RDG-Networks 0.3.7__py3-none-any.whl → 0.3.9__py3-none-any.whl

{RDG_Networks-0.3.7.dist-info → RDG_Networks-0.3.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: RDG-Networks
-Version: 0.3.7
+Version: 0.3.9
 Summary: Most of the code from the RDG Networks project
 Home-page: https://github.com/NiekMooij/RDG_networks
 Author: Niek Mooij
@@ -14,6 +14,14 @@ Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: shapely
 Requires-Dist: typing
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: home-page
+Dynamic: license
+Dynamic: requires-dist
+Dynamic: summary
 
 ## Overview
 

{RDG_Networks-0.3.7.dist-info → RDG_Networks-0.3.9.dist-info}/RECORD

@@ -1,5 +1,5 @@
 RDG_networks/Classes.py,sha256=_9X3JPHFAYYlaC8IZ_H9__sfz99G5l9UfPl65lL60_4,7977
-RDG_networks/__init__.py,sha256=tKoHFugrHAkce3wyw62MvOzcSfoBr2tpSp6da7Y54LQ,1764
+RDG_networks/__init__.py,sha256=8cc-h5ifS7RP1-N4b1Ow-4bA6MxgFETaS6SD0of54Fk,1575
 RDG_networks/draw_segments.py,sha256=U53N5GXmQHWKdM1Q1faP_EGKjc6enOu2mcsunzSFpP0,984
 RDG_networks/generate_line_network.py,sha256=lJ4rhObim3WcEQoebomewRQKWNJC5phFyFYRW7qjXIg,1127
 RDG_networks/generate_line_segments.py,sha256=QV8_k7q6TD5c7Hcb2Ms_apEdWYw4XdLr7rdJgh49v4Q,9004
@@ -8,15 +8,16 @@ RDG_networks/generate_line_segments_static.py,sha256=7KvHZi3krv-tAGydJR_gbMMmHKZ
 RDG_networks/get_intersection_segments.py,sha256=mXB5qCy1oOps4Vu1mX6flW6v_4Xxc71YK41yOWjJX8o,2797
 RDG_networks/sample_in_polygon.py,sha256=qpPpW-Da1vK8ZkVWMJ0zBsE8IgyMB619gCdybSkzKSQ,1605
 RDG_networks/save_to_stl.py,sha256=St8kGw6wl8uOGx8KhrZhBfe89-mOfp5JKhz0dEDBvc0,3894
-RDG_networks/thickness/Classes.py,sha256=gVe_q5Rh_1DBiJoZ8H0FyJ4xG-IAcespjUpUirxFfAA,8125
-RDG_networks/thickness/__init__.py,sha256=jyyA7Bp519TkOGNSYDVxPKxCgO9vTYpQvpFytnIuqQs,892
-RDG_networks/thickness/generate_line_segments_thickness.py,sha256=meLFptrXWt_povCTlEA0n_TYVfi_-HF9KUvW_tBpt4w,29194
-RDG_networks/thickness/generate_line_segments_thickness_orientation.py,sha256=oTEwQkXRBuoHvEdIGU30p21e2QHW1UlmApzRO1s5c64,16821
-RDG_networks/thickness/generate_line_segments_thickness_static.py,sha256=zvYkLZpmyl711Kr7LCEFbXeVUgxQuA1n9Z5jD8W2iXc,9021
+RDG_networks/thickness/Classes.py,sha256=zRhi2TFDwK1oARvAd1HlxnMWeHSj7KKO-u79_r23tXc,8176
+RDG_networks/thickness/__init__.py,sha256=DzH-mmdrk5e1LL7oq5kg0xaDjtWR7DiCeKKchArHSIs,703
+RDG_networks/thickness/generate_line_segments_thickness.py,sha256=q3MVKEC8w1MUpiRGF6o4MKh6VHBIs1nuIibsqsewDcQ,29037
+RDG_networks/thickness/generate_line_segments_thickness_correct.py,sha256=rvvqEMGYX7imosKedyXHyTkBV4C2_24K8UxthXDTe7Q,28627
+RDG_networks/thickness/generate_line_segments_thickness_static.py,sha256=6-2p4GOQFU-dP5Q9nYuaVqeb7wvxk2Fqld3A7cV2pY8,8964
+RDG_networks/thickness/orientate_network.py,sha256=4jii3y89Jlw1tPmTWoUyrKE7MlHq21JuoiuwnBa1Mkk,15484
 RDG_networks/thickness/sample_in_polygon.py,sha256=nJ-yqfoCCGfC6_EpGL3L1t1LOYdqWZd-7v5bxy6th34,1849
-RDG_Networks-0.3.7.dist-info/LICENSE.txt,sha256=BHUkX2GsdTr30sKmVZ1MLGR1njnx17EX_oUuuSVZZPE,598
-RDG_Networks-0.3.7.dist-info/METADATA,sha256=A_gS2IRz_hQxrek9dkl2BawsJ6SKYuBxIUBCdhkjb58,2422
-RDG_Networks-0.3.7.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-RDG_Networks-0.3.7.dist-info/entry_points.txt,sha256=DRd5hzsY9jAz5e_gkd3gNoIwqj6RAZEtISlV1qpsIE8,1038
-RDG_Networks-0.3.7.dist-info/top_level.txt,sha256=4gUUYafD5Al9V8ZSiViVGYHpRMMCsCBcGgCNodk9Syg,13
-RDG_Networks-0.3.7.dist-info/RECORD,,
+RDG_Networks-0.3.9.dist-info/LICENSE.txt,sha256=BHUkX2GsdTr30sKmVZ1MLGR1njnx17EX_oUuuSVZZPE,598
+RDG_Networks-0.3.9.dist-info/METADATA,sha256=hlDd-R21n_eTohn-xz3OU7-ZvLragLhxSHwNWTq0u4M,2577
+RDG_Networks-0.3.9.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+RDG_Networks-0.3.9.dist-info/entry_points.txt,sha256=coqOWe9rYYuz9VQvJGFomTzvEP7JY5T9V9gauMhSb_0,986
+RDG_Networks-0.3.9.dist-info/top_level.txt,sha256=4gUUYafD5Al9V8ZSiViVGYHpRMMCsCBcGgCNodk9Syg,13
+RDG_Networks-0.3.9.dist-info/RECORD,,

{RDG_Networks-0.3.7.dist-info → RDG_Networks-0.3.9.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{RDG_Networks-0.3.7.dist-info → RDG_Networks-0.3.9.dist-info}/entry_points.txt

@@ -6,10 +6,10 @@ generate_line_segments = RDG_networks.generate_line_segments:main
 generate_line_segments_dynamic = RDG_networks.generate_line_segments_dynamic:main
 generate_line_segments_static = RDG_networks.generate_line_segments_static:main
 generate_line_segments_thickness = RDG_networks.thickness.generate_line_segments_thickness:main
-generate_line_segments_thickness_orientation = RDG_networks.thickness.generate_line_segments_dynamic_orientation:main
 generate_line_segments_thickness_static = RDG_networks.generate_line_segments_thickness_static:main
 get_alignment_mean = RDG_networks.thickness.get_alignment_mean:main
 get_intersection_segments = RDG_networks.get_intersection_segments:main
+orientate_network = RDG_networks.thickness.orientate_network:main
 rotate_network = RDG_networks.thickness.rotate_network:main
 save_to_stl = RDG_networks.save_to_stl:main
 translate_network = RDG_networks.thickness.translate_network:main

