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Add ctk cli2 #497

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Add ctk cli2 #497

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a98459d
ENH: Addition of ctk_cli
fbudin69500 May 11, 2016
bae311d
BUG: Template argument name was modified in template declaration
fbudin69500 May 16, 2016
4b216a9
ENH: Addition of an example to use ctk_cli
fbudin69500 May 16, 2016
70a7aff
ENH: Generating new extension based on new module type.
fbudin69500 May 16, 2016
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2 changes: 1 addition & 1 deletion CMake/SlicerExtensionTemplatesGenerator.cmake
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Expand Up @@ -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()

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44 changes: 44 additions & 0 deletions Extensions/PythonCLIExtensionTemplate.s4ext
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#
# 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 https://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 https://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 https://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate/Screenshots/1.png

# 0 or 1: Define if the extension should be enabled after its installation.
enabled 1
2 changes: 1 addition & 1 deletion Extensions/Testing/CLIExtensionTemplate/CLIModuleTemplate/CLIModuleTemplate.cxx
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Expand Up @@ -15,7 +15,7 @@ namespace
{

template <typename TPixel>
int DoIt( int argc, char * argv[], T )
int DoIt( int argc, char * argv[], TPixel )
{
PARSE_ARGS;

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25 changes: 25 additions & 0 deletions Extensions/Testing/PythonCLIExtensionTemplate/CMakeLists.txt
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cmake_minimum_required(VERSION 2.8.9)

project(PythonCLIExtensionTemplate)

#-----------------------------------------------------------------------------
# Extension meta-information
set(EXTENSION_HOMEPAGE "https://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 "https://www.example.com/Slicer/Extensions/PythonCLIExtensionTemplate.png")
set(EXTENSION_SCREENSHOTURLS "https://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})
Binary file added Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIExtensionTemplate.png
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24 changes: 24 additions & 0 deletions Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/CMakeLists.txt
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#-----------------------------------------------------------------------------
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()
1 change: 1 addition & 0 deletions ...ensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
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1 change: 1 addition & 0 deletions ...tensionTemplate/PythonCLIModuleTemplate/Data/Baseline/PythonCLIModuleTemplateTest.raw.md5
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1 change: 1 addition & 0 deletions ...esting/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.nhdr.md5
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1 change: 1 addition & 0 deletions ...ting/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Data/Input/CTHeadAxial.raw.gz.md5
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36 changes: 36 additions & 0 deletions ...ons/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.py
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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)
52 changes: 52 additions & 0 deletions ...ns/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/PythonCLIModuleTemplate.xml
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<?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>https://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>
1 change: 1 addition & 0 deletions Extensions/Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/CMakeLists.txt
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add_subdirectory(Python)
17 changes: 17 additions & 0 deletions .../Testing/PythonCLIExtensionTemplate/PythonCLIModuleTemplate/Testing/Python/CMakeLists.txt
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#-----------------------------------------------------------------------------
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)
2 changes: 1 addition & 1 deletion SuperBuild.cmake
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Expand Up @@ -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)
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36 changes: 36 additions & 0 deletions SuperBuild/External_python-ctk_cli.cmake
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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}:https://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()
2 changes: 1 addition & 1 deletion Utilities/Templates/Modules/CLI/TemplateKey.cxx
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Expand Up @@ -15,7 +15,7 @@ namespace
{

template <typename TPixel>
int DoIt( int argc, char * argv[], T )
int DoIt( int argc, char * argv[], TPixel )
{
PARSE_ARGS;

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24 changes: 24 additions & 0 deletions Utilities/Templates/Modules/PythonCLI/CMakeLists.txt
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#-----------------------------------------------------------------------------
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()
1 change: 1 addition & 0 deletions Utilities/Templates/Modules/PythonCLI/Data/Baseline/PythonCLIModuleTemplateTest.nhdr.md5
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36 changes: 36 additions & 0 deletions Utilities/Templates/Modules/PythonCLI/PythonCLIModuleTemplate.py
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import itk
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See https://pypi.python.org/pypi/flake8-import-order

import logging
import sys

from ctk_cli import CLIArgumentParser

import itk

Useful resrouces: https://pypi.python.org/pypi/flake8-import-order and

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Additionally, would it be possible to use SimpleITK, wrapped ITK is not yet enabled by default.

Thanks for your help

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)
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