lassoan

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

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

# Define boundary points
import numpy as np

lassoan

# 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

import SampleData
sampleDataLogic = SampleData.SampleDataLogic()
masterVolumeNode = sampleDataLogic.downloadMRHead()

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

lassoan

# This example script demonstrates how a grow-cut
# operation can be performed without graphical user interface.

# The first half of the script downloads input data and creates seed segments.
# The second half of the script converts segments to merged labelmap (that's the required
# input format for grow-cut filter), computes the complete segmentation, and writes
# results into new segments.

# Generate input data
################################################

lassoan

# The module is now moved to SlicerSandbox extension:
#
#   https://github.com/PerkLab/SlicerSandbox/tree/master/SegmentCrossSectionArea
#

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

# 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

# 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

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

#

lassoan

# Generate input data
################################################

import SampleData
import numpy as np

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