fullwave25 1.2.6.dev1__tar.gz → 1.2.6.dev2__tar.gz

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/.bumpversion.toml

@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.2.6-dev1"
+current_version = "1.2.6-dev2"
 parse = """(?x)
     (?P<major>0|[1-9]\\d*)\\.
     (?P<minor>0|[1-9]\\d*)\\.

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fullwave25
-Version: 1.2.6.dev1
+Version: 1.2.6.dev2
 Summary: Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities
 Author: Masashi Sode, Gianmarco Pinton
 Maintainer: Masashi Sode

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/fullwave/__init__.py

@@ -60,7 +60,7 @@ try:
     __version__ = version("fullwave")
 except PackageNotFoundError:
     # Update via bump-my-version, not manually
-    __version__ = "1.2.6-dev1"
+    __version__ = "1.2.6-dev2"
 
 VERSION = __version__  # for convenience
 logger.info("Fullwave version: %s", __version__)

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/fullwave/solver/solver.py

@@ -15,6 +15,7 @@ from fullwave.utils import (
     MemoryTempfile,
     check_functions,
 )
+from fullwave.utils.signal_filter import apply_filter
 
 from .binary_manager import ensure_binary
 from .cuda_utils import get_cuda_architecture, retrieve_cuda_version
@@ -638,6 +639,80 @@ class Solver:
         error_msg = f"{path_fullwave_simulation_bin} does not exist"
         assert path_fullwave_simulation_bin.exists(), error_msg
 
+    @staticmethod
+    def _validate_filter_params(
+        highpass_cutoff_mhz: float | None,
+        bandpass_cutoff_mhz: tuple[float, float] | None,
+        *,
+        load_results: bool,
+    ) -> None:
+        """Validate high-pass / band-pass filter arguments passed to run().
+
+        Raises
+        ------
+        ValueError
+            If both filter options are set simultaneously, or if a filter is
+            requested without ``load_results=True``.
+
+        """
+        if highpass_cutoff_mhz is not None and bandpass_cutoff_mhz is not None:
+            error_msg = (
+                "highpass_cutoff_mhz and bandpass_cutoff_mhz cannot both be specified. "
+                "Use highpass_cutoff_mhz for a simple high-pass filter or "
+                "bandpass_cutoff_mhz for a band-pass filter."
+            )
+            logger.error(error_msg)
+            raise ValueError(error_msg)
+        if (highpass_cutoff_mhz is not None or bandpass_cutoff_mhz is not None) and (
+            not load_results
+        ):
+            error_msg = (
+                "Filtering requires load_results=True. "
+                "Set load_results=True or disable the filter options."
+            )
+            logger.error(error_msg)
+            raise ValueError(error_msg)
+
+    @staticmethod
+    def _apply_output_filter(
+        result: NDArray[np.float64],
+        dt: float,
+        highpass_cutoff_mhz: float | None,
+        bandpass_cutoff_mhz: tuple[float, float] | None,
+    ) -> NDArray[np.float64]:
+        """Apply the optional frequency filter to the reshaped sensor output.
+
+        Parameters
+        ----------
+        result : NDArray[np.float64]
+            Sensor data shaped ``[n_sensors, n_t]``.
+        dt : float
+            Grid time step in seconds.
+        highpass_cutoff_mhz : float | None
+            High-pass edge in MHz, or ``None``.
+        bandpass_cutoff_mhz : tuple[float, float] | None
+            ``(f_low_mhz, f_high_mhz)`` band-pass edges, or ``None``.
+
+        Returns
+        -------
+        NDArray[np.float64]
+            Filtered (or unchanged) sensor data.
+
+        """
+        if highpass_cutoff_mhz is not None:
+            logger.info("Applying high-pass filter at %.4g MHz...", highpass_cutoff_mhz)
+            return apply_filter(result, dt, f_low_hz=highpass_cutoff_mhz * 1e6)
+        if bandpass_cutoff_mhz is not None:
+            f_low_hz = bandpass_cutoff_mhz[0] * 1e6
+            f_high_hz = bandpass_cutoff_mhz[1] * 1e6
+            logger.info(
+                "Applying band-pass filter %.4g-%.4g MHz...",
+                bandpass_cutoff_mhz[0],
+                bandpass_cutoff_mhz[1],
+            )
+            return apply_filter(result, dt, f_low_hz=f_low_hz, f_high_hz=f_high_hz)
+        return result
+
     @staticmethod
     def _reshape_sensor_data(
         raw_sensor_output: NDArray[np.float64],
@@ -681,6 +756,8 @@ class Solver:
         load_results: bool = True,
         generate_input_only: bool = False,
         release_after_write: bool = False,
+        highpass_cutoff_mhz: float | None = None,
+        bandpass_cutoff_mhz: tuple[float, float] | None = None,
     ) -> NDArray[np.float64] | Path:
         r"""Run the fullwave simulation and return the result as a NumPy array.
 