RDG_networks/__init__.py

@@ -8,17 +8,17 @@ from .generate_line_segments_dynamic import generate_line_segments_dynamic
 from .generate_line_segments_static import generate_line_segments_static
 from .draw_segments import draw_segments
 from .thickness.generate_line_segments_thickness import generate_line_segments_thickness
-from .thickness.generate_line_segments_thickness_orientation import generate_line_segments_thickness_orientation
+from .thickness.orientate_network import orientate_network
 from .thickness.generate_line_segments_thickness_static import generate_line_segments_thickness_static
-from .thickness.generate_line_segments_thickness_orientation import translate_network
-from .thickness.generate_line_segments_thickness_orientation import clip_network
-from .thickness.generate_line_segments_thickness_orientation import rotate_network
-from .thickness.generate_line_segments_thickness_orientation import get_alignment_mean
+from .thickness.orientate_network import translate_network
+from .thickness.orientate_network import clip_network
+from .thickness.orientate_network import rotate_network
+from .thickness.orientate_network import get_alignment_mean
 from .save_to_stl import save_to_stl
 
 __all__ = ['generate_line_segments', 
            'generate_line_segments_thickness',
-           'generate_line_segments_thickness_orientation',
+           'orientate_network',
            'translate_network',
            'clip_network',
            'rotate_network',

RDG_networks/thickness/Classes.py

@@ -95,7 +95,7 @@ class Polygon:
         vertices (List[Tuple[float, float]]): A list of (x, y) coordinates representing the vertices of the polygon.
     """
 
-    def __init__(self, vertices: List[tuple], middle_segment=None):
+    def __init__(self, vertices: List[tuple], middle_segment=None, neighbors=None):
         """
         Initializes a Polygon instance with the provided vertices.
 
@@ -104,6 +104,7 @@ class Polygon:
         """
         self.vertices = vertices
         self.middle_segment = middle_segment
+        self.neighbors = neighbors
 
     def area(self) -> float:
         """

RDG_networks/thickness/__init__.py

@@ -1,16 +1,16 @@
 # __init__.py
 
 from .generate_line_segments_thickness import generate_line_segments_thickness
-from .generate_line_segments_thickness_orientation import generate_line_segments_thickness_orientation
+from .orientate_network import orientate_network
 from .generate_line_segments_thickness_static import generate_line_segments_thickness_static
-from .generate_line_segments_thickness_orientation import translate_network
-from .generate_line_segments_thickness_orientation import clip_network
-from .generate_line_segments_thickness_orientation import rotate_network
-from .generate_line_segments_thickness_orientation import get_alignment_mean
+from .orientate_network import translate_network
+from .orientate_network import clip_network
+from .orientate_network import rotate_network
+from .orientate_network import get_alignment_mean
 
 __all__ = [
            'generate_line_segments_thickness',
-           'generate_line_segments_thickness_orientation',
+           'orientate_network',
            'generate_line_segments_thickness_static',
            'translate_network',
            'clip_network',

RDG_networks/thickness/generate_line_segments_thickness.py

@@ -142,10 +142,10 @@ def pick_item_with_probability(
 def get_location_and_direction(
     polygon_arr: Dict[str, Dict[str, object]], 
     thickness: float, 
+    angle: float,
     nucleation_point: Tuple[float, float] = None,
     min_distance: float = 0,
-    max_attempts: int = 1000, 
-    angles: Union[str, List[float]] = 'uniform'
+    max_attempts: int = 1000
 ) -> Union[Tuple[str, Dict[str, object], Tuple[float, float], np.ndarray, np.ndarray], bool]:
     """
     Attempts to find a valid location and direction within a polygon for placing a new segment. The direction can either be randomly 
@@ -159,8 +159,8 @@ def get_location_and_direction(
             The thickness of the segment that needs to fit inside the polygon.
         max_attempts (int, optional): 
             The maximum number of attempts to find a valid location and direction. Defaults to 1000.
-        angles (Union[str, List[float]], optional): 
-            A string ('uniform' for random directions) or a list of angles (in radians) to choose the direction from. Defaults to 'uniform'.
+        angle (float): 
+            A float indicating the angle of the new segment.
         nucleation_point (Tuple[float, float], optional): 
             predified nucleation point for the segment. Defaults to None.
         min_distance (float, optional): 
@@ -178,16 +178,8 @@ def get_location_and_direction(
                 - The angle of the segment.
             - Returns `False` if no valid location and direction are found after the maximum attempts.
     """
-    
-    # Generate a new direction based on the angles parameter
-    if angles == 'uniform':
-        angle_new = random.uniform(-np.pi, np.pi)
-        direction = (np.cos(angle_new), np.sin(angle_new))
-        direction = direction / np.linalg.norm(direction)  # Normalize the direction vector
-    else:
-        angle_new = random.choice(angles)
-        direction = (np.cos(angle_new), np.sin(angle_new))
-        direction = np.array(direction) / np.linalg.norm(direction)
+    direction = (np.cos(angle), np.sin(angle))
+    direction = np.array(direction) / np.linalg.norm(direction)
     
     # Try to find a valid location and direction up to max_attempts
     attempt = 0
@@ -215,7 +207,7 @@ def get_location_and_direction(
         
         # Check if both endpoints of the segment are inside the polygon
         if is_inside_polygon(polygon['vertices'], p1) and is_inside_polygon(polygon['vertices'], p2):
-            return polygon_id, polygon, location_new, direction, perpendicular, angle_new
+            return polygon_id, polygon, location_new, direction, perpendicular, angle
         
         attempt += 1
     
@@ -425,7 +417,7 @@ def update_data(
     segments_dict[segment_new_1.id] = segment_new_1
     segments_dict[neighbor1_1].neighbors[id_1] = vertex_begin_1
     segments_dict[neighbor1_2].neighbors[id_1] = vertex_end_1
-    
+
     # Update the segments_dict for the second segment
     neighbors_initial_2 = {
         neighbor2_1: vertex_begin_2,
@@ -443,7 +435,20 @@ def update_data(
     segments_dict[neighbor2_2].neighbors[id_2] = vertex_end_2
     
     # Update the segment_thickness_dict with the base polygon
-    segment_thickness_dict[len(segment_thickness_dict) + 1] = Polygon(vertices=vertices0)
+    neighbors = cycle0.copy()
+    neighbors.remove(f'{len(segment_thickness_dict)+1}_1')
+    neighbors.remove(f'{len(segment_thickness_dict)+1}_2')
+    neighbors = [ i[:-2] if i not in ['b1', 'b2', 'b3', 'b4'] else i for i in neighbors ]
+    neighbors = list(set(neighbors))
+
+    segment_thickness_dict[len(segment_thickness_dict) + 1] = Polygon(vertices=vertices0, neighbors=neighbors)
+
+    for n in neighbors:
+        if n in ['b1', 'b2', 'b3', 'b4']:
+            continue
+
+        else:
+            segment_thickness_dict[int(n)].neighbors.append(len(segment_thickness_dict) + 1)
     
     return segments_dict, polygon_arr, segment_thickness_dict
     
@@ -451,7 +456,7 @@ def add_line_segment(
     segments_dict: Dict[int, LineSegment], 
     polygon_arr: Dict[str, Dict[str, object]], 
     segment_thickness_dict: Dict[int, Polygon], 
-    angles: str = 'uniform',
+    angle: float,
     thickness: float = 0,
     nucleation_point: Tuple[float, float] = None,
     min_distance: float = 0,
@@ -480,7 +485,7 @@ def add_line_segment(
     """
     
