Slicer4 ProgrammingTutorial SPujol-SPieper Nightly

Programming
in
Slicer4
Ph.D.
Sonia Pujol,
Surgical Planning Laboratory,
Harvard Medical School
Steve Pieper, Ph.D.

Paul Cézanne, Moulin sur la Couleuvre à Pontoise, 1881, Staatliche
Museen zu Berlin, Na:onalgalerie
Isomics Inc.
The NA-MIC Kit
S.Pujol, Ph.D. - S.Pieper, Ph.D.

NA-MIC ARR 2012-2017
3D Slicer version 4 (Slicer4.7.0-2017-07-12)
•  An end-user applica:on for
image analysis
•  An open-source environment
for soNware development
•  A soNware plaPorm that is

both easy to use for clinical
researchers and easy to
extend for programmers
Slicer Modules
•  Command Line Interface (CLI):
standalone executable with limited input/
output arguments
•  Scripted Modules (Python):

recommended for fast prototyping
•  Loadable Modules (C++ Plugins):

optimized for heaving computation
Slicer4 Highlights: Python
The Python console of Slicer4 gives access to

•  scene objects (MRML)
•  data arrays (volumes, models)
•  GUI elements that can be encapsulated in a
module (Qt)
•  Processing Libraries: numpy, VTK, ITK, CTK

Slicer4 Scripted Modules
•  Python scripted modules allow more

interac(ve func(onali(es (e.g. ‘Flythrough’
in Endoscopy module) and rapid prototyping
•  GUI based on Qt libraries accessed via Python

Tutorial Goal
•  This tutorial guides you through the steps of

crea:ng a very simple “Hello World” Python
scripted module and two small modules for
performing Laplacian filtering and sharpening.
•  For addi:onal details and pointers, visit the

Slicer Documenta:on page
hdp://wiki.slicer.org/slicerWiki/index.php/Documenta:on/
Nightly

Processing Examples in this Tutorial
Manipulation
with numpy
Image Data on
Disk (DICOM,
Nifti, nrrd…)
Manipulation
with VTK
MRML Scene
Manipulation
MRML: Medical Reality Markup Language, with ITK
the Slicer Data Representation (Slicer CLI)

Prerequisites
•  This course supposes that you have taken
the tutorial: ‘Slicer4 Data Loading and
Visualiza:on’- Sonia Pujol Ph.D.
•  The tutorial and HelloPython dataset are

available in the Slicer training
compendium

•  Programming experience is required, and
some familiarity with Python is essen:al.
Course Material
www.slicer.org à Slicer training à Slicer4 Programming Tutorial
Sample data set: spgr.nrrd Completed programming

(124-slice MRI volume)‫‏‬ examples:
Note: other volumes (for example, HelloPython, HelloLaplace,
provided by SampleData module) HelloSharpen
can be used just as well.
Unzip the HelloPython_Nightly.zip archive

Course Overview
•  Part A: Exploring Slicer via Python
•  Part B: “Hello world” simple Python scripted

module (HelloPython)
•  Part C: Implementa:on of Laplace operator

for a 3D volume (HelloLaplace)
•  Part D: Image sharpening using Laplace

operator and subtrac:on (HelloSharpen)
Part A: EXPLORING SLICER VIA
PYTHON

Python in Slicer
Slicer includes python 2.7 and a rich set of
standard libraries
•  Included:
Ø  numpy, VTK, CTK, PythonQt,
and most of standard python library

•  Not included:
Ø  scipy (scien:fic tools for python),
Ø  matplotlib (python 2D plo:ng library),
Ø  ipython (interac:ve python)
and some other popular packages that we have
found difficult to package for distribu:on
Python Console in Slicer
Select View à Python Interactor, or

click the button
Drag-and-drop the title bar to dock to

the side of application window or
move to other screen.

