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corner cases in _read_str, _read_int and _read_float #50

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corner cases in _read_str, _read_int and _read_float #50

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9f0a45f
handle more corner cases in _read_str
emiddell Dec 16, 2024
41c1114
for empty int/float/str datasets return None
emiddell Dec 17, 2024
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40 changes: 29 additions & 11 deletions snirf/pysnirf2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -355,7 +355,7 @@ def _read_dataset(dataset: h5py.Dataset):
]))


def _read_string(dataset: h5py.Dataset) -> str:
def _read_string(dataset: h5py.Dataset) -> str | None:
"""Reads the contents of an `h5py.Dataset` to a `str`.

Args:
Expand All @@ -365,20 +365,32 @@ def _read_string(dataset: h5py.Dataset) -> str:
"""
if type(dataset) is not h5py.Dataset:
raise TypeError("'dataset' must be type h5py.Dataset")

# Because many SNIRF files are saved with string values in length 1 arrays
try:
if dataset.ndim > 0:
return str(dataset[0].decode('ascii'))
if dataset.ndim > 0:
if len(dataset) > 0:
tentative_str = dataset[0]
else:
return str(dataset[()].decode('ascii'))
except AttributeError: # If we expected a string and got something else, `decode` isn't there
return None
else:
tentative_str = dataset[()]


if hasattr(tentative_str, 'decode'):
# tentative_str is a byte str -> decode
return str(tentative_str.decode('ascii'))
elif isinstance(tentative_str, np.ndarray) and tentative_str.dtype == np.dtype("S1"):
# tentative_str is a numpy array of bytes -> join -> decode
tentative_str = b''.join(tentative_str)
return str(tentative_str.decode('ascii'))
else:
warn(
'Expected dataset {} to be stringlike, is {} conversion may be incorrect'
.format(dataset.name, dataset.dtype), SnirfFormatError)
return str(dataset[0])
return str(tentative_str)


def _read_int(dataset: h5py.Dataset) -> int:
def _read_int(dataset: h5py.Dataset) -> int | None:
"""Reads the contents of an `h5py.Dataset` to an `int`.

Args:
Expand All @@ -389,12 +401,15 @@ def _read_int(dataset: h5py.Dataset) -> int:
if type(dataset) is not h5py.Dataset:
raise TypeError("'dataset' must be type h5py.Dataset")
if dataset.ndim > 0:
return int(dataset[0])
if len(dataset) > 0:
return int(dataset[0])
else:
return None
else:
return int(dataset[()])


def _read_float(dataset: h5py.Dataset) -> float:
def _read_float(dataset: h5py.Dataset) -> float | None:
"""Reads the contents of an `h5py.Dataset` to a `float`.

Args:
Expand All @@ -405,7 +420,10 @@ def _read_float(dataset: h5py.Dataset) -> float:
if type(dataset) is not h5py.Dataset:
raise TypeError("'dataset' must be type h5py.Dataset")
if dataset.ndim > 0:
return float(dataset[0])
if len(dataset) > 0:
return float(dataset[0])
else:
return None
else:
return float(dataset[()])

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