     # Get a valid location and direction, or return False if none is found
-    loc = get_location_and_direction(polygon_arr, thickness, nucleation_point, min_distance, max_attempts=max_attempts, angles=angles)
+    loc = get_location_and_direction(polygon_arr, angle=angle, thickness=thickness, nucleation_point=nucleation_point, min_distance=min_distance, max_attempts=max_attempts)
     if loc:
         polygon_id, polygon, location_new, direction_new, perpendicular, angle_new = loc
     else:
@@ -560,8 +565,7 @@ def generate_line_segments_thickness(
     Args:
         size (int): The number of line segments to generate.
         thickness_arr (List[float]): A list containing the thickness values for each segment to be generated.
-        angles (str): The angle distribution method for generating segments. Defaults to 'uniform'.
-                List[float]: list of angles in radians.
+        angles (str): Angle used in the generation of the segments.
         config (List[List[float]]): A list of configurations for the nucleation points and angles.
         epsilon (float): the minimum distance between two line.
         box_size (float): the size of the box.
@@ -606,8 +610,6 @@ def generate_line_segments_thickness(
             angles = [config[i]['angle']]
         else:
             nucleation_point = None
-            # if angles != 'uniform':
-            #     angles=[angles[i]]
 
         output = add_line_segment(segments_dict, 
                                     polygon_arr, 
@@ -615,7 +617,7 @@ def generate_line_segments_thickness(
                                     thickness=thickness_arr[i], 
                                     min_distance = epsilon,
                                     nucleation_point = nucleation_point, 
-                                    angles=angles,
+                                    angle=angles[i],
                                     box_size=box_size)
         if output:
             segments_dict, polygon_arr, segment_thickness_dict, location, angle = output
@@ -624,7 +626,7 @@ def generate_line_segments_thickness(
         else:
             if config:
                 print('Configuration not possible. Point is skipped.')
-            else:    
+            else:
                 print(f"Stopped at iteration {len(segment_thickness_dict)}, could not find a valid segment position.")
                 jammed = True
                 break

