Squashed commit of the following:

commit 46fe6aa
Merge: 6b2a13d 60d436b
Author: jrb20008 <joseph.bellemare@uconn.edu>
Date:   Tue Mar 25 12:23:57 2025 -0400

    Merge branch 'main' of https://github.uconn.edu/tjs20011/SDP-37-Model

commit 60d436b
Author: Joseph R Bellemare <joseph.bellemare@uconn.edu>
Date:   Tue Mar 25 12:21:55 2025 -0400

    Dataset generation (#4)

    * Squashed commit of the following:

    commit 4acc015
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Sun Mar 9 18:00:03 2025 -0400

        Added normalize function

        Added function to normalize the scale of meshes

    commit e685ab2
    Merge: 968cbac cc38025
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 21:28:20 2025 -0500

        Merge branch 'main' into shipgen-integration

    commit 968cbac
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:58:29 2025 -0500

        Added conversion

        Added helper functions to convert stl.Mesh's to triangle arrays

    commit 13a589f
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:47:02 2025 -0500

        Cleaned up Generate

    commit 22876e9
    Merge: f92334b adb4ab8
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:08:58 2025 -0500

        Merge branch 'main' into shipgen-integration

    commit f92334b
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:39:31 2025 -0500

        Renamed parameters

    commit f261895
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:37:13 2025 -0500

        Stopped warning message

    commit bf90105
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:26:12 2025 -0500

        Fixed unused parameter

    commit f79dbc1
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:14:46 2025 -0500

        Removed need to save stl's

    commit c640f6c
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:05:02 2025 -0500

        Improved typing

    commit 19cf09b
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 18:48:43 2025 -0500

        Added hull generator

    commit e8845c8
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 16:18:36 2025 -0500

        Uploaded streamlined ShipGen

        Uploaded a version of ShipGen modified from https://www.dropbox.com/sh/jg98r425v7ly89l/AAA49uMr7_mhaVmRDrPq0NU_a?dl=0 with all non-essential files removed

    * Added Custom Types

    Everything runs abut half as fast but it is much less error prone and more readable

    * Changed Raytrace Imports

    Change the Raytrace library so that mesh classes can be imported directly

    * Restructured Raytrace Library

    Moved the mesh classes into their own folder

    * Fixed Typo Related Bug

    Passing a Vector3 to the Vector3 constructor no longer causes an error

    * Redid Custom Types

    Custom types are now better integrated with numpy to get speed back to around where they were (well, 2/3rds the speed but whos counting)

    * Added Triangle output to Raytrace

    Raytracing functions now return a distance and a triangle. Subclasses now overwrite the raytrace_as_tri method

    * Added Explicate Reexports

    Added reexports to AUVSim

    * Created Generate Folder

    * Created Scan Utilities

    Added functions to help position AUVs and scan paths

    * Made CompositeMesh.triangles getter

    Modified CompositeMesh to make instantiating large quantities less intensive

    * Renamed AUV Utilities

    * Added Parallelism to AUV Utilities

    Made functions in the AUV utilities that take arrays in addition to their single value counter-parts

    * Added Hull Utilities

    Added utilities for generating hulls and placing anomalies

    * Created Outline

    Added an outline notebook that walks through how to create items for the dataset

    * Fixed Point Randomizer

    Fixed bug where random point had a 50% chance of not being on the triangle

    * Fixed Surface Normal

    * Fixed Outline

commit fd0b115
Author: Joseph R Bellemare <joseph.bellemare@uconn.edu>
Date:   Tue Mar 25 12:13:59 2025 -0400

    Typing Overhaul (#3)

    * Added Custom Types

    Everything runs abut half as fast but it is much less error prone and more readable

    * Changed Raytrace Imports

    Change the Raytrace library so that mesh classes can be imported directly

    * Restructured Raytrace Library

    Moved the mesh classes into their own folder

    * Fixed Typo Related Bug

    Passing a Vector3 to the Vector3 constructor no longer causes an error

    * Redid Custom Types

    Custom types are now better integrated with numpy to get speed back to around where they were (well, 2/3rds the speed but whos counting)

commit 6b2a13d
Author: jrb20008 <joseph.bellemare@uconn.edu>
Date:   Thu Mar 20 15:49:43 2025 -0400

    Squashed commit of the following:

    commit 4acc015
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Sun Mar 9 18:00:03 2025 -0400

