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Programming into Slicer3
Sonia Pujol, Ph.D.
Surgical Planning Laboratory
Harvard Medical School
Slicer3 for developers – Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing -1-
Slicer3
• An end-user application for image analysis
• An open-source environment for software
development
• A software platform that is both easy to use for
clinical researchers and easy to extend for
programmers
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Learning objective
Following this course, you’ll be able
1) to plug-in an external program into Slicer3
2) to implement an image filter and to run the
analysis from Slicer3
3) to write and run a test using the CTest tool
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National Alliance for Medical Image Computing -3-
Material
This course requires a user compiled version of the Slicer3 software
and the training dataset:
• Slicer 3 Software and building instructions
http://www.na-mic.org/Wiki/index.php/Slicer3:Downloads
http://www.na-mic.org/Wiki/index.php/Slicer3:Build_Instructions
• HelloWorld.zip archive
Disclaimer
It is the responsibility of the user of 3DSlicer to
comply with both the terms of the license and with
the applicable laws, regulations and rules.
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Overview
• Part A: integration of the HelloWorld program
into Slicer3
• Part B: implementation of a Discrete
Gaussian filter within the HelloWorld module
• Part C: implementation of a test for the
HelloWorld module
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Part A:
Integrating an
executable into Slicer3
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Slicer3 Execution Model
• This course is based on the Execution Model which
provides a mechanism for incorporating command
line programs as Slicer modules.
• The Slicer modules are described using XML files
which are used to generate the C++ command line
code and the Graphical User Interface (GUI).
www.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Documentation
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HelloWorld_CourseMaterial.tgz archive
unzip the HelloWorld.zip archive
HelloWorld.cxx
(application)
spgr.* HelloWorld.xml
(124 SPGR images) (Execution Model)
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HelloWorld.xml
<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
Demonstration</category> Open the file
<title>
Hello World</title> HelloWorld.xml
Module <description>
Slicer Developer Course</description>
Description <version>
1.0</version>
<documentation-url></documentation-url>
<license></license>
<contributor>
Sonia Pujol, Ph.D. </contributor>
<acknowledgements>
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes
of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. </acknowledgements>
<parameters>
<label>Input/Output</label>
<description>Input/output parameters</description>
<image>
Module <name>helloWorldInputVolume</name>
<label>Input Volume</label>
Parameters <channel>input</channel>
<index>0</index>
<default>None</default>
<description>Input volume</description>
</image>
<image>
<name>helloWorldOutputVolume</name>
<label>Output Volume</label>
<channel>output</channel>
<index>1</index>
<description>Output filtered</description>
Slicer3 for developers –
</image> Sonia Pujol, Ph.D.
</parameters>
National Alliance for Medical Image Computing
</executable> -9-
Module Description
<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
Demonstration</category>
<title>
Hello World</title>
<description>
Slicer Developer Course</description>
<version>
1.0</version>
<documentation-url></documentation-url>
<license></license>
<contributor> Sonia Pujol, Ph.D. </contributor>
<acknowledgements>
This work is part of the National Alliance for Medical Image
Computing (NAMIC), funded by the National Institutes of Health through the
NIH Roadmap for Medical Research, Grant U54 EB005149.
</acknowledgements>
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Module Parameters
<parameters>
<label>Input/Output</label>
<description>Input/output parameters</description>
<image>
<name>helloWorldInputVolume</name>
<label>Input Volume</label> A file that
Input <channel>input</channel> specifies
<index>0</index>
Volume <default>None</default>
the image
<description>Input volume</description>
</image>
<image>
<name>helloWorldOutputVolume</name>
<label>Output Volume</label>
Output <channel>output</channel>
<index>1</index>
Volume <default>None</default>
<description>Output filtered</description>
</image>
Slicer3 for developers – Sonia Pujol, Ph.D.
</parameters>
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</executable>
Modifying the source code
Open the file HelloWorld.cxx
# include <iostream>
int main(int argc, char * argv [])
{
std::cout<< “Hello World !”<<std::endl;
return 0 ;
}
Slicer3 for developers – Sonia Pujol, Ph.D.