RDG_networks/thickness/generate_line_segments_thickness_correct.py

@@ -0,0 +1,633 @@
+import math
+import numpy as np
+import random
+from typing import List, Dict, Tuple, Union, Optional
+from shapely.geometry import Polygon as Polygon_Shapely, LineString
+
+from .Classes import Line, LineSegment, Polygon
+from .sample_in_polygon import sample_in_polygon, is_inside_polygon
+
+def doLinesIntersect(line1: Line, line2: Line, box_size = 1) -> Tuple[bool, Union[Tuple[float, float], None]]:
+    """
+    Check if two lines intersect and return the intersection point.
+
+    Args:
+    - line1 (Line): The first line segment.
+    - line2 (Line): The second line segment.
+    - box_size (float): The size of the bounding box. Defaults to 1.
+
+    Returns:
+    - intersect (bool): True if the lines intersect, False otherwise.
+    - intersection_point (tuple or None): The intersection point (x, y) if lines intersect, None otherwise.
+    """
+    x1, y1 = line1.location
+    v1, w1 = line1.direction
+
+    x2, y2 = line2.location
+    v2, w2 = line2.direction
+
+    determinant = v1 * w2 - v2 * w1
+
+    if determinant == 0:
+        return False, (None, None)
+
+    t1 = ((x2 - x1) * w2 - (y2 - y1) * v2) / determinant
+    t2 = ((x2 - x1) * w1 - (y2 - y1) * v1) / determinant
+
+    intersect_x = x1 + v1 * t1
+    intersect_y = y2 + w2 * t2
+
+
+    if -1e-6 < intersect_x < box_size + 1e-6 and -1e-6 < intersect_y < box_size + 1e-6:
+        return True, (intersect_x, intersect_y)
+    else:
+        return False, (None, None)
+    
+def doSegmentsIntersect(
+    segment1: LineSegment, 
+    segment2: LineSegment,
+    box_size = 1
+) -> Tuple[bool, Tuple[Optional[float], Optional[float]]]:
+    """
+    Determines if two line segments intersect and returns the intersection point if they do.
+
+    Args:
+        segment1 (LineSegment): The first line segment.
+        segment2 (LineSegment): The second line segment.
+
+    Returns:
+        Tuple[bool, Tuple[Optional[float], Optional[float]]]:
+            - A boolean indicating whether the segments intersect.
+            - A tuple of the x and y coordinates of the intersection point if they intersect,
+              otherwise (None, None).
+    """
+    
+    # Create line equations based on the segments' start and end points
+    line1 = Line(location=segment1.start, direction=np.array(segment1.end) - np.array(segment1.start))
+    line2 = Line(location=segment2.start, direction=np.array(segment2.end) - np.array(segment2.start))
+    
+    # Check if the infinite extensions of the two lines intersect
+    intersect, (intersect_x, intersect_y) = doLinesIntersect(line1, line2, box_size)
+    
+    # If no intersection, return False
+    if not intersect:
+        return False, (None, None)
+    
+    # Check if the intersection point is within the bounds of both segments in the x-direction
+    xcheck = (
+        (segment1.end[0] <= intersect_x <= segment1.start[0]
+        or segment1.start[0] <= intersect_x <= segment1.end[0]
+        or abs(intersect_x - segment1.end[0]) < 1e-6
+        or abs(intersect_x - segment1.start[0]) < 1e-6)
+        and
+        (segment2.end[0] <= intersect_x <= segment2.start[0]
+        or segment2.start[0] <= intersect_x <= segment2.end[0]
+        or abs(intersect_x - segment2.end[0]) < 1e-6
+        or abs(intersect_x - segment2.start[0]) < 1e-6)
+    )
+    
+    # Check if the intersection point is within the bounds of both segments in the y-direction
+    ycheck = (
+        (segment1.end[1] <= intersect_y <= segment1.start[1]
+        or segment1.start[1] <= intersect_y <= segment1.end[1]
+        or abs(intersect_y - segment1.end[1]) < 1e-6
+        or abs(intersect_y - segment1.start[1]) < 1e-6)
+        and
+        (segment2.end[1] <= intersect_y <= segment2.start[1]
+        or segment2.start[1] <= intersect_y <= segment2.end[1]
+        or abs(intersect_y - segment2.end[1]) < 1e-6
+        or abs(intersect_y - segment2.start[1]) < 1e-6)
+    )
+    
+    # If the intersection point lies within the bounds of both segments, return True with the intersection point
+    if xcheck and ycheck:
+        return True, (intersect_x, intersect_y)
+    
+    # Otherwise, return False and no intersection point
+    return False, (None, None)
+
+def pick_item_with_probability(
+    polygon_arr: Dict[str, Dict[str, object]]
+) -> Tuple[str, Dict[str, object]]:
+    """
+    Randomly selects an item from the polygon array with a probability proportional to the area of the polygons.
+
+    Args:
+        polygon_arr (Dict[str, Dict[str, object]]): 
+            A dictionary where keys are polygon identifiers (e.g., 'p1', 'p2') and values are dictionaries containing polygon properties, 
+            including an 'area' key that stores the area of the polygon.
+
+    Returns:
+        Tuple[str, Dict[str, object]]: 
+            - The identifier of the selected polygon.
+            - The corresponding polygon data (dictionary) containing its properties.
+    """
+    
+    # Calculate the total weight (sum of areas of all polygons)
+    max_weight = sum(pol['area'] for pol in polygon_arr.values())
+    
+    # Generate a random threshold between 0 and the total weight
+    threshold = random.uniform(0, max_weight)
+    cumulative_weight = 0
+    
+    # Iterate through the polygons, accumulating weights
+    for item, pol in polygon_arr.items():
+        weight = pol['area']
+        cumulative_weight += weight
+        
+        # Return the polygon when the cumulative weight surpasses the threshold
+        if cumulative_weight >= threshold:
+            return item, pol
+
+def get_location_and_direction(
+    polygon_arr: Dict[str, Dict[str, object]], 
+    thickness: float, 
+    angle: float,
+    nucleation_point: Tuple[float, float] = None,
+    min_distance: float = 0,
+    max_attempts: int = 1000
+) -> Union[Tuple[str, Dict[str, object], Tuple[float, float], np.ndarray, np.ndarray], bool]:
+    """
+    Attempts to find a valid location and direction within a polygon for placing a new segment. The direction can either be randomly 
+    chosen (uniformly) or from a specified list of angles. It ensures that the segment lies within the polygon's bounds given the 
+    specified thickness.
+
+    Args:
+        polygon_arr (Dict[str, Dict[str, object]]): 
+            A dictionary where the keys are polygon identifiers and the values are dictionaries containing polygon properties, including 'vertices'.
+        thickness (float): 
+            The thickness of the segment that needs to fit inside the polygon.
+        max_attempts (int, optional): 
+            The maximum number of attempts to find a valid location and direction. Defaults to 1000.
+        angle (float): 
+            A float indicating the angle of the new segment.
+        nucleation_point (Tuple[float, float], optional): 
+            predified nucleation point for the segment. Defaults to None.
+        min_distance (float, optional): 
+            the minimum distance between two lines. Defaults to 0.
+
+    Returns:
+        Union[Tuple[str, Dict[str, object], Tuple[float, float], np.ndarray, np.ndarray], bool]:
+            - If a valid location and direction are found, returns a tuple containing:
+                - The polygon ID (`str`).
+                - The polygon data (`Dict[str, object]`).
+                - The new location as a tuple of floats (`Tuple[float, float]`).
+                - The direction vector as a numpy array (`np.ndarray`).
+                - The perpendicular vector to the direction as a numpy array (`np.ndarray`).
+                - The nucleation point [x,y] of the segment
+                - The angle of the segment.
+            - Returns `False` if no valid location and direction are found after the maximum attempts.
+    """
+    direction = (np.cos(angle), np.sin(angle))
+    direction = np.array(direction) / np.linalg.norm(direction)
+    
+    # Try to find a valid location and direction up to max_attempts
+    attempt = 0
+    while attempt < max_attempts:
+        polygon_id, polygon = pick_item_with_probability(polygon_arr)
+        
+        # Sample a location within the polygon
+        #check if nucleation point is given
+        if nucleation_point is not None:
+            location_new = nucleation_point
+        else:
+            location_new = sample_in_polygon(polygon['vertices'])
+        
+        # Compute the perpendicular vector to the direction
+        perpendicular = np.array([direction[1], -direction[0]])
+        perpendicular = perpendicular / np.linalg.norm(perpendicular)
+        
+        # Ensure the perpendicular vector is oriented consistently (y-component is non-negative)
+        if perpendicular[1] < 0:
+            perpendicular = -perpendicular
+        
+        # Compute the positions for the segment with thickness, shifted by half-thickness along the perpendicular direction
+        p1 = np.array(location_new) + (thickness/2 + min_distance) * perpendicular 
+        p2 = np.array(location_new) - (thickness/2 + min_distance) * perpendicular
+        
+        # Check if both endpoints of the segment are inside the polygon
+        if is_inside_polygon(polygon['vertices'], p1) and is_inside_polygon(polygon['vertices'], p2):
+            return polygon_id, polygon, location_new, direction, perpendicular, angle
+        
+        attempt += 1
+    
+    # If no valid location and direction is found, return False
+    return False
+
+def get_polygons(polygon_id, polygon_arr, neighbor1_1, neighbor1_2, vertex_begin_1, vertex_end_1, neighbor2_1, neighbor2_2, vertex_begin_2, vertex_end_2, segment_new_id_1, segment_new_id_2):
+    # Extract vertices and cycle (faces) of the original polygon
