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from core.modules.vistrails_module import Module, ModuleError
from Matrix import *
from Array import *
import scipy
from scipy import io, sparse
class ArrayUtilityModule(object):
my_namespace = 'scipy|matrix|utilities|Matlab'
class MatlabReader(ArrayUtilityModule, Module):
""" Read a Matlab .mat file into a SciPy matrix """
# Gather inputs here
def get_inputs(self):
if self.hasInputFromPort("Filename"):
self.fname = self.getInputFromPort("Filename")
else:
self.fname = self.getInputFromPort("File").name
# Set required members externally. This is just a helper function!
def set_member(self, name, val):
setattr(self, name, val)
# This is the work that the compute() method does
def process_compute(self):
m = io.loadmat(self.fname, None, 0)
vals = m.values()
for t in vals:
if type(t) == numpy.ndarray:
if t.dtype == 'object':
continue
mat = t
return (mat,)
# Take the returns from the processing and put them out on the outputs.
def set_outputs(self, results):
try:
out = Matrix()
out.set_matrix(sparse.csc_matrix(results[0]))
self.setResult("Matrix Output", out)
except:
pass
out_ar = NDArray()
out_ar.set_array(numpy.array(results[0]))
self.setResult("Array Output", out_ar)
# The compute method for vistrails compatibility
def compute(self):
self.get_inputs()
results = self.process_compute()
self.set_outputs(results)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
reg.add_input_port(cls, "File", (basic.File, 'File'))
reg.add_output_port(cls, "Matrix Output", (Matrix, 'Matrix Output'))
reg.add_output_port(cls, "Array Output", (NDArray, 'Array Output'))
class MatlabWriter(ArrayUtilityModule, Module):
""" Write a Matlab .mat file from a SciPy matrix """
def compute(self):
if self.hasInputFromPort("Filename"):
fname = self.getInputFromPort("Filename")
else:
fname = self.getInputFromPort("File").name
ar_list = self.getInputListFromPort("Arrays")
mat_list = self.getInputListFromPort("Matrices")
ar_dict = {}
for i in xrange(len(ar_list)):
ar_name = "array_" + str(i)
ar_dict[ar_name] = ar_list[i].get_array()
for i in xrange(len(mat_list)):
mat_name = "matrix_" + str(i)
ar_dict[mat_name] = mat_list[i].get_matrix()
io.savemat(fname, ar_dict)
@classmethod
def register(cls, reg, basic):
reg.add_module(cls, namespace=cls.my_namespace)
reg.add_input_port(cls, "Filename", (basic.String, 'Filename'))
reg.add_input_port(cls, "File", (basic.File, 'File'))
reg.add_input_port(cls, "Arrays", (NDArray, 'Arrays to Save'))
reg.add_input_port(cls, "Matrices", (Matrix, 'Matrices to Save'))
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