From 2baa6d68b35e522847c9534485793cdb5dae7714 Mon Sep 17 00:00:00 2001
From: Bas Nijholt <basnijholt@gmail.com>
Date: Fri, 20 Sep 2019 15:36:51 +0200
Subject: [PATCH] rename figures
---
figures.ipynb | 210 +++++++++---------
.../{adaptive_vs_grid.pdf => Learner1D.pdf} | Bin
figures/{adaptive_2D.pdf => Learner2D.pdf} | Bin
paper.md | 13 +-
4 files changed, 108 insertions(+), 115 deletions(-)
rename figures/{adaptive_vs_grid.pdf => Learner1D.pdf} (100%)
rename figures/{adaptive_2D.pdf => Learner2D.pdf} (100%)
diff --git a/figures.ipynb b/figures.ipynb
index a296429..eee3291 100644
--- a/figures.ipynb
+++ b/figures.ipynb
@@ -51,11 +51,98 @@
"import matplotlib.tri as mtri"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# 1D funcs\n",
+ "def f(x, offset=0.123):\n",
+ " a = 0.02\n",
+ " return x + a ** 2 / (a ** 2 + (x - offset) ** 2)\n",
+ "\n",
+ "\n",
+ "def g(x):\n",
+ " return np.tanh(x * 40)\n",
+ "\n",
+ "\n",
+ "def h(x):\n",
+ " return np.sin(100 * x) * np.exp(-x ** 2 / 0.1 ** 2)\n",
+ "\n",
+ "\n",
+ "funcs_1D = [\n",
+ " dict(function=f, bounds=(-1, 1), title=\"peak\"),\n",
+ " dict(function=g, bounds=(-1, 1), title=\"tanh\"),\n",
+ " dict(function=h, bounds=(-0.3, 0.3), title=\"wave packet\"),\n",
+ "]\n",
+ "\n",
+ "# 2D funcs\n",
+ "def ring(xy, offset=0.123):\n",
+ " a = 0.2\n",
+ " x, y = xy\n",
+ " return x + np.exp(-(x ** 2 + y ** 2 - 0.75 ** 2) ** 2 / a ** 4)\n",
+ "\n",
+ "\n",
+ "@functools.lru_cache()\n",
+ "def phase_diagram_setup(fname):\n",
+ " data = adaptive.utils.load(fname)\n",
+ " points = np.array(list(data.keys()))\n",
+ " values = np.array(list(data.values()), dtype=float)\n",
+ " bounds = [\n",
+ " (points[:, 0].min(), points[:, 0].max()),\n",
+ " (points[:, 1].min(), points[:, 1].max()),\n",
+ " ]\n",
+ " ll, ur = np.reshape(bounds, (2, 2)).T\n",
+ " inds = np.all(np.logical_and(ll <= points, points <= ur), axis=1)\n",
+ " points, values = points[inds], values[inds].reshape(-1, 1)\n",
+ " return interpolate.LinearNDInterpolator(points, values), bounds\n",
+ "\n",
+ "\n",
+ "def phase_diagram(xy, fname):\n",
+ " ip, _ = phase_diagram_setup(fname)\n",
+ " return np.round(ip(xy))\n",
+ "\n",
+ "\n",
+ "def density(x, eps=0):\n",
+ " e = [0.8, 0.2]\n",
+ " delta = [0.5, 0.5, 0.5]\n",
+ " c = 3\n",
+ " omega = [0.02, 0.05]\n",
+ "\n",
+ " H = np.array(\n",
+ " [\n",
+ " [e[0] + 1j * omega[0], delta[0], delta[1]],\n",
+ " [delta[0], e[1] + c * x + 1j * omega[1], delta[1]],\n",
+ " [delta[1], delta[2], e[1] - c * x + 1j * omega[1]],\n",
+ " ]\n",
+ " )\n",
+ " H += np.eye(3) * eps\n",
+ " return np.trace(np.linalg.inv(H)).imag\n",
+ "\n",
+ "\n",
+ "def level_crossing(xy):\n",
+ " x, y = xy\n",
+ " return density(x, y) + y\n",
+ "\n",
+ "\n",
+ "funcs_2D = [\n",
+ " dict(function=ring, bounds=[(-1, 1), (-1, 1)], npoints=33),\n",
+ " dict(\n",
+ " function=phase_diagram,\n",
+ " bounds=phase_diagram_setup(\"phase_diagram.pickle\")[1],\n",
+ " npoints=100,\n",
+ " fname=\"phase_diagram.pickle\",\n",
+ " ),\n",
+ " dict(function=level_crossing, bounds=[(-1, 1), (-3, 3)], npoints=50),\n",
+ "]"
+ ]
+ },
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Fig 1."
