(outputfile, mode) as hdf_file:
for inputfile in tqdm(inputfiles, disable=not progress):
with fits.open(inputfile) as f:
if version is None:
version = f[0].header['VERSION']
hdf_file.attrs['fact_tools_version'] = version
else:
if version != f[0].header['VERSION']:
raise ValueError(
'Merging output of different FACT-Tools versions not allowed'
)
if len(f) < 2:
continue
array = np.array(f[1].data[:])
# convert all names to snake case
array.dtype.names = rename_columns(array.dtype.names)
# add columns with theta in degrees
arrays = []
names = []
for in_col, out_col in zip(theta_columns, theta_deg_columns):
if in_col in array.dtype.names:
arrays.append(camera_distance_mm_to_deg(array[in_col]))
names.append(out_col)
if len(names) > 0:
array = recfunctions.append_fields(
array,
names=names,
data=arrays,
usemask=False,
)
if not initialized:
initialize_h5py(
hdf_file,
array,
key=key,
compression=compression,
)
initialized = True
append_to_h5py(hdf_file, array, key=key)
if 'timestamp' in array.dtype.names:
hdf_file[key]['timestamp'].attrs['timeformat'] = 'iso'