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Modifying the source code
Add the following lines to the file HelloWorld.cxx
# include <iostream>
#include “HelloWorldCLP.h”
int main(int argc, char * argv [])
{
PARSE_ARGS;
std::cout<< “Hello World !”<<std::endl;
return EXIT_SUCCESS ;
}
Slicer3 for developers – Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing -13-
Slicer architecture
.svn
Slicer3
Applications
Base
Slicer3-build CMake
Libs
Modules
Slicer3-lib Resources
Scripts
Testing
Utilities
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Slicer architecture
.svn
Slicer3
Applications
CLI
Base
Copy the 2 files CMake
HelloWorld.cxx
Libs
HelloWorld.xml
into the directory Modules
Slicer3\Applications\CLI
Resources
Scripts
Testing
Utilities
Slicer3 for developers – Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing -15-
Slicer architecture
.svn
Slicer3
Applications
CLI
Base
Open the file CMakeLists.txt
CMake
into the directory
Slicer3\Applications\CLI Libs
Modules
Resources
Scripts
Testing
Utilities
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Editing CMakeLists.txt – part 1
Add the following lines to CMakeLists.txt located
in Slicer3/Applications/CLI (above the SUBDIRS
lines):
SET (CLP HelloWorld)
SET (${CLP}_SOURCE ${CLP}.cxx)
GENERATECLP(${CLP}_SOURCE ${CLP}.xml)
GENERATECLP generates the file HelloWorldCLP.h for parsing
the command line arguments.
Slicer3 for developers – Sonia Pujol, Ph.D.
‘CLP’ means Command Line Processing
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Editing CMakeLists.txt – part 2
Add the following lines to CMakeLists.txt located in
Slicer3/Applications/CLI after the ‘GENERATECLP’ line
you just added
ADD_EXECUTABLE(${CLP} ${${CLP}_SOURCE})
TARGET_LINK_LIBRARIES (${CLP} ITKIO
ITKBasicFilters ITKCommon)
ADD_EXECUTABLE creates the stand-alone executable
HelloWorld.exe that can be run from a command line.
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Building Slicer3
Mac/Linux
Run ‘make’ in the directory Slicer3-build/Applications/CLI
Windows
• Step1: Select BuildBuild Slicer3 to build the solution
Slicer3.sln located in Slicer3-build/
• Step2: Close the solution Slicer3, and re-load it again in the
building environment
• Step3: Select the solution HelloWorld, and launch
‘BuildHelloWorld’
Slicer3 for developers – Sonia Pujol, Ph.D.
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Running Slicer3
Mac/Linux
Run ‘./Slicer3’ in Slicer3-build/
Windows
Run ‘./Slicer3.exe’ in Slicer3-build/
Slicer3 for developers – Sonia Pujol, Ph.D.
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HelloWorld module in Slicer3
Select the category
‘Demonstration’, and the
module ‘HelloWorld’ in the
Modules menu
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HelloWorld Module in Slicer3
The program ‘HelloWorld’ is
now integrated into Slicer3
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National Alliance for Medical Image Computing -22-
Part B:
Implementing an
image filter
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National Alliance for Medical Image Computing -23-
Goal
• In this section, we’ll implement a Gaussian
smoothing operator to ‘blur’ the images and
remove detail and noise.
• This implementation will allow us to run the filter
on volumes loaded in Slicer, and to integrate the
resulting filtered volumes as MRML nodes.
Slicer3 for developers – Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing -24-
Discrete Gaussian Filter
Variance
Discrete
Gaussian Filter
Input volume Output volume
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Editing the file HelloWorld.xml
<?xml version="1.0" encoding="utf-8"?>
<executable>
<category>
Demonstration</category>
<title>
Hello World</title>
<description> Add a new parameter
Slicer Developer Example</description>
<version> group to HelloWorld.xml
1.0</version>
<documentation-url></documentation-url>
<license></license>
<contributor>
Sonia Pujol</contributor>
<acknowledgements>
This work is part of the National Alliance for Medical Image Computing (NAMIC), funded by the National Institutes of Health
through the NIH Roadmap for Medical Research, Grant U54 EB005149. </acknowledgements>
<parameters>
<label>Input/Output</label>
<description>Input/output parameters</description>
….
