From fea224c047d3008d897a41bb9ea1c5f4628b14e5 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 21 Aug 2024 14:29:25 +0200
Subject: [PATCH 01/33] test: graph updated

---
 .../test_network_graph_simplificator.py       | 71 +++++++++++++++++--
 1 file changed, 67 insertions(+), 4 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index d1b496d67..7cfd28145 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -1,11 +1,10 @@
 import math
-import random
 from typing import Callable, Iterator
 
 import networkx as nx
 import numpy as np
 import pytest
-from shapely.geometry import LineString, Point
+from shapely.geometry import LineString
 
 from ra2ce.network import add_missing_geoms_graph
 from ra2ce.network.network_simplification.network_graph_simplificator import (
@@ -132,7 +131,7 @@ def _get_network_simplification_with_attribute_exclusion(
     def _get_nx_digraph_factory(self) -> Iterator[Callable[[], nx.MultiDiGraph]]:
         def create_nx_multidigraph():
             _nx_digraph = nx.MultiDiGraph()
-            for i in range(1, 16):
+            for i in range(1, 19):
                 _nx_digraph.add_node(i, x=i, y=i * 10)
 
             _nx_digraph.add_edge(1, 2, a=np.nan)
@@ -152,6 +151,10 @@ def create_nx_multidigraph():
             _nx_digraph.add_edge(13, 14, a="yes")
             _nx_digraph.add_edge(14, 15, a="yes")
             _nx_digraph.add_edge(15, 11, a="yes")
+            _nx_digraph.add_edge(1, 16, a="yes")
+            _nx_digraph.add_edge(16, 1, a="yes")
+            _nx_digraph.add_edge(16, 17, a="yes")
+            _nx_digraph.add_edge(16, 18, a="yes")
 
             _nx_digraph = add_missing_geoms_graph(_nx_digraph, "geometry")
             _nx_digraph.graph["crs"] = "EPSG:4326"
@@ -167,7 +170,8 @@ def _get_expected_result_graph_fixture(
     ) -> nx.MultiGraph:
         _nx_digraph = nx_digraph_factory()
         _result_digraph = nx.MultiGraph()
-        node_ids_degrees = {2: 1, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2}
+        # node_ids_degrees = {2: 1, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2}
+        node_ids_degrees = {2: 1, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2, 16: 4, 17: 1, 18: 1}
         for node_id, degree in node_ids_degrees.items():
             node_data = _nx_digraph.nodes[node_id]
             node_data["id"] = node_id
@@ -190,6 +194,21 @@ def _get_expected_result_graph_fixture(
             ),
         )
 
+        _result_digraph.add_edge(
+            2,
+            16,
+            a="None",
+            from_node=2,
+            to_node=16,
+            geometry=LineString(
+                [
+                    _nx_digraph.nodes[2]["geometry"],
+                    _nx_digraph.nodes[1]["geometry"],
+                    _nx_digraph.nodes[16]["geometry"],
+                ]
+            ),
+        )
+
         _result_digraph.add_edge(
             4,
             7.0,
@@ -276,6 +295,50 @@ def _get_expected_result_graph_fixture(
             ),
         )
 
+        _result_digraph.add_edge(
+            16,
+            4.0,
+            a="None",
+            from_node=16,
+            to_node=4,
+            geometry=LineString(
+                [
+                    _nx_digraph.nodes[16]["geometry"],
+                    _nx_digraph.nodes[1]["geometry"],
+                    _nx_digraph.nodes[2]["geometry"],
+                    _nx_digraph.nodes[3]["geometry"],
+                    _nx_digraph.nodes[4]["geometry"],
+                ]
+            ),
+        )
+
+        _result_digraph.add_edge(
+            16,
+            17,
+            a="None",
+            from_node=16,
+            to_node=17,
+            geometry=LineString(
+                [
+                    _nx_digraph.nodes[16]["geometry"],
+                    _nx_digraph.nodes[17]["geometry"],
+                ]
+            ),
+        )
+
+        _result_digraph.add_edge(
+            16,
+            18,
+            a="None",
+            from_node=16,
+            to_node=18,
+            geometry=LineString(
+                [
+                    _nx_digraph.nodes[16]["geometry"],
+                    _nx_digraph.nodes[18]["geometry"],
+                ]
+            ),
+        )
         _result_digraph.graph["crs"] = "EPSG:4326"
 
         snkit_network = NxToSnkitNetworkConverter(

From fd43031d7f79f73e80590c2f899fab2b7989ba07 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 21 Aug 2024 14:29:49 +0200
Subject: [PATCH 02/33] feat: deg_4 node filtering added

---
 .../snkit_network_merge_wrapper.py            | 24 +++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 3923a8324..b2501869f 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -26,6 +26,8 @@
 from snkit.network import Network as SnkitNetwork
 from tqdm import tqdm
 
+from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
+
 NxGraph = nx.Graph | nx.MultiGraph | nx.MultiDiGraph
 
 
@@ -94,6 +96,22 @@ def _get_merged_edges(
         updated_edges_gdf = updated_edges_gdf.drop(columns=["id"])
         return updated_edges_gdf
 
+    def _filter_degree_4(degree_4s: set) -> set:
+        degree_4_filtered = set()
+        snkit_network_wrapper = SnkitNetworkWrapper(
+            snkit_network=snkit_network,
+        )
+        networkx_graph = snkit_network_wrapper.to_networkx()
+        for degree_4_node_id in degree_4s:
+            # Get the predecessors (antecedents) and successors (precedents)
+            predecessors = list(networkx_graph.predecessors(degree_4_node_id))
+            successors = list(networkx_graph.successors(degree_4_node_id))
+
+            # Check if there is exactly one predecessor and one successor: 1->2, 2->3, 2->1, 3->2 => filters on 2
+            if len(predecessors) == 1 and len(successors) == 1:
+                degree_4_filtered.add(degree_4_node_id)
+        return degree_4_filtered
+
     def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
         # Convert edges to an adjacency list using vectorized operations
         edge_dict = defaultdict(set)
@@ -137,6 +155,12 @@ def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
 
     degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
     degree_2_set = set(degree_2)
+
+    degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
+    degree_4_set = set(degree_4)
+    degree_4 = _filter_degree_4(degree_4_set)
+
+    # ToDo: Add the filtered degree_2 and 4 sets to get the edge paths
     edge_paths = _get_edge_paths(degree_2_set, snkit_network)
 
     edge_ids_to_update = _get_edge_ids_to_update(edge_paths)

From 0d8faaaaa2c72053a7dd61a35ef5c25302332800 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 28 Aug 2024 11:28:16 +0200
Subject: [PATCH 03/33] chore: update the directionality of a few relevant
 functions

---
 .../snkit_network_merge_wrapper.py            | 38 ++++++++++++++-----
 .../snkit_to_nx_network_converter.py          |  6 +--
 .../test_network_graph_simplificator.py       | 14 +++----
 3 files changed, 37 insertions(+), 21 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index b2501869f..e9aea62ec 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -21,13 +21,12 @@
 import geopandas as gpd
 import networkx as nx
 import pandas as pd
+from networkx import MultiGraph
 from shapely.geometry import LineString, MultiLineString, MultiPoint, Point
 from shapely.ops import linemerge
 from snkit.network import Network as SnkitNetwork
 from tqdm import tqdm
 
-from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
-
 NxGraph = nx.Graph | nx.MultiGraph | nx.MultiDiGraph
 
 
@@ -97,6 +96,8 @@ def _get_merged_edges(
         return updated_edges_gdf
 
     def _filter_degree_4(degree_4s: set) -> set:
+        from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
+
         degree_4_filtered = set()
         snkit_network_wrapper = SnkitNetworkWrapper(
             snkit_network=snkit_network,
@@ -108,11 +109,13 @@ def _filter_degree_4(degree_4s: set) -> set:
             successors = list(networkx_graph.successors(degree_4_node_id))
 
             # Check if there is exactly one predecessor and one successor: 1->2, 2->3, 2->1, 3->2 => filters on 2
-            if len(predecessors) == 1 and len(successors) == 1:
+            if sorted(predecessors) == sorted(successors):
                 degree_4_filtered.add(degree_4_node_id)
         return degree_4_filtered
 
     def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
+        def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set:
+            return set(gdf[from_col]) ^ set(gdf[to_col])
         # Convert edges to an adjacency list using vectorized operations
         edge_dict = defaultdict(set)
         from_ids = snkit_network.edges["from_id"].values
@@ -125,7 +128,9 @@ def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
         edge_paths = []
 
         while node_set:
+            intermediates = set()
             popped_node = node_set.pop()
+            intermediates.add(popped_node)
             node_path = {popped_node}
             candidates = {popped_node}
             while candidates:
@@ -135,17 +140,28 @@ def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
                 for match in matches:
                     if match in node_set:
                         candidates.add(match)
+                        intermediates.add(match)
                         node_path.add(match)
                         node_set.remove(match)
                     else:
                         node_path.add(match)
             if len(node_path) >= 2:
-                edge_paths.append(
-                    snkit_network.edges.loc[
-                        (snkit_network.edges.from_id.isin(node_path))
-                        & (snkit_network.edges.to_id.isin(node_path))
+                intermediate_edges = snkit_network.edges[
+                    snkit_network.edges.from_id.isin(intermediates) &
+                    snkit_network.edges.to_id.isin(intermediates)
                     ]
-                )
+
+                unique_from_id = set(intermediate_edges["from_id"]) - set(intermediate_edges["to_id"])
+                entering_edge = snkit_network.edges[snkit_network.edges.to_id.isin(unique_from_id)]
+
+                unique_to_id = set(intermediate_edges["to_id"]) - set(intermediate_edges["from_id"])
+                leaving_edge = snkit_network.edges[snkit_network.edges.from_id.isin(unique_to_id)]
+
+                # Add the unique edges to the intermediate edges
+                edge_paths_gdf = intermediate_edges.append([entering_edge, leaving_edge])
+
+                # Append the result to edge_paths
+                edge_paths = edge_paths.append(edge_paths_gdf)
         return edge_paths
 
     if "degree" not in snkit_network.nodes.columns:
@@ -158,10 +174,12 @@ def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
 
     degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
     degree_4_set = set(degree_4)
-    degree_4 = _filter_degree_4(degree_4_set)
+    filtered_degree_4_set = _filter_degree_4(degree_4_set)
+
+    nodes_of_interest = degree_2_set | filtered_degree_4_set
 
     # ToDo: Add the filtered degree_2 and 4 sets to get the edge paths
-    edge_paths = _get_edge_paths(degree_2_set, snkit_network)
+    edge_paths = _get_edge_paths(sorted(nodes_of_interest), snkit_network)
 
     edge_ids_to_update = _get_edge_ids_to_update(edge_paths)
     edges_to_keep = snkit_network.edges[
diff --git a/ra2ce/network/network_simplification/snkit_to_nx_network_converter.py b/ra2ce/network/network_simplification/snkit_to_nx_network_converter.py
index 15f9128bd..7b3e0af21 100644
--- a/ra2ce/network/network_simplification/snkit_to_nx_network_converter.py
+++ b/ra2ce/network/network_simplification/snkit_to_nx_network_converter.py
@@ -33,7 +33,7 @@ class SnkitToNxNetworkConverter:
     edge_from_id_column_name: str = "from_id"
     edge_to_id_column_name: str = "to_id"
 
-    def convert(self) -> nx.MultiGraph:
+    def convert(self) -> nx.MultiDiGraph:
         """
         Converts the given `snkit.network.Network` into a matching
         `networkx.MultiGraph`.
@@ -42,10 +42,10 @@ def convert(self) -> nx.MultiGraph:
             snkit_network (SnkitNetwork): The snkit network to convert.
 
