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Allow length-1 datasets to be read as Nexus scalars #75

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Allow length-1 datasets to be read as Nexus scalars #75

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53 changes: 33 additions & 20 deletions src/nxmx/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,19 @@ def __len__(self):
return len(self._handle)


def h5scalar(ds: h5py.Dataset):
"""Read a scalar value from an HDF5 dataset

Sometimes scalars are stored as a length-1 1D dataset instead of a proper
scalar. This function allows for that, since NumPy has got stricter about
converting to scalars.
"""
if ds.size != 1:
raise TypeError("only length-1 arrays can be converted to Python scalars")
arr = np.squeeze(ds[()])
return arr.item()


def h5str(h5_value: str | np.bytes_ | bytes | None) -> str | None:
"""
Convert a value returned from an h5py attribute to str.
Expand Down Expand Up @@ -131,7 +144,7 @@ def __init__(self, handle):
self._entries = [
entry
for entry in find_class(handle, "NXentry")
if "definition" in entry and h5str(entry["definition"][()]) == "NXmx"
if "definition" in entry and h5str(h5scalar(entry["definition"])) == "NXmx"
]

@cached_property
Expand Down Expand Up @@ -178,7 +191,7 @@ def start_time(self) -> datetime.datetime:
should be provided in NXentry/NXinstrument/time_zone.
"""
if "start_time" in self._handle:
return dateutil.parser.isoparse(h5str(self._handle["start_time"][()]))
return dateutil.parser.isoparse(h5str(h5scalar(self._handle["start_time"])))

@cached_property
def end_time(self) -> datetime.datetime | None:
Expand All @@ -192,7 +205,7 @@ def end_time(self) -> datetime.datetime | None:
omitted.
"""
if "end_time" in self._handle:
return dateutil.parser.isoparse(h5str(self._handle["end_time"][()]))
return dateutil.parser.isoparse(h5str(h5scalar(self._handle["end_time"])))
return None

@cached_property
Expand All @@ -206,13 +219,13 @@ def end_time_estimated(self) -> datetime.datetime:
"""
if "end_time_estimated" in self._handle:
return dateutil.parser.isoparse(
h5str(self._handle["end_time_estimated"][()])
h5str(h5scalar(self._handle["end_time_estimated"]))
)

@cached_property
def definition(self) -> str:
"""NeXus NXDL schema to which this file conforms."""
return h5str(self._handle["definition"][()])
return h5str(h5scalar(self._handle["definition"]))


class NXdata(H5Mapping):
Expand Down Expand Up @@ -265,7 +278,7 @@ def data_scale_factor(self) -> str | None:
When omitted, the scaling factor is assumed to be 1.
"""
if "data_scale_factor" in self._handle:
return self._handle["data_scale_factor"][()]
return h5scalar(self._handle["data_scale_factor"])

@cached_property
def data_offset(self) -> str | None:
Expand All @@ -275,7 +288,7 @@ def data_offset(self) -> str | None:
When omitted, the offset is assumed to be 0.
"""
if "data_offset" in self._handle:
return self._handle["data_offset"][()]
return h5scalar(self._handle["data_offset"])


class NXtransformations(H5Mapping):
Expand Down Expand Up @@ -547,13 +560,13 @@ def __init__(self, handle):
@cached_property
def name(self) -> str:
"""Descriptive name of sample"""
return h5str(self._handle["name"][()])
return h5str(h5scalar(self._handle["name"]))

@cached_property
def depends_on(self) -> NXtransformationsAxis | None:
"""The axis on which the sample position depends"""
if "depends_on" in self._handle:
depends_on = h5str(self._handle["depends_on"][()])
depends_on = h5str(h5scalar(self._handle["depends_on"]))
if depends_on and depends_on != ".":
return NXtransformationsAxis(self._handle[depends_on])
return None
Expand All @@ -562,7 +575,7 @@ def depends_on(self) -> NXtransformationsAxis | None:
def temperature(self) -> pint.Quantity | None:
"""The temperature of the sample."""
if temperature := self._handle.get("temperature"):
return temperature[()] * units(temperature)
return h5scalar(temperature) * units(temperature)
return None

@cached_property
Expand Down Expand Up @@ -636,7 +649,7 @@ def name(self) -> str:
https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_diffrn_source.type.html
is highly recommended.
"""
return h5str(self._handle["name"][()])
return h5str(h5scalar(self._handle["name"]))

@cached_property
def short_name(self) -> str:
Expand Down Expand Up @@ -791,7 +804,7 @@ def distance_derived(self) -> bool | None:
derived from detector axis specifications.
"""
if "distance_derived" in self._handle:
return bool(self._handle["distance_derived"][()])
return bool(h5scalar(self._handle["distance_derived"]))
return None

@cached_property
Expand Down Expand Up @@ -834,7 +847,7 @@ def pixel_mask_applied(self) -> bool | None:
otherwise (optional).
"""
if "pixel_mask_applied" in self._handle:
return bool(self._handle["pixel_mask_applied"][()])
return bool(h5scalar(self._handle["pixel_mask_applied"]))
return None

@cached_property
Expand Down Expand Up @@ -884,14 +897,14 @@ def pixel_mask(self) -> h5py.Dataset | None:
def bit_depth_readout(self) -> int | None:
"""How many bits the electronics record per pixel (recommended)."""
if "bit_depth_readout" in self._handle:
return int(self._handle["bit_depth_readout"][()])
return int(h5scalar(self._handle["bit_depth_readout"]))
return None

@cached_property
def bit_depth_image(self) -> int | None:
"""The number of bits per pixel saved to the image data."""
if "bit_depth_image" in self._handle:
return int(self._handle["bit_depth_image"][()])
return int(h5scalar(self._handle["bit_depth_image"]))
return None

@cached_property
Expand All @@ -901,7 +914,7 @@ def sensor_material(self) -> str:
At times, radiation is not directly sensed by the detector. Rather, the detector
might sense the output from some converter like a scintillator. This is the name
of this converter material."""
return h5str(np.squeeze(self._handle["sensor_material"])[()])
return h5str(h5scalar(self._handle["sensor_material"]))

@cached_property
def sensor_thickness(self) -> pint.Quantity:
Expand All @@ -917,7 +930,7 @@ def underload_value(self) -> int | None:
to the underload_value.
"""
if "underload_value" in self._handle:
return int(self._handle["underload_value"][()].item())
return int(h5scalar(self._handle["underload_value"]))
return None

@cached_property
Expand All @@ -932,7 +945,7 @@ def saturation_value(self) -> int | None:
"""
if "saturation_value" in self._handle:
try:
return int(self._handle["saturation_value"][()].item())
return int(h5scalar(self._handle["saturation_value"]))
except TypeError as e:
logger.warning(f"Error extracting {self.path}/saturation_value: {e}")
return None
Expand Down Expand Up @@ -1058,7 +1071,7 @@ def name(self) -> str:
https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_diffrn_source.pdbx_synchrotron_site.html
controlled vocabulary is highly recommended.
"""
return h5str(self._handle["name"][()])
return h5str(h5scalar(self._handle["name"]))

@cached_property
def short_name(self) -> str | None:
Expand Down Expand Up @@ -1149,7 +1162,7 @@ def profile(self) -> str | None:
Any of these values: Gaussian | Airy | top-hat | rectangular
"""
if "profile" in self._handle:
return h5str(self._handle["profile"][()])
return h5str(h5scalar(self._handle["profile"]))
return None


Expand Down