+    vertices = polygon_arr[polygon_id]['vertices']
+    cycle = polygon_arr[polygon_id]['faces']
+    
+    # Get first cycle and vertices
+    index_start_1, index_end_1 = (cycle.index(neighbor1_1), cycle.index(neighbor1_2))
+    if index_start_1 < index_end_1:
+        cycle1 = [segment_new_id_1] + cycle[index_start_1:index_end_1+1]
+        vertices1 = [vertex_begin_1] + vertices[index_start_1:index_end_1] + [vertex_end_1]
+    else:
+        cycle1 = [segment_new_id_1] + cycle[index_start_1:] + cycle[:index_end_1+1]
+        vertices1 = [vertex_begin_1] + vertices[index_start_1:] + vertices[:index_end_1] + [vertex_end_1]
+        
+    # Get second cycle and vertices
+    index_start_2, index_end_2 = (cycle.index(neighbor2_2), cycle.index(neighbor2_1))
+    if index_start_2 < index_end_2:
+        cycle2 = [segment_new_id_2] + cycle[index_start_2:index_end_2+1]
+        vertices2 = [vertex_end_2] + vertices[index_start_2:index_end_2] + [vertex_begin_2]
+    else:
+        cycle2 = [segment_new_id_2] + cycle[index_start_2:] + cycle[:index_end_2+1]
+        vertices2 = [vertex_end_2] + vertices[index_start_2:] + vertices[:index_end_2] + [vertex_begin_2]
+    
+    # Get middle cycle and vertices
+    cycle0 = [neighbor1_1, segment_new_id_1, neighbor1_2]
+    vertices0 = [vertex_begin_1, vertex_end_1]
+    
+    index_start_0, index_end_0 = (cycle.index(neighbor1_2), cycle.index(neighbor2_2))
+    if index_start_0 < index_end_0:
+        cycle0 = cycle0 + cycle[index_start_0:index_end_0+1]
+        vertices0 = vertices0 + vertices[index_start_0:index_end_0] 
+        
+    elif index_start_0 > index_end_0:
+        cycle0 = cycle0 + cycle[index_start_0:] + cycle[:index_end_0+1]
+        vertices0 = vertices0 + vertices[index_start_0:] + vertices[:index_end_0]
+        
+    cycle0 = cycle0 + [segment_new_id_2]
+    vertices0 = vertices0 + [vertex_end_2] + [vertex_begin_2]
+    
+    index_start_0, index_end_0 = (cycle.index(neighbor2_1), cycle.index(neighbor1_1))
+    if index_start_0 < index_end_0:
+        cycle0 = cycle0 + cycle[index_start_0:index_end_0+1]
+        vertices0 = vertices0 + vertices[index_start_0:index_end_0] 
+        
+    elif index_start_0 > index_end_0:
+        cycle0 = cycle0 + cycle[index_start_0:] + cycle[:index_end_0+1]
+        vertices0 = vertices0 + vertices[index_start_0:] + vertices[:index_end_0]
+    
+    return cycle0, vertices0, cycle1, vertices1, cycle2, vertices2
+
+def get_new_segment(
+    line_segments_to_check: List[LineSegment],
+    location: Tuple[float, float], 
+    direction: Tuple[float, float], 
+    id: Optional[int] = None,
+    box_size: float = 1
+) -> LineSegment:
+    """
+    Creates a new line segment by extending a given location in a specified direction and 
+    determines its neighbors by checking intersections with other line segments.
+
+    Args:
+        line_segments_to_check (List[LineSegment]): List of existing line segments to check for intersections.
+        location (Tuple[float, float]): The starting point (x, y) for the new line segment.
+        direction (Tuple[float, float]): The direction vector in which to extend the line segment.
+        id (Optional[int]): Optional ID for the new line segment. If not provided, defaults to None.
+        box_size(optional[Int]]): The size of the box. Defaults to 1.
+
+    Returns:
+        LineSegment: A new line segment object with its neighbors based on intersections.
+    """
+    
+    # Create a temporary line segment extending from the location in both directions
+    s_temp = LineSegment(start=np.array(location) - 10*np.sqrt(2)*box_size * np.array(direction), end=np.array(location) + 10*np.sqrt(2)*box_size * np.array(direction))
+
+    intersection_points = []
+
+    # Check for intersections with existing line segments
+    for segment in line_segments_to_check:
+        intersect, (intersect_x, intersect_y) = doSegmentsIntersect(s_temp, segment, box_size)
+
+        if intersect:
+            segment_length = math.sqrt(
+                (location[0] - intersect_x) ** 2
+                + (location[1] - intersect_y) ** 2
+            )
+            intersection_points.append(
+                {"id": segment.id, "point": (intersect_x, intersect_y), "segment_length": segment_length}
+            )
+
+    # Divide intersections into ones behind and in front of the new line
+    intersections_b = [intersection for intersection in intersection_points if intersection["point"][0] < location[0]]
+    intersections_f = [intersection for intersection in intersection_points if intersection["point"][0] > location[0]]
+
+    if not intersections_b or not intersections_f:
+        intersections_b = [intersection for intersection in intersection_points if intersection["point"][1] < location[1]]
+        intersections_f = [intersection for intersection in intersection_points if intersection["point"][1] > location[1]]
+
+    # Determine the closest intersections for segment start and end
+    s_start = min(intersections_b, key=lambda x: x["segment_length"])
+    s_end = min(intersections_f, key=lambda x: x["segment_length"])
+    start, end = s_start['point'], s_end['point']
+    start_id, end_id = s_start['id'], s_end['id']
+
+    # Ensure the start comes before the end
+    if start[0] > end[0]:
+        start, end = end, start
+        start_id, end_id = end_id, start_id
+
+    # Create a new line segment and assign neighbors
+    neighbors_initial = {start_id: start, end_id: end}
+    segment_new = LineSegment(start=start, end=end, id=id, neighbors_initial=neighbors_initial, neighbors=neighbors_initial)
+    
+    return segment_new
+    
+def update_data(
+    segments_dict: Dict[int, LineSegment], 
+    polygon_arr: Dict[str, Dict[str, object]], 
+    polygon_id: str, 
+    segment_thickness_dict: Dict[int, Polygon], 
+    vertices0: List[Tuple[float, float]], 
+    vertices1: List[Tuple[float, float]], 
+    vertices2: List[Tuple[float, float]], 
+    cycle0: List[int], 
+    cycle1: List[int], 
+    cycle2: List[int], 
+    neighbor1_1: int, 
+    neighbor1_2: int, 
+    neighbor2_1: int, 
+    neighbor2_2: int, 
+    vertex_begin_1: Tuple[float, float], 
+    vertex_end_1: Tuple[float, float], 
+    vertex_begin_2: Tuple[float, float], 
+    vertex_end_2: Tuple[float, float], 
+    id_1: int, 
+    id_2: int
+) -> Tuple[Dict[int, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon]]:
+    """
+    Updates the segments, polygons, and segment thickness dictionaries by adding new data derived
+    from provided vertices and neighbor information.
+
+    Args:
+        segments_dict (Dict[int, LineSegment]): A dictionary of segments with segment ID as the key.
+        polygon_arr (Dict[str, Dict[str, object]]): A dictionary of polygons with polygon ID as the key.
+        polygon_id (str): The ID of the polygon being updated.
+        segment_thickness_dict (Dict[int, Polygon]): A dictionary mapping thickness information to polygon objects.
+        vertices0 (List[Tuple[float, float]]): Vertices of the base polygon.
+        vertices1 (List[Tuple[float, float]]): Vertices of the first new polygon.
+        vertices2 (List[Tuple[float, float]]): Vertices of the second new polygon.
+        cycle0 (List[int]): List of face indices for the base polygon.
+        cycle1 (List[int]): List of face indices for the first new polygon.
+        cycle2 (List[int]): List of face indices for the second new polygon.
+        neighbor1_1 (int): ID of the first neighbor of the first segment.
+        neighbor1_2 (int): ID of the second neighbor of the first segment.
+        neighbor2_1 (int): ID of the first neighbor of the second segment.
+        neighbor2_2 (int): ID of the second neighbor of the second segment.
+        vertex_begin_1 (Tuple[float, float]): Starting vertex of the first segment.
+        vertex_end_1 (Tuple[float, float]): Ending vertex of the first segment.
+        vertex_begin_2 (Tuple[float, float]): Starting vertex of the second segment.
+        vertex_end_2 (Tuple[float, float]): Ending vertex of the second segment.
+        id_1 (int): ID of the first new segment.
+        id_2 (int): ID of the second new segment.
+
+    Returns:
+        Tuple[Dict[int, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon]]:
+            - Updated dictionary of line segments.
+            - Updated dictionary of polygons.
+            - Updated dictionary of segment thickness.
+    """
+    
+    # Update polygon_arr (a dictionary of polygons)
+    polygon_new_1 = {
+        f'p{len(polygon_arr) + 1}': {
+            'vertices': vertices1, 
+            'area': Polygon(vertices=vertices1).area(), 
+            'faces': cycle1
+        }
+    }
+    polygon_new_2 = {
+        polygon_id: {
+            'vertices': vertices2, 
+            'area': Polygon(vertices=vertices2).area(), 
+            'faces': cycle2
+        }
+    }
+    polygon_arr.update(polygon_new_1)
+    polygon_arr.update(polygon_new_2)
+    
+    # Update the segments_dict for the first segment
+    neighbors_initial_1 = {
+        neighbor1_1: vertex_begin_1,
+        neighbor1_2: vertex_end_1
+    }
+    segment_new_1 = LineSegment(
+        start=vertex_begin_1, 
+        end=vertex_end_1, 
+        id=id_1, 
+        neighbors_initial=neighbors_initial_1, 
+        neighbors=neighbors_initial_1
+    )
+    segments_dict[segment_new_1.id] = segment_new_1
+    segments_dict[neighbor1_1].neighbors[id_1] = vertex_begin_1
+    segments_dict[neighbor1_2].neighbors[id_1] = vertex_end_1
+    
+    # Update the segments_dict for the second segment
+    neighbors_initial_2 = {
+        neighbor2_1: vertex_begin_2,
+        neighbor2_2: vertex_end_2
+    }
+    segment_new_2 = LineSegment(
