fail to build release 5.2rc03 on ArchLinux

[hubutui]

Error log:

CMake Error at Wrapping/CMakeUtilityFunctions.cmake:40 (math):
  math cannot parse the expression: ")

  set(ITK_WRAP_VECTOR_COMPONENTS + 1": syntax error, unexpected
  exp_CLOSEPARENT (1).
Call Stack (most recent call first):
  Wrapping/WrapBasicTypes.cmake:55 (INCREMENT)
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)


CMake Warning (dev) at Wrapping/CMakeUtilityFunctions.cmake:40 (math):
  Unexpected character in expression at position 1: "

Call Stack (most recent call first):
  Wrapping/WrapBasicTypes.cmake:63 (INCREMENT)
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Error at Wrapping/WrapBasicTypes.cmake:73 (message):
  ITK_WRAP_VECTOR_COMPONENTS must include ITK_WRAP_IMAGE_DIMS
Call Stack (most recent call first):
  Wrapping/ConfigureWrapping.cmake:131 (include)
  Wrapping/CMakeLists.txt:97 (include)

See the complete build log here

[thewtex]

How is the build invoked?

[hubutui]

  export CC=clang
  export CXX=clang++
  python setup.py build

I use clang instead of gcc, because I used to build python-itk 5.1.2 with clang.

[thewtex]

Does the same issue occur with the v5.2.0 tag (the current release branch)?

[hubutui]

yes, check the latest build log for v5.2.0 here.

[thewtex]

@hubutui , please try this branch #156

[hubutui]

I got this error when building with clang 11.1.0:

CMake Error at /usr/share/cmake-3.20/Modules/CheckIPOSupported.cmake:63 (message):
  IPO is not supported (check failed to compile).

check the complete build log here

I could build itk with gcc 10.2.0. I create pkg for ArchLinux with:

python setup.py build
python setup.py install --root="${pkgdir}" --optimize=1 --skip-build

But I fail to read example image with itk.imread(), error output:

Traceback (most recent call last):
  File "<input>", line 1, in <module>
    img = itk.imread('/home/hubutui/tmpdir/MRBrainTumor2.nrrd')
  File "/usr/lib/python3.9/site-packages/itk/support/extras.py", line 957, in imread
    reader = template_reader_type.New(**kwargs)
  File "/usr/lib/python3.9/site-packages/itk/support/template_class.py", line 660, in New
    return self._NewImageReader(
  File "/usr/lib/python3.9/site-packages/itk/support/template_class.py", line 191, in _NewImageReader
    ImageType = itk.Image[PixelType, dimension]
  File "/usr/lib/python3.9/site-packages/itk/support/template_class.py", line 529, in __getitem__
    raise itk.TemplateTypeError(self, key)
itk.support.extras.TemplateTypeError: itk.Image is not wrapped for input type `itk.SS, int`.

To limit the size of the package, only a limited number of
types are available in ITK Python. To print the supported
types, run the following command in your python environment:

    itk.Image.GetTypes()

Possible solutions:
* If you are an application user:
** Convert your input image into a supported format (see below).
** Contact developer to report the issue.
* If you are an application developer, force input images to be
loaded in a supported pixel type.

    e.g.: instance = itk.Image[itk.RGBPixel[itk.UC], int].New(my_input)

* (Advanced) If you are an application developer, build ITK Python yourself and
turned to `ON` the corresponding CMake option to wrap the pixel type or image
dimension you need. When configuring ITK with CMake, you can set
`ITK_WRAP_${type}` (replace ${type} with appropriate pixel type such as
`double`). If you need to support images with 4 or 5 dimensions, you can add
these dimensions to the list of dimensions in the CMake variable
`ITK_WRAP_IMAGE_DIMS`.

Supported input types:

itk.RGBPixel[itk.UC]
itk.RGBAPixel[itk.UC]
itk.Vector[itk.F,2]
itk.Vector[itk.F,4]
itk.CovariantVector[itk.F,2]
itk.CovariantVector[itk.F,4]
itk.SS
itk.UC
itk.US
itk.F
itk.D
itk.complex[itk.F]
itk.Vector[itk.D,2]
itk.Vector[itk.D,4]
itk.SI
itk.UI
itk.UL
itk.ULL
itk.B
itk.FixedArray[itk.F,2]
itk.FixedArray[itk.D,2]
itk.Offset[2]
itk.SymmetricSecondRankTensor[itk.D,2]
itk.Vector[itk.D,2]
itk.Vector[itk.D,4]
itk.Vector[itk.F,1]
itk.CovariantVector[itk.D,2]
itk.CovariantVector[itk.D,4]
itk.NormalBandNode[itk.Image[itk.F,2]]
itk.NormalBandNode[itk.Image[itk.D,2]]

and itk.Image.GetTypes() gives me:

