added flag to move scattering signal baseline to 0

Author: jtgasparik

pysp2/util/normalized_derivative_method.py

@@ -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 
@@ -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)

tests/baseline/test_plot_normalized_derivative.png

@@ -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)
@@ -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(), 

tests/test_ndm.py

@@ -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