From 35272e724ef1c48304de0e400478585d816dfeb1 Mon Sep 17 00:00:00 2001
From: Elizabeth <eberrigan@salk.edu>
Date: Thu, 18 Apr 2024 16:24:16 -0700
Subject: [PATCH 1/4] add helper function for getting points from geometry
---
sleap_roots/convhull.py | 19 ++++++++++-------
sleap_roots/points.py | 43 ++++++++++++++++++++++++++++++++++++-
tests/test_convhull.py | 1 -
tests/test_points.py | 47 +++++++++++++++++++++++++++++++++++++++--
4 files changed, 98 insertions(+), 12 deletions(-)
diff --git a/sleap_roots/convhull.py b/sleap_roots/convhull.py
index c15a169..12b3df2 100644
--- a/sleap_roots/convhull.py
+++ b/sleap_roots/convhull.py
@@ -4,7 +4,7 @@
from scipy.spatial import ConvexHull
from scipy.spatial.distance import pdist
from typing import Tuple, Optional, Union
-from sleap_roots.points import get_line_equation_from_points
+from sleap_roots.points import extract_points_from_geometry, get_line_equation_from_points
from shapely import box, LineString, normalize, Polygon
@@ -382,13 +382,9 @@ def get_chull_areas_via_intersection(
# Find the intersection between the hull perimeter and the extended line
intersection = extended_line.intersection(hull_perimeter)
- # Add intersection points to both lists
+ # Compute the intersection points and add to lists
if not intersection.is_empty:
- intersect_points = (
- np.array([[point.x, point.y] for point in intersection.geoms])
- if intersection.geom_type == "MultiPoint"
- else np.array([[intersection.x, intersection.y]])
- )
+ intersect_points = extract_points_from_geometry(intersection)
above_line.extend(intersect_points)
below_line.extend(intersect_points)
@@ -452,6 +448,10 @@ def get_chull_intersection_vectors(
Raises:
ValueError: If pts does not have the expected shape.
"""
+ if r0_pts.ndim == 1 or rn_pts.ndim == 1 or pts.ndim == 2:
+ print("Not enough instances or incorrect format to compute convex hull intersections.")
+ return (np.array([[np.nan, np.nan]]), np.array([[np.nan, np.nan]]))
+
# Check for valid pts input
if not isinstance(pts, np.ndarray) or pts.ndim != 3 or pts.shape[-1] != 2:
raise ValueError("pts must be a numpy array of shape (instances, nodes, 2).")
@@ -460,7 +460,7 @@ def get_chull_intersection_vectors(
raise ValueError("rn_pts must be a numpy array of shape (instances, 2).")
# Ensure r0_pts is a numpy array of shape (instances, 2)
if not isinstance(r0_pts, np.ndarray) or r0_pts.ndim != 2 or r0_pts.shape[-1] != 2:
- raise ValueError("r0_pts must be a numpy array of shape (instances, 2).")
+ raise ValueError(f"r0_pts must be a numpy array of shape (instances, 2).")
# Flatten pts to 2D array and remove NaN values
flattened_pts = pts.reshape(-1, 2)
@@ -481,6 +481,9 @@ def get_chull_intersection_vectors(
# Ensuring r0_pts does not contain NaN values
r0_pts_valid = r0_pts[~np.isnan(r0_pts).any(axis=1)]
+ # Expect two vectors in the end
+ if len(r0_pts_valid) < 2:
+ return (np.array([[np.nan, np.nan]]), np.array([[np.nan, np.nan]]))
# Get the vertices of the convex hull
hull_vertices = hull.points[hull.vertices]
diff --git a/sleap_roots/points.py b/sleap_roots/points.py
index 479f564..22bdfcf 100644
--- a/sleap_roots/points.py
+++ b/sleap_roots/points.py
@@ -3,11 +3,52 @@
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.lines import Line2D
-from shapely.geometry import LineString
+from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection
from shapely.ops import nearest_points
from typing import List, Optional, Tuple
+def extract_points_from_geometry(geometry):
+ """Extracts coordinates as a list of numpy arrays from any given Shapely geometry object.
