finally fixed from_pointcloud!

bdm_voxel_builder/__main__.py

@@ -7,7 +7,7 @@
 from bdm_voxel_builder.config_setup import Config
 from bdm_voxel_builder.environment import Environment
 from bdm_voxel_builder.helpers import (
-    pointcloud_from_ndarray,
+    pointcloud_from_grid_array,
     save_ndarray,
     save_pointcloud,
 )
@@ -45,7 +45,7 @@ def simulate(frame, config: Config = None, sim_state: Environment = None):
 
         save_ndarray(a1, note=note)
 
-        pointcloud, values = pointcloud_from_ndarray(a1, return_values=True)
+        pointcloud, values = pointcloud_from_grid_array(a1, return_values=True)
         save_pointcloud(pointcloud, values=values, note=note)
 
         sim_state.grids[algo.grid_to_dump].save_vdb()

bdm_voxel_builder/agent_algorithms/algo_10_a_slicer_agents.py

@@ -347,7 +347,7 @@ def check_print_chance(self, agent: Agent, state: Environment):
                     if print_density_below >= 0.33:
                         agent.build_chance = 1
                 elif self.overhang_limit <= 45 and print_density_below >= 0.5:
-                        agent.build_chance = 1
+                    agent.build_chance = 1
                 # elif self.overhang_limit <= 60:
                 #     if print_density_below >= 0.5 and print_density_below_2 >= 0.5:
                 #         self.build_chance = 1
@@ -357,9 +357,7 @@ def check_print_chance(self, agent: Agent, state: Environment):
         #     build chance: {agent.build_chance}.
         # """)
 
-
     def print_build_3x3(self, agent: Agent, state: Environment):
-
         """add index the print_dot list, and fill 3x3 voxel in the printed_clay grid"""
         built = False
         printed_clay = state.grids["printed_clay"]
@@ -388,7 +386,7 @@ def print_build(self, agent: Agent, state: Environment):
         """add index the print_dot list, and fill either:
         - one_voxel
         - voxels in cross shape
-        - or voxels in 3x3 square 
+        - or voxels in 3x3 square
         of the printed_clay grid"""
         built = False
         printed_clay = state.grids["printed_clay"]

bdm_voxel_builder/grid/base.py

@@ -11,13 +11,15 @@
 
 from bdm_voxel_builder import TEMP_DIR
 from bdm_voxel_builder.helpers import (
-    convert_array_to_pts,
+    convert_grid_array_to_pts,
     get_savepath,
-    get_xform_box2grid,
     pointcloud_to_grid_array,
     xform_to_compas,
     xform_to_vdb,
 )
+from bdm_voxel_builder.helpers.geometry import (
+    _get_xform_box2grid,
+)
 
 
 class Grid:
@@ -125,7 +127,7 @@ def get_number_of_active_voxels(self):
         return len(self.array[self.get_active_voxels()])
 
     def get_index_pts(self) -> list[list[float]]:
-        return convert_array_to_pts(self.array, get_data=False)
+        return convert_grid_array_to_pts(self.array)
 
     def get_index_pointcloud(self):
         return cg.Pointcloud(self.get_index_pts())
@@ -198,13 +200,18 @@ def from_pointcloud(
         if not grid_size:
             grid_size = max(pointcloud.aabb.dimensions) // voxel_edge_length + 1
 
-        T = get_xform_box2grid(pointcloud.aabb, grid_size=grid_size)
+        # TODO: Replace with multiplied version
+        Sc, R, Tl = _get_xform_box2grid(pointcloud.aabb, grid_size=grid_size)
+
+        pointcloud_transformed = pointcloud.copy()
 
-        pointcloud_transformed_for_grid = pointcloud.transformed(T) 
+        pointcloud_transformed.transform(Tl)
+        pointcloud_transformed.transform(R)
+        pointcloud_transformed.transform(Sc)
 
-        array = pointcloud_to_grid_array(pointcloud_transformed_for_grid, grid_size)
+        array = pointcloud_to_grid_array(pointcloud_transformed, grid_size)
 
