Skip to content

Commit

Permalink
Figures
Browse files Browse the repository at this point in the history
  • Loading branch information
@charnley
charnley committed Jan 4, 2025
1 parent ad83eb1 commit 3ff568e
Show file tree
Hide file tree
Showing 11 changed files with 51 additions and 91 deletions.
Binary file added docs/figures/fig_reorder_inertia.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/figures/fig_reorder_problem.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added docs/figures/fig_reorder_qml.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
0 notebooks/fig_rmsd_nothing.png → docs/figures/fig_rmsd_nothing.png
View file
File renamed without changes
0 notebooks/fig_rmsd_recentered.png → docs/figures/fig_rmsd_recentered.png
View file
File renamed without changes
0 notebooks/fig_rmsd_rotated.png → docs/figures/fig_rmsd_rotated.png
View file
File renamed without changes
Binary file removed notebooks/fig_reorder_inertia.png
View file
Binary file not shown.
Binary file removed notebooks/fig_reorder_problem.png
View file
Binary file not shown.
Binary file removed notebooks/fig_reorder_qml.png
View file
Binary file not shown.
82 changes: 32 additions & 50 deletions notebooks/explain_reorder.ipynb → notebooks/figures.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -111,6 +111,28 @@
"plot_funcs.set_global_style()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9da6930d-7d90-457a-b69e-783ae35fa3ec",
"metadata": {},
"outputs": [],
"source": [
"folder = Path(\"../docs/figures\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "244df06a-3276-4b72-9ae8-337481ffadb8",
"metadata": {},
"outputs": [],
"source": [
"def save_figure(fig, name):\n",
" filename = folder / name\n",
" fig.savefig(filename, bbox_inches=\"tight\")"
]
},
{
"cell_type": "markdown",
"id": "3cf67d24-ad0a-4130-a3cd-d3f8d79e59cd",
Expand Down Expand Up @@ -150,8 +172,7 @@
"\n",
" print(rmsdlib.rmsd(coord1, coord2))\n",
"\n",
" filename = \"fig_rmsd_nothing\"\n",
" fig.savefig(filename, bbox_inches=\"tight\")\n",
" save_figure(fig, \"fig_rmsd_nothing\")\n",
"\n",
" ##\n",
" \n",
Expand All @@ -166,8 +187,7 @@
"\n",
" print(rmsdlib.rmsd(coord1, coord2))\n",
" \n",
" filename = \"fig_rmsd_recentered\"\n",
" fig.savefig(filename, bbox_inches=\"tight\")\n",
" save_figure(fig, \"fig_rmsd_recentered\")\n",
"\n",
" ##\n",
"\n",
Expand All @@ -182,8 +202,7 @@
"\n",
" print(rmsdlib.rmsd(coord1, coord2))\n",
" \n",
" filename = \"fig_rmsd_rotated\"\n",
" fig.savefig(filename, bbox_inches=\"tight\")\n",
" save_figure(fig, \"fig_rmsd_rotated\")\n",
"\n",
"rmsd1()"
]
Expand Down Expand Up @@ -220,8 +239,7 @@
" plot_funcs.plot_molecule(ax, [\"\"]*3, coord)\n",
" plot_funcs.plot_representation(ax, atoms, coord)\n",
"\n",
" filename = \"fig_reorder_qml\"\n",
" fig.savefig(filename, bbox_inches=\"tight\")\n",
" save_figure(fig, \"fig_reorder_qml\")\n",
"\n",
"qml_illustration()"
]
Expand Down Expand Up @@ -263,8 +281,7 @@
" 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",
" save_figure(fig, \"fig_reorder_problem\")\n",
"\n",
"reorder()"
]
Expand Down Expand Up @@ -304,56 +321,21 @@
" plot_funcs.plot_molecule(ax, [\"\"]*3, coord2, hatch=\"\\\\\\\\\\\\\")\n",
"\n",
" pos = np.array([-1.2, 1.0])\n",
" plot_funcs.plot_inertia(ax, pos, atoms1, coord1)\n",
" plot_funcs.plot_inertia(ax, pos, atoms1, coord2)\n",
" plot_funcs.plot_inertia(ax, pos, atoms1, coord1, zorder=300)\n",
" plot_funcs.plot_inertia(ax, pos, atoms1, coord2, zorder=300)\n",
"\n",
" filename = \"fig_reorder_inertia\"\n",
" fig.savefig(filename, bbox_inches=\"tight\")\n",
"\n",
"show_inertia()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f4383e95-c349-44c2-a710-e236646173e3",
"metadata": {},
"outputs": [],
"source": [
"[[ 0.70710678 0.70710678 0. ]\n",
" [ 0.70710678 -0.70710678 0. ]\n",
" [ 0. 0. 1. ]]\n",
"[0 1]\n",
"[0.70710678 1.70710678]\n",
"[0.70710678 0.29289322]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "56beaea8-a833-4ce7-84e1-fbbfc9bfeff0",
"metadata": {},
"outputs": [],
"source": [
"1-1.70710678"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "4e01ea91-f201-4c0c-9997-9497668a4e15",
"metadata": {},
"outputs": [],
"source": [
"fig, ax = plot_funcs.get_plot()\n",
" save_figure(fig, \"fig_reorder_inertia\")\n",
"\n",
"ax.plot([0,1,2], [0,0,2], '-')\n"
"show_inertia()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "ab8c52f9-51bd-4f78-9564-187756cca3d5",
"id": "e19b1501-cf18-4e48-a18c-109ae9bd8e55",
"metadata": {},
"outputs": [],
"source": []
Expand Down
60 changes: 19 additions & 41 deletions notebooks/plot_funcs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,8 @@ def plot_molecule(ax, atoms, coords, hatch="/////", zorder=0):
return


