Fix warnings, build errors, improve build system and remove need for itk deprecated

[jcfr]

Summary of the changes:

• updates the minimum required version of CMake to 3.5
• fix warnings
• remove dependency to ITKDeprecated by copying the files itkDICOMSeriesFileNames.(cxx|h) as itkNiralDICOMSeriesFileNames.(cxx|h) . It also takes care of namespacing the class as itk::niral::DICOMSeriesFileNames
• simplify the build system: e.g introduction of niral_add_executable for module that do not follow the execution model convention.

This will allow to update Slicer extension like DTIPrep and remove the need for a specific version of ITK statically compiled with legacy code available.

This PR also depends on the following patches:

• https://github.com/NIRALUser/ImageNoise/pull/1 - Merged
• https://github.com/NIRALUser/PolyDataCompression/pull/1 - Merged
• https://github.com/NIRALUser/CurveCompare/pull/1 - Merged

Et voila, this set of changes allows to successfully build all modules (expect the unsupported ones)

$ cmake \
  -DSlicerExecutionModel_DIR:PATH=/home/jcfr/Projects/SlicerExecutionModel-Release/ \
  -DITK_DIR:PATH=/home/jcfr/Projects/Slicer-2-build/ITKv4-build/  \
  -DVTK_DIR:PATH=/home/jcfr/Projects/Slicer-2-build/VTKv8-build \
  -DBUILD_TESTING:BOOL=1 \
  -DCOMPILE_3D4DImageConversion:BOOL=1 \
  -DCOMPILE_CONVERTITKFORMATS:BOOL=1 \
  -DCOMPILE_CombineDWIs:BOOL=1 \
  -DCOMPILE_CurveCompare:BOOL=1 \
  -DCOMPILE_DTITensorNormalization:BOOL=1 \
  -DCOMPILE_IMAGESTAT:BOOL=1 \
  -DCOMPILE_ITKTransformTools:BOOL=1 \
  -DCOMPILE_ImageNoise:BOOL=1 \
  -DCOMPILE_MAURERDISTANCETRANSFORM:BOOL=1 \
  -DCOMPILE_MULTIATLASSEG:BOOL=1 \
  -DCOMPILE_NormalizeDWIGradientVectors:BOOL=1 \
  -DCOMPILE_ReadImageHeader:BOOL=1 \
  -DCOMPILE_PolyDataCompression:BOOL=1 \
../niral_utilities

-- The C compiler identification is GNU 5.2.1
-- The CXX compiler identification is GNU 5.2.1
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found Git: /usr/bin/git (found version "2.5.0") 
-- Setting build type to 'Debug' as none was specified.
-- Configuring executable: ImageMath
-- Configuring executable: ImageStat
-- Configuring executable: Crop4DImage
-- Configuring executable: CropDTI
-- Configuring executable: CropImage
-- Configuring executable: convertITKformats
-- Configuring executable: convertITKformats4D
-- Configuring executable: convertTextToImage
-- Configuring SEM CLI module: DWI_NiftiNrrdConversion
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_VISIBILITY - Success
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY
-- Performing Test COMPILER_HAS_HIDDEN_INLINE_VISIBILITY - Success
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring SEM CLI module: polydatatransform
-- Configuring SEM CLI module: polydatamerge
-- Configuring executable: MultiAtlasSeg
-- Configuring executable: DTITensorNormalization
-- Configuring SEM CLI module: MaurerDistanceTransform
-- Adding external project: ITKTransformTools
-- Adding external project: ReadImageHeader
-- Adding external project: ImageNoise
-- Adding external project: CombineDWIs
-- Adding external project: NormalizeDWIGradientVectors
-- Adding external project: 3D4DImageConversion
-- Adding external project: PolyDataCompression
-- Adding external project: CurveCompare
-- Configuring done
-- Generating done
-- Build files have been written to: /tmp/DTIPrep-build/niral_utilities-build

Cc: @styner @juanprietob

[styner]

Thanks JC!