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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.
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‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.py‎

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import itk
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from ctk_cli import *
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import sys
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import logging
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def SmoothingRecursiveGaussianImageFilter(inputVolume, outputVolume, sigma):
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reader = itk.ImageFileReader.New(FileName=inputVolume)
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filter = itk.SmoothingRecursiveGaussianImageFilter.New(reader)
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filter.SetSigma(sigma)
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writer = itk.ImageFileWriter.New(filter,FileName=outputVolume)
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writer.SetUseCompression(True)
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writer.Update()
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return 1
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def main():
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"""Parsing command line arguments and reading input files."""
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logging.basicConfig(level=logging.INFO)
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args=CLIArgumentParser().parse_args()
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# Run processing
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SmoothingRecursiveGaussianImageFilter(args.inputVolume,args.outputVolume,args.sigma)
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# Compare output with baseline
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reader1 = itk.ImageFileReader.New(FileName=args.outputVolume)
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reader2 = itk.ImageFileReader.New(FileName=args.baselineVolume)
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compareFilter=itk.ComparisonImageFilter.New(reader1)
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compareFilter.SetTestInput(reader1)
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compareFilter.SetValidInput(reader2)
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diff=compareFilter.GetTotalDifference()
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if diff < args.tolerance:
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return 0
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return 1
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if __name__ == "__main__":
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ret=main()
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if ret:
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sys.exit(ret)

‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CLIModuleTemplatePython.xml‎

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<?xml version="1.0" encoding="utf-8"?>
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<executable>
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<category>Examples</category>
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<title>CLIPythonModuleTemplate</title>
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<description><![CDATA[This is a CLI module that can be bundled in an extension]]></description>
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<version>0.0.1</version>
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<documentation-url>http://www.example.com/Slicer/Modules/CLIPythonModuleTemplate</documentation-url>
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<license>Slicer</license>
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<contributor>FirstName LastName (Institution), FirstName LastName (Institution)</contributor>
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<acknowledgements>This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN</acknowledgements>
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<parameters>
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<label>IO</label>
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<description><![CDATA[Input/output parameters]]></description>
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<double>
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<name>sigma</name>
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<longflag>sigma</longflag>
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<flag>s</flag>
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<label>Sigma</label>
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<description><![CDATA[A double value (in units of mm) passed to the algorithm]]></description>
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<default>1.0</default>
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</double>
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<image>
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<name>inputVolume</name>
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<label>Input Volume</label>
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<channel>input</channel>
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<index>0</index>
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<description><![CDATA[Input volume]]></description>
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</image>
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<image>
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<name>outputVolume</name>
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<label>Output Volume</label>
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<channel>output</channel>
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<index>1</index>
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<description><![CDATA[Output Volume]]></description>
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</image>
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<image>
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<name>baselineVolume</name>
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<label>Baseline Volume</label>
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<channel>input</channel>
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<index>2</index>
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<description><![CDATA[Output Volume]]></description>
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</image>
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<double>
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<name>tolerance</name>
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<longflag>tolerance</longflag>
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<flag>t</flag>
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<label>Tolerance</label>
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<description><![CDATA[Tolerance between the output image and the baseline (sum)]]></description>
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<default>0.0001</default>
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</double>
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</parameters>
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</executable>

‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CMakeLists.txt‎

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#-----------------------------------------------------------------------------
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set(MODULE_NAME CLIModuleTemplate)
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#-----------------------------------------------------------------------------
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set(PYTHON_MODULE_SCRIPT ${CMAKE_CURRENT_SOURCE_DIR}/${MODULE_NAME}Python.py)
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#-----------------------------------------------------------------------------
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if(BUILD_TESTING)
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add_subdirectory(Testing)
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endif()

‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CompareCLIPythonModule.py‎

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import itk
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import sys
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def main():
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"""Parsing command line arguments and reading input files."""
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## Read command line arguments (tolerance, baseline image, output image, module name, entry point, function arguments)
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## import module with mymodule=__import__(module_name)
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## Call function with arguments
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## use itk.ComparisonImageFilter to compare baseline and output image
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## Output result/save image difference
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if __name__ == "__main__":
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sys.exit(main())

‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/CompareCLIPythonModuleTemplate.xml‎

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<?xml version="1.0" encoding="utf-8"?>
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<executable>
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<category>Examples</category>
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<title>CLIModuleTemplate</title>
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<description><![CDATA[This is a CLI module compares the output of a Python script]]></description>
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<version>0.0.1</version>
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<documentation-url>http://www.example.com/Slicer/Modules/CLIModuleTemplate</documentation-url>
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<license>Slicer</license>
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<contributor>FirstName LastName (Institution), FirstName LastName (Institution)</contributor>
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<acknowledgements>This work was partially funded by NIH grant NXNNXXNNNNNN-NNXN</acknowledgements>
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<parameters>
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<label>IO</label>
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<description><![CDATA[Input/output parameters]]></description>
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<double>
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<name>sigma</name>
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<longflag>sigma</longflag>
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<flag>s</flag>
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<label>Sigma</label>
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<description><![CDATA[A double value (in units of mm) passed to the algorithm]]></description>
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<default>1.0</default>
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</double>
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<image>
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<name>inputVolume</name>
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<label>Input Volume</label>
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<channel>input</channel>
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<index>0</index>
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<description><![CDATA[Input volume]]></description>
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</image>
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<image>
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<name>outputVolume</name>
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<label>Output Volume</label>
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<channel>output</channel>
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<index>1</index>
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<description><![CDATA[Output Volume]]></description>
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</image>
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<image>
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<name>baselineVolume</name>
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<label>Baseline Volume</label>
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<channel>input</channel>
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<index>2</index>
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<description><![CDATA[Output Volume]]></description>
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</image>
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</parameters>
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</executable>

‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.nhdr.md5‎

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‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Baseline/CLIModuleTemplateTest.raw.md5‎

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‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.nhdr.md5‎

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‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Data/Input/CTHeadAxial.raw.gz.md5‎

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‎Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplatePython/Testing/CMakeLists.txt‎

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add_subdirectory(Python)

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