+        start=vertex_begin_2, 
+        end=vertex_end_2, 
+        id=id_2, 
+        neighbors_initial=neighbors_initial_2, 
+        neighbors=neighbors_initial_2
+    )
+    segments_dict[segment_new_2.id] = segment_new_2
+    segments_dict[neighbor2_1].neighbors[id_2] = vertex_begin_2
+    segments_dict[neighbor2_2].neighbors[id_2] = vertex_end_2
+    
+    # Update the segment_thickness_dict with the base polygon
+    segment_thickness_dict[len(segment_thickness_dict) + 1] = Polygon(vertices=vertices0)
+    
+    return segments_dict, polygon_arr, segment_thickness_dict
+    
+def add_line_segment(
+    segments_dict: Dict[int, LineSegment], 
+    polygon_arr: Dict[str, Dict[str, object]], 
+    segment_thickness_dict: Dict[int, Polygon], 
+    angle: float,
+    thickness: float = 0,
+    nucleation_point: Tuple[float, float] = None,
+    min_distance: float = 0,
+    box_size: float = 1,
+    max_attempts: int = 1000
+) -> Union[Tuple[Dict[int, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon], List[float], float], bool]:
+    """
+    Adds a new line segment to the segments and polygon data structures, with a given thickness and angle distribution.
+
+    Args:
+        segments_dict (Dict[int, LineSegment]): A dictionary containing the current line segments.
+        polygon_arr (Dict[str, Dict[str, object]]): A dictionary containing the current polygons and their properties.
+        segment_thickness_dict (Dict[int, Polygon]): A dictionary storing the thickness information mapped to polygons.
+        thickness (float): The thickness of the new segment to be added. Defaults to 0.
+        angles (str): The angle distribution method. Defaults to 'uniform'.
+        nucleation_point (Tuple[float, float]): A predefined nucleation point for the new segment. Defaults to None.
+        min_distance (float): The minimum distance between two lines. Defaults to 0.
+        box_size (float): The size of the box. Defaults to 1.
+        max_attempts (int): The maximum number of attempts to find a valid location and direction. Defaults to 1000.
+
+    Returns:
+        Union[Tuple[Dict[int, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon]], List[float], float, bool]:
+            - A tuple containing the updated segments dictionary, polygon dictionary, and thickness dictionary, 
+              or False if no valid location for the new segment is found.
+            -nucleation point in a list [x,y] and the angle of the segment in radians.
+    """
+    
+    # Get a valid location and direction, or return False if none is found
+    loc = get_location_and_direction(polygon_arr, angle=angle, thickness=thickness, nucleation_point=nucleation_point, min_distance=min_distance, max_attempts=max_attempts)
+    if loc:
+        polygon_id, polygon, location_new, direction_new, perpendicular, angle_new = loc
+    else:
+        print('No valid location found')
+        return False
+        
+    # Get the borders of the new segment with the given thickness
+    line_segments_to_check = [segments_dict[segment] for segment in polygon['faces']]
+    middle_segment = get_new_segment(line_segments_to_check, location=location_new, direction=direction_new, box_size=box_size)
+    s1 = get_new_segment(line_segments_to_check, location=np.array(location_new) + thickness * perpendicular / 2, direction=direction_new,box_size=box_size)
+    s2 = get_new_segment(line_segments_to_check, location=np.array(location_new) - thickness * perpendicular / 2, direction=direction_new, box_size=box_size)
+    
+    # Extract neighbor information and segment vertices
+    neighbor1_1, neighbor1_2 = list(s1.neighbors.keys())
+    vertex_begin_1, vertex_end_1 = list(s1.neighbors.values())
+    neighbor2_1, neighbor2_2 = list(s2.neighbors.keys())
+    vertex_begin_2, vertex_end_2 = list(s2.neighbors.values())
+    id_1 = str(int((len(segments_dict.keys()) - 2) / 2)) + '_1'
+    id_2 = str(int((len(segments_dict.keys()) - 2) / 2)) + '_2'
+    
+    # Get the resulting polygons after splitting
+    cycle0, vertices0, cycle1, vertices1, cycle2, vertices2 = get_polygons(
+        polygon_id,
+        polygon_arr, 
+        neighbor1_1, 
+        neighbor1_2, 
+        vertex_begin_1, 
+        vertex_end_1, 
+        neighbor2_1, 
+        neighbor2_2,
+        vertex_begin_2=vertex_begin_2,
+        vertex_end_2=vertex_end_2,
+        segment_new_id_1=id_1, 
+        segment_new_id_2=id_2
+    )
+    
+    # Update all relevant data structures
+    segments_dict, polygon_arr, segment_thickness_dict = update_data(
+        segments_dict, 
+        polygon_arr, 
+        polygon_id, 
+        segment_thickness_dict, 
+        vertices0, 
+        vertices1, 
+        vertices2, 
+        cycle0, 
+        cycle1, 
+        cycle2, 
+        neighbor1_1, 
+        neighbor1_2, 
+        neighbor2_1, 
+        neighbor2_2, 
+        vertex_begin_1, 
+        vertex_end_1, 
+        vertex_begin_2, 
+        vertex_end_2, 
+        id_1, 
+        id_2
+    )
+    
+    # Associate the middle segment with the newly created thickness entry
+    segment_thickness_dict[list(segment_thickness_dict.keys())[-1]].middle_segment = middle_segment
+    
+    return segments_dict, polygon_arr, segment_thickness_dict, location_new, angle_new
+
+def generate_line_segments_thickness(
+    size: int, 
+    thickness_arr: List[float], 
+    angles: str = 'uniform',
+    config: List[List[float]] = None, 
+    epsilon: float = 0,
+    box_size: float = 1 
+    ) -> Tuple[Dict[str, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon], np.ndarray]:
+    """
+    Generates a specified number of line segments and updates the polygon and segment thickness dictionaries.
+
+    Args:
+        size (int): The number of line segments to generate.
+        thickness_arr (List[float]): A list containing the thickness values for each segment to be generated.
+        angles (str): Angle used in the generation of the segments.
+        config (List[List[float]]): A list of configurations for the nucleation points and angles.
+        epsilon (float): the minimum distance between two line.
+        box_size (float): the size of the box.
+
+    Returns:
+        Tuple[Dict[str, LineSegment], Dict[str, Dict[str, object]], Dict[int, Polygon]]:
+            - Updated dictionary of line segments.
+            - Updated dictionary of polygons.
+            - Updated dictionary of segment thicknesses.
+            - Array of the nucleation points and angles [x,y,theta].
+    """
+    
+    # Initialize border segments for a square and its polygon representation
+    borders = [
+        LineSegment((box_size, 0), (0, 0), id='b1', neighbors_initial={'b2': (0, 0), 'b4': (box_size, 0)}, neighbors={'b2': (0, 0), 'b4': (box_size, 0)}),
+        LineSegment((0, box_size), (0, 0), id='b2', neighbors_initial={'b1': (0, 0), 'b3': (0, box_size)}, neighbors={'b1': (0, 0), 'b3': (0, box_size)}),
+        LineSegment((0, box_size), (box_size, box_size), id='b3', neighbors_initial={'b2': (0, box_size), 'b4': (box_size, box_size)}, neighbors={'b2': (0, box_size), 'b4': (box_size, box_size)}),
+        LineSegment((box_size, box_size), (box_size, 0), id='b4', neighbors_initial={'b1': (box_size, 0), 'b3': (box_size, box_size)}, neighbors={'b1': (box_size, 0), 'b3': (box_size, box_size)})
+    ]
+    
+    polygon_arr = {
+        'p1': {
+            'vertices': [(0, 0), (0, box_size), (box_size, box_size), (box_size, 0)], 
+            'area': box_size**2, 
+            'faces': ['b1', 'b2', 'b3', 'b4']
+        }
+    }
+
+    segments = borders
+    segments_dict = {segment.id: segment for segment in segments}
+    segment_thickness_dict = {}
+    generated_config = []
+
+    if config is not None and size > len(config):
+        print("The size of the configuration is smaller than the size of the segments. Generated a network of the same size as the configuration.")
+        size = len(config)
+
+    jammed = False
+    for i in range(size):
+        if config:
+            nucleation_point = config[i]['location']
+            angles = [config[i]['angle']]
+        else:
+            nucleation_point = None
+            # if angles != 'uniform':
+            #     angles=[angles[i]]
+
+        output = add_line_segment(segments_dict, 
+                                    polygon_arr, 
+                                    segment_thickness_dict, 
+                                    thickness=thickness_arr[i], 
+                                    min_distance = epsilon,
+                                    nucleation_point = nucleation_point, 
+                                    angle=angles[i],
+                                    box_size=box_size)
+        if output:
+            segments_dict, polygon_arr, segment_thickness_dict, location, angle = output
+            generated_config.append({ 'location': location, 'angle': angle, 'thickness': thickness_arr[i] })
+
+        else:
+            if config:
+                print('Configuration not possible. Point is skipped.')
+            else:    
+                print(f"Stopped at iteration {len(segment_thickness_dict)}, could not find a valid segment position.")
+                jammed = True
+                break
+            
+        # Uncomment the following line if you want progress feedback
+        percentage = np.round(i / size * 100, 3)
+        print(f'generate_segments: {percentage}% done', end='\r')
+    
+    data_dict = {'segments_dict': segments_dict, 
+                 'polygon_arr': polygon_arr, 
+                 'segment_thickness_dict': segment_thickness_dict, 
+                 'jammed': jammed,
+                 'generated_config': generated_config}
+    
+    return data_dict

