From a98459d9d10ad819d2f64219e17d14704d00d29f Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Wed, 11 May 2016 14:26:50 -0400
Subject: [PATCH 1/4] ENH: Addition of ctk_cli

ctk_cli [1] is a command line parsing python package that parses
arguments the same way SlicerExecutionModel does.
Using ctk_cli allows in Python scripts allows to have the same
user interface in Python or in C++.

[1] https://github.com/commontk/ctk-cli
---
 SuperBuild.cmake                         |  2 +-
 SuperBuild/External_python-ctk_cli.cmake | 36 ++++++++++++++++++++++++
 2 files changed, 37 insertions(+), 1 deletion(-)
 create mode 100644 SuperBuild/External_python-ctk_cli.cmake

diff --git a/SuperBuild.cmake b/SuperBuild.cmake
index c1c40204dc3..c5da79be547 100644
--- a/SuperBuild.cmake
+++ b/SuperBuild.cmake
@@ -100,7 +100,7 @@ if(Slicer_USE_SimpleITK)
 endif()
 
 if(Slicer_BUILD_CLI_SUPPORT)
-  list(APPEND Slicer_DEPENDENCIES SlicerExecutionModel)
+  list(APPEND Slicer_DEPENDENCIES SlicerExecutionModel python-ctk_cli)
 endif()
 
 if(Slicer_BUILD_EXTENSIONMANAGER_SUPPORT)
diff --git a/SuperBuild/External_python-ctk_cli.cmake b/SuperBuild/External_python-ctk_cli.cmake
new file mode 100644
index 00000000000..64c37751c2f
--- /dev/null
+++ b/SuperBuild/External_python-ctk_cli.cmake
@@ -0,0 +1,36 @@
+set(proj python-ctk_cli)
+
+# Set dependency list
+set(${proj}_DEPENDENCIES python python-setuptools)
+
+# Include dependent projects if any
+ExternalProject_Include_Dependencies(${proj} PROJECT_VAR proj DEPENDS_VAR ${proj}_DEPENDENCIES)
+
+if(${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+  # XXX - Add a test checking if <proj> is available
+endif()
+
+if(NOT DEFINED ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+  set(${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj} ${${CMAKE_PROJECT_NAME}_USE_SYSTEM_python})
+endif()
+
+set(ctk_cli_REPOSITORY ${git_protocol}://github.com/commontk/ctk-cli.git)
+set(ctk_cli_GIT_TAG 4346a22618b299c8eff84c6a179067ca68db43b9)
+
+if(NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj})
+
+  ExternalProject_Add(${proj}
+    ${${proj}_EP_ARGS}
+    GIT_REPOSITORY ${ctk_cli_REPOSITORY}
+    GIT_TAG ${ctk_cli_GIT_TAG}
+    SOURCE_DIR ${proj}
+    BUILD_IN_SOURCE 1
+    CONFIGURE_COMMAND ""
+    BUILD_COMMAND ""
+    INSTALL_COMMAND ${PYTHON_EXECUTABLE} setup.py install
+    DEPENDS
+      ${${proj}_DEPENDENCIES}
+    )
+else()
+  ExternalProject_Add_Empty(${proj} DEPENDS ${${proj}_DEPENDENCIES})
+endif()

From bae311d3d98ebd77ff53029d754775ccc5e88da6 Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Mon, 16 May 2016 16:08:36 -0400
Subject: [PATCH 2/4] BUG: Template argument name was modified in template
 declaration

Template argument name was modified in template declaration but not
when using it in the templated function.
---
 Utilities/Templates/Modules/CLI/TemplateKey.cxx | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Utilities/Templates/Modules/CLI/TemplateKey.cxx b/Utilities/Templates/Modules/CLI/TemplateKey.cxx
index 95b183e9613..1729d2734e4 100644
--- a/Utilities/Templates/Modules/CLI/TemplateKey.cxx
+++ b/Utilities/Templates/Modules/CLI/TemplateKey.cxx
@@ -15,7 +15,7 @@ namespace
 {
 
 template <typename TPixel>
-int DoIt( int argc, char * argv[], T )
+int DoIt( int argc, char * argv[], TPixel )
 {
   PARSE_ARGS;
 

