Drop scipy convex hull (#21)

* add convex_hull

* update

* convex hull

* normalize index

* updatec

* bind more

* fix spelling

* test include colinear

* more tests

* better API

* ready to release

* update docs

* update docs

* scipy to test requires

.gitignore

@@ -8,3 +8,4 @@ _generate/
 *env*
 wheelhouse
 !test.py
+site

.vscode/settings.json

@@ -94,7 +94,8 @@
         "slist": "cpp",
         "future": "cpp",
         "regex": "cpp",
-        "core": "cpp"
+        "core": "cpp",
+        "specialfunctions": "cpp"
     },
     "workbench.colorCustomizations": {
         "activityBar.background": "#143328",

Makefile

@@ -30,7 +30,7 @@ test_in_linux:
 
 PYTHON ?= python3
 python_install:
-	$(PYTHON) setup.py install
+	$(PYTHON) setup.py install --force
 python_build:
 	$(PYTHON) setup.py bdist_wheel
 python_sdist:

README.md

@@ -11,6 +11,8 @@ Credits goes to:
 
 Online document: <https://concave-hull.readthedocs.io/en/latest/>
 
+<!--intro-start-->
+
 ## Install
 
 ### via pip
@@ -48,14 +50,18 @@ concave_hull_indexes(
        *,
        concavity: float = 2.0,
        length_threshold: float = 0.0,
-       convex_hull_indexes: numpy.ndarray[numpy.int32[m, 1]] = None, # will use integrated scipy ConvexHull if None
+       # you can just ignore "convex_hull_indexes"
+       convex_hull_indexes: numpy.ndarray[numpy.int32[m, 1]] = None,
 ) -> numpy.ndarray[numpy.int32[m, 1]]
 
 # get concave hull points
 concave_hull(
        points: Union[numpy.ndarray, List, Tuple],
-       *args, *kwargs # will proxy all to covcave_hull_indexes
+       ... # same as
 ) -> Union[numpy.ndarray, List, Tuple]
+
+# P.S., we provide convex_hull (Graham scan)
+from concave_hull import convex_hull, convex_hull_indexes
 ```
 
 -   `concavity` is a relative measure of concavity. 1 results in a relatively
@@ -98,9 +104,6 @@ for simplex in convex_hull.simplices:
 idxes = concave_hull_indexes(
     points[:, :2],
     length_threshold=50,
-    # for concave_hull>=0.0.3
-    #   it's not necessary to provide convex_hull_indexes
-    # convex_hull_indexes=convex_hull.vertices.astype(np.int32),
 )
 # you can get coordinates by `points[idxes]`
 assert np.all(points[idxes] == concave_hull(points, length_threshold=50))
@@ -112,6 +115,8 @@ for f, t in zip(idxes[:-1], idxes[1:]):  # noqa
 plt.show()
 ```
 