</parameters>
<parameters>
<label>Discrete Gaussian Parameters</label>
<description>Parameters of the Discrete Gaussian Filter </description>
</parameters>
</executable>
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Editing the file HelloWorld.xml
<parameters>
<label>Discrete Gaussian Parameters</label>
<description>Parameters of the Discrete Gaussian Filter </description>
<double>
<name>variance</name>
<longflag>--variance</longflag>
<description>Variance ( width of the filter kernel) </description>
<label>Variance</label>
<default>0.5</default>
</double>
</parameters>
‘variance’
Add the parameter– Sonia Pujol, Ph.D. which corresponds to the
Slicer3 for developers
the for Medical Image Computing
variance ofAlliance Discrete Gaussian Filter to HelloWorld.xml
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Implementing I/O functionalities
Add the following lines to HelloWorld.cxx
#include <iostream>
#include "HelloWorldCLP.h"
#include "itkImage.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
int main(int argc, char * argv [])
{
PARSE_ARGS;
std::cout << "Hello World!" << std::endl;
return EXIT_SUCCESS ;
}
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National Alliance for Medical Image Computing -28-
Implementing Input/Output functionalities
Add the following command lines to set-up the reading
and writing functionalities in the ‘main’ procedure in
HelloWorld.cxx
int main ( int argc, char * argv[])
{
PARSE_ARGS;
std::cout << "Hello World!" << std::endl;
typedef itk::Image<short,3> ImageType;
typedef itk::ImageFileReader<ImageType> ReaderType;
typedef itk::ImageFileWriter<ImageType> WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
return EXIT_SUCCESS;
}
Slicer3 for developers – Sonia Pujol, Ph.D.
National Alliance for Medical Image Computing -29-
Implementing Input/Output functionalities
Set the input and output volumes parameters defined in
HelloWorld.xml
int main ( int argc, char * argv[])
{
PARSE_ARGS;
std::cout << "Hello World!" << std::endl;
typedef itk::Image< short, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName(helloWorldInputVolume.c_str() );
writer->SetFileName (helloWorldOutputVolume.c_str());
return EXIT_SUCCESS;
}
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National Alliance for Medical Image Computing -30-
Implementing the filter in HelloWorld.cxx
Implement the filter itk::DiscreteGaussianImageFilter
#include "itkDiscreteGaussianImageFilter.h"
int main ( int argc, char * argv[])
{
PARSE_ARGS;
std::cout << "Hello World!" << std::endl;
typedef itk::Image< short, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( helloWorldInputVolume.c_str() );
writer->SetFileName(helloWorldOutputVolume.c_str());
typedef itk::DiscreteGaussianImageFilter <ImageType, ImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
return EXIT_SUCCESS;
Slicer3 for developers – Sonia Pujol, Ph.D.
} National Alliance for Medical Image Computing -31-
Implementing the filter in HelloWorld.cxx
int main ( int argc, char * argv[])
{
PARSE_ARGS; Add the following lines
std::cout << "Hello World!" << std::endl;
typedef itk::Image< short, 3 > ImageType;
for the filter execution:
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( helloWorldInputVolume.c_str() );
writer->SetFileName (helloWorldOutputVolume.c_str());
typedef itk::DiscreteGaussianImageFilter <ImageType, ImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
try {
filter->SetInput(reader->GetOutput());
filter->SetVariance(variance);
writer->SetInput(filter->GetOutput());
writer->Update();
}
catch (itk::ExceptionObject &excep){
std::cerr << argv[0] << ": exception caught !" << std::endl;
Slicer3 for developers – Sonia Pujol, Ph.D.
