k-Wave-python 0.6.0__tar.gz → 0.6.2__tar.gz

k_wave_python-0.6.2/.git

@@ -0,0 +1 @@
+gitdir: /Users/Walter/git/k-wave-python/.git/worktrees/kwave-v0.6.2

k_wave_python-0.6.2/CLAUDE.md

@@ -0,0 +1,95 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## What is k-wave-python?
+
+Python implementation of the [k-Wave](http://www.k-wave.org/) acoustics toolbox for time-domain acoustic and ultrasound simulations. Two backends: a pure Python/NumPy/CuPy solver and C++ binaries (OMP/CUDA).
+
+## Commands
+
+```bash
+# Setup
+uv sync --extra dev --extra test
+uv run pre-commit install
+
+# Run tests
+uv run pytest                              # all tests
+uv run pytest tests/test_kgrid.py          # single file
+uv run pytest tests/test_kgrid.py::test_name  # single test
+uv run pytest -m integration               # MATLAB-reference tests only
+
+# Lint/format
+uv run ruff check . --fix
+uv run ruff format .
+uv run pre-commit run --all-files
+
+# Run an example
+uv run examples/ivp_homogeneous_medium.py
+
+# Build
+uv build
+```
+
+Always use `uv run` (not `uv run python`) for pytest, examples, and scripts.
+
+## Code Style
+
+- Line length: 140 (configured in `pyproject.toml` under `[tool.ruff]`)
+- Pre-commit hooks: ruff (lint + format), codespell, nb-clean
+- Ruff ignores F821 (nested function refs) and F722 (jaxtyping annotations)
+- Type annotations use `beartype` + `jaxtyping`
+
+## Architecture
+
+### Entry point
+
+`kwave/kspaceFirstOrder.py` — `kspaceFirstOrder()` is the unified API. It accepts `kgrid`, `medium`, `source`, `sensor` and dispatches to the appropriate backend.
+
+```
+kspaceFirstOrder(kgrid, medium, source, sensor, backend="python"|"cpp", device="cpu"|"gpu")
+```
+
+### Two backends
+
+- **Python backend** (`kwave/solvers/kspace_solver.py`): `Simulation` class implementing k-space pseudospectral method in NumPy/CuPy. Supports 1D/2D/3D. Uses CuPy for GPU when `device="gpu"`.
+- **C++ backend** (`kwave/solvers/cpp_simulation.py` + `kwave/executor.py`): Serializes to HDF5, invokes compiled C++ binary, reads results back. `save_only=True` writes HDF5 without running (for cluster jobs).
+
+### Core data classes
+
+- `kWaveGrid` (`kwave/kgrid.py`) — domain discretization, spacing, time array
+- `kWaveMedium` (`kwave/kmedium.py`) — sound speed, density, absorption, nonlinearity
+- `kSource` (`kwave/ksource.py`) — pressure/velocity sources with masks and signals
+- `kSensor` (`kwave/ksensor.py`) — sensor mask and recording configuration
+
+### Legacy path
+
+`kspaceFirstOrder2D()` / `kspaceFirstOrder3D()` in their respective files route through `kWaveSimulation` (`kwave/kWaveSimulation.py`) — a large legacy dataclass used by the C++ backend path. New code should use `kspaceFirstOrder()` directly.
+
+### PML handling
+
+When `pml_inside=False` (default), `kspaceFirstOrder()` expands the grid by `2*pml_size` before simulation and strips PML from full-grid output fields afterward. `pml_size="auto"` selects optimal sizes via `get_optimal_pml_size()`.
+
+### Key utilities
+
+- `kwave/utils/pml.py` — PML sizing (`get_pml()`, `get_optimal_pml_size()`)
+- `kwave/utils/mapgen.py` — geometry generators (`make_disc`, `make_ball`, `make_cart_circle`, etc.)
+- `kwave/utils/signals.py` — signal generation (tone bursts, filtering)
+- `kwave/utils/filters.py` — spatial smoothing, Gaussian filters
+- `kwave/utils/io.py` — HDF5 read/write
+- `kwave/utils/conversion.py` — unit conversion, `cart2grid`
+
+## Testing
+
+- Tests in `tests/`, configured via `[tool.pytest.ini_options]` in `pyproject.toml`
+- Integration tests (`@pytest.mark.integration`) compare against MATLAB reference data
+- Test fixtures in `tests/integration/conftest.py`: `load_matlab_ref` (fixture), `assert_fields_close` (helper function for field comparison)
+- MATLAB reference data for `@pytest.mark.integration` tests lives in `tests/matlab_test_data_collectors/python_testers/collectedValues/` (hardcoded in `conftest.py`)
+- `test_example_parity.py` (MATLAB-parity tests) reads `KWAVE_MATLAB_REF_DIR` (defaults to `~/git/k-wave-cupy/tests` if unset)
+
+## Naming Conventions
+
+- `backend="python"` or `"cpp"` (not "native")
+- `device="cpu"` or `"gpu"` (not `use_gpu` bool)
+- `quiet=True` to suppress output; `debug=True` for detailed output
+- `pml_size="auto"` for automatic PML sizing (not a separate boolean)

