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