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#21 Run qc5 on all test data
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@kwabenantim
kwabenantim committed Nov 28, 2024
1 parent 2b981dc commit 6bf42de
Showing 1 changed file with 93 additions and 45 deletions.
138 changes: 93 additions & 45 deletions tests/test_herg_qc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -111,10 +111,10 @@ def test_qc1(self):
[(0, 0, 0), False],
]

for (rseal, cm, rseries), expected in test_matrix:
for (rseal, cm, rseries), ex_pass in test_matrix:
self.assertEqual(
all_passed(hergqc.qc1(rseal, cm, rseries)),
expected,
ex_pass,
f"QC1: {rseal}, {cm}, {rseries}",
)

Expand Down Expand Up @@ -353,16 +353,16 @@ def test_qc3(self):
]

recording1 = np.asarray([0, 0.1] * (NOISE_LEN // 2) + [40] * 500)
for i, ex_pass, ex_rmsd_diff in test_matrix:
for i, ex_pass, ex_d_rmsd in test_matrix:
recording2 = np.asarray(
[0, 0.1] * (NOISE_LEN // 2) + [40 + i] * 500
)
pass_, rmsd_diff = hergqc.qc3(recording1, recording2)
pass_, d_rmsd = hergqc.qc3(recording1, recording2)
self.assertAlmostEqual(
rmsd_diff,
ex_rmsd_diff,
d_rmsd,
ex_d_rmsd,
1,
f"QC3: ({i}) {rmsd_diff} != {ex_rmsd_diff}",
f"QC3: ({i}) {d_rmsd} != {ex_d_rmsd}",
)
self.assertEqual(pass_, ex_pass, f"QC3: ({i}) {pass_} != {ex_pass}")

Expand All @@ -378,16 +378,16 @@ def test_qc3(self):
]

recording1 = np.asarray([0, 0.1] * (NOISE_LEN // 2) + [40] * 500)
for i, ex_pass, ex_rmsd_diff in test_matrix:
for i, ex_pass, ex_d_rmsd in test_matrix:
recording2 = np.asarray(
[0, 0.1 * i] * (NOISE_LEN // 2) + [40] * 500
)
pass_, rmsd_diff = hergqc.qc3(recording1, recording2)
pass_, d_rmsd = hergqc.qc3(recording1, recording2)
self.assertAlmostEqual(
rmsd_diff,
ex_rmsd_diff,
d_rmsd,
ex_d_rmsd,
1,
f"QC3: ({i}) {rmsd_diff} != {ex_rmsd_diff}",
f"QC3: ({i}) {d_rmsd} != {ex_d_rmsd}",
)
self.assertEqual(pass_, ex_pass, f"QC3: ({i}) {pass_} != {ex_pass}")

Expand Down Expand Up @@ -416,31 +416,31 @@ def test_qc3(self):
before = np.array(self.trace_sweeps_before[well])
after = np.array(self.trace_sweeps_after[well])

pass_raw, rmsd_diff_raw = hergqc.qc3(before[0, :], before[1, :])
pass_raw, d_rmsd_raw = hergqc.qc3(before[0, :], before[1, :])
ex_pass_raw = well not in failed_wells_raw
self.assertEqual(
pass_raw,
ex_pass_raw,
f"QC3: {well} (raw) {rmsd_diff_raw}",
f"QC3: {well} (raw) {d_rmsd_raw}",
)

pass_E4031, rmsd_diff_E4031 = hergqc.qc3(after[0, :], after[1, :])
pass_E4031, d_rmsd_E4031 = hergqc.qc3(after[0, :], after[1, :])
ex_pass_E4031 = well not in failed_wells_E4031
self.assertEqual(
pass_E4031,
ex_pass_E4031,
f"QC3: {well} (E4031) {rmsd_diff_E4031}",
f"QC3: {well} (E4031) {d_rmsd_E4031}",
)