+<!--intro-end-->
+
 ## Tests
 
 ```

concave_hull/__init__.py

@@ -1,20 +1,22 @@
 from typing import List, Tuple, Union
 
 import numpy as np
+import pybind11_concave_hull  # noqa
 from pybind11_concave_hull import __version__  # noqa
+from pybind11_concave_hull import clockwise, colinear  # noqa
 from pybind11_concave_hull import (  # noqa
     concave_hull_indexes as concave_hull_indexes_impl,
 )
-from pybind11_concave_hull import wgs84_to_east_north
-from scipy.spatial import ConvexHull
+from pybind11_concave_hull import convex_hull_indexes as convex_hull_indexes_impl
+from pybind11_concave_hull import orientation, wgs84_to_east_north  # noqa
 
 
 def concave_hull_indexes(
     points: Union[np.ndarray, List, Tuple],
     *,
     concavity: float = 2.0,
     length_threshold: float = 0.0,
-    convex_hull_indexes: np.ndarray = None,
+    convex_hull_indexes: np.ndarray = None,  # noqa
     is_wgs84: bool = False,
 ):
     """
@@ -35,8 +37,7 @@ def concave_hull_indexes(
     if is_wgs84:
         points = wgs84_to_east_north(points)
     if convex_hull_indexes is None:
-        convex_hull = ConvexHull(points)
-        convex_hull_indexes = convex_hull.vertices.astype(np.int32)
+        convex_hull_indexes = convex_hull_indexes_impl(points)
     return concave_hull_indexes_impl(
         points,
         concavity=concavity,
@@ -45,8 +46,53 @@ def concave_hull_indexes(
     )
 
 
-def concave_hull(points: Union[np.ndarray, List, Tuple], *args, **kwargs):
-    indexes = concave_hull_indexes(points, *args, **kwargs)
+def concave_hull(
+    points: Union[np.ndarray, List, Tuple],
+    *,
+    concavity: float = 2.0,
+    length_threshold: float = 0.0,
+    convex_hull_indexes: np.ndarray = None,  # noqa
+    is_wgs84: bool = False,
+):
+    indexes = concave_hull_indexes(
+        points,
+        concavity=concavity,
+        length_threshold=length_threshold,
+        convex_hull_indexes=convex_hull_indexes,
+        is_wgs84=is_wgs84,
+    )
+    return (
+        points[indexes]
+        if isinstance(points, np.ndarray)
+        else [points[i] for i in indexes]
+    )
+
+
+def convex_hull_indexes(
+    points: Union[np.ndarray, List, Tuple],
+    *,
+    include_colinear: bool = False,
+    order_only: bool = False,
+):
+    points = np.asarray(points, dtype=np.float64)
+    return convex_hull_indexes_impl(
+        points[:, :2],
+        include_colinear=include_colinear,
+        order_only=order_only,
+    )
+
+
+def convex_hull(
+    points: Union[np.ndarray, List, Tuple],
+    *,
+    include_colinear: bool = False,
+    order_only: bool = False,
+):
+    indexes = convex_hull_indexes(
+        points,
+        include_colinear=include_colinear,
+        order_only=order_only,
+    )
     return (
         points[indexes]
         if isinstance(points, np.ndarray)

docs/about/release-notes.md

@@ -10,6 +10,10 @@ To upgrade `concave_hull` to the latest version, use pip:
 pip install -U concave_hull
 ```
 
+## Version 0.0.6 (2023-04-05)
+
+*   Integrate Grahams-Scan algorithm, drop scipy dependency
+
 ## Version 0.0.5 (2023-03-04)
 
 *   Add macOS, Linux arm64 release

docs/index.md

@@ -2,114 +2,14 @@
 
 A very fast 2D concave hull algorithm.
 
