Repository: nialov/fractopo (language: python)

Issue:
Tracemap validation cannot handle shapefiles with z coordinates
Validation (`Validation(...).run_validation()`) fails with `TypeError: within_bounds() takes 6 positional arguments but 7 were given` if the tracemap shapefiles read by geopandas contain z coordinates.

I worked around this by removing the z coordinate prior to validation using this code:

```
from shapely.geometry import Polygon, MultiPolygon, LineString

class_lookup = dict(Polygon=Polygon, MultiPolygon=MultiPolygon, LineString=LineString)


def remove_z_coordinates(geometries):
    """
    :param geometries: Shapely geometry iterable
    :return: a list of Shapely geometries without z coordinates
    """
    return [shapely.wkb.loads(shapely.wkb.dumps(geometry, output_dimension=2)) for geometry in geometries]


trace_data.geometry = remove_z_coordinates(trace_data.geometry)
```

In case something similar is your preferred fix.

Thanks for developing a great tool!

Edit:  Simpler solution from one of the comments [here](https://gist.github.com/rmania/8c88377a5c902dfbc134795a7af538d8)
Tracemap validation cannot handle shapefiles with z coordinates
Validation (`Validation(...).run_validation()`) fails with `TypeError: within_bounds() takes 6 positional arguments but 7 were given` if the tracemap shapefiles read by geopandas contain z coordinates.

I worked around this by removing the z coordinate prior to validation using this code:

```
from shapely.geometry import Polygon, MultiPolygon, LineString

class_lookup = dict(Polygon=Polygon, MultiPolygon=MultiPolygon, LineString=LineString)


def remove_z_coordinates(geometries):
    """
    :param geometries: Shapely geometry iterable
    :return: a list of Shapely geometries without z coordinates
    """
    return [shapely.wkb.loads(shapely.wkb.dumps(geometry, output_dimension=2)) for geometry in geometries]


trace_data.geometry = remove_z_coordinates(trace_data.geometry)
```

In case something similar is your preferred fix.

Thanks for developing a great tool!

Edit:  Simpler solution from one of the comments [here](https://gist.github.com/rmania/8c88377a5c902dfbc134795a7af538d8)
Tracemap validation cannot handle shapefiles with z coordinates
Validation (`Validation(...).run_validation()`) fails with `TypeError: within_bounds() takes 6 positional arguments but 7 were given` if the tracemap shapefiles read by geopandas contain z coordinates.

I worked around this by removing the z coordinate prior to validation using this code:

```
from shapely.geometry import Polygon, MultiPolygon, LineString

class_lookup = dict(Polygon=Polygon, MultiPolygon=MultiPolygon, LineString=LineString)


def remove_z_coordinates(geometries):
    """
    :param geometries: Shapely geometry iterable
    :return: a list of Shapely geometries without z coordinates
    """
    return [shapely.wkb.loads(shapely.wkb.dumps(geometry, output_dimension=2)) for geometry in geometries]


trace_data.geometry = remove_z_coordinates(trace_data.geometry)
```

In case something similar is your preferred fix.

Thanks for developing a great tool!

Edit:  Simpler solution from one of the comments [here](https://gist.github.com/rmania/8c88377a5c902dfbc134795a7af538d8)


Discussion / hints:
Thank you a lot for the extensive issue report! I probably have not ever tested geometries with z-coordinates in `fractopo` so the validation functionality might not be the only part where the issue might arise! I will fix the issue shortly.

If you have any additional problems do not hesitate to create more issues, they are very helpful for me to iron out user problems that I have not thought of.
Thank you a lot for the extensive issue report! I probably have not ever tested geometries with z-coordinates in `fractopo` so the validation functionality might not be the only part where the issue might arise! I will fix the issue shortly.

If you have any additional problems do not hesitate to create more issues, they are very helpful for me to iron out user problems that I have not thought of.
Thank you a lot for the extensive issue report! I probably have not ever tested geometries with z-coordinates in `fractopo` so the validation functionality might not be the only part where the issue might arise! I will fix the issue shortly.

If you have any additional problems do not hesitate to create more issues, they are very helpful for me to iron out user problems that I have not thought of.

Fix patch:
diff --git a/docs_src/index.rst b/docs_src/index.rst
index b46b9f2f..3476780d 100644
--- a/docs_src/index.rst
+++ b/docs_src/index.rst
@@ -520,6 +520,7 @@ Copyright © 2020-2023, Nikolas Ovaskainen.
 
    validation/basics
    validation/errors
+   misc
 
 .. toctree::
    :maxdepth: 1
diff --git a/docs_src/misc.rst b/docs_src/misc.rst
new file mode 100644
index 00000000..675dab9e
--- /dev/null
+++ b/docs_src/misc.rst
@@ -0,0 +1,38 @@
+Miscellanous/FAQ
+================
+
+Geometries with Z-coordinates
+-----------------------------
+
+Currently ``fractopo`` has only partly been tested with geometries that
+have Z-coordinates (e.g. ``LineString([(0, 0, 0), (1, 1, 1)])``. Any
+issues you believe might be related to Z-coordinates should be reported
+on *GitHub*. To test for such issues using your data, try removing the
+Z-coordinates with e.g. the following code:
+
+   .. code:: python
+
+      from shapely.geometry import Polygon, MultiPolygon, LineString
+
+
+      def remove_z_coordinates(geometries):
+          """
+          :param geometries: Shapely geometry iterable
+          :return: a list of Shapely geometries without z coordinates
+          """
+          return [
+              shapely.wkb.loads(shapely.wkb.dumps(geometry, output_dimension=2))
+              for geometry in geometries
+          ]
+
+
+      trace_data.geometry = remove_z_coordinates(trace_data.geometry)
+
+Thanks to *Siyh* for the issue report and above code example
+(https://github.com/nialov/fractopo/issues/21).
+
+Furthermore, some validation and analysis remove Z-coordinates from
+geometric results. Specifically, use of ``Validation`` will remove
+Z-coordinates to avoid unexpected behaviour. Use of ``Network`` will by
+default remove z-coordinates but this can be disabled (See ``Network``
+input arguments)..
diff --git a/fractopo/analysis/network.py b/fractopo/analysis/network.py
index 75a1c1a1..de65e64b 100644
--- a/fractopo/analysis/network.py
+++ b/fractopo/analysis/network.py
@@ -5,6 +5,7 @@
 from dataclasses import dataclass, field
 from functools import wraps
 from pathlib import Path
+from textwrap import dedent
 from typing import Callable, Dict, List, Optional, Tuple, Union
 
