def aaaNumpyFile(self):
g =graph.Graph()
npfile = "/home/akreshuk/data/synapse_small_4d.npy"
reader = OpInputDataReader(graph=g)
reader.FilePath.setValue(npfile)
#out = reader.Output[:].wait()
#print out.shape
opFeatures = OpPixelFeaturesPresmoothed(graph=g)
opFeatures.Scales.setValue(self.scales)
opFeatures.FeatureIds.setValue(self.featureIds)
opFeatures.Input.connect(reader.Output)
opFeatures.Matrix.setValue(self.selectedFeatures[5])
out = opFeatures.Output[:].wait()
print out.shape
opFeaturesInterp = OpPixelFeaturesInterpPresmoothed(graph=g)
opFeaturesInterp.Scales.setValue(self.scales)
opFeaturesInterp.FeatureIds.setValue(self.featureIds)
opFeaturesInterp.Input.connect(reader.Output)
opFeaturesInterp.Matrix.setValue(self.selectedFeatures[5])
opFeaturesInterp.InterpolationScaleZ.setValue(2)
out = opFeaturesInterp.Output[:].wait()
print out.shape
def aaaAssert(self):
g = graph.Graph()
data = numpy.zeros((self.nx, self.ny, self.nz), dtype=numpy.float32)
for i in range(self.data3d.shape[2]):
data[:, :, i]=i
data = data.view(vigra.VigraArray)
data.axistags = vigra.VigraArray.defaultAxistags(3)
opFeaturesInterp = OpPixelFeaturesInterpPresmoothed(graph=g)
opFeaturesInterp.Input.setValue(data)
opFeaturesInterp.Scales.setValue(self.scales)
opFeaturesInterp.FeatureIds.setValue(self.featureIds)
opFeaturesInterp.InterpolationScaleZ.setValue(self.scaleZ)
opFeaturesInterp.Matrix.setValue(self.selectedFeatures[0])
out = opFeaturesInterp.Output[:].wait()
print "passed"
def runFeatures(self, data, dataInterp):
g = graph.Graph()
opFeatures = OpPixelFeaturesPresmoothed(graph=g)
opFeaturesInterp = OpPixelFeaturesInterpPresmoothed(graph=g)
opFeatures.Input.setValue(dataInterp)
opFeaturesInterp.Input.setValue(data)
opFeatures.Scales.setValue(self.scales)
opFeaturesInterp.Scales.setValue(self.scales)
opFeatures.FeatureIds.setValue(self.featureIds)
opFeaturesInterp.FeatureIds.setValue(self.featureIds)
opFeaturesInterp.InterpolationScaleZ.setValue(self.scaleZ)
#for i, imatrix in enumerate(self.selectedFeatures[0:1]):
for i, imatrix in enumerate(self.selectedFeatures):
opFeatures.Matrix.setValue(imatrix)
opFeaturesInterp.Matrix.setValue(imatrix)
outputInterpData = opFeatures.Output[:].wait()
outputInterpFeatures = opFeaturesInterp.Output[:].wait()
for iz in range(self.nz):
#for iz in range(2, 3):
#print iz, iz*self.scaleZ
try:
outputInterpDataSlice = opFeatures.Output[:, :, iz*self.scaleZ:iz*self.scaleZ+1, :].wait()
outputInterpFeaturesSlice = opFeaturesInterp.Output[:, :, iz, :].wait()
assert_array_almost_equal(outputInterpDataSlice, outputInterpFeaturesSlice, 1)
assert_array_almost_equal(outputInterpData[:, :, iz*self.scaleZ, 0], outputInterpFeatures[:, :, iz, 0], 1)
#assert_array_almost_equal(outputInterpDataSlice[:, :, 0, :], outputInterpData[:, :, iz*self.scaleZ, :], 3)
assert_array_almost_equal(outputInterpFeatures[:, :, iz, :], outputInterpFeaturesSlice[:, :, 0, :], 1)
except AssertionError:
print "failed for feature:", imatrix, i
print "failed for slice:", iz
print "inter data:", outputInterpData[:, :, iz*self.scaleZ, 0]
print "inter features:", outputInterpFeatures[:, :, iz, 0]
print "inter data slice:", outputInterpDataSlice[:, :, 0, 0]
print "inter features:", outputInterpFeaturesSlice[:, :, 0, 0]
raise AssertionError
