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佐久間 美波
2026-08-07 14:45:01 +09:00
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cube2mayavi_edge_corner.py
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#!/usr/bin/env python
# ./cube2mayavi_edge_corner.py -i 050Li3PS4-050LiI_PS4_I_zero.cube 050Li3PS4-050LiI_PS4_I_corner.cube 050Li3PS4-050LiI_PS4_I_edge.cube 050Li3PS4-050LiI_PS4_I_three.cube -iso 1.2e-09
import numpy as np
import os
from mayavi import mlab
ang_borr = 0.5291772109217
def read_cube(filename):
"""
.cubeファイルを読み込み、原子座標と3次元ボクセルデータを返す関数
"""
with open(filename, 'r') as f:
# ヘッダーの読み飛ばし（最初の2行はコメント）
f.readline()
f.readline()
# 3行目: 原子の数 と 原点座標
line = f.readline().split()
natoms = abs(int(line[0])) # 原子の数
origin = np.array([float(x) for x in line[1:4]]) # 原点
# 4-6行目: グリッドの分割数(N)とベクトル(X, Y, Z軸)
line = f.readline().split()
nx, x_vec = int(line[0]), np.array([float(x) for x in line[1:4]])
line = f.readline().split()
ny, y_vec = int(line[0]), np.array([float(x) for x in line[1:4]])
line = f.readline().split()
nz, z_vec = int(line[0]), np.array([float(x) for x in line[1:4]])
# 原子座標の読み込み
atoms = []
for _ in range(natoms):
line = f.readline().split()
atoms.append([float(x) for x in line[2:5]])
atoms = np.array(atoms)
# ボクセルデータの読み込み
data = []
for line in f:
data.extend([float(x) for x in line.split()])
vol_data = np.array(data).reshape(nx, ny, nz)
return vol_data, atoms, origin, (x_vec, y_vec, z_vec)
def draw_radial_scale(max_dist=10.0, step=1.0, axis='x'):
"""
原点から動径方向に目盛り（定規）を描画する
"""
if axis == 'y':
vec = np.array([0, 1, 0])
tick_dir = np.array([0.2, 0, 0])
elif axis == 'z':
vec = np.array([0, 0, 1])
tick_dir = np.array([0.2, 0, 0])
else: # default x
vec = np.array([1, 0, 0])
tick_dir = np.array([0, 0, 0.2])
# 1. メインの直線を引く
end_point = vec * max_dist
mlab.plot3d([0, end_point[0]], [0, end_point[1]], [0, end_point[2]],
tube_radius=0.02, color=(0, 0, 0))
# 2. 目盛りと数字を配置
for r in np.arange(step, max_dist + step, step):
pos = vec * r
t_start = pos - tick_dir
t_end = pos + tick_dir
mlab.plot3d([t_start[0], t_end[0]],
[t_start[1], t_end[1]],
[t_start[2], t_end[2]],
tube_radius=0.02, color=(0, 0, 0))
text_pos = pos + tick_dir * 1.5
mlab.text3d(text_pos[0], text_pos[1], text_pos[2],
f"{int(r)}", scale=0.25, color=(0, 0, 0))
def change_view(azimuth=30, elevation=60):
mlab.view(azimuth=azimuth, elevation=elevation)
def get_color_from_filename(filename):
"""
ファイル名から Edge, Corner などの判別を行い、RGBカラーを返す
"""
fname_lower = os.path.basename(filename).lower()
if 'zero' in fname_lower:
return (0.227, 0.373, 0.804) # 青色
elif 'corner' in fname_lower:
return (0.000, 0.733, 0.000) # 緑色
elif 'edge' in fname_lower:
return (0.850, 0.058, 0.058) # 赤色
elif 'three' in fname_lower:
return (0.943, 0.754, 0.000) # 黄色
else:
return (0.5, 0.5, 0.5) # 該当しない場合はグレー
def visualize_cubes(filenames, iso_val=None, cutoff=8):
"""
複数のcubeファイルを読み込んで可視化する
"""
mlab.figure(bgcolor=(1, 1, 1), size=(800, 600))
atoms_drawn = False
for filename in filenames:
print(f"Reading {filename}...")
vol_data, atoms, origin, vectors = read_cube(filename)
atoms = atoms * ang_borr
origin_ang = origin * ang_borr
dx = np.linalg.norm(vectors[0]) * ang_borr
dy = np.linalg.norm(vectors[1]) * ang_borr
dz = np.linalg.norm(vectors[2]) * ang_borr
# iso_val が未指定の場合はデータから自動計算
current_iso = iso_val
if current_iso is None:
current_iso = np.std(vol_data) * 2.0
print(f" -> Plotting isosurface at value: +/- {current_iso:.4e}")
# --- カットオフによるデータの球状マスク処理 ---
if cutoff is not None:
nx, ny, nz = vol_data.shape
x = origin_ang[0] + np.arange(nx) * dx
y = origin_ang[1] + np.arange(ny) * dy
z = origin_ang[2] + np.arange(nz) * dz
X, Y, Z = np.meshgrid(x, y, z, indexing='ij')
R = np.sqrt(X**2 + Y**2 + Z**2)
vol_data[R > cutoff] = 0.0
print(f" -> max_value: {np.max(vol_data):.4e}, min_value: {np.min(vol_data):.4e}")
# --- 確率密度 ---
src_in = mlab.pipeline.scalar_field(vol_data)
src_in.spacing = [dx, dy, dz]
src_in.origin = origin_ang
# ファイル名から色を取得
color = get_color_from_filename(filename)
# 等値面の描画
mlab.pipeline.iso_surface(src_in, contours=[current_iso], opacity=0.3, color=color)
# --- 原子の描画（最初の1回のみ実行） ---
if not atoms_drawn:
mlab.points3d(atoms[0, 0], atoms[0, 1], atoms[0, 2],
scale_factor=0.8, color=(0.576, 0.439, 0.8), resolution=20)
mlab.points3d(atoms[1:, 0], atoms[1:, 1], atoms[1:, 2],
scale_factor=0.8, color=(1, 1, 0), resolution=20)
# --- 結合の描画 ---
p_coord = atoms[0]
s_coords = atoms[1:]
for s_coord in s_coords:
mlab.plot3d([p_coord[0], s_coord[0]],
[p_coord[1], s_coord[1]],
[p_coord[2], s_coord[2]],
tube_radius=0.1, color=(0.6, 0.6, 0.6), opacity=1.0)
# 半径の基準となるうすい球の描画
mlab.points3d(0, 0, 0, scale_factor=cutoff * 2,
mode='sphere', color=(0, 0, 0), opacity=0.05, resolution=50)
atoms_drawn = True
# --- 実行部分 ---
if __name__ == "__main__":
import argparse
description = """Visualizes multiple cube files with different colors based on their filenames."""
par = argparse.ArgumentParser(description=description)
# 複数ファイルを受け取れるように nargs="+" を設定（既存のまま）
par.add_argument('-i', '--infiles', default=[], required=True, nargs="+",
help='input cube files (e.g., *_I_*.cube)')
par.add_argument('-iso', '--iso_val', required=False, type=float,
help='Threshold for isosurface (しきい値)')
args = par.parse_args()
# 複数ファイルをリストとして渡す
visualize_cubes(args.infiles, iso_val=args.iso_val)
mlab.show()