k-Wave-python 0.2.1__tar.gz → 0.3.1__tar.gz

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/.gitignore

@@ -14,4 +14,10 @@ kwave/bin/linux
 *.mat
 examples/__pycache__/
 src/
+.vscode/
+*.asv
 *.h5
+*.tar.gz
+*.whl
+*.png
+*.pyc

k_wave_python-0.3.1/.pre-commit-config.yaml

@@ -0,0 +1,23 @@
+repos:
+- repo: https://github.com/srstevenson/nb-clean.git
+  rev: 3.2.0
+  hooks:
+  - id: nb-clean
+    name: nb-clean
+    entry: nb-clean clean
+    language: python
+    types_or: [jupyter]
+    minimum_pre_commit_version: 2.9.2
+# - repo: https://github.com/pre-commit/pre-commit-hooks
+#   rev: v4.5.0  # Use the ref you want to point at
+#   hooks:
+#   -   id: trailing-whitespace
+# - repo: https://github.com/nbQA-dev/nbQA
+#   rev: 1.7.1
+#   hooks:
+#   - id: nbqa-ruff
+#     name: nbqa-ruff
+#     entry: nbqa ruff
+#     language: python
+#     types_or: [jupyter]
+#     minimum_pre_commit_version: 2.9.2

k_wave_python-0.3.1/.pytest_cache/v/cache/lastfailed

@@ -0,0 +1 @@
+{}

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/.pytest_cache/v/cache/nodeids