From 4b216a9f429efd9886d20af275fe9bd9e7052c9e Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Mon, 16 May 2016 16:16:21 -0400
Subject: [PATCH 3/4] ENH: Addition of an example to use ctk_cli

ctk_cli allows to parse python scripts command lines
the same way they would be parsed with
SlicerExecutionModel. This commit adds an example to
show how to use this package.
---
 CMake/SlicerExtensionTemplatesGenerator.cmake |  2 +-
 .../Modules/PythonCLI/CMakeLists.txt          | 24 +++++++++
 .../PythonCLIModuleTemplateTest.nhdr.md5      |  1 +
 .../PythonCLIModuleTemplateTest.raw.md5       |  1 +
 .../PythonCLI/Data/Input/CTHeadAxial.nhdr.md5 |  1 +
 .../Data/Input/CTHeadAxial.raw.gz.md5         |  1 +
 .../PythonCLI/PythonCLIModuleTemplate.py      | 36 +++++++++++++
 .../PythonCLI/PythonCLIModuleTemplate.xml     | 52 +++++++++++++++++++
 .../Modules/PythonCLI/Testing/CMakeLists.txt  |  1 +
 .../PythonCLI/Testing/Python/CMakeLists.txt   | 17 ++++++
 10 files changed, 135 insertions(+), 1 deletion(-)
 create mode 100644 Utilities/Templates/Modules/PythonCLI/CMakeLists.txt
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.nhdr.md5
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.raw.gz.md5
 create mode 100644 Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.py
 create mode 100644 Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.xml
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Testing/CMakeLists.txt
 create mode 100644 Utilities/Templates/Modules/PythonCLI/Testing/Python/CMakeLists.txt

diff --git a/CMake/SlicerExtensionTemplatesGenerator.cmake b/CMake/SlicerExtensionTemplatesGenerator.cmake
index 89ae8a8fa4e..5d6334db1d4 100644
--- a/CMake/SlicerExtensionTemplatesGenerator.cmake
+++ b/CMake/SlicerExtensionTemplatesGenerator.cmake
@@ -81,7 +81,7 @@ macro(_append_extension_template_generator_commands module_type)
 endmacro()
 
 # Loop over module type and add template generators
-foreach(type IN ITEMS CLI Loadable ScriptedLoadable)
+foreach(type IN ITEMS CLI PythonCLI Loadable ScriptedLoadable)
   _append_extension_template_generator_commands(${type})
 endforeach()
 
