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 1/3] 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 80a5a9b2331fc205330f003852f21eb7612a7618 Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Fri, 13 May 2016 11:23:31 -0400
Subject: [PATCH 2/3] 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.
---
 .../CLIModuleTemplate/CLIModuleTemplate.cxx                     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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;
 

From e3a73d06b11b6670caee2df0f8f400fbd7ab44a8 Mon Sep 17 00:00:00 2001
From: Francois Budin <francois.budin@gmail.com>
Date: Fri, 13 May 2016 11:34:42 -0400
Subject: [PATCH 3/3] 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.
---
 .../CLIModuleTemplatePython.py                | 36 +++++++++++++
 .../CLIModuleTemplatePython.xml               | 52 +++++++++++++++++++
 .../CLIModuleTemplatePython/CMakeLists.txt    | 12 +++++
 .../Baseline/CLIModuleTemplateTest.nhdr.md5   |  1 +
 .../Baseline/CLIModuleTemplateTest.raw.md5    |  1 +
 .../Data/Input/CTHeadAxial.nhdr.md5           |  1 +
 .../Data/Input/CTHeadAxial.raw.gz.md5         |  1 +
 .../Testing/CMakeLists.txt                    |  1 +
 .../Testing/Python/CMakeLists.txt             | 17 ++++++
 .../CLIExtensionTemplate/CMakeLists.txt       |  1 +
 10 files changed, 123 insertions(+)
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.py
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.xml
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CMakeLists.txt
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.nhdr.md5
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.raw.md5
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.nhdr.md5
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.raw.gz.md5
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/CMakeLists.txt
 create mode 100644 Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/Python/CMakeLists.txt

diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.py b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.py
new file mode 100644
index 00000000000..841dd166246
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.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/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.xml b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.xml
new file mode 100644
index 00000000000..d646ee7c4ca
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.xml
@@ -0,0 +1,52 @@
+<?xml version="1.0" encoding="utf-8"?>
+<executable>
+  <category>Examples</category>
+  <title>CLIPythonModuleTemplate</title>
+  <description><![CDATA[This is a CLI module that can be bundled in an extension]]></description>
+  <version>0.0.1</version>
+  <documentation-url>http://www.example.com/Slicer/Modules/CLIPythonModuleTemplate</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/CLIExtensionTemplate/CLIModuleTemplatePython/CMakeLists.txt b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CMakeLists.txt
new file mode 100644
index 00000000000..617808fa81b
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CMakeLists.txt
@@ -0,0 +1,12 @@
+
+#-----------------------------------------------------------------------------
+set(MODULE_NAME CLIModuleTemplate)
+
+#-----------------------------------------------------------------------------
+
+set(PYTHON_MODULE_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_NAME}Python.py)
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+  add_subdirectory(Testing)
+endif()
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.nhdr.md5 b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.nhdr.md5
new file mode 100644
index 00000000000..e3f7f4074cd
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.nhdr.md5
@@ -0,0 +1 @@
+fc6170ceeff3d8217a9dd6a1add2ec8c
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.raw.md5 b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.raw.md5
new file mode 100644
index 00000000000..6e640c3071f
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.raw.md5
@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559
\ No newline at end of file
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.nhdr.md5 b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.nhdr.md5
new file mode 100644
index 00000000000..734a0467eee
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.nhdr.md5
@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a
\ No newline at end of file
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.raw.gz.md5 b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.raw.gz.md5
new file mode 100644
index 00000000000..f555cb43501
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.raw.gz.md5
@@ -0,0 +1 @@
+3ebd710c9cf9d75750f4569b8caf6d07
\ No newline at end of file
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/CMakeLists.txt b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/CMakeLists.txt
new file mode 100644
index 00000000000..655007a0aab
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/CMakeLists.txt
@@ -0,0 +1 @@
+add_subdirectory(Python)
diff --git a/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/Python/CMakeLists.txt b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/Python/CMakeLists.txt
new file mode 100644
index 00000000000..7267f62eefa
--- /dev/null
+++ b/Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/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 ${CLP}PythonTest)
+ExternalData_add_test(${CLP}PythonData NAME ${testname} COMMAND ${Slicer_LAUNCHER_EXECUTABLE} ${PYTHON_MODULE_SCRIPT}
+  --sigma 2.5 DATA{${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}PythonData)
diff --git a/Extensions/Testing/CLIExtensionTemplate/CMakeLists.txt b/Extensions/Testing/CLIExtensionTemplate/CMakeLists.txt
index f32f2661026..ee2c3f56221 100644
--- a/Extensions/Testing/CLIExtensionTemplate/CMakeLists.txt
+++ b/Extensions/Testing/CLIExtensionTemplate/CMakeLists.txt
@@ -19,6 +19,7 @@ include(${Slicer_USE_FILE})
 #-----------------------------------------------------------------------------
 # Extension modules
 add_subdirectory(CLIModuleTemplate)
+add_subdirectory(CLIModuleTemplatePython)
 ## NEXT_MODULE
 
 #-----------------------------------------------------------------------------