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segmentationNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLSegmentationNode')
# set value to the size of the larges cracks in the segment surfaces
maximumHoleSizeMm = 2.0

############
masterVolumeNode = segmentationNode.GetNodeReference(segmentationNode.GetReferenceImageGeometryReferenceRole())

# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
# To show segment editor widget (useful for debugging):

lassoan

# This script randomly warps a 3D volume and adds random translations, rotations,
# and save each resulting 3D volume (and a screenshot for quick overview)
#
# The script can be executed by copy-pasting into 3D Slicer's Python console
# or in a Jupyter notebook running 3D Slicer kernel (provided by SlicerJupyter extension).
#
# Prerequisites:
# - Recent Slicer-4.11 version
# - SlicerIGT extension installed (for random deformations)

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# This gist contained a script that automatically removes table from a CT volume.

# The code was improved and turned into a Slicer module, available in the Sandbox extension:
# https://github.com/PerkLab/SlicerSandbox#remove-ct-table
#
# Source code:
# https://github.com/PerkLab/SlicerSandbox/blob/master/RemoveCtTable/RemoveCtTable.py#L251

lassoan

# Source data can be obtained from http://lifesciencedb.jp/bp3d/ (tested with partof_BP3D_4.0_obj_99)
# These input file must be loaded into the scene:
# - partof_inclusion_relation_list.txt and partof_element_parts.txt (loaded as Table nodes)
# - OBJ files

shNode = slicer.mrmlScene.GetSubjectHierarchyNode()
sceneItemID = shNode.GetSceneItemID()

def getItemParentsFmaIds(shNode, itemShItemId):
    existingParentShItemId = shNode.GetItemParent(itemShItemId)

lassoan

# Load dry bone CT of skull into the scene and run this script to automatically segment endocranium

masterVolumeNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLScalarVolumeNode")
smoothingKernelSizeMm = 3.0  # this is used for closing small holes in the se

# Compute bone threshold value automatically
import vtkITK
thresholdCalculator = vtkITK.vtkITKImageThresholdCalculator()
thresholdCalculator.SetInputData(masterVolumeNode.GetImageData())
thresholdCalculator.SetMethodToOtsu()

lassoan

# Load/generate input data
################################################

# Load master volume
import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRBrainTumor1()

# Define boundary points
import numpy as np

lassoan

# Get a dental CT scan
import SampleData
volumeNode = SampleData.SampleDataLogic().downloadDentalSurgery()[1]

# Define curve
curveNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLMarkupsCurveNode')
curveNode.CreateDefaultDisplayNodes()
curveNode.GetCurveGenerator().SetNumberOfPointsPerInterpolatingSegment(25) # add more curve points between control points than the default 10
curveNode.AddControlPoint(vtk.vtkVector3d(-45.85526315789473,	-104.59210526315789,	74.67105263157896))
curveNode.AddControlPoint(vtk.vtkVector3d(-50.9078947368421,	-90.06578947368418,	66.4605263157895))

lassoan

import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
from array import array
import logging
import vtk.util.numpy_support
import numpy as np

#

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volumesDir = r"c:\Users\andra\OneDrive\Projects\SlicerTesting4\20190523-AutoWWWL\volumes"
screenshotsDir = r"c:\Users\andra\OneDrive\Projects\SlicerTesting4\20190523-AutoWWWL\screenshots"

methods = [
    ["baseline", autoContrastSlicerDefault],
    ["hist-0.1-99.9", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 0.1, 99.9, 0.00, 0.0)], # = itksnap
    ["hist-1.0-99.9", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.9, 0.10, 0.0)],
    ["hist-1.0-99.0-x0.10", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.0, 0.10, 0.10)],
    ["hist-1.0-99.0-x0.20", lambda fn: autoContrastVtkImageHistogramStatisticsDefault(fn, 1.0, 99.0, 0.10, 0.20)],
    ]

lassoan

# Download a sample data set (chest CT)
import SampleData
masterVolumeNode = SampleData.SampleDataLogic().downloadCTChest()

# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass("vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(masterVolumeNode)

# Create temporary segment editor to get access to effects