def plot_representation(ax, atoms, coord):
def plot_representation(ax, atoms, coord, zorder=100):

# qml vectors
parameters = {
"elements": np.unique(atoms),
"pad": len(atoms),
Expand All @@ -75,17 +74,29 @@ def plot_representation(ax, atoms, coord):
c += offset
x, y = ax.transLimits.transform(c)

ins3 = ax.inset_axes(
axins = ax.inset_axes(
[x, y, REP_SIZE, REP_HEIGHT],
zorder=zorder + 1,
)

axins.imshow(np.expand_dims(vecs[idx], axis=1), cmap="gray")
axins.xaxis.set_ticks([])
axins.yaxis.set_ticks([])

# Add white stroke to insert axis
coords = ax.transAxes.inverted().transform(axins.get_tightbbox())
border = 0.009
w, h = coords[1] - coords[0] + 2 * border
ax.add_patch(
plt.Rectangle(
coords[0] - border, w, h, fc="white", transform=ax.transAxes, zorder=zorder
)
)
ins3.imshow(np.expand_dims(vecs[idx], axis=1), cmap="gray")
ins3.xaxis.set_ticks([])
ins3.yaxis.set_ticks([])

return


def plot_inertia(ax, pos, atoms, coord):
def plot_inertia(ax, pos, atoms, coord, zorder=100):

center = rmsdlib.get_cm(atoms, coord)
coord = coord - center
Expand All @@ -97,16 +108,10 @@ def plot_inertia(ax, pos, atoms, coord):

eigvec = eigvec.T
eigvec = eigvec[np.argsort(eigval)]
# eigvec = eigvec.T

eigvec *= -1

print(pos)
print(eigvec)

arrow_options = dict(
zorder=10,
# path_effects=[outline],
zorder=zorder,
head_width=0.1,
head_length=0.1,
fc="k",
Expand Down Expand Up @@ -148,26 +153,6 @@ def plot_inertia(ax, pos, atoms, coord):
)


# def do_dot(ax, coord1, coord2, size=24, **kwargs):
# ax.plot([coord1], [coord2], "o", markersize=size, linewidth=3, color="k", **kwargs)
# return


# def do_arrow(ax, pos_start, pos_end, rad=0.0, color="k"):
# edge_width = 2.0
# arrowstyle = "fancy,head_length={},head_width={},tail_width={}".format(
# 2 * edge_width, 3 * edge_width, edge_width
# )
# arrow = FancyArrowPatch(
# posA=pos_start,
# posB=pos_end,
# arrowstyle=arrowstyle,
# connectionstyle=f"arc3,rad=-{rad:f}",
# color=color,
# )
# ax.add_artist(arrow)


def set_axis_default(ax, lim=2.0, use_grid=True):

ax.set_box_aspect(1)
Expand Down Expand Up @@ -199,17 +184,10 @@ def set_global_style():
matplotlib.rc("font", **font)
matplotlib.rc("axes", labelweight="bold")

# Thicker spines
# matplotlib.rcParams["axes.linewidth"] = 1

# matplotlib.rcParams["xtick.major.width"] = 2
# matplotlib.rcParams["ytick.major.width"] = 2


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))

fig.tight_layout()
fig.subplots_adjust(hspace=0, wspace=0)
return fig, axs

0 comments on commit 3ff568e

Please sign in to comment.