RDG_networks/thickness/generate_line_segments_thickness_static.py

@@ -105,7 +105,7 @@ def seeds(number_of_lines, radius = 0.015, number_of_trials = 10000):
         if trial <= number_of_trials:
             nucleation_points += [new_points]
             angles = [0, np.pi/4, np.pi/2, 3*np.pi/4]
-            angle_new = random.uniform(0, 2*np.pi) #random.choice(angles)#np.pi #random.uniform(0, 2*np.pi)
+            angle_new = random.uniform(0, 2*np.pi)
             angle += [angle_new]
             Line[line_id] = [ new_points ,angle_new]
             line_id += 1

RDG_networks/thickness/{generate_line_segments_thickness_orientation.py → orientate_network.py}

@@ -1,8 +1,8 @@
 import numpy as np
+import math
 from typing import List, Dict, Tuple
 from shapely.geometry import Polygon as Polygon_Shapely
 from shapely.geometry import LineString, box
-from concurrent.futures import ProcessPoolExecutor
 from .Classes import LineSegment, Polygon
 
 def rotate(point, center, rotation_matrix):
@@ -13,7 +13,9 @@ def rotate(point, center, rotation_matrix):
     rotation_matrix: 2x2 numpy array representing the rotation matrix
     """
     translated_point = point - center
-    rotated_point = np.dot(rotation_matrix, translated_point)
+
+    # rotated_point = np.dot(rotation_matrix, translated_point)
+    rotated_point = rotation_matrix@translated_point
     final_point = rotated_point + center
 
     return final_point
@@ -30,16 +32,22 @@ def angle_between(v1, v2):
 
 def get_alignment_mean(line_vector_arr, director):
     """Get the mean alignment."""
-    S_all = []
+    S_all = 0
+    total_mass = 0
     for item in line_vector_arr:
         line_vector = item['line_vector']
+        vector_diff = np.array(line_vector[1]) - np.array(line_vector[0])
+
         area = item['area']
-        P2 = 0.5*(3*(np.cos(angle_between(line_vector, director)))**2-1)
-        S_all.append(P2*area)
+        align = math.cos(angle_between(vector_diff, director))**2
+        S_all += align*area
+        total_mass += area
 
-    return float(np.mean(S_all))
+    output = S_all / total_mass
 
-def compute_alignment_for_angle(
+    return output
+
+def compute_alignment(
     angle: float, 
     segment_thickness_dict: dict[str, Polygon],
     director: np.ndarray, 
@@ -69,7 +77,7 @@ def compute_alignment_for_angle(
     tuple[float, float]
         A tuple where the first element is the input angle and the second element is the computed alignment value.
     """
-    box_center = (np.array(box_measurements[0]) + np.array(box_measurements[2])) / 2
+    box_center = np.array((box_measurements[0]) + np.array(box_measurements[2])) / 2
 
     # Rotate network
     segment_thickness_dict_new = rotate_network(segment_thickness_dict, rotate_angle=angle, box_center=box_center)
@@ -79,13 +87,38 @@ def compute_alignment_for_angle(
 
     line_vectors = [
         {'line_vector': [seg.middle_segment.start, seg.middle_segment.end], 'area': seg.area()}
-        for seg in segment_thickness_dict_new.values()
+        for seg in segment_thickness_dict_new.values() if seg.middle_segment is not None
     ]
 
     alignment = get_alignment_mean(line_vectors, director)
-
+    
     return angle, alignment
 