        Added normalize function

        Added function to normalize the scale of meshes

    commit e685ab2
    Merge: 968cbac cc38025
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 21:28:20 2025 -0500

        Merge branch 'main' into shipgen-integration

    commit 968cbac
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:58:29 2025 -0500

        Added conversion

        Added helper functions to convert stl.Mesh's to triangle arrays

    commit 13a589f
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:47:02 2025 -0500

        Cleaned up Generate

    commit 22876e9
    Merge: f92334b adb4ab8
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 20:08:58 2025 -0500

        Merge branch 'main' into shipgen-integration

    commit f92334b
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:39:31 2025 -0500

        Renamed parameters

    commit f261895
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:37:13 2025 -0500

        Stopped warning message

    commit bf90105
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:26:12 2025 -0500

        Fixed unused parameter

    commit f79dbc1
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:14:46 2025 -0500

        Removed need to save stl's

    commit c640f6c
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 19:05:02 2025 -0500

        Improved typing

    commit 19cf09b
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 18:48:43 2025 -0500

        Added hull generator

    commit e8845c8
    Author: JoeBell <joe@onmyhonor.com>
    Date:   Tue Mar 4 16:18:36 2025 -0500

        Uploaded streamlined ShipGen

        Uploaded a version of ShipGen modified from https://www.dropbox.com/sh/jg98r425v7ly89l/AAA49uMr7_mhaVmRDrPq0NU_a?dl=0 with all non-essential files removed

commit 0405a26
Author: jrb20008 <joseph.bellemare@uconn.edu>
Date:   Sun Mar 9 19:59:52 2025 -0400

    Created AUVSim

    Created a module to generate basic AUV paths to follow the face of hulls

commit cc38025
Author: JoeBell <joe@onmyhonor.com>
Date:   Tue Mar 4 21:27:42 2025 -0500

    Fixed numpy version compatibility

commit adb4ab8
Author: JoeBell <joe@onmyhonor.com>
Date:   Tue Mar 4 20:03:31 2025 -0500

    Downgraded numpy

    Downgraded from numpy 2.x to numy 1.x for compatibility

commit 8eeecef
Merge: 4840eeb 373cc45
Author: JoeBell <joe@onmyhonor.com>
Date:   Tue Mar 4 17:40:20 2025 -0500

    Merge branch 'raytrace-update'

commit 4840eeb
Merge: 3ffe3b9 446bc2d
Author: Joseph R Bellemare <joseph.bellemare@uconn.edu>
Date:   Sun Mar 2 23:03:01 2025 -0500

    Merge pull request #2 from tjs20011/raytrace-update

    Raytrace update

commit 3ffe3b9
Merge: 9cc7468 4c24da0
Author: Joseph R Bellemare <joseph.bellemare@uconn.edu>
Date:   Thu Feb 20 19:11:19 2025 -0500

    Merge pull request #1 from tjs20011/raytrace-update

    Raytrace update

.gitignore

@@ -1,6 +1,5 @@
 # Created by venv; see https://docs.python.org/3/library/venv.html
 ShipD/
-ShipGen/
 Scripts/
 Lib/
 Include/

AUVSim/.gitignore

@@ -0,0 +1 @@
+__pycache__/

AUVSim/__init__.py

@@ -0,0 +1,5 @@
+from .auv import (
+    AUV as AUV,
+    AUVPath as AUVPath,
+    AUVPathGen as AUVPathGen,
+)

