Refactor meshing code (#140)

* Re-organize code
* Use delayed typing/TYPE_CHECKING to avoid circular imports (https://stackoverflow.com/a/69427502)
* Use relative imports where possible
* Fix bugs in notebooks

nanomesh/__init__.py

@@ -1,8 +1,9 @@
-# -*- coding: utf-8 -*-
-"""Documentation about nanomesh."""
 import logging
 import sys
 
+from .mesh2d import Mesher2D, compare_mesh_with_image, simple_triangulate
+from .mesh3d import Mesher3D
+from .mesh_container import TetraMesh, TriangleMesh
 from .plane import Plane
 from .volume import Volume
 
@@ -18,6 +19,12 @@
     '__author__',
     '__email__',
     '__version__',
+    'compare_mesh_with_image',
+    'Mesher2D',
+    'Mesher3D',
     'Plane',
+    'simple_triangulate',
+    'TetraMesh',
+    'TriangleMesh',
     'Volume',
 ]

nanomesh/_mesh_shared.py

@@ -3,7 +3,8 @@
 
 import numpy as np
 
-from nanomesh import Plane, Volume
+from .plane import Plane
+from .volume import Volume
 
 logger = logging.getLogger(__name__)
 

nanomesh/mesh2d/__init__.py

@@ -0,0 +1,10 @@
+from .helpers import compare_mesh_with_image, pad, simple_triangulate
+from .mesher import Mesher2D, generate_2d_mesh
+
+__all__ = [
+    'compare_mesh_with_image',
+    'generate_2d_mesh',
+    'Mesher2D',
+    'pad',
+    'simple_triangulate',
+]

nanomesh/mesh_utils.py → nanomesh/mesh2d/helpers.py

@@ -1,8 +1,13 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 import matplotlib.pyplot as plt
 import numpy as np
 import triangle as tr
 
-from nanomesh.mesh_container import TriangleMesh
+if TYPE_CHECKING:
+    from nanomesh.mesh_container import TriangleMesh
 
 
 def _legend_with_triplot_fix(ax: plt.Axes):
@@ -72,6 +77,8 @@ def simple_triangulate(points: np.ndarray,
     mesh : TriangleMesh
         Triangle mesh
     """
+    from nanomesh.mesh_container import TriangleMesh
+
     triangle_dict_in = {'vertices': points}
 
     if segments is not None:
@@ -118,6 +125,8 @@ def pad(mesh: TriangleMesh,
     ValueError
         When the value of `side` is invalid.
     """
+    from nanomesh.mesh_container import TriangleMesh
+
     if label is None:
         label = mesh.unique_labels.max() + 1
 

nanomesh/mesh2d.py → nanomesh/mesh2d/mesher.py

@@ -6,10 +6,10 @@
 import numpy as np
 from skimage import measure
 
-from nanomesh.mesh_utils import simple_triangulate
+from nanomesh._mesh_shared import BaseMesher
+from nanomesh.mesh_container import TriangleMesh
 
-from ._mesh_shared import BaseMesher
-from .mesh_container import TriangleMesh
+from .helpers import simple_triangulate
 
 logger = logging.getLogger(__name__)
 

nanomesh/mesh3d/__init__.py

@@ -0,0 +1,10 @@
+from .bounding_box import BoundingBox
+from .helpers import pad
+from .mesher import Mesher3D, generate_3d_mesh, get_region_markers
+
+__all__ = [
+    'BoundingBox',
+    'generate_3d_mesh',
+    'Mesher3D',
+    'pad',
+]

nanomesh/mesh3d/bounding_box.py

@@ -0,0 +1,73 @@
+from dataclasses import dataclass
+from typing import Tuple
+
+import numpy as np
+
+
+@dataclass
+class BoundingBox:
+    """Container for bounding box coordinates."""
+    xmin: float
+    xmax: float
+    ymin: float
+    ymax: float
+    zmin: float
+    zmax: float
+
+    @classmethod
+    def from_shape(cls, shape: tuple):
+        """Generate bounding box from data shape."""
+        xmin, ymin, zmin = 0, 0, 0
+        xmax, ymax, zmax = np.array(shape) - 1
+        return cls(xmin=xmin,
+                   ymin=ymin,
+                   zmin=zmin,
+                   xmax=xmax,
+                   ymax=ymax,
+                   zmax=zmax)
+
+    @property
+    def dimensions(self) -> Tuple[float, float, float]:
+        """Return dimensions of bounding box."""
+        return (
+            self.xmax - self.xmin,
+            self.ymax - self.ymin,
+            self.zmax - self.zmin,
+        )
+
+    @classmethod
+    def from_points(cls, points: np.array):
+        """Generate bounding box from set of points or coordinates."""
+        xmax, ymax, zmax = np.max(points, axis=0)
+        xmin, ymin, zmin = np.min(points, axis=0)
+
+        return cls(
+            xmin=xmin,
+            xmax=xmax,
+            ymin=ymin,
+            ymax=ymax,
+            zmin=zmin,
+            zmax=zmax,
+        )
+
+    def to_points(self) -> np.ndarray:
+        """Return (m,3) array with corner points."""
+        return np.array([
+            [self.xmin, self.ymin, self.zmin],
+            [self.xmin, self.ymin, self.zmax],
+            [self.xmin, self.ymax, self.zmin],
+            [self.xmin, self.ymax, self.zmax],
+            [self.xmax, self.ymin, self.zmin],
+            [self.xmax, self.ymin, self.zmax],
+            [self.xmax, self.ymax, self.zmin],
+            [self.xmax, self.ymax, self.zmax],
+        ])
+
+    @property
+    def center(self) -> np.ndarray:
+        """Return center of the bounding box."""
+        return np.array((
+            (self.xmin + self.xmax) / 2,
+            (self.ymin + self.ymax) / 2,
+            (self.zmin + self.zmax) / 2,
+        ))

nanomesh/mesh_utils_3d.py → nanomesh/mesh3d/helpers.py

@@ -1,16 +1,23 @@
+from __future__ import annotations
+
+from typing import TYPE_CHECKING
+
 import numpy as np
 
