def make_compare_images(image, reference_file, tolerance=0.1):
reader = imagereader.vmtkImageReader()
try:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.realpath(__file__))), 'vmtk-test-data', 'imagereference')
if not os.path.isdir(datadir): raise ValueError()
except ValueError:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.realpath(__file__))))),
'vmtk-test-data', 'imagereference')
if not os.path.isdir(datadir):
raise ValueError('the vmtk-test-data repository cannot be found at the same level as vmtk. expected it to be at', datadir)
reader.InputFileName = os.path.join(datadir, reference_file)
reader.Execute()
comp = imagecompare.vmtkImageCompare()
comp.Image = image
comp.ReferenceImage = reader.Image
comp.Method = 'subtraction'
comp.Tolerance = tolerance
comp.Execute()
return comp.Result
def make_compare_images(image, reference_file, tolerance=0.1):
reader = imagereader.vmtkImageReader()
try:
datadir = os.path.join(
os.path.dirname(os.path.dirname(os.path.realpath(__file__))),
'vmtk-test-data', 'imagereference')
if not os.path.isdir(datadir): raise ValueError()
except ValueError:
datadir = os.path.join(
os.path.dirname(
os.path.dirname(
os.path.dirname(
os.path.dirname(os.path.realpath(__file__))))),
'vmtk-test-data', 'imagereference')
if not os.path.isdir(datadir):
raise ValueError(
'the vmtk-test-data repository cannot be found at the same level as vmtk. expected it to be at',
datadir)
reader.InputFileName = os.path.join(datadir, reference_file)
reader.Execute()
comp = imagecompare.vmtkImageCompare()
comp.Image = image
comp.ReferenceImage = reader.Image
comp.Method = 'subtraction'
comp.Tolerance = tolerance
comp.Execute()
return comp.Result
def imageObjectEnhance():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
imageObjEn = imageEnhance.vmtkImageObjectEnhancement()
imageObjEn.Image = reader.Image
# default arguments
imageObjEn.SigmaMin = 1.0
imageObjEn.SigmaMax = 1.0
imageObjEn.NumberOfSigmaSteps = 1
imageObjEn.ScaledObjectness = 0
imageObjEn.Alpha = 0.5
imageObjEn.Beta = 0.5
imageObjEn.Gamma = 5.0
imageObjEn.ObjectDimension = 2
imageObjEn.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = imageObjEn.Image
viewer.Execute()
def test_read_vti_image(input_datadir, compare_images):
name = __name__ + '_test_read_vti_image.vti'
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir, 'vase.vti')
reader.Execute()
assert compare_images(reader.Image, name) == True
def levelset_seg():
'''
图像的水平集分割，生成等值面
'''
input_file = "vesselVoi.vti"
output_filename = 'vessellevelset.vtp'
reader = imagereader.vmtkImageReader()
# 图像序
reader.InputFileName = input_file
reader.Format = "vtkxml"
reader.UseITKIO = 0
reader.Execute()
levelset = levelsetseg.vmtkLevelSetSegmentation()
levelset.Image = reader.Image
levelset.LevelSetsType = "geodesic" # '["geodesic","curves","threshold","laplacian"]'
levelset.FeatureImageType = "gradient" # '["vtkgradient","gradient","upwind","fwhm"]'
levelset.Execute()
marchingcube = marchingcubes.vmtkMarchingCubes()
marchingcube.Image = levelset.LevelSetsOutput
marchingcube.Execute()
writer = surfacewriter.vmtkSurfaceWriter()
writer.Surface = marchingcube.Surface
writer.Format = "vtkxml"
writer.OutputFileName = output_filename
writer.Execute()
def transform_image(input_datadir):
import vmtk.vmtkimagereader as imagereader
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir,
'image-test-transform.nrrd')
reader.Execute()
return (reader.Image, reader.XyzToRasMatrixCoefficients)
def imagefeature():
'''
图像的水平集分割，生成等值面
'''
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
feature = imageFeatures.vmtkImageFeatures()
feature.Image = reader.Image
feature.FWHMRadius = [0.5, 0.5, 0.5]
feature.FeatureImageType = "gradient" # '["vtkgradient","gradient","upwind","fwhm"]'
feature.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = reader.Image
viewer.Execute()
def imagevoi(input_datadir, output_filename):
'''
提取图像感兴趣的区域
'''
print("Hello")
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
#print(len(filelist))
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
selector = imagevoiselector.vmtkImageVOISelector()
selector.Image = reader.Image
selector.Execute()
writer = imagewriter.vmtkImageWriter()
writer.Image = selector.Image
writer.Format = "vtkxml"
