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Ignore NaN reagents in create_fcs #29

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Ignore NaN reagents in create_fcs #29

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4 changes: 3 additions & 1 deletion src/flowio/create_fcs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,9 @@ def create_fcs(
# PnS - optional channel label
if opt_channel_names is not None:
# cannot have zero-length values in FCS keyword values
if opt_channel_names[i] not in [None, '']:
# equality test omits NaNs (result from "None" and "" in Pandas indices)
opt_channel_name = opt_channel_names[i]
if opt_channel_name not in [None, ''] and opt_channel_name == opt_channel_name:
text['P%dS' % chan_num] = opt_channel_names[i]

# Calculate initial text size, but it's tricky b/c the text contains the
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20 changes: 20 additions & 0 deletions tests/test_fcs_write.py
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Expand Up @@ -193,6 +193,26 @@ def test_create_fcs_with_opt_channel_labels(self):

self.assertEqual(p5s_label_value, p5s_label_truth)

def test_create_fcs_with_opt_channel_labels_none(self):
event_data = self.flow_data.events
channel_names = self.flow_data.channels
pnn_labels = [v['PnN'] for k, v in channel_names.items()]
pns_labels = [v['PnS'] for k, v in channel_names.items()]
pns_labels[0] = None
pns_labels[1] = float("nan")
pns_labels[2] = ""

export_file_path = "examples/fcs_files/test_fcs_export.fcs"
with open(export_file_path, 'wb') as fh:
create_fcs(fh, event_data, channel_names=pnn_labels, opt_channel_names=pns_labels)

exported_flow_data = FlowData(export_file_path)
os.unlink(export_file_path)

self.assertNotIn("p1s", exported_flow_data.text)
self.assertNotIn("p2s", exported_flow_data.text)
self.assertNotIn("p3s", exported_flow_data.text)

def test_create_fcs_with_std_metadata(self):
event_data = self.flow_data.events
channel_names = self.flow_data.channels
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