fullwave25 1.2.6.dev2__py3-none-any.whl → 1.2.6.dev4__py3-none-any.whl

fullwave/__init__.py

@@ -60,7 +60,7 @@ try:
     __version__ = version("fullwave")
 except PackageNotFoundError:
     # Update via bump-my-version, not manually
-    __version__ = "1.2.6-dev2"
+    __version__ = "1.2.6-dev4"
 
 VERSION = __version__  # for convenience
 logger.info("Fullwave version: %s", __version__)

fullwave/beamformer/beamformer.py

@@ -14,7 +14,8 @@ class Beamformer:
     For faster implementations, consider using libraries such as
     mach beamformer: https://github.com/Forest-Neurotech/mach
 
-    References:
+    References
+    ----------
     - Fullwave2 BMME890 implementation
     - https://github.com/gfpinton/fullwave_bmme890/blob/master/fullwave2_launcher_imaging_planewave.m
 

fullwave/medium.py

@@ -231,7 +231,8 @@ class MediumRelaxationMaps:
     ) -> None:
         """Check if the relaxation parameter updates have valid keys and matching shapes.
 
-        Raises:
+        Raises
+        ------
             ValueError: If the keys do not match the desired keys or
             if the shapes of the values do not match the domain shape.
 
@@ -1147,11 +1148,13 @@ class Medium:
         it uses the relaxation parameters look up table
         to generate the relaxation parameters.
 
-        Returns:
+        Returns
+        -------
             MediumRelaxationMaps: An instance of MediumRelaxationMaps
             built from the retrieved relaxation parameters.
 
-        Raises:
+        Raises
+        ------
             ValueError: If an unknown attenuation_builder is specified.
 
         """
@@ -1216,7 +1219,8 @@ class Medium:
     def build_exponential(self) -> MediumExponentialAttenuation:
         """Build MediumExponentialAttenuation from alpha and power maps.
 
-        Returns:
+        Returns
+        -------
             MediumExponentialAttenuation: An instance of MediumExponentialAttenuation
             built from the alpha and power maps.
 

fullwave/sensor.py

@@ -21,7 +21,7 @@ class Sensor:
     outcoords: NDArray[np.int64]
     sampling_modulus_time: int = 1
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         mask: NDArray[np.bool] | None = None,
         sampling_modulus_time: int = 1,
@@ -189,7 +189,8 @@ class Sensor:
     ) -> None:
         """Plot the transducer mask, optionally exporting and displaying the figure.
 
-        Raises:
+        Raises
+        ------
             ValueError: If the sensor is 3D because plotting is not supported.
 
         """

fullwave/solver/cuda_utils.py

@@ -113,7 +113,8 @@ def cuda_api_call(func: Callable) -> Callable:
     Decorator for CUDA API calls
     Raises RuntimeError if the CUDA call does not return CUDA_SUCCESS.
 
-    Returns:
+    Returns
+    -------
         Callable: The wrapped function that checks CUDA API call results.
 
     """
@@ -138,7 +139,8 @@ def cuda_api_call_warn(func: Callable) -> Callable:
 
     Prints a warning message if the CUDA call does not return CUDA_SUCCESS.
 
-    Returns:
+    Returns
+    -------
         Callable: The wrapped function that checks CUDA API call results.
 
     """
@@ -230,7 +232,8 @@ def get_cuda_device_specs() -> list[dict[str, Any]]:
         'cuda_cores': int
     }
 
-    Returns:
+    Returns
+    -------
         A list of dictionaries containing specifications for each CUDA device.
 
     """
@@ -325,7 +328,8 @@ def get_cuda_architecture() -> list[dict[str, Any]]:
         'architecture': str,
     }
 
-    Returns:
+    Returns
+    -------
         A list of dictionaries containing architecture information for each CUDA device.
 
     """
@@ -363,7 +367,8 @@ def get_cuda_architecture() -> list[dict[str, Any]]:
 def retrieve_cuda_version() -> float:
     """Retrieve the CUDA driver version.
 
-    Returns:
+    Returns
+    -------
         str: CUDA version in the format "major.minor" or "unknown" if retrieval fails.
 
     """

fullwave/solver/launcher.py

@@ -31,6 +31,7 @@ class Launcher:
         use_gpu: bool = True,
         cuda_device_id: str | int | list | None = None,
         save_gpu_memory: bool = False,
+        verify_gpu: bool = True,
     ) -> None:
         """Initialize a FullwaveLauncher instance.
 
@@ -62,6 +63,11 @@ class Launcher:
             depending on the hardware and the simulation settings.
             useful in 3D simulations with large grid sizes
             where GPU memory is a limiting factor.
+        verify_gpu : bool, optional
+            Whether to verify that the specified CUDA devices exist on the system.
+            Defaults to True. Set to False when generating input files only
+            (``generate_input_only=True``) on a machine that may not have
+            the target GPUs available.
 
         """
         self._path_fullwave_simulation_bin = path_fullwave_simulation_bin
@@ -69,7 +75,10 @@ class Launcher:
         assert self._path_fullwave_simulation_bin.exists(), error_msg
         self.is_3d = is_3d
         self.use_gpu = use_gpu
-        self.cuda_device_id = self._configure_cuda_device_id(cuda_device_id)
+        self.cuda_device_id = self._configure_cuda_device_id(
+            cuda_device_id,
+            verify_gpu=verify_gpu,
+        )
         self.save_gpu_memory = save_gpu_memory
         logger.debug("Launcher instance created.")
 