 import geopandas as gpd
@@ -53,12 +54,14 @@
     assign_branch_and_node_colors,
     bool_arrays_sum,
     calc_circle_radius,
+    check_for_z_coordinates,
     crop_to_target_areas,
     determine_boundary_intersecting_lines,
     focus_plot_to_bounds,
     numpy_to_python_type,
     pygeos_spatial_index,
     raise_determination_error,
+    remove_z_coordinates_from_geodata,
     sanitize_name,
     save_fig,
     spatial_index_intersection,
@@ -182,7 +185,10 @@ class Network:
 
     censoring_area: gpd.GeoDataFrame = field(default_factory=lambda: gpd.GeoDataFrame())
 
+    # Misc
+    # ==================
     cache_results: bool = True
+    remove_z_coordinates_from_inputs: bool = True
 
     # Private caching attributes
     # ==========================
@@ -243,6 +249,32 @@ def __post_init__(self):
         # Copy geodataframes instead of using pointers
         # Traces
         self.trace_gdf = self.trace_gdf.copy()
+        has_z_coordinates = check_for_z_coordinates(geodata=self.trace_gdf)
+        if has_z_coordinates:
+            log.warning(
+                dedent(
+                    """
+                Traces inputted into Network contain Z-coordinates.
+                They might not be correct in output geometries
+                and might cause unexpected errors.
+                """
+                ).strip()
+            )
+            if self.remove_z_coordinates_from_inputs:
+                log.warning(
+                    dedent(
+                        """
+                    Z-coordinates will be removed from the input traces and
+                    subsuquently from all outputs because Network input
+                    remove_z_coordinates_from_geodata is True.
+                    """
+                    ).strip()
+                )
+                trace_gdf_without_z_coords = remove_z_coordinates_from_geodata(
+                    geodata=self.trace_gdf
+                )
+                assert isinstance(trace_gdf_without_z_coords, gpd.GeoDataFrame)
+                self.trace_gdf = trace_gdf_without_z_coords
         # Area
         self.area_gdf = self.area_gdf.copy()
         # Branches
diff --git a/fractopo/branches_and_nodes.py b/fractopo/branches_and_nodes.py
index efe4aaa2..c839e111 100644
--- a/fractopo/branches_and_nodes.py
+++ b/fractopo/branches_and_nodes.py
@@ -40,6 +40,7 @@
     II_branch,
     X_node,
     Y_node,
+    check_for_z_coordinates,
     crop_to_target_areas,
     geom_bounds,
     get_trace_coord_points,
@@ -48,6 +49,7 @@
     numpy_to_python_type,
     point_to_point_unit_vector,
     pygeos_spatial_index,
+    remove_z_coordinates_from_geodata,
     spatial_index_intersection,
 )
 
@@ -291,7 +293,9 @@ def insert_point_to_linestring(
     t_coords = list(trace.coords)
     if not insert:
         t_coords.pop(idx)
-    t_coords.insert(idx, tuple(*point.coords))
+    t_coords.insert(idx, (point.x, point.y)) if not point.has_z else t_coords.insert(
+        idx, (point.x, point.y, point.z)
+    )
     # Closest points might not actually be the points which in between the
     # point is added. Have to use project and interpolate (?)
     # print(t_coords)
@@ -750,7 +754,7 @@ def filter_non_unique_traces(
     traces_set = set()
     idxs_to_keep = []
     for idx, geom in enumerate(traces.geometry.values):
-        assert isinstance(geom, LineString)
+        assert isinstance(geom, LineString), geom
 
         # Use a less strict coordinate precision when finding duplicates
         geom_wkt = dumps(geom, rounding_precision=int(-math.log10(snap_threshold)))
@@ -933,6 +937,15 @@ def branches_and_nodes(
         ),
     )
     traces_geosrs: gpd.GeoSeries = traces.geometry
+    if check_for_z_coordinates(geodata=traces_geosrs):
+        log.info(
+            "Removing z-coordinates from trace data before branch and node determination."
+        )
+        traces_without_z_coords = remove_z_coordinates_from_geodata(
+            geodata=traces_geosrs
+        )
+        assert isinstance(traces_without_z_coords, gpd.GeoSeries)
+        traces_geosrs = traces_without_z_coords
 
     # Filter out traces that are not unique by wkt
     # unary_union will fail to take them into account any way
@@ -951,7 +964,9 @@ def branches_and_nodes(
 
     # Collect into lists
     traces_list = [
-        trace for trace in traces.geometry.values if isinstance(trace, LineString)
+        trace
+        for trace in traces_geosrs.geometry.values
+        if isinstance(trace, LineString)
     ]
 
     # Snapping occurs multiple times due to possible side effects of each snap
diff --git a/fractopo/general.py b/fractopo/general.py
index 0bc9c538..2be7afc8 100644
--- a/fractopo/general.py
+++ b/fractopo/general.py
@@ -27,7 +27,7 @@
 from matplotlib import patheffects as path_effects
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
-from shapely import prepared
+from shapely import prepared, wkb
 from shapely.affinity import scale
 from shapely.geometry import (
     LineString,
@@ -1735,8 +1735,8 @@ def point_to_point_unit_vector(point: Point, other_point: Point) -> np.ndarray:
     >>> point_to_point_unit_vector(point, other_point)
     array([0.70710678, 0.70710678])
     """
-    x1, y1 = tuple(*point.coords)
-    x2, y2 = tuple(*other_point.coords)
+    x1, y1 = point.x, point.y
+    x2, y2 = other_point.x, other_point.y
     if any(np.isnan([x1, y1, x2, y2])):
         raise ValueError(
             f"Expected no nan values in point_to_point_unit_vector: {x1, y1, x2, y2}"
@@ -2030,6 +2030,45 @@ def write_geodataframe(geodataframe: gpd.GeoDataFrame, name: str, results_dir: P
         log.error(error_base.format(name, "ESRI Shapefile"), exc_info=True)
 
