def __init__(self, parent):

parent.title = "Tissue Model Creator" # TODO make this more human readable by adding spaces

parent.categories = ["Perk Tutor"]

parent.dependencies = []

parent.contributors = ["Matthew Holden (Queen's University)"] # replace with "Firstname Lastname (Org)"

parent.helpText = """

The purpose of the Tissue Model Creator module is to create a model based on a set of collected fiducial points. For help on how to use this module visit: <a href='http://www.github.com/PerkTutor/TissueModelCreator/wiki'>Tissue Model Creator</a>.

"""

parent.acknowledgementText = """

This work was was funded by Cancer Care Ontario and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO).

""" # replace with organization, grant and thanks.

parent.icon = qt.QIcon( "TissueModelCreator.png" )

self.parent = parent

# Add this test to the SelfTest module's list for discovery when the module

# is created. Since this module may be discovered before SelfTests itself,

# create the list if it doesn't already exist.

try:

slicer.selfTests

except AttributeError:

slicer.selfTests = {}

slicer.selfTests['TissueModelCreator'] = self.runTest

def runTest(self):

tester = TissueModelCreatorTest()

def __init__(self, parent = None):

if not parent:

self.parent = slicer.qMRMLWidget()

self.parent.setLayout(qt.QVBoxLayout())

self.parent.setMRMLScene(slicer.mrmlScene)

else:

self.parent = parent

self.layout = self.parent.layout()

if not parent:

self.setup()

self.parent.show()

def setup(self):

# Instantiate and connect widgets ...

# Comment these out when not debugging

#

# Reload and Test area

#

reloadCollapsibleButton = ctk.ctkCollapsibleButton()

reloadCollapsibleButton.text = "Reload && Test"

self.layout.addWidget(reloadCollapsibleButton)

reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)

# reload button

# (use this during development, but remove it when delivering

# your module to users)

self.reloadButton = qt.QPushButton("Reload")

self.reloadButton.toolTip = "Reload this module."

self.reloadButton.name = "TissueModelCreator Reload"

reloadFormLayout.addWidget(self.reloadButton)

self.reloadButton.connect('clicked()', self.onReload)

# reload and test button

# (use this during development, but remove it when delivering

# your module to users)

self.reloadAndTestButton = qt.QPushButton("Reload and Test")

self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."

reloadFormLayout.addWidget(self.reloadAndTestButton)

self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)

#

# Display Area

#

displayCollapsibleButton = ctk.ctkCollapsibleButton()

displayCollapsibleButton.text = "Display"

self.layout.addWidget(displayCollapsibleButton)

# Layout within the dummy collapsible button

displayFormLayout = qt.QFormLayout(displayCollapsibleButton)

#

# input fiducials selector

#

self.markupSelector = slicer.qMRMLNodeComboBox()

self.markupSelector.nodeTypes = ( ("vtkMRMLMarkupsFiducialNode"), "" )

self.markupSelector.addEnabled = False

self.markupSelector.removeEnabled = False

self.markupSelector.noneEnabled = False

self.markupSelector.showHidden = False

self.markupSelector.showChildNodeTypes = False

self.markupSelector.setMRMLScene( slicer.mrmlScene )

self.markupSelector.setToolTip( "Pick the markup node for the algorithm." )

displayFormLayout.addRow( "Select Markup Node: ", self.markupSelector )

#

# Depth slider

#

self.depthSlider = ctk.ctkSliderWidget()

self.depthSlider.maximum = 1000

self.depthSlider.minimum = 0

self.depthSlider.value = 100

self.depthSlider.setToolTip( "Select the depth of the tissue." )

displayFormLayout.addRow( "Depth (mm): ", self.depthSlider )

#

# Flip (ie flip) checkbox

#

self.flipCheckBox = qt.QCheckBox()

self.flipCheckBox.setCheckState( False )

self.flipCheckBox.setToolTip( "Flip the tissue so it is in the other direction." )

self.flipCheckBox.setText( "Flip" )

displayFormLayout.addRow( self.flipCheckBox )

#

# Force plane (ie plane) checkbox

#

self.planeCheckBox = qt.QCheckBox()

self.planeCheckBox.setCheckState( False )

self.planeCheckBox.setToolTip( "Force a plane to fit the collected points on the surface." )

self.planeCheckBox.setText( "Plane" )

displayFormLayout.addRow( self.planeCheckBox )