@@ -1,60 +1,34 @@
 [
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/cart2grid_test.py::test_cart2grid",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/expandMatrix_test.py::test_expand_matrix_test",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/fourierShift_test.py::test_fourier_shift",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/gaussianFilter_test.py::test_gaussianFilter",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/getColorMap_test.py::test_get_color_map",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/getWin_test.py::test_get_win",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_writeGrid",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_attributes",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_flags",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_matrix",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeArc_test.py::test_makeArc",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeBall_test.py::test_makeBall",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeBowl_test.py::test_makeBowl",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeCartCircle_test.py::test_makeCartCircle",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeCartSphere_test.py::test_makeCartSphere",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeCircle_test.py::test_makeCircle",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeDisc_test.py::test_makeDisc",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeLine_test.py::test_makeLine",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeMultiArc_test.py::test_makeMultiArc",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeMultiBowl_test.py::test_makeMultiBowl",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeSphere_test.py::test_makeSphere",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/makeSphericalSection_test.py::test_makeSphericalSection",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/maxND_test.py::test_maxND",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/minND_test.py::test_minND",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/reorderBinarySensorData_test.py::test_binary_sensor_data",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/reorderSensorData_test.py::test_reorderSensorData",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/revolve2D_test.py::test_revolve2D",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/scaleSI_test.py::test_scale_si",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/scaleTime_test.py::test_scale_time",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/scanConversion_test.py::test_scanConversion",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/test_interpcartdata.py::test_interpcartdata",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/test_resize.py::test_resize",
-  "tests/k-wave-python/tests/matlab_test_data_collectors/python_testers/unmaskSensorData_test.py::test_unmask_sensor_data",
   "tests/matlab_test_data_collectors/python_testers/angularSpectrumCW_test.py::test_angular_spectrum_cw",
   "tests/matlab_test_data_collectors/python_testers/angularSpectrum_test.py::test_angular_spectrum",
   "tests/matlab_test_data_collectors/python_testers/attenComp_test.py::test_atten_comp",
   "tests/matlab_test_data_collectors/python_testers/cart2grid_test.py::test_cart2grid",
+  "tests/matlab_test_data_collectors/python_testers/computeLinearTransform_test.py::test_compute_linear_transform",
   "tests/matlab_test_data_collectors/python_testers/create_cw_signals_test.py::test_create_cw_signals",
   "tests/matlab_test_data_collectors/python_testers/expandMatrix_test.py::test_expand_matrix_test",
+  "tests/matlab_test_data_collectors/python_testers/focusBowlONeil_test.py::test_focused_bowl_oneil",
   "tests/matlab_test_data_collectors/python_testers/fourierShift_test.py::test_fourier_shift",
   "tests/matlab_test_data_collectors/python_testers/gaussianFilter_test.py::test_gaussianFilter",
   "tests/matlab_test_data_collectors/python_testers/gaussian_test.py::test_gaussian",
+  "tests/matlab_test_data_collectors/python_testers/getAffineMatrix_test.py::test_get_affine_matrix",
   "tests/matlab_test_data_collectors/python_testers/getColorMap_test.py::test_get_color_map",
+  "tests/matlab_test_data_collectors/python_testers/getDeltaBLI_test.py::test_get_delta_bli",
   "tests/matlab_test_data_collectors/python_testers/getWin_test.py::test_get_win",
-  "tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_writeGrid",
   "tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_attributes",
   "tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_flags",
   "tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_grid",
   "tests/matlab_test_data_collectors/python_testers/h5io_test.py::test_write_matrix",
-  "tests/matlab_test_data_collectors/python_testers/kWaveGrid_test.py::test_get_color_map",