 
+def check_for_z_coordinates(geodata: Union[gpd.GeoDataFrame, gpd.GeoSeries]) -> bool:
+    """
+    Check if geopandas data contains Z-coordinates.
+    """
+    return any(geom.has_z for geom in geodata.geometry.values if hasattr(geom, "has_z"))
+
+
+def remove_z_coordinates_from_geodata(
+    geodata: Union[gpd.GeoDataFrame, gpd.GeoSeries]
+) -> Union[gpd.GeoDataFrame, gpd.GeoSeries]:
+    """
+    Remove Z-coordinates from geometries in geopandasgeodata.
+    """
+    geodata_without_z = geodata.copy()
+    geodata_without_z_geometries = geodata_without_z.geometry.apply(
+        remove_z_coordinates
+    )
+    if isinstance(geodata_without_z, gpd.GeoDataFrame):
+        geodata_without_z["geometry"] = geodata_without_z_geometries
+    else:
+        geodata_without_z = geodata_without_z_geometries
+
+    assert isinstance(geodata_without_z, (gpd.GeoDataFrame, gpd.GeoSeries))
+    return geodata_without_z
+
+
+def remove_z_coordinates(geometry: Union[BaseGeometry, BaseMultipartGeometry]) -> Any:
+    """
+    Remove z-coordinates from a geometry.
+
+    A ``shapely`` geometry should be provided. Output will always be the same
+    type of geometry with the z-coordinates removed.
+
+    :param geometry: Shapely geometry
+    :return: Shapely geometry with the same geometry type
+    """
+    return wkb.loads(wkb.dumps(geometry, output_dimension=2))
+
+
 def sanitize_name(name: str) -> str:
     """
     Return only alphanumeric parts of name string.
diff --git a/fractopo/tval/trace_validation.py b/fractopo/tval/trace_validation.py
index 25c2aac8..9a6d0f6a 100644
--- a/fractopo/tval/trace_validation.py
+++ b/fractopo/tval/trace_validation.py
@@ -7,13 +7,19 @@
 import logging
 from dataclasses import dataclass
 from itertools import chain
+from textwrap import dedent
 from typing import Any, List, Optional, Set, Tuple
 
 import geopandas as gpd
 from geopandas.sindex import PyGEOSSTRTreeIndex
 from shapely.geometry import LineString, MultiLineString, Point
 
-from fractopo.general import determine_general_nodes, is_empty_area
+from fractopo.general import (
+    check_for_z_coordinates,
+    determine_general_nodes,
+    is_empty_area,
+    remove_z_coordinates_from_geodata,
+)
 from fractopo.tval import trace_validators
 from fractopo.tval.trace_validation_utils import determine_trace_candidates
 from fractopo.tval.trace_validators import (
@@ -74,9 +80,17 @@ def __post_init__(self):
             else self.ERROR_COLUMN[0 : len(self.ERROR_COLUMN)]
         )
 
-        # Validate trace and area inputs
-        # for geom in self.area.geometry.values:
-        #     if not isinstance(geom, Polygon)
+        if check_for_z_coordinates(geodata=self.traces):
+            log.warning(
+                dedent(
+                    """
+                Traces inputted into Validation contain Z-coordinates. They
+                will be removed from the input traces and subsuquently from all
+                outputs.
+                """
+                ).strip()
+            )
+            self.traces = remove_z_coordinates_from_geodata(geodata=self.traces)
 
     def set_general_nodes(self):
         """
diff --git a/fractopo/tval/trace_validation_utils.py b/fractopo/tval/trace_validation_utils.py
index f0d83856..f69a288e 100644
--- a/fractopo/tval/trace_validation_utils.py
+++ b/fractopo/tval/trace_validation_utils.py
@@ -81,8 +81,16 @@ def segment_within_buffer(
             segmentize_linestring(ls, snap_threshold * overlap_detection_multiplier)
         )
     for start, end in all_segments:
-        if within_bounds(*start, min_x, min_y, max_x, max_y) and within_bounds(
-            *end, min_x, min_y, max_x, max_y
+        if within_bounds(
+            x=start[0], y=start[1], min_x=min_x, min_y=min_y, max_x=max_x, max_y=max_y
+        ) and within_bounds(
+            x=end[0],
+            y=end[1],
+            min_x=min_x,
+            min_y=min_y,
+            max_x=max_x,
+            max_y=max_y
+            # *end, min_x, min_y, max_x, max_y
         ):
             ls = LineString([start, end])
             if ls.length > snap_threshold * overlap_detection_multiplier and ls.within(
diff --git a/noxfile.py b/noxfile.py
index 1c1302fd..b5373178 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -252,10 +252,7 @@ def _api_docs(session):
 def _docs(session, auto_build: bool):
     """
     Make documentation.
-
-    Installation mimics readthedocs install.
     """
-
     auto_build_args = (
         [
             f"--ignore=**/{DOCS_AUTO_EXAMPLES_PATH.name}/**",
@@ -313,6 +310,7 @@ def auto_docs(session):
     """
     Make documentation and start sphinx-autobuild service.
     """
+    session.install("-r", str(DOCS_REQUIREMENTS_PATH))
     _docs(session=session, auto_build=True)
 
 
diff --git a/result b/result
deleted file mode 120000
index 9a1bd416..00000000
--- a/result
+++ /dev/null
@@ -1,1 +0,0 @@
-/nix/store/kwmdrlla71xgfnhpvnh9kqfvwbrb77yd-python3.10-fractopo-0.5.2
\ No newline at end of file


Test patch:
diff --git a/tests/__init__.py b/tests/__init__.py
index 907812b0..52e7a2a8 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -337,72 +337,6 @@ def make_invalid_target_areas():
 )
 