#

# Create Button

#

self.createButton = qt.QPushButton( "Create" )

self.createButton.toolTip = "Create a tissue model."

self.createButton.enabled = True

displayFormLayout.addRow( self.createButton )

#

# Status Label

#

self.statusLabel = qt.QLabel( "Status:" )

self.statusLabel.toolTip = "Status of whether the tissue model was successfully created."

self.statusLabel.enabled = True

displayFormLayout.addRow( self.statusLabel )

# connections

self.createButton.connect( 'clicked(bool)', self.onCreateButtonClicked )

# Add vertical spacer

self.layout.addStretch(1)

def cleanup(self):

pass

def onCreateButtonClicked(self):

logic = TissueModelCreatorLogic()

surfaceClosed = logic.run( self.markupSelector.currentNode(), self.depthSlider.value, self.planeCheckBox.checked, self.flipCheckBox.checked )

if ( surfaceClosed == True ):

self.statusLabel.setText( "Status: Success!" )

else:

self.statusLabel.setText( "Status: Failed!" )

def onReload(self,moduleName="TissueModelCreator"):

"""Generic reload method for any scripted module.

ModuleWizard will subsitute correct default moduleName.

"""

import imp, sys, os, slicer

widgetName = moduleName + "Widget"

# reload the source code

# - set source file path

# - load the module to the global space

filePath = eval('slicer.modules.%s.path' % moduleName.lower())

p = os.path.dirname(filePath)

if not sys.path.__contains__(p):

sys.path.insert(0,p)

fp = open(filePath, "r")

globals()[moduleName] = imp.load_module(

moduleName, fp, filePath, ('.py', 'r', imp.PY_SOURCE))

fp.close()

# rebuild the widget

# - find and hide the existing widget

# - create a new widget in the existing parent

parent = slicer.util.findChildren(name='%s Reload' % moduleName)[0].parent().parent()

for child in parent.children():

try:

child.hide()

except AttributeError:

pass

# Remove spacer items

item = parent.layout().itemAt(0)

while item:

parent.layout().removeItem(item)

item = parent.layout().itemAt(0)

# delete the old widget instance

if hasattr(globals()['slicer'].modules, widgetName):

getattr(globals()['slicer'].modules, widgetName).cleanup()

# create new widget inside existing parent

globals()[widgetName.lower()] = eval(

'globals()["%s"].%s(parent)' % (moduleName, widgetName))

globals()[widgetName.lower()].setup()

setattr(globals()['slicer'].modules, widgetName, globals()[widgetName.lower()])

def onReloadAndTest(self,moduleName="TissueModelCreator"):

try:

self.onReload()

evalString = 'globals()["%s"].%sTest()' % (moduleName, moduleName)

tester = eval(evalString)

tester.runTest()

except Exception, e:

import traceback

traceback.print_exc()

qt.QMessageBox.warning(slicer.util.mainWindow(),

"""This class should implement all the actual

computation done by your module. The interface

should be such that other python code can import

this class and make use of the functionality without

requiring an instance of the Widget

"""

def __init__(self):

pass

def run( self, markupNode, depth, fitPlane, flip ):

"""

Run the actual algorithm

"""

# Get all of the fiducial nodes and convert to vtkPoints

points = vtk.vtkPoints()

for i in range( 0, markupNode.GetNumberOfFiducials() ):

currentCoordinates = [ 0, 0, 0 ]

markupNode.GetNthFiducialPosition( i, currentCoordinates )

points.InsertNextPoint( currentCoordinates )

# Check that there is non-zero range in all coordinate directions

pointsBounds = [ 0, 0, 0, 0, 0, 0 ]

points.GetBounds( pointsBounds )

if ( pointsBounds[0] == pointsBounds [1] or pointsBounds[2] == pointsBounds [3] or pointsBounds[4] == pointsBounds [5] ):

print "Tissue Model Creator: Points have no extent in one or more coordinate directions."