+  "tests/matlab_test_data_collectors/python_testers/kWaveArray_test.py::test_kwave_array",
   "tests/matlab_test_data_collectors/python_testers/kWaveGrid_test.py::test_kwave_grid",
   "tests/matlab_test_data_collectors/python_testers/makeArc_test.py::test_makeArc",
   "tests/matlab_test_data_collectors/python_testers/makeBall_test.py::test_makeBall",
   "tests/matlab_test_data_collectors/python_testers/makeBowl_test.py::test_makeBowl",
+  "tests/matlab_test_data_collectors/python_testers/makeCartArc_test.py::test_makeCartArc",
+  "tests/matlab_test_data_collectors/python_testers/makeCartBowl_test.py::test_make_cart_bowl",
   "tests/matlab_test_data_collectors/python_testers/makeCartCircle_test.py::test_makeCartCircle",
+  "tests/matlab_test_data_collectors/python_testers/makeCartRect_test.py::test_make_cart_rect",
   "tests/matlab_test_data_collectors/python_testers/makeCartSphere_test.py::test_makeCartSphere",
+  "tests/matlab_test_data_collectors/python_testers/makeCartSphericalSegment_test.py::test_make_cart_spherical_segments",
   "tests/matlab_test_data_collectors/python_testers/makeCircle_test.py::test_makeCircle",
   "tests/matlab_test_data_collectors/python_testers/makeDisc_test.py::test_makeDisc",
   "tests/matlab_test_data_collectors/python_testers/makeLine_test.py::test_makeLine",
@@ -65,40 +39,27 @@
   "tests/matlab_test_data_collectors/python_testers/maxND_test.py::test_maxND",
   "tests/matlab_test_data_collectors/python_testers/minND_test.py::test_minND",
   "tests/matlab_test_data_collectors/python_testers/reorderBinarySensorData_test.py::test_binary_sensor_data",
-  "tests/matlab_test_data_collectors/python_testers/reorderSensorData_test.py::test_reorderSensorData",
   "tests/matlab_test_data_collectors/python_testers/reorderSensorData_test.py::test_reorder_sensor_data",
   "tests/matlab_test_data_collectors/python_testers/revolve2D_test.py::test_revolve2D",
   "tests/matlab_test_data_collectors/python_testers/scaleSI_test.py::test_scale_si",
   "tests/matlab_test_data_collectors/python_testers/scaleTime_test.py::test_scale_time",
   "tests/matlab_test_data_collectors/python_testers/scanConversion_test.py::test_scanConversion",
-  "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_brenner",
   "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_brenner2d",
   "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_brenner3d",
   "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_normvar",
-  "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_tannenbaum",
-  "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_tennenbaum",
   "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_tennenbaum2d",
   "tests/matlab_test_data_collectors/python_testers/sharpness_test.py::test_tennenbaum3d",
-  "tests/matlab_test_data_collectors/python_testers/smooth_test.py::test_brenner2d",
-  "tests/matlab_test_data_collectors/python_testers/smooth_test.py::test_brenner3d",
-  "tests/matlab_test_data_collectors/python_testers/smooth_test.py::test_normvar",
   "tests/matlab_test_data_collectors/python_testers/smooth_test.py::test_smooth",
-  "tests/matlab_test_data_collectors/python_testers/smooth_test.py::test_tennenbaum3d",
   "tests/matlab_test_data_collectors/python_testers/test_interpcartdata.py::test_interpcartdata",
+  "tests/matlab_test_data_collectors/python_testers/test_make_cart_disc.py::test_make_cart_disc",
   "tests/matlab_test_data_collectors/python_testers/test_resize.py::test_resize",
-  "tests/matlab_test_data_collectors/python_testers/test_resize.py::test_revolve2D",
   "tests/matlab_test_data_collectors/python_testers/toneBurst_test.py::test_tone_burst",
+  "tests/matlab_test_data_collectors/python_testers/trimCartPoints_test.py::test_trim_cart_points",
   "tests/matlab_test_data_collectors/python_testers/unmaskSensorData_test.py::test_unmask_sensor_data",
-  "tests/matlab_test_data_collectors/python_testers/writeMatrix_test.py::test_writeAttributes",
-  "tests/matlab_test_data_collectors/python_testers/writeMatrix_test.py::test_writeFlags",
-  "tests/matlab_test_data_collectors/python_testers/writeMatrix_test.py::test_writeGrid",
-  "tests/matlab_test_data_collectors/python_testers/writeMatrix_test.py::test_writeMatrix",
   "tests/test_binary_present.py::test_linux_afp_binaries_present",
-  "tests/test_binary_present.py::test_linux_binaries_present",
   "tests/test_binary_present.py::test_linux_cuda_binaries_present",
   "tests/test_binary_present.py::test_linux_omp_binaries_present",
   "tests/test_binary_present.py::test_windows_afp_binaries_present",
-  "tests/test_binary_present.py::test_windows_binaries_present",
   "tests/test_binary_present.py::test_windows_cuda_binaries_present",
   "tests/test_binary_present.py::test_windows_cufft6410_binaries_present",
   "tests/test_binary_present.py::test_windows_cufft64_binaries_present",
@@ -115,17 +76,8 @@
   "tests/test_cpp_io_in_parts.py::test_cpp_io_in_parts",