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: k-Wave-python
-Version: 0.6.0
+Version: 0.6.2
 Summary: Acoustics toolbox for time domain acoustic and ultrasound simulations in complex and tissue-realistic media.
 Project-URL: Homepage, http://www.k-wave.org/
 Project-URL: Documentation, https://waltersimson.com/k-wave-python/
 Project-URL: Repository, https://github.com/waltsims/k-wave-python
 Project-URL: Bug-tracker, https://github.com/waltsims/k-wave-python/issues
-Author-email: Farid Yagubbayli <farid.yagubbayli@tum.de>, Walter Simson <walter.simson@tum.de>
-Maintainer-email: Walter Simson <walter.simson@tum.de>, Farid Yagubbayli <farid.yagubbayli@tum.de>, David Sinden <david.sinden@mevis.fraunhofer.de>
+Author-email: Farid Yagubbayli <farid.yagubbayli@tum.de>, Walter Simson <walter.a.simson@gmail.com>
+Maintainer-email: Walter Simson <walter.a.simson@gmail.com>, Farid Yagubbayli <farid.yagubbayli@tum.de>, David Sinden <david.sinden@mevis.fraunhofer.de>
 License:                    GNU LESSER GENERAL PUBLIC LICENSE
                                Version 3, 29 June 2007
         
@@ -179,30 +179,32 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.10
 Requires-Dist: beartype==0.22.9
-Requires-Dist: deepdiff==8.6.1
+Requires-Dist: deepdiff==9.0.0
 Requires-Dist: deprecated>=1.2.14
-Requires-Dist: h5py==3.15.1
-Requires-Dist: jaxtyping==0.3.2
-Requires-Dist: matplotlib==3.10.7
+Requires-Dist: h5py==3.16.0
+Requires-Dist: jaxtyping==0.3.7
+Requires-Dist: matplotlib==3.10.9
 Requires-Dist: numpy<2.3.0,>=1.22.2
 Requires-Dist: opencv-python==4.13.0.92
 Requires-Dist: scipy==1.15.3
+Requires-Dist: tqdm>=4.60
 Provides-Extra: dev
-Requires-Dist: pre-commit==4.5.1; extra == 'dev'
+Requires-Dist: pre-commit==4.6.0; extra == 'dev'
 Provides-Extra: docs
-Requires-Dist: furo==2024.8.6; extra == 'docs'
+Requires-Dist: furo==2025.12.19; extra == 'docs'
 Requires-Dist: sphinx-copybutton==0.5.2; extra == 'docs'
 Requires-Dist: sphinx-mdinclude==0.6.2; extra == 'docs'
-Requires-Dist: sphinx-tabs==3.4.7; extra == 'docs'
-Requires-Dist: sphinx-toolbox==3.8.0; extra == 'docs'
+Requires-Dist: sphinx-tabs==3.4.5; extra == 'docs'
+Requires-Dist: sphinx-toolbox==4.1.2; extra == 'docs'
+Requires-Dist: sphinx<9; extra == 'docs'
 Provides-Extra: example
-Requires-Dist: gdown==5.2.0; extra == 'example'
+Requires-Dist: gdown==6.0.0; extra == 'example'
 Provides-Extra: test
-Requires-Dist: coverage==7.10.6; extra == 'test'
+Requires-Dist: coverage==7.14.0; extra == 'test'
 Requires-Dist: phantominator; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
 Requires-Dist: pytest-xdist; extra == 'test'
-Requires-Dist: requests==2.32.5; extra == 'test'
+Requires-Dist: requests==2.34.0; extra == 'test'
 Requires-Dist: testfixtures==8.3.0; extra == 'test'
 Description-Content-Type: text/markdown
 
