def write_image(system, vtk_filename, specifics = []):
plot_targets = lgeo.sort_data_by_type(system.data, specifics)
doc = xml.dom.minidom.Document()
pdb.set_trace()
vtktype = 'ImageData'
root_element = doc.createElementNS("VTK", "VTKFile")
root_element.setAttribute("type", vtktype)
root_element.setAttribute("version", "0.1")
root_element.setAttribute("byte_order", "LittleEndian")
doc.appendChild(root_element)
#ImageData Element
tempExtent = lgeo.array_to_string(['0', viewdims[0],
'0', viewdims[1], '0', viewdims[2]])
dataType = doc.createElementNS("VTK", vtktype)
dataType.setAttribute("WholeExtent", tempExtent)
dataType.setAttribute("Origin", "0 0 0")
dataType.setAttribute("Spacing", "1 1 1")
root_element.appendChild(dataType)
# Piece 0 (only one)
piece = doc.createElementNS("VTK", "Piece")
piece.setAttribute("Extent", tempExtent)
piece.setAttribute("NumberOfPoints", str(len(data[data.keys()[0]])))
piece.setAttribute("NumberOfCells", "0")
dataType.appendChild(piece)
### Points ####
points = doc.createElementNS("VTK", "Points")
piece.appendChild(points)
# Point location data
point_coords = doc.createElementNS("VTK", "DataArray")
point_coords.setAttribute("type", "Float32")
point_coords.setAttribute("format", "ascii")
point_coords.setAttribute("NumberOfComponents", "3")
points.appendChild(point_coords)
point_coords_string = lgeo.coords_to_string(data['time'], \
data['time'], [0.0]*len(data['time']))
point_coords_data = doc.createTextNode(point_coords_string)
point_coords.appendChild(point_coords_data)
#### Data at Points ####
point_data = doc.createElementNS("VTK", "PointData")
piece.appendChild(point_data)
# Array Data
for key in data.keys():
if key == 'time':
node= doc.createElementNS("VTK", "DataArray")
node.setAttribute("Name", "Points")
node.setAttribute("type", "Float32")
node.setAttribute("format", "ascii")
point_data.appendChild(node)
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
elif key == 'probability' or key == 'reaction_history':
continue
else:
node= doc.createElementNS("VTK", "DataArray")
node.setAttribute("Name", key)
node.setAttribute("type", "Int32")
node.setAttribute("format", "ascii")
point_data.appendChild(node)
string = lgeo.array_to_string(data[key])
node_Data = doc.createTextNode(string)
node.appendChild(node_Data)
#### Cell data (dummy) ####
cell_data = doc.createElementNS("VTK", "CellData")
piece.appendChild(cell_data)
#### Cells ####
cells = doc.createElementNS("VTK", "Cells")
piece.appendChild(cells)
# Cell locations
cell_connectivity = doc.createElementNS("VTK", "DataArray")
cell_connectivity.setAttribute("type", "Int32")
cell_connectivity.setAttribute("Name", "connectivity")
cell_connectivity.setAttribute("format", "ascii")
cells.appendChild(cell_connectivity)
# Cell location data
connectivity = doc.createTextNode("0")
cell_connectivity.appendChild(connectivity)
cell_offsets = doc.createElementNS("VTK", "DataArray")
cell_offsets.setAttribute("type", "Int32")
cell_offsets.setAttribute("Name", "offsets")
cell_offsets.setAttribute("format", "ascii")
cells.appendChild(cell_offsets)
offsets = doc.createTextNode("0")
cell_offsets.appendChild(offsets)
cell_types = doc.createElementNS("VTK", "DataArray")
cell_types.setAttribute("type", "UInt8")
cell_types.setAttribute("Name", "types")
cell_types.setAttribute("format", "ascii")
cells.appendChild(cell_types)
types = doc.createTextNode("11")
cell_types.appendChild(types)
outFile = open(vtk_filename, 'w')
doc.writexml(outFile, newl='\n')
outFile.close()
def write_image(system, vtk_filename, specifics=[]):
plot_targets = lgeo.sort_data_by_type(system.data, specifics)
doc = xml.dom.minidom.Document()
pdb.set_trace()
vtktype = 'ImageData'
root_element = doc.createElementNS("VTK", "VTKFile")
root_element.setAttribute("type", vtktype)
root_element.setAttribute("version", "0.1")
root_element.setAttribute("byte_order", "LittleEndian")
doc.appendChild(root_element)
#ImageData Element
tempExtent = lgeo.array_to_string(
['0', viewdims[0], '0', viewdims[1], '0', viewdims[2]])
dataType = doc.createElementNS("VTK", vtktype)
dataType.setAttribute("WholeExtent", tempExtent)
dataType.setAttribute("Origin", "0 0 0")
dataType.setAttribute("Spacing", "1 1 1")
root_element.appendChild(dataType)
# Piece 0 (only one)
piece = doc.createElementNS("VTK", "Piece")
piece.setAttribute("Extent", tempExtent)
piece.setAttribute("NumberOfPoints", str(len(data[data.keys()[0]])))