General Python Console Features
•  Command Line Edi:ng:
Ø  LeN/Right Arrow Keys, Home, End
Ø  Delete (Control-D)
Ø  Copy/Paste
•  Command Comple:on:
Ø  Tab Key
•  Input History:
Ø  Up/Down Arrow Keys

Add Volume
1. Select File à Add Data
2. Select Choose File(s) to add
3. Load the dataset spgr.nrrd

located in the directory
HelloPython/data

Add Volume
4. Verify in Description column

that file will be loaded as Volume

Access to MRML and Arrays
Run the following code in
the Python console
a = slicer.util.array('spgr’)

àUses the slicer.u:l package to
return a numpy array of the image
àThe variable 'a' is a numpy ndarray
of the volume data we just loaded
print(a)
!Shows a shortened view of the array

The intensity values of the spgr
image appear in the Python
console

Type the following command to
display the min and max
intensity value of the spgr image
print(a.min(),a.max())

àUse numpy array methods
to analyze and process the data

Voxel value:
min = 0
max = 355

Manipula:ng Arrays
Run the following code in the Python console,
(indent each new line with 2 spaces)
def toggle():
n = slicer.util.getNode('spgr')
a = slicer.util.array('spgr')
a[:] = a.max() - a
n.Modified()
print('Toggled')
toggle()
For practice: use up arrow and return

keys to execute toggle() over and over
The toggle func:on in more detail
•  def toggle():
Ø  Defines a python func:on
Ø  Body of func:on performs element-wise math on
en:re volume
Ø  Easy mix of scalar and volume math
•  Telling Slicer that the image data for node 'n'

has been modified causes the slice view
windows to refresh

Qt GUI in Python
Run the following code in the
Python console
b = qt.QPushButton('Toggle')
b.connect('clicked()',toggle)
b.show()
What do you think will happen when you run this code?
What about when you push the button?
Result with budon toggling
Original Result
Put the slicer view windows front to see the changes
In More Detail
•  Slicer uses PythonQt to expose the Qt library

in Python (hdp://pythonqt.sourceforge.net)

•  Sophis:cated interac:ve modules can be
wriden en:rely with Python code calling C++
code that is wrapped in Python
Ø  e.g. Endoscopy, SegmentEditor, SampleData,
ChangeTracker, and other slicer modules in the
Slicer source code

PART B: INTEGRATION OF THE
HELLOPYTHON TUTORIAL TO
SLICER4
Modules and Extensions
•  Module:
•  Defines user interface, processing, self-tests
•  Various types: Scripted (Python), Command
Line Interface (CLI), Loadable (C++)
•  Extension:
•  Collection of modules
•  Packaged in a single zip file and distributed
through the Extension Manager (Slicer app
store)

Create new extension
•  Create new extension: “Hello”
•  Choose destination folder by
clicking […] button
•  Select a folder (for example,
your Desktop)
•  Click Choose and OK

Set extension metadata
•  No need for setting metadata
now, just click OK.
•  Metadata can be edited later by
clicking “Edit Extension
Metadata”

Add module
•  Click “Add module to Extension”
•  Enter “HelloPython” as module
name (must not contain spaces
or special characters)
•  Click “OK”
Check “Add selected module…”

to load the module automatically
when Slicer is restarted

Adding modules to be loaded
For future reference only - no need to add the module manually if “Add
selected module to search paths” box (see previous slide) was checked.
Specify location of additional modules

that Slicer will load on startup:
•  Click “Add” and select file, or
•  Drag-and-drop the folder
or .py file in the path listbox
Edit module
•  Click “Edit” to open source code of the

module in default application associated
with .py files
•  If the source code is not opened
automatically then start an editor and
load the source code file: …\Desktop\Hello
\HelloPython\HelloPython.py
HelloPython.py
Module
Description
Module Widget
(GUI)
Module Logic
(processing, no
user interface)
Module Test
(automatic self-
tests)
Update Module Descrip:on
class HelloPython(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
"""
def __init__(self, parent): constructor

ScriptedLoadableModule.__init__(self, parent)
self.parent.title = "HelloPython" # TODO make this more human readable by adding spaces
self.parent.categories = ["Examples"]
self.parent.dependencies = []
self.parent.contributors = ["John Doe (AnyWare Corp.)"]
self.parent.helpText = """
This is an example of scripted loadable module bundled in an extension.
It performs a simple thresholding on the input volume and optionally captures a screenshot.
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.
and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
""" # replace with organization, grant and thanks.

