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zacsimile wants to merge 2 commits into from
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Add metadata to Octree and TriangleMesh and associated recipes #1284

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6bf774c
Add metadata to octree and trianglemesh and associated recipes
zacsimile Sep 22, 2022
15eb7d8
Fixed mdh calls. Saving doesn't work
zacsimile Sep 24, 2022
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8 changes: 7 additions & 1 deletion PYME/experimental/_octree.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@ cimport numpy as np
import numpy as np
cimport cython

from PYME.IO.MetaDataHandler import DictMDHandler

#size to initialize the storage to
INITIAL_NODES = 1000
NODE_DTYPE = [('depth', 'i4'), ('n_children', 'i4'), ('children', '8i4'),('parent', 'i4'), ('nPoints', 'i4'), ('centre', '3f4'), ('centroid', '3f4'),('point_idx', 'i4')]
Expand Down Expand Up @@ -101,6 +103,7 @@ cdef class Octree:
cdef node_d * _cnodes
cdef object _octant_offsets
cdef object _octant_sign
cdef public object mdh

cdef np.float32_t[50] _scale

Expand Down Expand Up @@ -132,11 +135,14 @@ cdef class Octree:

self._octant_sign = np.array([[2*(n&1) - 1, (n&2) -1, (n&4)/2 -1] for n in range(8)])

self.mdh = DictMDHandler()
self.mdh['Octree.BoundingBox'] = self._bounds
self.mdh['Octree.MaxDepth'] = self._maxdepth
self.mdh['Octree.SamplesPerNode'] = self._samples_per_node

#precalculate scaling factors for locating the centre of the next box down.
for n in range(50):
self._scale[n] = 1.0/(2.0**(n + 1))


def truncate_at_n_points(self, n_points=5):
out = Octree(self._bounds, self._maxdepth, samples_per_node=n_points)
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2 changes: 2 additions & 0 deletions PYME/experimental/_triangle_mesh.pxd
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Expand Up @@ -108,6 +108,8 @@ cdef class TriangleMesh(TrianglesBase):
cdef object _K
cdef public object smooth_curvature

cdef public object mdh

cdef _set_chalfedges(self, np.ndarray)#halfedge_t[:])
cdef _set_cfaces(self, np.ndarray)#face_d[:])
cdef _set_cvertices(self, np.ndarray)#vertex_d[:])
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7 changes: 7 additions & 0 deletions PYME/experimental/_triangle_mesh.pyx
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Expand Up @@ -9,6 +9,7 @@ from cpython.mem cimport PyMem_Malloc, PyMem_Realloc, PyMem_Free
import copy

from PYME.experimental import triangle_mesh_utils
from PYME.IO.MetaDataHandler import DictMDHandler

DEF MAX_VERTEX_COUNT = 2**31

Expand Down Expand Up @@ -255,6 +256,12 @@ cdef class TriangleMesh(TrianglesBase):

self._components_valid = 0

# Set up metadata
self.mdh = DictMDHandler()
self.mdh['TriangleMesh.Manifold'] = self.manifold
self.mdh['TriangleMesh.BoundingBox'] = self.bbox
self.mdh['TriangleMesh.SmoothCurvature'] = self.smooth_curvature

# Set fix_boundary, etc.
for key, value in kwargs.items():
setattr(self, key, value)
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2 changes: 2 additions & 0 deletions PYME/recipes/pointcloud.py
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Expand Up @@ -27,6 +27,8 @@ def execute(self, namespace):

ot = gen_octree_from_points(inp, min_pixel_size=self.minimum_pixel_size, max_depth=self.max_depth, samples_per_node=self.samples_per_node)

ot.mdh['Octree.MinimumPixelSize'] = self.minimum_pixel_size

namespace[self.output_octree] = ot


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6 changes: 6 additions & 0 deletions PYME/recipes/surface_fitting.py
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Expand Up @@ -168,6 +168,12 @@ def execute(self, namespace):
if self.cull_inner_surfaces:
surf.remove_inner_surfaces()

surf.mdh['DualMarchingCubes.ThresholdDensity'] = self.threshold_density
surf.mdh['DualMarchingCubes.NPointsMin'] = self.n_points_min
surf.mdh['DualMarchingCubes.Repair'] = self.repair
surf.mdh['DualMarchingCubes.Remesh'] = self.remesh
surf.mdh['DualMarchingCubes.CullInnerSurfaces'] = self.cull_inner_surfaces

namespace[self.output] = surf

@register_module('Isosurface')
Expand Down