piece.setAttribute("NumberOfCells", "0")
dataType.appendChild(piece)
### Points ####
points = doc.createElementNS("VTK", "Points")
piece.appendChild(points)
# Point location data
point_coords = doc.createElementNS("VTK", "DataArray")
point_coords.setAttribute("type", "Float32")
point_coords.setAttribute("format", "ascii")
point_coords.setAttribute("NumberOfComponents", "3")
points.appendChild(point_coords)
point_coords_string = lgeo.coords_to_string(data['time'], \
data['time'], [0.0]*len(data['time']))
point_coords_data = doc.createTextNode(point_coords_string)
point_coords.appendChild(point_coords_data)
#### Data at Points ####
point_data = doc.createElementNS("VTK", "PointData")
piece.appendChild(point_data)
# Array Data
for key in data.keys():
if key == 'time':
node = doc.createElementNS("VTK", "DataArray")
node.setAttribute("Name", "Points")
node.setAttribute("type", "Float32")
node.setAttribute("format", "ascii")
point_data.appendChild(node)
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
elif key == 'probability' or key == 'reaction_history':
continue
else:
node = doc.createElementNS("VTK", "DataArray")
node.setAttribute("Name", key)
node.setAttribute("type", "Int32")
node.setAttribute("format", "ascii")
point_data.appendChild(node)
string = lgeo.array_to_string(data[key])
node_Data = doc.createTextNode(string)
node.appendChild(node_Data)
#### Cell data (dummy) ####
cell_data = doc.createElementNS("VTK", "CellData")
piece.appendChild(cell_data)
#### Cells ####
cells = doc.createElementNS("VTK", "Cells")
piece.appendChild(cells)
# Cell locations
cell_connectivity = doc.createElementNS("VTK", "DataArray")
cell_connectivity.setAttribute("type", "Int32")
cell_connectivity.setAttribute("Name", "connectivity")
cell_connectivity.setAttribute("format", "ascii")
cells.appendChild(cell_connectivity)
# Cell location data
connectivity = doc.createTextNode("0")
cell_connectivity.appendChild(connectivity)
cell_offsets = doc.createElementNS("VTK", "DataArray")
cell_offsets.setAttribute("type", "Int32")
cell_offsets.setAttribute("Name", "offsets")
cell_offsets.setAttribute("format", "ascii")
cells.appendChild(cell_offsets)
offsets = doc.createTextNode("0")
cell_offsets.appendChild(offsets)
cell_types = doc.createElementNS("VTK", "DataArray")
cell_types.setAttribute("type", "UInt8")
cell_types.setAttribute("Name", "types")
cell_types.setAttribute("format", "ascii")
cells.appendChild(cell_types)
types = doc.createTextNode("11")
cell_types.appendChild(types)
outFile = open(vtk_filename, 'w')
doc.writexml(outFile, newl='\n')
outFile.close()
def write_unstructured(system, vtk_filename, specifics = []):
plot_targets = lgeo.sort_data_by_type(system.data, specifics)
doc = xml.dom.minidom.Document()
root_element = setup_element(doc, 'VTKFile',
{'type' : 'UnstructuredGrid',
'version' : '0.1',
'byte_order' : 'LittleEndian'})
doc.appendChild(root_element)
dataType = doc.createElementNS('VTK', 'UnstructuredGrid')
root_element.appendChild(dataType)
piece = setup_element(doc, 'Piece', {
'NumberOfPoints' : str(len(plot_targets['scalars'][
plot_targets['scalars'].keys()[0]])),
'NumberOfCells' : '0'})
dataType.appendChild(piece)
points = doc.createElementNS('VTK', 'Points')
piece.appendChild(points)
point_coords = setup_element(doc, 'DataArray', {
'type' : 'Float32',
'format' : 'ascii',
'NumberOfComponents' : '3'})
points.appendChild(point_coords)
point_data = doc.createElementNS('VTK', 'PointData')
piece.appendChild(point_data)
if len(plot_targets['coords'].keys()) > 0:
node = setup_element(doc, 'DataArray', {
'Name' : 'Points',
'type' : 'Float32',
'format' : 'ascii'})
point_data.appendChild(node)
keydex = plot_targets['coords'].keys()[0]
keydexes = plot_targets['coords'][keydex].keys()
point_coords_string = lgeo.coords_to_string(
plot_targets['coords'][keydex][keydexes[0]],
plot_targets['coords'][keydex][keydexes[1]],
plot_targets['coords'][keydex][keydexes[2]])
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
elif len(plot_targets['scalars'].keys()) > 0:
node = setup_element(doc, 'DataArray', {
'Name' : 'Points',
'type' : 'Float32',
'format' : 'ascii'})
point_data.appendChild(node)
keydex = plot_targets['scalars'].keys()[0]
point_coords_string = lgeo.coords_to_string(
plot_targets['scalars'][keydex],
plot_targets['scalars'][keydex],
plot_targets['scalars'][keydex])