@@ -740,6 +817,18 @@ class Solver:
             If True, the memory used by the input files will be released after writing them to disk.
             This is useful when run_on_memory is True to free up memory space for the simulation
             or when the input files are large. Default is False.
+        highpass_cutoff_mhz : float | None
+            Apply a high-pass filter to the sensor recordings after the simulation.
+            Removes low-frequency PML drift by attenuating frequencies below this value (in MHz).
+            Uses a cosine (Hann) taper to avoid Gibbs ringing.
+            Cannot be combined with ``bandpass_cutoff_mhz``.
+            Requires ``load_results=True``.  Default is ``None`` (no filtering).
+        bandpass_cutoff_mhz : tuple[float, float] | None
+            Apply a band-pass filter ``(f_low_mhz, f_high_mhz)`` to the sensor recordings
+            after the simulation.  Retains only frequencies inside the specified band.
+            Uses cosine (Hann) tapers on both edges.
+            Cannot be combined with ``highpass_cutoff_mhz``.
+            Requires ``load_results=True``.  Default is ``None`` (no filtering).
 
         Returns
         -------
@@ -757,6 +846,8 @@ class Solver:
             Static map simulations require input files to be stored on a disk.
             run_on_memory, on the other hand, removes the input files
             after the simulation is complete.
+            Also raised if both ``highpass_cutoff_mhz`` and ``bandpass_cutoff_mhz`` are given,
+            or if either filter option is set but ``load_results=False``.
 
         """
         # self._save_data_for_beamforming()
@@ -778,6 +869,12 @@ class Solver:
             logger.error(error_msg)
             raise ValueError(error_msg)
 
+        self._validate_filter_params(
+            highpass_cutoff_mhz,
+            bandpass_cutoff_mhz,
+            load_results=load_results,
+        )
+
         start_time = time.time()
         extended_medium = self.pml_builder.run(use_pml=self.use_pml)
         end_pml_builder_time = time.time()
@@ -867,7 +964,13 @@ class Solver:
                 f"{end_loading_time - start_loading_time:.2e} seconds."
             )
             logger.info(message)
-            return result
+
+            return self._apply_output_filter(
+                result,
+                self.grid.dt,
+                highpass_cutoff_mhz,
+                bandpass_cutoff_mhz,
+            )
         # if load_results is False, return the raw result
         # which is a list of file names
         return sim_result

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/fullwave/utils/__init__.py

@@ -1,6 +1,6 @@
 """misc utils for fullwave package."""
 
-from . import pulse, relaxation_parameters, signal_process
+from . import pulse, relaxation_parameters, signal_filter, signal_process
 from .memory_tempfile import MemoryTempfile
 from .scatterer import (
     generate_resolution_based_scatterer,
@@ -14,5 +14,6 @@ __all__ = [
     "generate_scatterer",
     "pulse",
     "relaxation_parameters",
+    "signal_filter",
     "signal_process",
 ]

