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Tweak density plotting function #175

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merged 3 commits into from
Oct 24, 2023
Merged

Tweak density plotting function #175

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dd80178
Update _density.py
AstyLavrinenko Oct 20, 2023
afa5e72
Plot structure cartesian coords
stefsmeets Oct 24, 2023
ab89780
Simplify color spec
stefsmeets Oct 24, 2023
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29 changes: 16 additions & 13 deletions src/gemdat/plots/_density.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from __future__ import annotations

from typing import TYPE_CHECKING, Sequence
from typing import TYPE_CHECKING, Optional, Sequence

import numpy as np
import plotly.express as px
Expand Down Expand Up @@ -71,13 +71,13 @@ def plot_points(points: np.ndarray,
point_size : int, optional
Size of the points
"""
colors = px.colors.qualitative.G10

assert len(points) == len(labels)

colors = dict(zip(labels, px.colors.qualitative.G10))

for i, (x, y, z) in enumerate(points):
color = colors[i % len(colors)]
label = labels[i]
color = colors[label]

fig.add_trace(
go.Scatter3d(x=[x],
Expand Down Expand Up @@ -158,7 +158,7 @@ def plot_volume(
showlegend=False))


def density(vol: Volume, structure: Structure) -> go.Figure:
def density(vol: Volume, structure: Optional[Structure] = None) -> go.Figure:
"""Create density plot from volume and structure.

Uses plotly as plotting backend.
Expand All @@ -167,22 +167,25 @@ def density(vol: Volume, structure: Structure) -> go.Figure:
---------
vol : Volume
Input volume
structure : Structure
structure : Structure, optional
Input structure

Returns
-------
fig : go.Figure
Output as plotly figure
"""
lattice = structure.lattice

fig = go.Figure()

plot_lattice_vectors(lattice, fig=fig)
plot_points(structure.cart_coords, structure.labels, fig=fig)
plot_lattice_vectors(vol.lattice, fig=fig)
plot_volume(vol, fig=fig)

if structure:
if structure.lattice == vol.lattice:
plot_points(structure.cart_coords, structure.labels, fig=fig)
else:
plot_structure(structure, fig=fig)

fig.update_layout(title='Density',
scene={
'aspectmode': 'manual',
Expand All @@ -191,9 +194,9 @@ def density(vol: Volume, structure: Structure) -> go.Figure:
'y': 1,
'z': 1
},
'xaxis_title': 'X (Angstrom)',
'yaxis_title': 'Y (Angstrom)',
'zaxis_title': 'Z (Angstrom)'
'xaxis_title': 'X (Ångstrom)',
'yaxis_title': 'Y (Ångstrom)',
'zaxis_title': 'Z (Ångstrom)'
},
legend={
'orientation': 'h',
Expand Down