         Returns:
-            `networkx.MultiGraph`: The converted graph.
+            `networkx.MultiDiGraph`: The converted graph.
         """
         # Define new graph
-        _nx_graph = nx.MultiGraph()
+        _nx_graph = nx.MultiDiGraph()
         _crs = self.snkit_network.edges.crs
 
         # Add nodes to the graph
diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 7cfd28145..27a999473 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -151,10 +151,10 @@ def create_nx_multidigraph():
             _nx_digraph.add_edge(13, 14, a="yes")
             _nx_digraph.add_edge(14, 15, a="yes")
             _nx_digraph.add_edge(15, 11, a="yes")
-            _nx_digraph.add_edge(1, 16, a="yes")
-            _nx_digraph.add_edge(16, 1, a="yes")
-            _nx_digraph.add_edge(16, 17, a="yes")
-            _nx_digraph.add_edge(16, 18, a="yes")
+            _nx_digraph.add_edge(1, 16, a=np.nan)
+            _nx_digraph.add_edge(16, 1, a=np.nan)
+            _nx_digraph.add_edge(16, 17, a=np.nan)
+            _nx_digraph.add_edge(16, 18, a=np.nan)
 
             _nx_digraph = add_missing_geoms_graph(_nx_digraph, "geometry")
             _nx_digraph.graph["crs"] = "EPSG:4326"
@@ -297,17 +297,15 @@ def _get_expected_result_graph_fixture(
 
         _result_digraph.add_edge(
             16,
-            4.0,
+            2.0,
             a="None",
             from_node=16,
-            to_node=4,
+            to_node=2,
             geometry=LineString(
                 [
                     _nx_digraph.nodes[16]["geometry"],
                     _nx_digraph.nodes[1]["geometry"],
                     _nx_digraph.nodes[2]["geometry"],
-                    _nx_digraph.nodes[3]["geometry"],
-                    _nx_digraph.nodes[4]["geometry"],
                 ]
             ),
         )

From 8088794c502531c19283ad636c3d760419e786ba Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 28 Aug 2024 17:04:48 +0200
Subject: [PATCH 04/33] feat: degree-4 path finding completed

---
 .../snkit_network_merge_wrapper.py            | 94 ++++++++++++++-----
 1 file changed, 73 insertions(+), 21 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index e9aea62ec..67528e615 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -95,6 +95,24 @@ def _get_merged_edges(
         updated_edges_gdf = updated_edges_gdf.drop(columns=["id"])
         return updated_edges_gdf
 
+    def _filter_degree_2(degree_2s: set) -> set:
+        from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
+
+        degree_2_filtered = set()
+        snkit_network_wrapper = SnkitNetworkWrapper(
+            snkit_network=snkit_network,
+        )
+        networkx_graph = snkit_network_wrapper.to_networkx()
+        for degree_2_node_id in degree_2s:
+            # Get the predecessors (antecedents) and successors (precedents)
+            predecessors = list(networkx_graph.predecessors(degree_2_node_id))
+            successors = list(networkx_graph.successors(degree_2_node_id))
+
+            # Check if there is exactly one predecessor and one successor: 1->2, 2->3, 2->1, 3->2 => filters on 2
+            if len(predecessors) == len(successors) == 1:
+                degree_2_filtered.add(degree_2_node_id)
+        return degree_2_filtered
+
     def _filter_degree_4(degree_4s: set) -> set:
         from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
 
@@ -116,6 +134,47 @@ def _filter_degree_4(degree_4s: set) -> set:
     def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
         def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set:
             return set(gdf[from_col]) ^ set(gdf[to_col])
+
+        def _find_and_append_degree_4_paths(
+                _edge_paths: list
+        ) -> None:
+            def retrieve_edge(node1: int|float, node2: int|float) -> gpd.GeoDataFrame:
+                """Retrieve the edge from snkit_network.edges GeoDataFrame between two nodes."""
+                edge = snkit_network.edges[
+                    (snkit_network.edges['from_id'] == node1) &
+                    (snkit_network.edges['to_id'] == node2)
+                    ]
+                return edge if not edge.empty else None
+
+            boundary_nodes = node_path.difference(filtered_degree_4_set)
+            intermediates_list = list(intermediates)
+            if len(boundary_nodes) == 2:
+                from_node, to_node = boundary_nodes
+
+                # Forward path: from_node -> intermediates -> to_node
+                forward_path = [
+                    retrieve_edge(intermediates_list[i], intermediates_list[i + 1])
+                    for i in range(len(intermediates) - 1)
+                ]
+                forward_path.insert(0, retrieve_edge(from_node, intermediates_list[0]))
+                forward_path.append(retrieve_edge(intermediates_list[-1], to_node))
+
+                if all(edge is not None for edge in forward_path):
+                    forward_gdf = pd.concat(forward_path)  # Combine edges into a single GeoDataFrame
+                    _edge_paths.append(forward_gdf)
+
+                # Backward path: to_node -> intermediates (reversed) -> from_node
+                backward_path = [
+                    retrieve_edge(intermediates_list[i + 1], intermediates_list[i])
+                    for i in range(len(intermediates) - 1)
+                ]
+                backward_path.insert(0, retrieve_edge(to_node, intermediates_list[-1]))
+                backward_path.append(retrieve_edge(intermediates_list[0], from_node))
+
+                if all(edge is not None for edge in backward_path):
+                    backward_gdf = pd.concat(backward_path)  # Combine edges into a single GeoDataFrame
+                    _edge_paths.append(backward_gdf)
+
         # Convert edges to an adjacency list using vectorized operations
         edge_dict = defaultdict(set)
         from_ids = snkit_network.edges["from_id"].values
@@ -125,7 +184,7 @@ def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set
             edge_dict[from_id].add(to_id)
             edge_dict[to_id].add(from_id)
 
-        edge_paths = []
+        _edge_paths = []
 
         while node_set:
             intermediates = set()
@@ -138,31 +197,24 @@ def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set
                 matches = edge_dict[popped_cand]
                 matches = matches - node_path
                 for match in matches:
+                    intermediates.add(popped_cand)
                     if match in node_set:
                         candidates.add(match)
-                        intermediates.add(match)
                         node_path.add(match)
                         node_set.remove(match)
                     else:
                         node_path.add(match)
             if len(node_path) >= 2:
-                intermediate_edges = snkit_network.edges[
-                    snkit_network.edges.from_id.isin(intermediates) &
-                    snkit_network.edges.to_id.isin(intermediates)
-                    ]
-
-                unique_from_id = set(intermediate_edges["from_id"]) - set(intermediate_edges["to_id"])
-                entering_edge = snkit_network.edges[snkit_network.edges.to_id.isin(unique_from_id)]
-
-                unique_to_id = set(intermediate_edges["to_id"]) - set(intermediate_edges["from_id"])
-                leaving_edge = snkit_network.edges[snkit_network.edges.from_id.isin(unique_to_id)]
-
-                # Add the unique edges to the intermediate edges
-                edge_paths_gdf = intermediate_edges.append([entering_edge, leaving_edge])
-
-                # Append the result to edge_paths
-                edge_paths = edge_paths.append(edge_paths_gdf)
-        return edge_paths
+                if any(node_path.intersection(filtered_degree_4_set)):
+                    _find_and_append_degree_4_paths(_edge_paths)
+                else:
+                    edge_paths_gdf = snkit_network.edges[
+                        snkit_network.edges.from_id.isin(intermediates) |
+                        snkit_network.edges.to_id.isin(intermediates)
+                        ]
+                    # Append the result to edge_paths
+                    _edge_paths.append(edge_paths_gdf)
+        return _edge_paths
 
     if "degree" not in snkit_network.nodes.columns:
         snkit_network.nodes["degree"] = snkit_network.nodes[id_col].apply(
@@ -171,14 +223,14 @@ def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set
 
     degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
     degree_2_set = set(degree_2)
+    filtered_degree_2_set = _filter_degree_2(degree_2_set)
 
     degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
     degree_4_set = set(degree_4)
     filtered_degree_4_set = _filter_degree_4(degree_4_set)
 
-    nodes_of_interest = degree_2_set | filtered_degree_4_set
+    nodes_of_interest = filtered_degree_2_set | filtered_degree_4_set
 
-    # ToDo: Add the filtered degree_2 and 4 sets to get the edge paths
     edge_paths = _get_edge_paths(sorted(nodes_of_interest), snkit_network)
 
     edge_ids_to_update = _get_edge_ids_to_update(edge_paths)

From 8e0794310c1fec30f203355ae908d0ac0a20f405 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 28 Aug 2024 17:40:18 +0200
Subject: [PATCH 05/33] chore: test updated

---
 .../test_network_graph_simplificator.py       | 31 +++++++++----------
 1 file changed, 14 insertions(+), 17 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 27a999473..879c51c91 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -170,8 +170,7 @@ def _get_expected_result_graph_fixture(
     ) -> nx.MultiGraph:
         _nx_digraph = nx_digraph_factory()
         _result_digraph = nx.MultiGraph()
-        # node_ids_degrees = {2: 1, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2}
-        node_ids_degrees = {2: 1, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2, 16: 4, 17: 1, 18: 1}
+        node_ids_degrees = {2: 3, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2, 16: 4, 17: 1, 18: 1}
         for node_id, degree in node_ids_degrees.items():
             node_data = _nx_digraph.nodes[node_id]
             node_data["id"] = node_id
@@ -182,7 +181,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             2,
             4.0,
-            a="None",
+            a=np.nan,
             from_node=2,
             to_node=4,
             geometry=LineString(
@@ -196,8 +195,8 @@ def _get_expected_result_graph_fixture(
 
         _result_digraph.add_edge(
             2,
-            16,
-            a="None",
+            16.0,
+            a=np.nan,
             from_node=2,
             to_node=16,
             geometry=LineString(
@@ -227,7 +226,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             7,
             8.0,
-            a="None",
+            a=np.nan,
             from_node=7,
             to_node=8,
             geometry=LineString(
@@ -239,8 +238,8 @@ def _get_expected_result_graph_fixture(
         )
         _result_digraph.add_edge(
             8,
-            11.0,
-            a="None",
+            11,
+            a=np.nan,
             from_node=8,
             to_node=11,
             geometry=LineString(
@@ -254,7 +253,7 @@ def _get_expected_result_graph_fixture(
         )
         _result_digraph.add_edge(
             8,
-            11.0,
+            11,
             a="yes",
             from_node=8,
             to_node=11,
@@ -270,8 +269,8 @@ def _get_expected_result_graph_fixture(
         )
         _result_digraph.add_edge(
             8,
-            12.0,
-            a="None",
+            12,
+            a=np.nan,
             from_node=8,
             to_node=12,
             geometry=LineString(
@@ -283,7 +282,7 @@ def _get_expected_result_graph_fixture(
         )
         _result_digraph.add_edge(
             11,
-            12.0,
+            12,
             a="yes",
             from_node=11,
             to_node=12,
@@ -298,7 +297,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             2.0,
-            a="None",
+            a=np.nan,
             from_node=16,
             to_node=2,
             geometry=LineString(
@@ -313,7 +312,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             17,
-            a="None",
+            a=np.nan,
             from_node=16,
             to_node=17,
             geometry=LineString(
@@ -327,7 +326,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             18,
-            a="None",
+            a=np.nan,
             from_node=16,
             to_node=18,
             geometry=LineString(
@@ -365,7 +364,5 @@ def test_simplify_graph(
         assert _graph_simple.nodes(data=True) == expected_result_graph_fixture.nodes(
             data=True
         )
-        # Compare edges topology
-        assert set(_graph_simple.edges()) == set(expected_result_graph_fixture.edges())
         # Compare edges with attributes
         assert _detailed_edge_comparison(_graph_simple, expected_result_graph_fixture)

From 6c19b6386b6520eeaa81ca097d523e1b57f41a29 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 28 Aug 2024 23:42:00 +0200
Subject: [PATCH 06/33] chore: test updated

---
 .../test_network_graph_simplificator.py       | 76 ++++++++++---------
 1 file changed, 42 insertions(+), 34 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 879c51c91..0da811513 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -26,19 +26,27 @@ def _detailed_edge_comparison(
     graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
 ) -> bool:
     def _dicts_comparison(
-        graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
+        _graph1: nx.MultiDiGraph | nx.MultiGraph, _graph2: nx.MultiDiGraph | nx.MultiGraph
     ) -> bool:
-        for u, v, k, data1 in graph1.edges(keys=True, data=True):
-            data2 = graph2.get_edge_data(u, v, k)
-            for key1, value1 in data1.items():
-                if key1 not in data2:
-                    return False
-                if isinstance(value1, float) and math.isnan(value1):
-                    if not math.isnan(data2[key1]):
-                        return False
-                    continue
-                if value1 != data2[key1]:
-                    return False
+        for u, v, k, data1 in _graph1.edges(keys=True, data=True):
+            geom1 = data1['geometry']
+            geom_found = 0
+
+            data2_dict = _graph2.get_edge_data(u, v)
+            for _, data2 in data2_dict.items():
+                if data2['geometry'] == geom1:
+                    geom_found = 1
+                    for key1, value1 in data1.items():
+                        if key1 not in data2:
+                            return False
+                        if isinstance(value1, float) and math.isnan(value1):
+                            if not math.isnan(data2[key1]):
+                                return False
+                            continue
+                        if value1 != data2[key1]:
+                            return False
+            if geom_found == 0:
+                return False
         return True
 
     check_1_2 = _dicts_comparison(graph1, graph2)
@@ -134,27 +142,27 @@ def create_nx_multidigraph():
             for i in range(1, 19):
                 _nx_digraph.add_node(i, x=i, y=i * 10)
 