+ "# loss_1D"
]
},
{
@@ -75,7 +162,7 @@
"fig, ax = plt.subplots(figsize=fig_size)\n",
"ax.scatter(xs, ys, c=\"k\")\n",
"ax.plot(xs, ys, c=\"k\")\n",
- "# ax.scatter()\n",
+ "\n",
"ax.annotate(\n",
" s=r\"$L_{1,2} = \\sqrt{\\Delta x^2 + \\Delta y^2}$\",\n",
" xy=(np.mean([xs[0], xs[1]]), np.mean([ys[0], ys[1]])),\n",
@@ -113,7 +200,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Fig 2."
+ "# adaptive_vs_grid"
]
},
{
@@ -122,24 +209,7 @@
"metadata": {},
"outputs": [],
"source": [
- "def f(x, offset=0.123):\n",
- " a = 0.02\n",
- " return x + a ** 2 / (a ** 2 + (x - offset) ** 2)\n",
- "\n",
- "\n",
- "def g(x):\n",
- " return np.tanh(x * 40)\n",
- "\n",
- "\n",
- "def h(x):\n",
- " return np.sin(100 * x) * np.exp(-x ** 2 / 0.1 ** 2)\n",
- "\n",
"\n",
- "funcs_1D = [\n",
- " dict(function=f, bounds=(-1, 1), title=\"peak\"),\n",
- " dict(function=g, bounds=(-1, 1), title=\"tanh\"),\n",
- " dict(function=h, bounds=(-0.3, 0.3), title=\"wave packet\"),\n",
- "]\n",
"fig, axs = plt.subplots(2, len(funcs_1D), figsize=(fig_width, 1.5 * fig_height))\n",
"n_points = 50\n",
"for i, ax in enumerate(axs.T.flatten()):\n",
@@ -168,14 +238,14 @@
"\n",
"axs[0][0].set_ylabel(r\"$\\textrm{homogeneous}$\")\n",
"axs[1][0].set_ylabel(r\"$\\textrm{adaptive}$\")\n",
- "plt.savefig(\"figures/adaptive_vs_grid.pdf\", bbox_inches=\"tight\", transparent=True)"
+ "plt.savefig(\"figures/Learner1D.pdf\", bbox_inches=\"tight\", transparent=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
- "# Fig 3. "
+ "# adaptive_2D"
]
},
{
@@ -184,66 +254,7 @@
"metadata": {},
"outputs": [],
"source": [
- "\n",
- "def f(xy, offset=0.123):\n",
- " a = 0.2\n",
- " x, y = xy\n",
- " return x + np.exp(-(x ** 2 + y ** 2 - 0.75 ** 2) ** 2 / a ** 4)\n",
- "\n",
- "\n",
- "@functools.lru_cache()\n",
- "def g_setup(fname):\n",
- " data = adaptive.utils.load(fname)\n",
- " points = np.array(list(data.keys()))\n",
- " values = np.array(list(data.values()), dtype=float)\n",
- " bounds = [\n",
- " (points[:, 0].min(), points[:, 0].max()),\n",
- " (points[:, 1].min(), points[:, 1].max()),\n",
- " ]\n",
- " ll, ur = np.reshape(bounds, (2, 2)).T\n",
- " inds = np.all(np.logical_and(ll <= points, points <= ur), axis=1)\n",
- " points, values = points[inds], values[inds].reshape(-1, 1)\n",
- " return interpolate.LinearNDInterpolator(points, values), bounds\n",
- "\n",
- "\n",
- "def g(xy, fname):\n",
- " ip, _ = g_setup(fname)\n",
- " return np.round(ip(xy))\n",
- "\n",
- "\n",
- "def density(x, eps=0):\n",
- " e = [0.8, 0.2]\n",
- " delta = [0.5, 0.5, 0.5]\n",
- " c = 3\n",
- " omega = [0.02, 0.05]\n",
- "\n",
- " H = np.array(\n",
- " [\n",
- " [e[0] + 1j * omega[0], delta[0], delta[1]],\n",
- " [delta[0], e[1] + c * x + 1j * omega[1], delta[1]],\n",
- " [delta[1], delta[2], e[1] - c * x + 1j * omega[1]],\n",
- " ]\n",
- " )\n",
- " H += np.eye(3) * eps\n",
- " return np.trace(np.linalg.inv(H)).imag\n",
- "\n",
- "\n",
- "def h(xy):\n",
- " x, y = xy\n",
- " return density(x, y) + y\n",
- "\n",
- "\n",
- "funcs = [\n",