writer.OutputFileName = output_filename
writer.WindowLevel = [150, 1200] #窗宽和窗位
writer.Execute()
def test_read_vti_image(input_datadir, compare_images):
name = __name__ + '_test_read_vti_image.vti'
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir, 'vase.vti')
reader.Execute()
assert compare_images(reader.Image, name) == True
def level_set_image(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(input_datadir, 'aorta-final-levelset.mha')
read.Execute()
return read.Image
def feature_image(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(input_datadir, 'aorta-feature-image.mha')
read.Execute()
return read.Image
def initial_level_sets(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(input_datadir, 'aorta-fastmarching-initial-levelset.mha')
read.Execute()
return read.Image
def feature_image(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(input_datadir, 'aorta-feature-image.mha')
read.Execute()
return read.Image
def level_set_image(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(input_datadir,
'aorta-final-levelset.mha')
read.Execute()
return read.Image
def initial_level_sets(input_datadir):
import vmtk.vmtkimagereader as reader
import os
read = reader.vmtkImageReader()
read.InputFileName = os.path.join(
input_datadir, 'aorta-fastmarching-initial-levelset.mha')
read.Execute()
return read.Image
def imageFeature():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
normalize = imagenormalize.vmtkImageNormalize()
normalize.Image = reader.Image
normalize.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = normalize.Image
viewer.Execute()
def pngToVti():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/Spine_Bone_Ext/'
outputFileName = 'vessel.vti'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
#print(len(filelist))
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0 ,512 ,0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
writer = imagewriter.vmtkImageWriter()
writer.Image = reader.Image
writer.Format = "vtkxml"
writer.OutputFileName = outputFileName
writer.WindowLevel = [150, 1200] #窗宽和窗位
writer.Execute()
def imageFeature():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
morphology = imagemorphology.vmtkImageMorphology()
morphology.Operation = "erode" # '["dilate","erode","open","close"]'
morphology.BallRadius = [1, 1, 1]
morphology.Image = reader.Image
morphology.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = morphology.Image
viewer.Execute()
def imageFeature():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/WU_Lung_Vessel_Ext/'
reader = imagereader.vmtkImageReader()
# 图像序
filelist = os.listdir(input_datadir)
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, len(filelist)]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
imageVesselEnhance = imagevesseEnhance.vmtkImageVesselEnhancement()
imageVesselEnhance.Image = reader.Image
imageVesselEnhance.Method = "vedm" #["frangi","sato","ved","vedm"]
imageVesselEnhance.SigmaStepMethod = "equispaced" #["equispaced","logarithmic"]
imageVesselEnhance.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = imageVesselEnhance.Image
viewer.Execute()
def ostsuerThreshold():
input_datadir = 'C:/Users/chenjiaxing/Desktop/CT-Data/png/Spine_Bone_Ext/'
reader = imagereader.vmtkImageReader()
# 单幅图像
# reader.InputFileName = os.path.join(input_datadir, '170.png')
# 图像序列
reader.InputFilePrefix = input_datadir
reader.InputFilePattern = "%s%d.png"
reader.DataExtent = [0, 512, 0, 512, 1, 188]
reader.Format = "png"
reader.UseITKIO = 0
reader.Execute()
otsuer = otsu.vmtkImageOtsuThresholds()
otsuer.Image = reader.Image
otsuer.NumberOfThresholds = 2
otsuer.Execute()
viewer = imageviewer.vmtkImageViewer()
viewer.Image = otsuer.Image
viewer.Execute()
def transform_image(input_datadir):
import vmtk.vmtkimagereader as imagereader
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir, 'image-test-transform.nrrd')
reader.Execute()
return (reader.Image, reader.XyzToRasMatrixCoefficients)
def aorta_image(input_datadir):
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta.mha')
reader.Execute()
return reader.Image
def aorta_image(input_datadir):
reader = imagereader.vmtkImageReader()
reader.InputFileName = os.path.join(input_datadir, 'aorta.mha')
reader.Execute()
return reader.Image