diff --git a/Utilities/Templates/Modules/PythonCLI/CMakeLists.txt b/Utilities/Templates/Modules/PythonCLI/CMakeLists.txt
new file mode 100644
index 00000000000..b6cc49745bd
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/CMakeLists.txt
@@ -0,0 +1,24 @@
+#-----------------------------------------------------------------------------
+set(MODULE_NAME PythonCLIModuleTemplate)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  ${MODULE_NAME}.xml
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+  # Additional build-time testing
+  add_subdirectory(Testing)
+endif()
diff --git a/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5 b/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
new file mode 100644
index 00000000000..e3f7f4074cd
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
@@ -0,0 +1 @@
+fc6170ceeff3d8217a9dd6a1add2ec8c
diff --git a/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5 b/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
new file mode 100644
index 00000000000..6e640c3071f
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559
\ No newline at end of file
diff --git a/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.nhdr.md5 b/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.nhdr.md5
new file mode 100644
index 00000000000..734a0467eee
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.nhdr.md5
@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a
\ No newline at end of file
diff --git a/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.raw.gz.md5 b/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.raw.gz.md5
new file mode 100644
index 00000000000..f555cb43501
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.raw.gz.md5
@@ -0,0 +1 @@
+3ebd710c9cf9d75750f4569b8caf6d07
\ No newline at end of file
diff --git a/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.py b/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.py
new file mode 100644
index 00000000000..841dd166246
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.py
@@ -0,0 +1,36 @@
+import itk
+from ctk_cli import *
+import sys
+import logging
+
+def SmoothingRecursiveGaussianImageFilter(inputVolume, outputVolume, sigma):
+    reader = itk.ImageFileReader.New(FileName=inputVolume)
+    filter = itk.SmoothingRecursiveGaussianImageFilter.New(reader)
+    filter.SetSigma(sigma)
+    writer = itk.ImageFileWriter.New(filter,FileName=outputVolume)
+    writer.SetUseCompression(True)
+    writer.Update()
+    return 1
+
+
+def main():
+    """Parsing command line arguments and reading input files."""
+    logging.basicConfig(level=logging.INFO)
+    args=CLIArgumentParser().parse_args()
+    # Run processing
+    SmoothingRecursiveGaussianImageFilter(args.inputVolume,args.outputVolume,args.sigma)
+    # Compare output with baseline
+    reader1 = itk.ImageFileReader.New(FileName=args.outputVolume)
+    reader2 = itk.ImageFileReader.New(FileName=args.baselineVolume)
+    compareFilter=itk.ComparisonImageFilter.New(reader1)
+    compareFilter.SetTestInput(reader1)
+    compareFilter.SetValidInput(reader2)
+    diff=compareFilter.GetTotalDifference()
+    if diff < args.tolerance:
+      return 0
+    return 1
+
+if __name__ == "__main__":
+    ret=main()
+    if ret:
+      sys.exit(ret)
diff --git a/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.xml b/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.xml
new file mode 100644
index 00000000000..604f1421566
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="utf-8"?>
+<executable>
+  <category>Examples</category>
+  <title>PythonCLIModuleTemplate</title>
+  <description><![CDATA[This is a Python CLI module that can be bundled in an extension]]></description>
+  <version>0.0.1</version>
+  <documentation-url>http://www.example.com/Slicer/Modules/PythonCLIModuleTemplate</documentation-url>
+  <license>Slicer</license>
+  <contributor>FirstName LastName (Institution), FirstName LastName (Institution)</contributor>
+  <acknowledgements>This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN</acknowledgements>
+  <parameters>
+    <label>IO</label>
+    <description><![CDATA[Input/output parameters]]></description>
+    <double>
+      <name>sigma</name>
+      <longflag>sigma</longflag>
+      <flag>s</flag>
+      <label>Sigma</label>
+      <description><![CDATA[A double value (in units of mm) passed to the algorithm]]></description>
+      <default>1.0</default>
+    </double>
+    <image>
+      <name>inputVolume</name>
+      <label>Input Volume</label>
+      <channel>input</channel>
+      <index>0</index>
+      <description><![CDATA[Input volume]]></description>
+    </image>
+    <image>
+      <name>outputVolume</name>
+      <label>Output Volume</label>
+      <channel>output</channel>
+      <index>1</index>
+      <description><![CDATA[Output Volume]]></description>
+    </image>
+    <image>
+      <name>baselineVolume</name>
+      <label>Baseline Volume</label>
+      <channel>input</channel>
+      <index>2</index>
+      <description><![CDATA[Output Volume]]></description>
+    </image>
+    <double>
+      <name>tolerance</name>
+      <longflag>tolerance</longflag>
+      <flag>t</flag>
+      <label>Tolerance</label>
+      <description><![CDATA[Tolerance between the output image and the baseline (sum)]]></description>
+      <default>0.0001</default>
+    </double>
+  </parameters>
+</executable>
diff --git a/Utilities/Templates/Modules/PythonCLI/Testing/CMakeLists.txt b/Utilities/Templates/Modules/PythonCLI/Testing/CMakeLists.txt
new file mode 100644
index 00000000000..655007a0aab
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Testing/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(Python)
diff --git a/Utilities/Templates/Modules/PythonCLI/Testing/Python/CMakeLists.txt b/Utilities/Templates/Modules/PythonCLI/Testing/Python/CMakeLists.txt
new file mode 100644
index 00000000000..82ea85b1231
--- /dev/null
+++ b/Utilities/Templates/Modules/PythonCLI/Testing/Python/CMakeLists.txt
@@ -0,0 +1,17 @@
+#-----------------------------------------------------------------------------
+set(BASELINE ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Baseline)
+set(INPUT ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Input)
+set(TEMP "${CMAKE_BINARY_DIR}/Testing/Temporary")
+
+set(CLP ${MODULE_NAME})
+
+#-----------------------------------------------------------------------------
+set(testname ${CLP}Test)
+ExternalData_add_test(${CLP}Data NAME ${testname} COMMAND ${Slicer_LAUNCHER_EXECUTABLE} ${MODULE_NAME}.py
+  --sigma 2.5 DATA{${INPUT}/CTHeadAxial.nhdr,CTHeadAxial.raw.gz} ${TEMP}/${CLP}Test.nhdr
+  DATA{${BASELINE}/${CLP}Test.nhdr,${CLP}Test.raw}
+  )
+set_property(TEST ${testname} PROPERTY LABELS ${CLP})
+
+#-----------------------------------------------------------------------------
+ExternalData_add_target(${CLP}Data)

