🧹 Remove redundant backsweep flag from GaussianActivationParameters (g…

…lotaran#1423)

Just a small additional clean-up after glotaran#1422 to get rid of the backsweep boolean flag, which is a residual of the < 0.8 model syntax when we had this as user input.

glotaran/builtin/elements/kinetic/element.py

@@ -136,7 +136,6 @@ def calculate_matrix_gaussian_activation(
                 np.array([[p.center for p in ps] for ps in parameters]),  # type:ignore[union-attr]
                 np.array([[p.width for p in ps] for ps in parameters]),  # type:ignore[union-attr]
                 scales,
-                parameters[0][0].backsweep,  # type:ignore[index]
                 parameters[0][0].backsweep_period,  # type:ignore[index]
             )
         else:
@@ -147,7 +146,6 @@ def calculate_matrix_gaussian_activation(
                 np.array([p.center for p in parameters]),  # type:ignore[union-attr]
                 np.array([p.width for p in parameters]),  # type:ignore[union-attr]
                 scales,
-                parameters[0].backsweep,  # type:ignore[union-attr]
                 parameters[0].backsweep_period,  # type:ignore[union-attr]
             )
         if activation.normalize:

glotaran/builtin/elements/kinetic/matrix.py

@@ -32,15 +32,14 @@ def calculate_matrix_gaussian_activation_on_index(
     centers: ArrayLike,
     widths: ArrayLike,
     scales: ArrayLike,
-    backsweep: bool,
-    backsweep_period: float | None,
+    backsweep_period: float,
 ):
     """Calculates a decay matrix with a gaussian irf."""
     for n_i in nb.prange(centers.size):
         center, width, scale = centers[n_i], widths[n_i], scales[n_i]
         for n_r in nb.prange(rates.size):
             r_n = rates[n_r]
-            backsweep_valid = backsweep and abs(r_n) * backsweep_period > 0.001
+            backsweep_valid = abs(r_n) * backsweep_period > 0.001
             alpha = (r_n * width) / SQRT2
             for n_t in nb.prange(times.size):
                 t_n = times[n_t]
@@ -52,11 +51,9 @@ def calculate_matrix_gaussian_activation_on_index(
                     matrix[n_t, n_r] += (
                         scale * 0.5 * (1 + erf(thresh)) * np.exp(alpha * (alpha - 2 * beta))
                     )
-                if backsweep and backsweep_valid:
+                if backsweep_valid:
                     x1 = np.exp(-r_n * (t_n - center + backsweep_period))
-                    x2 = np.exp(
-                        -r_n * ((backsweep_period / 2) - (t_n - center))  # type:ignore[operator]
-                    )
+                    x2 = np.exp(-r_n * ((backsweep_period / 2) - (t_n - center)))
                     x3 = np.exp(-r_n * backsweep_period)
                     matrix[n_t, n_r] += scale * (x1 + x2) / (1 - x3)
 
@@ -69,8 +66,7 @@ def calculate_matrix_gaussian_activation(
     all_centers: ArrayLike,
     all_widths: ArrayLike,
     scales: ArrayLike,
-    backsweep: bool,
-    backsweep_period: float | None,
+    backsweep_period: float,
 ):
     for n_w in nb.prange(all_centers.shape[0]):
         calculate_matrix_gaussian_activation_on_index(
@@ -80,6 +76,5 @@ def calculate_matrix_gaussian_activation(
             all_centers[n_w],
             all_widths[n_w],
             scales,
-            backsweep,
             backsweep_period,
         )

glotaran/builtin/items/activation/gaussian.py

@@ -81,7 +81,6 @@ class GaussianActivationParameters:
     center: float
     width: float
     scale: float
-    backsweep: bool
     backsweep_period: float
 
     def shift(self, value: float):
@@ -170,15 +169,13 @@ def parameters(
                 widths = widths * nr_gaussians
 
         scales = self.scale or [1.0] * nr_gaussians
-        backsweep = self.backsweep is not None
         backsweep_period = float(self.backsweep) if self.backsweep is not None else 0
 
         parameters: list[GaussianActivationParameters] = [
             GaussianActivationParameters(
                 float(center),
                 float(width),
                 float(scale),
-                backsweep,
                 backsweep_period,
             )
             for center, width, scale in zip(centers, widths, scales)

tests/builtin/items/activation/test_activation.py

@@ -18,7 +18,6 @@ def test_gaussian_activation():
     )
     parameter = activation.parameters(np.array([0]))
     assert len(parameter) == 1
-    assert parameter[0].backsweep
     assert parameter[0].backsweep_period == 2
     assert parameter[0].center == 1
     assert parameter[0].width == 10
@@ -33,7 +32,7 @@ def test_multi_gaussian_activation():
     )
     parameter = activation.parameters(np.array([0]))
     assert len(parameter) == 2
-    assert not parameter[0].backsweep
+    assert parameter[0].backsweep_period == 0
     assert parameter[0].center == 1
     assert parameter[0].width == 10
     assert parameter[1].center == 2