-            _nx_digraph.add_edge(1, 2, a=np.nan)
-            _nx_digraph.add_edge(2, 1, a=np.nan)
-            _nx_digraph.add_edge(2, 3, a=np.nan)
-            _nx_digraph.add_edge(3, 4, a=np.nan)
+            _nx_digraph.add_edge(1, 2, a='None')
+            _nx_digraph.add_edge(2, 1, a='None')
+            _nx_digraph.add_edge(2, 3, a='None')
+            _nx_digraph.add_edge(3, 4, a='None')
             _nx_digraph.add_edge(4, 5, a="yes")
             _nx_digraph.add_edge(5, 6, a="yes")
             _nx_digraph.add_edge(6, 7, a="yes")
-            _nx_digraph.add_edge(7, 8, a=np.nan)
-            _nx_digraph.add_edge(8, 9, a=np.nan)
-            _nx_digraph.add_edge(8, 12, a=np.nan)
+            _nx_digraph.add_edge(7, 8, a='None')
+            _nx_digraph.add_edge(8, 9, a='None')
+            _nx_digraph.add_edge(8, 12, a='None')
             _nx_digraph.add_edge(8, 13, a="yes")
-            _nx_digraph.add_edge(9, 10, a=np.nan)
-            _nx_digraph.add_edge(10, 11, a=np.nan)
+            _nx_digraph.add_edge(9, 10, a='None')
+            _nx_digraph.add_edge(10, 11, a='None')
             _nx_digraph.add_edge(11, 12, a="yes")
             _nx_digraph.add_edge(13, 14, a="yes")
             _nx_digraph.add_edge(14, 15, a="yes")
             _nx_digraph.add_edge(15, 11, a="yes")
-            _nx_digraph.add_edge(1, 16, a=np.nan)
-            _nx_digraph.add_edge(16, 1, a=np.nan)
-            _nx_digraph.add_edge(16, 17, a=np.nan)
-            _nx_digraph.add_edge(16, 18, a=np.nan)
+            _nx_digraph.add_edge(1, 16, a='None')
+            _nx_digraph.add_edge(16, 1, a='None')
+            _nx_digraph.add_edge(16, 17, a='None')
+            _nx_digraph.add_edge(16, 18, a='None')
 
             _nx_digraph = add_missing_geoms_graph(_nx_digraph, "geometry")
             _nx_digraph.graph["crs"] = "EPSG:4326"
@@ -169,7 +177,7 @@ def _get_expected_result_graph_fixture(
         self, nx_digraph_factory: nx.MultiDiGraph
     ) -> nx.MultiGraph:
         _nx_digraph = nx_digraph_factory()
-        _result_digraph = nx.MultiGraph()
+        _result_digraph = nx.MultiDiGraph()
         node_ids_degrees = {2: 3, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2, 16: 4, 17: 1, 18: 1}
         for node_id, degree in node_ids_degrees.items():
             node_data = _nx_digraph.nodes[node_id]
@@ -181,7 +189,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             2,
             4.0,
-            a=np.nan,
+            a='None',
             from_node=2,
             to_node=4,
             geometry=LineString(
@@ -196,7 +204,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             2,
             16.0,
-            a=np.nan,
+            a='None',
             from_node=2,
             to_node=16,
             geometry=LineString(
@@ -226,7 +234,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             7,
             8.0,
-            a=np.nan,
+            a='None',
             from_node=7,
             to_node=8,
             geometry=LineString(
@@ -239,7 +247,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             8,
             11,
-            a=np.nan,
+            a='None',
             from_node=8,
             to_node=11,
             geometry=LineString(
@@ -270,7 +278,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             8,
             12,
-            a=np.nan,
+            a='None',
             from_node=8,
             to_node=12,
             geometry=LineString(
@@ -297,7 +305,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             2.0,
-            a=np.nan,
+            a='None',
             from_node=16,
             to_node=2,
             geometry=LineString(
@@ -312,7 +320,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             17,
-            a=np.nan,
+            a='None',
             from_node=16,
             to_node=17,
             geometry=LineString(
@@ -326,7 +334,7 @@ def _get_expected_result_graph_fixture(
         _result_digraph.add_edge(
             16,
             18,
-            a=np.nan,
+            a='None',
             from_node=16,
             to_node=18,
             geometry=LineString(

From 9b15a735f95478a3980b88f2940a623076d07e29 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Thu, 29 Aug 2024 11:27:37 +0200
Subject: [PATCH 07/33] chore: forward and backward formation updated

---
 .../snkit_network_merge_wrapper.py            | 58 ++++++++++---------
 1 file changed, 32 insertions(+), 26 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 67528e615..b7d02010a 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -132,9 +132,6 @@ def _filter_degree_4(degree_4s: set) -> set:
         return degree_4_filtered
 
     def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
-        def unique_ids_from_to(gdf: gpd.GeoDataFrame, from_col: str, to_col: str) -> set:
-            return set(gdf[from_col]) ^ set(gdf[to_col])
-
         def _find_and_append_degree_4_paths(
                 _edge_paths: list
         ) -> None:
@@ -145,36 +142,45 @@ def retrieve_edge(node1: int|float, node2: int|float) -> gpd.GeoDataFrame:
                     (snkit_network.edges['to_id'] == node2)
                     ]
                 return edge if not edge.empty else None
-
-            boundary_nodes = node_path.difference(filtered_degree_4_set)
-            intermediates_list = list(intermediates)
+            
+            def construct_path(start_node: int|float, end_node: int|float, intermediates: list):
+                path = []
+                current_node = start_node
+                _intermediates = intermediates.copy()
+
+                while _intermediates:
+                    for next_node in _intermediates:
+                        edge = retrieve_edge(current_node, next_node)
+                        if edge is not None:
+                            path.append(edge)
+                            _intermediates.remove(next_node)
+                            current_node = next_node
+                            break
+
+                final_edge = retrieve_edge(current_node, end_node)
+                if final_edge is not None:
+                    path.append(final_edge)
+
+                if len(path) > 0 and all(edge is not None for edge in path):
+                    return pd.concat(path)  # Combine edges into a single GeoDataFrame
+                return None
+
+            boundary_nodes = list(node_path - filtered_degree_4_set)
             if len(boundary_nodes) == 2:
                 from_node, to_node = boundary_nodes
+                intermediates = list(node_path & filtered_degree_4_set)
 
-                # Forward path: from_node -> intermediates -> to_node
-                forward_path = [
-                    retrieve_edge(intermediates_list[i], intermediates_list[i + 1])
-                    for i in range(len(intermediates) - 1)
-                ]
-                forward_path.insert(0, retrieve_edge(from_node, intermediates_list[0]))
-                forward_path.append(retrieve_edge(intermediates_list[-1], to_node))
-
-                if all(edge is not None for edge in forward_path):
-                    forward_gdf = pd.concat(forward_path)  # Combine edges into a single GeoDataFrame
+                # Construct and append the forward path
+                forward_gdf = construct_path(from_node, to_node, intermediates)
+                if forward_gdf is not None:
                     _edge_paths.append(forward_gdf)
 
-                # Backward path: to_node -> intermediates (reversed) -> from_node
-                backward_path = [
-                    retrieve_edge(intermediates_list[i + 1], intermediates_list[i])
-                    for i in range(len(intermediates) - 1)
-                ]
-                backward_path.insert(0, retrieve_edge(to_node, intermediates_list[-1]))
-                backward_path.append(retrieve_edge(intermediates_list[0], from_node))
-
-                if all(edge is not None for edge in backward_path):
-                    backward_gdf = pd.concat(backward_path)  # Combine edges into a single GeoDataFrame
+                # Construct and append the backward path
+                backward_gdf = construct_path(to_node, from_node, intermediates)
+                if backward_gdf is not None:
                     _edge_paths.append(backward_gdf)
 
+
         # Convert edges to an adjacency list using vectorized operations
         edge_dict = defaultdict(set)
         from_ids = snkit_network.edges["from_id"].values

From 7f6423c5055f25e5631bc6a87c06655cfed294f3 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 15:29:33 +0200
Subject: [PATCH 08/33] fix: networkx_graph property added to
 snkit_network_wrapper

---
 .../snkit_network_merge_wrapper.py                 | 14 ++------------
 .../snkit_network_wrapper.py                       |  9 +++++++++
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index b7d02010a..8ea3538a1 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -41,6 +41,7 @@
 
 def merge_edges(
     snkit_network: SnkitNetwork,
+    networkx_graph: NxGraph,
     aggregate_func: str | dict,
     by: str | list,
     id_col: str,
@@ -50,6 +51,7 @@ def merge_edges(
 
     Args:
         snkit_network (SnkitNetwork): network to merge.
+        networkx_graph (NxGraph): networkx graph to merge
         aggregate_func (str | dict): Aggregation function to apply.
         by (str | list): Arguments (column names).
         id_col (str, optional): Name of the column representing the 'id'.
@@ -96,13 +98,7 @@ def _get_merged_edges(
         return updated_edges_gdf
 
     def _filter_degree_2(degree_2s: set) -> set:
-        from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
-
         degree_2_filtered = set()
-        snkit_network_wrapper = SnkitNetworkWrapper(
-            snkit_network=snkit_network,
-        )
-        networkx_graph = snkit_network_wrapper.to_networkx()
         for degree_2_node_id in degree_2s:
             # Get the predecessors (antecedents) and successors (precedents)
             predecessors = list(networkx_graph.predecessors(degree_2_node_id))
@@ -114,13 +110,7 @@ def _filter_degree_2(degree_2s: set) -> set:
         return degree_2_filtered
 
     def _filter_degree_4(degree_4s: set) -> set:
-        from ra2ce.network.network_simplification.snkit_network_wrapper import SnkitNetworkWrapper
-
         degree_4_filtered = set()
-        snkit_network_wrapper = SnkitNetworkWrapper(
-            snkit_network=snkit_network,
-        )
-        networkx_graph = snkit_network_wrapper.to_networkx()
         for degree_4_node_id in degree_4s:
             # Get the predecessors (antecedents) and successors (precedents)
             predecessors = list(networkx_graph.predecessors(degree_4_node_id))
diff --git a/ra2ce/network/network_simplification/snkit_network_wrapper.py b/ra2ce/network/network_simplification/snkit_network_wrapper.py
index 4e9803736..58054dcae 100644
--- a/ra2ce/network/network_simplification/snkit_network_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_wrapper.py
@@ -47,6 +47,14 @@ class SnkitNetworkWrapper:
     edge_from_id_column_name: str = "from_id"
     edge_to_id_column_name: str = "to_id"
 
+    def __init__(self, snkit_network: Network, node_id_column_name: str = "id",
+                 edge_from_id_column_name: str = "from_id", edge_to_id_column_name: str = "to_id") -> None:
+        self.snkit_network = snkit_network
+        self.node_id_column_name = node_id_column_name
+        self.edge_from_id_column_name = edge_from_id_column_name
+        self.edge_to_id_column_name = edge_to_id_column_name
+        self.networkx_graph: NxGraph = self.to_networkx()
+
     @classmethod
     def from_networkx(
         cls,
@@ -91,6 +99,7 @@ def filter_excluded_attributes() -> list[str]:
         # Overwrite the existing network with the merged edges.
         self.snkit_network = merge_edges(
             snkit_network=self.snkit_network,
+            networkx_graph=self.networkx_graph,
             aggregate_func=_aggregate_function,
             by=_attributes_to_exclude,
             id_col="id",

From e2b69920e8841b4b6b77cf427333ba29a25649da Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 15:37:24 +0200
Subject: [PATCH 09/33] doc: comment added for clarification of
 _filter_degree_2

---
 .../network_simplification/snkit_network_merge_wrapper.py    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 8ea3538a1..0638f988c 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -100,11 +100,12 @@ def _get_merged_edges(
     def _filter_degree_2(degree_2s: set) -> set:
         degree_2_filtered = set()
         for degree_2_node_id in degree_2s:
-            # Get the predecessors (antecedents) and successors (precedents)
+            # Get the predecessors (antecedents) and successors (precedents) to make sure for each node with the degree
+            # of 2 there is only one predecessor and successor. E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
             predecessors = list(networkx_graph.predecessors(degree_2_node_id))
             successors = list(networkx_graph.successors(degree_2_node_id))
 
-            # Check if there is exactly one predecessor and one successor: 1->2, 2->3, 2->1, 3->2 => filters on 2
+            # Check if there is one predecessor and one successor.
             if len(predecessors) == len(successors) == 1:
                 degree_2_filtered.add(degree_2_node_id)
         return degree_2_filtered

From c345d0538d153c6be719a1a62a92ab6748cd1f2e Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 15:39:57 +0200
Subject: [PATCH 10/33] doc: comment added for clarification of
 _filter_degree_4

---
 .../network_simplification/snkit_network_merge_wrapper.py    | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 0638f988c..264ed62b0 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -113,11 +113,12 @@ def _filter_degree_2(degree_2s: set) -> set:
     def _filter_degree_4(degree_4s: set) -> set:
         degree_4_filtered = set()
         for degree_4_node_id in degree_4s:
-            # Get the predecessors (antecedents) and successors (precedents)
+            # Get the predecessors (antecedents) and successors (precedents) for filtering.
+            # E.g. : 1->2, 2->3, 2->1, 3->2 => filters on 2
             predecessors = list(networkx_graph.predecessors(degree_4_node_id))
             successors = list(networkx_graph.successors(degree_4_node_id))
 
-            # Check if there is exactly one predecessor and one successor: 1->2, 2->3, 2->1, 3->2 => filters on 2
+            # Check if the predecessors and successors are the same nodes
             if sorted(predecessors) == sorted(successors):
                 degree_4_filtered.add(degree_4_node_id)
         return degree_4_filtered

From c125d6d7f6a4420eb7205d8e98594802f291df88 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 15:54:13 +0200
Subject: [PATCH 11/33] doc: minor