 
-# def random_data_column(iterable):
-#     """
-#     Make random data column contents.
-#     """
-#     return ["aaa" for _ in iterable]
-
-
-# geoms are all LineStrings and no errors
-
-
-# def valid_gdf_get():
-#     """
-#     Get valid gdf.
-#     """
-#     return gpd.GeoDataFrame(
-#         {
-#             GEOMETRY_COLUMN: valid_traces,
-#             ERROR_COLUMN: valid_error_srs,
-#             "random_col": random_data_column(valid_traces),
-#             "random_col2": random_data_column(valid_traces),
-#             "random_col3": random_data_column(valid_traces),
-#             "random_col4": random_data_column(valid_traces),
-#         }
-#     )
-
-
-# def invalid_gdf_get():
-#     """
-#     Get invalid gdf.
-#     """
-#     return gpd.GeoDataFrame(
-#         {
-#             GEOMETRY_COLUMN: invalid_traces,
-#             ERROR_COLUMN: invalid_error_srs,
-#             "random_col": random_data_column(invalid_traces),
-#         }
-#     )
-
-
-# def invalid_gdf_null_get():
-#     """
-#     Get gdf with None and empty geometries.
-#     """
-#     return gpd.GeoDataFrame(
-#         {
-#             GEOMETRY_COLUMN: [None, LineString()],
-#             ERROR_COLUMN: [[], []],
-#             "random_col": random_data_column(range(2)),
-#         }
-#     )
-
-
-# def valid_area_gdf_get():
-#     """
-#     Get a valid area gdf.
-#     """
-#     return gpd.GeoDataFrame({GEOMETRY_COLUMN: valid_areas_geoseries})
-
-
-# def invalid_area_gdf_get():
-#     """
-#     Get an invalid area gdf.
-#     """
-#     return gpd.GeoDataFrame({GEOMETRY_COLUMN: invalid_areas_geoseries})
-
-
 faulty_error_srs = pd.Series([[] for _ in valid_traces.geometry.values])
 faulty_error_srs[0] = np.nan
 faulty_error_srs[1] = "this cannot be transformed to list?"
@@ -410,35 +344,6 @@ def make_invalid_target_areas():
 faulty_error_srs[5] = 5.12315235
 
 
-# def valid_gdf_with_faulty_error_col_get():
-#     """
-#     Get valid gdf with faulty error column.
-#     """
-#     return gpd.GeoDataFrame(
-#         {
-#             GEOMETRY_COLUMN: valid_traces,
-#             ERROR_COLUMN: faulty_error_srs,
-#             "random_col": random_data_column(valid_traces),
-#         }
-#     )
-
-
-# def iterate_validators():
-#     """
-#     Iterate over validators.
-#     """
-#     for validator in (
-#         GeomNullValidator,
-#         GeomTypeValidator,
-#         MultiJunctionValidator,
-#         VNodeValidator,
-#         MultipleCrosscutValidator,
-#         UnderlappingSnapValidator,
-#         TargetAreaSnapValidator,
-#     ):
-#         yield validator
-
-
 nice_integer_coordinates = integers(-10, 10)
 nice_float = floats(
     allow_nan=False, allow_infinity=False, min_value=-1e5, max_value=1e5
@@ -497,20 +402,6 @@ def get_nice_traces():
     return nice_traces.copy()
 
 
-# def get_traces_geosrs():
-#     """
-#     Get traces GeoSeries.
-#     """
-#     return traces_geosrs.copy()
-
-
-# def get_areas_geosrs():
-#     """
-#     Get areas GeoSeries.
-#     """
-#     return areas_geosrs.copy()
-
-
 def get_geosrs_identicals():
     """
     Get GeoSeries with identical geometries.
@@ -597,7 +488,15 @@ def get_geosrs_identicals():
 kb7_trace_50_path = Path("tests/sample_data/KB7/KB7_tulkinta_50.geojson")
 kb7_area_path = Path("tests/sample_data/KB7/KB7_tulkinta_alue.geojson")
 
-kb7_traces = read_geofile(kb7_trace_50_path)
+kb7_traces_50 = read_geofile(kb7_trace_50_path)
+kb7_traces_50_z = kb7_traces_50.copy()
+kb7_traces_50_z.update(
+    {
+        "geometry": kb7_traces_50.geometry.apply(
+            lambda geom: LineString([(*coord, 10.0) for coord in geom.coords])
+        )
+    }
+)
 kb7_area = read_geofile(kb7_area_path)
 
 test_tracevalidate_params = [
@@ -826,12 +725,19 @@ def get_geosrs_identicals():
 intersected_3_times = LineString([Point(-3, -4), Point(-3, -1)])
 test_validation_params = [
     (
-        kb7_traces,  # traces
+        kb7_traces_50,  # traces
         kb7_area,  # area
         "kb7",  # name
         True,  # auto_fix
         [SharpCornerValidator.ERROR],  # assume_errors
     ),
+    (
+        kb7_traces_50_z,  # traces
+        kb7_area,  # area
+        "kb7_z_coordinates",  # name
+        True,  # auto_fix
+        [SharpCornerValidator.ERROR],  # assume_errors
+    ),
     (
         hastholmen_traces,  # traces
         hastholmen_area,  # area
@@ -933,6 +839,22 @@ def get_geosrs_identicals():
         True,  # auto_fix
         [TargetAreaSnapValidator.ERROR],  # assume_errors
     ),
+    (
+        gpd.GeoDataFrame(
+            geometry=[
+                LineString([(0, 0, 0), (1, 1, 1)]),
+                LineString([(2, 2, 2), (3, 3, 3)]),
+            ]
+        ),  # traces
+        gpd.GeoDataFrame(
+            geometry=[
+                Polygon([(-5, -5), (5, -5), (5, 5), (-5, 5)]),
+            ]
+        ),  # area
+        "traces-with-z-coordinates",  # name
+        True,  # auto_fix
+        [],  # assume_errors
+    ),
 ]
 