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
point_coords.appendChild(copy(node_Data))
for key in plot_targets['scalars'].keys():
node = setup_element(doc, 'DataArray', {
'Name' : key,
'type' : 'Float32',
'format' : 'ascii'})
point_data.appendChild(node)
string = lgeo.array_to_string(plot_targets['scalars'][key])
node_Data = doc.createTextNode(string)
node.appendChild(node_Data)
cell_data = doc.createElementNS("VTK", "CellData")
piece.appendChild(cell_data)
cells = doc.createElementNS("VTK", "Cells")
piece.appendChild(cells)
cell_connectivity = setup_element(doc, 'DataArray', {
'type' : 'Int32',
'Name' : 'connectivity',
'format' : 'ascii'})
cells.appendChild(cell_connectivity)
connectivity = doc.createTextNode("0")
cell_connectivity.appendChild(connectivity)
cell_offsets = setup_element(doc, 'DataArray', {
'type' : 'Int32',
'Name' : 'offsets',
'format' : 'ascii'})
cells.appendChild(cell_offsets)
offsets = doc.createTextNode("0")
cell_offsets.appendChild(offsets)
cell_types = setup_element(doc, 'DataArray', {
'type' : 'UInt8',
'Name' : 'types',
'format' : 'ascii'})
cells.appendChild(cell_types)
types = doc.createTextNode("11")
cell_types.appendChild(types)
out_file = open('.'.join(vtk_filename.split('.')[:-1] + ['vtu']), 'w')
doc.writexml(out_file, newl='\n')
out_file.close()
def write_unstructured(system, vtk_filename, specifics=[]):
plot_targets = lgeo.sort_data_by_type(system.data, specifics)
doc = xml.dom.minidom.Document()
root_element = setup_element(doc, 'VTKFile', {
'type': 'UnstructuredGrid',
'version': '0.1',
'byte_order': 'LittleEndian'
})
doc.appendChild(root_element)
dataType = doc.createElementNS('VTK', 'UnstructuredGrid')
root_element.appendChild(dataType)
piece = setup_element(
doc, 'Piece', {
'NumberOfPoints':
str(len(
plot_targets['scalars'][plot_targets['scalars'].keys()[0]])),
'NumberOfCells':
'0'
})
dataType.appendChild(piece)
points = doc.createElementNS('VTK', 'Points')
piece.appendChild(points)
point_coords = setup_element(doc, 'DataArray', {
'type': 'Float32',
'format': 'ascii',
'NumberOfComponents': '3'
})
points.appendChild(point_coords)
point_data = doc.createElementNS('VTK', 'PointData')
piece.appendChild(point_data)
if len(plot_targets['coords'].keys()) > 0:
node = setup_element(doc, 'DataArray', {
'Name': 'Points',
'type': 'Float32',
'format': 'ascii'
})
point_data.appendChild(node)
keydex = plot_targets['coords'].keys()[0]
keydexes = plot_targets['coords'][keydex].keys()
point_coords_string = lgeo.coords_to_string(
plot_targets['coords'][keydex][keydexes[0]],
plot_targets['coords'][keydex][keydexes[1]],
plot_targets['coords'][keydex][keydexes[2]])
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
elif len(plot_targets['scalars'].keys()) > 0:
node = setup_element(doc, 'DataArray', {
'Name': 'Points',
'type': 'Float32',
'format': 'ascii'
})
point_data.appendChild(node)
keydex = plot_targets['scalars'].keys()[0]
point_coords_string = lgeo.coords_to_string(
plot_targets['scalars'][keydex], plot_targets['scalars'][keydex],
plot_targets['scalars'][keydex])
node_Data = doc.createTextNode(point_coords_string)
node.appendChild(node_Data)
point_coords.appendChild(copy(node_Data))
for key in plot_targets['scalars'].keys():
node = setup_element(doc, 'DataArray', {
'Name': key,
'type': 'Float32',
'format': 'ascii'
})
point_data.appendChild(node)
string = lgeo.array_to_string(plot_targets['scalars'][key])
node_Data = doc.createTextNode(string)
node.appendChild(node_Data)
cell_data = doc.createElementNS("VTK", "CellData")
piece.appendChild(cell_data)
cells = doc.createElementNS("VTK", "Cells")
piece.appendChild(cells)
cell_connectivity = setup_element(doc, 'DataArray', {
'type': 'Int32',
'Name': 'connectivity',
'format': 'ascii'
})
cells.appendChild(cell_connectivity)
connectivity = doc.createTextNode("0")
cell_connectivity.appendChild(connectivity)
cell_offsets = setup_element(doc, 'DataArray', {
'type': 'Int32',
'Name': 'offsets',
'format': 'ascii'
})
cells.appendChild(cell_offsets)
offsets = doc.createTextNode("0")
cell_offsets.appendChild(offsets)
cell_types = setup_element(doc, 'DataArray', {
'type': 'UInt8',
'Name': 'types',
'format': 'ascii'
})
cells.appendChild(cell_types)
types = doc.createTextNode("11")
cell_types.appendChild(types)
out_file = open('.'.join(vtk_filename.split('.')[:-1] + ['vtu']), 'w')
doc.writexml(out_file, newl='\n')
out_file.close()
