def find_captures_4_unfolded_terminal_test():
"""Example capture window contains 1 long terminal capturethat has unfolded.
Tests: find_captures returns 1 capture
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_4.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(5_511_887, 5_604_585)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = True
filters = [filtering.LengthFilter(100, None)]
delay = 0
end_tol = 0
channel_number = 2
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 1
def find_captures_3_multicapture_nonterminal_test():
"""Example capture window contains 1 long terminal capture & 1 medium capture.
Tests: find_captures returns...
3 captures when terminal_capture_only = False
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_3.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(1_187_841, 1_280_674)
actual_captures = [(1_200_088, 1_201_033, False), (1_252_611, 1_280_674, True)]
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 3
end_tol = 0
channel_number = 2
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == len(actual_captures)
for test_capture in captures:
test_start = test_capture.window.start
test_end = test_capture.window.end
ejected = test_capture.ejected
assert (test_start, test_end, ejected) in actual_captures
def find_captures_3_multicapture_terminal_test():
"""Example capture window contains 1 long terminal capture & 2 medium/short captures.
Tests: find_captures returns...
1 capture when terminal_capture_only = True
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_3.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(1_187_841, 1_280_674)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = True
filters = [filtering.LengthFilter(100, None)]
delay = 0
end_tol = 0
channel_number = 2
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 1
def find_captures_2_nocaptures_test():
"""Example capture window contains no captures.
Test: find_captures returns no captures"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_2.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(3_423_474, 3_516_439)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 10
end_tol = 0
channel_number = 1
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 0
def find_captures_1_double_capture_noterminal_2_test():
"""Example capture window contains 2 long captures, neither terminal.
Also contains a few short blips.
Test: terminal_capture_only = False returns 2 captures"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_1.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(4_765_695, 4_858_482)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 0
end_tol = 0
channel_number = 1
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 2
def find_captures_0_single_capture_terminal_test():
data_file = "src/tests/data/capture_windows/test_data_capture_window_0.txt.gz"
window = Window(3_572_989, 3_665_680)
data = picoampere_signal_from_data_file(data_file)
actual_captures = [(33822 + window.start, 92691 + window.start, True)]
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = True
filters = [filtering.LengthFilter(100, None)]
delay = 0
end_tol = 0
channel_number = 1
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == len(actual_captures)
for test_capture in captures:
test_start = test_capture.window.start
test_end = test_capture.window.end
ejected = test_capture.ejected
assert (test_start, test_end, ejected) in actual_captures
def find_captures_7_capture_no_open_channel_test():
"""Example capture window contains 1 long terminal capture. Open pore region
is extremely, extremely short. Test by cutting off the open pore region.
Tests: find_captures returns 1 capture; open pore returns alt value.
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_7.txt.gz"
data = picoampere_signal_from_data_file(data_file)[100:]
window = Window(2_919_913, 3_013_723)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 100
end_tol = 0
channel_number = 2
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 1
# Rough check; should be ~229.05 & anything close is okay.
# The function is nondeterministic & should return this exact value, but if
# future changes are made, some tolerance can be allowed.
expected_open_channel_pA = 230
open_channel_pA = np.array([capture.open_channel_pA_calculated for capture in captures])
all_currents_within_bounds = all(
(np.isclose(open_channel_pA, expected_open_channel_pA, atol=0.5))
)
assert (
all_currents_within_bounds
), f"All captures should have calculated an open channel current close to {expected_open_channel_pA}."
def find_captures_5_unfolded_terminal_test():
"""Example capture window contains 1 long terminal capture. It was captured
almost immediately, causing a very short open pore region.
Tests: find_captures returns 1 capture
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_5.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(965_676, 1_059_216)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = True
filters = [filtering.LengthFilter(100, None)]
delay = 0
end_tol = 0
channel_number = 1
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 1
open_channel_pA = np.array([capture.open_channel_pA_calculated for capture in captures])
low_expected_open_channel_pA = 228.5
high_expected_open_channel_pA = 230
# Rough check; should be ~229.05 & anything close is okay.
# The function is nondeterministic & should return this exact value, but if
# future changes are made, some tolerance can be allowed.
all_currents_within_bounds = all(
(open_channel_pA > low_expected_open_channel_pA)
& (open_channel_pA < high_expected_open_channel_pA)
)
assert (
all_currents_within_bounds
), f"Expect all capture open channel currents to be between '{low_expected_open_channel_pA}' and '{high_expected_open_channel_pA}'."
def find_captures_8_capture_no_open_channel_test():
"""Example capture window contains 2 captures: both long, 1 terminal.
Test non-terminal long capture.
Tests: find_captures returns 2 captures.
Checks exact capture boundaries with delay = 3
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_8.txt.gz"
data = picoampere_signal_from_data_file(data_file)
window = Window(4_875_289, 4_969_337)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 3
end_tol = 0
channel_number = 2
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 2
actual_captures = [
(11310 + window.start, 22098 + window.start, False),
(26617 + window.start, 94048 + window.start, True),
]
for test_capture in captures:
test_start = test_capture.window.start
test_end = test_capture.window.end
ejected = test_capture.ejected
assert (test_start, test_end, ejected) in actual_captures
def find_captures_6_clog_no_open_channel_test():
"""Example capture window contains 1 long terminal capture. Open pore region
is extremely, extremely short. Test by cutting off the open pore region.
Tests: find_captures returns 1 capture; open pore returns alt value.
"""
data_file = "src/tests/data/capture_windows/test_data_capture_window_6.txt.gz"
data = picoampere_signal_from_data_file(data_file)[100:]
window = Window(2_769_436, 2_863_265)
signal_threshold_frac = 0.7
alt_open_channel_pA = 230
terminal_capture_only = False
filters = [filtering.LengthFilter(100, None)]
delay = 100
end_tol = 0
channel_number = 1
captures = segment.find_captures(
data,
channel_number,
window,
signal_threshold_frac,
alt_open_channel_pA,
terminal_capture_only=terminal_capture_only,
filters=filters,
delay=delay,
end_tol=end_tol,
)
assert len(captures) == 1
open_channel_pA = np.array([capture.open_channel_pA_calculated for capture in captures])
expected_open_channel_pA = 230
all_currents_within_bounds = all(
(np.isclose(open_channel_pA, expected_open_channel_pA, atol=0.5))
)
assert (
all_currents_within_bounds
), f"All calculated open channel currents should be close to {expected_open_channel_pA}"