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Modified vtk.py to import 4.2 version vtk files. #297

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Modified vtk.py to import 4.2 version vtk files. #297

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115 changes: 73 additions & 42 deletions raysect/primitive/mesh/vtk.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,14 +46,17 @@
class VTKHandler:

@classmethod
def import_vtk(cls, filename, scaling=1.0, mode=VTK_AUTOMATIC, **kwargs):
def my_import_vtk(cls, filename, scaling=1e-3, mode=VTK_AUTOMATIC, **kwargs):
"""
Create a mesh instance from a VTK mesh data file (.vtk).

.. warning ::
Currently only supports VTK DataFile v2.0 and unstructured grid data with
3 element (triangular) cells.

.. warning ::
Trying to update the version to be able to read VTK DataFile 4.2.

:param str filename: Mesh file path.
:param double scaling: Scale the mesh by this factor (default=1.0).
:param str mode: The file format to load: 'ascii', 'binary', 'auto' (default='auto').
Expand Down Expand Up @@ -87,11 +90,11 @@ def _load_ascii(cls, filename, scaling):
with open(filename, 'r') as f:

# parse the file header
assert f.readline().strip() == "# vtk DataFile Version 2.0"
assert f.readline().strip() == "# vtk DataFile Version 4.2"
mesh_name = f.readline().strip()
assert f.readline().strip() == "ASCII"

if not f.readline().strip() == "DATASET UNSTRUCTURED_GRID":
if not f.readline().strip() == "DATASET POLYDATA":
raise RuntimeError("Unrecognised dataset encountered in vtk file.")

vertices = cls._ascii_read_vertices(f, scaling)
Expand All @@ -109,36 +112,47 @@ def _ascii_read_vertices(cls, f, scaling):

vertices = np.empty((num_points, 3))

for i in range(num_points):
i=0

while i < num_points:
coordinates = f.readline().split()
vertices[i, 0] = float(coordinates[0]) * scaling
vertices[i, 1] = float(coordinates[1]) * scaling
vertices[i, 2] = float(coordinates[2]) * scaling

j=0

while j < np.size(coordinates):
vertices[i, 0] = float(coordinates[j]) * scaling
vertices[i, 1] = float(coordinates[j+1]) * scaling
vertices[i, 2] = float(coordinates[j+2]) * scaling
j += 3
i += 1

return vertices

@classmethod
def _ascii_read_triangles(cls, f):

match = re.match("CELLS\s*([0-9]*)\s*([0-9]*)", f.readline())
#match = re.match("CELLS\s*([0-9]*)\s*([0-9]*)", f.readline())
match = False

while not match:
match = re.match("POLYGONS\s*([0-9]*)\s*([0-9]*)", f.readline())

if not match:
raise RuntimeError("Unrecognised dataset encountered in vtk file.")
num_triangles = int(match.group(1))
triangles = np.empty((num_triangles, 3), dtype=np.int32)
for i in range(num_triangles):
triangle_specification = f.readline().split()

#assert triangle specification[0] == 3
triangles[i, 0] = int(triangle_specification[1])
triangles[i, 1] = int(triangle_specification[2])
triangles[i, 2] = int(triangle_specification[3])

assert f.readline().split()[0] == 'CELL_TYPES'
for i in range(num_triangles):
assert int(f.readline().strip()) == 5

return triangles

@classmethod
def export_vtk(cls, mesh, filename, triangle_data=None, vertex_data=None, mode=VTK_ASCII):
def my_export_vtk(cls, mesh, filename, triangle_data=None, vertex_data=None, mode=VTK_ASCII):
"""
Write a mesh instance to a vtk mesh file (.vtk) with optional cell and point data.

Expand All @@ -152,7 +166,8 @@ def export_vtk(cls, mesh, filename, triangle_data=None, vertex_data=None, mode=V
equal to the number of vertices in the mesh.
:param str mode: The file format to write: 'ascii' or 'binary' (default='ascii').
"""

print('\n\n***WARNING***\n\nMY_EXPORT_VTK: still to be revised & NO normals & other missing data\n\n')

if not isinstance(mesh, Mesh):
raise ValueError("The mesh argument to write_vtk() must be a valid Raysect Mesh primitive object.")

