def SerializeVTKTable(table):
tmp = tempfile.mktemp()
writer = vtk.vtkTableWriter()
writer.SetFileName(tmp)
writer.SetFileTypeToBinary()
writer.SetInputData(table)
writer.Update()
with open(tmp, 'r') as fp:
data = fp.read()
os.remove(tmp)
data = base64.b64encode(data)
return data
def SerializeVTKTable(table):
tmp = tempfile.mktemp()
writer = vtk.vtkTableWriter()
writer.SetFileName(tmp)
writer.SetFileTypeToBinary()
writer.SetInputData(table)
writer.Update()
with open(tmp, 'r') as fp:
data = fp.read()
os.remove(tmp)
data = base64.b64encode(data)
return data
def execute(inputs, outputs, script):
# prepend some R code to the beginning of the script
# this allows us to capture useful error output information
script = "con <- file(\"/tmp/R_errors.txt\", \"w\")\nsink(con, type=\"message\")\n" + script
# Setup the pipeline
rcalc = vtk.vtkRCalculatorFilter()
rcalc.SetRscript(script)
readers = []
input_tables = []
input_trees = []
for name, type, format, value in inputs:
if type == 'Table':
input_tables.append(name)
input = vtk.vtkTableReader()
elif type == 'Tree':
input_trees.append(name)
input = vtk.vtkTreeReader()
data_value = base64.b64decode(value)
input.SetBinaryInputString(data_value, len(data_value))
input.SetReadFromInputString(1)
readers.append(input)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(input_tables))
index = 0
for name in input_tables:
names.SetValue(index, name)
index += 1
rcalc.PutTables(names)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(input_trees))
index = 0
for name in input_trees:
names.SetValue(index, name)
index += 1
rcalc.PutTrees(names)
# Multi inputs
if len(inputs) > 1:
input = vtk.vtkMultiBlockDataGroupFilter()
for reader in readers:
input.AddInputConnection(reader.GetOutputPort())
rcalc.AddInputConnection(input.GetOutputPort())
output_tables = []
output_trees = []
for o in outputs:
if o['type'] == 'Table':
output_tables.append(o['name'])
elif o['type'] == 'Tree':
output_trees.append(o['name'])
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(output_tables))
index = 0
for name in output_tables:
names.SetValue(index, name)
index += 1
rcalc.GetTables(names)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(output_trees))
index = 0
for name in output_trees:
names.SetValue(index, name)
index += 1
rcalc.GetTrees(names)
try:
rcalc.Update()
output = rcalc.GetOutput()
except vtk.ErrorEventException:
f = file("/tmp/R_errors.txt", "r")
error_msg = f.read()
raise Exception(error_msg)
print str(output)
output_dataobjects = []
if len(outputs) > 1:
iter = output.NewIterator()
iter.InitTraversal()
while not iter.IsDoneWithTraversal():
dataobject = iter.GetCurrentDataObject()
output_dataobjects.append(dataobject)
iter.GoToNextItem()
iter.FastDelete()
else:
output_dataobjects.append(output)
output_json = {'output': []}
index = 0
for dataobject in output_dataobjects:
output = outputs[index]
index += 1
if output['type'] == 'Table':
writer = vtk.vtkTableWriter()
elif output['type'] == 'Tree':
writer = vtk.vtkTreeWriter()
tmp = tempfile.mktemp()
writer.SetFileName(tmp)
writer.SetFileTypeToBinary()
writer.SetInputData(dataobject)
writer.Update()
with open(tmp, 'r') as fp:
data = fp.read()
os.remove(tmp)
data = base64.b64encode(data)
output_json['output'].append({
'name': output['name'],
'type': output['type'],
'data': data
})
return output_json
def execute(inputs, outputs, script):
# prepend some R code to the beginning of the script
# this allows us to capture useful error output information
script = "con <- file(\"/tmp/R_errors.txt\", \"w\")\nsink(con, type=\"message\")\n" + script
# Setup the pipeline
rcalc = vtk.vtkRCalculatorFilter()
rcalc.SetRscript(script)
readers = []
input_tables = []
input_trees = []
for name, type, format, value in inputs:
if type == 'Table':
input_tables.append(name)
input = vtk.vtkTableReader()
elif type == 'Tree':
input_trees.append(name)
input = vtk.vtkTreeReader()
data_value = base64.b64decode(value)
input.SetBinaryInputString(data_value, len(data_value))
input.SetReadFromInputString(1)
readers.append(input)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(input_tables))
index = 0
for name in input_tables:
names.SetValue(index, name)
index += 1
rcalc.PutTables(names)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(input_trees))
index = 0
for name in input_trees:
names.SetValue(index, name)
index += 1
rcalc.PutTrees(names)
# Multi inputs
if len(inputs) > 1:
input = vtk.vtkMultiBlockDataGroupFilter()
for reader in readers:
input.AddInputConnection(reader.GetOutputPort())
rcalc.AddInputConnection(input.GetOutputPort())
output_tables = []
output_trees = []
for o in outputs:
if o['type'] == 'Table':
output_tables.append(o['name'])
elif o['type'] == 'Tree':
output_trees.append(o['name'])
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(output_tables))
index = 0
for name in output_tables:
names.SetValue(index, name)
index += 1
rcalc.GetTables(names)
names = vtk.vtkStringArray()
names.SetNumberOfComponents(1)
names.SetNumberOfTuples(len(output_trees))
index = 0
for name in output_trees:
names.SetValue(index, name)
index += 1
rcalc.GetTrees(names)
try:
rcalc.Update()
output = rcalc.GetOutput()
except vtk.ErrorEventException:
f = file("/tmp/R_errors.txt", "r")
error_msg = f.read()
raise Exception(error_msg)
print str(output)
output_dataobjects = []
if len(outputs) > 1:
iter = output.NewIterator();
iter.InitTraversal()
while not iter.IsDoneWithTraversal():
dataobject = iter.GetCurrentDataObject()
output_dataobjects.append(dataobject)
iter.GoToNextItem()
iter.FastDelete()
else:
output_dataobjects.append(output)
output_json = {'output': []}
index = 0
for dataobject in output_dataobjects:
output = outputs[index]
index += 1
if output['type'] == 'Table':
writer = vtk.vtkTableWriter()
elif output['type'] == 'Tree':
writer = vtk.vtkTreeWriter()
tmp = tempfile.mktemp()
writer.SetFileName(tmp)
writer.SetFileTypeToBinary()
writer.SetInputData(dataobject)
writer.Update()
with open(tmp, 'r') as fp:
data = fp.read()
os.remove(tmp)
data = base64.b64encode(data)
output_json['output'].append({'name': output['name'], 'type': output['type'], 'data': data})
return output_json