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Fix dask TriMesh rasterization #4935

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May 18, 2021
Merged

Fix dask TriMesh rasterization #4935

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1e32913
Fix dask TriMesh rasterization
philippjfr May 18, 2021
55f5164
Add warning
philippjfr May 18, 2021
bf47c35
Add tests
philippjfr May 18, 2021
4dd1986
Fix flakes
philippjfr May 18, 2021
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39 changes: 32 additions & 7 deletions holoviews/operation/datashader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -987,16 +987,42 @@ class trimesh_rasterize(aggregate):
def _precompute(self, element, agg):
from datashader.utils import mesh
if element.vdims and getattr(agg, 'column', None) not in element.nodes.vdims:
simplices = element.dframe([0, 1, 2, 3])
verts = element.nodes.dframe([0, 1])
simplex_dims = [0, 1, 2, 3]
vert_dims = [0, 1]
elif element.nodes.vdims:
simplices = element.dframe([0, 1, 2])
verts = element.nodes.dframe([0, 1, 3])
simplex_dims = [0, 1, 2]
vert_dims = [0, 1, 3]
else:
raise ValueError("Cannot shade TriMesh without value dimension.")
datatypes = [element.interface.datatype, element.nodes.interface.datatype]
if set(datatypes) == {'dask'}:
dims, node_dims = element.dimensions(), element.nodes.dimensions()
simplices = element.data[[dims[sd].name for sd in simplex_dims]]
verts = element.nodes.data[[node_dims[vd].name for vd in vert_dims]]
else:
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if datatypes == 'dask':
if datatypes[0] == 'dask':
p, n = 'simplexes', 'vertices'
else:
p, n = 'vertices', 'simplexes'
self.param.warning(
"TriMesh %s were provided as dask DataFrame but %s "
"were not. Datashader will not use dask to parallelize "
"rasterization unless both are provided as dask "
"DataFrames." % (p, n))
simplices = element.dframe(simplex_dims)
verts = element.nodes.dframe(vert_dims)
for c, dtype in zip(simplices.columns[:3], simplices.dtypes):
if dtype.kind != 'i':
simplices[c] = simplices[c].astype('int')
return {'mesh': mesh(verts, simplices), 'simplices': simplices,
'vertices': verts}
mesh = mesh(verts, simplices)
if hasattr(mesh, 'persist'):
mesh = mesh.persist()
return {
'mesh': mesh,
'simplices': simplices,
'vertices': verts
}

def _precompute_wireframe(self, element, agg):
if hasattr(element, '_wireframe'):
Expand Down Expand Up @@ -1037,7 +1063,6 @@ def _process(self, element, key=None):
precomputed = self._precompute_wireframe(element, agg)
else:
precomputed = self._precompute(element, agg)

bounds = (x_range[0], y_range[0], x_range[1], y_range[1])
params = self._get_agg_params(element, x, y, agg, bounds)

Expand Down
153 changes: 111 additions & 42 deletions holoviews/tests/operation/testdatashader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,11 @@

import numpy as np

from holoviews import (Dimension, Curve, Points, Image, Dataset, RGB, Path,
Graph, TriMesh, QuadMesh, NdOverlay, Contours, Spikes,
Spread, Area, Rectangles, Segments, Polygons)
from holoviews import (
Dimension, Curve, Points, Image, Dataset, RGB, Path, Graph, TriMesh,
QuadMesh, NdOverlay, Contours, Spikes, Spread, Area, Rectangles,
Segments, Polygons, Nodes
)
from holoviews.streams import Tap
from holoviews.element.comparison import ComparisonTestCase
from numpy import nan
Expand Down Expand Up @@ -879,64 +881,127 @@ def setUp(self):
if ds_version <= '0.6.4':
raise SkipTest('Regridding operations require datashader>=0.7.0')

self.simplexes = [(0, 1, 2), (3, 2, 1)]
self.vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
self.simplexes_vdim = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
self.vertices_vdim = [(0., 0., 1), (0., 1., 2), (1., 0, 3), (1, 1, 4)]

def test_rasterize_trimesh_no_vdims(self):
simplices = [(0, 1, 2), (3, 2, 1)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices))
trimesh = TriMesh((self.simplexes, self.vertices))
img = rasterize(trimesh, width=3, height=3, dynamic=False)
image = Image(np.array([[True, True, True], [True, True, True], [True, True, True]]),
bounds=(0, 0, 1, 1), vdims=Dimension('Any', nodata=0))
self.assertEqual(img, image)

def test_rasterize_trimesh_no_vdims_zero_range(self):
simplices = [(0, 1, 2), (3, 2, 1)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices))
trimesh = TriMesh((self.simplexes, self.vertices))
img = rasterize(trimesh, height=2, x_range=(0, 0), dynamic=False)
image = Image(([], [0.25, 0.75], np.zeros((2, 0))),
bounds=(0, 0, 0, 1), xdensity=1, vdims=Dimension('Any', nodata=0))
self.assertEqual(img, image)

def test_rasterize_trimesh_with_vdims_as_wireframe(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices), vdims=['z'])
trimesh = TriMesh((self.simplexes_vdim, self.vertices), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, aggregator='any', interpolation=None, dynamic=False)
image = Image(np.array([[True, True, True], [True, True, True], [True, True, True]]),
bounds=(0, 0, 1, 1), vdims=Dimension('Any', nodata=0))
array = np.array([
[True, True, True],
[True, True, True],
[True, True, True]
])
image = Image(array, bounds=(0, 0, 1, 1), vdims=Dimension('Any', nodata=0))
self.assertEqual(img, image)