---
 .../network_simplification/snkit_network_merge_wrapper.py      | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 264ed62b0..850c285ef 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -117,7 +117,6 @@ def _filter_degree_4(degree_4s: set) -> set:
             # E.g. : 1->2, 2->3, 2->1, 3->2 => filters on 2
             predecessors = list(networkx_graph.predecessors(degree_4_node_id))
             successors = list(networkx_graph.successors(degree_4_node_id))
-
             # Check if the predecessors and successors are the same nodes
             if sorted(predecessors) == sorted(successors):
                 degree_4_filtered.add(degree_4_node_id)
@@ -135,7 +134,7 @@ def retrieve_edge(node1: int|float, node2: int|float) -> gpd.GeoDataFrame:
                     ]
                 return edge if not edge.empty else None
             
-            def construct_path(start_node: int|float, end_node: int|float, intermediates: list):
+            def construct_path(start_node: int|float, end_node: int|float, intermediates: list) -> pd.DataFrame | None:
                 path = []
                 current_node = start_node
                 _intermediates = intermediates.copy()

From ff454d5241dbda954f344b726785f234c55ed96d Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 16:05:13 +0200
Subject: [PATCH 12/33] fix: _filter_node replaced two repeating functions

---
 .../snkit_network_merge_wrapper.py            | 44 ++++++++-----------
 1 file changed, 18 insertions(+), 26 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 850c285ef..6b4b1e500 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -97,30 +97,22 @@ def _get_merged_edges(
         updated_edges_gdf = updated_edges_gdf.drop(columns=["id"])
         return updated_edges_gdf
 
-    def _filter_degree_2(degree_2s: set) -> set:
-        degree_2_filtered = set()
-        for degree_2_node_id in degree_2s:
-            # Get the predecessors (antecedents) and successors (precedents) to make sure for each node with the degree
-            # of 2 there is only one predecessor and successor. E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
-            predecessors = list(networkx_graph.predecessors(degree_2_node_id))
-            successors = list(networkx_graph.successors(degree_2_node_id))
-
-            # Check if there is one predecessor and one successor.
-            if len(predecessors) == len(successors) == 1:
-                degree_2_filtered.add(degree_2_node_id)
-        return degree_2_filtered
-
-    def _filter_degree_4(degree_4s: set) -> set:
-        degree_4_filtered = set()
-        for degree_4_node_id in degree_4s:
-            # Get the predecessors (antecedents) and successors (precedents) for filtering.
-            # E.g. : 1->2, 2->3, 2->1, 3->2 => filters on 2
-            predecessors = list(networkx_graph.predecessors(degree_4_node_id))
-            successors = list(networkx_graph.successors(degree_4_node_id))
-            # Check if the predecessors and successors are the same nodes
-            if sorted(predecessors) == sorted(successors):
-                degree_4_filtered.add(degree_4_node_id)
-        return degree_4_filtered
+    def _filter_node(_node_set: set, _degrees: int) -> set:
+        _filtered = set()
+        for _node_id in _node_set:
+            # Get the predecessors (antecedents) and successors (precedents) to make sure for to filter correctly
+            # For _node_set with all degree 2: this filters on the nodes that have only one predecessor and successor.
+            # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
+            # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
+            # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
+            predecessors = list(networkx_graph.predecessors(_node_id))
+            successors = list(networkx_graph.successors(_node_id))
+
+            # Check the degree of the _node_set and the corresponding criterium.
+            if ((_degrees == 2 and len(predecessors) == len(successors) == 1) or
+                    (_degrees == 4 and sorted(predecessors) == sorted(successors))):
+                _filtered.add(_node_id)
+        return _filtered
 
     def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
         def _find_and_append_degree_4_paths(
@@ -220,11 +212,11 @@ def construct_path(start_node: int|float, end_node: int|float, intermediates: li
 
     degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
     degree_2_set = set(degree_2)
-    filtered_degree_2_set = _filter_degree_2(degree_2_set)
+    filtered_degree_2_set = _filter_node(degree_2_set, _degrees=2)
 
     degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
     degree_4_set = set(degree_4)
-    filtered_degree_4_set = _filter_degree_4(degree_4_set)
+    filtered_degree_4_set = _filter_node(degree_4_set, _degrees=4)
 
     nodes_of_interest = filtered_degree_2_set | filtered_degree_4_set
 

From fa1daf0ce3a2c7d313e737abcfafcfa12a40e13e Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 16:16:16 +0200
Subject: [PATCH 13/33] fix: code made compacter and more comments added

---
 .../snkit_network_merge_wrapper.py            | 25 +++++++++----------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 6b4b1e500..5aa9fa373 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -100,11 +100,9 @@ def _get_merged_edges(
     def _filter_node(_node_set: set, _degrees: int) -> set:
         _filtered = set()
         for _node_id in _node_set:
-            # Get the predecessors (antecedents) and successors (precedents) to make sure for to filter correctly
+            # Get the predecessors (antecedents) and successors (precedents) for filtering:
             # For _node_set with all degree 2: this filters on the nodes that have only one predecessor and successor.
-            # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
             # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
-            # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
             predecessors = list(networkx_graph.predecessors(_node_id))
             successors = list(networkx_graph.successors(_node_id))
 
@@ -205,20 +203,21 @@ def construct_path(start_node: int|float, end_node: int|float, intermediates: li
                     _edge_paths.append(edge_paths_gdf)
         return _edge_paths
 
+    # Adds degree column which is needed to find the to-be-simplified nodes and edges.
     if "degree" not in snkit_network.nodes.columns:
         snkit_network.nodes["degree"] = snkit_network.nodes[id_col].apply(
             lambda x: _node_connectivity_degree(x, snkit_network)
         )
-
-    degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
-    degree_2_set = set(degree_2)
-    filtered_degree_2_set = _filter_node(degree_2_set, _degrees=2)
-
-    degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
-    degree_4_set = set(degree_4)
-    filtered_degree_4_set = _filter_node(degree_4_set, _degrees=4)
-
-    nodes_of_interest = filtered_degree_2_set | filtered_degree_4_set
+    # Filter on the nodes with degree 2 and 4 which suffice the following criteria:
+    # For _node_set with all degree 2: this filters on the nodes that have only one predecessor and successor.
+    # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
+    # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
+    # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
+    nodes_of_interest = set()
+    for degree in [2,4]:
+        nodes_with_degree_set = set(list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == degree]))
+        filtered_nodes_with_degree_set = _filter_node(nodes_with_degree_set, _degrees=degree)
+        nodes_of_interest = nodes_of_interest | filtered_nodes_with_degree_set
 
     edge_paths = _get_edge_paths(sorted(nodes_of_interest), snkit_network)
 

From 0402c96f214958b6dc0ff85acf2e012a419113d9 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 16:23:05 +0200
Subject: [PATCH 14/33] fix: last commit almost reverted

---
 .../snkit_network_merge_wrapper.py            | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 5aa9fa373..9df6bd173 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -100,9 +100,11 @@ def _get_merged_edges(
     def _filter_node(_node_set: set, _degrees: int) -> set:
         _filtered = set()
         for _node_id in _node_set:
-            # Get the predecessors (antecedents) and successors (precedents) for filtering:
+            # Get the predecessors (antecedents) and successors (precedents) to make sure for to filter correctly
             # For _node_set with all degree 2: this filters on the nodes that have only one predecessor and successor.
+            # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
             # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
+            # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
             predecessors = list(networkx_graph.predecessors(_node_id))
             successors = list(networkx_graph.successors(_node_id))
 
@@ -208,16 +210,21 @@ def construct_path(start_node: int|float, end_node: int|float, intermediates: li
         snkit_network.nodes["degree"] = snkit_network.nodes[id_col].apply(
             lambda x: _node_connectivity_degree(x, snkit_network)
         )
+
     # Filter on the nodes with degree 2 and 4 which suffice the following criteria:
     # For _node_set with all degree 2: this filters on the nodes that have only one predecessor and successor.
     # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
     # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
     # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
-    nodes_of_interest = set()
-    for degree in [2,4]:
-        nodes_with_degree_set = set(list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == degree]))
-        filtered_nodes_with_degree_set = _filter_node(nodes_with_degree_set, _degrees=degree)
-        nodes_of_interest = nodes_of_interest | filtered_nodes_with_degree_set
+    degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
+    degree_2_set = set(degree_2)
+    filtered_degree_2_set = _filter_node(degree_2_set, _degrees=2)
+
+    degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
+    degree_4_set = set(degree_4)
+    filtered_degree_4_set = _filter_node(degree_4_set, _degrees=4)
+
+    nodes_of_interest = filtered_degree_2_set | filtered_degree_4_set
 
     edge_paths = _get_edge_paths(sorted(nodes_of_interest), snkit_network)
 

From 71d52e59c94d28a1d0292cc2645dfdbd6772dbb8 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 16:37:27 +0200
Subject: [PATCH 15/33] doc: comments added to _get_edge_paths

---
 .../snkit_network_merge_wrapper.py                    | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 9df6bd173..a0a63afe7 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -175,28 +175,39 @@ def construct_path(start_node: int|float, end_node: int|float, intermediates: li
 
         _edge_paths = []
 
+        # find the edge paths for the nodes in node_set
         while node_set:
+            # for each node in node_set find other nodes on the path
             intermediates = set()
             popped_node = node_set.pop()
+            # intermediates are the nodes in the node_path that are between two other nodes in the path
             intermediates.add(popped_node)
             node_path = {popped_node}
             candidates = {popped_node}
             while candidates:
                 popped_cand = candidates.pop()
+                # matches are the nodes that belong to a node_path
                 matches = edge_dict[popped_cand]
                 matches = matches - node_path
                 for match in matches:
                     intermediates.add(popped_cand)
+                    # if the found node on the path is in the node_set, then keep looking for other connected nodes on
+                    # the path
                     if match in node_set:
                         candidates.add(match)
                         node_path.add(match)
                         node_set.remove(match)
+                    # If the found node is not in node_set stop.
                     else:
                         node_path.add(match)
+            # After finding all nodes on a path find the edges that are connected to these nodes.
+            # Finding the edges is different for the nodes in the node path with degree 2 and 4.
             if len(node_path) >= 2:
                 if any(node_path.intersection(filtered_degree_4_set)):
+                    # node_path has nodes with degree 4 => get the forward and backward paths
                     _find_and_append_degree_4_paths(_edge_paths)
                 else:
+                    # node_path has nodes with degree 4 => find the edges connected to the intermediates
                     edge_paths_gdf = snkit_network.edges[
                         snkit_network.edges.from_id.isin(intermediates) |
                         snkit_network.edges.to_id.isin(intermediates)

From 32c4a7f26c9c1e10478f7a9d1953aafc8e578a8d Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 17:12:10 +0200
Subject: [PATCH 16/33] chore: minor

---
 .../snkit_network_merge_wrapper.py            | 96 ++++++++++---------
 1 file changed, 51 insertions(+), 45 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index a0a63afe7..0b362b01b 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -20,6 +20,7 @@
 
 import geopandas as gpd
 import networkx as nx
+import numpy as np
 import pandas as pd
 from networkx import MultiGraph
 from shapely.geometry import LineString, MultiLineString, MultiPoint, Point
@@ -114,65 +115,71 @@ def _filter_node(_node_set: set, _degrees: int) -> set:
                 _filtered.add(_node_id)
         return _filtered
 
-    def _get_edge_paths(node_set: set, snkit_network: SnkitNetwork) -> list:
+    def _get_edge_paths(node_set: set, _snkit_network: SnkitNetwork) -> list:
+        def _get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from_id",
+                                to_id_column: str = "to_id") -> defaultdict:
+            # Convert the edges of a GeoDataFrame to an adjacency list using vectorized operations.
+            _edge_dict = defaultdict(set)
+            # Extract the 'from_id' and 'to_id' columns as numpy arrays for efficient processing
+            from_ids = edges_gdf[from_id_column].values
+            to_ids = edges_gdf[to_id_column].values
+            # Vectorized operation to populate the adjacency list
+            for from_id, to_id in np.nditer([from_ids, to_ids]):
+                _edge_dict[from_id].add(to_id)
+                _edge_dict[to_id].add(from_id)
+
+            return _edge_dict
+
+        def _retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
+            """Retrieve the edge from snkit_network.edges GeoDataFrame between two nodes."""
+            edge = _snkit_network.edges[
+                (_snkit_network.edges['from_id'] == node1) &
+                (_snkit_network.edges['to_id'] == node2)
+                ]
+            return edge if not edge.empty else None
+
+        def _construct_path(start_node: int | float, end_node: int | float, __intermediates: list) -> pd.DataFrame | None:
+            path = []
+            current_node = start_node
+            _intermediates = __intermediates.copy()
+
+            while _intermediates:
+                for next_node in _intermediates:
+                    edge = _retrieve_edge(current_node, next_node)
+                    if edge is not None:
+                        path.append(edge)
+                        _intermediates.remove(next_node)
+                        current_node = next_node
+                        break
+
+            final_edge = _retrieve_edge(current_node, end_node)
+            if final_edge is not None:
+                path.append(final_edge)
+
+            if len(path) > 0 and all(edge is not None for edge in path):
+                return pd.concat(path)  # Combine edges into a single GeoDataFrame
+            return None
+
         def _find_and_append_degree_4_paths(
                 _edge_paths: list
         ) -> None:
-            def retrieve_edge(node1: int|float, node2: int|float) -> gpd.GeoDataFrame:
-                """Retrieve the edge from snkit_network.edges GeoDataFrame between two nodes."""
-                edge = snkit_network.edges[
-                    (snkit_network.edges['from_id'] == node1) &
-                    (snkit_network.edges['to_id'] == node2)
-                    ]
-                return edge if not edge.empty else None
-            
-            def construct_path(start_node: int|float, end_node: int|float, intermediates: list) -> pd.DataFrame | None:
-                path = []
-                current_node = start_node
-                _intermediates = intermediates.copy()
-
-                while _intermediates:
-                    for next_node in _intermediates:
-                        edge = retrieve_edge(current_node, next_node)
-                        if edge is not None:
-                            path.append(edge)
-                            _intermediates.remove(next_node)
-                            current_node = next_node
-                            break
-
-                final_edge = retrieve_edge(current_node, end_node)
-                if final_edge is not None:
-                    path.append(final_edge)
-
-                if len(path) > 0 and all(edge is not None for edge in path):
-                    return pd.concat(path)  # Combine edges into a single GeoDataFrame
-                return None
-
             boundary_nodes = list(node_path - filtered_degree_4_set)
             if len(boundary_nodes) == 2:
                 from_node, to_node = boundary_nodes
-                intermediates = list(node_path & filtered_degree_4_set)
+                _intermediates = list(node_path & filtered_degree_4_set)
 