@@ -152,13 +161,20 @@ class Launcher:
                 raise ValueError(message)
 
     @staticmethod
-    def _configure_cuda_device_id(cuda_device_id: str | int | list | None) -> str:
+    def _configure_cuda_device_id(
+        cuda_device_id: str | int | list | None,
+        *,
+        verify_gpu: bool = True,
+    ) -> str:
         """Verify and assign the CUDA device ID.
 
         Parameters
         ----------
         cuda_device_id : str | int | None
             The CUDA device ID to verify and assign.
+        verify_gpu : bool, optional
+            Whether to verify that the specified CUDA devices exist.
+            Defaults to True.
 
         Returns
         -------
@@ -167,7 +183,8 @@ class Launcher:
 
         """
         output = Launcher._parse_cuda_device_id(cuda_device_id)
-        Launcher._verify_cuda_devices_exist(output)
+        if verify_gpu:
+            Launcher._verify_cuda_devices_exist(output)
         return output
 
     def run(

fullwave/solver/pml_builder.py

@@ -5,13 +5,11 @@ import logging
 from collections import OrderedDict
 from dataclasses import dataclass, field
 from functools import cached_property
-from itertools import starmap
 from pathlib import Path
 
 import matplotlib.pyplot as plt
 import numexpr as ne
 import numpy as np
-from joblib import Parallel, delayed
 from numpy.typing import NDArray
 
 import fullwave
@@ -115,7 +113,7 @@ class PMLBuilder:
     pml_mask_x: NDArray[np.float64] = field(init=False)
     pml_mask_y: NDArray[np.float64] = field(init=False)
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         grid: fullwave.Grid,
         medium: fullwave.Medium,
@@ -834,21 +832,24 @@ class PMLBuilder:
 
         items = list(rename_dict.items())
 
-        results = Parallel(n_jobs=self.medium_org.n_jobs, backend="threading")(
-            delayed(_compute_one)(
-                key_fw2,
-                key_py,
-                relaxation_param_dict,
-                alpha_target_higher_nu,
-                d_target_higher_nu,
-                alpha_target_pml,
-                d_target_pml,
-                n_polynomial,
-                self.is_3d,
-                self._apply_transition_and_pml,
-            )
-            for key_fw2, key_py in items
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [
+                executor.submit(
+                    _compute_one,
+                    key_fw2,
+                    key_py,
+                    relaxation_param_dict,
+                    alpha_target_higher_nu,
+                    d_target_higher_nu,
+                    alpha_target_pml,
+                    d_target_pml,
+                    n_polynomial,
+                    self.is_3d,
+                    self._apply_transition_and_pml,
+                )
+                for key_fw2, key_py in items
+            ]
+            results = [f.result() for f in futures]
         out_dict = dict(results)
 
         logger.debug("Calculating PML a and b coefficients...")
@@ -876,13 +877,9 @@ class PMLBuilder:
             # Return keys + values so parent can update dict safely
             return (f"a_pml_{axis}{nu}", a, f"b_pml_{axis}{nu}", b)
 
-        results = Parallel(
-            n_jobs=self.medium_org.n_jobs,  # use all cores
-            backend="loky",  # process-based; safe default for Python code
-            prefer="processes",
-        )(
-            starmap(delayed(_worker), tasks),
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [executor.submit(_worker, nu, axis) for nu, axis in tasks]
+            results = [f.result() for f in futures]
 
         for a_key, a_val, b_key, b_val in results:
             out_dict[a_key] = a_val
@@ -898,7 +895,7 @@ class PMLBuilder:
 
         return extended_medium
 
-    def _apply_pml_3d(  # noqa: PLR0915
+    def _apply_pml_3d(
         self,
         extended_medium: fullwave.MediumRelaxationMaps,
         theoritical_reflection_coefficient: float,
@@ -1119,21 +1116,24 @@ class PMLBuilder:
             raise ValueError(error_msg)
 
         items = list(rename_dict.items())
-        results = Parallel(n_jobs=self.medium_org.n_jobs, backend="threading")(
-            delayed(_compute_one)(
-                key_fw2,
-                key_py,
-                relaxation_param_dict,
-                alpha_target_higher_nu,
-                d_target_higher_nu,
-                alpha_target_pml,
-                d_target_pml,
-                n_polynomial,
-                self.is_3d,
-                self._apply_transition_and_pml,
-            )
-            for key_fw2, key_py in items
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [
+                executor.submit(
+                    _compute_one,
+                    key_fw2,
+                    key_py,
+                    relaxation_param_dict,
+                    alpha_target_higher_nu,
+                    d_target_higher_nu,
+                    alpha_target_pml,
+                    d_target_pml,
+                    n_polynomial,
+                    self.is_3d,
+                    self._apply_transition_and_pml,
+                )
+                for key_fw2, key_py in items
+            ]
+            results = [f.result() for f in futures]
         out_dict = dict(results)
 
         logger.debug("Calculating PML a and b coefficients...")
@@ -1162,13 +1162,9 @@ class PMLBuilder:
             # Return keys + values so parent can update dict safely
             return (f"a_pml_{axis}{nu}", a, f"b_pml_{axis}{nu}", b)
 
-        results = Parallel(
-            n_jobs=self.medium_org.n_jobs,  # use all cores
-            backend="loky",  # process-based; safe default for Python code
-            prefer="processes",
-        )(
-            starmap(delayed(_worker), tasks),
-        )
+        with concurrent.futures.ThreadPoolExecutor() as executor:
+            futures = [executor.submit(_worker, nu, axis) for nu, axis in tasks]
+            results = [f.result() for f in futures]
 
         for a_key, a_val, b_key, b_val in results:
             out_dict[a_key] = a_val
@@ -1184,7 +1180,7 @@ class PMLBuilder:
 
         return extended_medium
 
-    def _apply_transition_and_pml(  # noqa: C901, PLR0912, PLR0915
+    def _apply_transition_and_pml(  # noqa: PLR0912
         self,
         input_array: NDArray[np.float64],
         value_target: float,
@@ -1465,7 +1461,7 @@ class PMLBuilder:
 class PMLBuilderExponentialAttenuation(PMLBuilder):
     """A class to set up PML for exponential attenuation media."""
 