pass_subtracted, rmsd_diff_subtracted = hergqc.qc3(
pass_subtracted, d_rmsd_subtracted = hergqc.qc3(
before[0, :] - after[0, :],
before[1, :] - after[1, :],
)
ex_pass_subtracted = well not in failed_wells_subtracted
self.assertEqual(
pass_subtracted,
ex_pass_subtracted,
f"QC3: {well} (subtracted) {rmsd_diff_subtracted}",
f"QC3: {well} (subtracted) {d_rmsd_subtracted}",
)

def test_qc4(self):
Expand All @@ -461,18 +461,18 @@ def test_qc4(self):
(5.0, False),
]

for i, expected in test_matrix:
for i, ex_pass in test_matrix:
rseals = [r_lo, i * r_lo]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

rseals = [r_hi, i * r_hi]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

Expand All @@ -487,18 +487,18 @@ def test_qc4(self):
(5.0, False),
]

for i, expected in test_matrix:
for i, ex_pass in test_matrix:
cms = [c_lo, i * c_lo]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

cms = [c_hi, i * c_hi]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

Expand All @@ -513,18 +513,18 @@ def test_qc4(self):
(5.0, False),
]

for i, expected in test_matrix:
for i, ex_pass in test_matrix:
rseriess = [r_lo, i * r_lo]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

rseriess = [r_hi, i * r_hi]
self.assertEqual(
all_passed(hergqc.qc4(rseals, cms, rseriess)),
expected,
ex_pass,
f"({i}: {rseals}, {cms}, {rseriess})",
)

Expand Down Expand Up @@ -609,23 +609,71 @@ def test_qc5(self):
# qc5 checks that the maximum current during the second half of the
# staircase changes by at least 75% of the raw trace after E-4031 addition
test_matrix = [
(-1.0, True),
(0.1, True),
(0.2, True), # max_diffc - max_diff = -0.5
(0.25, True), # max_diffc - max_diff = 0.0
(0.3, False), # max_diffc - max_diff = 0.5
(0.5, False),
(1.0, False),
(-1.0, True, -12.5),
(0.1, True, -1.5),
(0.2, True, -0.5),
(0.24, True, -0.1),
(0.25, True, 0),
(0.26, False, 0.1),
(0.3, False, 0.5),
(0.5, False, 2.5),
(1.0, False, 7.5),
]

recording1 = np.asarray([0, 0.1] * (NOISE_LEN // 2) + [10] * 500)
for i, expected in test_matrix:
for i, ex_pass, ex_d_max_diff in test_matrix:
recording2 = np.asarray(
[0, 0.1] * (NOISE_LEN // 2) + [10 * i] * 500)
result = hergqc.qc5(recording1, recording2)
self.assertEqual(result[0], expected, f"({i}: {result[1]})")
[0, 0.1] * (NOISE_LEN // 2) + [10 * i] * 500
)
pass_, d_max_diff = hergqc.qc5(recording1, recording2)
self.assertAlmostEqual(
d_max_diff,
ex_d_max_diff,
1,
f"QC5: ({i}) {d_max_diff} != {ex_d_max_diff}",
)
self.assertEqual(pass_, ex_pass, f"QC5: ({i}) {pass_} != {ex_pass}")

