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pd_vtk.py
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pd_vtk.py
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#!python
'''
Copyright 2017 - 2021 Vale
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
https://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
'''
import numpy as np
import pandas as pd
try:
import pyvista as pv
except:
# we use this base class in enviroments that dont support VTK
class pv(object):
class UniformGrid(object):
pass
def read(*argv):
pass
''' GetDataObjectType
PolyData == 0
VTK_STRUCTURED_GRID = 2
VTK_RECTILINEAR_GRID = 3
VTK_UNSTRUCTURED_GRID = 4
UniformGrid == 6
VTK_MULTIBLOCK_DATA_SET = 13
'''
def pv_read(fp):
''' simple import safe pyvista reader '''
if pv is None: return
return pv.read(fp)
def pv_save(meshes, fp, binary=True):
''' simple import safe pyvista writer '''
if pv is None: return
if not isinstance(meshes, list):
meshes.save(fp, binary)
elif len(meshes) == 1:
meshes[0].save(fp, binary)
else:
pv.MultiBlock(meshes).save(fp, binary)
def vtk_cells_to_flat(cells):
r = []
p = 0
while p < len(cells):
n = cells[p]
r.extend(cells[p+1:p+1+n])
p += n + 1
return r
def vtk_cells_to_faces(cells):
faces = vtk_cells_to_flat(cells)
return np.reshape(faces, (len(faces) // 3, 3))
def vtk_flat_to_cells(flat, nodes = None):
#print(flat)
#print(nodes)
if nodes is None:
nodes = pd.Series(np.arange(len(flat)), flat.index)
n = 0
cells = []
for i in flat.index[::-1]:
n += 1
cells.insert(0, nodes[i])
if flat[i] == 0:
cells.insert(0, n)
n = 0
return np.array(cells)
def pd_detect_xyz(df, z = True):
xyz = None
dfcs = set(df.columns)
for s in [['x','y','z'], ['mid_x','mid_y','mid_z'], ['xworld','yworld','zworld'], ['xc','yc','zc']]:
if z == False:
s.pop()
for c in [str.lower, str.upper,str.capitalize]:
cs = list(map(c, s))
if dfcs.issuperset(cs):
xyz = cs
break
else:
continue
# break also the outter loop if the inner loop ended due to a break
break
if xyz is None and z:
return pd_detect_xyz(df, False)
return xyz
def vtk_nf_to_mesh(nodes, faces):
if len(nodes) == 0:
return pv.PolyData()
if len(faces) == 0:
return pv.PolyData(np.array(nodes))
meshfaces = np.hstack(np.concatenate((np.full((len(faces), 1), 3, dtype=np.int_), faces), 1))
return pv.PolyData(np.array(nodes), meshfaces)
def vtk_df_to_mesh(df, xyz = None):
if pv is None: return
if xyz is None:
xyz = pd_detect_xyz(df)
if xyz is None:
print('geometry/xyz information not found')
return None
print("xyz:",','.join(xyz))
if len(xyz) == 2:
xyz.append('z')
if 'z' not in df:
if '0' in df:
# geotiff first/only spectral channel
print('using first channel as Z value')
df['z'] = df['0']
else:
print('using 0 as Z value')
df['z'] = 0
#pdata = df[xyz].dropna(0, 'all')
#pdata.fillna(0, inplace=True)
pdata = df[xyz]
if 'n' in df and df['n'].max() > 0:
if 'node' in df:
cells = vtk_flat_to_cells(df['n'], df['node'])
nodes = df['node'].drop_duplicates().sort_values()
pdata = pdata.loc[nodes.index]
else:
cells = vtk_flat_to_cells(df['n'])
mesh = pv.PolyData(pdata.values.astype(np.float), cells)
else:
mesh = pv.PolyData(pdata.values.astype(np.float))
if 'colour' in df:
mesh.point_arrays['colour'] = df.loc[pdata.index, 'colour']
return mesh
# dmbm_to_vtk
def vtk_dmbm_to_ug(df):
''' datamine block model to uniform grid '''
df_min = df.min(0)
xyzc = ['XC','YC','ZC']
size = df_min[['XINC','YINC','ZINC']].astype(np.int_)
dims = np.add(df_min[['NX','NY','NZ']] ,1).astype(np.int_)
origin = df_min[['XMORIG','YMORIG','ZMORIG']]
grid = pv.UniformGrid(dims, size, origin)
n_predefined = 13
vl = [df.columns[_] for _ in range(13, df.shape[1])]
cv = [dict()] * grid.GetNumberOfCells()
for i,row in df.iterrows():
cell = grid.find_closest_cell(row[xyzc].values)
if cell >= 0:
cv[cell] = row[vl].to_dict()
cvdf = pd.DataFrame.from_records(cv)
for v in vl:
grid.cell_arrays[v] = cvdf[v]
return grid
def vtk_plot_meshes(meshes, point_labels=False):
