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Make visualization.py work again #8

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merged 6 commits into from
Sep 9, 2021
Merged

Make visualization.py work again #8

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7ac0d8e
Fix the issue 'Axes3D currently only supports the aspect argument 'au…
shervinea Sep 9, 2021
5e72ee0
Fix the issue 'AttributeError: 'list' object has no attribute 'ndim''
shervinea Sep 9, 2021
4cac1ce
Fix issue 'TypeError: 'float' object is not subscriptable'
shervinea Sep 9, 2021
b767532
Remove superfluous import
shervinea Sep 9, 2021
da0fd61
Mimic previous light source by adjusting parameters accordingly
shervinea Sep 9, 2021
17f142a
Indicate working matplotlib version with the current state of the vis…
shervinea Sep 9, 2021
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23 changes: 15 additions & 8 deletions enzynet/visualization.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,10 @@

# MIT License

from typing import List, Optional, Text, Tuple
from typing import Optional, Text, Tuple

import numpy as np
import matplotlib.colors as mcolors
import matplotlib.pyplot as plt

from enzynet import pdb
Expand Down Expand Up @@ -52,7 +53,11 @@ def plot_volume(vol: np.ndarray, pdb_id: Text, v_size: int, num: int,
plt.rc('font', family='serif')
fig = plt.figure(figsize=(4,4))
ax = fig.gca(projection='3d')
ax.set_aspect('equal')

# Reproduces the functionality of ax.set_aspect('equal').
# Source: https://github.com/matplotlib/matplotlib/issues/17172#issuecomment-830139107
ax.set_box_aspect(
[ub - lb for lb, ub in (getattr(ax, f'get_{a}lim')() for a in 'xyz')])

# Parameters.
len_vol = vol.shape[0]
Expand Down Expand Up @@ -94,9 +99,9 @@ def plot_volume(vol: np.ndarray, pdb_id: Text, v_size: int, num: int,
ax.zaxis._axinfo["grid"]['linewidth'] = 0.1

# Change thickness of ticks.
ax.xaxis._axinfo["tick"]['linewidth'] = 0.1
ax.yaxis._axinfo["tick"]['linewidth'] = 0.1
ax.zaxis._axinfo["tick"]['linewidth'] = 0.1
ax.xaxis._axinfo["tick"]['linewidth'][True] = 0.1
ax.yaxis._axinfo["tick"]['linewidth'][True] = 0.1
ax.zaxis._axinfo["tick"]['linewidth'][True] = 0.1

# Change tick placement.
ax.xaxis._axinfo['tick']['inward_factor'] = 0
Expand All @@ -115,7 +120,7 @@ def plot_volume(vol: np.ndarray, pdb_id: Text, v_size: int, num: int,
def cuboid_data(
pos: Tuple[float, float, float],
size: Tuple[int, int, int]=(1,1,1)
) -> Tuple[List[List[float]], List[List[float]], List[List[float]]]:
) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
"""Gets coordinates of cuboid."""
# Gets the (left, outside, bottom) point.
o = [a - b / 2 for a, b in zip(pos, size)]
Expand All @@ -132,15 +137,17 @@ def cuboid_data(
[o[2], o[2], o[2] + h, o[2] + h, o[2]],
[o[2], o[2], o[2] + h, o[2] + h, o[2]]]

return x, y, z
return np.array(x), np.array(y), np.array(z)


def plot_cube_at(pos: Tuple[float, float, float] = (0,0,0),
ax: Optional[plt.gca] = None) -> None:
"""Plots a cube element at position pos."""
lightsource = mcolors.LightSource(azdeg=135, altdeg=0)
if ax != None:
X, Y, Z = cuboid_data(pos)
ax.plot_surface(X, Y, Z, color='g', rstride=1, cstride=1, alpha=1)
ax.plot_surface(X, Y, Z, color='g', rstride=1, cstride=1, alpha=1,
lightsource=lightsource)


def plot_cube_weights_at(pos: Tuple[float, float, float] = (0, 0, 0),
Expand Down
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ keras
tensorflow

# Plot
matplotlib
matplotlib==3.4.1

# Biology
biopython
Expand Down