Merge pull request #72 from golmschenk/infinite_data_points

Infinite data points removal

docs/source/tutorials/crafting_standard_datasets.md

@@ -35,6 +35,7 @@ In the previous section, we only changed the length of that the uniform lengthen
 
 ```python
 def default_light_curve_observation_post_injection_transform(x: LightCurveObservation, length: int, randomize: bool = True) -> (Tensor, Tensor):
+    x = remove_infinite_flux_data_points_from_light_curve_observation(x)
     x = remove_nan_flux_data_points_from_light_curve_observation(x)
     if randomize:
         x = randomly_roll_light_curve_observation(x)

src/qusi/internal/light_curve.py

@@ -48,6 +48,21 @@ def remove_nan_flux_data_points_from_light_curve(light_curve: LightCurve) -> Lig
     return light_curve
 
 
+def remove_infinite_flux_data_points_from_light_curve(light_curve: LightCurve) -> LightCurve:
+    """
+    Removes infinite values from a light curve. If there is an infinite value in either the times or the
+    fluxes, both corresponding values are removed.
+
+    :param light_curve: The light curve.
+    :return: The light curve with infinite values removed.
+    """
+    light_curve = deepcopy(light_curve)
+    infinite_flux_indexes = np.isinf(light_curve.fluxes)
+    light_curve.fluxes = light_curve.fluxes[~infinite_flux_indexes]
+    light_curve.times = light_curve.times[~infinite_flux_indexes]
+    return light_curve
+
+
 def randomly_roll_light_curve(light_curve: LightCurve) -> LightCurve:
     """
     Randomly rolls a light curve. That is, a random position in the light curve is chosen, the light curve

src/qusi/internal/light_curve_dataset.py

@@ -25,12 +25,13 @@
 from qusi.internal.light_curve import (
     LightCurve,
     randomly_roll_light_curve,
-    remove_nan_flux_data_points_from_light_curve,
+    remove_nan_flux_data_points_from_light_curve, remove_infinite_flux_data_points_from_light_curve,
 )
 from qusi.internal.light_curve_observation import (
     LightCurveObservation,
     randomly_roll_light_curve_observation,
     remove_nan_flux_data_points_from_light_curve_observation,
+    remove_infinite_flux_data_points_from_light_curve_observation,
 )
 from qusi.internal.light_curve_transforms import (
     from_light_curve_observation_to_fluxes_array_and_label_array,
@@ -357,6 +358,7 @@ def default_light_curve_observation_post_injection_transform(
     :param randomize: Whether to have randomization in the transforms.
     :return: The transformed light curve observation.
     """
+    x = remove_infinite_flux_data_points_from_light_curve_observation(x)
     x = remove_nan_flux_data_points_from_light_curve_observation(x)
     if randomize:
         x = randomly_roll_light_curve_observation(x)
@@ -382,6 +384,7 @@ def default_light_curve_post_injection_transform(
     :param randomize: Whether to have randomization in the transforms.
     :return: The transformed light curve.
     """
+    x = remove_infinite_flux_data_points_from_light_curve(x)
     x = remove_nan_flux_data_points_from_light_curve(x)
     if randomize:
         x = randomly_roll_light_curve(x)

src/qusi/internal/light_curve_observation.py

@@ -3,7 +3,9 @@
 
 from typing_extensions import Self
 
-from qusi.internal.light_curve import LightCurve, randomly_roll_light_curve, remove_nan_flux_data_points_from_light_curve
+from qusi.internal.light_curve import (LightCurve, randomly_roll_light_curve,
+                                       remove_nan_flux_data_points_from_light_curve,
+                                       remove_infinite_flux_data_points_from_light_curve)
 
 
 @dataclass
@@ -48,6 +50,23 @@ def remove_nan_flux_data_points_from_light_curve_observation(
     return light_curve_observation
 
 
+def remove_infinite_flux_data_points_from_light_curve_observation(
+    light_curve_observation: LightCurveObservation,
+) -> LightCurveObservation:
+    """
+    Removes the inf values from a light curve in a light curve observation. If there is an inf in either the times or the
+    fluxes, both corresponding values are removed.
+
+    :param light_curve_observation: The light curve observation.
+    :return: The light curve observation with inf values removed.
+    """
+    light_curve_observation = deepcopy(light_curve_observation)
+    light_curve_observation.light_curve = remove_infinite_flux_data_points_from_light_curve(
+        light_curve_observation.light_curve
+    )
+    return light_curve_observation
+
+
 def randomly_roll_light_curve_observation(light_curve_observation: LightCurveObservation) -> LightCurveObservation:
     """
     Randomly rolls a light curve observation. That is, a random position in the light curve is chosen, the light curve

src/qusi/transform.py

@@ -1,11 +1,12 @@
 """
 Data transform related public interface.
 """
-from qusi.internal.light_curve import randomly_roll_light_curve, remove_nan_flux_data_points_from_light_curve
+from qusi.internal.light_curve import randomly_roll_light_curve, remove_nan_flux_data_points_from_light_curve, \
+    remove_infinite_flux_data_points_from_light_curve
 from qusi.internal.light_curve_dataset import default_light_curve_post_injection_transform, \
     default_light_curve_observation_post_injection_transform
 from qusi.internal.light_curve_observation import remove_nan_flux_data_points_from_light_curve_observation, \
-    randomly_roll_light_curve_observation
+    randomly_roll_light_curve_observation, remove_infinite_flux_data_points_from_light_curve_observation
 from qusi.internal.light_curve_transforms import from_light_curve_observation_to_fluxes_array_and_label_array, \
     pair_array_to_tensor, make_uniform_length, normalize_tensor_by_modified_z_score
 
@@ -20,4 +21,6 @@
     'randomly_roll_light_curve_observation',
     'remove_nan_flux_data_points_from_light_curve',
     'remove_nan_flux_data_points_from_light_curve_observation',
+    'remove_infinite_flux_data_points_from_light_curve',
+    'remove_infinite_flux_data_points_from_light_curve_observation',
 ]

tests/unit_tests/test_transform.py

@@ -0,0 +1,17 @@
+import numpy as np
+
+from qusi.internal.light_curve import LightCurve, remove_infinite_flux_data_points_from_light_curve
+
+
+def test_remove_infinite_flux_data_points_from_light_curve():
+    times = np.array([0.0, 1.0, 2.0])
+    fluxes = np.array([0.0, np.inf, 20.0])
+    light_curve = LightCurve.new(
+        times=times,
+        fluxes=fluxes,
+    )
+    updated_light_curve = remove_infinite_flux_data_points_from_light_curve(light_curve=light_curve)
+    expected_times = np.array([0.0, 2.0])
+    expected_fluxes = np.array([0.0, 20.0])
+    assert np.array_equal(updated_light_curve.times, expected_times)
+    assert np.array_equal(updated_light_curve.fluxes, expected_fluxes)