# TODO: Test on select data
# Test on data
failed_wells = [
'A10', 'A12', 'A13', 'A15', 'A19', 'A20', 'A24', 'B05', 'B07', 'B09',
'B11', 'B12', 'B13', 'B15', 'B18', 'B19', 'B21', 'B23', 'C02', 'C04',
'C05', 'C07', 'C08', 'C09', 'C11', 'C12', 'C14', 'C17', 'C18', 'C19',
'C20', 'C21', 'C22', 'C24', 'D02', 'D05', 'D09', 'D10', 'D11', 'D12',
'D14', 'D17', 'D18', 'D19', 'D21', 'E04', 'E10', 'E11', 'E13', 'E14',
'E15', 'E16', 'E17', 'E18', 'E19', 'E22', 'E23', 'F01', 'F03', 'F04',
'F06', 'F07', 'F09', 'F10', 'F12', 'F13', 'F14', 'F15', 'F16', 'F18',
'F19', 'F20', 'F21', 'F22', 'F24', 'G03', 'G06', 'G08', 'G09', 'G12',
'G13', 'G14', 'G15', 'G16', 'G18', 'G19', 'G20', 'G23', 'G24', 'H01',
'H02', 'H03', 'H04', 'H06', 'H07', 'H08', 'H10', 'H11', 'H14', 'H15',
'H16', 'H18', 'H19', 'H21', 'H23', 'H24', 'I01', 'I04', 'I05', 'I06',
'I07', 'I08', 'I10', 'I11', 'I12', 'I13', 'I14', 'I16', 'I17', 'I18',
'I21', 'J07', 'J10', 'J12', 'J15', 'J16', 'J17', 'J18', 'J19', 'J20',
'J21', 'J23', 'J24', 'K02', 'K03', 'K06', 'K07', 'K11', 'K12', 'K13',
'K14', 'K16', 'K18', 'K20', 'K22', 'K23', 'K24', 'L01', 'L02', 'L03',
'L04', 'L05', 'L07', 'L08', 'L10', 'L11', 'L12', 'L13', 'L16', 'L17',
'L18', 'L24', 'M01', 'M02', 'M03', 'M04', 'M06', 'M08', 'M09', 'M11',
'M12', 'M14', 'M15', 'M16', 'M17', 'M18', 'M19', 'M21', 'N04', 'N06',
'N07', 'N08', 'N11', 'N13', 'N14', 'N16', 'N18', 'N20', 'N21', 'N22',
'N24', 'O01', 'O02', 'O03', 'O07', 'O08', 'O10', 'O12', 'O15', 'O16',
'O17', 'O18', 'O19', 'O20', 'O21', 'O22', 'O24', 'P01', 'P03', 'P05',
'P06', 'P07', 'P08', 'P09', 'P10', 'P12', 'P13', 'P14', 'P15', 'P17',
'P18', 'P20', 'P21', 'P22', 'P24'
]

for well in self.all_wells:
before = np.array(self.trace_sweeps_before[well])
after = np.array(self.trace_sweeps_after[well])

pass_, d_max_diff = hergqc.qc5(
before[0, :], after[0, :], hergqc.qc5_win
)
ex_pass = well not in failed_wells
self.assertEqual(
pass_,
ex_pass,
f"QC5: {well} {d_max_diff}",
)

def test_qc5_1(self):
hergqc = self.clone_herg_qc("test_qc5_1")
Expand All @@ -644,11 +692,11 @@ def test_qc5_1(self):
]

recording1 = np.asarray([0, 0.1] * (NOISE_LEN // 2) + [10] * 500)
for i, expected in test_matrix:
for i, ex_pass in test_matrix:
recording2 = np.asarray(
[0, 0.1] * (NOISE_LEN // 2) + [10 * i] * 500)
result = hergqc.qc5_1(recording1, recording2)
self.assertEqual(result[0], expected, f"({i}: {result[1]})")
self.assertEqual(result[0], ex_pass, f"({i}: {result[1]})")

# TODO: Test on select data

Expand All @@ -667,11 +715,11 @@ def test_qc6(self):
(10, True), # valc - val = -1.1
(100, True), # valc - val = -10.1
]
for i, expected in test_matrix:
for i, ex_pass in test_matrix:
recording = np.asarray(
[0, 0.1] * (NOISE_LEN // 2) + [0.1 * i] * 500)
result = hergqc.qc6(recording, win=[NOISE_LEN, -1])
self.assertEqual(result[0], expected, f"({i}: {result[1]})")
self.assertEqual(result[0], ex_pass, f"({i}: {result[1]})")

# TODO: Test on select data

Expand All @@ -688,7 +736,7 @@ def test_run_qc(self):
("D01", False),
]

for well, expected in test_matrix:
for well, ex_pass in test_matrix:
with self.subTest(well):
# Take values from the first sweep only
before = np.array(self.trace_sweeps_before[well])
Expand All @@ -714,4 +762,4 @@ def test_run_qc(self):
if not QC.qc_passed(label):
trace += f"{well} {label}: {result}\n"

self.assertEqual(QC.all_passed(), expected, trace)
self.assertEqual(QC.all_passed(), ex_pass, trace)

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