-    def __init__(  # noqa: PLR0915
+    def __init__(
         self,
         grid: fullwave.Grid,
         medium: fullwave.Medium,

fullwave/solver/solver.py

@@ -309,7 +309,7 @@ class Solver:
     generates the required input files, and runs the simulation executable.
     """
 
-    def __init__(  # noqa: PLR0912, PLR0915, C901
+    def __init__(  # noqa: PLR0912
         self,
         work_dir: Path,
         grid: fullwave.Grid,
@@ -329,6 +329,7 @@ class Solver:
         use_isotropic_relaxation: bool = True,
         cuda_device_id: str | int | list | None = None,
         save_gpu_memory: bool = False,
+        verify_gpu: bool = True,
     ) -> None:
         """Initialize a Solver instance for the fullwave simulation.
 
@@ -415,6 +416,11 @@ class Solver:
             depending on the hardware and the simulation settings.
             useful in 3D simulations with large grid sizes
             where GPU memory is a limiting factor.
+        verify_gpu : bool, optional
+            Whether to verify that the specified CUDA devices exist on the system.
+            Defaults to True. Set to False when generating input files only
+            (``generate_input_only=True``) on a machine that may not have
+            the target GPUs available.
 
         Raises
         ------
@@ -555,6 +561,7 @@ class Solver:
             use_gpu=self.use_gpu,
             cuda_device_id=self.cuda_device_id,
             save_gpu_memory=self.save_gpu_memory,
+            verify_gpu=verify_gpu,
         )
 
         if use_exponential_attenuation:
@@ -758,6 +765,7 @@ class Solver:
         release_after_write: bool = False,
         highpass_cutoff_mhz: float | None = None,
         bandpass_cutoff_mhz: tuple[float, float] | None = None,
+        gpu_memory_estimate: bool = False,
     ) -> NDArray[np.float64] | Path:
         r"""Run the fullwave simulation and return the result as a NumPy array.
 
@@ -829,6 +837,9 @@ class Solver:
             Uses cosine (Hann) tapers on both edges.
             Cannot be combined with ``highpass_cutoff_mhz``.
             Requires ``load_results=True``.  Default is ``None`` (no filtering).
+        gpu_memory_estimate : bool
+            Whether to estimate GPU memory usage before running the simulation.
+            Default is True. If True, it estimates the GPU memory usage.
 
         Returns
         -------
@@ -937,6 +948,9 @@ class Solver:
         )
         logger.debug(message)
 
+        if gpu_memory_estimate:
+            self._estimate_gpu_memory(sensor)
+
         if generate_input_only:
             logger.info(
                 "Input data generation completed in %s. Skipping simulation execution.",
@@ -975,6 +989,250 @@ class Solver:
         # which is a list of file names
         return sim_result
 