   "tests/test_cpp_running_simulations.py::test_cpp_running_simulations",
   "tests/test_executor.py::TestExecutor::test_system_call_correct",
-  "tests/test_filterutils.py::test_brenner_sharpness2",
-  "tests/test_filterutils.py::test_brenner_sharpness3",
-  "tests/test_filterutils.py::test_create_cw_signals",
   "tests/test_filterutils.py::test_envelope_detection",
   "tests/test_filterutils.py::test_fwhm",
-  "tests/test_filterutils.py::test_gaussian",
-  "tests/test_filterutils.py::test_gaussian_filter",
-  "tests/test_filterutils.py::test_norm_var_sharpness",
-  "tests/test_filterutils.py::test_smooth",
-  "tests/test_filterutils.py::test_tannenbaum_sharpness2",
-  "tests/test_filterutils.py::test_tannenbaum_sharpness3",
   "tests/test_ivp_3D_simulation.py::test_ivp_3D_simulation",
   "tests/test_ivp_axisymmetric_simulation.py::test_ivp_axisymmetric_simulation",
   "tests/test_ivp_binary_sensor_mask.py::test_ivp_binary_sensor_mask",
@@ -139,24 +91,20 @@
   "tests/test_kutils.py::test_check_stability",
   "tests/test_kutils.py::test_focus",
   "tests/test_kutils.py::test_get_alpha_filters_1D",
-  "tests/test_kutils.py::test_get_alpha_filters_2D",
   "tests/test_kutils.py::test_get_alpha_filters_2d",
+  "tests/test_kutils.py::test_make_time",
   "tests/test_kutils.py::test_prime_factors",
   "tests/test_misc.py::test_find_closest",
-  "tests/test_misc.py::test_focused_bowl_oneil",
   "tests/test_misc.py::test_round_even_down",
   "tests/test_misc.py::test_round_even_up",
   "tests/test_misc.py::test_round_odd_down",
   "tests/test_misc.py::test_round_odd_up",
-  "tests/test_na_controlling_the_PML.py::test_na_controlling_the_PML",
   "tests/test_na_controlling_the_PML.py::test_na_controlling_the_pml",
   "tests/test_na_optimising_performance.py::test_na_optimising_performance",
-  "tests/test_pmlutils.py::test_get_optimal_pml_size_1D",
   "tests/test_pmlutils.py::test_get_optimal_pml_size_1d",
   "tests/test_pmlutils.py::test_get_optimal_pml_size_2D",
   "tests/test_pmlutils.py::test_get_optimal_pml_size_3D",
   "tests/test_pr_2D_FFT_line_sensor.py::test_pr_2D_FFT_line_sensor",
-  "tests/test_pr_2D_TR_circular_sensor.py::test_pr_2D_TR_circular_sensor",
   "tests/test_pr_2D_TR_circular_sensor.py::test_pr_2d_tr_circular_sensor",
   "tests/test_pr_2D_TR_directional_sensors.py::test_pr_2D_TR_directional_sensors",
   "tests/test_pr_2D_TR_line_sensor.py::test_pr_2D_TR_line_sensor",
@@ -166,7 +114,6 @@
   "tests/test_sd_directional_array_elements.py::test_sd_directional_array_elements",
   "tests/test_sd_directivity_modelling_2D.py::test_sd_directivity_modelling_2D",
   "tests/test_sd_directivity_modelling_3D.py::test_sd_directivity_modelling_3D",
-  "tests/test_sd_focussed_detector_2D.py::test_sd_focussed_detector_2D",
   "tests/test_sd_focussed_detector_2D.py::test_sd_focussed_detector_2d",
   "tests/test_sd_sensor_directivity_2D.py::test_sd_sensor_directivity_2D",
   "tests/test_tvsp_3D_simulation.py::test_tvsp_3D_simulation",
@@ -179,7 +126,6 @@
   "tests/test_us_defining_transducer.py::test_us_defining_transducer",
   "tests/test_us_transducer_as_sensor.py::test_us_transducer_as_sensor",
   "tests/test_utils.py::test_add_noise",
-  "tests/test_utils.py::test_add_noise_peak",
   "tests/test_utils.py::test_apply_filter_bandpass",
   "tests/test_utils.py::test_apply_filter_highpass",
   "tests/test_utils.py::test_apply_filter_lowpass",
@@ -194,16 +140,6 @@
   "tests/test_utils.py::test_gradient_spacing_ndim",
   "tests/test_utils.py::test_gradient_spect_1D",
   "tests/test_utils.py::test_gradient_spect_2D",
-  "tests/test_utils.py::test_grid2cart",
-  "tests/test_utils.py::test_grid2cart_1D",
-  "tests/test_utils.py::test_grid2cart_2D",
-  "tests/test_utils.py::test_grid2cart_3D",
-  "tests/test_utils.py::test_hounsfield2soundspeed",
-  "tests/test_utils.py::test_interpCartData",
-  "tests/test_utils.py::test_interp_cart_data",
-  "tests/test_utils.py::test_interpftn",
-  "tests/test_utils.py::test_make_cart_circle",
-  "tests/test_utils.py::test_make_cart_sphere",
   "tests/test_utils.py::test_nepers2db",
   "tests/test_utils.py::test_num_dim",
   "tests/test_utils.py::test_power_kramers_kronig",
@@ -212,14 +148,11 @@
   "tests/test_utils.py::test_resize_2D_nearest_larger",
   "tests/test_utils.py::test_resize_2D_nearest_smaller",
   "tests/test_utils.py::test_resize_2D_splinef2d",
-  "tests/test_utils.py::test_ring_up_down",
   "tests/test_utils.py::test_signal_length",
   "tests/test_utils.py::test_signal_offset",
   "tests/test_utils.py::test_spect",
-  "tests/test_utils.py::test_tone_burst_gaussian",
-  "tests/test_utils.py::test_tone_burst_rectangular",
-  "tests/test_utils.py::test_tone_burst_ring",
   "tests/test_utils.py::test_tone_error",
+  "tests/test_utils.py::test_trim_zeros",
   "tests/test_water.py::test_water_absorption",
   "tests/test_water.py::test_water_density",
   "tests/test_water.py::test_water_non_linearity",

