Exposing private functions (#195)

* points_on_circle, unit_fibonacci_sphere, circ_mask, bli_function are not private anymore
* added css and js files to paths for build_docs action
* removed __about__

.github/workflows/build_docs.yml

@@ -12,6 +12,8 @@ on:
       - '**.md'
       - '**.ipynb'
       - '**.sh'
+      - '**.css'
+      - '**.js'
 
 jobs:
   build-and-publish:

CHANGELOG.md

@@ -13,6 +13,14 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 ### Removed
 - Removed the uncertainty propagation notebook example. For a more in depth example of using linear uncertainty propagation see [this repository](https://github.com/ucl-bug/linear-uncertainty)
 
+### Added
+- Exposed `points_on_circle` function to generate points on a circle
+- Exposed `unit_fibonacci_sphere` function
+- Exposed `fibonacci_sphere` function
+- Exposed `sphere_mask` function for creating spherical binary masks
+- Exposed `circ_mask` function for creating circular binary masks
+- Exposed bli_function that is used to compute the band limited interpolant
+
 ## [0.1.3] - 2023-06-28
 ### Added
 - Added off grid sensors [@tomelse]

docs/notebooks/harmonic/helmholtz_problem.ipynb

@@ -46,7 +46,7 @@
     "from matplotlib import pyplot as plt\n",
     "\n",
     "from jwave import FiniteDifferences, FourierSeries\n",
-    "from jwave.geometry import Domain, Medium, _circ_mask\n",
+    "from jwave.geometry import Domain, Medium, circ_mask\n",
     "from jwave.utils import plot_complex_field, show_positive_field\n",
     "\n",
     "key = random.PRNGKey(42)  # Random seed"
@@ -119,8 +119,8 @@
     "sound_speed = sound_speed.at[20:105, 20:200].set(1.0)\n",
     "sound_speed = (\n",
     "    sound_speed\n",
-    "    * (1 - _circ_mask(N, 90, [64, 180]))\n",
-    "    * (1 - _circ_mask(N, 50, [64, 22]))\n",
+    "    * (1 - circ_mask(N, 90, [64, 180]))\n",
+    "    * (1 - circ_mask(N, 50, [64, 22]))\n",
     "    * 0.5\n",
     "    + 1\n",
     ")\n",

docs/notebooks/ivp/custom_sensors.ipynb

@@ -30,7 +30,7 @@
     "from jwave import FourierSeries\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
     "from jwave.geometry import *\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "from jwave.utils import show_field\n",
     "\n",
     "domain = Domain((128, 128), (0.1e-3, 0.1e-3))\n",
@@ -48,10 +48,10 @@
     "# Defining the initial pressure\n",
     "\n",
     "N = domain.N\n",
-    "mask1 = _circ_mask(N, 8, (50, 50))\n",
-    "mask2 = _circ_mask(N, 5, (80, 60))\n",
-    "mask3 = _circ_mask(N, 10, (64, 64))\n",
-    "mask4 = _circ_mask(N, 30, (64, 64))\n",
+    "mask1 = circ_mask(N, 8, (50, 50))\n",
+    "mask2 = circ_mask(N, 5, (80, 60))\n",
+    "mask3 = circ_mask(N, 10, (64, 64))\n",
+    "mask4 = circ_mask(N, 30, (64, 64))\n",
     "p0 = 5.0 * mask1 + 3.0 * mask2 + 4.0 * mask3 + 0.5 * mask4\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",

docs/notebooks/ivp/different_discretizations.ipynb

@@ -20,7 +20,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from jwave.geometry import Domain, Medium, TimeAxis, _circ_mask\n",
+    "from jwave.geometry import Domain, Medium, TimeAxis, circ_mask\n",
     "from jwave.acoustics.time_varying import simulate_wave_propagation\n",
     "from jwave import FiniteDifferences, FourierSeries\n",
     "from jwave.signal_processing import smooth\n",
@@ -50,7 +50,7 @@
     "\n",
     "# Smoothed initial pressure distribution\n",
     "Nx = domain.N\n",
-    "p0 = 5.0 * _circ_mask(Nx, 5, (128, 40))\n",
+    "p0 = 5.0 * circ_mask(Nx, 5, (128, 40))\n",
     "p0 = smooth(p0)\n",
     "\n",
     "# Getting time axis\n",

docs/notebooks/ivp/heterogeneous_medium.ipynb

@@ -25,7 +25,7 @@
     "from jwave import FourierSeries\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
     "from jwave.geometry import *\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "from jwave.utils import show_field, show_positive_field\n",
     "\n",
     "domain = Domain((128, 128), (0.1e-3, 0.1e-3))"
@@ -87,7 +87,7 @@
     "# Defining the initial pressure\n",
     "\n",
     "N = domain.N\n",
-    "p0 = _circ_mask(N, 3, (64, 30))\n",
+    "p0 = circ_mask(N, 3, (64, 30))\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",
     "p0 = FourierSeries(p0, domain)"
@@ -244,7 +244,7 @@
     "density = FiniteDifferences(np.expand_dims(density, -1), domain, accuracy=8)\n",
     "\n",
     "N = domain.N\n",
-    "p0 = _circ_mask(N, 3, (64, 30))\n",
+    "p0 = circ_mask(N, 3, (64, 30))\n",
     "\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",
     "p0 = FiniteDifferences(p0, domain, accuracy=8)"

docs/notebooks/ivp/homogeneous_medium.ipynb

@@ -147,9 +147,9 @@
     "from jax import numpy as jnp\n",
     "\n",
     "from jwave import FourierSeries\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "\n",
-    "p0 = 1.0 * jnp.expand_dims(_circ_mask(N, 4, (80, 60)), -1)\n",
+    "p0 = 1.0 * jnp.expand_dims(circ_mask(N, 4, (80, 60)), -1)\n",
     "p0 = FourierSeries(p0, domain)"
    ]
   },

docs/notebooks/others/save_video.ipynb

@@ -24,7 +24,7 @@
     "from jwave import FourierSeries\n",
     "from jwave.geometry import Domain, Medium, TimeAxis\n",
     "from jwave.acoustics import simulate_wave_propagation\n",
-    "from jwave.geometry import _circ_mask\n",
+    "from jwave.geometry import circ_mask\n",
     "\n",
     "domain = Domain((128, 128), (0.1e-3, 0.1e-3))"
    ]
@@ -54,7 +54,7 @@
     "\n",
     "# Defining the initial pressure\n",
     "N = domain.N\n",
-    "p0 = _circ_mask(N, 3, (64, 30))\n",
+    "p0 = circ_mask(N, 3, (64, 30))\n",
     "p0 = 1.0 * jnp.expand_dims(p0, -1)\n",
     "p0 = FourierSeries(p0, domain)"
    ]