+    def _estimate_gpu_memory(
+        self,
+        sensor: fullwave.Sensor,
+    ) -> None:
+        """Estimate and log GPU memory usage per device.
+
+        Provides a pre-launch estimate so users can verify that the simulation
+        fits in GPU memory before the binary starts allocating.
+
+        Parameters
+        ----------
+        sensor : fullwave.Sensor
+            The sensor that will actually be written to the input files (may
+            differ from ``self.sensor`` when ``record_whole_domain=True``).
+
+        """
+        # show that this is an experimental feature
+        logger.info("Estimating GPU memory usage... (experimental feature, may be inaccurate)")
+        device_ids = self.fullwave_launcher.cuda_device_id.split(",")
+        n_gpus = len(device_ids)
+
+        grid = self.pml_builder.extended_grid
+        source = self.pml_builder.extended_source
+        medium = self.pml_builder.extended_medium
+
+        depth = grid.nx
+        lateral = grid.ny * grid.nz if self.is_3d else grid.ny
+        halo_depth = 8
+
+        float_bytes = 4
+        int_bytes = 4
+
+        c_map = medium.sound_speed
+        c_range = int(np.rint(c_map.max()) - np.rint(c_map.min()))
+        n_deriv_levels = 1 if c_range == 0 else c_range + 1
+
+        n_source_timesteps = source.icmat.shape[1]
+
+        gb = 1024.0**3
+
+        base_depth = depth // n_gpus
+        remainder = depth % n_gpus
+
+        for rank, dev_id in enumerate(device_ids):
+            depth_this = base_depth + (1 if rank < remainder else 0)
+
+            if n_gpus == 1:
+                n_halo_sides = 0
+            elif rank == 0 or rank == n_gpus - 1:
+                n_halo_sides = 1
+            else:
+                n_halo_sides = 2
+            local_depth = depth_this + n_halo_sides * halo_depth
+            slab = local_depth * lateral
+
+            n_sources = max(source.n_sources // n_gpus, 0)
+            n_sensors = max(sensor.n_sensors // n_gpus, 0)
+            n_air_local = max(medium.n_air // n_gpus, 0)
+
+            if self.use_exponential_attenuation:
+                total = self._mem_exponential(
+                    slab,
+                    n_deriv_levels,
+                    n_sources,
+                    n_source_timesteps,
+                    save_gpu_memory=self.save_gpu_memory,
+                    n_sensors=n_sensors,
+                    float_bytes=float_bytes,
+                    int_bytes=int_bytes,
+                    is_3d=self.is_3d,
+                )
+            else:
+                total = self._mem_relaxation(
+                    slab,
+                    n_deriv_levels,
+                    n_sources,
+                    n_source_timesteps,
+                    save_gpu_memory=self.save_gpu_memory,
+                    n_air=n_air_local,
+                    n_sensors=n_sensors,
+                    n_relax=self.n_relax_mechanisms,
+                    float_bytes=float_bytes,
+                    int_bytes=int_bytes,
+                    is_3d=self.is_3d,
+                )
+
+            mode = "exponential" if self.use_exponential_attenuation else "relaxation"
+            saving = ", save_gpu_memory=True" if self.save_gpu_memory else ""
+            logger.info(
+                "GPU memory estimate [GPU %s] (%s mode%s): "
+                "%.2f GB  (depth=%d +%d halo, lateral=%d)",
+                dev_id.strip(),
+                mode,
+                saving,
+                total / gb,
+                depth_this,
+                n_halo_sides * halo_depth,
+                lateral,
+            )
+
+    @staticmethod
+    def _mem_exponential(
+        slab: int,
+        n_deriv_levels: int,
+        n_sources: int,
+        n_source_timesteps: int,
+        *,
+        save_gpu_memory: bool,
+        n_sensors: int,
+        float_bytes: int,
+        int_bytes: int,
+        is_3d: bool,
+    ) -> int:
+        """Return estimated GPU bytes for exponential-attenuation solver.
+
+        Parameters
+        ----------
+        slab : int
+            Grid points per GPU slab (local_depth * lateral).
+        n_deriv_levels : int
+            Number of derivative-map levels.
+        n_sources : int
+            Approximate source count on this GPU.
+        n_source_timesteps : int
+            Number of source time steps.
+        save_gpu_memory : bool
+            Whether memory-saving mode is active.
+        n_sensors : int
+            Approximate sensor count on this GPU.
+        float_bytes : int
+            Bytes per float (4).
+        int_bytes : int
+            Bytes per int (4).
+        is_3d: bool,
+            Whether the simulation is 3D (affects sensor memory).
+
+        Returns
+        -------
+        int
+            Total estimated bytes.
+
+        """
+        fb = float_bytes
+        ib = int_bytes
+        ndim = 3 if is_3d else 2
+        n_fields = 4 if is_3d else 3  # p, u, [v], w
+
+        # wave fields: n_fields pairs x 2 time levels
+        mem = n_fields * 2 * slab * fb
+        # material: rho + K + beta + a_exp
+        mem += 4 * slab * fb
+        # derivative maps (dmap + dcmap)
+        mem += 9 * 2 * n_deriv_levels * fb + slab * ib
+        # source (icmat + coords)
+        if n_sources > 0:
+            mem += n_sources * fb if save_gpu_memory else n_sources * n_source_timesteps * fb
+            mem += ndim * n_sources * ib
+        # sensor (genoutframe + coordsout_local + p_idx_array)
+        if n_sensors > 0:
+            mem += n_sensors * fb
+            mem += (ndim + 1) * n_sensors * ib
+            mem += n_sensors * ib
+        return mem
+
+    @staticmethod
+    def _mem_relaxation(
+        slab: int,
+        n_deriv_levels: int,
+        n_sources: int,
+        n_source_timesteps: int,
+        *,
+        save_gpu_memory: bool,
+        n_air: int,
+        n_sensors: int,
+        n_relax: int,
+        float_bytes: int,
+        int_bytes: int,
+        is_3d: bool,
+    ) -> int:
+        """Return estimated GPU bytes for relaxation (power-law) solver.
+
+        Parameters
+        ----------
+        slab : int
+            Grid points per GPU slab (local_depth * lateral).
+        n_deriv_levels : int
+            Number of derivative-map levels.
+        n_sources : int
+            Approximate source count on this GPU.
+        n_source_timesteps : int
+            Number of source time steps.
+        save_gpu_memory : bool
+            Whether memory-saving mode is active.
+        n_air : int
+            Number of zero-pressure (air) coordinates on this GPU.
+        n_sensors : int
+            Approximate sensor count on this GPU.
+        n_relax : int
+            Number of relaxation mechanisms.
+        float_bytes : int
+            Bytes per float (4).
+        int_bytes : int
+            Bytes per int (4).
+        is_3d: bool,
+            Whether the simulation is 3D (affects sensor memory).
+
+        Returns
+        -------
+        int
+            Total estimated bytes.
+
+        """
+        fb = float_bytes
+        ib = int_bytes
+        ndim = 3 if is_3d else 2
+        n_fields = 4 if is_3d else 3  # p, u, [v], w
+
+        # wave fields: n_fields pairs x 2 time levels
+        mem = n_fields * 2 * slab * fb
+        # relaxation psi:
+        mem += 2 * (ndim * n_relax * 2 * slab * fb)
+        # material: rho + K + beta
+        mem += 3 * slab * fb
+        # kappa: 2 arrays (kappa_x1, kappa_x2)
+        mem += 2 * slab * fb
+        # PML: pml_x1 + pml_x2, each has 2 * n_relax arrays
+        mem += 2 * (2 * n_relax) * slab * fb
+        # (dmap + dcmap)
+        mem += 9 * 2 * n_deriv_levels * fb + slab * ib
+        # source (icmat + coords)
+        if n_sources > 0:
+            mem += n_sources * fb if save_gpu_memory else n_sources * n_source_timesteps * fb
+            mem += ndim * n_sources * ib
+
+        # air
+        if n_air > 0:
+            mem += ndim * n_air * ib
+        # sensor
+        if n_sensors > 0:
+            mem += n_sensors * fb
+            mem += (ndim + 1) * n_sensors * ib
+            mem += n_sensors * ib
+        return mem
+
     def print_info(self) -> None:
         """Print the Solver instance information."""
         print(str(self))

