Point In Face #1056
Point In Face #1056
Conversation
|
@ philipc2 do you think this should be an internal function or exposed to the user? |
ASV BenchmarkingBenchmark Comparison ResultsBenchmarks that have improved:
Benchmarks that have stayed the same:
|
aaronzedwick
added
run-benchmark
uxarray/grid/grid.py
Outdated
| # Get the face's edges for the whole subset | ||
| face_edge_cartesian = _get_cartesian_face_edge_nodes( | ||
| subset.face_node_connectivity.values, | ||
| subset.n_face, | ||
| subset.n_max_face_nodes, | ||
| subset.node_x.values, | ||
| subset.node_y.values, | ||
| subset.node_z.values, | ||
| ) |
There was a problem hiding this comment.
This is very expensive to re-compute each time we call this function. Consider adding an internal property or storing this in Grid._ds like we do with our other methods.
There was a problem hiding this comment.
I can do that, but it is a new subset each time the operation is run. So won't it be recomputed anyway? It should only be a face or a few at max for each subset.
There was a problem hiding this comment.
A more efficient approach would be to store it in the original Grid, where it can be computed once, and then once we subset, it should return a Grid with the face_edge_nodes_xyx appropriately indexed.
Though, if it is only a few faces at most, the perfromance may be negligible, but we need to consider the cases where we may be running millions of point in polygon queries for higher-resolution grids.
There was a problem hiding this comment.
Oh, okay yeah that would work. I didn't realize it would keep it through the subset operation.
There was a problem hiding this comment.
The subset actually keeps the entire array for the whole grid. I can still make it work, that way, but that is why the tests where failing.
There was a problem hiding this comment.
So the subset actually keeps the entire array for the whole grid. I can still make it work, that way, but that is why the tests where failing.
Yeah, we should always ensure that the subset never contains the entire array for any variable.
benchmarks/mpas_ocean.py
Outdated
| class PointInPolygon(GridBenchmark): | ||
| def time_whole_grid(self, resolution): | ||
| point_xyz = np.array([self.uxgrid.face_x[0].values, self.uxgrid.face_y[0].values, self.uxgrid.face_z[0].values]) | ||
|
|
||
| self.uxgrid.get_faces_containing_point(point_xyz=point_xyz) |
There was a problem hiding this comment.
From the GH Actions report, it appears that a single Point in Face query is taking approximately 27.0±0.1ms
Ideally, we want to get this number significantly down.
There was a problem hiding this comment.
Did some digging:
Please include the following in a custom setup function:
_ = uxds.uxgrid.face_edge_connectivity
We don't want this to be included in the timing. I believe much of the 27ms is attributed to that.
This is for a 30km Grid
There was a problem hiding this comment.
Also, consider including a single sample point query in the setup, since there is also some overhead with the KD tree construction.
There was a problem hiding this comment.
This is the performance I get for a 30km grid after doing the things mentioned above. pretty good for 30km grids
Only issue, is that it doesn't find any faces.
Here is my sample code I used.
import uxarray as ux
import numpy as np
import cProfile
profiler = cProfile.Profile()
grid_path = "/Users/philipc/PycharmProjects/uxarray/unstructured-grid-viz-cookbook/meshfiles/x1.655362.grid.nc"
data_path = "/Users/philipc/PycharmProjects/uxarray/unstructured-grid-viz-cookbook/meshfiles/x1.655362.data.nc"
uxds = ux.open_dataset(grid_path, data_path)
uxds.uxgrid.normalize_cartesian_coordinates()
_ = uxds.uxgrid.face_edge_connectivity
point = np.array([0.0, 0.0, 1.0])
res = uxds.uxgrid.get_faces_containing_point(point)
profiler.enable()
res = uxds.uxgrid.get_faces_containing_point(point)
profiler.disable()
profiler.dump_stats('pface.prof')
print(res)Can do snakeviz pface.prof to view the profiler.
There was a problem hiding this comment.
Thanks for looking into this for me! I am trying to implement these changes now. In terms of it not finding any faces, does the mesh have holes in it? There may not be a face at the pole possibly?
There was a problem hiding this comment.
The grid is a global MPAS atmosphere grid with no holes.
There was a problem hiding this comment.
I may have been on an older version of the code. Just ran it again after pulling and it works. A single face is detected. Going to run a few more tests.
There was a problem hiding this comment.
Is it working locally for you? It does for me, but the CI is failing. Not sure why.
There was a problem hiding this comment.
It seems like it is working for the poles at least on my end. Haven't tested other points
aaronzedwick
added
run-benchmark
aaronzedwick
added
run-benchmark
|
Try to print array shape and check why is it assesing this? works on my local also, it must be something with dependency or library versions. |
uxarray/grid/grid.py
Outdated
| @@ -2415,3 +2443,26 @@ def get_faces_at_constant_longitude(self, lon: float): | |||
|
|
|||
| faces = constant_lon_intersections_face_bounds(lon, self.face_bounds_lon.values) | |||
| return faces | |||
|
|
|||
| def get_faces_containing_point(self, point_xyz): | |||
There was a problem hiding this comment.
We should change point_xyz to point, which can be either cartesian or spherical. Many times the user will want to query a spherical point, which we can convert to x, y, z.
Closes #905
Overview
Expected Usage
PR Checklist
General
Testing
Documentation
_) and have been added todocs/internal_api/index.rstdocs/user_api/index.rst