@@ -211,52 +213,42 @@ Description-Content-Type: text/markdown
 [![Support](https://img.shields.io/discord/1234942672418897960?style=flat&logo=discord)](https://discord.gg/your-invite-code)
 [![Documentation Status](https://readthedocs.org/projects/k-wave-python/badge/?version=latest)](https://k-wave-python.readthedocs.io/en/latest/?badge=latest)
 [![codecov](https://codecov.io/gh/waltsims/k-wave-python/graph/badge.svg?token=6ofwtPiDNG)](https://codecov.io/gh/waltsims/k-wave-python)
-[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/waltsims/k-wave-python/master)
 
-This project is a Python implementation of v1.4.0 of the [MATLAB toolbox k-Wave](http://www.k-wave.org/) as well as an
-interface to the pre-compiled v1.3 of k-Wave simulation binaries, which support NVIDIA sm 5.0 (Maxwell) to sm 9.0a (Hopper) GPUs.
-
-**New in v0.6.0:** Unified `kspaceFirstOrder()` API with a pure NumPy/CuPy solver. See the [API guide](https://k-wave-python.readthedocs.io/en/latest/get_started/new_api.html).
+A Python implementation of [k-Wave](http://www.k-wave.org/) — an acoustics toolbox for time-domain simulation of acoustic wave fields. Includes a pure NumPy/CuPy solver (`backend="python"`) and an interface to the pre-compiled k-Wave C++ binaries (`backend="cpp"`) with NVIDIA GPU support (sm 5.0–9.0a).
 
 ## Mission
 
-With this project, we hope to increase the accessibility and reproducibility of [k-Wave](http://www.k-wave.org/) simulations
-for medical imaging, algorithmic prototyping, and testing. Many tools and methods of [k-Wave](http://www.k-wave.org/) can
-be found here, but this project has and will continue to diverge from the original [k-Wave](http://www.k-wave.org/) APIs
-to leverage pythonic practices.
+Increase the accessibility and reproducibility of [k-Wave](http://www.k-wave.org/) simulations for medical imaging, algorithmic prototyping, and testing.
 
 ## Getting started
 
 ![](_static/example_bmode.png)
 
-A large [collection of examples](../examples/) exists to get started with k-wave-python. All examples can be run in Google Colab notebooks with a few clicks. One can begin with e.g. the [B-mode reconstruction example notebook](https://colab.research.google.com/github/waltsims/k-wave-python/blob/HEAD/examples/us_bmode_linear_transducer/us_bmode_linear_transducer.ipynb).
+A [collection of examples](../examples/) covers common simulation scenarios. Run any example locally:
+
+```bash
+uv run examples/ivp_homogeneous_medium.py
+```
 
-This example file steps through the process of:
- 1. Generating a simulation medium
- 2. Configuring a transducer
- 3. Running the simulation
- 4. Reconstructing the simulation
+No GPU required — all examples run on CPU with NumPy.
 
