def test_export_fcs_as_raw(self):
# This test uses a file where the preprocessing makes the orig & raw events different.
# The purpose here is to verify that importing the exported file has the same raw events
# as the original file's raw events.
fcs_file_path = "examples/data/8_color_data_set/fcs_files/101_DEN084Y5_15_E01_008_clean.fcs"
sample = Sample(fcs_path_or_data=fcs_file_path)
sample.export("test_fcs_export.fcs",
source='raw',
directory="examples")
exported_fcs_file = "examples/test_fcs_export.fcs"
exported_sample = Sample(fcs_path_or_data=exported_fcs_file)
os.unlink(exported_fcs_file)
self.assertIsInstance(exported_sample, Sample)
# When the events are exported, they are saved as single precision (32-bit). We'll test the
# arrays with the original sample data converted to 32-bit float. The original sample data
# was also originally in 32-bit. Comparing both in single precision is then the most
# "correct" thing to do here.
np.testing.assert_array_equal(
sample._raw_events.astype(np.float32),
exported_sample._raw_events.astype(np.float32))
def test_export_fcs_as_raw_with_gain(self):
# This test uses a file where the preprocessing makes the orig & raw events different.
# File data1.fcs has 2 channels that specify a gain value other than 1.0.
# The purpose here is to verify that importing the exported file has the same raw events
# as the original file's raw events.
sample = Sample(fcs_path_or_data=data1_fcs_path,
cache_original_events=True)
sample.export("test_fcs_export.fcs",
source='raw',
directory="examples")
exported_fcs_file = "examples/test_fcs_export.fcs"
exported_sample = Sample(fcs_path_or_data=exported_fcs_file)
os.unlink(exported_fcs_file)
self.assertIsInstance(exported_sample, Sample)
# When the events are exported, they are saved as single precision (32-bit). We'll test the
# arrays with the original sample data converted to 32-bit float. The original sample data
# was also originally in 32-bit. Comparing both in single precision is then the most
# "correct" thing to do here.
np.testing.assert_array_equal(
sample._raw_events.astype(np.float32),
exported_sample._raw_events.astype(np.float32))
def test_export_exclude_negative_scatter(self):
# there are 2 negative SSC-A events in this file (of 65016 total events)
fcs_file_path = "examples/data/100715.fcs"
sample = Sample(fcs_path_or_data=fcs_file_path)
sample.filter_negative_scatter()
neg_scatter_count = len(sample.negative_scatter_indices)
exported_fcs_file = "examples/test_fcs_export.fcs"
sample.export(exported_fcs_file,
source='raw',
exclude_neg_scatter=True)
exported_sample = Sample(exported_fcs_file)
os.unlink(exported_fcs_file)
orig_event_count = sample.event_count
exp_event_count = exported_sample.event_count
self.assertEqual(exp_event_count, orig_event_count - neg_scatter_count)
def test_create_csv(self):
fcs_file_path = "examples/test_comp_example.fcs"
comp_file_path = Path("examples/comp_complete_example.csv")
sample = Sample(fcs_path_or_data=fcs_file_path,
compensation=comp_file_path)
sample.export("test_fcs_export.csv",
source='comp',
directory="examples")
exported_csv_file = "examples/test_fcs_export.csv"
exported_df = pd.read_csv(exported_csv_file)
exported_sample = Sample(exported_df)
os.unlink(exported_csv_file)
self.assertIsInstance(exported_sample, Sample)
# TODO: Need to investigate why the exported comp data isn't exactly equal
np.testing.assert_almost_equal(sample._comp_events[:, :],
exported_sample._raw_events[:, :],
decimal=3)
def test_create_fcs(self):
fcs_file_path = "examples/test_comp_example.fcs"
comp_file_path = Path("examples/comp_complete_example.csv")
sample = Sample(fcs_path_or_data=fcs_file_path,
compensation=comp_file_path)
sample.export("test_fcs_export.fcs",
source='comp',
directory="examples")
exported_fcs_file = "examples/test_fcs_export.fcs"
exported_sample = Sample(fcs_path_or_data=exported_fcs_file)
os.unlink(exported_fcs_file)
self.assertIsInstance(exported_sample, Sample)
# TODO: Excluding time channel here, as the difference was nearly 0.01. Need to investigate why the
# exported comp data isn't exactly equal
np.testing.assert_almost_equal(sample._comp_events[:, :-1],
exported_sample._raw_events[:, :-1],
decimal=3)