def test_rasterize_trimesh(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices), vdims=['z'])
trimesh = TriMesh((self.simplexes_vdim, self.vertices), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, dynamic=False)
image = Image(np.array([[1.5, 1.5, np.NaN], [0.5, 1.5, np.NaN], [np.NaN, np.NaN, np.NaN]]),
bounds=(0, 0, 1, 1))
array = np.array([
[ 1.5, 1.5, np.NaN],
[ 0.5, 1.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_dask_trimesh(self):
simplex_df = pd.DataFrame(self.simplexes_vdim, columns=['v0', 'v1', 'v2', 'z'])
vertex_df = pd.DataFrame(self.vertices, columns=['x', 'y'])

simplex_ddf = dd.from_pandas(simplex_df, npartitions=2)
vertex_ddf = dd.from_pandas(vertex_df, npartitions=2)

tri_nodes = Nodes(vertex_ddf, ['x', 'y', 'index'])
trimesh = TriMesh((simplex_ddf, tri_nodes), vdims=['z'])

ri = rasterize.instance()
img = ri(trimesh, width=3, height=3, dynamic=False, precompute=True)

cache = ri._precomputed
self.assertEqual(len(cache), 1)
self.assertIn(trimesh._plot_id, cache)
self.assertIsInstance(cache[trimesh._plot_id]['mesh'], dd.DataFrame)

array = np.array([
[ 1.5, 1.5, np.NaN],
[ 0.5, 1.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_dask_trimesh_with_node_vdims(self):
simplex_df = pd.DataFrame(self.simplexes, columns=['v0', 'v1', 'v2'])
vertex_df = pd.DataFrame(self.vertices_vdim, columns=['x', 'y', 'z'])

simplex_ddf = dd.from_pandas(simplex_df, npartitions=2)
vertex_ddf = dd.from_pandas(vertex_df, npartitions=2)

tri_nodes = Nodes(vertex_ddf, ['x', 'y', 'index'], ['z'])
trimesh = TriMesh((simplex_ddf, tri_nodes))

ri = rasterize.instance()
img = ri(trimesh, width=3, height=3, dynamic=False, precompute=True)

cache = ri._precomputed
self.assertEqual(len(cache), 1)
self.assertIn(trimesh._plot_id, cache)
self.assertIsInstance(cache[trimesh._plot_id]['mesh'], dd.DataFrame)

array = np.array([
[ 2., 3., np.NaN],
[ 1.5, 2.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_trimesh_node_vdim_precedence(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0., 1), (0., 1., 2), (1., 0, 3), (1, 1, 4)]
trimesh = TriMesh((simplices, Points(vertices, vdims=['node_z'])), vdims=['z'])
nodes = Points(self.vertices_vdim, vdims=['node_z'])
trimesh = TriMesh((self.simplexes_vdim, nodes), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, dynamic=False)
image = Image(np.array([[2., 3., np.NaN], [1.5, 2.5, np.NaN], [np.NaN, np.NaN, np.NaN]]),
bounds=(0, 0, 1, 1), vdims='node_z')

array = np.array([
[ 2., 3., np.NaN],
[ 1.5, 2.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1), vdims='node_z')
self.assertEqual(img, image)

def test_rasterize_trimesh_node_explicit_vdim(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0., 1), (0., 1., 2), (1., 0, 3), (1, 1, 4)]
trimesh = TriMesh((simplices, Points(vertices, vdims=['node_z'])), vdims=['z'])
nodes = Points(self.vertices_vdim, vdims=['node_z'])
trimesh = TriMesh((self.simplexes_vdim, nodes), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, dynamic=False, aggregator=ds.mean('z'))
image = Image(np.array([[1.5, 1.5, np.NaN], [0.5, 1.5, np.NaN], [np.NaN, np.NaN, np.NaN]]),
bounds=(0, 0, 1, 1))

array = np.array([
[ 1.5, 1.5, np.NaN],
[ 0.5, 1.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_trimesh_zero_range(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices), vdims=['z'])
trimesh = TriMesh((self.simplexes_vdim, self.vertices), vdims=['z'])
img = rasterize(trimesh, x_range=(0, 0), height=2, dynamic=False)
image = Image(([], [0.25, 0.75], np.zeros((2, 0))),
bounds=(0, 0, 0, 1), xdensity=1)
Expand All @@ -952,21 +1017,25 @@ def test_rasterize_trimesh_vertex_vdims(self):
self.assertEqual(img, image)

def test_rasterize_trimesh_ds_aggregator(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices), vdims=['z'])
trimesh = TriMesh((self.simplexes_vdim, self.vertices), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, dynamic=False, aggregator=ds.mean('z'))
image = Image(np.array([[1.5, 1.5, np.NaN], [0.5, 1.5, np.NaN], [np.NaN, np.NaN, np.NaN]]),
bounds=(0, 0, 1, 1))
array = np.array([
[ 1.5, 1.5, np.NaN],
[ 0.5, 1.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_trimesh_string_aggregator(self):
simplices = [(0, 1, 2, 0.5), (3, 2, 1, 1.5)]
vertices = [(0., 0.), (0., 1.), (1., 0), (1, 1)]
trimesh = TriMesh((simplices, vertices), vdims=['z'])
trimesh = TriMesh((self.simplexes_vdim, self.vertices), vdims=['z'])
img = rasterize(trimesh, width=3, height=3, dynamic=False, aggregator='mean')
image = Image(np.array([[1.5, 1.5, np.NaN], [0.5, 1.5, np.NaN], [np.NaN, np.NaN, np.NaN]]),
bounds=(0, 0, 1, 1))
array = np.array([
[ 1.5, 1.5, np.NaN],
[ 0.5, 1.5, np.NaN],
[np.NaN, np.NaN, np.NaN]
])
image = Image(array, bounds=(0, 0, 1, 1))
self.assertEqual(img, image)

def test_rasterize_quadmesh(self):
Expand Down