 ## Installation
 
-To install the most recent build of k-Wave-python from PyPI, run:
+Using [uv](https://docs.astral.sh/uv/) (recommended):
+
+```bash
+uv add k-wave-python
+```
+
+Or with pip:
 
 ```bash
 pip install k-wave-python
 ```
-> **Note for MacOS:**
-> 
-> k-wave-python offers initial support for MacOS, but you will need to install the following dependencies using the [brew package manager](https://docs.brew.sh/Installation) along with the Python package:
-> ```bash
-> brew install fftw hdf5 zlib libomp
-> ```
-After installing the Python package, the required binaries will be downloaded and installed the first time you run a
-simulation.
 
 ## Development
 
-If you're enjoying k-Wave-python and want to contribute, development instructions can be
-found [here](https://k-wave-python.readthedocs.io/en/latest/development/development_environment.html).
+Development instructions can be found [here](https://k-wave-python.readthedocs.io/en/latest/development/development_environment.html).
 
 ## Related Projects
 
@@ -273,7 +265,7 @@ The documentation for k-wave-python can be found [here](https://k-wave-python.re
 ## Citation
 ```bibtex
 @software{k-Wave-Python,
-author = {Yagubbbayli, Farid and Sinden, David and Simson, Walter},
+author = {Yagubbayli, Farid and Sinden, David and Simson, Walter},
 license = {GPL-3.0},
 title = {{k-Wave-Python}},
 url = {https://github.com/waltsims/k-wave-python}
@@ -281,4 +273,4 @@ url = {https://github.com/waltsims/k-wave-python}
 ```
 ## Contact
 
-e-mail [wsimson@stanford.edu](mailto:wsimson@stanford.edu).
+e-mail [walter.a.simson@gmail.com](mailto:walter.a.simson@gmail.com).

k_wave_python-0.6.2/docs/README.md

@@ -0,0 +1,66 @@
+# k-wave-python
+
+[![Support](https://img.shields.io/discord/1234942672418897960?style=flat&logo=discord)](https://discord.gg/your-invite-code)
+[![Documentation Status](https://readthedocs.org/projects/k-wave-python/badge/?version=latest)](https://k-wave-python.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/waltsims/k-wave-python/graph/badge.svg?token=6ofwtPiDNG)](https://codecov.io/gh/waltsims/k-wave-python)
+
+A Python implementation of [k-Wave](http://www.k-wave.org/) — an acoustics toolbox for time-domain simulation of acoustic wave fields. Includes a pure NumPy/CuPy solver (`backend="python"`) and an interface to the pre-compiled k-Wave C++ binaries (`backend="cpp"`) with NVIDIA GPU support (sm 5.0–9.0a).
+
+## Mission
+
+Increase the accessibility and reproducibility of [k-Wave](http://www.k-wave.org/) simulations for medical imaging, algorithmic prototyping, and testing.
+
+## Getting started
+
+![](_static/example_bmode.png)
+
+A [collection of examples](../examples/) covers common simulation scenarios. Run any example locally:
+
+```bash
+uv run examples/ivp_homogeneous_medium.py
+```
+
+No GPU required — all examples run on CPU with NumPy.
+
+## Installation
+
+Using [uv](https://docs.astral.sh/uv/) (recommended):
+
+```bash
+uv add k-wave-python
+```
+
+Or with pip:
+
+```bash
+pip install k-wave-python
+```
+
+## Development
+
+Development instructions can be found [here](https://k-wave-python.readthedocs.io/en/latest/development/development_environment.html).
+
+## Related Projects
+
+1. [k-Wave](https://github.com/ucl-bug/k-wave): A MATLAB toolbox for the time-domain simulation of acoustic wave fields.
+2. [j-wave](https://github.com/ucl-bug/jwave): Differentiable acoustic simulations in JAX.
+3. [ADSeismic.jl](https://github.com/kailaix/ADSeismic.jl): a finite difference acoustic simulator with support for AD
+   and JIT compilation in Julia.
+4. [stride](https://github.com/trustimaging/stride): a general optimisation framework for medical ultrasound tomography.
+
+## Documentation
+
+The documentation for k-wave-python can be found [here](https://k-wave-python.readthedocs.io/en/latest/).
+
+## Citation
+```bibtex
+@software{k-Wave-Python,
+author = {Yagubbayli, Farid and Sinden, David and Simson, Walter},
+license = {GPL-3.0},
+title = {{k-Wave-Python}},
+url = {https://github.com/waltsims/k-wave-python}
+}
+```
+## Contact
+
+e-mail [walter.a.simson@gmail.com](mailto:walter.a.simson@gmail.com).