Implement Module GUI
class HelloPythonWidget(ScriptedLoadableModuleWidget):
…
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
…
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button

parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# HelloWorld button
helloWorldButton = qt.QPushButton("Hello world")
helloWorldButton.toolTip = "Print 'Hello world' in standard output."
parametersFormLayout.addWidget(helloWorldButton)
Update helloWorldButton.connect('clicked(bool)', self.onHelloWorldButtonClicked)
widget to # Add vertical spacer

self.layout.addStretch(1)
have only
a single # Set local var as instance attribute
self.helloWorldButton = helloWorldButton
button
def onHelloWorldButtonClicked(self):
logic = HelloPythonLogic()
result = logic.process()
qt.QMessageBox.information(slicer.util.mainWindow(),
'Slicer Python', result)
Reload module
•  Save HelloPython.py file

•  Click “Reload” button to update the
module based on changes in the
source code
•  If the module GUI is not updated or
disappears then check the Python
console for error messages

Implement Module Logic
Replace content of logic class with a single method.
class HelloPythonLogic(ScriptedLoadableModuleLogic):
"""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.
Uses ScriptedLoadableModuleLogic base class, available at:
"""
def process(self):
return "Hello world!"

Run the module
Click on Help and
Acknowledgment
in the Hello Python module
Click on the Hello World button

Implement self-test
Replace test_HelloPython1 with a simple test.
Use asserts, such as assertIsNone(…), assertTrue(…)to test that
the module works correctly.
class HelloPythonTest(ScriptedLoadableModuleTest):
def setUp(self):
slicer.mrmlScene.Clear(0)
def runTest(self):
self.setUp()
self.test_HelloPython1()
def test_HelloPython1(self):
self.delayDisplay("Starting the test")

logic = HelloPythonLogic()
result = logic.process()
self.assertIsNotNone(result)
self.delayDisplay('Test passed!')
If an extension is submitted to the Extension Manager (Slicer App Store) then all
tests of all of its modules are executed for every release and results are reported
on the dashboard: http://slicer.cdash.org/index.php?project=Slicer4
Test the module
•  Save HelloPython.py file

•  Click “Reload and Test” button to
update the module based on
changes in the source code and
run all the tests

Part C:
Implemen:ng the
Text
Laplace* Operator
*named aNer Pierre-Simon, Marquis de Laplace (1749-1827)

Overview
The goal of this sec:on is to build an image
analysis module that implements a Laplacian
filter on volume data

•  Use qMRML widgets: widgets
that automa:cally track the
state of the Slicer MRML scene
•  Use VTK filters to manipulate

volume data

Add module to exis:ng extension
•  Open Extension Wizard module (press
Ctrl+F shortcut, type exte, and select
Extension Wizard from list)
•  Click “Select Extension”, select your
extension folder (…Desktop/Hello)
•  Click Add module to Extension”
•  Enter “HelloLaplace” as module name


Edit module

HelloLaplace module in default
application associated with .py files
\HelloPython\HelloLaplace.py
Implement Module GUI (Part 1)
class HelloLaplaceWidget(ScriptedLoadableModuleWidget):
…
self.outputSelector.setToolTip( "Pick the output to the algorithm." )