k_wave_python-0.3.1/.readthedocs.yaml

@@ -0,0 +1,14 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+sphinx:
+   configuration: docs/conf.py
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs

k_wave_python-0.3.1/.ruff_cache/.gitignore

@@ -0,0 +1 @@
+*

k_wave_python-0.3.1/.ruff_cache/CACHEDIR.TAG

@@ -0,0 +1 @@
+Signature: 8a477f597d28d172789f06886806bc55

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/Dockerfile

@@ -4,7 +4,8 @@ RUN apt-get update
 RUN apt-get install -y gfortran libopenblas-dev liblapack-dev libgl1-mesa-glx libglib2.0-0 libgl1-mesa-glx libglib2.0-0 git
 RUN pip install --upgrade pip
 COPY pyproject.toml .
-COPY README.md .
+#COPY README.md .
+COPY docs/ docs
 COPY LICENSE .
 COPY kwave/ kwave
 RUN pip install '.[test]'

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: k-Wave-python
-Version: 0.2.1
+Version: 0.3.1
 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/
@@ -687,38 +687,42 @@ Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.8
-Requires-Dist: deepdiff==5.2.3
-Requires-Dist: h5py==3.6.0
-Requires-Dist: matplotlib==3.6.3
-Requires-Dist: numpy<1.25.0,>=1.22.2
-Requires-Dist: opencv-python==4.7.0.68
-Requires-Dist: scikit-image==0.19.3
-Requires-Dist: scipy==1.7.3
-Requires-Dist: uff-reader==0.0.2
+Requires-Dist: beartype==0.16.4
+Requires-Dist: deepdiff==6.7.1
+Requires-Dist: h5py==3.10.0
+Requires-Dist: matplotlib==3.7.2
+Requires-Dist: nptyping==2.5.0
+Requires-Dist: numpy<1.27.0,>=1.22.2
+Requires-Dist: opencv-python==4.9.0.80
+Requires-Dist: scipy==1.10.1
+Provides-Extra: dev
+Requires-Dist: pre-commit==3.5.0; extra == 'dev'
 Provides-Extra: docs
-Requires-Dist: furo==2022.12.7; extra == 'docs'
+Requires-Dist: furo==2023.9.10; extra == 'docs'
 Requires-Dist: m2r2==0.3.2; extra == 'docs'
-Requires-Dist: sphinx-copybutton==0.5.1; extra == 'docs'
-Requires-Dist: sphinx-tabs==3.4.1; extra == 'docs'
-Requires-Dist: sphinx-toolbox==3.2.0; extra == 'docs'
+Requires-Dist: sphinx-copybutton==0.5.2; extra == 'docs'
+Requires-Dist: sphinx-tabs==3.4.4; extra == 'docs'
+Requires-Dist: sphinx-toolbox==3.5.0; extra == 'docs'
 Provides-Extra: example
-Requires-Dist: gdown==4.6.0; extra == 'example'
+Requires-Dist: gdown==4.7.3; extra == 'example'
 Provides-Extra: test
 Requires-Dist: phantominator; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
+Requires-Dist: requests==2.31.0; extra == 'test'
 Description-Content-Type: text/markdown
 
 # k-Wave-python
+[![Documentation Status](https://readthedocs.org/projects/k-wave-python/badge/?version=latest)](https://k-wave-python.readthedocs.io/en/latest/?badge=latest)
 
-This project is a Python implementation of most 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.
+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.
 
 ## Mission
 
-With this project, we hope to increase 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
+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
-in order to leverage pythonic practices.
+to leverage pythonic practices.
 