fullwave25-1.2.6.dev2/fullwave/utils/signal_filter.py

@@ -0,0 +1,161 @@
+"""FFT-based frequency-domain filtering for sensor data.
+
+GPU backend: CuPy when available; falls back silently to NumPy.
+No new hard dependencies — CuPy is already listed under the ``examples`` optional extra.
+"""
+
+from __future__ import annotations
+
+import logging
+from typing import TYPE_CHECKING
+
+import numpy as np
+
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
+logger = logging.getLogger("__main__." + __name__)
+
+# Module-level cache to avoid repeated import overhead
+_CUPY_AVAILABLE: bool | None = None
+
+
+def _check_cupy() -> bool:
+    """Return True if CuPy is importable; result is cached after the first call."""
+    global _CUPY_AVAILABLE  # noqa: PLW0603
+    if _CUPY_AVAILABLE is None:
+        try:
+            import cupy  # noqa: F401
+
+            _CUPY_AVAILABLE = True
+        except ImportError:
+            _CUPY_AVAILABLE = False
+    return _CUPY_AVAILABLE
+
+
+def _build_frequency_mask(
+    n_fft: int,
+    dt: float,
+    f_low_hz: float | None = None,
+    f_high_hz: float | None = None,
+    taper_ratio: float = 0.1,
+) -> NDArray[np.float64]:
+    """Build a frequency-domain gain mask with cosine (Hann) tapers.
+
+    Parameters
+    ----------
+    n_fft : int
+        FFT length (number of time samples before zero-padding, i.e. ``n_t``).
+    dt : float
+        Simulation time step in seconds.
+    f_low_hz : float | None
+        High-pass cut-off frequency in Hz.  Frequencies below this value are
+        attenuated.  The mask transitions smoothly from 0 to 1 in a window of
+        width ``f_low_hz * taper_ratio`` centred at ``f_low_hz``.
+    f_high_hz : float | None
+        Low-pass cut-off frequency in Hz.  Frequencies above this value are
+        attenuated.  The mask transitions smoothly from 1 to 0 in a window of
+        width ``f_high_hz * taper_ratio`` centred at ``f_high_hz``.
+    taper_ratio : float
+        Fractional width of each cosine taper relative to its centre frequency.
+        Default is 0.1 (10 %).
+
+    Returns
+    -------
+    NDArray[np.float64]
+        Frequency-domain gain mask of shape ``[n_fft // 2 + 1]``.
+
+    """
+    freqs = np.fft.rfftfreq(n_fft, d=dt)
+    mask = np.ones(len(freqs), dtype=np.float64)
+
+    if f_low_hz is not None:
+        half_width = f_low_hz * taper_ratio / 2.0
+        f_start = f_low_hz - half_width
+        f_end = f_low_hz + half_width
+        width = f_end - f_start  # == f_low_hz * taper_ratio
+
+        in_taper = (freqs >= f_start) & (freqs <= f_end)
+        below_taper = freqs < f_start
+
+        mask[below_taper] = 0.0
+        mask[in_taper] = 0.5 * (1.0 - np.cos(np.pi * (freqs[in_taper] - f_start) / width))
+
+    if f_high_hz is not None:
+        half_width = f_high_hz * taper_ratio / 2.0
+        f_start = f_high_hz - half_width
+        f_end = f_high_hz + half_width
+        width = f_end - f_start  # == f_high_hz * taper_ratio
+
+        in_taper = (freqs >= f_start) & (freqs <= f_end)
+        above_taper = freqs > f_end
+
+        lp_taper = np.ones(len(freqs), dtype=np.float64)
+        lp_taper[in_taper] = 0.5 * (1.0 + np.cos(np.pi * (freqs[in_taper] - f_start) / width))
+        lp_taper[above_taper] = 0.0
+        mask *= lp_taper
+
+    return mask
+
+
+def apply_filter(
+    data: NDArray[np.float64],
+    dt: float,
+    f_low_hz: float | None = None,
+    f_high_hz: float | None = None,
+    taper_ratio: float = 0.1,
+    *,
+    use_gpu: bool = True,
+) -> NDArray[np.float64]:
+    """Apply a frequency-domain filter to sensor data.
+
+    The filter is built as a cosine-tapered gain mask (see :func:`_build_frequency_mask`).
+    When CuPy is available and ``use_gpu=True``, the FFT operations run on the GPU
+    for maximum throughput; otherwise NumPy is used transparently.
+
+    Parameters
+    ----------
+    data : NDArray[np.float64]
+        Sensor time traces, shape ``[n_sensors, n_t]``.
+    dt : float
+        Simulation time step in seconds.
+    f_low_hz : float | None
+        High-pass edge frequency in Hz.  Pass ``None`` to skip high-passing.
+    f_high_hz : float | None
+        Low-pass edge frequency in Hz.  Pass ``None`` to skip low-passing.
+    taper_ratio : float
+        Fractional taper width relative to each cut-off frequency.  Default 0.1.
+    use_gpu : bool
+        If ``True`` (default), attempt to use CuPy for GPU-accelerated FFTs.
+        Falls back to NumPy silently if CuPy is unavailable.
+
+    Returns
+    -------
+    NDArray[np.float64]
+        Filtered data, same shape as ``data``.
+
+    """
+    n_t = data.shape[1]
+    mask = _build_frequency_mask(
+        n_t,
+        dt,
+        f_low_hz=f_low_hz,
+        f_high_hz=f_high_hz,
+        taper_ratio=taper_ratio,
+    )
+
+    if use_gpu and _check_cupy():
+        import cupy as cp
+
+        logger.debug("apply_filter: using CuPy GPU backend")
+        data_gpu = cp.asarray(data, dtype=cp.float64)
+        mask_gpu = cp.asarray(mask, dtype=cp.float64)
+        spec = cp.fft.rfft(data_gpu, axis=1)
+        spec *= mask_gpu[cp.newaxis, :]
+        filtered = cp.fft.irfft(spec, n=n_t, axis=1)
+        return cp.asnumpy(filtered)
+
+    logger.debug("apply_filter: using NumPy CPU backend")
+    spec = np.fft.rfft(data, axis=1)
+    spec *= mask[np.newaxis, :]
+    return np.fft.irfft(spec, n=n_t, axis=1)

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fullwave25"
-version = "1.2.6-dev1" # Update via bump-my-version, not manually
+version = "1.2.6-dev2" # Update via bump-my-version, not manually
 description = "Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities"
 readme = "README.md"
 requires-python = ">=3.10"

{fullwave25-1.2.6.dev1 → fullwave25-1.2.6.dev2}/uv.lock

@@ -735,7 +735,7 @@ wheels = [
 
 [[package]]
 name = "fullwave25"
-version = "1.2.6.dev1"
+version = "1.2.6.dev2"
 source = { editable = "." }
 dependencies = [
     { name = "joblib" },