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Refactor sorter #233

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Merged
merged 7 commits into from
Sep 17, 2025
Merged

Refactor sorter #233

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8394557
refactor sorter
noellehmcheng Sep 10, 2025
5d04aae
fix sorter abstract class sort method to include optional parameters
noellehmcheng Sep 12, 2025
b83252a
refactor calculate_stratigraphic_order in project class
noellehmcheng Sep 12, 2025
b5767ef
style: style fixes by ruff and autoformatting by black
noellehmcheng Sep 12, 2025
a5c2728
add libjpeg-turbo installation to yml file
noellehmcheng Sep 12, 2025
8fe398a
Merge branch 'noelle/sorter' of https://github.com/Loop3D/map2loop in…
noellehmcheng Sep 12, 2025
c1984e1
fix dtm in SorterObservationProjections
noellehmcheng Sep 15, 2025
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6 changes: 3 additions & 3 deletions .github/workflows/linting_and_testing.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,23 +53,23 @@ jobs:
if: ${{ matrix.os == 'windows-latest' && (matrix.python-version == '3.9' || matrix.python-version == '3.10') }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge "gdal=3.4.3" python=${{ matrix.python-version }} -y
conda run -n test conda install -c loop3d -c conda-forge "gdal=3.4.3" python=${{ matrix.python-version }} libjpeg-turbo -y
conda run -n test conda install -c loop3d -c conda-forge --file dependencies.txt python=${{ matrix.python-version }} -y
conda run -n test conda install pytest python=${{ matrix.python-version }} -y

- name: Install dependencies for windows python 3.11
if: ${{ matrix.os == 'windows-latest' && matrix.python-version == '3.11' }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge gdal "netcdf4=*=nompi_py311*" python=${{ matrix.python-version }} -y
conda run -n test conda install -c loop3d -c conda-forge gdal "netcdf4=*=nompi_py311*" python=${{ matrix.python-version }} libjpeg-turbo -y
conda run -n test conda install -c loop3d -c conda-forge --file dependencies.txt python=${{ matrix.python-version }} -y
conda run -n test conda install pytest python=${{ matrix.python-version }} -y

- name: Install dependencies for other environments
if: ${{ !(matrix.os == 'windows-latest' && (matrix.python-version == '3.9' || matrix.python-version == '3.10' || matrix.python-version == '3.11')) }}
run: |
conda run -n test conda info
conda run -n test conda install -c loop3d -c conda-forge python=${{ matrix.python-version }} gdal pytest --file dependencies.txt -y
conda run -n test conda install -c loop3d -c conda-forge python=${{ matrix.python-version }} gdal pytest libjpeg-turbo --file dependencies.txt -y

- name: Install map2loop
run: |
Expand Down
10 changes: 7 additions & 3 deletions map2loop/project.py
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Original file line number Diff line number Diff line change
Expand Up @@ -569,7 +569,9 @@ def calculate_stratigraphic_order(self, take_best=False):
self.stratigraphic_column.stratigraphicUnits,
self.topology.get_unit_unit_relationships(),
self.contact_extractor.contacts,
self.map_data,
self.map_data.get_map_data(Datatype.GEOLOGY),
self.map_data.get_map_data(Datatype.STRUCTURE),
self.map_data.get_map_data(Datatype.DTM),
)
for sorter in sorters
]
Expand Down Expand Up @@ -601,7 +603,9 @@ def calculate_stratigraphic_order(self, take_best=False):
self.stratigraphic_column.stratigraphicUnits,
self.topology.get_unit_unit_relationships(),
self.contact_extractor.contacts,
self.map_data,
self.map_data.get_map_data(Datatype.GEOLOGY),
self.map_data.get_map_data(Datatype.STRUCTURE),
self.map_data.get_map_data(Datatype.DTM),
)

@beartype.beartype
Expand Down Expand Up @@ -1165,4 +1169,4 @@ def save_geotiff_raster(
target_ds.SetProjection(geol.crs.to_string())
target_ds = None
source_layer = None
source_ds = None
source_ds = None
58 changes: 37 additions & 21 deletions map2loop/sorter.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,11 @@
import pandas
import numpy as np
import math
from .mapdata import MapData
from typing import Union
from osgeo import gdal
import geopandas

from map2loop.utils import value_from_raster
from .logging import getLogger

logger = getLogger(__name__)
Expand Down Expand Up @@ -41,7 +43,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame = None,
structure_data: geopandas.GeoDataFrame = None,
dtm_data: gdal.Dataset = None,
) -> list:
"""
Execute sorter method (abstract method)
Expand All @@ -50,7 +54,9 @@ def sort(
units (pandas.DataFrame): the data frame to sort (columns must contain ["layerId", "name", "minAge", "maxAge", "group"])
units_relationships (pandas.DataFrame): the relationships between units (columns must contain ["Index1", "Unitname1", "Index2", "Unitname2"])
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available
geology_data (geopandas.GeoDataFrame): the geology data
structure_data (geopandas.GeoDataFrame): the structure data
dtm_data (ggdal.Dataset): the dtm data