                 # Construct and append the forward path
-                forward_gdf = construct_path(from_node, to_node, intermediates)
+                forward_gdf = _construct_path(from_node, to_node, _intermediates)
                 if forward_gdf is not None:
                     _edge_paths.append(forward_gdf)
 
                 # Construct and append the backward path
-                backward_gdf = construct_path(to_node, from_node, intermediates)
+                backward_gdf = _construct_path(to_node, from_node, _intermediates)
                 if backward_gdf is not None:
                     _edge_paths.append(backward_gdf)
 
-
         # Convert edges to an adjacency list using vectorized operations
-        edge_dict = defaultdict(set)
-        from_ids = snkit_network.edges["from_id"].values
-        to_ids = snkit_network.edges["to_id"].values
-
-        for from_id, to_id in zip(from_ids, to_ids):
-            edge_dict[from_id].add(to_id)
-            edge_dict[to_id].add(from_id)
-
+        edge_dict = _get_adjacency_list(edges_gdf=snkit_network.edges)
         _edge_paths = []
 
         # find the edge paths for the nodes in node_set
@@ -207,12 +214,11 @@ def construct_path(start_node: int|float, end_node: int|float, intermediates: li
                     # node_path has nodes with degree 4 => get the forward and backward paths
                     _find_and_append_degree_4_paths(_edge_paths)
                 else:
-                    # node_path has nodes with degree 4 => find the edges connected to the intermediates
+                    # node_path has nodes with degree 2 => find the edges connected to the intermediates
                     edge_paths_gdf = snkit_network.edges[
                         snkit_network.edges.from_id.isin(intermediates) |
                         snkit_network.edges.to_id.isin(intermediates)
                         ]
-                    # Append the result to edge_paths
                     _edge_paths.append(edge_paths_gdf)
         return _edge_paths
 

From ce5d9f27074aaa038d71260c69fd18aef102d482 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 17:34:58 +0200
Subject: [PATCH 17/33] chore: _ removed from the inned functions

---
 .../snkit_network_merge_wrapper.py            | 65 +++++++++----------
 1 file changed, 30 insertions(+), 35 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 0b362b01b..cbf86281e 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -61,7 +61,7 @@ def merge_edges(
         SnkitNetwork: _description_
     """
 
-    def _node_connectivity_degree(node, snkit_network: SnkitNetwork) -> int:
+    def node_connectivity_degree(node, snkit_network: SnkitNetwork) -> int:
         return len(
             snkit_network.edges[
                 (snkit_network.edges.from_id == node)
@@ -69,13 +69,13 @@ def _node_connectivity_degree(node, snkit_network: SnkitNetwork) -> int:
             ]
         )
 
-    def _get_edge_ids_to_update(edges_list: list) -> list:
+    def get_edge_ids_to_update(edges_list: list) -> list:
         ids_to_update = []
         for edges in edges_list:
             ids_to_update.extend(edges.id.tolist())
         return ids_to_update
 
-    def _get_merged_edges(
+    def get_merged_edges(
         paths_to_group: list,
         by: list,
         aggfunc: str | dict,
@@ -98,7 +98,7 @@ def _get_merged_edges(
         updated_edges_gdf = updated_edges_gdf.drop(columns=["id"])
         return updated_edges_gdf
 
-    def _filter_node(_node_set: set, _degrees: int) -> set:
+    def filter_node(_node_set: set, _degrees: int) -> set:
         _filtered = set()
         for _node_id in _node_set:
             # Get the predecessors (antecedents) and successors (precedents) to make sure for to filter correctly
@@ -115,8 +115,8 @@ def _filter_node(_node_set: set, _degrees: int) -> set:
                 _filtered.add(_node_id)
         return _filtered
 
-    def _get_edge_paths(node_set: set, _snkit_network: SnkitNetwork) -> list:
-        def _get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from_id",
+    def get_edge_paths(node_set: set, _snkit_network: SnkitNetwork) -> list:
+        def get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from_id",
                                 to_id_column: str = "to_id") -> defaultdict:
             # Convert the edges of a GeoDataFrame to an adjacency list using vectorized operations.
             _edge_dict = defaultdict(set)
@@ -130,7 +130,7 @@ def _get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from
 
             return _edge_dict
 
-        def _retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
+        def retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
             """Retrieve the edge from snkit_network.edges GeoDataFrame between two nodes."""
             edge = _snkit_network.edges[
                 (_snkit_network.edges['from_id'] == node1) &
@@ -138,21 +138,21 @@ def _retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
                 ]
             return edge if not edge.empty else None
 
-        def _construct_path(start_node: int | float, end_node: int | float, __intermediates: list) -> pd.DataFrame | None:
+        def construct_path(start_node: int | float, end_node: int | float, __intermediates: list) -> pd.DataFrame | None:
             path = []
             current_node = start_node
             _intermediates = __intermediates.copy()
 
             while _intermediates:
                 for next_node in _intermediates:
-                    edge = _retrieve_edge(current_node, next_node)
+                    edge = retrieve_edge(current_node, next_node)
                     if edge is not None:
                         path.append(edge)
                         _intermediates.remove(next_node)
                         current_node = next_node
                         break
 
-            final_edge = _retrieve_edge(current_node, end_node)
+            final_edge = retrieve_edge(current_node, end_node)
             if final_edge is not None:
                 path.append(final_edge)
 
@@ -160,27 +160,29 @@ def _construct_path(start_node: int | float, end_node: int | float, __intermedia
                 return pd.concat(path)  # Combine edges into a single GeoDataFrame
             return None
 
-        def _find_and_append_degree_4_paths(
+        def find_and_append_degree_4_paths(
                 _edge_paths: list
-        ) -> None:
+        ) -> list:
+            _edge_paths_results = _edge_paths
             boundary_nodes = list(node_path - filtered_degree_4_set)
             if len(boundary_nodes) == 2:
                 from_node, to_node = boundary_nodes
                 _intermediates = list(node_path & filtered_degree_4_set)
 
                 # Construct and append the forward path
-                forward_gdf = _construct_path(from_node, to_node, _intermediates)
+                forward_gdf = construct_path(from_node, to_node, _intermediates)
                 if forward_gdf is not None:
-                    _edge_paths.append(forward_gdf)
+                    _edge_paths_results.append(forward_gdf)
 
                 # Construct and append the backward path
-                backward_gdf = _construct_path(to_node, from_node, _intermediates)
+                backward_gdf = construct_path(to_node, from_node, _intermediates)
                 if backward_gdf is not None:
-                    _edge_paths.append(backward_gdf)
+                    _edge_paths_results.append(backward_gdf)
+            return _edge_paths_results
 
         # Convert edges to an adjacency list using vectorized operations
-        edge_dict = _get_adjacency_list(edges_gdf=snkit_network.edges)
-        _edge_paths = []
+        edge_dict = get_adjacency_list(edges_gdf=snkit_network.edges)
+        _edge_paths: list = []
 
         # find the edge paths for the nodes in node_set
         while node_set:
@@ -212,7 +214,7 @@ def _find_and_append_degree_4_paths(
             if len(node_path) >= 2:
                 if any(node_path.intersection(filtered_degree_4_set)):
                     # node_path has nodes with degree 4 => get the forward and backward paths
-                    _find_and_append_degree_4_paths(_edge_paths)
+                    _edge_paths = find_and_append_degree_4_paths(_edge_paths)
                 else:
                     # node_path has nodes with degree 2 => find the edges connected to the intermediates
                     edge_paths_gdf = snkit_network.edges[
@@ -225,7 +227,7 @@ def _find_and_append_degree_4_paths(
     # Adds degree column which is needed to find the to-be-simplified nodes and edges.
     if "degree" not in snkit_network.nodes.columns:
         snkit_network.nodes["degree"] = snkit_network.nodes[id_col].apply(
-            lambda x: _node_connectivity_degree(x, snkit_network)
+            lambda x: node_connectivity_degree(x, snkit_network)
         )
 
     # Filter on the nodes with degree 2 and 4 which suffice the following criteria:
@@ -233,29 +235,22 @@ def _find_and_append_degree_4_paths(
     # E.g. filters on 2 in 1->2, 1->5, 2->3, 3->4, 3->5
     # For _node_set with all degree 4: Check if the predecessors and successors are the same nodes.
     # E.g. filters on 2 in 1->2, 2->3, 2->1, 3->2.
-    degree_2 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2])
-    degree_2_set = set(degree_2)
-    filtered_degree_2_set = _filter_node(degree_2_set, _degrees=2)
+    degree_2_set = set(list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 2]))
+    filtered_degree_2_set = filter_node(degree_2_set, _degrees=2)
 
-    degree_4 = list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4])
-    degree_4_set = set(degree_4)
-    filtered_degree_4_set = _filter_node(degree_4_set, _degrees=4)
+    degree_4_set = set(list(snkit_network.nodes[id_col].loc[snkit_network.nodes.degree == 4]))
+    filtered_degree_4_set = filter_node(degree_4_set, _degrees=4)
 
     nodes_of_interest = filtered_degree_2_set | filtered_degree_4_set
 
-    edge_paths = _get_edge_paths(sorted(nodes_of_interest), snkit_network)
+    edge_paths = get_edge_paths(sorted(nodes_of_interest), snkit_network)
 
-    edge_ids_to_update = _get_edge_ids_to_update(edge_paths)
+    edge_ids_to_update = get_edge_ids_to_update(edge_paths)
     edges_to_keep = snkit_network.edges[
         ~snkit_network.edges["id"].isin(edge_ids_to_update)
     ]
 
-    updated_edges = _get_merged_edges(
-        paths_to_group=edge_paths,
-        by=by,
-        aggfunc=aggregate_func,
-        net=snkit_network,
-    )
+    updated_edges = get_merged_edges(paths_to_group=edge_paths, by=by, aggfunc=aggregate_func, net=snkit_network)
     edges_to_keep = edges_to_keep.drop(columns=["id"])
     updated_edges = updated_edges.reset_index(drop=True)
 
@@ -270,7 +265,7 @@ def _find_and_append_degree_4_paths(
 
     merged_snkit_network = SnkitNetwork(nodes=new_nodes_gdf, edges=new_edges_gdf)
     merged_snkit_network.nodes["degree"] = merged_snkit_network.nodes[id_col].apply(
-        lambda x: _node_connectivity_degree(x, merged_snkit_network)
+        lambda x: node_connectivity_degree(x, merged_snkit_network)
     )
 
     return merged_snkit_network

From 61acd5edc28365617a25476aa4c7bc34cd9fa6ca Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 17:35:13 +0200
Subject: [PATCH 18/33] chore: _ removed from the inned functions

---
 .../network_simplification/test_network_graph_simplificator.py  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 0da811513..d627b1a41 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -25,7 +25,7 @@
 def _detailed_edge_comparison(
     graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
 ) -> bool:
-    def _dicts_comparison(
+    def dicts_comparison(
         _graph1: nx.MultiDiGraph | nx.MultiGraph, _graph2: nx.MultiDiGraph | nx.MultiGraph
     ) -> bool:
         for u, v, k, data1 in _graph1.edges(keys=True, data=True):

From efb3477f2370427dba62ca9f40c95f97002c4932 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Wed, 4 Sep 2024 17:35:21 +0200
Subject: [PATCH 19/33] chore: _ removed from the inned functions

---
 .../test_network_graph_simplificator.py                       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index d627b1a41..b147edba6 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -49,8 +49,8 @@ def dicts_comparison(
                 return False
         return True
 
-    check_1_2 = _dicts_comparison(graph1, graph2)
-    check_2_1 = _dicts_comparison(graph2, graph1)
+    check_1_2 = dicts_comparison(graph1, graph2)
+    check_2_1 = dicts_comparison(graph2, graph1)
 
     if check_1_2 and check_2_1:
         return True

From 7a72adbc9ac8575d957f1808be2e964d1a8e2a5b Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Sun, 8 Sep 2024 00:38:51 +0200
Subject: [PATCH 20/33] fix: array to int to create a dict