parametersFormLayout.addRow("Output Volume: ", self.outputSelector)
We only need
#
input and # threshold value
#
output volume self.imageThresholdSliderWidget = ctk.ctkSliderWidget()
self.imageThresholdSliderWidget.singleStep = 0.1
selectors, so
X
self.imageThresholdSliderWidget.minimum = -100
self.imageThresholdSliderWidget.maximum = 100
remove self.imageThresholdSliderWidget.value = 0.5
self.imageThresholdSliderWidget.setToolTip("Set threshold value for computing the
threshold output image. Voxels that have intensities lower than this value will set to zero.")
parametersFormLayout.addRow("Image threshold", self.imageThresholdSliderWidget)
value and
#
check box # check box to trigger taking screen shots for later use in tutorials
#
sections from self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
the self.enableScreenshotsFlagCheckBox.setToolTip("If checked, take screen shots for
tutorials. Use Save Data to write them to disk.")
HelloLaplace parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
Widget
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
…
class HelloLaplaceWidget(ScriptedLoadableModuleWidget):
…
def onSelect(self):
self.applyButton.enabled =
self.inputSelector.currentNode() and
self.outputSelector.currentNode()
Update Apply def onApplyButton(self):
button event logic = HelloLaplaceLogic()
handler logic.run(self.inputSelector.currentNode(),
self.outputSelector.currentNode())
(onApplyButton) # make the output volume appear in all the slice views
to only use input slicer.util.setSliceViewerLayers(
background = self.outputSelector.currentNode())
and output
volumes #
# HelloLaplaceLogic
#

Reload module
•  Save HelloLaplace.py file

•  Click “Reload” button to update the
module based on changes in the
source code
•  “Image threshold” slider and
“Enable screenshots” checkbox
should disappear
•  If the module GUI is not updated or
disappears then check the Python
console for error messages

In More Detail
•  CTK is a Qt Add-On Library with many useful

widgets, par:cularly for visualiza:on and medical
imaging see hdp://commontk.org
•  Qt Widgets, Layouts, and Op(ons are well
documented at hdp://qt-project.org
•  qMRMLNodeComboBox is a powerful slicer widget
that monitors the scene and allows you to select/
create nodes of specified types (we used
vtkMRMLScalarVolumeNode). Documented here:
hdp://apidocs.slicer.org/master/

class HelloLaplaceLogic(ScriptedLoadableModuleLogic):
…
def run(self, inputVolume, outputVolume):
if not self.isValidInputOutputData(inputVolume, outputVolume):

return False
Update logging.info('Processing started')
processing laplacian = vtk.vtkImageLaplacian()

laplacian.SetInputData (inputVolume.GetImageData())
method to laplacian.SetDimensionality(3)
compute output laplacian.Update()
by a VTK filter. # Copy image origin, spacing, directions from input

ijkToRAS = vtk.vtkMatrix4x4()
inputVolume.GetIJKToRASMatrix(ijkToRAS)
outputVolume.SetIJKToRASMatrix(ijkToRAS)
outputVolume.SetAndObserveImageData(laplacian.GetOutput())
logging.info('Processing completed')
return True

In More Detail
•  vtkImageLaplacian is a vtkImageAlgorithm operates

on vtkImageData (see hdp://vtk.org)

•  vtkMRMLScalarVolumeNode is a Slicer MRML class
that contains vtkImageData, plus orienta:on
informa:on ijkToRAS matrix (see hdp://www.slicer.
org/slicerWiki/index.php/Coordinate_systems)

In More Detail (Con:nued)
•  Global slicer package gives python access to:

Ø  Convenience func:ons: slicer.u(l
hdp://slicer.readthedocs.io/en/latest/developer_guide/slicer.html#module-slicer.u:l
Ø  Data: slicer.mrmlScene
hdp://apidocs.slicer.org/master/classvtkMRMLScene.html
Ø  CLI modules: slicer.cli
Ø  Scripted modules: by impor:ng Python classes
Ø  Loadable modules: slicer.modules.(modulename).logic()
hdp://apidocs.slicer.org/master/classvtkSlicerModuleLogic.html
Ø  Applica:on GUI: slicer.app
hdp://apidocs.slicer.org/master/classqSlicerApplica:on.html

Running the module
1. Note that Input Volume combobox
auto-selected new volume
2. Create new volume for output
3. Run the module

Output of HelloLaplace
Result of Laplace Operator
on spgr volume

Part D:
Image Sharpening with
Laplace Operator and
subtrac:on

Overview
The goal of this sec:on is to add a
processing op:on for image sharpening.
•  We’ll implement this

opera:on using our
HelloLaplace module
and an exis:ng Slicer
Command Line Module
‘Subtract Scalar Volumes’