- " dict(function=f, bounds=[(-1, 1), (-1, 1)], npoints=33),\n",
- " dict(\n",
- " function=g,\n",
- " bounds=g_setup(\"phase_diagram.pickle\")[1],\n",
- " npoints=100,\n",
- " fname=\"phase_diagram.pickle\",\n",
- " ),\n",
- " dict(function=h, bounds=[(-1, 1), (-3, 3)], npoints=50),\n",
- "]\n",
- "fig, axs = plt.subplots(2, len(funcs), figsize=(fig_width, 1.5 * fig_height))\n",
+ "fig, axs = plt.subplots(2, len(funcs_2D), figsize=(fig_width, 1.5 * fig_height))\n",
"\n",
"plt.subplots_adjust(hspace=-0.1, wspace=0.1)\n",
"\n",
@@ -262,7 +273,7 @@
" ax.xaxis.set_ticks([])\n",
" ax.yaxis.set_ticks([])\n",
" kind = \"homogeneous\" if i % 2 == 0 else \"adaptive\"\n",
- " d = funcs[i // 2] if kind == \"homogeneous\" else funcs[(i - 1) // 2]\n",
+ " d = funcs_2D[i // 2] if kind == \"homogeneous\" else funcs_2D[(i - 1) // 2]\n",
" bounds = d[\"bounds\"]\n",
" npoints = d[\"npoints\"]\n",
" f = d[\"function\"]\n",
@@ -302,7 +313,7 @@
"\n",
"axs[0][0].set_ylabel(r\"$\\textrm{homogeneous}$\")\n",
"axs[1][0].set_ylabel(r\"$\\textrm{adaptive}$\")\n",
- "plt.savefig(\"figures/adaptive_2D.pdf\", bbox_inches=\"tight\", transparent=True)"
+ "plt.savefig(\"figures/Learner2D.pdf\", bbox_inches=\"tight\", transparent=True)"
]
},
{
@@ -467,7 +478,7 @@
" ncol=1,\n",
")\n",
"\n",
- "# On grid\n",
+ "# On grid, uncomment for homogeneous plot\n",
"# axs.plot(learner.bounds, [-(i + 0.5) * step, -(i + 0.5) * step], c='k', ls='--')\n",
"# xs_hom = np.linspace(*learner.bounds, i)\n",
"# ys_hom = f(xs_hom) - (i + 3) * step\n",
@@ -573,27 +584,6 @@
"source": [
"import scipy\n",
"\n",
- "\n",
- "def f(x, offset=0.123):\n",
- " a = 0.02\n",
- " return x + a ** 2 / (a ** 2 + (x - offset) ** 2)\n",
- "\n",
- "\n",
- "def g(x):\n",
- " return np.tanh(x * 40)\n",
- "\n",
- "\n",
- "def h(x):\n",
- " return np.sin(100 * x) * np.exp(-x ** 2 / 0.1 ** 2)\n",
- "\n",
- "\n",
- "funcs_1D = [\n",
- " dict(function=f, bounds=(-1, 1), title=\"peak\"),\n",
- " dict(function=g, bounds=(-1, 1), title=\"tanh\"),\n",
- " dict(function=h, bounds=(-0.3, 0.3), title=\"wave packet\"),\n",
- "]\n",
- "\n",
- "\n",
"def err(xs, ys, xs_rand):\n",
" ip = scipy.interpolate.interp1d(xs, ys)\n",
" abserr = np.abs(ip(xs_rand) - f(xs_rand))\n",
@@ -784,7 +774,7 @@
" return x ** 2 + y ** 3\n",
"\n",
"bounds = [(-1, 1), (-1, 1)]\n",
- "npoints = 300\n",
+ "npoints = 17**2\n",
"\n",
"def isoline_loss_function(y_iso, sigma, priority=1):\n",
" from adaptive.learner.learnerND import default_loss\n",
@@ -833,13 +823,15 @@
"\n",
" if with_tri:\n",
" xy = np.array([learner.tri.get_vertices(s)\n",
- " for s in learner.tri.simplices]).reshape(-1, 2)\n",
- " triang = mtri.Triangulation(*xy.T)\n",
+ " for s in learner.tri.simplices])\n",
+ " print(f'{len(xy)} triangles')\n",
+ " triang = mtri.Triangulation(*xy.reshape(-1, 2).T)\n",
" ax.triplot(triang, c=\"w\", lw=0.2, alpha=0.8)\n",
"\n",
" # Isolines\n",
" vertices, lines = learner._get_iso(level, which='line')\n",
" paths = np.array([[vertices[i], vertices[j]] for i, j in lines]).T\n",