From 70a7aff60fa995b16109abd7e35953c78e74fb36 Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Mon, 16 May 2016 17:23:57 -0400
Subject: [PATCH 4/4] ENH: Generating new extension based on new module type.

Generating a new extension implementing a PythonCLI module by
calling the target SlicerGenerateExtensionTemplates.
---
 Extensions/PythonCLIExtensionTemplate.s4ext   |  44 +++++++++++++++
 .../CLIModuleTemplate/CLIModuleTemplate.cxx   |   2 +-
 .../PythonCLIExtensionTemplate/CMakeLists.txt |  25 +++++++++
 .../PythonCLIExtensionTemplate.png            | Bin 0 -> 17838 bytes
 .../PythonCLIModuleTemplate/CMakeLists.txt    |  24 ++++++++
 .../PythonCLIModuleTemplateTest.nhdr.md5      |   1 +
 .../PythonCLIModuleTemplateTest.raw.md5       |   1 +
 .../Data/Input/CTHeadAxial.nhdr.md5           |   1 +
 .../Data/Input/CTHeadAxial.raw.gz.md5         |   1 +
 .../PythonCLIModuleTemplate.py                |  36 ++++++++++++
 .../PythonCLIModuleTemplate.xml               |  52 ++++++++++++++++++
 .../Testing/CMakeLists.txt                    |   1 +
 .../Testing/Python/CMakeLists.txt             |  17 ++++++
 13 files changed, 204 insertions(+), 1 deletion(-)
 create mode 100644 Extensions/PythonCLIExtensionTemplate.s4ext
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/CMakeLists.txt
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIExtensionTemplate.png
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/CMakeLists.txt
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.nhdr.md5
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.raw.gz.md5
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.py
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.xml
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/CMakeLists.txt
 create mode 100644 Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/Python/CMakeLists.txt

diff --git a/Extensions/PythonCLIExtensionTemplate.s4ext b/Extensions/PythonCLIExtensionTemplate.s4ext
new file mode 100644
index 00000000000..2ce8e785a1a
--- /dev/null
+++ b/Extensions/PythonCLIExtensionTemplate.s4ext
@@ -0,0 +1,44 @@
+#
+# First token of each non-comment line is the keyword and the rest of the line
+# (including spaces) is the value.
+# - the value can be blank
+#
+
+# This is source code manager (i.e. svn)
+scm local
+scmurl Testing/PythonCLIExtensionTemplate
+scmrevision NA
+
+# list dependencies
+# - These should be names of other modules that have .s4ext files
+# - The dependencies will be built first
+depends NA
+
+# Inner build directory (default is ".")
+build_subdirectory .
+
+# homepage
+homepage http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PythonCLIExtensionTemplate
+
+# Firstname1 Lastname1 ([SubOrg1, ]Org1), Firstname2 Lastname2 ([SubOrg2, ]Org2)
+# For example: Jane Roe (Superware), John Doe (Lab1, Nowhere), Joe Bloggs (Noware)
+contributors John Doe (AnyWare Corp.)
+
+# Match category in the xml description of the module (where it shows up in Modules menu)
+category Examples
+
+# url to icon (png, size 128x128 pixels)
+iconurl http://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate.png
+
+# Give people an idea what to expect from this code
+#  - Is it just a test or something you stand behind?
+status 
+
+# One line stating what the module does
+description This is an example of a simple extension
+
+# Space separated list of urls
+screenshoturls http://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate/Screenshots/1.png
+
+# 0 or 1: Define if the extension should be enabled after its installation.
+enabled 1
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx
index 28f2121d40c..f0cc177539d 100644
--- a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx
@@ -15,7 +15,7 @@ namespace
 {
 
 template <typename TPixel>
-int DoIt( int argc, char * argv[], T )
+int DoIt( int argc, char * argv[], TPixel )
 {
   PARSE_ARGS;
 