 test_determine_v_nodes_params = [
@@ -1093,6 +1015,7 @@ def get_geosrs_identicals():
         0.001,  # snap_threshold
         True,  # circular_target_area
         False,  # try_export_of_data
+        True,  # remove_z_coordinates_from_inputs
     ),
     (
         kb11_traces,  # traces
@@ -1103,6 +1026,7 @@ def get_geosrs_identicals():
         0.001,  # snap_threshold
         False,  # circular_target_area
         False,  # try_export_of_data
+        True,  # remove_z_coordinates_from_inputs
     ),
     (
         kb11_traces.iloc[0:100],  # traces
@@ -1113,6 +1037,7 @@ def get_geosrs_identicals():
         0.001,  # snap_threshold
         False,  # circular_target_area
         True,  # try_export_of_data
+        True,  # remove_z_coordinates_from_inputs
     ),
     (
         v_node_network_error_gdf,  # traces
@@ -1123,6 +1048,29 @@ def get_geosrs_identicals():
         0.001,  # snap_threshold
         False,  # circular_target_area
         False,  # try_export_of_data
+        True,  # remove_z_coordinates_from_inputs
+    ),
+    (
+        kb7_traces_50_z,  # traces
+        kb7_area,  # area
+        "KB7_Z-coords",  # name
+        True,  # determine_branches_nodes
+        True,  # truncate_traces
+        0.001,  # snap_threshold
+        False,  # circular_target_area
+        False,  # try_export_of_data
+        True,  # remove_z_coordinates_from_inputs
+    ),
+    (
+        kb7_traces_50_z,  # traces
+        kb7_area,  # area
+        "KB7_Z-coords",  # name
+        True,  # determine_branches_nodes
+        True,  # truncate_traces
+        0.001,  # snap_threshold
+        False,  # circular_target_area
+        False,  # try_export_of_data
+        False,  # remove_z_coordinates_from_inputs
     ),
 ]
 
@@ -1408,6 +1356,15 @@ def get_geosrs_identicals():
         50,
         False,
     ),
+    (
+        # LineString with z-coordinates
+        LineString([(0, 0, 0), (1, 1, 1)]),
+        MultiLineString([LineString([(0, 0, 0), (1, 1, 1)])]),
+        0.001,
+        1.1,
+        50,
+        True,
+    ),
 ]
 
 test_segmentize_linestring_params = [
@@ -2025,7 +1982,7 @@ def test_multinetwork_plot_multi_length_distribution_slow_params():
     snap_threshold=0.001,
 )
 KB7_NETWORK_PARAMS = dict(
-    trace_gdf=kb7_traces,
+    trace_gdf=kb7_traces_50,
     area_gdf=kb7_area,
     name="kb7",
     circular_target_area=False,
diff --git a/tests/analysis/test_network.py b/tests/analysis/test_network.py
index f457f56b..c35a01e4 100644
--- a/tests/analysis/test_network.py
+++ b/tests/analysis/test_network.py
@@ -69,7 +69,7 @@ def test_azimuth_set_relationships_regression(
     """
     azimuth_set_names: Tuple[str, ...] = ("1", "2", "3")[0 : len(azimuth_set_ranges)]
     relations_df: pd.DataFrame = Network(
-        tests.kb7_traces,  # type: ignore
+        tests.kb7_traces_50,  # type: ignore
         tests.kb7_area,  # type: ignore
         name="kb7",
         determine_branches_nodes=True,
@@ -96,7 +96,7 @@ def test_length_set_relationships_regression(num_regression):
     )
     trace_length_set_names: Tuple[str, ...] = ("a", "b", "c")
     relations_df: pd.DataFrame = Network(
-        tests.kb7_traces,  # type: ignore
+        tests.kb7_traces_50,  # type: ignore
         tests.kb7_area,  # type: ignore
         name="kb7",
         determine_branches_nodes=True,
@@ -121,6 +121,7 @@ def test_length_set_relationships_regression(num_regression):
     snap_threshold,
     circular_target_area,
     try_export_of_data,
+    remove_z_coordinates_from_inputs,
     """,
     tests.test_network_params,
 )
@@ -133,6 +134,7 @@ def test_network(
     snap_threshold,
     circular_target_area,
     try_export_of_data,
+    remove_z_coordinates_from_inputs,
     file_regression,
     data_regression,
     tmp_path,
@@ -154,6 +156,7 @@ def test_network(
         trace_length_set_ranges=((0.1, 1), (1, 2)),
         branch_length_set_ranges=((0.1, 1), (1, 2)),
         circular_target_area=circular_target_area,
+        remove_z_coordinates_from_inputs=remove_z_coordinates_from_inputs,
     )
 