fullwave/solver/utils.py

@@ -17,10 +17,12 @@ def load_dat_data(dat_file_path: Path, dtype: DTypeLike = np.float32) -> NDArray
         dat_file_path (Path): Path to the .dat file.
         dtype: Data type to use when reading the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if dat_file_path does not exist.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
     """
@@ -58,7 +60,8 @@ def load_dat_and_reshape(
         n_sensors: Number of sensors
         dtype: Data type to use when reading the file.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
     """
@@ -88,7 +91,8 @@ def initialize_relaxation_param_dict(
 ) -> dict[str, NDArray[np.float64]]:
     """Initialize a dictionary with relaxation parameters.
 
-    Returns:
+    Returns
+    -------
         dict[str, NDArray[np.float64]]: Dictionary of relaxation parameters.
 
     """
@@ -125,10 +129,12 @@ def load_data_with_time_step(
         dtype: Data type to use when reading the file.
         time_step: Time step index to load.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if file_path does not exist.
 
     """
@@ -159,10 +165,12 @@ def load_data_with_sensor_index(
         sensor_index: Sensor index to load.
         dtype: Data type to use when reading the file.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.float64]: Array of data read from the file.
 
-    Raises:
+    Raises
+    ------
         ValueError: if file_path does not exist.
 
     """

fullwave/source.py

@@ -30,7 +30,7 @@ class Source:
     w0: NDArray[np.float64] | None = None
     incoords_w: NDArray[np.int64] | None = None
 
-    def __init__(  # noqa: C901 PLR0912 PLR0915
+    def __init__(  # noqa: PLR0912
         self,
         p0: NDArray[np.float64] | None = None,
         mask: NDArray[np.bool] | None = None,

fullwave/transducer.py

@@ -22,7 +22,8 @@ logger = logging.getLogger("__main__." + __name__)
 def _make_pos_int(val: float | tuple[float] | tuple[int]) -> NDArray[np.int64]:
     """Force value to be a positive integer.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: Array with positive integers.
 
     """
@@ -202,7 +203,7 @@ class TransducerGeometry:
         ) = self._create_element_coords()
         logger.debug("TransducerGeometry instance created.")
 
-    def _init_dimensions(  # noqa: C901, PLR0912
+    def _init_dimensions(  # noqa: PLR0912
         self,
         grid: Grid,
         element_width_px: int | None,
@@ -313,7 +314,7 @@ class TransducerGeometry:
             assert len(position_m) == 3, "position_m must have 3 elements for 3D transducer"
         return position_px, position_m
 
-    def _create_element_coords(  # noqa: PLR0912, PLR0915
+    def _create_element_coords(  # noqa: PLR0912
         self,
     ) -> tuple[NDArray[np.int64], NDArray[np.int64], NDArray[np.int64], NDArray[np.int64]]:
         """Build flat coordinate arrays for source and sensor pixels.
@@ -813,15 +814,15 @@ class Transducer:
     def source_coords(self) -> NDArray[np.int64]:
         """Coordinates of active source pixels; shape [N_src, ndim]."""
         active_ids = np.where(self.active_source_elements)[0] + 1
-        mask = np.isin(self.transducer_geometry._source_ids, active_ids)  # noqa: SLF001
-        return self.transducer_geometry._source_coords[mask]  # noqa: SLF001
+        mask = np.isin(self.transducer_geometry._source_ids, active_ids)
+        return self.transducer_geometry._source_coords[mask]
 
     @property
     def sensor_coords(self) -> NDArray[np.int64]:
         """Coordinates of active sensor pixels; shape [N_snsr, ndim]."""
         active_ids = np.where(self.active_sensor_elements)[0] + 1
-        mask = np.isin(self.transducer_geometry._sensor_ids, active_ids)  # noqa: SLF001
-        return self.transducer_geometry._sensor_coords[mask]  # noqa: SLF001
+        mask = np.isin(self.transducer_geometry._sensor_ids, active_ids)
+        return self.transducer_geometry._sensor_coords[mask]
 
     @property
     def element_id_to_element_surface(self) -> dict[int, NDArray[np.int64]]:
@@ -986,8 +987,8 @@ class Transducer:
     @property
     def element_id_to_element_center(self) -> dict[int, NDArray[np.int64]]:
         """Return the dictionary mapping element IDs to their center coordinates."""
-        coords = self.transducer_geometry._source_coords  # noqa: SLF001
-        ids = self.transducer_geometry._source_ids  # noqa: SLF001
+        coords = self.transducer_geometry._source_coords
+        ids = self.transducer_geometry._source_ids
         n = self.transducer_geometry.number_elements
         ndim = coords.shape[1] if len(coords) else (3 if self.is_3d else 2)
         out: dict[int, NDArray[np.int64]] = {}
@@ -1049,7 +1050,7 @@ class Transducer:
 
         it plots whole transducer geometry including the inactive/active source and sensor elements.
         """
-        import matplotlib.pyplot as plt
+        import matplotlib.pyplot as plt  # noqa: PLC0415
 