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/CMakeLists.txt b/Extensions/Testing/PythonCLIExtensionTemplate/CMakeLists.txt
new file mode 100644
index 00000000000..a45b67b2db9
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/CMakeLists.txt
@@ -0,0 +1,25 @@
+cmake_minimum_required(VERSION 2.8.9)
+
+project(PythonCLIExtensionTemplate)
+
+#-----------------------------------------------------------------------------
+# Extension meta-information
+set(EXTENSION_HOMEPAGE "http://slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/PythonCLIExtensionTemplate")
+set(EXTENSION_CATEGORY "Examples")
+set(EXTENSION_CONTRIBUTORS "John Doe (AnyWare Corp.)")
+set(EXTENSION_DESCRIPTION "This is an example of a simple extension")
+set(EXTENSION_ICONURL "http://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate.png")
+set(EXTENSION_SCREENSHOTURLS "http://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate/Screenshots/1.png")
+
+#-----------------------------------------------------------------------------
+# Extension dependencies
+find_package(Slicer REQUIRED)
+include(${Slicer_USE_FILE})
+
+#-----------------------------------------------------------------------------
+# Extension modules
+add_subdirectory(PythonCLIModuleTemplate)
+## NEXT_MODULE
+
+#-----------------------------------------------------------------------------
+include(${Slicer_EXTENSION_CPACK})
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIExtensionTemplate.png b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIExtensionTemplate.png
new file mode 100644
index 0000000000000000000000000000000000000000..6aae6ab703e9fb715c775e67ab172a1c21db80cd
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diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/CMakeLists.txt b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/CMakeLists.txt
new file mode 100644
index 00000000000..b6cc49745bd
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/CMakeLists.txt
@@ -0,0 +1,24 @@
+#-----------------------------------------------------------------------------
+set(MODULE_NAME PythonCLIModuleTemplate)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  ${MODULE_NAME}.xml
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+  # Additional build-time testing
+  add_subdirectory(Testing)
+endif()
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5 b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
new file mode 100644
index 00000000000..e3f7f4074cd
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
@@ -0,0 +1 @@
+fc6170ceeff3d8217a9dd6a1add2ec8c
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5 b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
new file mode 100644
index 00000000000..6e640c3071f
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559
\ No newline at end of file
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.nhdr.md5 b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.nhdr.md5
new file mode 100644
index 00000000000..734a0467eee
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.nhdr.md5
@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a
\ No newline at end of file
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.raw.gz.md5 b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.raw.gz.md5
new file mode 100644
index 00000000000..f555cb43501
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.raw.gz.md5
@@ -0,0 +1 @@
+3ebd710c9cf9d75750f4569b8caf6d07
\ No newline at end of file
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.py b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.py
new file mode 100644
index 00000000000..841dd166246
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.py
@@ -0,0 +1,36 @@
+import itk
+from ctk_cli import *
+import sys
+import logging
+
+def SmoothingRecursiveGaussianImageFilter(inputVolume, outputVolume, sigma):
+    reader = itk.ImageFileReader.New(FileName=inputVolume)
+    filter = itk.SmoothingRecursiveGaussianImageFilter.New(reader)
+    filter.SetSigma(sigma)
+    writer = itk.ImageFileWriter.New(filter,FileName=outputVolume)
+    writer.SetUseCompression(True)
+    writer.Update()
+    return 1
+
+
+def main():
+    """Parsing command line arguments and reading input files."""
