fix: Handling of zero values when using plot_fields with scale=dB

Author: dmarek-flex

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed interpolation handling for permittivity and conductivity gradients in CustomMedium.
 - Restored original batch-load logging by suppressing per-task “Loading simulation…” messages. 
 - Fixed output range of `tidy3d.plugins.invdes.FilterAndProject` to be between 0 and 1.
+- Handling of zero values when using `sim_data.plot_field` with `scale=dB`.
 
 ## [2.10.0] - 2025-12-18
 

tests/test_data/test_sim_data.py

@@ -2,6 +2,8 @@
 
 from __future__ import annotations
 
+import warnings
+
 import matplotlib.pyplot as plt
 import numpy as np
 import pydantic.v1 as pydantic
@@ -624,3 +626,49 @@ def test_plot_field_monitor_data_unsupported_scale():
             val="real",
             scale="invalid",
         )
+
+
+def test_plot_field_with_zeros_db_scale():
+    """Test that plotting field data with zeros using dB scale doesn't produce warnings."""
+    sim_data = make_sim_data()
+
+    # Get the existing field data and modify it to include zeros
+    field_monitor_data = sim_data["field"]
+    ex_data = field_monitor_data.Ex
+
+    # Create modified data with some zeros
+    values = ex_data.values.copy()
+    values[np.abs(values) < np.abs(values).max() * 0.3] = 0  # Set small values to zero
+    ex_with_zeros = ex_data.copy(data=values)
+
+    # Create new field data with zeros
+    field_data_with_zeros = field_monitor_data.updated_copy(Ex=ex_with_zeros)
+    f_sel = ex_data.f.values[0]
+    x_sel = ex_data.x.values[0]
+
+    # Plot with dB scale - this should not produce divide by zero warnings
+    with warnings.catch_warnings():
+        warnings.filterwarnings("error", message="divide by zero")
+        sim_data.plot_field_monitor_data(
+            field_monitor_data=field_data_with_zeros,
+            field_name="Ex",
+            val="abs",
+            scale="dB",
+            f=f_sel,
+            x=x_sel,
+        )
+        plt.close()
+
+    # Also test with vmin specified (zeros replaced with floor value)
+    with warnings.catch_warnings():
+        warnings.filterwarnings("error", message="divide by zero")
+        sim_data.plot_field_monitor_data(
+            field_monitor_data=field_data_with_zeros,
+            field_name="Ex",
+            val="abs",
+            scale="dB",
+            f=f_sel,
+            x=x_sel,
+            vmin=-50,
+        )
+        plt.close()

tidy3d/components/data/sim_data.py

@@ -545,7 +545,13 @@ def plot_field_monitor_data(
                 ("E", "abs^2"): 10,
                 ("H", "abs^2"): 10,
             }.get((field_name[0], val), 20)
-            field_data = db_factor * np.log10(np.abs(field_data))
+            # Replace zeros to prevent log10(0) warnings, preserving NaN values
+            fill_val = np.nan
+            if vmin is not None:
+                fill_val = 10 ** (vmin / db_factor)
+            field_data = np.abs(field_data)
+            field_data = field_data.where((field_data > 0) | np.isnan(field_data), fill_val)
+            field_data = db_factor * np.log10(field_data)
             field_data.name += " (dB)"
             cmap_type = "sequential"
         elif scale == "lin":