+
+ This function supports Point, MultiPoint, LineString, and GeometryCollection types.
+ It recursively extracts coordinates from complex geometries and aggregates them into a single list.
+ For unsupported geometry types, it returns an empty list.
+
+ Parameters:
+ - geometry (shapely.geometry.base.BaseGeometry): A Shapely geometry object from which to extract points.
+
+ Returns:
+ - List[np.ndarray]: A list of numpy arrays, where each array represents the coordinates of a point.
+ The list will be empty if the geometry type is unsupported or contains no coordinates.
+
+ Raises:
+ - TypeError: If the input is not a recognized Shapely geometry type.
+
+ Example:
+ >>> from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection
+ >>> point = Point(1, 2)
+ >>> multipoint = MultiPoint([(1, 2), (3, 4)])
+ >>> linestring = LineString([(0, 0), (1, 1), (2, 2)])
+ >>> geom_col = GeometryCollection([point, multipoint, linestring])
+ >>> extract_points_from_geometry(geom_col)
+ [array([1, 2]), array([1, 2]), array([3, 4]), array([0, 0]), array([1, 1]), array([2, 2])]
+ """
+ if isinstance(geometry, Point):
+ return [np.array([geometry.x, geometry.y])]
+ elif isinstance(geometry, MultiPoint):
+ return [np.array([point.x, point.y]) for point in geometry.geoms]
+ elif isinstance(geometry, LineString):
+ return [np.array([x, y]) for x, y in zip(*geometry.xy)]
+ elif isinstance(geometry, GeometryCollection):
+ points = []
+ for geom in geometry.geoms:
+ points.extend(extract_points_from_geometry(geom))
+ return points
+ else:
+ raise TypeError(f"Unsupported geometry type: {type(geometry).__name__}")
+
+
def get_count(pts: np.ndarray):
"""Get number of roots.
diff --git a/tests/test_convhull.py b/tests/test_convhull.py
index a33c279..f506312 100644
--- a/tests/test_convhull.py
+++ b/tests/test_convhull.py
@@ -314,7 +314,6 @@ def test_basic_functionality(pts_shape_3_6_2):
@pytest.mark.parametrize(
"invalid_input",
[
- (np.array([1, 2]), np.array([3, 4]), np.array([[[1, 2], [3, 4]]]), None),
(np.array([[1, 2, 3]]), np.array([[3, 4]]), np.array([[[1, 2], [3, 4]]]), None),
# Add more invalid inputs as needed
],
diff --git a/tests/test_points.py b/tests/test_points.py
index 6ac3a1d..ed042a8 100644
--- a/tests/test_points.py
+++ b/tests/test_points.py
@@ -1,9 +1,9 @@
import numpy as np
import pytest
-from shapely.geometry import LineString
+from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection
from sleap_roots import Series
from sleap_roots.lengths import get_max_length_pts
-from sleap_roots.points import filter_plants_with_unexpected_ct, get_count, join_pts
+from sleap_roots.points import extract_points_from_geometry, filter_plants_with_unexpected_ct, get_count, join_pts
from sleap_roots.points import (
get_all_pts_array,
get_nodes,
@@ -738,3 +738,46 @@ def test_filter_plants_with_unexpected_ct_incorrect_input_types():
expected_count = "not a float"
with pytest.raises(ValueError):
filter_plants_with_unexpected_ct(primary_pts, lateral_pts, expected_count)
+
+
+def test_extract_from_point():
+ point = Point(1, 2)
+ expected = [np.array([1, 2])]
+ assert np.array_equal(extract_points_from_geometry(point), expected)
+
+def test_extract_from_multipoint():
+ multipoint = MultiPoint([(1, 2), (3, 4)])
+ expected = [np.array([1, 2]), np.array([3, 4])]
+ results = extract_points_from_geometry(multipoint)
+ assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
+def test_extract_from_linestring():
+ linestring = LineString([(0, 0), (1, 1), (2, 2)])
+ expected = [np.array([0, 0]), np.array([1, 1]), np.array([2, 2])]
+ results = extract_points_from_geometry(linestring)
+ assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
+def test_extract_from_geometrycollection():
+ geom_collection = GeometryCollection([Point(1, 2), LineString([(0, 0), (1, 1)])])
+ expected = [np.array([1, 2]), np.array([0, 0]), np.array([1, 1])]
+ results = extract_points_from_geometry(geom_collection)
+ assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
+def test_extract_from_empty_multipoint():
+ empty_multipoint = MultiPoint()
+ expected = []
+ assert extract_points_from_geometry(empty_multipoint) == expected
+
+def test_extract_from_empty_linestring():
+ empty_linestring = LineString()
+ expected = []
+ assert extract_points_from_geometry(empty_linestring) == expected
+
+def test_extract_from_unsupported_type():
+ with pytest.raises(NameError):
+ extract_points_from_geometry(Polygon([(0, 0), (1, 1), (1, 0)])) # Polygon is unsupported
+
+def test_extract_from_empty_geometrycollection():
+ empty_geom_collection = GeometryCollection()
+ expected = []
+ assert extract_points_from_geometry(empty_geom_collection) == expected
\ No newline at end of file
From 93741fcecaf0c2c6dd478b10dde0ed05ff6d8976 Mon Sep 17 00:00:00 2001
From: eberrigan <berri104@gmail.com>
Date: Tue, 23 Apr 2024 10:15:05 -0700
Subject: [PATCH 2/4] lint
---
sleap_roots/convhull.py | 9 +++++++--
sleap_roots/points.py | 16 ++++++++--------
2 files changed, 15 insertions(+), 10 deletions(-)
diff --git a/sleap_roots/convhull.py b/sleap_roots/convhull.py
index 12b3df2..88ad97c 100644
--- a/sleap_roots/convhull.py
+++ b/sleap_roots/convhull.py
@@ -4,7 +4,10 @@
from scipy.spatial import ConvexHull
from scipy.spatial.distance import pdist
from typing import Tuple, Optional, Union
-from sleap_roots.points import extract_points_from_geometry, get_line_equation_from_points
+from sleap_roots.points import (
+ extract_points_from_geometry,
+ get_line_equation_from_points,
+)
from shapely import box, LineString, normalize, Polygon
@@ -449,7 +452,9 @@ def get_chull_intersection_vectors(
ValueError: If pts does not have the expected shape.
"""
if r0_pts.ndim == 1 or rn_pts.ndim == 1 or pts.ndim == 2:
- print("Not enough instances or incorrect format to compute convex hull intersections.")
+ print(
+ "Not enough instances or incorrect format to compute convex hull intersections."
+ )
return (np.array([[np.nan, np.nan]]), np.array([[np.nan, np.nan]]))
# Check for valid pts input
diff --git a/sleap_roots/points.py b/sleap_roots/points.py
index 22bdfcf..fd9acbc 100644
--- a/sleap_roots/points.py
+++ b/sleap_roots/points.py
@@ -10,21 +10,21 @@
def extract_points_from_geometry(geometry):
"""Extracts coordinates as a list of numpy arrays from any given Shapely geometry object.
-
- This function supports Point, MultiPoint, LineString, and GeometryCollection types.
- It recursively extracts coordinates from complex geometries and aggregates them into a single list.
+
+ This function supports Point, MultiPoint, LineString, and GeometryCollection types.
+ It recursively extracts coordinates from complex geometries and aggregates them into a single list.
For unsupported geometry types, it returns an empty list.
-
+
Parameters:
- geometry (shapely.geometry.base.BaseGeometry): A Shapely geometry object from which to extract points.
-
+
Returns:
- - List[np.ndarray]: A list of numpy arrays, where each array represents the coordinates of a point.
+ - List[np.ndarray]: A list of numpy arrays, where each array represents the coordinates of a point.
The list will be empty if the geometry type is unsupported or contains no coordinates.
-
+
Raises:
- TypeError: If the input is not a recognized Shapely geometry type.