         fig, ax = plt.subplots(1, 1, figsize=(10, 10))
         plot_mask = np.zeros(self.transducer_geometry.stored_grid_size)
@@ -1089,7 +1090,7 @@ class Transducer:
 
         it plots whole transducer geometry including the inactive/active source and sensor elements.
         """
-        import matplotlib.pyplot as plt
+        import matplotlib.pyplot as plt  # noqa: PLC0415
 
         fig, ax = plt.subplots(1, 1, figsize=(10, 10))
         plot_mask = np.zeros(self.transducer_geometry.stored_grid_size)

fullwave/utils/check_functions.py

@@ -7,7 +7,8 @@ from typing import Any
 def check_instance(target_var: Any, instances: list[Any] | Any) -> None:  # noqa: ANN401
     """Check whether target_var is an instance of the specified type.
 
-    Raises:
+    Raises
+    ------
         TypeError: If target_var is not an instance of instance.
 
     """
@@ -21,7 +22,8 @@ def check_instance(target_var: Any, instances: list[Any] | Any) -> None:  # noqa
 def check_path_exists(target_path: Path) -> None:
     """Check whether the provided target_path exists.
 
-    Raises:
+    Raises
+    ------
         ValueError: If target_path does not exist.
 
     """
@@ -37,7 +39,8 @@ def check_compatible_value(
 ) -> None:
     """Check whether the provided value is in the list of compatible values.
 
-    Raises:
+    Raises
+    ------
         ValueError: If value is not in compatible_values.
 
     """

fullwave/utils/coordinates.py

@@ -16,7 +16,8 @@ def make_circle_idx(
         cen: The center of the circle.
         rad: The radius of the circle.
 
-    Returns:
+    Returns
+    -------
         mask: The mask of the circle.
 
     """
@@ -32,7 +33,8 @@ def map_to_coords(
 ) -> NDArray[np.int64]:
     """Map the mask map to coordinates.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """
@@ -103,7 +105,8 @@ def map_to_coords_with_sort(map_data: NDArray[np.int64]) -> NDArray[np.int64]:
     Args:
         map_data: The mask map.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """
@@ -124,7 +127,8 @@ def map_to_coordinates(
         is_3d: Whether the grid is 3D or not.
         sort: Whether to sort the coordinates by the first dimension.
 
-    Returns:
+    Returns
+    -------
         NDArray[np.int64]: An array of coordinates corresponding to non-zero elements in the mask.
 
     """

fullwave/utils/memory_tempfile.py

@@ -31,7 +31,7 @@ class MemoryTempfile:
     and create temporary files and directories.
     """
 
-    def __init__(  # noqa: C901, PLR0912
+    def __init__(  # noqa: PLR0912
         self,
         *,
         preferred_paths: list | None = None,
@@ -182,7 +182,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> str:
         """Create a temporary directory.
 
@@ -207,7 +207,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
         *,
         text: bool = False,
     ) -> tuple[int, str]:
@@ -241,7 +241,7 @@ class MemoryTempfile:
         self,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.TemporaryDirectory[str]:
         """Create a temporary directory and return a TemporaryDirectory object.
 
@@ -275,7 +275,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.SpooledTemporaryFile:
         """Create a spooled temporary file.
 
@@ -329,7 +329,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
         *,
         delete: bool = True,
     ) -> tempfile.NamedTemporaryFile:
@@ -379,7 +379,7 @@ class MemoryTempfile:
         newline: str | None = None,
         suffix: str | None = None,
         prefix: str | None = None,
-        dir: str | None = None,  # noqa: A002
+        dir: str | None = None,
     ) -> tempfile.TemporaryFile:
         """Create and return a temporary file.
 

fullwave/utils/plot_utils.py

@@ -13,7 +13,7 @@ from numpy.typing import NDArray
 from tqdm import tqdm
 
 
-def plot_array(  # noqa: C901, D417, PLR0912
+def plot_array(  # noqa: PLR0912
     x: NDArray[np.float64 | np.int64 | np.bool],
     aspect: float | None = None,
     vmin: float | None = None,
@@ -553,7 +553,7 @@ def plot_wave_propagation_animation(
     animation_data.save(export_name, writer="ffmpeg", dpi=dpi)
 
 
-def plot_wave_propagation_with_map(  # noqa: PLR0915, C901
+def plot_wave_propagation_with_map(
     propagation_map: NDArray[np.float64],
     c_map: NDArray[np.float64],
     rho_map: NDArray[np.float64],
@@ -868,7 +868,7 @@ def plot_wave_propagation_with_map(  # noqa: PLR0915, C901
     plt.close("all")
 
 
-def plot_wave_propagation_snapshot(  # noqa: PLR0915
+def plot_wave_propagation_snapshot(
     propagation_map: NDArray[np.float64],
     c_map: NDArray[np.float64],
     rho_map: NDArray[np.float64],

fullwave/utils/signal_filter.py

@@ -25,7 +25,7 @@ def _check_cupy() -> bool:
     global _CUPY_AVAILABLE  # noqa: PLW0603
     if _CUPY_AVAILABLE is None:
         try:
-            import cupy  # noqa: F401
+            import cupy  # noqa: F401, PLC0415
 
             _CUPY_AVAILABLE = True
         except ImportError:
@@ -145,7 +145,7 @@ def apply_filter(
     )
 
     if use_gpu and _check_cupy():
-        import cupy as cp
+        import cupy as cp  # noqa: PLC0415
 
         logger.debug("apply_filter: using CuPy GPU backend")
         data_gpu = cp.asarray(data, dtype=cp.float64)