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/__init__.py

@@ -3,23 +3,45 @@ import json
 import logging
 import os
 import platform
+import stat
+import warnings
 from pathlib import Path
 from typing import List
 from urllib.request import urlretrieve
 
 # Test installation with:
 # python3 -m pip install -i https://test.pypi.org/simple/ --extra-index-url=https://pypi.org/simple/ k-Wave-python==0.3.0
-__version__ = "0.6.0"
+__version__ = "0.6.2"
 
 # Constants and Configurations
 URL_BASE = "https://github.com/waltsims/"
-BINARY_VERSION = "v1.3.0"
-PREFIX = f"{URL_BASE}kspaceFirstOrder-{{}}-{{}}/releases/download/{BINARY_VERSION}/"
+BINARY_VERSION = "v1.4.1"
+# Pin both Windows binaries to v1.3.0. v1.4.x windows builds switched compiler /
+# OpenMP / FFT / CUDA runtime stacks and neither v1.4.x release ships its runtime
+# DLLs (cufft, cudart, vcomp, vcruntime140_1, fftw3f, etc.). v1.3.0 binaries are
+# self-contained with their Intel-era DLL bundle (listed in WINDOWS_DLLS below,
+# downloaded with the OMP request and used by both .exe files since they share
+# kwave/bin/windows/). OMP DLL bundling is fixed in kspacefirstorder-unified#14
+# (awaiting validation); CUDA DLL bundling is tracked in kspacefirstorder-unified#17.
+WINDOWS_OMP_VERSION = "v1.3.0"
+WINDOWS_CUDA_VERSION = "v1.3.0"
 PLATFORM = platform.system().lower()
 
 if PLATFORM not in ["linux", "windows", "darwin"]:
     raise NotImplementedError(f"k-wave-python is currently unsupported on this operating system: {PLATFORM}.")
 
+# darwin C++ binary is arm64-only; universal2 coverage tracked for v0.6.5
+DARWIN_BINARY_ARCH = "arm64"
+_darwin_unsupported = PLATFORM == "darwin" and platform.machine() != DARWIN_BINARY_ARCH
+if _darwin_unsupported:
+    warnings.warn(
+        f"k-wave-python's macOS C++ binary is {DARWIN_BINARY_ARCH}-only. "
+        f"Detected {platform.machine()} — the C++ backend (backend='cpp') will not run on this machine. "
+        "Use backend='python' instead. Universal2 (Intel + Apple Silicon) coverage is tracked for v0.6.5.",
+        RuntimeWarning,
+        stacklevel=2,
+    )
+
 # TODO: install directly in to /bin/ directory system directory is no longer needed
 # TODO: deprecate in 0.5.0
 BINARY_PATH = Path(__file__).parent / "bin" / PLATFORM
@@ -44,21 +66,24 @@ ARCHITECTURES = ["omp", "cuda"]
 
 
 def get_windows_release_urls(architecture: str) -> list:
+    version = WINDOWS_OMP_VERSION if architecture == "omp" else WINDOWS_CUDA_VERSION
     specific_filenames = [EXECUTABLE_PREFIX + architecture + ".exe"]
     if architecture == "omp":
         specific_filenames += WINDOWS_DLLS
-    release_urls = [PREFIX.format(architecture.upper(), PLATFORM.lower()) + filename for filename in specific_filenames]
-    return release_urls
+    base = f"{URL_BASE}kspaceFirstOrder-{architecture.upper()}-{PLATFORM.lower()}/releases/download/{version}/"
+    return [base + filename for filename in specific_filenames]
 