+    logging.basicConfig(level=logging.INFO)
+    args=CLIArgumentParser().parse_args()
+    # Run processing
+    SmoothingRecursiveGaussianImageFilter(args.inputVolume,args.outputVolume,args.sigma)
+    # Compare output with baseline
+    reader1 = itk.ImageFileReader.New(FileName=args.outputVolume)
+    reader2 = itk.ImageFileReader.New(FileName=args.baselineVolume)
+    compareFilter=itk.ComparisonImageFilter.New(reader1)
+    compareFilter.SetTestInput(reader1)
+    compareFilter.SetValidInput(reader2)
+    diff=compareFilter.GetTotalDifference()
+    if diff < args.tolerance:
+      return 0
+    return 1
+
+if __name__ == "__main__":
+    ret=main()
+    if ret:
+      sys.exit(ret)
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.xml b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.xml
new file mode 100644
index 00000000000..604f1421566
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="utf-8"?>
+<executable>
+  <category>Examples</category>
+  <title>PythonCLIModuleTemplate</title>
+  <description><![CDATA[This is a Python CLI module that can be bundled in an extension]]></description>
+  <version>0.0.1</version>
+  <documentation-url>http://www.example.com/Slicer/Modules/PythonCLIModuleTemplate</documentation-url>
+  <license>Slicer</license>
+  <contributor>FirstName LastName (Institution), FirstName LastName (Institution)</contributor>
+  <acknowledgements>This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN</acknowledgements>
+  <parameters>
+    <label>IO</label>
+    <description><![CDATA[Input/output parameters]]></description>
+    <double>
+      <name>sigma</name>
+      <longflag>sigma</longflag>
+      <flag>s</flag>
+      <label>Sigma</label>
+      <description><![CDATA[A double value (in units of mm) passed to the algorithm]]></description>
+      <default>1.0</default>
+    </double>
+    <image>
+      <name>inputVolume</name>
+      <label>Input Volume</label>
+      <channel>input</channel>
+      <index>0</index>
+      <description><![CDATA[Input volume]]></description>
+    </image>
+    <image>
+      <name>outputVolume</name>
+      <label>Output Volume</label>
+      <channel>output</channel>
+      <index>1</index>
+      <description><![CDATA[Output Volume]]></description>
+    </image>
+    <image>
+      <name>baselineVolume</name>
+      <label>Baseline Volume</label>
+      <channel>input</channel>
+      <index>2</index>
+      <description><![CDATA[Output Volume]]></description>
+    </image>
+    <double>
+      <name>tolerance</name>
+      <longflag>tolerance</longflag>
+      <flag>t</flag>
+      <label>Tolerance</label>
+      <description><![CDATA[Tolerance between the output image and the baseline (sum)]]></description>
+      <default>0.0001</default>
+    </double>
+  </parameters>
+</executable>
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/CMakeLists.txt b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/CMakeLists.txt
new file mode 100644
index 00000000000..655007a0aab
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(Python)
diff --git a/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/Python/CMakeLists.txt b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/Python/CMakeLists.txt
new file mode 100644
index 00000000000..82ea85b1231
--- /dev/null
+++ b/Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/Python/CMakeLists.txt
@@ -0,0 +1,17 @@
+#-----------------------------------------------------------------------------
+set(BASELINE ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Baseline)
+set(INPUT ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/Input)
+set(TEMP "${CMAKE_BINARY_DIR}/Testing/Temporary")
+
+set(CLP ${MODULE_NAME})
+
+#-----------------------------------------------------------------------------
+set(testname ${CLP}Test)
+ExternalData_add_test(${CLP}Data NAME ${testname} COMMAND ${Slicer_LAUNCHER_EXECUTABLE} ${MODULE_NAME}.py
+  --sigma 2.5 DATA{${INPUT}/CTHeadAxial.nhdr,CTHeadAxial.raw.gz} ${TEMP}/${CLP}Test.nhdr
+  DATA{${BASELINE}/${CLP}Test.nhdr,${CLP}Test.raw}
+  )
+set_property(TEST ${testname} PROPERTY LABELS ${CLP})
+
+#-----------------------------------------------------------------------------
+ExternalData_add_target(${CLP}Data)