Nationalreturn EXIT_FAILURE;} Computing
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return EXIT_SUCCESS;}
Final Version of HelloWorld.cxx
int main ( int argc, char * argv[])
{
PARSE_ARGS;
std::cout << "Hello World!" << std::endl;
typedef itk::Image< short, 3 > ImageType;
typedef itk::ImageFileReader< ImageType > ReaderType;
typedef itk::ImageFileWriter< ImageType > WriterType;
ReaderType::Pointer reader = ReaderType::New();
WriterType::Pointer writer = WriterType::New();
reader->SetFileName( helloWorldInputVolume.c_str() );
writer->SetFileName (helloWorldOutputVolume.c_str());
typedef itk::DiscreteGaussianImageFilter <ImageType, ImageType> FilterType;
FilterType::Pointer filter = FilterType::New();
try { - Linux and Mac:
filter->SetInput(reader->GetOutput());
filter->SetVariance(variance);
Type make in
writer->SetInput(filter->GetOutput()); Slicer3-build/
writer->Update();} - Windows: build
catch (itk::ExceptionObject &excep){ Slicer3.sln
std::cerr << argv[0] << ": exception caught !" << std::endl;
Slicer3 for developers – Sonia Pujol, Ph.D.
return EXIT_FAILURE;}
National Alliance for Medical Image Computing
return EXIT_SUCCESS;} -33-
Running Slicer3
Mac/Linux
Run ‘./Slicer3’ in Slicer3-build/
Windows
Run ‘./Slicer3.exe’ in Slicer3-build/
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Running the Filter
Go in FileAdd Volume and
load the dataset spgr.nrrd
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Running the Filter
Browse to the Category ‘Demonstration’
in the Modules menu, and select the
module ‘HelloWorld’
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Running the Filter
Select the input volume ‘spgr.nhdr’, the
output volume ‘Create New’.
Enter the value ‘0.9’ for the variance and
click on Apply
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Running the Filter
Slicer displays the filtered volume
‘HelloWorldVolume1’.
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National Alliance for Medical Image Computing -38-
Running the Filter
Select the Foreground volume
‘spgr.nhdr’ and fade between the
Background and Foreground images
to visualize the effect of the filter.
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Part C: Testing
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Goal
• This section describes a simple example for testing that
the ‘help’ functionality of our newly implemented module
‘HelloWorld’ works correctly.
• CTest is a core element of Slicer3’s quality control system
for software development.
http://www.cmake.org/Wiki/CMake_Testing_With_CTest
• The goal of ‘HelloWorldTest1’ is to test the following
command:
./HelloWorld --help
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HelloWorld Test 1
To implement this test, add the following lines to the
CMakeLists.txt file located in the directory:
Slicer3\Applications\CLI\CMakeLists.txt and build Slicer3
SET (SLICER_EXE ${Slicer3_BINARY_DIR}/Slicer3 )
IF (WIN32)
ADD_TEST(HelloWorldTest1 ${SLICER_EXE} --launch
${EXECUTABLE_OUTPUT_PATH}/${CMAKE_BUILD_TYPE}/${CLP} --help)
ELSE(WIN32)
ADD_TEST(HelloWorldTest1 ${SLICER_EXE} --launch ${EXECUTABLE_OUTPUT_PATH}/${CLP} --help)
ENDIF (WIN32)
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HelloWorld Test 1
SET( SLICER_EXE ${Slicer3_BINARY_DIR}/Slicer3 )
IF (WIN32)
ADD_TEST(HelloWorldTest1 ${SLICER_EXE} --launch
${EXECUTABLE_OUTPUT_PATH}/${CMAKE_BUILD_TYPE}/${CLP} --help)
ELSE(WIN32)
ADD_TEST(HelloWorldTest1 ${SLICER_EXE} --launch
${EXECUTABLE_OUTPUT_PATH}/${CLP} --help)
ENDIF (WIN32)
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National Alliance for Medical Image Computing -43-
Running HelloWorldTest1
Mac/Linux
In Slicer3-build/ run
../Slicer3-lib/CMake-build/bin/ctest -R HelloWorldTest1
Windows
In Slicer3-build/ run
../Slicer3-lib/CMake-build/bin/ctest.exe -R HelloWorldTest1
Slicer3 for developers – Sonia Pujol, Ph.D.
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Running HelloWorldTest1
When the module successfully passes the test,
the output below is generated:
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National Alliance for Medical Image Computing -45-
Conclusion
• This course described functionalities for integrating,
developing and testing external program within Slicer3.
• The Execution Model of Slicer3 provides a simple
mechanism for incorporating command line programs
as Slicer modules.
• www.slicer.org
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