---
 .../network_simplification/snkit_network_merge_wrapper.py     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index cbf86281e..d1e471b13 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -125,8 +125,8 @@ def get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from_
             to_ids = edges_gdf[to_id_column].values
             # Vectorized operation to populate the adjacency list
             for from_id, to_id in np.nditer([from_ids, to_ids]):
-                _edge_dict[from_id].add(to_id)
-                _edge_dict[to_id].add(from_id)
+                _edge_dict[int(from_id)].add(int(to_id))
+                _edge_dict[int(to_id)].add(int(from_id))
 
             return _edge_dict
 

From ea8ef06bd11e869da12926e297f27761c1228452 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 08:51:18 +0200
Subject: [PATCH 21/33] fix: removed default values + private variables

---
 .../snkit_network_merge_wrapper.py                     | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index d1e471b13..32a113623 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -116,8 +116,8 @@ def filter_node(_node_set: set, _degrees: int) -> set:
         return _filtered
 
     def get_edge_paths(node_set: set, _snkit_network: SnkitNetwork) -> list:
-        def get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str = "from_id",
-                                to_id_column: str = "to_id") -> defaultdict:
+        def get_adjacency_list(edges_gdf: gpd.GeoDataFrame, from_id_column: str,
+                                to_id_column: str) -> defaultdict:
             # Convert the edges of a GeoDataFrame to an adjacency list using vectorized operations.
             _edge_dict = defaultdict(set)
             # Extract the 'from_id' and 'to_id' columns as numpy arrays for efficient processing
@@ -138,10 +138,10 @@ def retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
                 ]
             return edge if not edge.empty else None
 
-        def construct_path(start_node: int | float, end_node: int | float, __intermediates: list) -> pd.DataFrame | None:
+        def construct_path(start_node: int | float, end_node: int | float, intermediates: list) -> pd.DataFrame | None:
             path = []
             current_node = start_node
-            _intermediates = __intermediates.copy()
+            _intermediates = intermediates.copy()
 
             while _intermediates:
                 for next_node in _intermediates:
@@ -181,7 +181,7 @@ def find_and_append_degree_4_paths(
             return _edge_paths_results
 
         # Convert edges to an adjacency list using vectorized operations
-        edge_dict = get_adjacency_list(edges_gdf=snkit_network.edges)
+        edge_dict = get_adjacency_list(edges_gdf=snkit_network.edges, from_id_column="from_id", to_id_column="to_id")
         _edge_paths: list = []
 
         # find the edge paths for the nodes in node_set

From 9260b0666690167e63873d8c4f0525d02b62796c Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 08:58:24 +0200
Subject: [PATCH 22/33] fix: while loop is replaced

---
 .../snkit_network_merge_wrapper.py            | 25 +++++++++++--------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
index 32a113623..eac76f852 100644
--- a/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_merge_wrapper.py
@@ -138,19 +138,22 @@ def retrieve_edge(node1: int | float, node2: int | float) -> gpd.GeoDataFrame:
                 ]
             return edge if not edge.empty else None
 
-        def construct_path(start_node: int | float, end_node: int | float, intermediates: list) -> pd.DataFrame | None:
+        def construct_path(start_node: int | float, end_node: int | float, intermediate_nodes: list) -> pd.DataFrame | None:
             path = []
             current_node = start_node
-            _intermediates = intermediates.copy()
-
-            while _intermediates:
-                for next_node in _intermediates:
-                    edge = retrieve_edge(current_node, next_node)
-                    if edge is not None:
-                        path.append(edge)
-                        _intermediates.remove(next_node)
-                        current_node = next_node
-                        break
+            _intermediates = intermediate_nodes.copy()
+
+            _explored_nodes = []
+            # Ensure we go through all the items.
+            for _ in range(len(intermediate_nodes)):
+                # Filter out nodes already used for edge retrieval
+                _to_explore = filter(lambda x: x not in _explored_nodes, intermediate_nodes)
+                for _next_node in _to_explore:
+                    _edge = retrieve_edge(current_node, _next_node)
+                    if _edge is not None:
+                        path.append(_edge)
+                        _explored_nodes.append(_next_node)
+                        current_node = _next_node
 
             final_edge = retrieve_edge(current_node, end_node)
             if final_edge is not None:

From f18be85e4155eddde15787438f341c81f067c5dc Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 09:18:16 +0200
Subject: [PATCH 23/33] fix: add_edge_with_attributes added to make the test
 compacter

---
 .../test_network_graph_simplificator.py       | 188 ++++--------------
 1 file changed, 41 insertions(+), 147 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index b147edba6..52ef574f0 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -4,6 +4,8 @@
 import networkx as nx
 import numpy as np
 import pytest
+from altgraph.Graph import Graph
+from networkx import DiGraph
 from shapely.geometry import LineString
 
 from ra2ce.network import add_missing_geoms_graph
@@ -176,6 +178,23 @@ def create_nx_multidigraph():
     def _get_expected_result_graph_fixture(
         self, nx_digraph_factory: nx.MultiDiGraph
     ) -> nx.MultiGraph:
+        def add_edge_with_attributes(graph_to_shape: Graph | DiGraph, edge_u: int | float, edge_v: int | float, a_value: str, edge_node_ids: list) -> Graph | DiGraph:
+            # Create a copy of the input graph
+            shaped_graph = graph_to_shape.copy()
+
+            # Extract geometries programmatically using edge_node_ids
+            geometry_list = [graph_to_shape.nodes[n_id]["geometry"] for n_id in edge_node_ids]
+
+            shaped_graph.add_edge(
+                edge_u,
+                edge_v,
+                a=a_value,
+                from_node=edge_u,
+                to_node=edge_v,
+                geometry=LineString(geometry_list),
+            )
+            return shaped_graph
+
         _nx_digraph = nx_digraph_factory()
         _result_digraph = nx.MultiDiGraph()
         node_ids_degrees = {2: 3, 4: 2, 7: 2, 8: 4, 11: 3, 12: 2, 16: 4, 17: 1, 18: 1}
@@ -186,163 +205,38 @@ def _get_expected_result_graph_fixture(
             _result_digraph.add_node(node_id, **node_data)
         _result_digraph = add_missing_geoms_graph(_result_digraph, "geometry")
 
-        _result_digraph.add_edge(
-            2,
-            4.0,
-            a='None',
-            from_node=2,
-            to_node=4,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[2]["geometry"],
-                    _nx_digraph.nodes[3]["geometry"],
-                    _nx_digraph.nodes[4]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 2, 4.0, 'None', [2, 3, 4]
         )
-
-        _result_digraph.add_edge(
-            2,
-            16.0,
-            a='None',
-            from_node=2,
-            to_node=16,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[2]["geometry"],
-                    _nx_digraph.nodes[1]["geometry"],
-                    _nx_digraph.nodes[16]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 2, 16.0, 'None', [2, 1, 16]
         )
-
-        _result_digraph.add_edge(
-            4,
-            7.0,
-            a="yes",
-            from_node=4,
-            to_node=7,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[4]["geometry"],
-                    _nx_digraph.nodes[5]["geometry"],
-                    _nx_digraph.nodes[6]["geometry"],
-                    _nx_digraph.nodes[7]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 4, 7.0, 'yes', [4, 5, 6, 7]
         )
-        _result_digraph.add_edge(
-            7,
-            8.0,
-            a='None',
-            from_node=7,
-            to_node=8,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[7]["geometry"],
-                    _nx_digraph.nodes[8]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 7, 8.0, 'None', [7, 8]
         )
-        _result_digraph.add_edge(
-            8,
-            11,
-            a='None',
-            from_node=8,
-            to_node=11,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[8]["geometry"],
-                    _nx_digraph.nodes[9]["geometry"],
-                    _nx_digraph.nodes[10]["geometry"],
-                    _nx_digraph.nodes[11]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 8, 11, 'None', [8, 9, 10, 11]
         )
-        _result_digraph.add_edge(
-            8,
-            11,
-            a="yes",
-            from_node=8,
-            to_node=11,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[8]["geometry"],
-                    _nx_digraph.nodes[13]["geometry"],
-                    _nx_digraph.nodes[14]["geometry"],
-                    _nx_digraph.nodes[15]["geometry"],
-                    _nx_digraph.nodes[11]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 8, 11, 'yes', [8, 13, 14, 15, 11]
         )
-        _result_digraph.add_edge(
-            8,
-            12,
-            a='None',
-            from_node=8,
-            to_node=12,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[8]["geometry"],
-                    _nx_digraph.nodes[12]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 8, 12, 'None', [8, 12]
         )
-        _result_digraph.add_edge(
-            11,
-            12,
-            a="yes",
-            from_node=11,
-            to_node=12,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[11]["geometry"],
-                    _nx_digraph.nodes[12]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 11, 12, 'yes', [11, 12]
         )
-
-        _result_digraph.add_edge(
-            16,
-            2.0,
-            a='None',
-            from_node=16,
-            to_node=2,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[16]["geometry"],
-                    _nx_digraph.nodes[1]["geometry"],
-                    _nx_digraph.nodes[2]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 16, 2.0, 'None', [16, 1, 2]
         )
-
-        _result_digraph.add_edge(
-            16,
-            17,
-            a='None',
-            from_node=16,
-            to_node=17,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[16]["geometry"],
-                    _nx_digraph.nodes[17]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 16, 17, 'None', [16, 17]
         )
-
-        _result_digraph.add_edge(
-            16,
-            18,
-            a='None',
-            from_node=16,
-            to_node=18,
-            geometry=LineString(
-                [
-                    _nx_digraph.nodes[16]["geometry"],
-                    _nx_digraph.nodes[18]["geometry"],
-                ]
-            ),
+        _result_digraph = add_edge_with_attributes(
+            _result_digraph, 16, 18, 'None', [16, 18]
         )
         _result_digraph.graph["crs"] = "EPSG:4326"
 

From 6d328a19a324f50cd562a1f1ced1012a42115d04 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 09:25:13 +0200
Subject: [PATCH 24/33] fix: add_nodes_from replaced the for loop

---
 .../network_simplification/test_network_graph_simplificator.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 52ef574f0..79e730bbd 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -141,8 +141,7 @@ def _get_network_simplification_with_attribute_exclusion(
     def _get_nx_digraph_factory(self) -> Iterator[Callable[[], nx.MultiDiGraph]]:
         def create_nx_multidigraph():
             _nx_digraph = nx.MultiDiGraph()
-            for i in range(1, 19):
-                _nx_digraph.add_node(i, x=i, y=i * 10)
+            _nx_digraph.add_nodes_from([(i, {'x': i, 'y': i * 10}) for i in range(1, 19)])
 
             _nx_digraph.add_edge(1, 2, a='None')
             _nx_digraph.add_edge(2, 1, a='None')

From 01c6da9ab13f8b43a7cb093c2ad286ae6801b97e Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 09:27:52 +0200
Subject: [PATCH 25/33] chore: default values are removed

---
 .../network_simplification/snkit_network_wrapper.py    | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_wrapper.py b/ra2ce/network/network_simplification/snkit_network_wrapper.py
index 14802d1ce..819bed6ff 100644
--- a/ra2ce/network/network_simplification/snkit_network_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_wrapper.py
@@ -43,12 +43,12 @@ class SnkitNetworkWrapper:
     """
 
     snkit_network: Network
-    node_id_column_name: str = "id"
-    edge_from_id_column_name: str = "from_id"
-    edge_to_id_column_name: str = "to_id"
+    node_id_column_name: str
+    edge_from_id_column_name: str
+    edge_to_id_column_name: str
 
-    def __init__(self, snkit_network: Network, node_id_column_name: str = "id",
-                 edge_from_id_column_name: str = "from_id", edge_to_id_column_name: str = "to_id") -> None:
+    def __init__(self, snkit_network: Network, node_id_column_name: str,
+                 edge_from_id_column_name: str, edge_to_id_column_name: str) -> None:
         self.snkit_network = snkit_network
         self.node_id_column_name = node_id_column_name
         self.edge_from_id_column_name = edge_from_id_column_name

From 34fec8dde687926ce2565ff2946713f1f3d52822 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 09:30:27 +0200
Subject: [PATCH 26/33] chore: self.to_networkx() replaced

---
 ra2ce/network/network_simplification/snkit_network_wrapper.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_wrapper.py b/ra2ce/network/network_simplification/snkit_network_wrapper.py
index 819bed6ff..0cfeb41ca 100644
--- a/ra2ce/network/network_simplification/snkit_network_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_wrapper.py
@@ -95,7 +95,7 @@ def filter_excluded_attributes() -> list[str]:
         # Overwrite the existing network with the merged edges.
         self.snkit_network = merge_edges(
             snkit_network=self.snkit_network,
-            networkx_graph=self.networkx_graph,
+            networkx_graph=self.to_networkx(),
             aggregate_func=_aggregate_function,
             by=_attributes_to_exclude,
             id_col="id",

From 29d461a6ca213857f7806106e31b970a19ff767a Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Tue, 10 Sep 2024 10:06:05 +0200
Subject: [PATCH 27/33] chore: test revised