     assert area.shape[0] == len(network.representative_points())
@@ -431,7 +434,7 @@ def test_network_circular_target_area(trace_gdf, area_gdf, name, data_regression
 @pytest.mark.parametrize(
     "trace_gdf,area_gdf,network_name,snap_threshold",
     [
-        (tests.kb7_traces, tests.kb7_area, "kb7", 0.001),
+        (tests.kb7_traces_50, tests.kb7_area, "kb7", 0.001),
         (tests.kb11_traces, tests.kb11_area, "kb11", 0.001),
     ],
 )
diff --git a/tests/analysis/test_network/test_network_traces0_area0_Geta1_1_1000_True_True_0_001_True_False_True_.yml b/tests/analysis/test_network/test_network_traces0_area0_Geta1_1_1000_True_True_0_001_True_False_True_.yml
new file mode 100644
index 00000000..beb10b1b
--- /dev/null
+++ b/tests/analysis/test_network/test_network_traces0_area0_Geta1_1_1000_True_True_0_001_True_False_True_.yml
@@ -0,0 +1,94 @@
+Area: 1953.54
+Areal Frequency B20: 1.11
+Areal Frequency P20: 0.47
+Branch Boundary 0 Intersect Count: 2145
+Branch Boundary 1 Intersect Count: 60
+Branch Boundary 2 Intersect Count: 0
+Branch Max Length: 16.52
+Branch Mean Length: 0.7
+Branch Min Length: 0.02
+C - C: 1174
+C - E: 50
+C - I: 850
+Censoring: .nan
+Connection Frequency: 0.51
+Connections per Branch: 1.49
+Connections per Trace: 2.17
+Dimensionless Intensity B22: 0.54
+Dimensionless Intensity P22: 1.25
+E: 60
+E - E: 0
+Fracture Density (Mauldon): 0.47
+Fracture Intensity (Mauldon): 0.6
+Fracture Intensity B21: 0.78
+Fracture Intensity P21: 0.78
+I: 1102
+I - E: 10
+I - I: 121
+Number of Branches: 2175.0
+Number of Branches (Real): 2205
+Number of Traces: 919.0
+Number of Traces (Real): 949
+Radius: 24.94
+Relative Censoring: .nan
+Trace Boundary 0 Intersect Count: 889
+Trace Boundary 1 Intersect Count: 60
+Trace Boundary 2 Intersect Count: 0
+Trace Max Length: 34.86
+Trace Mean Length: 1.6
+Trace Mean Length (Mauldon): 1.28
+Trace Min Length: 0.08
+X: 260
+Y: 736
+branch exponential Kolmogorov-Smirnov distance D: 0.19
+branch exponential lambda: 0.5
+branch exponential loglikelihood: -174.45
+branch lengths cut off proportion: 0.95
+branch lognormal Kolmogorov-Smirnov distance D: .nan
+branch lognormal loglikelihood: -152.66
+branch lognormal mu: -693.78
+branch lognormal sigma: 18.15
+branch lognormal vs. exponential R: 2.08
+branch lognormal vs. exponential p: 0.04
+branch power_law Kolmogorov-Smirnov distance D: 0.03
+branch power_law alpha: 3.11
+branch power_law cut-off: 2.13
+branch power_law exponent: -2.11
+branch power_law sigma: 0.21
+branch power_law vs. exponential R: 2.08
+branch power_law vs. exponential p: 0.04
+branch power_law vs. lognormal R: -1.87
+branch power_law vs. lognormal p: 0.06
+branch power_law vs. truncated_power_law R: 0.0
+branch power_law vs. truncated_power_law p: 1.0
+branch truncated_power_law Kolmogorov-Smirnov distance D: 0.03
+branch truncated_power_law alpha: 3.11
+branch truncated_power_law exponent: -2.11
+branch truncated_power_law lambda: 0.0
+branch truncated_power_law loglikelihood: -152.69
+trace exponential Kolmogorov-Smirnov distance D: 0.21
+trace exponential lambda: 0.25
+trace exponential loglikelihood: -290.54
+trace lengths cut off proportion: 0.87
+trace lognormal Kolmogorov-Smirnov distance D: 0.03
+trace lognormal loglikelihood: -261.94
+trace lognormal mu: -684.92
+trace lognormal sigma: 19.81
+trace lognormal vs. exponential R: 2.42
+trace lognormal vs. exponential p: 0.02
+trace power_law Kolmogorov-Smirnov distance D: 0.03
+trace power_law alpha: 2.75
+trace power_law cut-off: 3.12
+trace power_law exponent: -1.75
+trace power_law sigma: 0.16
+trace power_law vs. exponential R: 2.42
+trace power_law vs. exponential p: 0.02
+trace power_law vs. lognormal R: 0.15
+trace power_law vs. lognormal p: 0.88
+trace power_law vs. truncated_power_law R: -0.15
+trace power_law vs. truncated_power_law p: 0.9
+trace truncated_power_law Kolmogorov-Smirnov distance D: 0.03
+trace truncated_power_law alpha: 2.74
+trace truncated_power_law exponent: -1.74
+trace truncated_power_law lambda: 0.0
+trace truncated_power_law loglikelihood: -261.93
diff --git a/tests/analysis/test_network/test_network_traces1_area1_KB11_True_True_0_001_False_False_True_.yml b/tests/analysis/test_network/test_network_traces1_area1_KB11_True_True_0_001_False_False_True_.yml
new file mode 100644
index 00000000..a31bdc39
--- /dev/null
+++ b/tests/analysis/test_network/test_network_traces1_area1_KB11_True_True_0_001_False_False_True_.yml
@@ -0,0 +1,94 @@
+Area: 1237.9
+Areal Frequency B20: 1.63
+Areal Frequency P20: 0.53
+Branch Boundary 0 Intersect Count: 2072
+Branch Boundary 1 Intersect Count: 0
+Branch Boundary 2 Intersect Count: 0
+Branch Max Length: 5.72
+Branch Mean Length: 0.78
+Branch Min Length: 0.01
+C - C: 1521
+C - E: 100
+C - I: 410
+Censoring: .nan
+Connection Frequency: 0.88
+Connections per Branch: 1.76
+Connections per Trace: 3.36
+Dimensionless Intensity B22: 0.98
+Dimensionless Intensity P22: 2.79
+E: 114
+E - E: 1
+Fracture Density (Mauldon): .nan
+Fracture Intensity (Mauldon): .nan
+Fracture Intensity B21: 1.26
+Fracture Intensity P21: 1.26
+I: 478
+I - E: 12
+I - I: 28
+Number of Branches: 2015.0
+Number of Branches (Real): 2072
+Number of Traces: 651.0
+Number of Traces (Real): 709
+Radius: .nan
+Relative Censoring: .nan
+Trace Boundary 0 Intersect Count: 709
+Trace Boundary 1 Intersect Count: 0
+Trace Boundary 2 Intersect Count: 0
+Trace Max Length: 33.11
+Trace Mean Length: 2.21
+Trace Mean Length (Mauldon): .nan