Add module to exis:ng extension
•  Open Extension Wizard module (press
Ctrl+F shortcut, type exte, and select
Extension Wizard from list)
•  Click “Select Extension”, select your
extension folder (…Desktop/Hello)
•  Click Add module to Extension”
•  Enter “HelloSharpen” as module name


Edit module

HelloSharpen module in default
application associated with .py files
\HelloPython\HelloSharpen.py
class HelloSharpenWidget(ScriptedLoadableModuleWidget):
…
self.outputSelector.setToolTip( "Pick the output to the algorithm." )

parametersFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# threshold value
#
self.imageThresholdSliderWidget = ctk.ctkSliderWidget()
Remove self.imageThresholdSliderWidget.singleStep = 0.1
X
self.imageThresholdSliderWidget.minimum = -100
unneeded self.imageThresholdSliderWidget.maximum = 100
self.imageThresholdSliderWidget.value = 0.5
slider and self.imageThresholdSliderWidget.setToolTip("Set threshold value for computing the
output image. Voxels that have intensities lower than this value will set to zero.")
checkbox parametersFormLayout.addRow("Image threshold", self.imageThresholdSliderWidget)
(same as for #
# check box to trigger taking screen shots for later use in tutorials
HelloLaplace #
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
module) self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip("If checked, take screen shots for
tutorials. Use Save Data to write them to disk.")
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
…
class HelloSharpenWidget(ScriptedLoadableModuleWidget):
…
def onSelect(self):
self.applyButton.enabled =
self.inputSelector.currentNode() and
self.outputSelector.currentNode()
Update Apply def onApplyButton(self):
button event logic = HelloSharpenLogic()
handler logic.run(self.inputSelector.currentNode(),
self.outputSelector.currentNode())
(onApplyButton) # make the output volume appear in all the slice views
to only use input slicer.util.setSliceViewerLayers(
background = self.outputSelector.currentNode())
and output
volumes #
# HelloSharpenLogic
#

class HelloSharpenLogic(ScriptedLoadableModuleLogic):
…
if not self.isValidInputOutputData(inputVolume, outputVolume):

return False
Update
processing logging.info('Processing started')
method to # Compute Laplacian by scripted module

import HelloLaplace
compute output laplaceLogic = HelloLaplace.HelloLaplaceLogic()
by using success = laplaceLogic.run(inputVolume, outputVolume)
if not success:
HelloLaplace return False
module and # Subtract Laplacian from input volume using CLI module
SubtractVolumes parameters = {}
parameters['inputVolume1'] = inputVolume.GetID()
CLI module. parameters['inputVolume2'] = outputVolume.GetID()
parameters['outputVolume'] = outputVolume.GetID()
slicer.cli.runSync(slicer.modules.subtractscalarvolumes, None,
parameters)
return True

In More Detail
•  slicer.cli gives access to Command Line

Interface (CLI) modules
•  CLI modules allow packaging of arbitrary C++
code (oNen ITK-based) into slicer with
automa:cally generated GUI and python
wrapping
•  Note: if only ITK filters needed, they can be
accessed directly from Python, using
SimpleITK
Run module
1. Note that Input Volume combobox
autoselected new volume
2. Create new volume for output
3. Run the module

Output of HelloSharpen
Result of Laplacian
Sharpening Operator on
spgr volume

Adjus:ng output display
Adjust Window/Level with
Left-Mouse-Drag in Slice
Window

Improve Module Logic
Set output volume’s window/level automatically,
by copying the input volume’s window/level.
class HelloSharpenLogic(ScriptedLoadableModuleLogic):
…
…
slicer.cli.runSync(slicer.modules.subtractscalarvolumes, None,
parameters)
# Copy window/level (brightness/contrast) setting to output

inputDisplay = inputVolume.GetDisplayNode()
outputDisplay = outputVolume.GetDisplayNode()
outputDisplay.SetAutoWindowLevel(False)
outputDisplay.SetWindow(inputDisplay.GetWindow())
outputDisplay.SetLevel(inputDisplay.GetLevel())
return True

