BD facs diva support #46
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…some channels as in FACS Diva
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Comandeering to resolve conflicts |
eyurtsev
reviewed
Apr 26, 2023
| 'fake bitmask error': os.path.join(BASE_PATH, 'fake_bitmask_error', | ||
| 'fcs1_cleaned.lmd'), | ||
| 'Cytek xP5': os.path.join(BASE_PATH, 'Cytek_xP5', 'Cytek_xP5.fcs'), | ||
| 'guava muse': os.path.join(BASE_PATH, 'GuavaMuse', |
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Could you add guava muse file back to the test suite?
fcsparser/tests/test_fcs_reader.py
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| self.assertListEqual(channel_names, pns_names) | ||
| self.assertListEqual(list(channel_meta["$PnS"]), pns_names) | ||
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| # self.assertListEqual(channel_names, pnn_names) |
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Suggested change
| # self.assertListEqual(channel_names, pnn_names) | |
| # self.assertListEqual(channel_names, pnn_names) |
fcsparser/tests/test_fcs_reader.py
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| self.assertListEqual(list(channel_meta["$PnS"]), pns_names) | ||
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| # self.assertListEqual(channel_names, pnn_names) | ||
| # self.assertListEqual(list(data.columns.values), pnn_names) |
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Suggested change
| # self.assertListEqual(list(data.columns.values), pnn_names) | |
| # self.assertListEqual(list(data.columns.values), pnn_names) |
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@CaRniFeXeR thanks for the PR! I added CI to run to make sure unit-test are running as part of the PR. Would you be able to address the failing tests and add back missing tests? |
eyurtsev
reviewed
Apr 26, 2023
fcsparser/api.py
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| s_key = '$P{0}S'.format(i) | ||
| name_n = "" | ||
| name_s = "" | ||
| if n_key in text.keys(): |
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Here's a short hand version
name_n = text.get(n_key, "")
name_s = text.get(s_key, "")
fcsparser/api.py
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| channel_names_n = [] | ||
| channel_names_s = [] | ||
| for i in self.channel_numbers: |
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sting interpolation using named arguments rather than indexed arguments
for channel_number in self.channel_numbers:
n_key = f'$P{channel_number}N'
s_key = f'$P{channel_number}S'
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BD facs diva devices only have channel_name_s set for some but not all channels. If not present for all channels fcsparser fallbacks to the channel_names_n.
This pull request includes two main adaptations:
All adaptations have corresponding unit tests