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_update_pns(self):
fseg = TextSegment(
self.data.shape[0],
self.long_channels,
self.channels,
self.data.max(axis=0),
data_start=1000,
)
fseg.update_pns({"a": "aa", "b": "bb"})
assert fseg.pns == ["aa", "bb", "c", "d"]
text_str = fseg.to_string()
assert "$P1S/aa" in text_str
assert "$P2S/bb" in text_str
def test_update_pnn(self):
fseg = TextSegment(
self.data.shape[0],
self.long_channels,
self.channels,
self.data.max(axis=0),
data_start=1000,
)
fseg.update_pnn({"A": "AA", "B": "BB"})
assert fseg.pnn == ["AA", "BB", "C", "D"]
text_str = fseg.to_string()
assert "$P1N/AA" in text_str
assert "$P2N/BB" in text_str
def test_from_string(self):
with open("tests/TextSegment.txt", "rb") as fp:
s = fp.readline()
fseq = TextSegment.from_string(s)
assert fseq.data_start == 4064
assert fseq.data_end == 119207043
def test_cal_datapos(self):
textend = 2
datasize = 8
start_expected = 4
end_expected = 11
start, end = TextSegment.cal_datapos(textend, datasize)
assert start == start_expected
assert end == end_expected
textend = 999
datasize = 9000
start_expected = 1007
end_expected = 10006
start, end = TextSegment.cal_datapos(textend, datasize)
assert start == start_expected
assert end == end_expected
def test_locations(self):
fseg = TextSegment(
self.data.shape[0],
self.long_channels,
self.channels,
self.data.max(axis=0),
data_start=1000,
)
assert fseg.text_start == 256
assert fseg.text_end == 564
assert fseg.data_start == 1000
assert fseg.data_end == 0
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_cal_max_text_ends(self):
assert TextSegment.cal_max_text_ends({}, "/", 0) == 124
def test_dict_to_string(self):
text = {}
text["BEGINDATA"] = "256"
text["BYTEORD"] = "1,2,3,4" # little endian
assert (TextSegment.dict_to_string(
text, "/") == "/$BEGINDATA/256/$BYTEORD/1,2,3,4/")
def test_data_pos(self):
assert TextSegment.cal_datapos(10, 100) == (14, 113)