{fullwave25-1.2.6.dev2.dist-info → fullwave25-1.2.6.dev4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fullwave25
-Version: 1.2.6.dev2
+Version: 1.2.6.dev4
 Summary: Fullwave 2.5: Ultrasound wave propagation simulation with heterogeneous power law attenuation modelling capabilities
 Author: Masashi Sode, Gianmarco Pinton
 Maintainer: Masashi Sode
@@ -13,7 +13,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Physics
 Requires-Python: >=3.10
-Requires-Dist: joblib>=1.5.3
 Requires-Dist: matplotlib>=3.10.7
 Requires-Dist: numba>=0.63.1
 Requires-Dist: numexpr>=2.14.1

{fullwave25-1.2.6.dev2.dist-info → fullwave25-1.2.6.dev4.dist-info}/RECORD

@@ -1,11 +1,11 @@
-fullwave/__init__.py,sha256=N4GYVSocXju_a_cRIHpvcD7NZLZncFlAEoBefisiHd8,1780
+fullwave/__init__.py,sha256=Wb8_IQQeLRrptNyonXRvriurzqUtnqV92_E4kr3MU4c,1780
 fullwave/grid.py,sha256=YbxAAgdYKR8AXwobtTZzHm9C4KR4D5--51zgbs0aQGY,7435
-fullwave/medium.py,sha256=NPg3NxLhR6roeroHM32lv-7rk0CALIExHrhSXpHh9MI,48302
-fullwave/sensor.py,sha256=q9T3_u8YS6b3Awo-FVqt-QYF05GFBhxqPO2OaL7Mvho,9311
-fullwave/source.py,sha256=dPh03qSh_-ASpmlC0HDFJGaolact2IP_wniXUoG6rUI,18758
-fullwave/transducer.py,sha256=LFS4tulRSwzU2R8FAvgif7oDSzirRsiXVm4wvqKoW50,48592
+fullwave/medium.py,sha256=A3EoRNs1CM9gB2MISWp5n0ikRDEk9uQqEO6YSdp12jQ,48360
+fullwave/sensor.py,sha256=McHyaSKxM11_Kfb_2hfnOtV9Z1UMBCLkeovncLT8_bA,9308
+fullwave/source.py,sha256=gFitSme70CHecVVik31_Fv7Md7PEZ_4zGsKYohDivz4,18745
+fullwave/transducer.py,sha256=uC9EcKJVpP9gTqKKLrq30sKizT1fhaRVDQcAuhuS9RI,48526
 fullwave/beamformer/__init__.py,sha256=tNPq_5lfLXfAdueyfQtdTxLTVEV6nEDkeSGAeTf7Q5s,88
-fullwave/beamformer/beamformer.py,sha256=cZzZDy3dS9YVUKA-O8TZAOqmlaziIAvXJTNVBkqUJf4,5587
+fullwave/beamformer/beamformer.py,sha256=0jE_B5UlxDDBsUcQSHa5d1q3uSTSCyqgNiUJrU10juI,5601
 fullwave/constants/__init__.py,sha256=WOmkhLsSe86D71gwKsa4Tz8QPeOdayLGgvBCh7UEOPk,104
 fullwave/constants/material_properties.py,sha256=SouMKD4ONzYl0VU8ZsC2I_85y-ZLj9scRNwAArCD7bg,2729
 fullwave/medium_builder/__init__.py,sha256=QVz0sA4niq51O94RnXUVlHutx7FYEIa1TRcR5fDc_Ps,201
@@ -21,12 +21,12 @@ fullwave/medium_builder/presets/data/.keep,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5
 fullwave/medium_builder/presets/data/abdominal_wall/i2365f_etfw1.mat,sha256=N3JFFxc9HW1S-NaTPcPlFgXWGIzlrr9X40JbDapTo4g,67348
 fullwave/solver/__init__.py,sha256=E0Jg5akBpicqTjku1puw9rAIoKiw7TwtYNDPiv8G5IY,30
 fullwave/solver/binary_manager.py,sha256=oz3WLUX2m0HHXCVaI8tBokDyHEUZcERzdCJWErE6Ig8,5011
-fullwave/solver/cuda_utils.py,sha256=iWa_6bicQwSsKGyp47hfAlyGBRZAGfN-sg2frzrQaVU,11352
+fullwave/solver/cuda_utils.py,sha256=n7p3TJYbLAXmIzSMS5Q_8m4OWg5U9VG5_3hAxa0uTYI,11407
 fullwave/solver/input_file_writer.py,sha256=7wE86-ZnxwLhRw2adXUC8yAB3p9iH92E0t0Ew8q_lDQ,44617
-fullwave/solver/launcher.py,sha256=CsXSzcb7qphUeBAN8hGoFKuAYQO94_h__aoE_pJFgSE,9911
-fullwave/solver/pml_builder.py,sha256=hsjY1_uHLmb4KTGWGLzw0YPXT8q9zkZ53HEDzZqZFJs,70673
-fullwave/solver/solver.py,sha256=44SrAdojKEXCv9F9Z-PfAmTArjOBXkxG4dmrWNqu3Ro,41220
-fullwave/solver/utils.py,sha256=3lota1TDzwAo5kxlrvy30CEnSEyVe4Iqxnh4bpCBHiw,5389
+fullwave/solver/launcher.py,sha256=zh-3HY4iKGmjreALu9WczDpWX3d74nOcIns9xVvnUIg,10531