+def get_max_alignment(
+    segment_thickness_dict: dict, 
+    director: np.ndarray, 
+    box_measurements: list[float], 
+    grid_points: int = 360
+) -> float:
+    """Find the angle with the maximum alignment using parallel processing."""
+    # Create a list of angles to evaluate
+    angles = np.linspace(0, np.pi, grid_points)
+
+    results = []
+    for a in angles:
+        result = compute_alignment(a, segment_thickness_dict, director, box_measurements)
+        results.append(result)
+
+    # Find the angle with the maximum alignment
+    max_alignment = 0
+    max_angle = None
+    for angle, alignment in results:
+        if alignment > max_alignment:
+            max_alignment = alignment
+            max_angle = angle
+
+    return max_angle
+
 def rotate_network(
     segment_thickness_dict: dict[str, Polygon],
     rotate_angle: float, 
@@ -137,7 +170,7 @@ def rotate_network(
         middle_segment_new = LineSegment(start=start, end=end)
         
         # Store the rotated segment in the new dictionary
-        segment_thickness_dict_new[id] = Polygon(vertices=vertices_new, middle_segment=middle_segment_new)
+        segment_thickness_dict_new[id] = Polygon(vertices=vertices_new, middle_segment=middle_segment_new, neighbors=segment.neighbors)
 
     return segment_thickness_dict_new
 
@@ -204,7 +237,7 @@ def clip_network(
                 middle_segment_new = LineSegment(start=start, end=end)
 
             # Create a new clipped polygon with updated vertices and middle segment
-            pol_new = Polygon(vertices=vertices_new, middle_segment=middle_segment_new)
+            pol_new = Polygon(vertices=vertices_new, middle_segment=middle_segment_new, neighbors=segment.neighbors)
             pol_new.sort_vertices()  # Ensure vertices are sorted
             segment_thickness_dict_new[id] = pol_new
 
@@ -252,78 +285,16 @@ def translate_network(
             middle_segment_new = LineSegment(start=start, end=end)
         
         # Store the translated segment in the new dictionary
-        segment_thickness_dict_new[id] = Polygon(vertices=vertices_new, middle_segment=middle_segment_new)
+        segment_thickness_dict_new[id] = Polygon(vertices=vertices_new, middle_segment=middle_segment_new, neighbors=segment.neighbors)
 
     return segment_thickness_dict_new
 
-def get_alignment_mean(line_vector_arr, director):
-    """Get the mean alignment."""
-    S_all = []
-    for item in line_vector_arr:
-        line_vector = item['line_vector']
-        area = item['area']
-        P2 = 0.5*(3*(np.cos(angle_between(line_vector, director)))**2-1)
-        S_all.append(P2*area)
-
-    return float(np.mean(S_all))
-
-def compute_alignment_for_angle(
-    segment_thickness_dict: dict,
-    angle: float, 
-    box_center,
-    director: np.ndarray, 
-) -> tuple[float, float]:
-    """Compute the alignment for a given angle."""
-    
-    # Rotate the segment network for the given angle
-    segment_thickness_dict_rotated = rotate_network(segment_thickness_dict, rotate_angle=angle, box_center=box_center)
-    
-    # Create line vectors from the rotated segments
-    line_vectors = [] 
-    for s in segment_thickness_dict_rotated.values():
-        line_vectors.append({'line_vector': np.array([s.middle_segment.start, s.middle_segment.end]), 'area': s.area()})
-
-    # Compute the alignment for the current angle
-    alignment = get_alignment_mean(line_vectors, director)
-    return angle, alignment
-
-def get_max_alignment_angle(
-    segment_thickness_dict: dict, 
-    director: np.ndarray, 
-    box_measurements: list[float], 
-    grid_points: int = 360
-) -> float:
-    """Find the angle with the maximum alignment using parallel processing."""
-    
-    # Create a list of angles to evaluate
-    angles = np.linspace(0, 2 * np.pi, grid_points)
-
-    # Use ProcessPoolExecutor for parallel computation of alignment
-    with ProcessPoolExecutor() as executor:
-        # Submit tasks to the pool for each angle
-        results = list(executor.map(
-            compute_alignment_for_angle, 
-            [segment_thickness_dict] * len(angles),  # Same segment dictionary for all angles
-            angles,                                 # Different angles
-            [box_measurements] * len(angles),       # Same box measurements for all angles
-            [director] * len(angles)                # Same director for all angles
-        ))
-
-    # Find the angle with the maximum alignment
-    max_alignment = 0
-    max_angle = 0
-    for angle, alignment in results:
-        if alignment > max_alignment:
-            max_alignment = alignment
-            max_angle = angle
-
-    return max_angle
-
-def generate_line_segments_thickness_orientation(
+def orientate_network(
     data_dict: Dict[str, dict], 
     orientation: List[int], 
     grid_points: int = 360, 
-    box_measurements: List[Tuple[float, float]] = [(0, 0), (0, 1), (1, 1), (1, 0)]
+    box_measurements: List[Tuple[float, float]] = [(0, 0), (0, 1), (1, 1), (1, 0)],
+    director: np.ndarray = np.array([0, 1])
 ) -> List[Dict[str, dict]]:
     """
     Generates a set of networks of line segments with different thicknesses and orientations, and clips them to fit 
@@ -354,36 +325,33 @@ def generate_line_segments_thickness_orientation(
     
     # Extract the segment thickness dictionary from the input data
     segment_thickness_dict = data_dict['segment_thickness_dict']
-
-    # Define the director vector along the y-axis
-    director = np.array([0, 1])
     
     # Find the angle that aligns the network most with the y-axis
-    max_angle = get_max_alignment_angle(segment_thickness_dict, director, box_measurements, grid_points)
-
+    max_angle = get_max_alignment(segment_thickness_dict, director, box_measurements, grid_points)
+    
     # Store the initial unmodified configuration
     output = [{'orientation': 'original', 'data_dict': data_dict}]
     
     # Loop through each given orientation, rotate, clip, and translate the network
     for o in orientation:
         # Compute the rotation angle for the current orientation relative to max alignment
-        rotate_angle = o - max_angle
+        rotate_angle = -max_angle + o
         
         # Rotate the network by the computed angle
-        segment_thickness_dict_new = rotate_network(segment_thickness_dict, rotate_angle=rotate_angle, box_center=box_center)
+        segment_thickness_dict_rotated = rotate_network(segment_thickness_dict, rotate_angle=rotate_angle, box_center=box_center)
 
         # Clip the rotated network to fit within the bounding box
-        segment_thickness_dict_new = clip_network(segment_thickness_dict_new, box_measurements=box_measurements)
+        segment_thickness_dict_clipped = clip_network(segment_thickness_dict_rotated, box_measurements=box_measurements)
 
         # Translate the clipped network to start at the origin (0,0)
         translation_vector = -np.array(box_measurements[0])
-        segment_thickness_dict_new = translate_network(segment_thickness_dict_new, translation_vector)
+        segment_thickness_dict_translated = translate_network(segment_thickness_dict_clipped, translation_vector)
     
         # Prepare a new data dictionary with the transformed segment information
         data_dict_new = {
             'segments_dict': None,
             'polygon_arr': None,
-            'segment_thickness_dict': segment_thickness_dict_new,
+            'segment_thickness_dict': segment_thickness_dict_translated,
             'jammed': None,
             'generated_config': None
         }