-        return cls(grid_size=grid_size, name=name, xform=T, array=array)
+        return cls(grid_size=grid_size, name=name, xform=Tl * R * Sc, array=array)
 
     @classmethod
     def from_ply(

bdm_voxel_builder/helpers/__init__.py

@@ -25,10 +25,10 @@
 )
 from .geometry import (
     box_from_corner_frame,
-    convert_array_to_pts,
+    convert_grid_array_to_pts,
     get_xform_box2grid,
     ply_to_compas,
-    pointcloud_from_ndarray,
+    pointcloud_from_grid_array,
     pointcloud_to_grid_array,
 )
 from .math import remap, remap_trim

bdm_voxel_builder/helpers/file.py

@@ -25,11 +25,11 @@ def get_savepath(dir: Path, suffix: str, note: str = None):
     return Path(dir) / filename
 
 
-def get_nth_newest_file_in_folder(folder_path: os.PathLike, n = 0):
+def get_nth_newest_file_in_folder(folder_path: os.PathLike, n=0):
     folder_path = Path(folder_path)
 
     # Get a list of files in the folder
-    files = list(folder_path.glob('*'))
+    files = list(folder_path.glob("*"))
 
     # Sort the files by change time (modification time) in descending order
     files.sort(key=lambda x: x.stat().st_mtime, reverse=True)
@@ -45,6 +45,5 @@ def save_pointcloud(
     json_dump(dict_, get_savepath(TEMP_DIR, ".json", note=note))
 
 
-
 def save_ndarray(arr: npt.NDArray, note: str = None):
     np.save(get_savepath(TEMP_DIR, ".npy", note=note), arr)

bdm_voxel_builder/helpers/geometry.py

@@ -19,19 +19,7 @@ def box_from_corner_frame(frame: cg.Frame, xsize: float, ysize: float, zsize: fl
     return cg.Box(xsize=xsize, ysize=ysize, zsize=zsize, frame=center_frame)
 
 
-def _convert_array_to_pts_wo_data(arr: npt.NDArray) -> list[list[float]]:
-    pts = []
-    for i, j, k in zip(*np.nonzero(arr), strict=False):
-        pts.append([i, j, k])
-    return pts
-
-
-def convert_array_to_pts(
-    arr: npt.NDArray, get_data=True
-) -> list[list[float] | npt.NDArray]:
-    if not get_data:
-        return _convert_array_to_pts_wo_data(arr)
-
+def convert_grid_array_to_pts(arr: npt.NDArray) -> npt.NDArray:
     indicies = np.indices(arr.shape)
     pt_location = np.logical_not(arr == 0)
 
@@ -52,13 +40,45 @@ def get_xform_box2grid(
 
     scale_factor = float(max(grid_size) - 1) / max(box.dimensions)
 
-    S = cg.Scale.from_factors([scale_factor] * 3)
+    Sc = cg.Scale.from_factors([scale_factor] * 3)
 
     v = cg.Vector(box.xmin, box.ymin, box.zmin) * scale_factor
 
-    Tr = cg.Translation.from_vector(v.inverted())
+    Tl = cg.Translation.from_vector(v.inverted())
+
+    return Tl * R * Sc
+
+
+def _get_xform_box2grid(
+    box: cg.Box, grid_size: tuple[int, int, int]
+) -> cg.Transformation:
+    """Get the linear transformation between two bounding boxes with uniform
+    scaling."""
+    Sc = get_scaling_box2grid(box, grid_size)
+    R = get_rotation_box2grid(box)
+    Tl = get_translation_box2grid(box, grid_size)
+
+    return Sc, R, Tl
+
+
+
+def get_translation_box2grid(
+    box: cg.Box, grid_size: tuple[int, int, int]
+) -> cg.Translation:
+    """Get the translation between bounding box and grid."""
+    v = cg.Vector(box.xmin, box.ymin, box.zmin)
+
+    return cg.Translation.from_vector(v.inverted())
+
+
+def get_scaling_box2grid(box: cg.Box, grid_size: tuple[int, int, int]) -> cg.Scale:
+    """Get the scaling needed between bounding box and grid."""
+    return cg.Scale.from_factors([float(max(grid_size) - 1) / max(box.dimensions)] * 3)
+
 
