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import matplotlib.pyplot as plt
%matplotlib inline
import SimpleITK as sitk
# Download data to work on
from downloaddata import fetch_data as fdata


    

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from myshow import myshow, myshow3d


    

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img_T1 = sitk.ReadImage(fdata("nac-hncma-atlas2013-Slicer4Version/Data/A1_grayT1.nrrd"))
img_T2 = sitk.ReadImage(fdata("nac-hncma-atlas2013-Slicer4Version/Data/A1_grayT2.nrrd"))
img_labels = sitk.ReadImage(fdata("nac-hncma-atlas2013-Slicer4Version/Data/hncma-atlas.nrrd"))


    

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sitk.Show(img_T1)


    

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pt = (110, 120, 132)


    

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seg = sitk.Image(img_T1.GetSize(), sitk.sitkUInt8)
seg.CopyInformation(img_T1)
seg[pt] = 1
seg = sitk.BinaryDilate(seg, 3)


    

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img_T1_255 = sitk.Cast(sitk.RescaleIntensity(img_T1), sitk.sitkUInt8)
sitk.Show(sitk.LabelOverlay(img_T1_255, seg))


    

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sitk.ConnectedThreshold?


    

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seg = sitk.ConfidenceConnected(img_T1, [pt], numberOfIterations=0, multiplier=2)
sitk.Show(sitk.LabelOverlay(img_T1_255, seg))


    

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sitk.VectorConfidenceConnected?


    

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img_multi = sitk.Compose(img_T1, img_T2)
seg = sitk.VectorConfidenceConnected(img_multi, [pt], numberOfIterations=2, multiplier=4.5)
sitk.Show(sitk.LabelOverlay(img_T1_255, seg))


    

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size = img_multi.GetSize()
myshow3d(sitk.LabelOverlay(img_T1_255,seg),yslices=range(50,size[1]-50,15), zslices=range(50,size[2]-50,15), dpi=30)


    

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for m in (2.5, 3.0, 3.5, 4.0):
    seg = sitk.VectorConfidenceConnected(img_multi, [pt], numberOfIterations=2, multiplier=m)
    myshow3d(sitk.LabelOverlay(img_T1_255,seg),yslices=range(50,size[1]-50,15), zslices=range(50,size[2]-50,15), dpi=30, title="VectorConfidence multi="+str(m))


    

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sitk.Show(sitk.LabelOverlay(img_T1_255, seg))
sitk.Show(sitk.LaplacianRecursiveGaussian(img_T1,sigma=1.0))


    

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components = (img_T1, img_T2, sitk.LaplacianRecursiveGaussian(img_T1, .5), sitk.LaplacianRecursiveGaussian(img_T1, .5))
components = [sitk.Cast(img, sitk.sitkFloat32) for img in components]
img_multi = sitk.Compose(components)


    

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