def format_data(self, data):
"""
This accepts data input in the form:
***** (observation) *****
{"density": {"mean": "XX 1000/mm3", "std": "YY 1000/mm3"}}
***** (prediction) *****
{"density": {"value": "ZZ 1000/mm3"}}
It splits the values of mean, std, value to numeric quantities
and their units (via quantities package).
"""
for key, val in data["density"].items():
try:
quantity_parts = val.split(" ")
number = float(quantity_parts[0])
units_str = " ".join(quantity_parts[1:])
assert (units_str == self.units.symbol)
data["density"][key] = quantities.Quantity(number, self.units)
except AssertionError:
raise sciunit.Error(
"Values not in appropriate format. Required units: ",
self.units.symbol)
except:
raise sciunit.Error("Values not in appropriate format.")
return data
def format_data(self, data):
"""
This accepts data input in the form:
***** (observation) *****
{'Layer 1': {'height': {'mean': 'X0 um', 'std': 'Y0 um'}},
'Layer 2/3': {'height': {'mean': 'X1 um', 'std': 'Y1 um'}},
... }
***** (prediction) *****
{ 'Layer 1': {'height': {'value': 'X0 um'}},
'Layer 2/3': {'height': {'value': 'X1 um'}},
... }
and splits the values of mean and std to numeric quantities
and their units (via quantities package).
"""
for key0 in data.keys():
for key, val in data[key0]["height"].items():
try:
quantity_parts = val.split(" ")
number = float(quantity_parts[0])
units_str = " ".join(quantity_parts[1:])
assert (units_str == self.units.symbol)
data[key0]["height"][key] = quantities.Quantity(
number, self.units)
except AssertionError:
raise sciunit.Error(
"Values not in appropriate format. Required units: ",
self.units.symbol)
except:
raise sciunit.Error("Values not in appropriate format.")
return data
def format_data(self, data):
"""
This accepts data input in the form:
***** (observation) *****
list of Nunit neo.SpikeTrains with annotations 'exc', 'inh'
***** (prediction) *****
list of Nunit neo.SpikeTrains with annotations 'exc', 'inh'
"""
neu_types = []
for st in data:
try: # neo SpikeTrains?
assert type(st) is neo.core.spiketrain.SpikeTrain
except:
raise sciunit.Error("List elements are not " +
"neo.core.spiketrain.SpikeTrains.")
try: # has neu_type annotations?
assert 'neu_type' in st.annotations
except:
raise sciunit.Error("SpikeTrain has no neu_type annotation.")
neu_types.append(st.annotations['neu_type'])
neu_types = set(neu_types)
try:
assert any('exc' == s for s in neu_types)
except:
raise sciunit.Error("There are no exc units.")
try:
assert any('inh' == s for s in neu_types)
except:
raise sciunit.Error("There are no inh units.")
pass
def format_data(self, data):
"""
This accepts data input in the form:
***** (observation) *****
{"cell_kind": { "cell_part_1": {'morph_feature_name_11': {'mean value': 'X11_mean units_str', 'std': 'X11_std units_str'},
'morph_feature_name_12': {'mean value': 'X12_mean units_str', 'std': 'X12_std units_str'},
... },
"cell_part_2": {'morph_feature_name_21': {'mean value': 'X21_mean units_str', 'std': 'X21_std units_str'},
'morph_feature_name_22': {'mean value': 'X22_mean units_str', 'std': 'X22_std units_str'},
... },
... }
}
***** (prediction) *****
{"cell1_ID": { 'cell_part_1': {'morph_feature_name_11': {'value': 'X11 units_str'},
'morph_feature_name_12': {'value': 'X12 units_str'},
... },
'cell_part_2': {'morph_feature_name_21': {'value': 'X21 units_str'},
'morph_feature_name_22': {'value': 'X22 units_str'},
... },
... }
"cell2_ID": { 'cell_part_1': {'morph_feature_name_11': {'value': 'Y11 units_str'},
'morph_feature_name_12': {'value': 'Y12 units_str'},
... },