Expand All @@ -170,12 +185,13 @@ def _write_ascii(cls, mesh, filename, triangle_data=None, vertex_data=None):

with open(filename, 'w') as f:

# # vtk DataFile Version 2.0
# My Raysect mesh data
# # vtk DataFile Version 4.2
# vtk output
# ASCII
mesh_name = (mesh.name or 'RaysectMesh').replace(" ", "_")
f.write('# vtk DataFile Version 2.0\n')
f.write('{}\n'.format(mesh_name))
f.write('# vtk DataFile Version 4.2\n')
#f.write('{}\n'.format(mesh_name))
f.write('vtk output\n')
f.write('ASCII\n')

cls._ascii_write_geometry(f, mesh)
Expand All @@ -194,32 +210,39 @@ def _ascii_write_geometry(cls, f, mesh):
num_triangles = mesh.data.triangles.shape[0]
num_vertices = mesh.data.vertices.shape[0]

# DATASET UNSTRUCTURED_GRID
# POINTS 5081 float
# 5.12135678592 3.59400404579 5.20377763887
# 5.07735666785 3.40460816029 5.27386350545
# DATASET POLYDATA
# POINTS 36013 float
# 5.12135678592 3.59400404579 5.20377763887 5.07735666785 3.40460816029 5.27386350545
# ...
f.write('DATASET UNSTRUCTURED_GRID\n')
f.write('DATASET POLYDATA\n')
f.write('POINTS {} float\n'.format(num_vertices))
for i in range(num_vertices):
f.write('{} {} {}\n'.format(vertices[i, 0], vertices[i, 1], vertices[i, 2]))

# CELLS 9804 39216
i = 0

while i < num_vertices:
j = 0
while i < num_vertices and j < 3:
f.write('{} {} {} '.format(vertices[i, 0], vertices[i, 1], vertices[i, 2]))
i += 1
j += 1
f.write('\n')

f.write('METADATA\nINFORMATION 2\n')
f.write('NAME L2_NORM_RANGE LOCATION vtkDataArray\n')
f.write('DATA 2 2.37105 2.7879\n')
f.write('NAME L2_NORM_FINITE_RANGE LOCATION vtkDataArray\n')
f.write('DATA 2 2.37105 2.7879\n\n')


# POLYGONS 9804 39216

# 3 447 4361 446
# 3 444 4248 445
# ...
f.write('CELLS {} {}\n'.format(num_triangles, 4 * num_triangles))
f.write('POLYGONS {} {}\n'.format(num_triangles, 4 * num_triangles))
for i in range(num_triangles):
f.write('3 {} {} {}\n'.format(triangles[i, 0], triangles[i, 1], triangles[i, 2]))

# CELL_TYPES 9804
# 5
# 5
# ...
f.write('CELL_TYPES {}\n'.format(num_triangles))
for i in range(num_triangles):
f.write('5\n')

@classmethod
def _ascii_write_vertex_data(cls, f, mesh, vertex_data):
raise NotImplementedError("write_vtk() does not currently support mesh vertex data.")
Expand All @@ -237,7 +260,7 @@ def _ascii_write_triangle_data(cls, f, mesh, triangle_data):
# ...

num_triangles = mesh.data.triangles.shape[0]
f.write('CELL_DATA {}\n'.format(num_triangles))
f.write('\nCELL_DATA {}\n'.format(num_triangles))

error_msg = "The triangle_data argument in write_vtk() must be a dictionary or arrays/lists " \
"with length equal to the number of triangles."
Expand All @@ -253,11 +276,19 @@ def _ascii_write_triangle_data(cls, f, mesh, triangle_data):
except TypeError:
raise ValueError(error_msg)

f.write('SCALARS {} FLOAT\n'.format(var_name.replace(" ", "_")))
f.write('LOOKUP_TABLE default\n')
for value in values:
f.write('{}\n'.format(value))
f.write('FIELD FieldData 1\n')
f.write('GroupIds 1 {} float\n'.format(num_triangles))

i = 0

while i < num_triangles:
j = 0
while i < num_triangles and j < 9:
f.write('{} '.format(values[i]))
i += 1
j += 1
f.write('\n')


import_vtk = VTKHandler.import_vtk
export_vtk = VTKHandler.export_vtk
my_import_vtk = VTKHandler.my_import_vtk
my_export_vtk = VTKHandler.my_export_vtk