Merge pull request #71 from autotwin/spheres

autotwin · Sep 13, 2024 · 789d243 · 789d243
2 parents ddf542e + dbe546a
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diff --git a/.github/workflows/python.yml b/.github/workflows/python.yml
@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     runs-on: ${{ matrix.os }}
     steps:
     - name: checkout
@@ -41,7 +41,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.9', '3.10', '3.11', '3.12']
     runs-on: ${{ matrix.os }}
     steps:
     - uses: actions/checkout@v4

diff --git a/book/SUMMARY.md b/book/SUMMARY.md
@@ -6,6 +6,8 @@
 
 - [Installation](installation.md)
 - [Mathematics](mathematics.md)
+- [Examples](examples/README.md)
+  - [Spheres](examples/spheres/README.md)
 
 # Reference Guide
 

diff --git a/book/examples/README.md b/book/examples/README.md
@@ -0,0 +1,3 @@
+# Examples
+
+Following are examples created with `automesh`.
diff --git a/book/examples/spheres/README.md b/book/examples/spheres/README.md
@@ -0,0 +1,117 @@
+# Spheres
+
+## Segmentation
+
+Using [spheres.py](spheres.py), 
+
+```python
+<!-- cmdrun cat spheres.py -->
+```
+
+create very coarse spheres of varying
+resolution (`radius=1`, `radius=3`, and `radius=5`), as shown below:
+
+![spheres.png](spheres.png)
+
+For the `radius=1` case, the underyling data structure appears as:
+
+```python
+spheres["ball_1"]
+
+array([[[0, 0, 0],
+        [0, 1, 0],
+        [0, 0, 0]],
+
+       [[0, 1, 0],
+        [1, 1, 1],
+        [0, 1, 0]],
+
+       [[0, 0, 0],
+        [0, 1, 0],
+        [0, 0, 0]]], dtype=uint8)
+```
+
+For the `radius=3` case, the underyling data structure appears as:
+
+```python
+spheres["ball_3"]
+
+array([[[0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 1, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0]],
+
+       [[0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 1, 1, 1, 0, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 0, 1, 1, 1, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0]],
+
+       [[0, 0, 0, 0, 0, 0, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 0, 0, 0, 0, 0, 0]],
+
+       [[0, 0, 0, 1, 0, 0, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [1, 1, 1, 1, 1, 1, 1],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 0, 0, 1, 0, 0, 0]],
+
+       [[0, 0, 0, 0, 0, 0, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 0, 0, 0, 0, 0, 0]],
+
+       [[0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 1, 1, 1, 0, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 1, 1, 1, 1, 1, 0],
+        [0, 0, 1, 1, 1, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0]],
+
+       [[0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 1, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 0, 0, 0]]], dtype=uint8)
+```
+
+Because of the large size of `ball_5`, its data structure is not shown
+here.
+
+These data structures are saved to
+
+* [spheres_ball_1_.npy](spheres_ball_1_.npy)
+* [spheres_ball_3_.npy](spheres_ball_3_.npy)
+* [spheres_ball_5_.npy](spheres_ball_5_.npy)
+
+## Mesh
+
+```sh
+cargo run -- -i book/examples/spheres/spheres_ball_1_.npy -o book/examples/spheres/spheres_ball_1_.inp -x 3 -y 3 -z 3
+```
+
+```sh
+cargo run -- -i book/examples/spheres/spheres_ball_3_.npy -o book/examples/spheres/spheres_ball_3_.inp -x 7 -y 7 -z 7
+```
+
+```sh
+cargo run -- -i book/examples/spheres/spheres_ball_5_.npy -o book/examples/spheres/spheres_ball_5_.inp -x 11 -y 11 -z 11
+```
diff --git a/book/examples/spheres/spheres.png b/book/examples/spheres/spheres.png
diff --git a/book/examples/spheres/spheres.py b/book/examples/spheres/spheres.py
@@ -0,0 +1,82 @@
+"""This module demonstrates how to create a voxelized sphere and export
+it as a .npy file.
+
+Items that need to be installed into the virtual environment:
+    pip install scikit-image
+
+"""
+
+import matplotlib.pyplot as plt
+from matplotlib.colors import LightSource
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+from pathlib import Path
+from typing import Final
+
+from skimage.morphology import ball
+
+
+# User input begin
+
+spheres = {
+    "ball_1": ball(radius=1),
+    "ball_3": ball(radius=3),
+    "ball_5": ball(radius=5),
+}
+
+aa = Path(__file__)
+bb = aa.with_suffix(".png")