 
 URL_DICT = {
     "linux": {
-        "cuda": [URL_BASE + f"kspaceFirstOrder-CUDA-{PLATFORM}/releases/download/v1.3.1/{EXECUTABLE_PREFIX}CUDA"],
+        "cuda": [URL_BASE + f"kspaceFirstOrder-CUDA-{PLATFORM}/releases/download/{BINARY_VERSION}/{EXECUTABLE_PREFIX}CUDA"],
         "omp": [URL_BASE + f"kspaceFirstOrder-OMP-{PLATFORM}/releases/download/{BINARY_VERSION}/{EXECUTABLE_PREFIX}OMP"],
     },
     "darwin": {
         "cuda": [],
-        "omp": [URL_BASE + f"k-wave-omp-{PLATFORM}/releases/download/v0.3.0rc3/{EXECUTABLE_PREFIX}OMP"],
+        "omp": (
+            [] if _darwin_unsupported else [URL_BASE + f"k-wave-omp-{PLATFORM}/releases/download/{BINARY_VERSION}/{EXECUTABLE_PREFIX}OMP"]
+        ),
     },
     "windows": {architecture: get_windows_release_urls(architecture) for architecture in ARCHITECTURES},
 }
@@ -77,6 +102,31 @@ def _hash_file(filepath: str) -> str:
     return md5.hexdigest()
 
 
+def _ensure_executable(binary_filepath) -> None:
+    # Self-heal the executable bit on Linux/macOS. urlretrieve creates files
+    # at 0644, and prior versions of this package didn't fix that up, so users
+    # upgrading with a cached non-executable binary on disk would otherwise
+    # stay stuck (the cache check below returns True and skips re-download).
+    # Any OS-level failure here (broken symlink, read-only FS, wrong ownership,
+    # TOCTOU race) is degraded to a warning so it never aborts `import kwave`.
+    if PLATFORM == "windows":
+        return
+    try:
+        current_mode = os.stat(binary_filepath).st_mode
+        desired_mode = current_mode | stat.S_IXUSR | stat.S_IXGRP | stat.S_IXOTH
+        if current_mode == desired_mode:
+            return
+        os.chmod(binary_filepath, desired_mode)
+    except OSError:  # pragma: no cover - defensive; degrades to warning, never fatal
+        # Don't abort import. The user can chmod +x manually or reinstall
+        # into a writable location.
+        logging.warning(
+            "kwave: cannot set executable bit on %s — backend='cpp' may fail with "
+            "Permission denied. Run `chmod +x` manually or reinstall.",
+            binary_filepath,
+        )
+
+
 def _is_binary_present(binary_name: str, binary_type: str) -> bool:
     binary_filepath = BINARY_PATH / binary_name
     binary_file_exists = os.path.exists(binary_filepath)
@@ -106,6 +156,8 @@ def _is_binary_present(binary_name: str, binary_type: str) -> bool:
     if existing_metadata["url"] not in latest_urls:
         return False
 
+    _ensure_executable(binary_filepath)
+
     # No need to check `version` field for now
     # because we version is already present in the URL
     return True
@@ -176,6 +228,7 @@ def download_binaries(system_os: str, bin_type: str):
         try:
             binary_filepath = os.path.join(BINARY_PATH, filename)
             urlretrieve(url, binary_filepath)
+            _ensure_executable(binary_filepath)
             _record_binary_metadata(binary_version=binary_version, binary_filepath=binary_filepath, binary_url=url, filename=filename)
 
         except TimeoutError:

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/compat.py

@@ -70,5 +70,9 @@ def options_to_kwargs(simulation_options=None, execution_options=None):
             kwargs["num_threads"] = opts.num_threads
         if opts.device_num is not None:
             kwargs["device_num"] = opts.device_num
+        # Read _binary_path directly: the property auto-resolves to a default,
+        # so it can't distinguish a user-set path from one.
+        if opts._binary_path is not None:
+            kwargs["binary_path"] = opts._binary_path
 
     return kwargs

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/enums.py

@@ -1,5 +1,17 @@
 from enum import Enum
 
+
+class AlphaMode(str, Enum):
+    """Controls which absorption/dispersion terms are included in the equation of state."""
+
+    NO_ABSORPTION = "no_absorption"
+    NO_DISPERSION = "no_dispersion"
+    STOKES = "stokes"
+
+    def __str__(self):
+        return self.value
+
+
 ################################################################
 # literals that link the discrete cosine and sine transform types with
 # their type definitions in the functions dtt1D, dtt2D, and dtt3D

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/executor.py

@@ -52,9 +52,16 @@ class Executor:
                     raise subprocess.CalledProcessError(proc.returncode, command, stdout, stderr)
 
         except subprocess.CalledProcessError as e:
-            # This ensures stdout is printed regardless of show_sim_logs value if an error occurs
             print(e.stdout)
             print(e.stderr, file=sys.stderr)
+            if sys.platform == "darwin" and e.stderr and any(s in e.stderr for s in ("Library not loaded", "image not found", "dyld")):
+                print(
+                    "\nMissing macOS libraries for the C++ backend.\n"
+                    "Install them with:\n\n"
+                    "    brew install fftw hdf5 zlib libomp\n\n"
+                    "Alternatively, use backend='python' which requires no extra dependencies.",
+                    file=sys.stderr,
+                )
             raise
 
         sensor_data = self.parse_executable_output(output_filename)

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/kWaveSimulation_helper/create_absorption_variables.py

@@ -12,19 +12,19 @@ def create_absorption_variables(kgrid: kWaveGrid, medium: kWaveMedium, equation_
     # define the lossy derivative operators and proportionality coefficients
     """
     Selects and returns absorption and dispersion operators and coefficients for the given medium based on the equation of state.
-    
+
     Parameters:
         kgrid (kWaveGrid): Grid object providing wavenumber array via `kgrid.k`.
         medium (kWaveMedium): Medium properties used to compute absorption/dispersion coefficients.
         equation_of_state (str): One of `"absorbing"`, `"stokes"`, or `"lossless"` determining which variables to produce.
-    
+
     Returns:
         tuple: (nabla1, nabla2, tau, eta)
             - nabla1: First-order absorption operator or `None` when not applicable.
             - nabla2: Dispersion operator or `None` when not applicable.
             - tau: Absorbing coefficient or `None` when not applicable.
             - eta: Dispersive coefficient or `None` when not applicable.
-    
+
     Behavior:
         - "absorbing": returns (nabla1, nabla2, tau, eta) computed for an absorbing medium.
         - "stokes": returns (None, None, tau, None) where `tau` is the Stokes absorbing coefficient.
@@ -127,4 +127,4 @@ def apply_alpha_filter(medium, nabla1, nabla2):
     # shift the parameters back
     nabla1 = np.fft.ifftshift(nabla1)
     nabla2 = np.fft.ifftshift(nabla2)
-    return nabla1, nabla2
+    return nabla1, nabla2

{k_wave_python-0.6.0 → k_wave_python-0.6.2}/kwave/kgrid.py

@@ -108,7 +108,7 @@ class kWaveGrid(object):
     @t_array.setter
     def t_array(self, t_array):
         # check for 'auto' input
-        if t_array == "auto":
+        if isinstance(t_array, str) and t_array == "auto":
             # set values to auto
             self.Nt = "auto"
             self.dt = "auto"