if pv is None: return
p = pv.Plotter()
c = 0
for mesh in meshes:
if mesh is not None:
p.add_mesh(mesh, opacity=0.5)
if point_labels:
p.add_point_labels(mesh.points, np.arange(mesh.n_points))
c += 1
if c:
print("display", c, "meshes")
p.show()
def vtk_mesh_to_df(mesh):
df = pd.DataFrame()
if hasattr(mesh, 'n_blocks'):
for block in mesh:
df = df.append(vtk_mesh_to_df(block))
else:
arr_n = np.zeros(mesh.n_points, dtype=np.int)
arr_node = np.arange(mesh.n_points, dtype=np.int)
print("GetDataObjectType", mesh.GetDataObjectType())
# VTK_STRUCTURED_POINTS = 1
# VTK_STRUCTURED_GRID = 2
# VTK_UNSTRUCTURED_GRID = 4
# 6 = UniformGrid
# VTK_UNIFORM_GRID = 10
if mesh.GetDataObjectType() in [2,4,6]:
points = mesh.cell_centers().points
arr_node = np.arange(mesh.GetNumberOfCells(), dtype=np.int)
arr_n = np.zeros(mesh.GetNumberOfCells())
arr_data = [pd.Series(mesh.get_array(name),name=name) for name in mesh.cell_arrays]
else:
arr_data = []
# in some cases, n_faces may be > 0 but with a empty faces array
if mesh.n_faces and len(mesh.faces):
face_size = int(mesh.faces[0])
arr_flat = vtk_cells_to_flat(mesh.faces)
points = mesh.points.take(arr_flat, 0)
arr_node = arr_node.take(arr_flat)
arr_n = np.tile(np.arange(face_size, dtype=np.int), len(points) // face_size)
for name in mesh.point_arrays:
arr_data.append(pd.Series(mesh.get_array(name).take(arr_flat), name=name))
else:
points = mesh.points
arr_data = [pd.Series(mesh.point_arrays[name],name=name) for name in mesh.point_arrays]
df = pd.concat([pd.DataFrame(points,columns=['x','y','z']), pd.Series(arr_n,name='n'), pd.Series(arr_node,name='node')] + arr_data,1)
return df
def vtk_mesh_info(mesh):
print(mesh)
#.IsA('vtkMultiBlockDataSet'):
if hasattr(mesh, 'n_blocks'):
for n in range(mesh.n_blocks):
print("block",n,"name",mesh.get_block_name(n))
vtk_mesh_info(mesh.get(n))
else:
for preference in ['point', 'cell', 'field']:
arr_list = mesh.cell_arrays
if preference == 'point':
arr_list = mesh.point_arrays
if preference == 'field':
arr_list = mesh.field_arrays
for name in arr_list:
arr = mesh.get_array(name, preference)
# check if this array is unicode, obj, str or other text types
if arr.dtype.num >= 17:
d = np.unique(arr)
else:
d = '{%f <=> %f}' % mesh.get_data_range(name, preference)
print(name,preference,arr.dtype.name,d,len(arr))
print('')
return mesh
def vtk_array_string_to_index(mesh):
print("converting string arrays to integer index:")
for name in mesh.cell_arrays:
arr = mesh.cell_arrays[name]
if arr.dtype.num >= 17:
print(name,"(cell)",arr.dtype)
mesh.cell_arrays[name] = pd.factorize(arr)[0]
for name in mesh.point_arrays:
arr = mesh.point_arrays[name]
if arr.dtype.num >= 17:
print(name,"(point)",arr.dtype)
mesh.point_arrays[name] = pd.factorize(arr)[0]
return mesh
def vtk_info(fp):
if pv is None: return
return vtk_mesh_info(pv.read(fp))
class vtk_Voxel(pv.UniformGrid):
@classmethod
def from_bmf(cls, bm, n_schema = None):
if n_schema is None:
n_schema = bm.model_n_schemas()-1
size = np.resize(bm.model_schema_size(n_schema), 3)
dims = bm.model_schema_dimensions(n_schema)
o0 = bm.model_schema_extent(n_schema)
origin = np.add(bm.model_origin(), o0[:3])
return cls(np.add(dims, 1, dtype = np.int_, casting = 'unsafe'), size, origin[:3])
@classmethod
def from_mesh(cls, mesh, cell_size = 10, ndim = 3):
mesh = mesh.copy()
if ndim == 2:
mesh.points[:, 2] = 0
bb = np.transpose(np.reshape(mesh.GetBounds(), (3,2)))
dims = np.add(np.ceil(np.divide(np.subtract(bb[1], bb[0]), cell_size)), 3)
if ndim == 2:
dims[2] = 1
origin = np.subtract(bb[0], cell_size)
#grid = pv.UniformGrid(dims.astype(np.int), np.full(3, cell_size, dtype=np.int), origin)
return cls(dims.astype(np.int), np.full(3, cell_size, dtype=np.int), origin)
@classmethod
def from_df(cls, df, cell_size, xyz = ['x','y','z']):
bb0 = df[xyz].min()
bb1 = df[xyz].max()
dims = np.add(np.ceil(np.divide(np.subtract(bb1, bb0), cell_size)), 3)
origin = np.subtract(bb0, cell_size)
