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Ignore secondary annotations (undefined annotations in TYPE_DCT) #25

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Ignore secondary annotations (undefined annotations in TYPE_DCT) #25

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143f2c2
Added section in tmd.io.load_neuron to remove structural
BCJongbloets Jan 21, 2020
dd52ed7
CHanged LoadNeuronError to a printed warning to allow the data
BCJongbloets Jan 21, 2020
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16 changes: 15 additions & 1 deletion tmd/io/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def make_tree(data):


def load_neuron(input_file, line_delimiter='\n', soma_type=None,
tree_types=None, remove_duplicates=True):
tree_types=None, remove_duplicates=True, verbose=True):
'''
Io method to load an swc or h5 file into a Neuron object.
TODO: Check if tree is connected to soma, otherwise do
Expand Down Expand Up @@ -79,6 +79,20 @@ def load_neuron(input_file, line_delimiter='\n', soma_type=None,
except IndexError:
raise LoadNeuronError('Soma points not in the expected format')

# Remove structural annotations other than defined in TYPE_DICT
# Presence of those annotations impede loading of data when generating
# csr_matrix.
in_type_dct = _np.zeros((len(data), len(TYPE_DCT))).astype(bool)
for ind, TYPE in enumerate(TYPE_DCT.values()):
in_type_dct[:, ind] = data[:, 1] == int(TYPE)
in_type_dct = _np.sum(in_type_dct, axis=1).astype(bool)
if verbose and len(data) > _np.sum(in_type_dct):
print('LoadNeuronWarning: Loaded neuron data contains structural '
'annotations that are ignored in current TMD '
' package. Processed data only contains: %s'
% str(TYPE_DCT))
data = data[in_type_dct, :]

# Extract soma information from swc
soma = Soma.Soma(x=_np.transpose(data)[SWC_DCT['x']][soma_ids],
y=_np.transpose(data)[SWC_DCT['y']][soma_ids],
Expand Down