AUVSim/auv.py

@@ -0,0 +1,65 @@
+from Raytrace import TriangleMesh
+from Raytrace.SideScan import SideScan
+import numpy as np
+from typing import Any
+from CustomTypes import Ray, Vector3, Vector3Array
+
+class AUV:
+    ideal_distance:float # Currently unused
+    start_pos:Vector3
+    start_facing:Vector3
+    def __init__(self,
+                 position:Vector3,
+                 facing:Vector3,
+                 ideal_distance:float = -1,
+                 ):
+        self.start_pos = position
+        self.start_facing = facing
+        self.ideal_distance = ideal_distance
+class AUVPath:
+    positions:Vector3Array
+    facings:Vector3Array
+
+    def __init__(self, positions:Vector3Array, facings:Vector3Array):
+        self.positions = positions
+        self.facings = facings
+    @property
+    def rays(self) -> list[Ray]:
+        return list(map(Ray, self.facings, self.positions))
+
+class AUVPathGen:
+    mesh:TriangleMesh
+    auv:AUV
+    def __init__(self, mesh:TriangleMesh, auv:AUV):
+        self.mesh = mesh
+        self.auv = auv
+    def get_path(self, travel_distance:float, samples:int) -> AUVPath:
+        travel_step = travel_distance / (samples - 1)
+        positions = [self.auv.start_pos]
+        facings = [self.auv.start_facing]
+
+        # Utility functions
+        # HACK: There should be a function to generate one side ray
+        #       instead of generating a list with length one.
+        get_side_ray = lambda face, pos:\
+            SideScan.generate_rays(Ray(face, pos), 0, 1, 2)[0]
+        get_dist = lambda ray: self.mesh.raytrace(ray)
+        normalize = lambda vector: vector / np.sqrt(np.dot(vector, vector))
+
+        for _ in range(samples - 1):
+            # find distance at current state
+            prev_dist = get_dist(get_side_ray(facings[-1], positions[-1]))
+            # move frowards
+            positions.append(positions[-1] + facings[-1] * travel_step)
+            # shoot side ray
+            # NOTE: facing has not yet been updated
+            side_ray = get_side_ray(facings[-1], positions[-1])
+            ray_dist = self.mesh.raytrace(side_ray)
+            # point in the direction that the hull is sloping
+            rise = (ray_dist - prev_dist) * side_ray.direction
+            if not (np.isfinite(ray_dist) and np.isfinite(prev_dist)):
+                rise = Vector3(0, 0, 0)
+            new_facing = normalize(facings[-1] + rise)
+            facings.append(new_facing)
+
+        return AUVPath(Vector3Array(positions), Vector3Array(facings))

CustomTypes/.gitignore

@@ -0,0 +1 @@
+__pycache__/

CustomTypes/__init__.py

@@ -0,0 +1,11 @@
+from .custom_np import CustomNP as CustomNP
+from .custom_types import (
+    Vector3 as Vector3,
+    Triangle as Triangle,
+    Ray as Ray,
+)
+from .custom_arrays import (
+    FloatArray as FloatArray,
+    TriangleArray as TriangleArray,
+    Vector3Array as Vector3Array,
+)

CustomTypes/custom_arrays.py

@@ -0,0 +1,54 @@
+from typing import Any, Iterable, Literal, overload
+import numpy as np
+
+from . import CustomNP, Triangle, Vector3
+
+class FloatArray(CustomNP):
+    def __new__(cls,
+                content: Iterable[float]|np.ndarray|None = None,
+                ):
+        if isinstance(content, np.ndarray):
+            if content.ndim != 1: raise ValueError(content.shape) # must be 1d
+            return content.view(cls)
+        if content is None:
+            return np.ndarray((0,), float).view(cls)
+        return np.array(content).view(cls)
+    def __getitem__(self, index):
+        if isinstance(index, slice): return super().__getitem__(index).view(type(self))
+        return super().__getitem__(index)
+
+class Vector3Array(CustomNP):
+    def __new__(cls,
+                content: Iterable[Vector3]|np.ndarray|None = None,
+                ):
+        if isinstance(content, np.ndarray):
+            if content.ndim == 1: content = content.reshape((1,) + content.shape)
+            if content.ndim != 2: raise ValueError(content.shape) # must be 1d or 2d
+            if content.shape[1]  != 3: raise ValueError(content.shape) # must be shape (n, 3)
+            return content.view(cls)
+        if content is None:
+            return np.ndarray((0, 3), float).view(cls)
+        return np.array(content).view(cls)
+    def __getitem__(self, index):
+        if isinstance(index, slice): return super().__getitem__(index).view(type(self))
+        return super().__getitem__(index)
+
+class TriangleArray(CustomNP):
+    def __new__(cls,
+                content: Iterable[Triangle]|np.ndarray|None = None,
+                ):
+        if isinstance(content, np.ndarray):
+            if content.ndim == 2: content = content.reshape((1,) + content.shape)
+            if content.ndim != 3: raise ValueError(content.shape) # must be 2d or 3d
+            if content.shape[1] != 3 or content.shape[2] != 3: raise ValueError(content.shape) # must be shape (n, 3, 3)
+            return content.view(cls)
+        if content is None:
+            return np.ndarray((0, 3, 3), float).view(cls)
+        return np.array(content).view(cls)
+    def __getitem__(self, index):
+        if isinstance(index, slice): return super().__getitem__(index).view(type(self))
+        return super().__getitem__(index)
+    @property
+    def verticies(self) -> tuple[Vector3Array, Vector3Array, Vector3Array]:
+        v0, v1, v2 = self.swapaxes(0, 1)
+        return (v0.view(Vector3Array), v1.view(Vector3Array), v2.view(Vector3Array))