+Trace Min Length: 0.0
+X: 270
+Y: 824
+branch exponential Kolmogorov-Smirnov distance D: 0.06
+branch exponential lambda: 1.28
+branch exponential loglikelihood: -79.84
+branch lengths cut off proportion: 0.95
+branch lognormal Kolmogorov-Smirnov distance D: 0.06
+branch lognormal loglikelihood: -80.11
+branch lognormal mu: 0.4
+branch lognormal sigma: 0.49
+branch lognormal vs. exponential R: -1.29
+branch lognormal vs. exponential p: 0.2
+branch power_law Kolmogorov-Smirnov distance D: 0.05
+branch power_law alpha: 4.98
+branch power_law cut-off: 2.46
+branch power_law exponent: -3.98
+branch power_law sigma: 0.39
+branch power_law vs. exponential R: -1.28
+branch power_law vs. exponential p: 0.2
+branch power_law vs. lognormal R: -1.25
+branch power_law vs. lognormal p: 0.21
+branch power_law vs. truncated_power_law R: -1.56
+branch power_law vs. truncated_power_law p: 0.06
+branch truncated_power_law Kolmogorov-Smirnov distance D: 0.05
+branch truncated_power_law alpha: 1.0
+branch truncated_power_law exponent: -0.0
+branch truncated_power_law lambda: 1.02
+branch truncated_power_law loglikelihood: -79.84
+trace exponential Kolmogorov-Smirnov distance D: 0.17
+trace exponential lambda: 0.29
+trace exponential loglikelihood: -188.02
+trace lengths cut off proportion: 0.88
+trace lognormal Kolmogorov-Smirnov distance D: 0.06
+trace lognormal loglikelihood: -181.37
+trace lognormal mu: -24.65
+trace lognormal sigma: 3.41
+trace lognormal vs. exponential R: 1.84
+trace lognormal vs. exponential p: 0.07
+trace power_law Kolmogorov-Smirnov distance D: 0.05
+trace power_law alpha: 3.32
+trace power_law cut-off: 4.82
+trace power_law exponent: -2.32
+trace power_law sigma: 0.25
+trace power_law vs. exponential R: 1.79
+trace power_law vs. exponential p: 0.07
+trace power_law vs. lognormal R: -0.1
+trace power_law vs. lognormal p: 0.92
+trace power_law vs. truncated_power_law R: -0.39
+trace power_law vs. truncated_power_law p: 0.65
+trace truncated_power_law Kolmogorov-Smirnov distance D: 0.06
+trace truncated_power_law alpha: 3.1
+trace truncated_power_law exponent: -2.1
+trace truncated_power_law lambda: 0.02
+trace truncated_power_law loglikelihood: -181.28
diff --git a/tests/analysis/test_network/test_network_traces2_area2_KB11_0_100_True_True_0_001_False_True_True_.txt b/tests/analysis/test_network/test_network_traces2_area2_KB11_0_100_True_True_0_001_False_True_True_.txt
new file mode 100644
index 00000000..9289054d
--- /dev/null
+++ b/tests/analysis/test_network/test_network_traces2_area2_KB11_0_100_True_True_0_001_False_True_True_.txt
@@ -0,0 +1,9971 @@
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new file mode 100644
index 00000000..885073ac
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+branch exponential loglikelihood: -19.55
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+branch lognormal Kolmogorov-Smirnov distance D: 0.36
+branch lognormal loglikelihood: -15.64
+branch lognormal mu: -1942.0
+branch lognormal sigma: 88.84
+branch lognormal vs. exponential R: 0.68
+branch lognormal vs. exponential p: 0.49
+branch power_law Kolmogorov-Smirnov distance D: 0.36
+branch power_law alpha: 1.25
+branch power_law cut-off: 3.98
+branch power_law exponent: -0.25
+branch power_law sigma: 0.17
+branch power_law vs. exponential R: 0.68
+branch power_law vs. exponential p: 0.49
+branch power_law vs. lognormal R: 0.0
+branch power_law vs. lognormal p: 1.0
+branch power_law vs. truncated_power_law R: -0.32
+branch power_law vs. truncated_power_law p: 0.49
+branch truncated_power_law Kolmogorov-Smirnov distance D: 0.4
+branch truncated_power_law alpha: 1.1
+branch truncated_power_law exponent: -0.1
+branch truncated_power_law lambda: 0.0
+branch truncated_power_law loglikelihood: -15.41
+trace exponential Kolmogorov-Smirnov distance D: 0.36
+trace exponential lambda: 0.0
+trace exponential loglikelihood: -19.55
+trace lengths cut off proportion: 0.0
+trace lognormal Kolmogorov-Smirnov distance D: 0.36
+trace lognormal loglikelihood: -15.64
+trace lognormal mu: -1942.0
+trace lognormal sigma: 88.84
+trace lognormal vs. exponential R: 0.68
+trace lognormal vs. exponential p: 0.49
+trace power_law Kolmogorov-Smirnov distance D: 0.36
+trace power_law alpha: 1.25
+trace power_law cut-off: 3.98
+trace power_law exponent: -0.25
+trace power_law sigma: 0.17
+trace power_law vs. exponential R: 0.68
+trace power_law vs. exponential p: 0.49
+trace power_law vs. lognormal R: 0.0
+trace power_law vs. lognormal p: 1.0
+trace power_law vs. truncated_power_law R: -0.32
+trace power_law vs. truncated_power_law p: 0.49
+trace truncated_power_law Kolmogorov-Smirnov distance D: 0.4
+trace truncated_power_law alpha: 1.1
+trace truncated_power_law exponent: -0.1
+trace truncated_power_law lambda: 0.0
+trace truncated_power_law loglikelihood: -15.41
diff --git a/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_.txt b/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_.txt
new file mode 100644
index 00000000..479193be
--- /dev/null
+++ b/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_.txt
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new file mode 100644
index 00000000..4e9adb18
--- /dev/null
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diff --git a/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_True_.txt b/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_True_.txt
new file mode 100644
index 00000000..479193be
--- /dev/null
