/
quantities.py
137 lines (110 loc) · 4.15 KB
/
quantities.py
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# Needed for quantities
from __future__ import absolute_import
import exdir
import quantities as pq
import numpy as np
from collections import defaultdict
def convert_back_quantities(value):
"""Convert quantities back from dictionary."""
result = value
if isinstance(value, dict):
if "unit" in value and "value" in value and "uncertainty" in value:
try:
result = pq.UncertainQuantity(value["value"],
value["unit"],
value["uncertainty"])
except Exception:
pass
elif "unit" in value and "value" in value:
try:
result = pq.Quantity(value["value"], value["unit"])
except Exception:
pass
else:
try:
for key, value in result.items():
result[key] = convert_back_quantities(value)
except AttributeError:
pass
return result
def convert_quantities(value):
"""Convert quantities to dictionary."""
result = value
if isinstance(value, pq.Quantity):
result = {
"value": value.magnitude.tolist(),
"unit": value.dimensionality.string
}
if isinstance(value, pq.UncertainQuantity):
assert value.dimensionality == value.uncertainty.dimensionality
result["uncertainty"] = value.uncertainty.magnitude.tolist()
elif isinstance(value, np.ndarray):
result = value.tolist()
elif isinstance(value, np.integer):
result = int(value)
elif isinstance(value, np.float):
result = float(value)
else:
# try if dictionary like objects can be converted if not return the
# original object
# Note, this might fail if .items() returns a strange combination of
# objects
try:
new_result = {}
for key, val in value.items():
new_key = convert_quantities(key)
new_result[new_key] = convert_quantities(val)
result = new_result
except AttributeError:
pass
return result
class DatasetPlugin(exdir.plugin_interface.Dataset):
def prepare_read(self, dataset_data):
values = dataset_data.data
attrs = dataset_data.attrs
if "unit" in attrs:
item_dict = {
"value": values,
"unit": attrs["unit"]
}
if "uncertainty" in attrs:
item_dict["uncertainty"] = attrs["uncertainty"]
values = convert_back_quantities(item_dict)
dataset_data.data = values
return dataset_data
def prepare_write(self, dataset_data):
data = dataset_data.data
attrs = {}
meta = dataset_data.meta
if isinstance(data, pq.Quantity):
# TODO consider adding a helper class that wraps defaultdict and converts back again
if "plugins" not in meta:
meta["plugins"] = {}
if "quantities" not in meta["plugins"]:
meta["plugins"]["quantities"] = {}
meta["plugins"]["quantities"]["required"] = True
result = data.magnitude
attrs["unit"] = data.dimensionality.string
if isinstance(data, pq.UncertainQuantity):
attrs["uncertainty"] = data.uncertainty
else:
result = data
dataset_data.data = data
dataset_data.attrs = attrs
dataset_data.meta = dict(meta)
return dataset_data
class AttributePlugin(exdir.plugin_interface.Attribute):
def prepare_read(self, attribute_data):
attribute_data.attrs = convert_back_quantities(attribute_data.attrs)
return attribute_data
def prepare_write(self, attribute_data):
attribute_data.attrs = convert_quantities(attribute_data.attrs)
return attribute_data
def plugins():
return [exdir.plugin_interface.Plugin(
"quantities",
dataset_plugins=[DatasetPlugin()],
attribute_plugins=[AttributePlugin()],
read_before=["numpy_attributes"],
write_before=["numpy_attributes"]
)]