---
 .../network_simplification/test_network_graph_simplificator.py  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 79e730bbd..e5b7bb67b 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -182,7 +182,7 @@ def add_edge_with_attributes(graph_to_shape: Graph | DiGraph, edge_u: int | floa
             shaped_graph = graph_to_shape.copy()
 
             # Extract geometries programmatically using edge_node_ids
-            geometry_list = [graph_to_shape.nodes[n_id]["geometry"] for n_id in edge_node_ids]
+            geometry_list = [_nx_digraph.nodes[n_id]["geometry"] for n_id in edge_node_ids]
 
             shaped_graph.add_edge(
                 edge_u,

From e3802b1cb80b2f6740982ef0b980b88783b0fc3b Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Fri, 13 Sep 2024 11:23:59 +0200
Subject: [PATCH 28/33] chore: removed unnecessaty self.to_networkx()

---
 .../network_simplification/snkit_network_wrapper.py      | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_wrapper.py b/ra2ce/network/network_simplification/snkit_network_wrapper.py
index 0cfeb41ca..e5173638d 100644
--- a/ra2ce/network/network_simplification/snkit_network_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_wrapper.py
@@ -53,13 +53,12 @@ def __init__(self, snkit_network: Network, node_id_column_name: str,
         self.node_id_column_name = node_id_column_name
         self.edge_from_id_column_name = edge_from_id_column_name
         self.edge_to_id_column_name = edge_to_id_column_name
-        self.networkx_graph: NxGraph = self.to_networkx()
 
     @classmethod
     def from_networkx(
-        cls,
-        networkx_graph: NxGraph,
-        column_names_dict: dict[str, str],
+            cls,
+            networkx_graph: NxGraph,
+            column_names_dict: dict[str, str],
     ) -> SnkitNetworkWrapper:
         """
         Generates a `SnkitNetworkWrapper` based on the given `NxGraph`.
@@ -108,7 +107,7 @@ def process_network(self) -> None:
         )  # length in m
         self.snkit_network.edges = self.snkit_network.edges[
             self.snkit_network.edges["length"] != 0
-        ]  # Remove zero-length edges
+            ]  # Remove zero-length edges
 
         def convert_to_line_string(geometry_to_convert) -> MultiLineString:
             if isinstance(geometry_to_convert, MultiLineString):

From 8b5f7a7f8d0b43964f3d14101b67204d003fcd15 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Fri, 13 Sep 2024 16:47:45 +0200
Subject: [PATCH 29/33] chore: formatted

---
 .../snkit_network_wrapper.py                  | 25 +++++++++++++------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/ra2ce/network/network_simplification/snkit_network_wrapper.py b/ra2ce/network/network_simplification/snkit_network_wrapper.py
index e5173638d..8ebab34fd 100644
--- a/ra2ce/network/network_simplification/snkit_network_wrapper.py
+++ b/ra2ce/network/network_simplification/snkit_network_wrapper.py
@@ -47,8 +47,13 @@ class SnkitNetworkWrapper:
     edge_from_id_column_name: str
     edge_to_id_column_name: str
 
-    def __init__(self, snkit_network: Network, node_id_column_name: str,
-                 edge_from_id_column_name: str, edge_to_id_column_name: str) -> None:
+    def __init__(
+        self,
+        snkit_network: Network,
+        node_id_column_name: str,
+        edge_from_id_column_name: str,
+        edge_to_id_column_name: str,
+    ) -> None:
         self.snkit_network = snkit_network
         self.node_id_column_name = node_id_column_name
         self.edge_from_id_column_name = edge_from_id_column_name
@@ -56,9 +61,9 @@ def __init__(self, snkit_network: Network, node_id_column_name: str,
 
     @classmethod
     def from_networkx(
-            cls,
-            networkx_graph: NxGraph,
-            column_names_dict: dict[str, str],
+        cls,
+        networkx_graph: NxGraph,
+        column_names_dict: dict[str, str],
     ) -> SnkitNetworkWrapper:
         """
         Generates a `SnkitNetworkWrapper` based on the given `NxGraph`.
@@ -87,9 +92,13 @@ def filter_excluded_attributes() -> list[str]:
         _attributes_to_exclude = filter_excluded_attributes()
 
         if "demand_edge" not in _attributes_to_exclude:
-            _aggregate_function = self._aggrfunc(cols, _attributes_to_exclude, with_demand=True)
+            _aggregate_function = self._aggrfunc(
+                cols, _attributes_to_exclude, with_demand=True
+            )
         else:
-            _aggregate_function = self._aggrfunc(cols, _attributes_to_exclude, with_demand=False)
+            _aggregate_function = self._aggrfunc(
+                cols, _attributes_to_exclude, with_demand=False
+            )
 
         # Overwrite the existing network with the merged edges.
         self.snkit_network = merge_edges(
@@ -107,7 +116,7 @@ def process_network(self) -> None:
         )  # length in m
         self.snkit_network.edges = self.snkit_network.edges[
             self.snkit_network.edges["length"] != 0
-            ]  # Remove zero-length edges
+        ]  # Remove zero-length edges
 
         def convert_to_line_string(geometry_to_convert) -> MultiLineString:
             if isinstance(geometry_to_convert, MultiLineString):

From 727b5f26d38b523b2a118f029dbc5704c5685cd2 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Mon, 16 Sep 2024 10:04:14 +0200
Subject: [PATCH 30/33] chore: graph1 renamed

---
 .../test_network_graph_simplificator.py       | 107 ++++++++++--------
 1 file changed, 59 insertions(+), 48 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index e5b7bb67b..b36e24be9 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -25,18 +25,19 @@
 
 
 def _detailed_edge_comparison(
-    graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
+        graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
 ) -> bool:
     def dicts_comparison(
-        _graph1: nx.MultiDiGraph | nx.MultiGraph, _graph2: nx.MultiDiGraph | nx.MultiGraph
+            graph_a: nx.MultiDiGraph | nx.MultiGraph,
+            graph_b: nx.MultiDiGraph | nx.MultiGraph,
     ) -> bool:
-        for u, v, k, data1 in _graph1.edges(keys=True, data=True):
-            geom1 = data1['geometry']
+        for u, v, k, data1 in graph_a.edges(keys=True, data=True):
+            geom1 = data1["geometry"]
             geom_found = 0
 
-            data2_dict = _graph2.get_edge_data(u, v)
+            data2_dict = graph_b.get_edge_data(u, v)
             for _, data2 in data2_dict.items():
-                if data2['geometry'] == geom1:
+                if data2["geometry"] == geom1:
                     geom_found = 1
                     for key1, value1 in data1.items():
                         if key1 not in data2:
@@ -63,7 +64,7 @@ def dicts_comparison(
 class TestNetworkGraphSimplificator:
     @pytest.fixture(name="network_graph_simplificator_factory")
     def _get_network_graph_simplificator(
-        self,
+            self,
     ) -> Iterator[Callable[[], NetworkGraphSimplificator]]:
         def get_network_graph_simplificator() -> NetworkGraphSimplificator:
             return NetworkGraphSimplificator(
@@ -73,8 +74,8 @@ def get_network_graph_simplificator() -> NetworkGraphSimplificator:
         yield get_network_graph_simplificator
 
     def test_validate_fixture_init(
-        self,
-        network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
+            self,
+            network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
     ):
         # 1. Define test data.
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -90,9 +91,9 @@ def _get_multigraph_fixture(self) -> Iterator[nx.MultiGraph]:
         yield _graph
 
     def test__graph_create_unique_ids_with_missing_id_data(
-        self,
-        network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
-        multigraph_fixture: nx.MultiGraph,
+            self,
+            network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
+            multigraph_fixture: nx.MultiGraph,
     ):
         # 1. Define test data
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -110,9 +111,9 @@ def test__graph_create_unique_ids_with_missing_id_data(
         assert all(_new_id_name in _keys for _keys in _dicts_keys)
 
     def test__graph_create_unique_ids_with_existing_id(
-        self,
-        network_graph_simplificator_factory: NetworkGraphSimplificator,
-        multigraph_fixture: nx.MultiGraph,
+            self,
+            network_graph_simplificator_factory: NetworkGraphSimplificator,
+            multigraph_fixture: nx.MultiGraph,
     ):
         # 1. Define test data
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -131,7 +132,7 @@ def test__graph_create_unique_ids_with_existing_id(
 class TestNetworkSimplificationWithAttributeExclusion:
     @pytest.fixture(name="network_simplification_with_attribute_exclusion")
     def _get_network_simplification_with_attribute_exclusion(
-        self,
+            self,
     ) -> Iterator[NetworkSimplificationWithAttributeExclusion]:
         yield NetworkSimplificationWithAttributeExclusion(
             nx_graph=None, attributes_to_exclude=[]
@@ -141,29 +142,31 @@ def _get_network_simplification_with_attribute_exclusion(
     def _get_nx_digraph_factory(self) -> Iterator[Callable[[], nx.MultiDiGraph]]:
         def create_nx_multidigraph():
             _nx_digraph = nx.MultiDiGraph()
-            _nx_digraph.add_nodes_from([(i, {'x': i, 'y': i * 10}) for i in range(1, 19)])
+            _nx_digraph.add_nodes_from(
+                [(i, {"x": i, "y": i * 10}) for i in range(1, 19)]
+            )
 
-            _nx_digraph.add_edge(1, 2, a='None')
-            _nx_digraph.add_edge(2, 1, a='None')
-            _nx_digraph.add_edge(2, 3, a='None')
-            _nx_digraph.add_edge(3, 4, a='None')
+            _nx_digraph.add_edge(1, 2, a="None")
+            _nx_digraph.add_edge(2, 1, a="None")
+            _nx_digraph.add_edge(2, 3, a="None")
+            _nx_digraph.add_edge(3, 4, a="None")
             _nx_digraph.add_edge(4, 5, a="yes")
             _nx_digraph.add_edge(5, 6, a="yes")
             _nx_digraph.add_edge(6, 7, a="yes")
-            _nx_digraph.add_edge(7, 8, a='None')
-            _nx_digraph.add_edge(8, 9, a='None')
-            _nx_digraph.add_edge(8, 12, a='None')
+            _nx_digraph.add_edge(7, 8, a="None")
+            _nx_digraph.add_edge(8, 9, a="None")
+            _nx_digraph.add_edge(8, 12, a="None")
             _nx_digraph.add_edge(8, 13, a="yes")
-            _nx_digraph.add_edge(9, 10, a='None')
-            _nx_digraph.add_edge(10, 11, a='None')
+            _nx_digraph.add_edge(9, 10, a="None")
+            _nx_digraph.add_edge(10, 11, a="None")
             _nx_digraph.add_edge(11, 12, a="yes")
             _nx_digraph.add_edge(13, 14, a="yes")
             _nx_digraph.add_edge(14, 15, a="yes")
             _nx_digraph.add_edge(15, 11, a="yes")
-            _nx_digraph.add_edge(1, 16, a='None')
-            _nx_digraph.add_edge(16, 1, a='None')
-            _nx_digraph.add_edge(16, 17, a='None')
-            _nx_digraph.add_edge(16, 18, a='None')
+            _nx_digraph.add_edge(1, 16, a="None")
+            _nx_digraph.add_edge(16, 1, a="None")
+            _nx_digraph.add_edge(16, 17, a="None")
+            _nx_digraph.add_edge(16, 18, a="None")
 
             _nx_digraph = add_missing_geoms_graph(_nx_digraph, "geometry")
             _nx_digraph.graph["crs"] = "EPSG:4326"
@@ -175,14 +178,22 @@ def create_nx_multidigraph():
 
     @pytest.fixture(name="expected_result_graph_fixture")
     def _get_expected_result_graph_fixture(
-        self, nx_digraph_factory: nx.MultiDiGraph
+            self, nx_digraph_factory: nx.MultiDiGraph
     ) -> nx.MultiGraph:
-        def add_edge_with_attributes(graph_to_shape: Graph | DiGraph, edge_u: int | float, edge_v: int | float, a_value: str, edge_node_ids: list) -> Graph | DiGraph:
+        def add_edge_with_attributes(
+                graph_to_shape: Graph | DiGraph,
+                edge_u: int | float,
+                edge_v: int | float,
+                a_value: str,
+                edge_node_ids: list,
+        ) -> Graph | DiGraph:
             # Create a copy of the input graph
             shaped_graph = graph_to_shape.copy()
 
             # Extract geometries programmatically using edge_node_ids
-            geometry_list = [_nx_digraph.nodes[n_id]["geometry"] for n_id in edge_node_ids]
+            geometry_list = [
+                _nx_digraph.nodes[n_id]["geometry"] for n_id in edge_node_ids
+            ]
 
             shaped_graph.add_edge(
                 edge_u,
@@ -205,37 +216,37 @@ def add_edge_with_attributes(graph_to_shape: Graph | DiGraph, edge_u: int | floa
         _result_digraph = add_missing_geoms_graph(_result_digraph, "geometry")
 
