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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Open in desktop
Original file line numberDiff line numberDiff 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 DownExpand 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
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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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

View file


Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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

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matteomoscheni
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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

View file


Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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

View file


Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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

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matteomoscheni
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1
commit into

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Choose a base branch

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


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115 changes: 73 additions & 42 deletions
raysect/primitive/mesh/vtk.py

View file


Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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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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Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
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

View file


Open in desktop

Original file line numberDiff line numberDiff 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 DownExpand 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

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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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 numberDiff line numberDiff 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 DownExpand 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