Error extracting vertices from lines

[ccastelblanco]

Hello,

I would like to have your help please with an error I am experiencing when I try to use the function extract_xyz. I am trying to get the coordinates of some fault data to drape the lines over a DEM. After passing the faults gdf and the dem raster to the function extract_xyz like "gg.vector.extract_xyz(gdf=faults, dem=dem, reset_index=False)", the following error appears:

`---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\indexes\base.py:3653, in Index.get_loc(self, key)
3652 try:
-> 3653 return self._engine.get_loc(casted_key)
3654 except KeyError as err:

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas_libs\index.pyx:147, in pandas._libs.index.IndexEngine.get_loc()

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas_libs\index.pyx:176, in pandas._libs.index.IndexEngine.get_loc()

File pandas_libs\hashtable_class_helper.pxi:2606, in pandas._libs.hashtable.Int64HashTable.get_item()

File pandas_libs\hashtable_class_helper.pxi:2630, in pandas._libs.hashtable.Int64HashTable.get_item()

KeyError: 1

The above exception was the direct cause of the following exception:

KeyError Traceback (most recent call last)
Cell In[63], line 2
1 faults = gdf_f_clip[gdf_f_clip.is_valid]
----> 2 faults_xyz = gg.vector.extract_xyz(gdf=faults, dem=dem, reset_index=False)

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\gemgis\vector.py:1940, in extract_xyz(gdf, dem, minz, maxz, extent, reset_index, drop_index, drop_id, drop_points, drop_level0, drop_level1, target_crs, bbox, remove_total_bounds, threshold_bounds)
1938 # Extracting xyz
1939 if isinstance(dem, rasterio.io.DatasetReader):
-> 1940 gdf = extract_xyz_rasterio(gdf=gdf,
1941 dem=dem,
1942 reset_index=False,
1943 drop_id=False,
1944 drop_index=False,
1945 drop_level0=False,
1946 drop_level1=False,
1947 drop_points=False,
1948 remove_total_bounds=remove_total_bounds,
1949 threshold_bounds=threshold_bounds)
1951 elif isinstance(dem, np.ndarray):
1952 gdf = extract_xyz_array(gdf=gdf,
1953 dem=dem,
1954 extent=extent,
(...)
1961 remove_total_bounds=remove_total_bounds,
1962 threshold_bounds=threshold_bounds)

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\gemgis\vector.py:1298, in extract_xyz_rasterio(gdf, dem, minz, maxz, reset_index, drop_index, drop_id, drop_points, drop_level0, drop_level1, target_crs, bbox, remove_total_bounds, threshold_bounds)
1296 # Extracting X and Y coordinates if they are not present in the GeoDataFrame
1297 if not {'X', 'Y'}.issubset(gdf.columns):
-> 1298 gdf = extract_xy(gdf=gdf,
1299 reset_index=False,
1300 drop_index=False,
1301 drop_id=False,
1302 drop_points=False,
1303 drop_level0=False,
1304 drop_level1=False,
1305 overwrite_xy=False,
1306 target_crs=None,
1307 bbox=None,
1308 remove_total_bounds=remove_total_bounds,
1309 threshold_bounds=threshold_bounds)
1311 # If the CRS of the gdf and the dem are identical, just extract the heights using the rasterio sample method
1312 # NB: for points outside the bounds of the raster, nodata values will be returned
1313 if gdf.crs == dem.crs:

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\gemgis\vector.py:744, in extract_xy(gdf, reset_index, drop_index, drop_id, drop_points, drop_level0, drop_level1, overwrite_xy, target_crs, bbox, remove_total_bounds, threshold_bounds)
742 # Extracting x,y coordinates from line vector data
743 if all(gdf.geom_type == "LineString"):
--> 744 gdf = extract_xy_linestrings(gdf=gdf,
745 reset_index=False,
746 drop_id=False,
747 drop_index=False,
748 drop_points=False,
749 overwrite_xy=overwrite_xy,
750 target_crs=crs,
751 bbox=bbox)
753 # Extracting x,y coordinates from point vector data
754 elif all(gdf.geom_type == "Point"):

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\gemgis\vector.py:480, in extract_xy_linestrings(gdf, reset_index, drop_id, drop_index, drop_points, drop_level0, drop_level1, overwrite_xy, target_crs, bbox)
477 gdf['points'] = [shapely.get_coordinates(geometry=gdf.geometry[i],
478 include_z=True) for i in range(len(gdf))]
479 else:
--> 480 gdf['points'] = [shapely.get_coordinates(geometry=gdf.geometry[i],
481 include_z=False) for i in range(len(gdf))]
483 # Creating DataFrame from exploded columns
484 df = pd.DataFrame(data=gdf).explode('points')