return False

# Create a polydata object from the points

# The reversiness doesn't matter - we will fix it later if it os wrong

if ( fitPlane ):

surfacePolyData = self.PointsToPlanePolyData( points, True )

else:

surfacePolyData = self.PointsToSurfacePolyData( points, True )

surfaceCleaner = vtk.vtkCleanPolyData()

surfaceCleaner.SetInputData( surfacePolyData )

surfaceCleaner.Update()

surfacePolyData = surfaceCleaner.GetOutput()

mean = self.CalculateMean( points )

surfaceBase = [ 0, 0, 0 ]

surfaceDir1 = [ 0, 0, 0 ]

surfaceDir2 = [ 0, 0, 0 ]

surfaceNormal = [ 0, 0, 0 ]

self.CalculatePlane( surfacePolyData.GetPoints(), surfaceBase, surfaceDir1, surfaceDir2, surfaceNormal )

if ( flip == True ):

surfaceNormal[ 0 ] = - surfaceNormal[ 0 ]

surfaceNormal[ 1 ] = - surfaceNormal[ 1 ]

surfaceNormal[ 2 ] = - surfaceNormal[ 2 ]

extremePointIndex = self.FindExtremePoint( surfacePolyData.GetPoints(), surfaceBase, surfaceNormal )

reverse = self.ReverseNormals( extremePointIndex, surfacePolyData, surfaceNormal )

# Reverse the normals if necessary

reverseFilter = vtk.vtkReverseSense()

reverseFilter.SetInputData( surfacePolyData )

reverseFilter.SetReverseCells( reverse )

reverseFilter.SetReverseNormals( reverse )

reverseFilter.Update()

surfacePolyData = reverseFilter.GetOutput()

untransDeepPolyData = vtk.vtkPolyData()

untransDeepPolyData.DeepCopy( surfacePolyData )

# Make the normals opposite the surface's normals

reverseFilter = vtk.vtkReverseSense()

reverseFilter.SetInputData( untransDeepPolyData )

reverseFilter.SetReverseCells( True )

reverseFilter.SetReverseNormals( True )

reverseFilter.Update()

untransDeepPolyData = reverseFilter.GetOutput()

deepTransform = vtk.vtkTransform()

deepTransform.Translate( depth * surfaceNormal[0], depth * surfaceNormal[1], depth * surfaceNormal[2] )

deepTransformFilter = vtk.vtkTransformPolyDataFilter()

deepTransformFilter.SetInputData( untransDeepPolyData )

deepTransformFilter.SetTransform( deepTransform )

deepTransformFilter.Update()

deepPolyData = deepTransformFilter.GetOutput()

surfaceHullPoints = self.GetBoundaryPoints( surfacePolyData )

deepHullPoints = self.GetBoundaryPoints( deepPolyData )

# Apparently, the joining needs an offset for the plane, but not for the surface reconstruction

if ( fitPlane ):

jointHullPolyData = self.JoinBoundaryPoints( surfaceHullPoints, deepHullPoints, 1 )

else:

jointHullPolyData = self.JoinBoundaryPoints( surfaceHullPoints, deepHullPoints, 0 )

# Append all of the polydata together

tissuePolyDataAppend = vtk.vtkAppendPolyData()

tissuePolyDataAppend.AddInputData( surfacePolyData )

tissuePolyDataAppend.AddInputData( deepPolyData )

tissuePolyDataAppend.AddInputData( jointHullPolyData )

tissuePolyDataAppend.Update()

# Clean up so the surface is closed

tissueCleaner = vtk.vtkCleanPolyData()

tissueCleaner.SetInputData( tissuePolyDataAppend.GetOutput() )

tissueCleaner.Update()

tissueModelPolyData = tissueCleaner.GetOutput()

# Add the data to a model

tissueModel = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )

slicer.mrmlScene.AddNode( tissueModel )

tissueModel.SetName( "TissueModel" )

tissueModel.SetAndObservePolyData( tissueModelPolyData )

tissueModel.SetScene( slicer.mrmlScene )

# Finally display the model

tissueModelDisplay = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )

slicer.mrmlScene.AddNode( tissueModelDisplay )

tissueModel.SetAndObserveDisplayNodeID( tissueModelDisplay.GetID() )

tissueModelDisplay.SetScene( slicer.mrmlScene )

tissueModelDisplay.SetInputPolyDataConnection( tissueModel.GetPolyDataConnection() )

# Check to make sure the model is a closed surface

edgesFilter = vtk.vtkFeatureEdges()

edgesFilter.FeatureEdgesOff()

edgesFilter.BoundaryEdgesOn()

edgesFilter.NonManifoldEdgesOn()

edgesFilter.SetInputData( tissueModel.GetPolyData() )

edgesFilter.Update()

if ( edgesFilter.GetOutput().GetNumberOfCells() != 0 ):

print "Tissue Model Creator: Surface is not closed."

