Add ctk cli2

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()
 

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()

Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5

@@ -0,0 +1 @@
+fc6170ceeff3d8217a9dd6a1add2ec8c

Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5

@@ -0,0 +1 @@
+0749d4d3f07a217030f9ae33d94c4559

Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.nhdr.md5

@@ -0,0 +1 @@
+6e5c289c73e14ba7a1b0f8aaf6ed249a

Utilities/Templates/Modules/PythonCLI/Data/Input/CTHeadAxial.raw.gz.md5

@@ -0,0 +1 @@
+3ebd710c9cf9d75750f4569b8caf6d07

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)

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>

Utilities/Templates/Modules/PythonCLI/Testing/CMakeLists.txt

@@ -0,0 +1 @@
+add_subdirectory(Python)

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)