+ " print('{} line segments'.format(len(paths.T)))\n",
" ax.plot(*paths, c='k')\n",
"\n",
" values = np.array(list(learner.data.values()))\n",
diff --git a/figures/adaptive_vs_grid.pdf b/figures/Learner1D.pdf
similarity index 100%
rename from figures/adaptive_vs_grid.pdf
rename to figures/Learner1D.pdf
diff --git a/figures/adaptive_2D.pdf b/figures/Learner2D.pdf
similarity index 100%
rename from figures/adaptive_2D.pdf
rename to figures/Learner2D.pdf
diff --git a/paper.md b/paper.md
index e44df2a..effba5e 100755
--- a/paper.md
+++ b/paper.md
@@ -61,14 +61,14 @@ The most significant advantage of these *local* algorithms is that they allow fo
{#fig:adaptive_vs_grid}
+When the features are homogeneously spaced, such as with the wave packet, adaptive sampling is not as effective as in the other cases.](figures/Learner1D.pdf){#fig:Learner1D}
![Comparison of homogeneous sampling (top) with adaptive sampling (bottom) for different two-dimensional functions where the number of points in each column is identical.
On the left is a circle with a linear background $x + a ^ 2 / (a ^ 2 + (x - x_\textrm{offset}) ^ 2)$.
In the middle a topological phase diagram from [\onlinecite{nijholt2016orbital}] its function can be -1 or 1, which indicate the presence or abscence of a Majorana bound state.
On the right we plot level crossings for a two level quantum system.
In all cases using Adaptive results in a better plot.
-](figures/adaptive_2D.pdf){#fig:adaptive_2D}
+](figures/Learner2D.pdf){#fig:Learner2D}
#### We provide a reference implementation, the Adaptive package, and demonstrate its performance.
@@ -133,7 +133,7 @@ The amortized complexity of the point suggestion algorithm is, therefore, $\math
An example of such a loss function for a one-dimensional function is the interpoint distance.
This loss will suggest to sample a point in the middle of an interval with the largest Euclidean distance and thereby ensure the continuity of the function.
A more complex loss function that also takes the first neighbouring intervals into account is one that adds more points where the second derivative (or curvature) is the highest.
-Figure @fig:adaptive_vs_grid shows a comparison between a result using this loss and a function that is sampled on a grid.
+Figure @fig:Learner1D shows a comparison between a result using this loss and a function that is sampled on a grid.
#### With many points, due to the loss being local, parallel sampling incurs no additional cost.
So far, the description of the general algorithm did not include parallelism.
@@ -218,7 +218,7 @@ $$
$$
This error approaches zero as the approximation becomes better.
-{#fig:line_loss_error}
@@ -232,11 +232,12 @@ Here, we see that for homogeneous sampling to get the same error as sampling wit
## isoline and isosurface sampling
We can find isolines or isosurfaces using a loss function that prioritizes intervals that are closer to the function values that we are interested in.
-See @fig:isoline.
+See Fig. @fig:isoline.
-{#fig:isoline}
# Implementation and benchmarks
--
GitLab