-Released as a python package for easy integration. All credits goes to:
-
--   <https://github.com/mapbox/concaveman>
--   <https://github.com/sadaszewski/concaveman-cpp>
-
-## Install
-
-### via pip
-
-```bash
-pip install -U concave_hull
-```
-
-### from source
-
-```bash
-git clone --recursive https://github.com/cubao/concave_hull
-pip install ./concave_hull
-```
-
-Or
-
-```bash
-pip install git+https://github.com/cubao/concave_hull.git
-```
-
-(you can build wheels for later reuse by ` pip wheel git+https://github.com/cubao/concave_hull.git`)
-
-## Usage
-
-Signature:
-
-```python
-# import
-from concave_hull import concave_hull, concave_hull_indexes
-
-# get concave hull indexes
-concave_hull_indexes(
-       points: Union[numpy.ndarray, List, Tuple],
-       *,
-       concavity: float = 2.0,
-       length_threshold: float = 0.0,
-       convex_hull_indexes: numpy.ndarray[numpy.int32[m, 1]] = None, # will use integrated scipy ConvexHull if None
-) -> numpy.ndarray[numpy.int32[m, 1]]
-
-# get concave hull points
-concave_hull(
-       points: Union[numpy.ndarray, List, Tuple],
-       *args, *kwargs # will proxy all to covcave_hull_indexes
-) -> Union[numpy.ndarray, List, Tuple]
-```
-
--   `concavity` is a relative measure of concavity. 1 results in a relatively
-    detailed shape, Infinity results in a convex hull. You can use values lower
-    than 1, but they can produce pretty crazy shapes.
--   `length_threshold`: when a segment length is under this threshold, it stops
-    being considered for further detalization. Higher values result in simpler
-    shapes.
-
-(document from <https://github.com/mapbox/concaveman>)
-
-Example (see full code in [`test.py`](https://github.com/cubao/concave_hull/blob/master/test.py)):
-
-```python
-import matplotlib.pyplot as plt
-import numpy as np
-from scipy.spatial import ConvexHull
-
-from concave_hull import concave_hull, concave_hull_indexes
-
-points = []
-c = np.array([250, 250])
-for x in np.arange(100, 400, 5 * np.pi):
-    for y in np.arange(100, 400, 5 * np.pi):
-        if x > c[0] and y > c[1]:
-            continue
-        r = np.linalg.norm(c - [x, y])
-        if r > 150:
-            continue
-        points.append([x, y])
-points = np.array(points)
-convex_hull = ConvexHull(points[:, :2])  # it's already N-by-2, I'm just emphasizing
-
-# https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.ConvexHull.html
-
-plt.plot(points[:, 0], points[:, 1], "o")
-for simplex in convex_hull.simplices:
-    plt.plot(points[simplex, 0], points[simplex, 1], "g-", alpha=0.5)
-
-idxes = concave_hull_indexes(
-    points[:, :2],
-    length_threshold=50,
-    # for concave_hull>=0.0.3
-    #   it's not necessary to provide convex_hull_indexes
-    # convex_hull_indexes=convex_hull.vertices.astype(np.int32),
-)
-# you can get coordinates by `points[idxes]`
-assert np.all(points[idxes] == concave_hull(points, length_threshold=50))
-
-for f, t in zip(idxes[:-1], idxes[1:]):  # noqa
-    seg = points[[f, t]]
-    plt.plot(seg[:, 0], seg[:, 1], "r-", alpha=0.5)
-# plt.savefig('hull.png')
-plt.show()
-```
-
 ![](hull.png)
 
+{%
+   include-markdown "../README.md"
+   start="<!--intro-start-->"
+   end="<!--intro-end-->"
+%}
+
 <div class="text-center">
 <a href="https://github.com/cubao/concave_hull" class="btn btn-primary" role="button">Code on GitHub</a>
 <a href="https://pypi.org/project/concave-hull" class="btn btn-primary" role="button">Package on PyPi</a>

docs/requirements.txt

@@ -1 +1,2 @@
-mkdocs>=1.3.0
+mkdocs==1.4.2
+mkdocs-include-markdown-plugin==4.0.3

docs/usage.md

@@ -0,0 +1,10 @@
+# Usage
+
+## test_basic.py
+
+```python
+{%
+    include-markdown "../tests/test_basic.py"
+    comments=false
+%}
+```

mkdocs.yml

@@ -9,9 +9,11 @@ edit_uri: blob/master/docs/
 theme: readthedocs
 nav:
   - Home: index.md
+  - Usage: usage.md
   - WGS84: wgs84.md
   - About:
       - Release Notes: about/release-notes.md
       - License: about/license.md
-
+plugins:
+  - include-markdown
 copyright: Copyright &copy; 2023 <a href="https://cubao.readthedocs.io/">cubao team</a>.

setup.py

@@ -122,7 +122,7 @@ def build_extension(self, ext):
 # logic and declaration, and simpler if you include description/version in a file.
 setup(
     name="concave_hull",
-    version="0.0.5",
+    version="0.0.6",
     author="tzx",
     author_email="[email protected]",
     url="https://concave-hull.readthedocs.io",
@@ -133,6 +133,6 @@ def build_extension(self, ext):
     ext_modules=[CMakeExtension("concave_hull")],
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,
-    install_requires=["numpy", "scipy"],
-    extras_require={"test": ["pytest>=6.0"]},
+    install_requires=["numpy"],
+    extras_require={"test": ["pytest>=6.0", "scipy"]},
 )