def test_repeated_delimiter_text_segment(self):
parser = FCSParser()
raw_text = '/flow_speed/3 m//s/x/a///y/b/////'
text = parser._extract_text_dict(raw_text)
self.assertDictEqual(text, {
'flow_speed': '3 m/s',
'x': 'a/',
'y': 'b//'
})
def test_cloning_an_fcs_file_with_a_subset_of_data(self):
""" Reading a FCS file, modifying and writing to disk """
fname = file_formats['IntelliCyt iQue']
fcs_parser = FCSParser(fname)
# Only save a subset of the data points
new_fcs_parser = fcs_parser.clone(data=fcs_parser.data[:1000])
with tempfile.NamedTemporaryFile(suffix='.fcs') as written_fcs:
new_fcs_parser.write_to_file(written_fcs.name)
new_fcs_parser = FCSParser(written_fcs.name)
self.assertTrue(new_fcs_parser.data.shape == fcs_parser.data[:1000].shape)
def test_reading_and_writing_fcs_file(self):
""" Reading a FCS file and writing to disk the same """
fname = file_formats['IntelliCyt iQue']
fcs_parser = FCSParser(fname)
with tempfile.NamedTemporaryFile(suffix='.fcs') as written_fcs:
fcs_parser.write_to_file(written_fcs.name)
# use filecmp to compare the files
self.assertTrue(filecmp.cmp(fname, written_fcs.name))
# read the written file and assert that the annotations, and data are equal
new_fcs_parser = FCSParser(written_fcs.name)
self.assertDictEqual(fcs_parser.annotation, new_fcs_parser.annotation)
self.assertTrue(numpy.array_equal(fcs_parser.data, new_fcs_parser.data))
# compare the md5 checksum for the original and written file
self._compare_file_md5(fname, written_fcs.name)
def test_reading_in_memory_fcs_file(self):
"""Find data segment of an in-memory FCS file."""
values = array(
[[
4.99655876159667968750e+01, -1.78884857177734375000e+02,
3.53545867919921875000e+02, -6.63189687500000000000e+04,
1.53373974609375000000e+03, 1.71934411621093750000e+03,
1.16922687500000000000e+05, -1.85308218002319335938e+00,
1.55241485595703125000e+02, -1.56457653808593750000e+03,
7.68178787231445312500e+01, 1.61987319946289062500e+02,
6.21571679687500000000e+04, 3.74284629821777343750e+01,
1.23476585388183593750e+02, 3.87178945312500000000e+04
],
[
7.65274276733398437500e+01, 8.52657958984375000000e+02,
8.35975280761718750000e+02, 1.33687671875000000000e+05,
2.55060937500000000000e+03, 2.26837988281250000000e+03,
1.47379843750000000000e+05, 4.53825866699218750000e+02,
4.73883544921875000000e+02, 1.25524226562500000000e+05,
-8.64693832397460937500e+00, 9.53993377685546875000e+01,
-1.18802871093750000000e+04, 8.17031021118164062500e+01,
2.03511352539062500000e+02, 5.58651601562500000000e+04
],
[
8.48738250732421875000e+01, 1.49076705932617187500e+02,
2.49545867919921875000e+02, 7.83013671875000000000e+04,
6.49180541992187500000e+02, 5.83344177246093750000e+02,
1.45864812500000000000e+05, 1.76183197021484375000e+02,
2.59241485595703125000e+02, 8.90778906250000000000e+04,
1.03054801940917968750e+02, 1.69987319946289062500e+02,
7.94623906250000000000e+04, -6.35836944580078125000e+01,
1.13396583557128906250e+02, -6.63863593750000000000e+04
],
[
1.02074172973632812500e+02, 1.37832305908203125000e+02,
3.85545867919921875000e+02, 4.68581250000000000000e+04,
1.88981237792968750000e+03, 1.81534411621093750000e+03,
1.36448781250000000000e+05, 3.93574859619140625000e+02,
4.83241485595703125000e+02, 1.06751273437500000000e+05,
6.74475479125976562500e+01, 1.77987319946289062500e+02,
4.96691835937500000000e+04, -3.04502067565917968750e+01,
2.20916580200195312500e+02, -1.28346718750000000000e+04
]])
fname = FILE_IDENTIFIER_TO_PATH['mq fcs 3.0']
with open(fname, 'rb') as f:
data = f.read()
matrix = FCSParser.from_data(data).data
diff = numpy.abs(values - matrix[0:4, :])
self.assertTrue(numpy.all(diff < 10**-8))
def __init__(
self,
initdata: Union["URLPath", "FCSData", tuple],
channels: list = None,):
"""Create a new FCS object.
Args:
initdata: Either tuple of meta and data from fcsparser, string filepath or another FCSData object.
meta: Dict of fcsmeta named tuples.
Returns:
FCSData object.
"""
if isinstance(initdata, self.__class__):
self.data = initdata.data.copy()
self.mask = initdata.mask.copy()
self.channels = initdata.channels.copy()
elif isinstance(initdata, (URLPath, str)):
parser = FCSParser(str(initdata), data_set=DEFAULT_DATASET, encoding=DEFAULT_ENCODING)
self.data = parser.data
self.mask = np.ones(self.data.shape)
if parser.channel_names_s:
self.channels = create_meta_from_fcs(parser.annotation, parser.channel_names_s)
else:
self.channels = create_meta_from_fcs(parser.annotation, parser.channel_names_n)
elif isinstance(initdata, tuple):
self.data, self.mask = initdata
if channels is None:
raise ValueError("Channels needed when initializing from np data")
self.channels = create_meta_from_data(self.data, channels)
else:
raise RuntimeError(
"Invalid data for FCS. Either Path, similar object or tuple of data and metadata needed.")
self.data = self.data.astype("float32", copy=False)
self.channels = [Marker.convert(c) for c in self.channels]