def test_convert_back_quantities():
pq_dict = {"value": 1, "unit": "m"}
result = convert_back_quantities(pq_dict)
assert result == pq.Quantity(1, "m")
pq_dict = {"value": [1, 2, 3], "unit": "m"}
result = convert_back_quantities(pq_dict)
assert np.array_equal(result, pq.Quantity([1, 2, 3], "m"))
pq_dict = {"value": [1, 2, 3]}
result = convert_back_quantities(pq_dict)
assert result == pq_dict
result = convert_back_quantities(1)
assert result == 1
result = convert_back_quantities(2.3)
assert result == 2.3
pq_dict = {"unit": "m", "uncertainty": [3, 4], "value": [1.0, 2.0]}
result = convert_back_quantities(pq_dict)
pq_value = pq.UncertainQuantity([1, 2], "m", [3, 4])
assert isinstance(result, pq.UncertainQuantity)
assert result.magnitude.tolist() == pq_value.magnitude.tolist()
assert result.dimensionality.string == pq_value.dimensionality.string
assert result.uncertainty.magnitude.tolist(
) == pq_value.uncertainty.magnitude.tolist()
pq_dict = {
"quantity": {
"unit": "m",
"value": 1
},
"uq_quantity": {
"unit": "m",
"uncertainty": [3, 4],
"value": [1.0, 2.0]
}
}
pq_values = {
"quantity": pq.Quantity(1, "m"),
"uq_quantity": pq.UncertainQuantity([1, 2], "m", [3, 4])
}
result = convert_back_quantities(pq_values)
assert result == pq_values
pq_values = {"list": [1, 2, 3], "quantity": {"unit": "m", "value": 1}}
result = convert_back_quantities(pq_values)
assert result == {"list": [1, 2, 3], "quantity": pq.Quantity(1, "m")}
def test_convert_quantities():
pq_value = pq.Quantity(1, "m")
result = convert_quantities(pq_value)
assert result == {"value": 1, "unit": "m"}
pq_value = pq.Quantity([1, 2, 3], "m")
result = convert_quantities(pq_value)
assert result == {"value": [1, 2, 3], "unit": "m"}
result = convert_quantities(np.array([1, 2, 3]))
assert result == [1, 2, 3]
result = convert_quantities(1)
assert result == 1
result = convert_quantities(2.3)
assert result == 2.3
pq_value = pq.UncertainQuantity([1, 2], "m", [3, 4])
result = convert_quantities(pq_value)
assert result == {"unit": "m", "uncertainty": [3, 4], "value": [1.0, 2.0]}
pq_values = {
"quantity": pq.Quantity(1, "m"),
"uq_quantity": pq.UncertainQuantity([1, 2], "m", [3, 4])
}
result = convert_quantities(pq_values)
assert (result == {
"quantity": {
"unit": "m",
"value": 1
},
"uq_quantity": {
"unit": "m",
"uncertainty": [3, 4],
"value": [1.0, 2.0]
}
})
pq_values = {"list": [1, 2, 3], "quantity": pq.Quantity(1, "m")}
pq_dict = {"list": [1, 2, 3], "quantity": {"unit": "m", "value": 1}}
result = convert_quantities(pq_values)
assert result == pq_dict
def __init__(self):
self.cell = Organelle("cell")
self.nucleus = Organelle('nucleus')
self.cell.diameter = pq.Quantity(5, 'um')
self.cell.volume = pq.Quantity(50, 'um**3')
self.nucleus.diameter = pq.Quantity(2, 'um')
self.nucleus.volume = pq.UncertainQuantity(2.9, 'um**3', 0.2)
pq.nucleur_volume = pq.UnitQuantity('nuclear volume',
self.nucleus.volume,
symbol='NucVol')
pq.cell_volume = pq.UnitQuantity('cellular volume',
self.cell.volume,
symbol='CellVol')
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_from_firebase(value):
"""
Converts quantities back from dictionary
"""
result = value
if isinstance(value, dict):
if "_force_dict" in value:
del value["_force_dict"]
if 'units' in value and "value" in value:
value['unit'] = value['units']
del(value['units'])
if "unit" in value and "value" in value:
if "uncertainty" in value:
try:
result = pq.UncertainQuantity(value["value"],
value["unit"],
value["uncertainty"])
except Exception:
pass
else:
try:
result = pq.Quantity(value["value"], value["unit"])
except Exception:
pass
else:
try:
for key, value in result.items():
result[key] = convert_from_firebase(value)
except AttributeError:
pass
if isinstance(result, str):
if result == 'NaN':
result = np.nan
elif isinstance(result, list):
result = [v if v != 'NaN' else np.nan for v in result]
return result
def test_quantity_uncertain():
t = pq.UncertainQuantity(7., pq.second, 1.)
q1 = Quantity(t)
assert q1.dumps() == r'\SI{7.0 +- 1.0}{\second}'
options={
'round-precision': 4,
'round-mode': 'figures'
})
math = Math(data=['F=', q1])
subsection.append(math)
section.append(subsection)
subsection = Subsection('Scalars without units')
world_population = 7400219037
N = Quantity(world_population,
options={
'round-precision': 2,
'round-mode': 'figures'
},
format_cb="{0:23.17e}".format)
subsection.append(Math(data=['N=', N]))
section.append(subsection)
subsection = Subsection('Scalars with uncertainties')
width = pq.UncertainQuantity(7.0, pq.meter, .4)
length = pq.UncertainQuantity(6.0, pq.meter, .3)
area = Quantity(width * length,
options='separate-uncertainty',
format_cb=lambda x: "{0:.1f}".format(float(x)))
subsection.append(Math(data=['A=', area]))
section.append(subsection)
doc.append(section)
doc.generate_pdf('quantities_ex')
def __init__(self):
self.Kd = pq.UncertainQuantity(1.2, pq.nM, 0.1) # From literature
self.koff = pq.Quantity(5.5e-5, 1 / pq.s).rescale(1 / pq.min)
self.kon = pq.Quantity(4.6e4, 1 / (pq.s * pq.M))
self.kon = self.kon.rescale(1 / (pq.min * pq.nM))