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\gemgis\vector.py:480, in (.0)
477 gdf['points'] = [shapely.get_coordinates(geometry=gdf.geometry[i],
478 include_z=True) for i in range(len(gdf))]
479 else:
--> 480 gdf['points'] = [shapely.get_coordinates(geometry=gdf.geometry[i],
481 include_z=False) for i in range(len(gdf))]
483 # Creating DataFrame from exploded columns
484 df = pd.DataFrame(data=gdf).explode('points')

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\geopandas\geoseries.py:629, in GeoSeries.getitem(self, key)
628 def getitem(self, key):
--> 629 return self._wrapped_pandas_method("getitem", key)

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\geopandas\geoseries.py:622, in GeoSeries._wrapped_pandas_method(self, mtd, *args, **kwargs)
620 def _wrapped_pandas_method(self, mtd, *args, **kwargs):
621 """Wrap a generic pandas method to ensure it returns a GeoSeries"""
--> 622 val = getattr(super(), mtd)(*args, **kwargs)
623 if type(val) == Series:
624 val.class = GeoSeries

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\series.py:1007, in Series.getitem(self, key)
1004 return self._values[key]
1006 elif key_is_scalar:
-> 1007 return self._get_value(key)
1009 if is_hashable(key):
1010 # Otherwise index.get_value will raise InvalidIndexError
1011 try:
1012 # For labels that don't resolve as scalars like tuples and frozensets

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\series.py:1116, in Series._get_value(self, label, takeable)
1113 return self._values[label]
1115 # Similar to Index.get_value, but we do not fall back to positional
-> 1116 loc = self.index.get_loc(label)
1118 if is_integer(loc):
1119 return self._values[loc]

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\indexes\multi.py:2812, in MultiIndex.get_loc(self, key)
2809 return mask
2811 if not isinstance(key, tuple):
-> 2812 loc = self._get_level_indexer(key, level=0)
2813 return _maybe_to_slice(loc)
2815 keylen = len(key)

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\indexes\multi.py:3160, in MultiIndex._get_level_indexer(self, key, level, indexer)
3157 return slice(i, j, step)
3159 else:
-> 3160 idx = self._get_loc_single_level_index(level_index, key)
3162 if level > 0 or self._lexsort_depth == 0:
3163 # Desired level is not sorted
3164 if isinstance(idx, slice):
3165 # test_get_loc_partial_timestamp_multiindex

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\indexes\multi.py:2752, in MultiIndex._get_loc_single_level_index(self, level_index, key)
2750 return -1
2751 else:
-> 2752 return level_index.get_loc(key)

File c:\Users\carli\anaconda3\envs\gemgis\lib\site-packages\pandas\core\indexes\base.py:3655, in Index.get_loc(self, key)
3653 return self._engine.get_loc(casted_key)
3654 except KeyError as err:
-> 3655 raise KeyError(key) from err
3656 except TypeError:
3657 # If we have a listlike key, _check_indexing_error will raise
3658 # InvalidIndexError. Otherwise we fall through and re-raise
3659 # the TypeError.
3660 self._check_indexing_error(key)

KeyError: 1`

Additionally, I tried to run the related cell in the example "42_draping_linestrings_over_dem_in_pyvista.ipynb" but an error results as well.

I appreciate your kind help to fix this.

Kind regards,

Carlos

[AlexanderJuestel]

Hello @ccastelblanco,

Would it be possible for you to provide the data for us? Then I can check directly where the error is :)

Cheers
Alex

[ccastelblanco]

Thank you! Yes, sure. Here I attach the files:

test_files.zip

I appreciate your help!

[AlexanderJuestel]

Hey @ccastelblanco,

I think the error was that you also have MultiLineStrings in your data. That is why GemGIS could not handle it. We currently support only GeoDataFrames/Shape Files with one geometry type. A solution that worked for me now is the following. Here, the MultiLineStrings are exploded into single LineStrings and the index was reset.

faults = faults.explode().reset_index(drop=True)
faults_xyz = gg.vector.extract_xyz(faults, dem)

Let me know if that worked. I will also convert your issue to a discussion :)

[AlexanderJuestel]

@ccastelblanco I think I tracked down the line of code that is causing the issue. However, it would be too much of a workaround to post it here. Are you okay with the solution above for now? Then I would fix things in the code and it would be available in the next version!

[AlexanderJuestel]

A fix for your issue was implemented in a0a81d3 and will be released with version 1.1 of GemGIS :)

[AlexanderJuestel]

I also fixed tutorial 42 that you were using and fixed an error while extracting coordinates :)

[ccastelblanco]

Thank you very much! Yes, finally it works.

I appreciate your time helping me with this.

Regards,

[AlexanderJuestel]

No worries, problems of others only make our package better! So, I hope to have you back here soon!