'cell_part_2': {'morph_feature_name_21': {'value': 'Y21 units_str'},
'morph_feature_name_22': {'value': 'Y22 units_str'},
... },
... }
... }
It splits the values of mean, std and value to numeric quantities
and their units (via quantities package)
"""
dim_non = ['order', 'number', 'asymmetry', 'rate']
dim_um = ['radii', 'length', 'distance', 'extent']
dim_umSq = ['area']
dim_umCb = ['volume']
dim_deg = ['angle']
for dict1 in data.values(
): # Dict. with cell's part-features dictionary pairs for each cell
for dict2 in dict1.values(
): # Dict. with feature name-value pairs for each cell part:
# neuron, apical_dendrite, basal_dendrite or axon
for dict3 in dict2.values(
): # Dict. with 'value', 'mean' and 'std' values
for key, val in dict3.items():
quantity_parts = val.split()
number, units_str = float(quantity_parts[0]), " ".join(
quantity_parts[1:])
try:
if any(sub_str in key for sub_str in dim_um):
assert (units_str == quantities.um | units_str == quantities.mm), \
sciunit.Error("Values not in appropriate format. Required units: mm or um")
elif any(sub_str in key for sub_str in dim_non):
assert (units_str == quantities.dimensionless), \
sciunit.Error("Values not in appropriate format. Required units: ",
quantities.dimensionless)
finally:
dict3[key] = quantities.Quantity(number, units_str)
return data
def validate_observation(self, observation):
# Checking format of the observation data
for dict1 in observation.values(
): # Dict. with cell's part-features dictionary pairs for each cell
for dict2 in dict1.values(
): # Dict. with feature name-value pairs for each cell part:
# neuron, apical_dendrite, basal_dendrite or axon
for dict3 in dict2.values(
): # Dict. with 'value' or 'mean' and 'std' values
for val in dict3.values():
assert type(val) is quantities.Quantity, \
sciunit.Error(("Observation must be of the form "
"{'mean': 'XX units_str','std': 'YY units_str'}"))
def format_data(self, data):
"""
This accepts data input in the form:
***** (observation) *****
{ "AA":{
"SO": {"mean": "X0"},
"SP": {"mean": "X1"},
"SR": {"mean": "X2"},
"SLM":{"mean": "X3"}
},
"BP": {...},
"BS": {...},
"CCKBC":{...},
"Ivy":{...},
"OLM":{...},
"PC":{...},
"PPA":{...},
"SCA":{...},
"Tri":{...}
}
***** (prediction) *****
{ "AA":{
"SO": {"value": "X0"},
"SP": {"value": "X1"},
"SR": {"value": "X2"},
"SLM":{"value": "X3"},
"OUT":{"value": "X4"}
},
"BP": {...},
"BS": {...},
"CCKBC":{...},
"Ivy":{...},
"OLM":{...},
"PC":{...},
"PPA":{...},
"SCA":{...},
"Tri":{...}
}
Returns a new dictionary of the form
{ "AA":[X0, X1, X2, X3, X4], "BP":[...] , "BS":[...], "CCKBC":[...], "Ivy":[...], "OLM":[...],
"PC":[...], "PPA":[...], "SCA":[...], "Tri":[...] }
"""
data_new_dict = dict()
for key0, dict0 in data.items(
): # dict0: a dictionary containing the synapses fraction in each of the
# Hippocampus CA1 layers (SO, SP, SR, SLM) and OUT (for prediction data only)
# for each m-type cell (AA, BP, BS, CCKBC, Ivy, OLM, PC, PPA, SCA, Tri)
data_list_1 = list()
for dict1 in dict0.values(): # dict1: a dictionary of the form
# {"mean": "X0"} (observation) or {"value": "X"} (prediction)
try:
synapses_fraction = float(dict1.values()[0])
assert (synapses_fraction <= 1.0)
data_list_1.extend([synapses_fraction])
except:
raise sciunit.Error(
"Values not in appropriate format. Synapses fraction of an m-type cell"
"must be dimensionless and not larger than 1.0")
if "OUT" not in dict0.keys():
data_list_1.extend([0.0]) # observation data
data_list_1_q = quantities.Quantity(data_list_1, self.units)
data_new_dict[key0] = data_list_1_q
return data_new_dict
