import SimpleITK as sitk

import urllib
import os.path

destination = '/tmp/TralitusSaltrator.jpg'
source = 'http://files.figshare.com/1546044/IMG_0974.jpg'

if not os.path.isfile(destination):
    urllib.urlretrieve(source,destination)

colorimage = sitk.ReadImage(destination)


image = sitk.VectorMagnitude(colorimage)

imshow(sitk.GetArrayFromImage(image));

import matplotlib.pyplot as plt
import matplotlib.cm as cm

imshow(sitk.GetArrayFromImage(image),cmap=cm.gray);

rgsmootherfilter = sitk.SmoothingRecursiveGaussianImageFilter()
rgsmootherfilter.SetSigma(2.5)
rgsmootherfilter.SetNormalizeAcrossScale(1)
rgsmoothedimage  = rgsmootherfilter.Execute(image)

imshow(sitk.GetArrayFromImage(rgsmoothedimage),cmap=cm.gray);

rgsmoothedimage  = rgsmootherfilter.Execute(image,3.5,1)

imshow(sitk.GetArrayFromImage(rgsmoothedimage),cmap=cm.gray);

medianfilter = sitk.MedianImageFilter()
medianfilter.SetRadius(3)
medianimage  = medianfilter.Execute(image)

imshow(sitk.GetArrayFromImage(medianimage),cmap=cm.gray);

medianimage  = medianfilter.Execute(image,[3,3])

imshow(sitk.GetArrayFromImage(medianimage),cmap=cm.gray);

curvatureflowfilter = sitk.CurvatureFlowImageFilter()
curvatureflowfilter.SetTimeStep(0.01)
curvatureflowfilter.SetNumberOfIterations(30)
curvatureflowimage  = curvatureflowfilter.Execute(image)

imshow(sitk.GetArrayFromImage(curvatureflowimage),cmap=cm.gray);

rgsmootherfilter.SetSigma(2.5)

imshow(sitk.GetArrayFromImage(curvatureflowimage),cmap=cm.gray);

grayscale_erode_filter = sitk.GrayscaleErodeImageFilter()
grayscale_eroded_image = grayscale_erode_filter.Execute(image)
grayscale_erode_filter.SetKernelRadius(3)
grayscale_erode_filter.SetKernelType(sitk.sitkBall)
imshow(sitk.GetArrayFromImage(grayscale_eroded_image),cmap=cm.gray);

grayscale_dilate_filter = sitk.GrayscaleDilateImageFilter()
grayscale_dilate_image = grayscale_dilate_filter.Execute(image)
grayscale_dilate_filter.SetKernelRadius(3)
grayscale_dilate_filter.SetKernelType(sitk.sitkBall)
imshow(sitk.GetArrayFromImage(grayscale_dilate_image),cmap=cm.gray);

canny_filter = sitk.CannyEdgeDetectionImageFilter()
float_image =  sitk.Cast(image, sitk.sitkFloat32)
canny_filter.SetLowerThreshold(50);
canny_filter.SetVariance(15);
canny_edges = canny_filter.Execute(float_image)
imshow(sitk.GetArrayFromImage(canny_edges),cmap=cm.gray);

rglaplacianfilter = sitk.LaplacianRecursiveGaussianImageFilter()
rglaplacianfilter.SetSigma(2.5)
rglaplacianfilter.SetNormalizeAcrossScale(1)
rglaplacianimage  = rglaplacianfilter.Execute(image)

imshow(sitk.GetArrayFromImage(rglaplacianimage),cmap=cm.gray);

otsu_filter = sitk.OtsuThresholdImageFilter()
otsu_image = otsu_filter.Execute(image)
imshow(sitk.GetArrayFromImage(otsu_image),cmap=cm.gray);

hole_filling_filter = sitk.VotingBinaryHoleFillingImageFilter()
hole_filling_filter.SetRadius(2)
hole_filling_filter.SetMajorityThreshold(1)
hole_filling_filter.SetBackgroundValue(0)
hole_filling_filter.SetForegroundValue(1)
hole_filled_image = hole_filling_filter.Execute(otsu_image)
imshow(sitk.GetArrayFromImage(hole_filled_image),cmap=cm.gray);

hole_filling_filter = sitk.VotingBinaryIterativeHoleFillingImageFilter()
hole_filling_filter.SetRadius(2)
hole_filling_filter.SetMajorityThreshold(1)
hole_filling_filter.SetBackgroundValue(0)
hole_filling_filter.SetForegroundValue(1)
hole_filled_image = hole_filling_filter.Execute(otsu_image)
imshow(sitk.GetArrayFromImage(hole_filled_image),cmap=cm.gray);

dir(sitk)