return cls(dims.astype(np.int), np.full(3, cell_size, dtype=np.int), origin)
@property
def shape(self):
shape = np.subtract(self.dimensions, 1)
return shape[shape.nonzero()]
def get_ndarray(self, name = None, preference='cell'):
if name is None:
return np.ndarray(self.shape)
return self.get_array(name, preference).reshape(self.shape)
def set_ndarray(self, name, array, preference='cell'):
if preference=='cell':
self.cell_arrays[name] = array.flat
else:
self.point_arrays[name] = array.flat
def GetCellCenter(self, cellId):
return vtk_Voxel.sGetCellCenter(self, cellId)
# DEPRECATED: use cell_centers().points
@staticmethod
def sGetCellCenter(self, cellId):
cell = self.GetCell(cellId)
bounds = np.reshape(cell.GetBounds(), (3,2))
return bounds.mean(1)
def vtk_texture_to_array(tex):
' WORKING drop in replacement for to_array()'
img = tex.to_image()
sh = (img.dimensions[1], img.dimensions[0])
if img.active_scalars.ndim > 1:
sh = (img.dimensions[1], img.dimensions[0], tex.n_components)
return img.active_scalars.reshape(sh)
def vtk_to_gltf(vtk_meshes):
import pygltflib
from pygltflib.utils import ImageFormat
import PIL.Image
import skimage.io
import io
buffer0 = io.BytesIO()
accessors = []
bufferviews = []
meshes = []
texcoords = []
textures = []
images = []
samplers = []
materials = []
for mesh in vtk_meshes:
nodes = mesh.points
faces = vtk_cells_to_faces(mesh.faces)
tcoor = mesh.t_coords
meshes.append(pygltflib.Mesh(primitives=[pygltflib.Primitive(attributes=pygltflib.Attributes(POSITION=len(accessors),TEXCOORD_0=len(texcoords)+2), indices=len(accessors)+1, material=0)]))
# POSITION
view_blob = nodes.astype(np.float32).tobytes()
bufferview = pygltflib.BufferView(buffer=0,byteOffset=buffer0.tell(),byteLength=len(view_blob),target=pygltflib.ARRAY_BUFFER)
accessor = pygltflib.Accessor(bufferView=len(bufferviews),componentType=pygltflib.FLOAT,count=len(nodes),type=pygltflib.VEC3,max=nodes.max(axis=0).tolist(),min=nodes.min(axis=0).tolist())
buffer0.write(view_blob)
bufferviews.append(bufferview)
accessors.append(accessor)
# indices
view_blob = faces.astype(np.int).tobytes()
bufferview = pygltflib.BufferView(buffer=0,byteOffset=buffer0.tell(),byteLength=len(view_blob),target=pygltflib.ELEMENT_ARRAY_BUFFER)
accessor = pygltflib.Accessor(bufferView=len(bufferviews),componentType=pygltflib.UNSIGNED_INT,count=faces.size,type=pygltflib.SCALAR,max=[],min=[])
buffer0.write(view_blob)
bufferviews.append(bufferview)
accessors.append(accessor)
# TEXCOORD
view_blob = tcoor.astype(np.float32).tobytes()
bufferview = pygltflib.BufferView(buffer=0,byteOffset=buffer0.tell(),byteLength=len(view_blob),target=pygltflib.ARRAY_BUFFER)
accessor = pygltflib.Accessor(bufferView=len(bufferviews),componentType=pygltflib.FLOAT,count=len(tcoor),type=pygltflib.VEC2,max=[],min=[])
buffer0.write(view_blob)
bufferviews.append(bufferview)
accessors.append(accessor)
for i in mesh.textures:
byteoffset = buffer0.tell()
img = vtk_texture_to_array(mesh.textures[i])
skimage.io.imsave(buffer0, img, format='png')
# buffers chunks MUST be multiple of 4
while buffer0.tell() % 4 > 0:
buffer0.write(b'\0')
materials.append(pygltflib.Material(doubleSided=True, alphaCutoff=None, pbrMetallicRoughness=pygltflib.PbrMetallicRoughness(baseColorTexture=pygltflib.TextureInfo(index=len(textures), texCoord=0))))
textures.append(pygltflib.Texture(source=len(images)))
images.append(pygltflib.Image(mimeType=pygltflib.IMAGEPNG,bufferView=len(bufferviews)))
bufferviews.append(pygltflib.BufferView(buffer=0,byteOffset=byteoffset,byteLength=buffer0.tell()-byteoffset))
gltf = pygltflib.GLTF2(
scene=0,
scenes=[pygltflib.Scene(nodes=[0])],
nodes=[pygltflib.Node(mesh=0)],
meshes=meshes,
accessors=accessors,
bufferViews=bufferviews,
buffers=[
pygltflib.Buffer(byteLength=buffer0.tell())
],
images=images,
samplers=samplers,
textures=textures,
materials=materials
)
gltf.set_binary_blob(buffer0.getbuffer())
print(gltf)
return gltf
if __name__=="__main__":
pass