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

Author: dmarek-flex

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed output range of `tidy3d.plugins.invdes.FilterAndProject` to be between 0 and 1.
 - Cropped adjoint monitor sizes in 2D simulations to planar geometry intersection.
 - Fixed `Batch.download()` silently succeeding when background downloads fail (e.g., gzip extraction errors).
+- 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/base_sim/data/sim_data.py

@@ -5,7 +5,7 @@
 import pathlib
 from abc import ABC
 from os import PathLike
-from typing import Any, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 import pydantic.v1 as pd
@@ -132,6 +132,40 @@ def _field_component_value(
 
         return field_value
 
+    @staticmethod
+    def _apply_log_scale(
+        field_data: xr.DataArray,
+        vmin: Optional[float] = None,
+        db_factor: float = 1.0,
+    ) -> xr.DataArray:
+        """Prepare field data for log-scale plotting by handling zeros.
+
+        Takes absolute value of the data, replaces zeros with a fill value
+        (to prevent log10(0) warnings), and applies log10 scaling.
+
+        Parameters
+        ----------
+        field_data : xr.DataArray
+            The field data to prepare.
+        vmin : float, optional
+            The minimum value for the color scale. If provided, zeros are replaced
+            with ``10 ** (vmin / db_factor)`` instead of NaN.
+        db_factor : float
+            Factor to multiply the log10 result by (e.g., 20 for dB scale of field,
+            10 for dB scale of power). Default is 1 (pure log10 scale).
+
+        Returns
+        -------
+        xr.DataArray
+            The log-scaled field data.
+        """
+        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)
+        return db_factor * np.log10(field_data)
+
     def get_monitor_by_name(self, name: str) -> AbstractMonitor:
         """Return monitor named 'name'."""
         return self.simulation.get_monitor_by_name(name)

tidy3d/components/data/sim_data.py

@@ -545,7 +545,7 @@ 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))
+            field_data = self._apply_log_scale(field_data, vmin=vmin, db_factor=db_factor)
             field_data.name += " (dB)"
             cmap_type = "sequential"
         elif scale == "lin":