def test_buffer_export(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, "export.fcs")
text_start = 256
fseg = TextSegment(
self.data.shape[0],
self.long_channels,
self.channels,
self.data.max(axis=0),
text_start=text_start,
)
header = HeaderSegment(text_start, fseg.text_end, fseg.data_start,
fseg.data_end)
fcs = Fcs(self.data, self.long_channels, self.channels)
with open(filename, "wb") as fp:
fcs.export(fp)
with open(filename, "rb") as fp:
assert fp.read(58).decode("UTF-8") == header.to_string()
fp.seek(text_start)
assert (fp.read(header.text_end - fseg.text_start +
1).decode("UTF-8").strip() == fseg.to_string())
fp.seek(fseg.data_start)
dseg = DataSegment.from_string(
fp.read(fseg.data_end - fseg.data_start + 1),
fseg.datatype,
len(fseg.pnn),
fseg.tot,
fseg.endian,
)
assert np.array_equal(dseg.values, self.data)
def test_data(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, self.name)
df = DataFrame(self.data, columns=self.channels)
df.to_fcs(filename)
fcs = Fcs.from_file(filename)
assert np.array_equal(fcs.values, self.data)
def test_count(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, self.name)
df = DataFrame(self.data, columns=self.channels)
df.to_fcs(filename)
fcs = Fcs.from_file(filename)
assert fcs.count == len(self.data)
def test_read_text_segment(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, self.name)
cols = pd.MultiIndex.from_tuples(
list(zip(self.channels, self.long_channels)),
names=["short", "long"],
)
df = DataFrame(self.data, columns=cols)
df.to_fcs(filename)
seg = Fcs.read_text_segment(filename)
assert seg.pnn == self.channels
assert seg.pns == self.long_channels
def test_read_text_segment(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, "test.fcs")
cols = pd.MultiIndex.from_tuples(
list(zip(self.channels, self.long_channels)),
names=["short", "long"],
)
df = DataFrame(self.data, columns=cols)
df.to_fcs(filename)
self.s3.upload_file(filename, self.bucket_name, "test.fcs")
parse_func = create_open_func(S3ReadBuffer, bucket=self.bucket_name)
with parse_func("test.fcs") as fp:
seg = Fcs.read_text_segment(fp)
assert seg.pnn == self.channels
assert seg.pns == self.long_channels
def test_write_text_segment(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, "export.fcs")
fcs = Fcs(self.data, self.long_channels, self.channels)
fcs.export(filename)
fseg = TextSegment(
self.data.shape[0],
self.long_channels,
["w", "x", "y", "z"],
self.data.max(axis=0),
text_start=256,
)
Fcs.write_text_segment(filename, fseg)
tseg = Fcs.read_text_segment(filename)
assert tseg.pns == ["w", "x", "y", "z"]
def test_from_fcs(self):
with TmpDir() as dir_:
filename = os.path.join(dir_, "test.fcs")
cols = pd.MultiIndex.from_tuples(
list(zip(self.channels, self.long_channels)),
names=["short", "long"],
)
df = DataFrame(self.data, columns=cols)
df.to_fcs(filename)
self.s3.upload_file(filename, self.bucket_name, "test.fcs")
parse_func = create_open_func(S3ReadBuffer, bucket=self.bucket_name)
with parse_func("test.fcs") as fp:
fcs = Fcs.from_file(fp)
assert fcs.short_channels == self.channels
assert fcs.long_channels == self.long_channels
assert fcs.count == len(self.data)
assert np.array_equal(fcs.values, self.data)