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import core.modules
import core.modules.module_registry
from core.modules.vistrails_module import Module, ModuleError
from scipy import sparse
from Array import *
from Matrix import *
class ArrayConvertModule(object):
my_namespace = 'numpy|array|convert'
class ArrayDumpToFile(ArrayConvertModule, Module):
""" Pickle the input array and dump it to the specified file. This
array can then be read in via pickle.load or numpy.load """
def compute(self):
a = self.getInputFromPort("Array")
fn = self.getInputFromPort("Filename")
a.dump_to_file(fn)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="ArrayToPickledFile", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
class ArrayDumpToString(ArrayConvertModule, Module):
""" Pickle the input array and dump it to a string. This array
can then be read in via pickle.loads or numpy.loads """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Output String", a.dump_to_string())
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, name="ArrayToPickledString", namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
class ArrayToFile(ArrayConvertModule, Module):
""" Write the data to a file. If a separator char is given, the file
will be written in ASCII with the given char acting as a delimiter. If
no separator is given, the file is written in Binary. The array
is always written in row-major format regardless of the order of the
input array. """
def compute(self):
a = self.getInputFromPort("Array")
fn = self.getInputFromPort("Filename")
sep = ""
if self.hasInputFromPort("Separator"):
sep = self.getInputFromPort("Separator")
a.tofile(fn, sep)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
reg.add_input_port(cls, "Separator", (basic.String, 'Separator'), True)
class ArrayToString(ArrayConvertModule, Module):
""" Convert the array to a Python string. The output string will
be represented in row-major form regardless of the ordering of the
input array. """
def compute(self):
a = self.getInputFromPort("Array")
self.setResult("Output String", a.tostring())
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Output String", (basic.String, 'Output String'))
class ArrayToMatrix(ArrayConvertModule, Module):
""" Convert the input Numpy Array to a Scipy Matrix. The input array
must be no more than 2-dimensional """
def compute(self):
a = self.getInputFromPort("Array")
try:
mat = sparse.csc_matrix(a.get_array())
out_mat = Matrix()
out_mat.set_matrix(mat)
self.setResult("Output Matrix", out_mat)
except:
raise ModuleError("Could not convert input array to matrix")
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array'))
reg.add_output_port(cls, "Output Matrix", (Matrix, 'Output Matrix'))
class ArrayToVTKImageData(ArrayConvertModule, Module):
""" Convert the array to a vtImageData dataset. This works well for
arrays up to (and including) rank 3. Behavior is undefined for array of
rank > 3."""
def compute(self):
import vtk
a = self.getInputFromPort("Array")
sh = a.get_shape()
if len(sh) < 2:
sh = tuple([sh[0], 1, 0])
if len(sh) < 3:
sh = tuple([sh[0], sh[1], 0])
(num_sigs, num_times, num_freqs) = sh
num_pts = a.get_num_elements()
vtk_set = core.modules.module_registry.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkStructuredPoints').module()
vtk_set.vtkInstance = vtk.vtkImageData()
vtk_set.vtkInstance.SetDimensions(sh[0], sh[1], sh[2]+1)
vtk_set.vtkInstance.SetScalarTypeToFloat()
scalars = vtk.vtkFloatArray()
ar = a.get_array()
for ar_x in xrange(sh[0]):
for ar_y in xrange(sh[1]):
if sh[2] == 0:
val = ar[ar_x, ar_y]
vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, 0, 0, val)
else:
for ar_z in xrange(sh[2]):
val = ar[ar_x, ar_y, ar_z]
vtk_set.vtkInstance.SetScalarComponentFromFloat(ar_x, ar_y, ar_z, 0, val)
if self.hasInputFromPort("SpacingX"):
x = self.getInputFromPort("SpacingX")
else:
x = 1.0
if self.hasInputFromPort("SpacingY"):
y = self.getInputFromPort("SpacingY")
else:
y = 1.0
if self.hasInputFromPort("SpacingZ"):
z = self.getInputFromPort("SpacingZ")
else:
z = 1.0
vtk_set.vtkInstance.SetSpacing(x,y,z)
self.setResult("vtkImageData", vtk_set)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Array", (NDArray, 'Input Array Volume'))
reg.add_input_port(cls, "SpacingX", (basic.Float, 'X Spacing'))
reg.add_input_port(cls, "SpacingY", (basic.Float, 'Y Spacing'))
reg.add_input_port(cls, "SpacingZ", (basic.Float, 'Z Spacing'))
reg.add_output_port(cls, "vtkImageData", (reg.registry.get_descriptor_by_name('edu.utah.sci.vistrails.vtk', 'vtkImageData').module))
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