+
+# Visualize the elements.
+# width, height = 8, 4
+width, height = 6, 3
+fig = plt.figure(figsize=(width, height))
+# fig = plt.figure(figsize=(8, 8))
+
+el, az, roll = 63, -110, 0
+cmap = plt.get_cmap(name="tab10")
+num_colors = len(spheres)
+voxel_alpha: Final[float] = 0.9
+
+colors = cmap(np.linspace(0, 1, num_colors))
+lightsource = LightSource(azdeg=325, altdeg=45)  # azimuth, elevation
+# lightsource = LightSource(azdeg=325, altdeg=90)  # azimuth, elevation
+dpi: Final[int] = 300  # resolution, dots per inch
+serialize: Final[bool] = False  # turn to True to save .png and .npy files
+# User input end
+
+
+idx = 1
+for title, struc in spheres.items():
+    ax = fig.add_subplot(1, 3, idx, projection=Axes3D.name)
+    ax.voxels(
+        struc,
+        facecolors=colors[idx-1],
+        edgecolor=colors[idx-1],
+        alpha=voxel_alpha,
+        lightsource=lightsource)
+    ax.set_title(title)
+    idx += 1
+
+    # Set labels for the axes
+    ax.set_xlabel("x")
+    ax.set_ylabel("y")
+    ax.set_zlabel("z")
+
+    # Set the camera view
+    ax.set_aspect("equal")
+    ax.view_init(elev=el, azim=az, roll=roll)
+
+    if serialize:
+        cc = aa.with_stem("spheres_" + title + "_")
+        dd = cc.with_suffix(".npy")
+        # Save the data in .npy format
+        np.save(dd, struc)
+        print(f"Saved: {dd}")
+
+fig.tight_layout()
+plt.show()
+
+if serialize:
+    fig.savefig(bb, dpi=dpi)
+    print(f"Saved: {bb}")
diff --git a/book/examples/spheres/spheres_ball_1_.inp b/book/examples/spheres/spheres_ball_1_.inp
@@ -0,0 +1,49 @@
+*HEADING
+autotwin.automesh
+version 0.1.3
+autogenerated on 2024-09-11 23:05:42.323084 UTC
+**
+*NODE, NSET=ALLNODES
+     1,      1.000000e0,      1.000000e0,      0.000000e0
+     2,      2.000000e0,      1.000000e0,      0.000000e0
+     3,      1.000000e0,      2.000000e0,      0.000000e0
+     4,      2.000000e0,      2.000000e0,      0.000000e0
+     5,      1.000000e0,      0.000000e0,      1.000000e0
+     6,      2.000000e0,      0.000000e0,      1.000000e0
+     7,      0.000000e0,      1.000000e0,      1.000000e0
+     8,      1.000000e0,      1.000000e0,      1.000000e0
+     9,      2.000000e0,      1.000000e0,      1.000000e0
+    10,      3.000000e0,      1.000000e0,      1.000000e0
+    11,      0.000000e0,      2.000000e0,      1.000000e0
+    12,      1.000000e0,      2.000000e0,      1.000000e0
+    13,      2.000000e0,      2.000000e0,      1.000000e0
+    14,      3.000000e0,      2.000000e0,      1.000000e0
+    15,      1.000000e0,      3.000000e0,      1.000000e0
+    16,      2.000000e0,      3.000000e0,      1.000000e0
+    17,      1.000000e0,      0.000000e0,      2.000000e0
+    18,      2.000000e0,      0.000000e0,      2.000000e0
+    19,      0.000000e0,      1.000000e0,      2.000000e0
+    20,      1.000000e0,      1.000000e0,      2.000000e0
+    21,      2.000000e0,      1.000000e0,      2.000000e0
+    22,      3.000000e0,      1.000000e0,      2.000000e0
+    23,      0.000000e0,      2.000000e0,      2.000000e0
+    24,      1.000000e0,      2.000000e0,      2.000000e0
+    25,      2.000000e0,      2.000000e0,      2.000000e0
+    26,      3.000000e0,      2.000000e0,      2.000000e0
+    27,      1.000000e0,      3.000000e0,      2.000000e0
+    28,      2.000000e0,      3.000000e0,      2.000000e0
+    29,      1.000000e0,      1.000000e0,      3.000000e0
+    30,      2.000000e0,      1.000000e0,      3.000000e0
+    31,      1.000000e0,      2.000000e0,      3.000000e0
+    32,      2.000000e0,      2.000000e0,      3.000000e0
+**
+*ELEMENT, TYPE=C3D8R, ELSET=EB1
+    1,     1,     2,     4,     3,     8,     9,    13,    12
+    2,     5,     6,     9,     8,    17,    18,    21,    20
+    3,     7,     8,    12,    11,    19,    20,    24,    23
+    4,     8,     9,    13,    12,    20,    21,    25,    24
+    5,     9,    10,    14,    13,    21,    22,    26,    25
+    6,    12,    13,    16,    15,    24,    25,    28,    27
+    7,    20,    21,    25,    24,    29,    30,    32,    31
+**
+*SOLID SECTION, ELSET=EB1, MATERIAL=Default-Steel
diff --git a/book/examples/spheres/spheres_ball_1_.npy b/book/examples/spheres/spheres_ball_1_.npy