Image Sharpening Results
original Laplacian Sharpen

Going Further
•  Review scripted modules in Slicer for more
examples
hdps://github.com/Slicer/Slicer/tree/master/Modules/Scripted
•  Explore numpy for numerical array

manipula:on
http://docs.scipy.org/doc/numpy/reference

•  Explore SimpleITK for image processing
using ITK
hdps://itk.org/SimpleITKDoxygen/html/classes.html

Conclusion
This course demonstrated how to

program custom behavior in Slicer
with Python

Acknowledgments

National Alliance for Medical Image
Computing
NIH U54EB005149

Neuroimage Analysis Center
NIH P41RR013218

Sidong Liu and Fan Zhang, The University of Sydney

Andras Lasso, PerkLab, Queen’s University


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Programming

Steve Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

• A soNware plaPorm that is

• Scripted Modules (Python):

• Loadable Modules (C++ Plugins):

The Python console of Slicer4 gives access to

S.Pujol, Ph.D. - S.Pieper, Ph.D.

• Python scripted modules allow more

• GUI based on Qt libraries accessed via Python

S.Pujol, Ph.D. - S.Pieper, Ph.D.

• This tutorial guides you through the steps of

• For addi:onal details and pointers, visit the

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

• The tutorial and HelloPython dataset are

Sample data set: spgr.nrrd Completed programming

Unzip the HelloPython_Nightly.zip archive

• Part B: “Hello world” simple Python scripted

• Part C: Implementa:on of Laplace operator

• Part D: Image sharpening using Laplace

S.Pujol, Ph.D. - S.Pieper, Ph.D.

Select View à Python Interactor, or

Drag-and-drop the title bar to dock to

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

3. Load the dataset spgr.nrrd

S.Pujol, Ph.D. - S.Pieper, Ph.D.

4. Verify in Description column

S.Pujol, Ph.D. - S.Pieper, Ph.D.

!Shows a shortened view of the array

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

For practice: use up arrow and return

• Telling Slicer that the image data for node 'n'

S.Pujol, Ph.D. - S.Pieper, Ph.D.

• Slicer uses PythonQt to expose the Qt library

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

Check “Add selected module…”

S.Pujol, Ph.D. - S.Pieper, Ph.D.

Specify location of additional modules

• Click “Edit” to open source code of the

def __init__(self, parent): constructor

S.Pujol, Ph.D. - S.Pieper, Ph.D.

# Layout within the dummy collapsible button

widget to # Add vertical spacer

• Save HelloPython.py file

S.Pujol, Ph.D. - S.Pieper, Ph.D.

Replace content of logic class with a single method.

S.Pujol, Ph.D. - S.Pieper, Ph.D.

Click on the Hello World button

S.Pujol, Ph.D. - S.Pieper, Ph.D.

self.delayDisplay("Starting the test")

• Save HelloPython.py file

S.Pujol, Ph.D. - S.Pieper, Ph.D.

•  A soNware plaPorm that is

•  Scripted Modules (Python):

•  Loadable Modules (C++ Plugins):

•  Python scripted modules allow more

•  GUI based on Qt libraries accessed via Python

•  This tutorial guides you through the steps of

•  For addi:onal details and pointers, visit the

•  The tutorial and HelloPython dataset are

•  Part B: “Hello world” simple Python scripted

•  Part C: Implementa:on of Laplace operator

•  Part D: Image sharpening using Laplace

•  Telling Slicer that the image data for node 'n'

•  Slicer uses PythonQt to expose the Qt library

•  Click “Edit” to open source code of the

def init(self, parent): constructor

•  Save HelloPython.py file

•  Save HelloPython.py file

•  Use VTK ﬁlters to manipulate

•  Click “Edit” to open source code of the

•  Save HelloLaplace.py file

•  CTK is a Qt Add-On Library with many useful

•  vtkImageLaplacian is a vtkImageAlgorithm operates

•  Global slicer package gives python access to:

•  We’ll implement this

•  Click “Edit” to open source code of the

•  slicer.cli gives access to Command Line

•  Explore numpy for numerical array