-
+
Example:
>>> from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection
>>> point = Point(1, 2)
From 5033de5979837741bc76f816ae99d04c13bdfae5 Mon Sep 17 00:00:00 2001
From: eberrigan <berri104@gmail.com>
Date: Tue, 23 Apr 2024 10:52:16 -0700
Subject: [PATCH 3/4] Black
---
tests/test_points.py | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/tests/test_points.py b/tests/test_points.py
index ed042a8..54c37d6 100644
--- a/tests/test_points.py
+++ b/tests/test_points.py
@@ -3,7 +3,12 @@
from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection
from sleap_roots import Series
from sleap_roots.lengths import get_max_length_pts
-from sleap_roots.points import extract_points_from_geometry, filter_plants_with_unexpected_ct, get_count, join_pts
+from sleap_roots.points import (
+ extract_points_from_geometry,
+ filter_plants_with_unexpected_ct,
+ get_count,
+ join_pts,
+)
from sleap_roots.points import (
get_all_pts_array,
get_nodes,
@@ -745,39 +750,48 @@ def test_extract_from_point():
expected = [np.array([1, 2])]
assert np.array_equal(extract_points_from_geometry(point), expected)
+
def test_extract_from_multipoint():
multipoint = MultiPoint([(1, 2), (3, 4)])
expected = [np.array([1, 2]), np.array([3, 4])]
results = extract_points_from_geometry(multipoint)
assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
def test_extract_from_linestring():
linestring = LineString([(0, 0), (1, 1), (2, 2)])
expected = [np.array([0, 0]), np.array([1, 1]), np.array([2, 2])]
results = extract_points_from_geometry(linestring)
assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
def test_extract_from_geometrycollection():
geom_collection = GeometryCollection([Point(1, 2), LineString([(0, 0), (1, 1)])])
expected = [np.array([1, 2]), np.array([0, 0]), np.array([1, 1])]
results = extract_points_from_geometry(geom_collection)
assert all(np.array_equal(result, exp) for result, exp in zip(results, expected))
+
def test_extract_from_empty_multipoint():
empty_multipoint = MultiPoint()
expected = []
assert extract_points_from_geometry(empty_multipoint) == expected
+
def test_extract_from_empty_linestring():
empty_linestring = LineString()
expected = []
assert extract_points_from_geometry(empty_linestring) == expected
+
def test_extract_from_unsupported_type():
with pytest.raises(NameError):
- extract_points_from_geometry(Polygon([(0, 0), (1, 1), (1, 0)])) # Polygon is unsupported
+ extract_points_from_geometry(
+ Polygon([(0, 0), (1, 1), (1, 0)])
+ ) # Polygon is unsupported
+
def test_extract_from_empty_geometrycollection():
empty_geom_collection = GeometryCollection()
expected = []
- assert extract_points_from_geometry(empty_geom_collection) == expected
\ No newline at end of file
+ assert extract_points_from_geometry(empty_geom_collection) == expected
From 5a51eab3f530fd242eeb5d18a124dd9457b8f411 Mon Sep 17 00:00:00 2001
From: eberrigan <berri104@gmail.com>
Date: Tue, 23 Apr 2024 10:58:53 -0700
Subject: [PATCH 4/4] pydoc style
---
sleap_roots/points.py | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/sleap_roots/points.py b/sleap_roots/points.py
index fd9acbc..6d5c5c1 100644
--- a/sleap_roots/points.py
+++ b/sleap_roots/points.py
@@ -15,15 +15,12 @@ def extract_points_from_geometry(geometry):
It recursively extracts coordinates from complex geometries and aggregates them into a single list.
For unsupported geometry types, it returns an empty list.
- Parameters:
- - geometry (shapely.geometry.base.BaseGeometry): A Shapely geometry object from which to extract points.
+ Args:
+ geometry (shapely.geometry.base.BaseGeometry): A Shapely geometry object from which to extract points.
Returns:
- - List[np.ndarray]: A list of numpy arrays, where each array represents the coordinates of a point.
- The list will be empty if the geometry type is unsupported or contains no coordinates.
-
- Raises:
- - TypeError: If the input is not a recognized Shapely geometry type.
+ List[np.ndarray]: A list of numpy arrays, where each array represents the coordinates of a point.
+ The list will be empty if the geometry type is unsupported or contains no coordinates.
Example:
>>> from shapely.geometry import Point, MultiPoint, LineString, GeometryCollection