CustomTypes/custom_arrays.pyi

@@ -0,0 +1,53 @@
+import numpy as np
+from typing import Any, Iterable, Literal, Self, Type, TypeVar, overload
+
+from . import CustomNP, Triangle, Vector3
+
+class FloatArray(CustomNP[tuple[int, Literal[3]], np.dtype[np.float_]]):
+    @overload
+    def __new__(cls) -> FloatArray:...
+    @overload
+    def __new__(cls, content: Iterable[float]) -> FloatArray:...
+    @overload
+    def __new__(cls, content: np.ndarray[tuple[int], np.dtype[np.float_]]) -> FloatArray:...
+
+    @overload # type: ignore
+    def __getitem__(self, index:int) -> float: ...
+    @overload
+    def __getitem__(self, index:slice) -> Self: ...
+
+class Vector3Array(CustomNP[tuple[int, Literal[3]], np.dtype[np.float_]]):
+    @overload
+    def __new__(cls) -> Vector3Array:...
+    @overload
+    def __new__(cls, content: Iterable[Vector3]) -> Vector3Array:...
+    @overload
+    def __new__(cls, content: np.ndarray[tuple[int, Literal[3]], np.dtype[np.float_]]) -> Vector3Array:...
+
+    @overload # type: ignore
+    def __getitem__(self, index:int) -> Vector3: ...
+    @overload
+    def __getitem__(self, index:tuple[int, Literal[0, 1, 2]]) -> float: ...
+    @overload
+    def __getitem__(self, index:slice) -> Self: ...
+
+class TriangleArray(CustomNP[tuple[int, Literal[3], Literal[3]], np.dtype[np.float_]]):
+    @overload
+    def __new__(cls) -> TriangleArray:...
+    @overload
+    def __new__(cls, content: Iterable[Triangle]) -> TriangleArray:...
+    @overload
+    def __new__(cls, content: np.ndarray[tuple[int, Literal[3], Literal[3]], np.dtype[np.float_]]) -> TriangleArray:...
+
+    @overload # type: ignore
+    def __getitem__(self, index:int) -> Triangle: ...
+    @overload
+    def __getitem__(self, index:tuple[int, Literal[0, 1, 2]]) -> Vector3: ...
+    @overload
+    def __getitem__(self, index:tuple[int, Literal[0, 1, 2], Literal[0, 1, 2]]) -> float: ...
+    @overload
+    def __getitem__(self, index:slice) -> Self: ...
+
+    @property
+    def verticies(self) -> tuple[Vector3Array, Vector3Array, Vector3Array]: ...
+

CustomTypes/custom_np.py

@@ -0,0 +1,21 @@
+
+from typing import Generic, TypeVar, Self
+import numpy as np
+
+
+_S = TypeVar('_S', bound=tuple)
+_T = TypeVar('_T', bound=np.dtype)
+class CustomNP(np.ndarray[_S, _T]):
+    def __add__(self, other):
+        return super().__add__(other).view(type(self))
+    def __sub__(self, other):
+        return super().__sub__(other).view(type(self))
+    def __mul__(self, other):
+        return super().__mul__(other).view(type(self))
+    def __truediv__(self, other):
+        return super().__truediv__(other).view(type(self))
+    def __rtruediv__(self, other):
+        return super().__rtruediv__(other).view(type(self))
+    @property
+    def nd(self):
+        return self.view(np.ndarray)

CustomTypes/custom_np.pyi

@@ -0,0 +1,15 @@
+from typing import TypeVar, Self
+import numpy as np
+
+
+_S = TypeVar('_S', bound=tuple)
+_T = TypeVar('_T', bound=np.dtype)
+class CustomNP(np.ndarray[_S, _T]):
+    def __add__(self, other:Self) -> Self: ... # type: ignore
+    def __sub__(self, other:Self) -> Self: ... # type: ignore
+    def __mul__(self, other:Self|float) -> Self: ... # type: ignore
+    def __truediv__(self, other:Self|float) -> Self: ... # type: ignore
+    def __rtruediv__(self, other:float) -> Self: ... # type: ignore
+
+    @property
+    def nd(self) -> np.ndarray: ...