 ## Installation
 
@@ -728,7 +732,7 @@ To install the most recent build of k-Wave-python from PyPI, run:
 pip install k-wave-python
 ```
 
-After installing the python package, the required binaries will be downloaded and installed the first time you run a
+After installing the Python package, the required binaries will be downloaded and installed the first time you run a
 simulation.
 
 ## Getting started
@@ -740,8 +744,9 @@ After installation, run the B-mode reconstruction example in the `examples` dire
 ```bash
 git clone https://github.com/waltsims/k-wave-python
 cd k-wave-python
+git checkout v0.3.0
 pip install '.[example]' 
-python3 examples/bmode_reconstruction_example.py
+python3 examples/us_bmode_linear_transducer/us_bmode_linear_transducer.py
 ```
 
 This example file steps through the process of:
@@ -754,13 +759,13 @@ This example file steps through the process of:
 This example expects an NVIDIA GPU by default to simulate with k-Wave.
 
 To test the reconstruction on a machine with a GPU,
-set `RUN_SIMULATION` [on line 14 of `bmode_reconstruction_example.py`](https://github.com/waltsims/k-wave-python/blob/master/examples/bmode_reconstruction_example.py#L18)
-to `True` and the example will run without the pre-computed data.
+set `RUN_SIMULATION` [on line 30 of `bmode_reconstruction_example.py`](https://github.com/waltsims/k-wave-python/blob/master/examples/bmode_reconstruction_example.py#L30)
+to `True`, and the example will run without the pre-computed data.
 
 ## Development
 
 If you're enjoying k-Wave-python and want to contribute, development instructions can be
-found [here](https://waltersimson.com/k-wave-python/development/development_environment.html).
+found [here](https://k-wave-python.readthedocs.io/en/latest/development/development_environment.html).
 
 ## Related Projects
 
@@ -772,8 +777,8 @@ found [here](https://waltersimson.com/k-wave-python/development/development_envi
 
 ## Documentation
 
-The documentation for k-wave-python can be found [here](http://waltersimson.com/k-wave-python/)
+The documentation for k-wave-python can be found [here](https://k-wave-python.readthedocs.io/en/latest/).
 
 ## Contact
 
-e-mail [walter.simson@tum.de](mailto:walter.simson@tum.de).
+e-mail [wsimson@stanford.edu](mailto:wsimson@stanford.edu).

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/docs/README.md

@@ -1,14 +1,15 @@
 # k-Wave-python
+[![Documentation Status](https://readthedocs.org/projects/k-wave-python/badge/?version=latest)](https://k-wave-python.readthedocs.io/en/latest/?badge=latest)
 
-This project is a Python implementation of most 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.
+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.
 
 ## Mission
 
-With this project, we hope to increase 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
+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
-in order to leverage pythonic practices.
+to leverage pythonic practices.
 
 ## Installation
 
@@ -18,7 +19,7 @@ To install the most recent build of k-Wave-python from PyPI, run:
 pip install k-wave-python
 ```
 
-After installing the python package, the required binaries will be downloaded and installed the first time you run a
+After installing the Python package, the required binaries will be downloaded and installed the first time you run a
 simulation.
 
 ## Getting started
@@ -30,8 +31,9 @@ After installation, run the B-mode reconstruction example in the `examples` dire
 ```bash
 git clone https://github.com/waltsims/k-wave-python
 cd k-wave-python
+git checkout v0.3.0
 pip install '.[example]' 
-python3 examples/bmode_reconstruction_example.py
+python3 examples/us_bmode_linear_transducer/us_bmode_linear_transducer.py
 ```
 
 This example file steps through the process of:
@@ -44,13 +46,13 @@ This example file steps through the process of:
 This example expects an NVIDIA GPU by default to simulate with k-Wave.
 
 To test the reconstruction on a machine with a GPU,
-set `RUN_SIMULATION` [on line 14 of `bmode_reconstruction_example.py`](https://github.com/waltsims/k-wave-python/blob/master/examples/bmode_reconstruction_example.py#L18)
-to `True` and the example will run without the pre-computed data.
+set `RUN_SIMULATION` [on line 30 of `bmode_reconstruction_example.py`](https://github.com/waltsims/k-wave-python/blob/master/examples/bmode_reconstruction_example.py#L30)
+to `True`, and the example will run without the pre-computed data.
 
 ## Development
 
 If you're enjoying k-Wave-python and want to contribute, development instructions can be
-found [here](https://waltersimson.com/k-wave-python/development/development_environment.html).
+found [here](https://k-wave-python.readthedocs.io/en/latest/development/development_environment.html).
 
 ## Related Projects
 
@@ -62,8 +64,8 @@ found [here](https://waltersimson.com/k-wave-python/development/development_envi
 
 ## Documentation
 
-The documentation for k-wave-python can be found [here](http://waltersimson.com/k-wave-python/)
+The documentation for k-wave-python can be found [here](https://k-wave-python.readthedocs.io/en/latest/).
 
 ## Contact
 
-e-mail [walter.simson@tum.de](mailto:walter.simson@tum.de).
+e-mail [wsimson@stanford.edu](mailto:wsimson@stanford.edu).