return False

return True

def PointsToSurfacePolyData( self, inPoints, reverse ):

# Create a polydata object from the points

pointsPolyData = vtk.vtkPolyData()

pointsPolyData.SetPoints( inPoints )

# Create the surface filter from the polydata

surfaceFilter = vtk.vtkSurfaceReconstructionFilter()

surfaceFilter.SetInputData( pointsPolyData )

surfaceFilter.Update()

# Do the contouring filter, and reverse to ensure it works properly

contourFilter = vtk.vtkContourFilter()

contourFilter.SetValue( 0, 0.0 )

contourFilter.SetInputData( surfaceFilter.GetOutput() )

contourFilter.Update()

# Reverse the normals if necessary

reverseFilter = vtk.vtkReverseSense()

reverseFilter.SetInputData( contourFilter.GetOutput() )

reverseFilter.SetReverseCells( reverse )

reverseFilter.SetReverseNormals( reverse )

reverseFilter.Update()

# Reset the scaling to let the surface match the points

fiducialBounds = [ 0, 0, 0, 0, 0, 0 ]

pointsPolyData.GetBounds( fiducialBounds )

tissueBounds = [ 0, 0, 0, 0, 0, 0 ]

reverseFilter.GetOutput().GetBounds( tissueBounds )

scaleX = ( fiducialBounds[1] - fiducialBounds[0] ) / ( tissueBounds[1] - tissueBounds[0] )

scaleY = ( fiducialBounds[3] - fiducialBounds[2] ) / ( tissueBounds[3] - tissueBounds[2] )

scaleZ = ( fiducialBounds[5] - fiducialBounds[4] ) / ( tissueBounds[5] - tissueBounds[4] )

transform = vtk.vtkTransform()

transform.Translate( fiducialBounds[0], fiducialBounds[2], fiducialBounds[4] )

transform.Scale( scaleX, scaleY, scaleZ )

transform.Translate( - tissueBounds[0], - tissueBounds[2], - tissueBounds[4] )

transformFilter = vtk.vtkTransformPolyDataFilter()

transformFilter.SetInputData( reverseFilter.GetOutput() )

transformFilter.SetTransform( transform )

transformFilter.Update()

return transformFilter.GetOutput()

def PointsToPlanePolyData( self, inPoints, reverse ):

# Create the oriented bounding box

# This gives us one plane on the bounding box, not the plane of best fit

corner = [ 0, 0, 0 ]

maxVector = [ 0, 0, 0 ]

midVector = [ 0, 0, 0 ]

minVector = [ 0, 0, 0 ]

size = [ 0, 0, 0 ]

obb = vtk.vtkOBBTree()

obb.ComputeOBB( inPoints, corner, maxVector, midVector, minVector, size )

# Calculate the mean of the points on the plane

base = self.CalculateMean( inPoints )

relBase = [ 0, 0, 0 ]

# Find the projection of the mean point in the minVector direction

vtk.vtkMath().Subtract( base, corner, relBase )

normal = minVector[:]

vtk.vtkMath().Normalize( normal )

dot = vtk.vtkMath().Dot( relBase, normal )

dot = 0

proj = normal[:]

vtk.vtkMath().MultiplyScalar( proj, dot )

print dot

# Find the points on the plane

origin = [ 0, 0, 0 ]

point1 = [ 0, 0, 0 ]

point2 = [ 0, 0, 0 ]

vtk.vtkMath().Add( corner, proj, origin )

vtk.vtkMath().Add( origin, maxVector, point1 )

vtk.vtkMath().Add( origin, midVector, point2 )

# Construct the plane

plane = vtk.vtkPlaneSource()

plane.SetOrigin( origin )

plane.SetPoint1( point1 )

plane.SetPoint2( point2 )

plane.Update()

return plane.GetOutput()

def CalculateMean( self, inPoints ):

mean = [ 0, 0, 0 ]

for i in range( 0, inPoints.GetNumberOfPoints() ):

currPoint = [ 0, 0, 0 ]

inPoints.GetPoint( i, currPoint )

mean[ 0 ] = mean[ 0 ] + currPoint[ 0 ]

mean[ 1 ] = mean[ 1 ] + currPoint[ 1 ]

mean[ 2 ] = mean[ 2 ] + currPoint[ 2 ]

if ( inPoints.GetNumberOfPoints() > 0 ):

mean[ 0 ] = mean[ 0 ] / inPoints.GetNumberOfPoints()

mean[ 1 ] = mean[ 1 ] / inPoints.GetNumberOfPoints()

mean[ 2 ] = mean[ 2 ] / inPoints.GetNumberOfPoints()

return mean

def CalculatePlane( self, inPoints, base, dir1, dir2, normal ):

