From 527de6c339e56ead036ab5ed5d94d06d77673ae6 Mon Sep 17 00:00:00 2001
From: RoyThomsonMonash <roy.thomson@monash.edu>
Date: Thu, 25 Jan 2024 10:04:20 +1100
Subject: [PATCH] fix: Typo in intrusion flag, ignoring intrusions for contact
 calculations, remove errant sorter from take_best option

---
 map2loop/mapdata.py | 5 ++++-
 map2loop/project.py | 2 +-
 map2loop/sorter.py  | 4 +++-
 3 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/map2loop/mapdata.py b/map2loop/mapdata.py
index b90b170f..48d3b0c7 100644
--- a/map2loop/mapdata.py
+++ b/map2loop/mapdata.py
@@ -719,7 +719,7 @@ def parse_geology_map(self) -> tuple:
             geology["INTRUSIVE"] = self.raw_data[Datatype.GEOLOGY][config["rocktype_column"]].astype(str).str.contains(config["intrusive_text"])
             geology["ROCKTYPE1"] = self.raw_data[Datatype.GEOLOGY][config["rocktype_column"]].astype(str)
         else:
-            geology["INSTRUSIVE"] = False
+            geology["INTRUSIVE"] = False
             geology["ROCKTYPE1"] = ""
 
         if config["alt_rocktype_column"] in self.raw_data[Datatype.GEOLOGY]:
@@ -1213,6 +1213,9 @@ def extract_all_contacts(self, save_contacts=True):
         """
         geology = self.get_map_data(Datatype.GEOLOGY).copy()
         geology = geology.dissolve(by="UNITNAME", as_index=False)
+        # Remove intrusions
+        geology = geology[geology["INTRUSIVE"]==False]
+        geology = geology[geology["SILL"]==False]
         # Remove faults from contact geomety
         if self.get_map_data(Datatype.FAULT) is not None:
             faults = self.get_map_data(Datatype.FAULT).copy()
diff --git a/map2loop/project.py b/map2loop/project.py
index a3fe4390..0a24dd32 100644
--- a/map2loop/project.py
+++ b/map2loop/project.py
@@ -348,7 +348,7 @@ def calculate_stratigraphic_order(self, take_best=False):
         Use unit relationships, unit ages and the sorter to create a stratigraphic column
         """
         if take_best:
-            sorters = [SorterUseHint(), SorterAgeBased(), SorterAlpha(), SorterUseNetworkX(), SorterMaximiseContacts(), SorterObservationProjections()]
+            sorters = [SorterUseHint(), SorterAgeBased(), SorterAlpha(), SorterUseNetworkX()]
             columns = [sorter.sort(self.stratigraphic_column.stratigraphicUnits,
                                    self.map2model.get_unit_unit_relationships(),
                                    self.map2model.get_sorted_units(),
diff --git a/map2loop/sorter.py b/map2loop/sorter.py
index 63f72f03..3c30da69 100644
--- a/map2loop/sorter.py
+++ b/map2loop/sorter.py
@@ -205,7 +205,7 @@ def sort(self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, st
         while graph.number_of_nodes() > 0:
             if cnode is None:
                 df = pandas.DataFrame(columns=["unit", "num_neighbours"])
-                df["unit"] = units
+                df["unit"] = list(graph.nodes)
                 df["num_neighbours"] = df.apply(lambda row: len(list(graph.neighbors(row["unit"]))), axis=1)
                 df.sort_values(by=["num_neighbours"], inplace=True)
                 df.reset_index(inplace=True, drop=True)
@@ -320,6 +320,8 @@ def sort(self, units: pandas.DataFrame, unit_relationships: pandas.DataFrame, st
             return stratigraphic_order_hint
 
         geol = map_data.get_map_data(Datatype.GEOLOGY).copy()
+        geol = geol[geol["INTRUSIVE"]==False]
+        geol = geol[geol["SILL"]==False]
         orientations = map_data.get_map_data(Datatype.STRUCTURE).copy()
 
         verbose = False