{k_wave_python-0.2.1 → k_wave_python-0.3.1}/kwave/__init__.py

@@ -1,15 +1,13 @@
+import logging
 import os
 import sys
 import urllib.request
 from os import environ
 from pathlib import Path
 
-from kwave.kgrid import kWaveGrid
-from kwave.kmedium import kWaveMedium
-from kwave.ktransducer import NotATransducer
-from kwave.options import SimulationOptions
-
-VERSION = '0.2.1'
+# 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 = '0.3.1'
 # Set environment variable to binaries to get rid of user warning
 # This code is a crutch and should be removed when kspaceFirstOrder
 # is refactored
@@ -61,7 +59,7 @@ def binaries_present() -> bool:
 
     for binary in binary_list[system]:
         if not os.path.exists(os.path.join(binary_path, binary)):
-            print(f"{binary} not found")
+            logging.log(logging.WARN,  f"{binary} not found")
             return False
     return True
 
@@ -98,7 +96,7 @@ def download_binaries(system_os: str, bin_type: str):
         # Extract the file name from the GitHub release URL
         filename = url.split("/")[-1]
 
-        print(f"Downloading {filename} to {binary_path}...")
+        logging.log(logging.INFO, f"Downloading {filename} to {binary_path}...")
 
         # Create the directory if it does not yet exist
         os.makedirs(binary_path, exist_ok=True)

k_wave_python-0.3.1/kwave/data.py

@@ -0,0 +1,120 @@
+from dataclasses import dataclass
+from typing import Any
+
+import numpy as np
+
+
+class Vector(np.ndarray):
+    def __new__(cls, elements: list):
+        assert 1 <= len(elements) <= 3
+        elements = list(elements)
+        obj = np.array(elements).view(cls)
+        return obj
+
+    @property
+    def x(self):
+        return self[0]
+
+    @x.setter
+    def x(self, value):
+        self[0] = value
+
+    @property
+    def y(self):
+        if self.shape[0] > 1:
+            return self[1]
+        return np.nan
+
+    @y.setter
+    def y(self, value):
+        if self.shape[0] > 1:
+            self[1] = value
+
+    @property
+    def z(self):
+        if self.shape[0] > 2:
+            return self[2]
+        return np.nan
+
+    @z.setter
+    def z(self, value):
+        if self.shape[0] > 2:
+            self[2] = value
+
+    def assign_dim(self, dim: int, val: Any):
+        self[dim - 1] = val
+
+    def append(self, value):
+        new_coordinates = list(self) + [value]
+        return Vector(new_coordinates)
+
+
+@dataclass
+class FlexibleVector(object):
+    """
+    This class is very similar to Numpy.ndarray but there are differences:
+        - It can have 3 elements at max
+        - Its elements can be anything
+        - The elements do not have to be same type,
+                e.g. this is valid: Array([<scalar>, <List>, <Tuple of Tuples>])
+
+    WARNING: The class will be deprecated once we refactor the kWaveGrid class to use the Vector class instead!
+    """
+    data: list
+
+    def __post_init__(self):
+        assert 1 <= len(self) <= 3
+
+    def __len__(self):
+        return len(self.data)
+
+    def __getitem__(self, item):
+        return self.data[item]
+
+    def __setitem__(self, key, value):
+        self.data[key] = value
+
+    @property
+    def x(self):
+        return self[0]
+
+    @x.setter
+    def x(self, val):
+        self[0] = val
+
+    @property
+    def y(self):
+        return self[1] if len(self) >= 2 else np.nan
+
+    @y.setter
+    def y(self, val):
+        assert len(self) >= 2
+        self[1] = val
+
+    @property
+    def z(self):
+        """
+        :return: 3rd dimension element. 0 if not defined
+        """
+        return self[2] if len(self) == 3 else np.nan
+
+    @z.setter
+    def z(self, val):
+        assert len(self) == 3
+        self[2] = val
+
+    def numpy(self):
+        return np.asarray(self.data)
+
+    def assign_dim(self, dim, val):
+        if dim == 1:
+            self.x = val
+        if dim == 2:
+            self.y = val
+        if dim == 3:
+            self.z = val
+
+    def append(self, val):
+        assert len(self.data) <= 2
+        self.data.append(val)
+        return self