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diff --git a/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_True_.yml b/tests/analysis/test_network/test_network_traces4_area4_KB7_Z_coords_True_True_0_001_False_False_True_.yml
new file mode 100644
index 00000000..4e9adb18
--- /dev/null
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diff --git a/tests/analysis/test_network/test_network_traces5_area5_KB7_Z_coords_True_True_0_001_False_False_False_.txt b/tests/analysis/test_network/test_network_traces5_area5_KB7_Z_coords_True_True_0_001_False_False_False_.txt
new file mode 100644
index 00000000..479193be
--- /dev/null
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diff --git a/tests/analysis/test_network/test_network_traces5_area5_KB7_Z_coords_True_True_0_001_False_False_False_.yml b/tests/analysis/test_network/test_network_traces5_area5_KB7_Z_coords_True_True_0_001_False_False_False_.yml
new file mode 100644
index 00000000..4e9adb18
--- /dev/null
+++ b/tests/analysis/test_network/test_network_traces5_area5_KB7_Z_coords_True_True_0_001_False_False_False_.yml
@@ -0,0 +1,94 @@
+Area: 534.68
+Areal Frequency B20: 0.16
+Areal Frequency P20: 0.08
+Branch Boundary 0 Intersect Count: 91
+Branch Boundary 1 Intersect Count: 0
+Branch Boundary 2 Intersect Count: 0
+Branch Max Length: 4.11
+Branch Mean Length: 0.76
+Branch Min Length: 0.02
+C - C: 33
+C - E: 8
+C - I: 33
+Censoring: .nan
+Connection Frequency: 0.06
+Connections per Branch: 1.29
+Connections per Trace: 1.57
+Dimensionless Intensity B22: 0.09
+Dimensionless Intensity P22: 0.15
+E: 16
+E - E: 1
+Fracture Density (Mauldon): .nan
+Fracture Intensity (Mauldon): .nan
+Fracture Intensity B21: 0.12
+Fracture Intensity P21: 0.12
+I: 59
+I - E: 6
+I - I: 10
+Number of Branches: 83.0
+Number of Branches (Real): 91
+Number of Traces: 42.0
+Number of Traces (Real): 50
+Radius: .nan
+Relative Censoring: .nan
+Trace Boundary 0 Intersect Count: 50
+Trace Boundary 1 Intersect Count: 0
+Trace Boundary 2 Intersect Count: 0
+Trace Max Length: 5.7
+Trace Mean Length: 1.26
+Trace Mean Length (Mauldon): .nan
+Trace Min Length: 0.06
+X: 8
+Y: 25
+branch exponential Kolmogorov-Smirnov distance D: 0.12
+branch exponential lambda: 1.28
+branch exponential loglikelihood: -30.02
+branch lengths cut off proportion: 0.56
+branch lognormal Kolmogorov-Smirnov distance D: 0.07
+branch lognormal loglikelihood: -29.08
+branch lognormal mu: -0.98
+branch lognormal sigma: 1.05
+branch lognormal vs. exponential R: 0.71
+branch lognormal vs. exponential p: 0.48
+branch power_law Kolmogorov-Smirnov distance D: 0.11
+branch power_law alpha: 2.39
+branch power_law cut-off: 0.53
+branch power_law exponent: -1.39
+branch power_law sigma: 0.22
+branch power_law vs. exponential R: -0.14
+branch power_law vs. exponential p: 0.89
+branch power_law vs. lognormal R: -1.07
+branch power_law vs. lognormal p: 0.28
+branch power_law vs. truncated_power_law R: -1.35
+branch power_law vs. truncated_power_law p: 0.07
+branch truncated_power_law Kolmogorov-Smirnov distance D: 0.07
+branch truncated_power_law alpha: 1.34
+branch truncated_power_law exponent: -0.34
+branch truncated_power_law lambda: 0.52
+branch truncated_power_law loglikelihood: -28.71
+trace exponential Kolmogorov-Smirnov distance D: 0.16
+trace exponential lambda: 0.85
+trace exponential loglikelihood: -41.93
+trace lengths cut off proportion: 0.28
+trace lognormal Kolmogorov-Smirnov distance D: 0.12
+trace lognormal loglikelihood: -39.55
+trace lognormal mu: -1.35
+trace lognormal sigma: 1.42
+trace lognormal vs. exponential R: 1.18
+trace lognormal vs. exponential p: 0.24
+trace power_law Kolmogorov-Smirnov distance D: 0.1
+trace power_law alpha: 2.07
+trace power_law cut-off: 0.48
+trace power_law exponent: -1.07
+trace power_law sigma: 0.18
+trace power_law vs. exponential R: 0.44
+trace power_law vs. exponential p: 0.66
+trace power_law vs. lognormal R: -1.01
+trace power_law vs. lognormal p: 0.31
+trace power_law vs. truncated_power_law R: -1.35
+trace power_law vs. truncated_power_law p: 0.07
+trace truncated_power_law Kolmogorov-Smirnov distance D: 0.12
+trace truncated_power_law alpha: 1.39
+trace truncated_power_law exponent: -0.39
+trace truncated_power_law lambda: 0.24
+trace truncated_power_law loglikelihood: -38.95
diff --git a/tests/test_general.py b/tests/test_general.py
index 328fd81b..1699fdc2 100644
--- a/tests/test_general.py
+++ b/tests/test_general.py
@@ -9,7 +9,7 @@
 import pytest
 from hypothesis import example, given
 from hypothesis.strategies import booleans, floats
-from shapely.geometry import Point, Polygon
+from shapely.geometry import LineString, Point, Polygon
 
 import tests
 from fractopo import general
@@ -179,3 +179,25 @@ def test_determine_valid_intersection_points(intersection_geoms: gpd.GeoSeries,
         )
         assert isinstance(result, list)
         assert all(isinstance(val, Point) for val in result)
+
+
+@pytest.mark.parametrize(
+    "geodata",
+    [
+        gpd.GeoSeries([LineString([(0, 0, 0), (1, 1, 1)])]),
+        gpd.GeoSeries(
+            [
+                LineString([(0, 0, 0), (1, 1, 1)]),
+                LineString([(10, 10, 10), (20, 20, 20)]),
+            ]
+        ),
+        gpd.GeoSeries([LineString([(0, 0), (1, 1)])]),
+    ],
+)
+def test_total_bounds(geodata):
+    """
+    Test total_bounds.
+    """
+    result = general.total_bounds(geodata=geodata)
+    assert isinstance(result, tuple)
+    assert len(result) == 4