CustomTypes/custom_types.py

@@ -0,0 +1,42 @@
+from typing import Any, Iterable, Literal, Self, overload
+import numpy as np
+from . import CustomNP
+
+class Vector3(CustomNP):
+    def __new__(cls,
+                x: float | tuple[float, float, float] | Self, y = 0, z = 0):
+        if isinstance(x, tuple):
+            x, y, z = x
+        elif isinstance(x, Vector3):
+            x, y, z = x
+        assert isinstance(x, (float, int, np.floating))
+        return np.array([x, y, z]).view(cls)
+    def __str__(self):
+        return f"({self[0]}, {self[1]}, {self[2]})"
+    def __repr__(self):
+        return f"Vector3({self[0]}, {self[1]}, {self[2]})"
+
+class Triangle(CustomNP):
+    def __new__(cls,
+                v0: Vector3 | tuple[Vector3, Vector3, Vector3],
+                v1: Vector3 = Vector3(0, 0, 0),
+                v2: Vector3 = Vector3(0, 0, 0),
+                ) -> 'Triangle':
+        if isinstance(v0, tuple): 
+            v0, v1, v2 = v0
+        return np.array([v0, v1, v2]).view(cls)
+
+    def __str__(self) -> str:
+        return f"({self[0]}, {self[1]}, {self[2]})"
+    def __repr__(self) -> str:
+        return f"Vector3({self[0]}, {self[1]}, {self[2]})"
+
+class Ray:
+    direction:Vector3
+    origin:Vector3
+    def __init__(self,
+                 direction:Vector3,
+                 origin:Vector3,
+                 ) -> None:
+        self.direction = direction
+        self.origin = origin

CustomTypes/custom_types.pyi

@@ -0,0 +1,40 @@
+from typing import Any, Iterable, Iterator, Literal, TypeAlias, TypeVar, overload
+import numpy as np
+from . import CustomNP
+
+class Vector3(CustomNP[tuple[Literal[3]], np.dtype[np.float_]]):
+    @overload
+    def __new__(cls, x: float, y: float, z: float) -> Vector3: ...
+    @overload
+    def __new__(cls, x: tuple[float, float, float]) -> Vector3: ...
+    @overload
+    def __new__(cls, x: Vector3) -> Vector3: ...
+
+    def __getitem__(self, index:Literal[0, 1, 2]) -> float: ... # type: ignore
+
+class Triangle(CustomNP[tuple[Literal[3], Literal[3]], np.dtype[np.float_]], Iterable[Vector3]):
+    @overload
+    def __new__(cls, v0: Vector3, v1: Vector3, v2: Vector3) -> Triangle: ...
+    @overload
+    def __new__(cls, v0: tuple[Vector3, Vector3, Vector3]) -> Triangle: ...
+    @overload
+    def __new__(cls, v0: Triangle) -> Triangle: ...
+
+    @overload # type: ignore
+    def __getitem__(self, index:Literal[0, 1, 2]) -> Vector3: ...
+    @overload
+    def __getitem__(self, index:tuple[Literal[0, 1, 2], Literal[0, 1, 2]]) -> float: ...
+
+    def __add__(self, other:Triangle) -> Triangle: ... # type: ignore
+    def __sub__(self, other:Triangle) -> Triangle: ... # type: ignore
+
+    def __iter__(self) -> Iterator[Vector3]: ...
+class Ray:
+    direction:Vector3
+    origin:Vector3
+    def __init__(self,
+                 direction:Vector3,
+                 origin:Vector3,
+                 ) -> None:
+        self.direction = direction
+        self.origin = origin

Generate/.gitignore

@@ -0,0 +1 @@
+__pycache__/

Generate/__init__.py

@@ -0,0 +1,13 @@
+from .auv import(
+    place_auvs_over_points as place_auvs_over_points,
+    generate_paths as generate_paths,
+    scan_paths as scan_paths,
+)
+from .hull import (
+    generate_hulls as generate_hulls,
+    generate_points_on_hull as generate_points_on_hull,
+    generate_vertical_bounds as generate_vertical_bounds,
+    load_anomalies as load_anomalies,
+    pick_anomalies as pick_anomalies,
+    place_anomalies_at_points as place_anomalies_at_points,
+)