# Create arrays for the dataset

points2D = vtk.vtkPoints()

arrayX = vtk.vtkDoubleArray()

arrayX.SetNumberOfComponents( 1 )

arrayX.SetName ( 'X' )

arrayY = vtk.vtkDoubleArray()

arrayY.SetNumberOfComponents( 1 )

arrayY.SetName ( 'Y' )

arrayZ = vtk.vtkDoubleArray()

arrayZ.SetNumberOfComponents( 1 )

arrayZ.SetName ( 'Z' )

# Add the points to the table

for i in range( 0, inPoints.GetNumberOfPoints() ):

currPoint = [ 0, 0, 0 ]

inPoints.GetPoint( i, currPoint )

arrayX.InsertNextValue( currPoint[ 0 ] )

arrayY.InsertNextValue( currPoint[ 1 ] )

arrayZ.InsertNextValue( currPoint[ 2 ] )

# Create a table for the dataset

table = vtk.vtkTable()

table.AddColumn( arrayX )

table.AddColumn( arrayY )

table.AddColumn( arrayZ )

# Setting up the PCA

pca = vtk.vtkPCAStatistics()

pca.SetInputData( vtk.vtkStatisticsAlgorithm.INPUT_DATA, table )

pca.SetColumnStatus( 'X', 1 )

pca.SetColumnStatus( 'Y', 1 )

pca.SetColumnStatus( 'Z', 1 )

pca.RequestSelectedColumns()

pca.SetDeriveOption( True )

pca.Update()

eigvec = vtk.vtkDoubleArray()

pca.GetEigenvectors( eigvec )

eigvec.GetTuple( 0, dir1 )

eigvec.GetTuple( 1, dir2 )

eigvec.GetTuple( 2, normal )

mean = self.CalculateMean( inPoints )

base[0] = mean[0]

base[1] = mean[1]

base[2] = mean[2]

def GetBoundaryPoints( self, inPolyData ):

featureEdges = vtk.vtkFeatureEdges()

featureEdges.FeatureEdgesOff()

featureEdges.NonManifoldEdgesOff()

featureEdges.ManifoldEdgesOff()

featureEdges.BoundaryEdgesOn()

featureEdges.SetInputData( inPolyData )

featureEdges.Update()

stripper = vtk.vtkStripper()

stripper.SetInputData( featureEdges.GetOutput() )

stripper.Update()

cleaner = vtk.vtkCleanPolyData()

cleaner.SetInputData( stripper.GetOutput() )

cleaner.Update()

return cleaner.GetOutput().GetPoints()

def JoinBoundaryPoints( self, hullPoints1, hullPoints2, offset ):

if ( hullPoints1.GetNumberOfPoints() != hullPoints2.GetNumberOfPoints() ):

return

joiningAppend = vtk.vtkAppendPolyData()

numPoints = hullPoints1.GetNumberOfPoints()

for i in range( 0, numPoints ):

currPointsForSurface = vtk.vtkPoints()

point1 = [ 0, 0, 0 ]

hullPoints1.GetPoint( ( i - offset )% numPoints, point1 )

currPointsForSurface.InsertNextPoint( point1[ 0 ], point1[ 1 ], point1[ 2 ] )

point2 = [ 0, 0, 0 ]

hullPoints2.GetPoint( ( - i ) % numPoints, point2 )

currPointsForSurface.InsertNextPoint( point2[ 0 ], point2[ 1 ], point2[ 2 ] )

# Observe that the deep is flipped from the surface

# Must proceed in opposite orders

point3 = [ 0, 0, 0 ]

hullPoints1.GetPoint( ( i + 1 - offset ) % numPoints, point3 )

currPointsForSurface.InsertNextPoint( point3[ 0 ], point3[ 1 ], point3[ 2 ] )

point4 = [ 0, 0, 0 ]

hullPoints2.GetPoint( ( - ( i + 1 ) ) % numPoints, point4 )

currPointsForSurface.InsertNextPoint( point4[ 0 ], point4[ 1 ], point4[ 2 ] )