-    return Tr * R * S
+def get_rotation_box2grid(box: cg.Box) -> cg.Rotation:
+    """Get the rotation needed between bounding box and grid."""
+    return cg.Rotation.from_frame_to_frame(box.frame, cg.Frame.worldXY())
 
 
 def ply_to_array(ply_path: os.PathLike, precision: str = None):
@@ -75,7 +95,7 @@ def ply_to_compas(ply_path: os.PathLike, precision: str = None):
     return cg.Pointcloud(ply.parser.vertices)
 
 
-def pointcloud_from_ndarray(arr: npt.NDArray, return_values=False):
+def pointcloud_from_grid_array(arr: npt.NDArray, return_values=False):
     pts, values = sort_pts_by_values(arr)
 
     pointcloud = cg.Pointcloud(pts)
@@ -87,25 +107,23 @@ def pointcloud_from_ndarray(arr: npt.NDArray, return_values=False):
 
 
 def pointcloud_to_grid_array(
-    pointcloud: cg.Pointcloud, grid_size: tuple[int, int, int], dtype=int, value=1
+    pointcloud: cg.Pointcloud, grid_size: tuple[int, int, int], dtype=np.int8, value=1
 ):
     """Convert a pointcloud to a grid."""
     if not isinstance(grid_size, Sequence):
         grid_size = (grid_size, grid_size, grid_size)
 
     grid_array = np.zeros(grid_size)
 
-    pts = np.array(pointcloud).floor().astype(dtype=dtype)
+    indices = np.array(pointcloud.points).round().astype(np.int8)
 
-    if pts.min() < 0:
+    if indices.min() < 0:
         raise ValueError(
             "Pointcloud contains negative values, needs to be transformed to index grid."
         )  # noqa: E501
 
-    for i, j, k in pts:
-        if (i, j, k) > grid_size:
-            raise ValueError(
-                "Pointcloud contains values that are larger than grid size."
-            )
+    for i, j, k in indices:
+        if max((i, j, k)) >= max(grid_size):
+            raise IndexError(f"Index out of bounds: {i,j,k} in {grid_size}")
         grid_array[i, j, k] = value
-    return grid_array
+    return grid_array.astype(dtype)

bdm_voxel_builder/helpers/math.py

@@ -1,4 +1,3 @@
-
 def remap_trim(
     x,
     output_domain,

bdm_voxel_builder/visualizer/compas_viewer.py

@@ -3,7 +3,7 @@
 from compas_viewer import Viewer
 
 from bdm_voxel_builder import TEMP_DIR
-from bdm_voxel_builder.helpers import convert_array_to_pts, get_savepath
+from bdm_voxel_builder.helpers import convert_grid_array_to_pts, get_savepath
 from bdm_voxel_builder.visualizer.base import Visualizer
 
 
@@ -46,7 +46,7 @@ def draw(self, iteration_count=None):
                 continue
             parent = self.scene.get_node_by_name(grid.name)
 
-            pts = convert_array_to_pts(grid.array, get_data=False)
+            pts = convert_grid_array_to_pts(grid.array)
 
             iteration = iteration_count or len(parent.children)
             name = f"{grid.name}_{iteration}"

bdm_voxel_builder/visualizer/matplotlib.py

@@ -8,7 +8,7 @@
 from bdm_voxel_builder import TEMP_DIR
 from bdm_voxel_builder.config_setup import Config
 from bdm_voxel_builder.environment import Environment
-from bdm_voxel_builder.helpers import convert_array_to_pts, get_savepath
+from bdm_voxel_builder.helpers import convert_grid_array_to_pts, get_savepath
 from bdm_voxel_builder.visualizer.base import Visualizer
 
 
@@ -94,7 +94,7 @@ def clear(self):
 
     def draw(self):
         for grid in self.grids:
-            pts = np.array(convert_array_to_pts(grid.array)).transpose()
+            pts = np.array(convert_grid_array_to_pts(grid.array)).transpose()
             self.ax1.scatter(
                 pts[0, :],
                 pts[1, :],