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Merged
rcjackson merged 1 commit into from
Mar 11, 2026
Merged

baseline correction flag #81

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7 changes: 6 additions & 1 deletion pysp2/util/normalized_derivative_method.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import numpy as np
import xarray as xr

def central_difference(S, num_records=None, normalize=True):
def central_difference(S, num_records=None, normalize=True, baseline_to_zero=True):

"""
Compute fourth order derivative S'(t) using the
Expand Down Expand Up @@ -39,6 +39,11 @@ def central_difference(S, num_records=None, normalize=True):

for ch in channels:
y = S[ch].isel(event_index=slice(0, num_records)).values

# Baseline shift: make each record's minimum be 0
if baseline_to_zero:
y_min = np.nanmin(y, axis=1, keepdims=True) # shape (n_records, 1)
y = y - y_min
d = np.full_like(y, np.nan, dtype=np.float64)

# Interior points (vectorized)
Expand Down
Binary file modified tests/baseline/test_plot_normalized_derivative.png
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4 changes: 2 additions & 2 deletions tests/test_ndm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ def test_central_difference():
my_sp2b = pysp2.io.read_sp2(pysp2.testing.EXAMPLE_SP2B)
my_ini = pysp2.io.read_config(pysp2.testing.EXAMPLE_INI)
my_binary = pysp2.util.gaussian_fit(my_sp2b, my_ini, parallel=False)
dSdt = pysp2.util.central_difference(my_binary, normalize=False)
dSdt = pysp2.util.central_difference(my_binary, normalize=False, baseline_to_zero=False)

np.testing.assert_almost_equal(dSdt['Data_ch4'].isel(event_index=5876, time=0).item(),
8.3333333333e6, decimal=2)
Expand All @@ -15,7 +15,7 @@ def test_central_difference():
1.5e7, decimal=2)
assert np.isfinite(dSdt).all()

dSdt_norm = pysp2.util.central_difference(my_binary, normalize=True)
dSdt_norm = pysp2.util.central_difference(my_binary, normalize=True, baseline_to_zero=False)
np.testing.assert_almost_equal(dSdt_norm['Data_ch4'].isel(event_index=5876, time=0).item(),
8.3333333333e6/-30168, decimal=2)
np.testing.assert_almost_equal(dSdt_norm['Data_ch4'].isel(event_index=5876, time=99).item(),
Expand Down
4 changes: 2 additions & 2 deletions tests/test_vis.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,10 +14,10 @@ def test_plot_normalized_derivative():
my_sp2b = pysp2.io.read_sp2(pysp2.testing.EXAMPLE_SP2B)
my_ini = pysp2.io.read_config(pysp2.testing.EXAMPLE_INI)
my_binary = pysp2.util.gaussian_fit(my_sp2b, my_ini, parallel=False)
dSdt_norm = pysp2.util.central_difference(my_binary, normalize=True)
dSdt_norm = pysp2.util.central_difference(my_binary, normalize=True, baseline_to_zero=True)

# Test the plotting function for channel 0 and record number 2
ax = plot_normalized_derivative(dSdt_norm, record_no=304, chn=0)
ax = plot_normalized_derivative(dSdt_norm, record_no=499, chn=0)
fig = ax.figure

return fig
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