+fullwave/solver/pml_builder.py,sha256=gtkZjXG8ujvC0HMFjJ9RLaURQqjZKelLsj6FNE35P5k,70706
+fullwave/solver/solver.py,sha256=Ziz7fOF_tq7ygv5MRhc2zULexcFK3Ft-raZl6JvwEcA,49836
+fullwave/solver/utils.py,sha256=vM8Nwe4JFscb1hpkGoQHydsxC5_Xt93XQMmEOk5hVFg,5474
 fullwave/solver/bins/_gpu/2d/num_relax=2/fullwave2_2d_2_relax_multi_gpu_cuda118,sha256=bIzyHFzr_bsIBSlCcRA3M9LlTSRrBVn6ASJHyozvcwU,1245432
 fullwave/solver/bins/_gpu/2d/num_relax=2/fullwave2_2d_2_relax_multi_gpu_cuda124,sha256=NiYCmOzZIcvAzR7-Mjs3PtUzZGd31jSVQB1IT9nQrLU,1416160
 fullwave/solver/bins/_gpu/2d/num_relax=2/fullwave2_2d_2_relax_multi_gpu_cuda129,sha256=TkyC8OqvFzRoSa_0XRWPmnlDBjPf8tG5NJaGQVFy_PY,1779992
@@ -37,17 +37,17 @@ fullwave/solver/bins/_gpu/3d/num_relax=2/fullwave2_3d_2_relax_multi_gpu_cuda129,
 fullwave/solver/bins/_gpu/3d/num_relax=2/fullwave2_3d_2_relax_multi_gpu_cuda130,sha256=8hzQfyodLl070a7nM-QCmv7ygijLMgRNvZxNOisRYSA,1571848
 fullwave/solver/bins/database/relaxation_params_database_num_relax=2_20260113_0957.mat,sha256=Fei5ie9wgAAN43pIdSFf6xVaPPDgOaBBZodi3qK6WtQ,168056
 fullwave/utils/__init__.py,sha256=yz_pbPte2XrSofb16mdqLmUxr2rXUE7FIzOjCT9y1IE,461
-fullwave/utils/check_functions.py,sha256=ezpwLvTSpriIfguvoWvdiVKjZxMy1m9diP6XZWDIL5E,1484
-fullwave/utils/coordinates.py,sha256=iIfvfrTQ1DA_WG6o2DbCtrjOY3wk076pKOmv7KsLIBs,4358
-fullwave/utils/memory_tempfile.py,sha256=5mBbIYDQ4lCt08HnQHsGy2Df5VWJa_6fDMyxIhPfw7U,14440
+fullwave/utils/check_functions.py,sha256=benZqFjOQF7aaQDTBGaOq-eplJ-dC8Dz4jcqPE-9HSk,1514
+fullwave/utils/coordinates.py,sha256=TEVQE9JXUIVFoKEyg8ZZMeGh31elbpecHnDgbljHQ14,4402
+fullwave/utils/memory_tempfile.py,sha256=BzMRNvINzLYdtV8NcSNjrTr2F9Qow8vYl1o7RUXFWH8,14350
 fullwave/utils/numerical.py,sha256=khdi2KE3y_Ky9cEnmGXvVHjeYuKfb-8gQTV1a8nx9uA,3260
-fullwave/utils/plot_utils.py,sha256=PuOTYljHh5DeM6r6Bg_kh1gofa8OVtctKCX2k48Q2ho,37257
+fullwave/utils/plot_utils.py,sha256=wXR6YMnlO0tCUeKoAELKRyi5K_kepKIBqLjlFSRKito,37205
 fullwave/utils/pulse.py,sha256=aqnCdBxivACouIGlot1aE2k4V9nctUxNCEPzdBpsupg,2811
 fullwave/utils/relaxation_parameters.py,sha256=DEHjr67eHGR-DqEaNsQViokseIsDywtjBjB1DvF4-OM,14106
 fullwave/utils/scatterer.py,sha256=CLqD085f9pqX4cF1YiT2IkzT5P0o1xp45Do7lf5BLnM,24049
-fullwave/utils/signal_filter.py,sha256=ZxnOXup8iQ-xFzVduvDNiPsq_3BvX6fQrqrHn7FTTdU,5193
+fullwave/utils/signal_filter.py,sha256=_Tf42aBygGtIUrcSPybYqvZoAW2o_4dd-hHTEvZ8--E,5219
 fullwave/utils/signal_process.py,sha256=MP38r37JSPHN4sT-lIReXS5BT2GT_tkRxD0Y1wQ-lNs,5153
-fullwave25-1.2.6.dev2.dist-info/METADATA,sha256=Q4yUUXQOVVVeqmz0ZOOLWuvEq_8WEcK584Y2ZMp4LUM,19027
-fullwave25-1.2.6.dev2.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
-fullwave25-1.2.6.dev2.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
-fullwave25-1.2.6.dev2.dist-info/RECORD,,
+fullwave25-1.2.6.dev4.dist-info/METADATA,sha256=b2tSzbymlgrVigxYrdeWk8pvQ31Tzv9ZIGTQlNWW4Ac,18998
+fullwave25-1.2.6.dev4.dist-info/WHEEL,sha256=QccIxa26bgl1E6uMy58deGWi-0aeIkkangHcxk2kWfw,87
+fullwave25-1.2.6.dev4.dist-info/licenses/LICENSE,sha256=46mU2C5kSwOnkqkw9XQAJlhBL2JAf1_uCD8lVcXyMRg,7652
+fullwave25-1.2.6.dev4.dist-info/RECORD,,