More pictures

notebooks/explain_reorder.ipynb

@@ -217,22 +217,21 @@
     "    \n",
     "    fig, ax = plot_funcs.get_plot()\n",
     "    plot_funcs.set_axis_default(ax)\n",
-    "    plot_funcs.plot_molecule(ax, atoms, coord)\n",
+    "    plot_funcs.plot_molecule(ax, [\"\"]*3, coord)\n",
     "    plot_funcs.plot_representation(ax, atoms, coord)\n",
     "\n",
+    "    filename = \"fig_reorder_problem\"\n",
+    "    fig.savefig(filename, bbox_inches=\"tight\")\n",
+    "\n",
     "qml_illustration()"
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "37612822-a13a-4c97-a512-40073a161690",
+   "cell_type": "markdown",
+   "id": "faa92f45-9f5f-4f4e-9021-dd3e1c9d271a",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "\n",
-    "import matplotlib\n",
-    "matplotlib.pyplot.close()"
+    "# Reorder problem"
    ]
   },
   {
@@ -241,7 +240,34 @@
    "id": "9d6ce450-e2f3-42ca-9904-bcfe6873d92d",
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "def reorder():\n",
+    "\n",
+    "    coord1 = [\n",
+    "        [0,0,0],\n",
+    "        [1,1,0],\n",
+    "        [2,0,0],\n",
+    "    ]\n",
+    "    coord1 = np.array(coord1, dtype=float) / 1.2\n",
+    "    coord1 -= rmsdlib.centroid(coord1)\n",
+    "    coord2 = np.array(coord1, copy=True)\n",
+    "    atoms1 = [6, 6, 6]\n",
+    "\n",
+    "    coord2 /= 1.5\n",
+    "    coord2 -= rmsdlib.centroid(coord1)\n",
+    "    coord2[:,1] -= 0.5\n",
+    "    coord1[:,1] += 0.2\n",
+    "    \n",
+    "    fig, ax = plot_funcs.get_plot()\n",
+    "    plot_funcs.set_axis_default(ax)\n",
+    "    plot_funcs.plot_molecule(ax, [\"1\", \"2\", \"3\"], coord1)\n",
+    "    plot_funcs.plot_molecule(ax, [\"2\", \"3\", \"1\"], coord2, hatch=\"\\\\\\\\\\\\\")\n",
+    "\n",
+    "    filename = \"fig_reorder_problem\"\n",
+    "    fig.savefig(filename, bbox_inches=\"tight\")\n",
+    "\n",
+    "reorder()"
+   ]
   },
   {
    "cell_type": "code",

notebooks/plot_funcs.py

@@ -6,7 +6,12 @@
 
 import rmsd as rmsdlib
 
-outline = patheffects.withStroke(linewidth=6, foreground="w")
+outline = patheffects.withStroke(linewidth=5, foreground="w")
+
+FIGURE_SIZE = 4
+MARKER_SIZE = 400
+REP_SIZE = 0.1
+REP_HEIGHT = 0.15
 
 
 def plot_molecule(ax, atoms, coords, hatch="/////"):
@@ -19,7 +24,7 @@ def plot_molecule(ax, atoms, coords, hatch="/////"):
     ax.scatter(
         X,
         Y,
-        s=500.0,
+        s=MARKER_SIZE,
         hatch=hatch,
         facecolor="#fff",
         edgecolor="#000",
@@ -71,7 +76,7 @@ def plot_representation(ax, atoms, coord):
         x, y = ax.transLimits.transform(c)
 
         ins3 = ax.inset_axes(
-            [x, y, 0.02, 0.1],
+            [x, y, REP_SIZE, REP_HEIGHT],
         )
         ins3.imshow(np.expand_dims(vecs[idx], axis=1), cmap="gray")
         ins3.xaxis.set_ticks([])
@@ -100,15 +105,31 @@ def plot_representation(ax, atoms, coord):
 #     ax.add_artist(arrow)
 
 
-def set_axis_default(ax, lim=2.0):
+def set_axis_default(ax, lim=2.0, use_grid=True):
 
+    ax.set_box_aspect(1)
     ax.set_xlim(-lim, lim)
     ax.set_ylim(-lim, lim)
-    ax.grid(True)
+    ax.grid(use_grid)
 
-    ax.tick_params(width=0, length=0)
     ax.tick_params(axis="both", which="major", labelsize=0)
 
+    for tick in ax.xaxis.get_major_ticks():
+
+        tick.tick1line.set_visible(False)
+        tick.tick2line.set_visible(False)
+
+        tick.label1.set_visible(False)
+        tick.label2.set_visible(False)
+
+    for tick in ax.yaxis.get_major_ticks():
+
+        tick.tick1line.set_visible(False)
+        tick.tick2line.set_visible(False)
+
+        tick.label1.set_visible(False)
+        tick.label2.set_visible(False)
+
 
 def set_global_style():
     font = {"weight": "bold", "size": 18, "family": "serif"}
@@ -122,7 +143,7 @@ def set_global_style():
     # matplotlib.rcParams["ytick.major.width"] = 2
 
 
-def get_plot(n_ax=1, size=5):
+def get_plot(n_ax=1, size=FIGURE_SIZE):
     """Get a jupyter-sized plot"""
     fig, axs = plt.subplots(1, n_ax, sharey=True, sharex=True, figsize=(size * n_ax, size))
 
@@ -157,8 +178,6 @@ def fix_borders(ax, visibles=[False, False, True, True], fix_bounds=True):
     min_y = np.min(yticks)
     max_y = np.max(yticks)
 
-    # TODO Better ax.set_xlim()
-
     for direction, visible in zip(directions, visibles):
 
         spine = spines[direction]