# We know what the triangles should look like, so create them manually

# Note: The order here is important - ensure the triangles face the correct way

triangle1 = vtk.vtkTriangle()

triangle1.GetPointIds().SetId( 0, 0 )

triangle1.GetPointIds().SetId( 1, 1 )

triangle1.GetPointIds().SetId( 2, 2 )

triangle2 = vtk.vtkTriangle()

triangle2.GetPointIds().SetId( 0, 3 )

triangle2.GetPointIds().SetId( 1, 2 )

triangle2.GetPointIds().SetId( 2, 1 )

triangles = vtk.vtkCellArray()

triangles.InsertNextCell( triangle1 )

triangles.InsertNextCell( triangle2 )

currPolyDataForSurface = vtk.vtkPolyData()

currPolyDataForSurface.SetPoints( currPointsForSurface )

currPolyDataForSurface.SetPolys( triangles )

joiningAppend.AddInputData( currPolyDataForSurface )

joiningAppend.Update()

return joiningAppend.GetOutput()

def FindExtremePoint( self, surfacePoints, surfaceBase, surfaceNormal ):

extremePointIndex = 1

extremePointProjection = 0

# Find the point with the smallest projection (ie most negative) onto the surface normal

for i in range( surfacePoints.GetNumberOfPoints() ):

currPoint = [ 0, 0, 0 ]

surfacePoints.GetPoint( i, currPoint )

currProjection = ( currPoint[ 0 ] - surfaceBase [ 0 ] ) * surfaceNormal [ 0 ] + ( currPoint[ 1 ] - surfaceBase [ 1 ] ) * surfaceNormal [ 1 ] + ( currPoint[ 2 ] - surfaceBase [ 2 ] ) * surfaceNormal [ 2 ]

if ( currProjection < extremePointProjection ):

extremePointProjection = currProjection

extremePointIndex = i

return extremePointIndex

def ReverseNormals( self, extremePointIndex, surfacePolyData, surfaceNormal ):

normalArray = surfacePolyData.GetPointData().GetNormals()

extremePointNormal = [ 0, 0, 0 ]

normalArray.GetTuple( extremePointIndex, extremePointNormal )

if ( vtk.vtkMath.Dot( extremePointNormal, surfaceNormal ) > 0 ):

return True

"""

This is the test case for your scripted module.

"""

def delayDisplay(self,message,msec=1000):

"""This utility method displays a small dialog and waits.

This does two things: 1) it lets the event loop catch up

to the state of the test so that rendering and widget updates

have all taken place before the test continues and 2) it

shows the user/developer/tester the state of the test

so that we'll know when it breaks.

"""

print(message)

self.info = qt.QDialog()

self.infoLayout = qt.QVBoxLayout()

self.info.setLayout(self.infoLayout)

self.label = qt.QLabel(message,self.info)

self.infoLayout.addWidget(self.label)

qt.QTimer.singleShot(msec, self.info.close)

self.info.exec_()

def setUp(self):

""" Do whatever is needed to reset the state - typically a scene clear will be enough.

"""

slicer.mrmlScene.Clear(0)

def runTest(self):

"""Run as few or as many tests as needed here.

"""

self.setUp()

self.test_TissueModelCreator1()

def test_TissueModelCreator1(self):

""" Ideally you should have several levels of tests. At the lowest level

tests sould exercise the functionality of the logic with different inputs

(both valid and invalid). At higher levels your tests should emulate the

way the user would interact with your code and confirm that it still works

the way you intended.

One of the most important features of the tests is that it should alert other

developers when their changes will have an impact on the behavior of your

module. For example, if a developer removes a feature that you depend on,

your test should break so they know that the feature is needed.

"""

self.delayDisplay("Starting the test")

#

# first, get some data

#

import urllib

downloads = (

('http://slicer.kitware.com/midas3/download?items=5767', 'FA.nrrd', slicer.util.loadVolume),

)

for url,name,loader in downloads:

filePath = slicer.app.temporaryPath + '/' + name

if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:

print('Requesting download %s from %s...\n' % (name, url))

urllib.urlretrieve(url, filePath)

if loader:

print('Loading %s...\n' % (name,))

loader(filePath)

self.delayDisplay('Finished with download and loading\n')

volumeNode = slicer.util.getNode(pattern="FA")

logic = TissueModelCreatorLogic()

self.assertTrue( logic.hasImageData(volumeNode) )