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 2, 4.0, 'None', [2, 3, 4]
+            _result_digraph, 2, 4.0, "None", [2, 3, 4]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 2, 16.0, 'None', [2, 1, 16]
+            _result_digraph, 2, 16.0, "None", [2, 1, 16]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 4, 7.0, 'yes', [4, 5, 6, 7]
+            _result_digraph, 4, 7.0, "yes", [4, 5, 6, 7]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 7, 8.0, 'None', [7, 8]
+            _result_digraph, 7, 8.0, "None", [7, 8]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 8, 11, 'None', [8, 9, 10, 11]
+            _result_digraph, 8, 11, "None", [8, 9, 10, 11]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 8, 11, 'yes', [8, 13, 14, 15, 11]
+            _result_digraph, 8, 11, "yes", [8, 13, 14, 15, 11]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 8, 12, 'None', [8, 12]
+            _result_digraph, 8, 12, "None", [8, 12]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 11, 12, 'yes', [11, 12]
+            _result_digraph, 11, 12, "yes", [11, 12]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 16, 2.0, 'None', [16, 1, 2]
+            _result_digraph, 16, 2.0, "None", [16, 1, 2]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 16, 17, 'None', [16, 17]
+            _result_digraph, 16, 17, "None", [16, 17]
         )
         _result_digraph = add_edge_with_attributes(
-            _result_digraph, 16, 18, 'None', [16, 18]
+            _result_digraph, 16, 18, "None", [16, 18]
         )
         _result_digraph.graph["crs"] = "EPSG:4326"
 
@@ -251,10 +262,10 @@ def add_edge_with_attributes(graph_to_shape: Graph | DiGraph, edge_u: int | floa
         return SnkitToNxNetworkConverter(snkit_network=snkit_network).convert()
 
     def test_simplify_graph(
-        self,
-        network_simplification_with_attribute_exclusion: NetworkSimplificationWithAttributeExclusion,
-        nx_digraph_factory: Callable[[], nx.MultiDiGraph],
-        expected_result_graph_fixture: nx.MultiDiGraph,
+            self,
+            network_simplification_with_attribute_exclusion: NetworkSimplificationWithAttributeExclusion,
+            nx_digraph_factory: Callable[[], nx.MultiDiGraph],
+            expected_result_graph_fixture: nx.MultiDiGraph,
     ):
         network_simplification_with_attribute_exclusion.nx_graph = nx_digraph_factory()
         network_simplification_with_attribute_exclusion.attributes_to_exclude = ["a"]

From ca3bdacd8065453827cb936ac594a279dfe3c916 Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Mon, 16 Sep 2024 10:07:41 +0200
Subject: [PATCH 31/33] chore: reformatting

---
 .../test_network_graph_simplificator.py       | 46 +++++++++----------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index b36e24be9..226536af6 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -25,11 +25,11 @@
 
 
 def _detailed_edge_comparison(
-        graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
+    graph1: nx.MultiDiGraph | nx.MultiGraph, graph2: nx.MultiDiGraph | nx.MultiGraph
 ) -> bool:
     def dicts_comparison(
-            graph_a: nx.MultiDiGraph | nx.MultiGraph,
-            graph_b: nx.MultiDiGraph | nx.MultiGraph,
+        graph_a: nx.MultiDiGraph | nx.MultiGraph,
+        graph_b: nx.MultiDiGraph | nx.MultiGraph,
     ) -> bool:
         for u, v, k, data1 in graph_a.edges(keys=True, data=True):
             geom1 = data1["geometry"]
@@ -64,7 +64,7 @@ def dicts_comparison(
 class TestNetworkGraphSimplificator:
     @pytest.fixture(name="network_graph_simplificator_factory")
     def _get_network_graph_simplificator(
-            self,
+        self,
     ) -> Iterator[Callable[[], NetworkGraphSimplificator]]:
         def get_network_graph_simplificator() -> NetworkGraphSimplificator:
             return NetworkGraphSimplificator(
@@ -74,8 +74,8 @@ def get_network_graph_simplificator() -> NetworkGraphSimplificator:
         yield get_network_graph_simplificator
 
     def test_validate_fixture_init(
-            self,
-            network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
+        self,
+        network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
     ):
         # 1. Define test data.
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -91,9 +91,9 @@ def _get_multigraph_fixture(self) -> Iterator[nx.MultiGraph]:
         yield _graph
 
     def test__graph_create_unique_ids_with_missing_id_data(
-            self,
-            network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
-            multigraph_fixture: nx.MultiGraph,
+        self,
+        network_graph_simplificator_factory: Callable[[], NetworkGraphSimplificator],
+        multigraph_fixture: nx.MultiGraph,
     ):
         # 1. Define test data
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -111,9 +111,9 @@ def test__graph_create_unique_ids_with_missing_id_data(
         assert all(_new_id_name in _keys for _keys in _dicts_keys)
 
     def test__graph_create_unique_ids_with_existing_id(
-            self,
-            network_graph_simplificator_factory: NetworkGraphSimplificator,
-            multigraph_fixture: nx.MultiGraph,
+        self,
+        network_graph_simplificator_factory: NetworkGraphSimplificator,
+        multigraph_fixture: nx.MultiGraph,
     ):
         # 1. Define test data
         _network_graph_simplificator = network_graph_simplificator_factory()
@@ -132,7 +132,7 @@ def test__graph_create_unique_ids_with_existing_id(
 class TestNetworkSimplificationWithAttributeExclusion:
     @pytest.fixture(name="network_simplification_with_attribute_exclusion")
     def _get_network_simplification_with_attribute_exclusion(
-            self,
+        self,
     ) -> Iterator[NetworkSimplificationWithAttributeExclusion]:
         yield NetworkSimplificationWithAttributeExclusion(
             nx_graph=None, attributes_to_exclude=[]
@@ -178,14 +178,14 @@ def create_nx_multidigraph():
 
     @pytest.fixture(name="expected_result_graph_fixture")
     def _get_expected_result_graph_fixture(
-            self, nx_digraph_factory: nx.MultiDiGraph
+        self, nx_digraph_factory: nx.MultiDiGraph
     ) -> nx.MultiGraph:
         def add_edge_with_attributes(
-                graph_to_shape: Graph | DiGraph,
-                edge_u: int | float,
-                edge_v: int | float,
-                a_value: str,
-                edge_node_ids: list,
+            graph_to_shape: Graph | DiGraph,
+            edge_u: int | float,
+            edge_v: int | float,
+            a_value: str,
+            edge_node_ids: list,
         ) -> Graph | DiGraph:
             # Create a copy of the input graph
             shaped_graph = graph_to_shape.copy()
@@ -262,10 +262,10 @@ def add_edge_with_attributes(
         return SnkitToNxNetworkConverter(snkit_network=snkit_network).convert()
 
     def test_simplify_graph(
-            self,
-            network_simplification_with_attribute_exclusion: NetworkSimplificationWithAttributeExclusion,
-            nx_digraph_factory: Callable[[], nx.MultiDiGraph],
-            expected_result_graph_fixture: nx.MultiDiGraph,
+        self,
+        network_simplification_with_attribute_exclusion: NetworkSimplificationWithAttributeExclusion,
+        nx_digraph_factory: Callable[[], nx.MultiDiGraph],
+        expected_result_graph_fixture: nx.MultiDiGraph,
     ):
         network_simplification_with_attribute_exclusion.nx_graph = nx_digraph_factory()
         network_simplification_with_attribute_exclusion.attributes_to_exclude = ["a"]

From 2308cd8c5b597c1dab16fb3ae278e3999d4ff25f Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Mon, 16 Sep 2024 10:11:52 +0200
Subject: [PATCH 32/33] chore: attribute to exclude renamed

---
 .../test_network_graph_simplificator.py       | 50 ++++++++++---------
 1 file changed, 26 insertions(+), 24 deletions(-)

diff --git a/tests/network/network_simplification/test_network_graph_simplificator.py b/tests/network/network_simplification/test_network_graph_simplificator.py
index 226536af6..474352e56 100644
--- a/tests/network/network_simplification/test_network_graph_simplificator.py
+++ b/tests/network/network_simplification/test_network_graph_simplificator.py
@@ -146,27 +146,27 @@ def create_nx_multidigraph():
                 [(i, {"x": i, "y": i * 10}) for i in range(1, 19)]
             )
 
-            _nx_digraph.add_edge(1, 2, a="None")
-            _nx_digraph.add_edge(2, 1, a="None")
-            _nx_digraph.add_edge(2, 3, a="None")
-            _nx_digraph.add_edge(3, 4, a="None")
-            _nx_digraph.add_edge(4, 5, a="yes")
-            _nx_digraph.add_edge(5, 6, a="yes")
-            _nx_digraph.add_edge(6, 7, a="yes")
-            _nx_digraph.add_edge(7, 8, a="None")
-            _nx_digraph.add_edge(8, 9, a="None")
-            _nx_digraph.add_edge(8, 12, a="None")
-            _nx_digraph.add_edge(8, 13, a="yes")
-            _nx_digraph.add_edge(9, 10, a="None")
-            _nx_digraph.add_edge(10, 11, a="None")
-            _nx_digraph.add_edge(11, 12, a="yes")
-            _nx_digraph.add_edge(13, 14, a="yes")
-            _nx_digraph.add_edge(14, 15, a="yes")
-            _nx_digraph.add_edge(15, 11, a="yes")
-            _nx_digraph.add_edge(1, 16, a="None")
-            _nx_digraph.add_edge(16, 1, a="None")
-            _nx_digraph.add_edge(16, 17, a="None")
-            _nx_digraph.add_edge(16, 18, a="None")
+            _nx_digraph.add_edge(1, 2, bridge="None")
+            _nx_digraph.add_edge(2, 1, bridge="None")
+            _nx_digraph.add_edge(2, 3, bridge="None")
+            _nx_digraph.add_edge(3, 4, bridge="None")
+            _nx_digraph.add_edge(4, 5, bridge="yes")
+            _nx_digraph.add_edge(5, 6, bridge="yes")
+            _nx_digraph.add_edge(6, 7, bridge="yes")
+            _nx_digraph.add_edge(7, 8, bridge="None")
+            _nx_digraph.add_edge(8, 9, bridge="None")
+            _nx_digraph.add_edge(8, 12, bridge="None")
+            _nx_digraph.add_edge(8, 13, bridge="yes")
+            _nx_digraph.add_edge(9, 10, bridge="None")
+            _nx_digraph.add_edge(10, 11, bridge="None")
+            _nx_digraph.add_edge(11, 12, bridge="yes")
+            _nx_digraph.add_edge(13, 14, bridge="yes")
+            _nx_digraph.add_edge(14, 15, bridge="yes")
+            _nx_digraph.add_edge(15, 11, bridge="yes")
+            _nx_digraph.add_edge(1, 16, bridge="None")
+            _nx_digraph.add_edge(16, 1, bridge="None")
+            _nx_digraph.add_edge(16, 17, bridge="None")
+            _nx_digraph.add_edge(16, 18, bridge="None")
 
             _nx_digraph = add_missing_geoms_graph(_nx_digraph, "geometry")
             _nx_digraph.graph["crs"] = "EPSG:4326"
@@ -184,7 +184,7 @@ def add_edge_with_attributes(
             graph_to_shape: Graph | DiGraph,
             edge_u: int | float,
             edge_v: int | float,
-            a_value: str,
+            value_to_exclude: str,
             edge_node_ids: list,
         ) -> Graph | DiGraph:
             # Create a copy of the input graph
@@ -198,7 +198,7 @@ def add_edge_with_attributes(
             shaped_graph.add_edge(
                 edge_u,
                 edge_v,
-                a=a_value,
+                bridge=value_to_exclude,
                 from_node=edge_u,
                 to_node=edge_v,
                 geometry=LineString(geometry_list),
@@ -268,7 +268,9 @@ def test_simplify_graph(
         expected_result_graph_fixture: nx.MultiDiGraph,
     ):
         network_simplification_with_attribute_exclusion.nx_graph = nx_digraph_factory()
-        network_simplification_with_attribute_exclusion.attributes_to_exclude = ["a"]
+        network_simplification_with_attribute_exclusion.attributes_to_exclude = [
+            "bridge"
+        ]
 
         _graph_simple = network_simplification_with_attribute_exclusion.simplify_graph()
 

From b63d5ad33f7917cb4238ad002d9cfadc4acdd9ea Mon Sep 17 00:00:00 2001
From: asgarpou <sahand.asgarpour@deltares.nl>
Date: Mon, 16 Sep 2024 11:34:46 +0200
Subject: [PATCH 33/33] chore: network.ini updated for optimal route with
 hazard example

---
 examples/data/optimal_routes_analysis_with_hazard/network.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/data/optimal_routes_analysis_with_hazard/network.ini b/examples/data/optimal_routes_analysis_with_hazard/network.ini
index 6e62313f4..a9446eeff 100644
--- a/examples/data/optimal_routes_analysis_with_hazard/network.ini
+++ b/examples/data/optimal_routes_analysis_with_hazard/network.ini
@@ -32,6 +32,6 @@ hazard_crs = EPSG:32736
 [cleanup]
 snapping_threshold = None
 segmentation_length = None
-merge_lines = True
+merge_lines = False
 merge_on_id = False
 cut_at_intersections = False
\ No newline at end of file