-from nanomesh.mesh3d import BoundingBox
-from nanomesh.mesh_container import TriangleMesh
 from nanomesh.utils import pairwise
 
+from .bounding_box import BoundingBox
+
+if TYPE_CHECKING:
+    from nanomesh.mesh_container import TriangleMesh
+
 
-def pad3d(mesh: TriangleMesh,
-          *,
-          side: str,
-          width: int,
-          label: int = None) -> TriangleMesh:
-    """Pad a tetra mesh.
+def pad(mesh: TriangleMesh,
+        *,
+        side: str,
+        width: int,
+        label: int = None) -> TriangleMesh:
+    """Pad a triangle mesh.
 
     Parameters
     ----------
@@ -137,7 +144,7 @@ def pad3d(mesh: TriangleMesh,
 
     cells = np.vstack([mesh.cells, new_triangles])
 
-    new_mesh = TriangleMesh(points=points, cells=cells)
+    new_mesh = mesh.__class__(points=points, cells=cells)
 
     center = extra_coords.mean(axis=0)
     center[col] = (center[col] + edge_value) / 2

nanomesh/mesh3d.py → nanomesh/mesh3d/mesher.py

@@ -1,88 +1,23 @@
+from __future__ import annotations
+
 import logging
-from dataclasses import dataclass
-from typing import List, Tuple, Union
+from typing import TYPE_CHECKING, List, Tuple, Union
 
 import matplotlib.pyplot as plt
 import meshio
 import numpy as np
 from skimage import measure, morphology
 
-from nanomesh import Volume
-from nanomesh.mesh_utils import simple_triangulate
+from nanomesh._mesh_shared import BaseMesher
+from nanomesh.mesh2d import simple_triangulate
+from nanomesh.volume import Volume
 
-from ._mesh_shared import BaseMesher
-from .mesh_container import TriangleMesh
+from .bounding_box import BoundingBox
 
 logger = logging.getLogger(__name__)
 
-
-@dataclass
-class BoundingBox:
-    """Container for bounding box coordinates."""
-    xmin: float
-    xmax: float
-    ymin: float
-    ymax: float
-    zmin: float
-    zmax: float
-
-    @classmethod
-    def from_shape(cls, shape: tuple):
-        """Generate bounding box from data shape."""
-        xmin, ymin, zmin = 0, 0, 0
-        xmax, ymax, zmax = np.array(shape) - 1
-        return cls(xmin=xmin,
-                   ymin=ymin,
-                   zmin=zmin,
-                   xmax=xmax,
-                   ymax=ymax,
-                   zmax=zmax)
-
-    @property
-    def dimensions(self) -> Tuple[float, float, float]:
-        """Return dimensions of bounding box."""
-        return (
-            self.xmax - self.xmin,
-            self.ymax - self.ymin,
-            self.zmax - self.zmin,
-        )
-
-    @classmethod
-    def from_points(cls, points: np.array):
-        """Generate bounding box from set of points or coordinates."""
-        xmax, ymax, zmax = np.max(points, axis=0)
-        xmin, ymin, zmin = np.min(points, axis=0)
-
-        return cls(
-            xmin=xmin,
-            xmax=xmax,
-            ymin=ymin,
-            ymax=ymax,
-            zmin=zmin,
-            zmax=zmax,
-        )
-
-    def to_points(self) -> np.ndarray:
-        """Return (m,3) array with corner points."""
-        return np.array([
-            [self.xmin, self.ymin, self.zmin],
-            [self.xmin, self.ymin, self.zmax],
-            [self.xmin, self.ymax, self.zmin],
-            [self.xmin, self.ymax, self.zmax],
-            [self.xmax, self.ymin, self.zmin],
-            [self.xmax, self.ymin, self.zmax],
-            [self.xmax, self.ymax, self.zmin],
-            [self.xmax, self.ymax, self.zmax],
-        ])
-
-    @property
-    def center(self) -> np.ndarray:
-        """Return center of the bounding box."""
-        return np.array((
-            (self.xmin + self.xmax) / 2,
-            (self.ymin + self.ymax) / 2,
-            (self.zmin + self.zmax) / 2,
-        ))
+if TYPE_CHECKING:
+    from nanomesh.mesh_container import TriangleMesh
 
 
 def get_point_in_prop(
@@ -165,7 +100,11 @@ def add_corner_points(mesh: TriangleMesh, bbox: BoundingBox) -> None:
     mesh.points = np.vstack([mesh.points, corners])
 
 
-def close_side(mesh, *, side: str, bbox: BoundingBox, ax: plt.Axes = None):
+def close_side(mesh: TriangleMesh,
+               *,
+               side: str,
+               bbox: BoundingBox,
+               ax: plt.Axes = None):
     """Fill a side of the bounding box with triangles.
 
     Parameters
@@ -190,6 +129,7 @@ def close_side(mesh, *, side: str, bbox: BoundingBox, ax: plt.Axes = None):
     ValueError
         When the value of `side` is invalid.
     """
+    from nanomesh.mesh_container import TriangleMesh
     all_points = mesh.points
 
     if side == 'top':
@@ -301,6 +241,8 @@ def generate_contour(
             By default takes the average of the min and max value. Can be
             ignored if a binary image is passed to `Mesher3D`.
         """
+        from nanomesh.mesh_container import TriangleMesh
+
         points, cells, *_ = measure.marching_cubes(
             self.image,
             level=level,