Returns:
list: sorted list of unit names
Expand All @@ -75,7 +81,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame = None,
structure_data: geopandas.GeoDataFrame = None,
dtm_data: gdal.Dataset = None,
) -> list:
"""
Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm.
Expand All @@ -84,7 +92,6 @@ def sort(
units (pandas.DataFrame): the data frame to sort
units_relationships (pandas.DataFrame): the relationships between units
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available

Returns:
list: the sorted unit names
Expand Down Expand Up @@ -140,7 +147,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame = None,
structure_data: geopandas.GeoDataFrame = None,
dtm_data: gdal.Dataset = None,
) -> list:
"""
Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm.
Expand All @@ -150,7 +159,6 @@ def sort(
units_relationships (pandas.DataFrame): the relationships between units
stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available

Returns:
list: the sorted unit names
Expand Down Expand Up @@ -192,7 +200,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame = None,
structure_data: geopandas.GeoDataFrame = None,
dtm_data: gdal.Dataset = None,
) -> list:
"""
Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm.
Expand All @@ -202,7 +212,6 @@ def sort(
units_relationships (pandas.DataFrame): the relationships between units
stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available

Returns:
list: the sorted unit names
Expand Down Expand Up @@ -280,7 +289,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame = None,
structure_data: geopandas.GeoDataFrame = None,
dtm_data: gdal.Dataset = None,
) -> list:
"""
Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm.
Expand All @@ -290,7 +301,6 @@ def sort(
units_relationships (pandas.DataFrame): the relationships between units
stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available

Returns:
list: the sorted unit names
Expand Down Expand Up @@ -362,7 +372,9 @@ def sort(
units: pandas.DataFrame,
unit_relationships: pandas.DataFrame,
contacts: pandas.DataFrame,
map_data: MapData,
geology_data: geopandas.GeoDataFrame,
structure_data: geopandas.GeoDataFrame,
dtm_data: gdal.Dataset
) -> list:
"""
Execute sorter method takes unit data, relationships and a hint and returns the sorted unit names based on this algorithm.
Expand All @@ -372,19 +384,25 @@ def sort(
units_relationships (pandas.DataFrame): the relationships between units
stratigraphic_order_hint (list): a list of unit names to use as a hint to sorting the units
contacts (pandas.DataFrame): unit contacts with length of the contacts in metres
map_data (map2loop.MapData): a catchall so that access to all map data is available
geology_data (geopandas.GeoDataFrame): the geology data
structure_data (geopandas.GeoDataFrame): the structure data
dtm_data (ggdal.Dataset): the dtm data

Returns:
list: the sorted unit names
"""
import networkx as nx
import networkx.algorithms.approximation as nx_app
from shapely.geometry import LineString, Point
from map2loop.m2l_enums import Datatype

geol = map_data.get_map_data(Datatype.GEOLOGY).copy()
geol = geol.drop(geol.index[np.logical_or(geol["INTRUSIVE"], geol["SILL"])])
orientations = map_data.get_map_data(Datatype.STRUCTURE).copy()
geol = geology_data.copy()
if "INTRUSIVE" in geol.columns:
geol = geol.drop(geol.index[geol["INTRUSIVE"]])
if "SILL" in geol.columns:
geol = geol.drop(geol.index[geol["SILL"]])
orientations = structure_data.copy()
inv_geotransform = gdal.InvGeoTransform(dtm_data.GetGeoTransform())
dtm_array = np.array(dtm_data.GetRasterBand(1).ReadAsArray().T)

# Create a map of maps to store younger/older observations
ordered_unit_observations = []
Expand Down Expand Up @@ -434,11 +452,9 @@ def sort(
continue

# Get heights for intersection point and start of ray
height = map_data.get_value_from_raster(Datatype.DTM, start.x, start.y)
height = value_from_raster(inv_geotransform, dtm_array, start.x, start.y)
first_intersect_point = Point(start.x, start.y, height)
height = map_data.get_value_from_raster(
Datatype.DTM, second_intersect_point.x, second_intersect_point.y
)
height = value_from_raster(inv_geotransform, dtm_array, second_intersect_point.x, second_intersect_point.y)
second_intersect_point = Point(second_intersect_point.x, start.y, height)

# Check vertical difference between points and compare to projected dip angle
Expand Down
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