def load(fname, sme):
"""
Load the SME Structure from disk
Parameters
----------
fname : str
file to load
sme : SME_Structure
empty sme structure with default values set
Returns
-------
sme : SME_Structure
loaded sme structure
"""
try:
ff = FlexFile.read(fname)
sme = from_flex(ff, sme)
ff.close()
return sme
except Exception as ex:
logger.error(ex)
try:
sme = load_v1(fname, sme)
except:
raise ex
return sme
def test_read_write(tmp_fname):
file = FlexFile()
file.header["Hello"] = "World"
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert isinstance(f2.header, dict)
assert f2.header["Hello"] == "World"
def test_header_numpy_arrays(tmp_fname):
file = FlexFile()
file.header["Hello"] = np.ones(3)
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert isinstance(f2.header, dict)
assert np.all(np.asarray(f2.header["Hello"]) == 1)
def test_empty_data(tmp_fname):
file = FlexFile()
ext = BinaryDataExtension(data=[])
file.extensions["img"] = ext
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert f2["img"].data.size == 0
def test_read_write_multi(tmp_fname):
file = FlexFile()
ext = MultipleDataExtension(data={"bla": np.zeros(10)})
file.extensions["img"] = ext
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert f2["img"].data["bla"].size == 10
assert np.all(f2["img"].data["bla"] == 0)
def test_read_write(tmp_fname):
file = FlexFile()
ext = BinaryDataExtension(data=np.zeros(10))
file.extensions["img"] = ext
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert f2["img"].data.size == 10
assert np.all(f2["img"].data == 0)
def test_read_write(tableclass, tmp_fname, table):
file = FlexFile()
ext = tableclass(data=table)
file.extensions["tab"] = ext
file.write(tmp_fname)
del file
f2 = FlexFile.read(tmp_fname)
assert f2["tab"].data.size == 10 * 2
assert np.all(f2["tab"].data == 1)
assert len(f2["tab"].data.columns) == 2
assert "A" in f2["tab"].data.columns
assert "B" in f2["tab"].data.columns
def read(cls, filename, format=None):
if format is None:
format = cls.determine_filetype_based_on_filename(filename)
if format == "flex":
ff = FlexFile.read(filename)
spec = ff["spectrum"]
return spec
elif format == "fits":
hdulist = fits.open(filename)
spec = cls.read_fits_hdu(hdulist[1])
return spec
elif format == "npz":
data = np.load(filename, allow_pickle=True)
data = {k: v[()] for k, v in data.items()}
spec = cls.from_dict(data)
return spec
else:
raise ValueError(
f"Format not understood expected one of ('flex', 'fits') but got {format}"
)
file.header["np_str"] = np.str("World")
# FITS can handle either long header keys, or long entries
# But not both at the same time...
file.header["really_long_entry"] = "bla"
file.header["really_l"] = "bla" * 100
file.header["really_long_text_with_HIERARCH"] = "bla" * 100
file.extensions["np"] = ext
file.extensions["tab"] = tab
file.extensions["bin"] = ext_bin
d = file.to_json()
d2 = FlexFile.from_json(d)
d = file.to_json("test.json")
d2 = FlexFile.from_json("test.json")
d = file.to_fits("test.fits", overwrite=True)
d2 = FlexFile.from_fits("test.fits")
file.write("test.flex")
f2 = FlexFile.read("test.flex")
f2["np"].data["data"][:5] = 1
print(f2["np"].data)
del f2
f2 = FlexFile.read("test.flex")
print(f2["np"].data)
def load(self, filename=None):
if filename is None:
filename = self.savefilename
ff = FlexFile.read(filename)
return ff.header