Merge pull request #43 from nvaytet/lic_tweaks

Lic tweaks

docs/plotting.ipynb

@@ -63,7 +63,8 @@
     "osyris.histogram2d(\n",
     "    data[\"hydro\"][\"density\"], data[\"hydro\"][\"B_field\"],\n",
     "    {\"data\": data[\"hydro\"][\"mass\"], \"norm\": \"log\"}, # layer 1\n",
-    "    {\"data\": data[\"amr\"][\"level\"], \"operation\": \"mean\", \"mode\": \"contour\", \"colors\": \"k\"}, # layer 2\n",
+    "    {\"data\": data[\"amr\"][\"level\"], \"operation\": \"mean\",\n",
+    "     \"mode\": \"contour\", \"colors\": \"k\"}, # layer 2\n",
     "    loglog=True)"
    ]
   },
@@ -215,10 +216,7 @@
    "outputs": [],
    "source": [
     "# Create figure\n",
-    "fig = plt.figure(figsize=(10, 3.5))\n",
-    "ax1 = fig.add_subplot(121)\n",
-    "ax2 = fig.add_subplot(122)\n",
-    "plt.subplots_adjust(wspace=0.5)\n",
+    "fig, ax = plt.subplots(1, 2, figsize=(12, 4.5))\n",
     "\n",
     "# Define region to plot\n",
     "dx = 2000.0 * osyris.units(\"au\")\n",
@@ -235,16 +233,13 @@
     "                  \"linestyles\": [\"solid\",\"dashed\",\"solid\"],\n",
     "                  \"cmap\": None,\n",
     "                  \"labels\": False},\n",
-    "             dx=dx,\n",
-    "             origin=center,\n",
-    "             direction=\"z\", ax=ax1)\n",
+    "             dx=dx, origin=center, direction=\"z\", ax=ax[0])\n",
     "\n",
     "osyris.plane({\"data\": data[\"hydro\"][\"temperature\"], \"norm\": \"log\", \"mode\": \"contourf\",\n",
-    "              \"levels\": np.logspace(0.9, 2, 21), \"cmap\": \"hot\"},\n",
-    "             {\"data\": data[\"amr\"][\"level\"], \"mode\": \"contour\", \"colors\": \"w\", \"levels\": [6, 7, 8]},\n",
-    "             dx=dx,\n",
-    "             origin=center,\n",
-    "             direction=\"z\", ax=ax2)"
+    "              \"levels\": np.logspace(0.9, 2, 11), \"cmap\": \"hot\"},\n",
+    "             {\"data\": data[\"amr\"][\"level\"], \"mode\": \"contour\", \"colors\": \"w\",\n",
+    "              \"levels\": [6, 7, 8]},\n",
+    "             dx=dx, origin=center, direction=\"z\", ax=ax[1])"
    ]
   },
   {
@@ -506,7 +501,9 @@
    "source": [
     "## Line integral convolution vector field visualizations\n",
     "\n",
-    "Osyris now supports line integral convolution (LIC) visualizations of vector fields. This visualization method, although computationally intensive, offers an excellent representation of the vector field (especially near discontinuities) provided we have enough resolution.\n",
+    "Osyris now supports line integral convolution (LIC) visualizations of vector fields.\n",
+    "This visualization method, although computationally intensive,\n",
+    "offers an excellent representation of the vector field (especially near discontinuities).\n",
     "\n",
     "**Note:** This feature requires the [lic](https://pypi.org/project/lic/) package to be installed.\n",
     "\n",
@@ -520,16 +517,20 @@
    "outputs": [],
    "source": [
     "osyris.plane({\"data\": data[\"hydro\"][\"velocity\"], \"mode\": \"lic\"},\n",
-    "             dx=2000 * osyris.units(\"au\"),\n",
-    "             origin=center,\n",
-    "             direction=\"z\", resolution=1000)"
+    "             dx=2000 * osyris.units(\"au\"), direction=\"z\",\n",
+    "             origin=center, cmap=\"binary\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The LIC can be colored by a scalar field using the `color` keyword, and the length of the lines of the LIC can also be modified using the `length` keyword (whose default value is 30):"
+    "The LIC can be colored by a scalar field using the `color` keyword,\n",
+    "and the length of the lines of the LIC can also be modified using the `length` keyword.\n",
+    "\n",
+    "In the following example,\n",
+    "we use the colors to show the gas density overlayed onto the velocity flow structure on the left,\n",
+    "while on the right we use the colors to recover some information on the magnitude of the velocities."
    ]
   },
   {
@@ -538,19 +539,26 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "fig, ax = plt.subplots(1, 2, figsize=(12, 4))\n",
+    "\n",
+    "dx = 2000 * osyris.units(\"au\")\n",
+    "\n",
     "osyris.plane({\"data\": data[\"hydro\"][\"velocity\"], \"mode\": \"lic\",\n",
-    "              \"color\": data[\"hydro\"][\"density\"], \"norm\": \"log\", \"length\":30},\n",
-    "             dx=2000 * osyris.units(\"au\"),\n",
-    "             origin=center,\n",
-    "             direction=\"z\", resolution=1000)"
+    "              \"color\": data[\"hydro\"][\"density\"], \"norm\": \"log\",\n",
+    "              \"length\":60}, ax=ax[0],\n",
+    "             dx=dx, origin=center, direction=\"z\")\n",
+    "osyris.plane({\"data\": data[\"hydro\"][\"velocity\"], \"mode\": \"lic\",\n",
+    "              \"color\": data[\"hydro\"][\"velocity\"], \"norm\": \"linear\",\n",
+    "              \"length\":60, \"cmap\": \"plasma\"}, ax=ax[1],\n",
+    "             dx=dx, origin=center, direction=\"z\")"
    ]
   },
   {
-   "cell_type": "markdown",
+   "cell_type": "code",
+   "execution_count": null,
    "metadata": {},
-   "source": [
-    "Overlaying this plot with velocity arrows allows us to retrieve some information on the magnitude of the vector field."
-   ]
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = osyris
-version = 2.3.1
+version = 2.3.2
 author = Neil Vaytet
 author_email = [email protected]
 description = A package to visualize AMR data from the RAMSES code

src/osyris/plot/wrappers.py

@@ -2,6 +2,8 @@
 # Copyright (c) 2021 Osyris contributors (https://github.com/nvaytet/osyris)
 from .. import config
 from ..core import Array
+from contextlib import redirect_stderr
+import io
 import matplotlib.pyplot as plt
 from matplotlib.cm import ScalarMappable
 from matplotlib.collections import PatchCollection
@@ -175,7 +177,7 @@ def line_integral_convolution(ax,
                               z,
                               cbar=False,
                               cblabel=None,
-                              length=30,
+                              length=None,
                               color=None,
                               **kwargs):
     """
@@ -185,7 +187,10 @@ def line_integral_convolution(ax,
     from lic import lic
 
     # Compute line integral convolution
-    lic_res = lic(z[..., 1], z[..., 0], length=length)
+    if length is None:
+        length = int(max(z.shape[:-1]) * 15 / 128)
+    with redirect_stderr(io.StringIO()) as _:
+        lic_res = lic(z[..., 1], z[..., 0], length=length)
 
     if color is not None:
         plot_args = {**kwargs}