<itkTemplate itk::Image>
Options:
  [<itkCType bool>, 2]
  [<itkCType double>, 2]
  [<itkCType float>, 2]
  [<itkCType signed int>, 2]
  [<itkCType signed short>, 2]
  [<itkCType unsigned char>, 2]
  [<itkCType unsigned int>, 2]
  [<itkCType unsigned long long>, 2]
  [<itkCType unsigned long>, 2]
  [<itkCType unsigned short>, 2]
  [<class 'itk.itkCovariantVectorPython.itkCovariantVectorD2'>, 2]
  [<class 'itk.itkCovariantVectorPython.itkCovariantVectorD4'>, 2]
  [<class 'itk.itkCovariantVectorPython.itkCovariantVectorF2'>, 2]
  [<class 'itk.itkCovariantVectorPython.itkCovariantVectorF4'>, 2]
  [<class 'itk.itkFixedArrayPython.itkFixedArrayD2'>, 2]
  [<class 'itk.itkFixedArrayPython.itkFixedArrayF2'>, 2]
  [<class 'itk.itkOffsetPython.itkOffset2'>, 2]
  [<class 'itk.itkRGBAPixelPython.itkRGBAPixelUC'>, 2]
  [<class 'itk.itkRGBPixelPython.itkRGBPixelUC'>, 2]
  [<class 'itk.itkSparseFieldFourthOrderLevelSetImageFilterPython.itkNormalBandNodeID2'>, 2]
  [<class 'itk.itkSparseFieldFourthOrderLevelSetImageFilterPython.itkNormalBandNodeIF2'>, 2]
  [<class 'itk.itkSymmetricSecondRankTensorPython.itkSymmetricSecondRankTensorD2'>, 2]
  [<class 'itk.itkVectorPython.itkVectorD2'>, 2]
  [<class 'itk.itkVectorPython.itkVectorD2'>, 3]
  [<class 'itk.itkVectorPython.itkVectorD4'>, 2]
  [<class 'itk.itkVectorPython.itkVectorD4'>, 3]
  [<class 'itk.itkVectorPython.itkVectorF1'>, 2]
  [<class 'itk.itkVectorPython.itkVectorF2'>, 2]
  [<class 'itk.itkVectorPython.itkVectorF4'>, 2]
  [<class 'itk.stdcomplexPython.stdcomplexF'>, 2]

Did I use the wrong method to build and create pkg for python-itk?

[thewtex]

IPO is not supported (check failed to compile).

@hubutui please test this patch:
InsightSoftwareConsortium/ITK#2498

To limit the size of the package, only a limited number of
types are available in ITK Python. To print the supported
types, run the following command in your python environment:

The default build does not enable support for all pixel types. To add support for more pixels type, enable CMake configurations such as:

ITKPythonPackage/scripts/internal/manylinux-build-wheels.sh

Lines 126 to 128 in e019220

	-DITK_WRAP_unsigned_short:BOOL=ON \
	-DITK_WRAP_double:BOOL=ON \
	-DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \

[hubutui]

OK, I could now build python-itk with pull 156 and pull 2498 patches applied.

cd ${srcdir}/ITK-5.2.0
patch -p1 -i https://github.com/InsightSoftwareConsortium/ITK/pull/2498
cd ${srcdir}/ITKPythonPackage-5.2.0
patch -p1 -i https://github.com/InsightSoftwareConsortium/ITKPythonPackage/pull/156
  python setup.py build -- \
    -DITK_WRAP_unsigned_short:BOOL=ON \
    -DITK_WRAP_double:BOOL=ON \
    -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \
    -DITK_SOURCE_DIR="${srcdir}/ITK-5.2.0"

However, I still fail to read the example image with itk.imread() with a similar error message as above.

Are these wheels from PyPI build with:

    -DITK_WRAP_unsigned_short:BOOL=ON \
    -DITK_WRAP_double:BOOL=ON \
    -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \

?
I could confirm that if I install from PyPi, I could read the example image.

[thewtex]

itk.Image is not wrapped for input type itk.SS, int

This indicated the signed short pixel type, which is wrapped by default.

[, 2]

The error message says 2D signed short images are wrapped. However, I do not see 3D listed.

-DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \

As with #156, we may need to remove the quotes.

[hubutui]

@thewtex I'm confused, if I run

python setup.py build -- \
    -DITK_WRAP_unsigned_short:BOOL=ON \
    -DITK_WRAP_double:BOOL=ON \
    -DITK_WRAP_IMAGE_DIMS:STRING=2;3;4 \
    -DITK_SOURCE_DIR="${srcdir}/ITK-5.2.0"

doesn't it means:

python setup.py build -- \
    -DITK_WRAP_unsigned_short:BOOL=ON \
    -DITK_WRAP_double:BOOL=ON \
    -DITK_WRAP_IMAGE_DIMS:STRING=2
3
4 -DITK_SOURCE_DIR="${srcdir}/ITK-5.2.0"

?

[thewtex]

@hubutui yes, how about "-DITK_WRAP_IMAGE_DIMS:STRING=2;3;4"

[hubutui]

I could build python-itk with:

cd ${srcdir}/ITK-5.2.0
patch -p1 -i https://github.com/InsightSoftwareConsortium/ITK/pull/2498
cd ${srcdir}/ITKPythonPackage-5.2.0
patch -p1 -i https://github.com/InsightSoftwareConsortium/ITKPythonPackage/pull/156
  python setup.py build -- \
    -DITK_WRAP_unsigned_short:BOOL=ON \
    -DITK_WRAP_double:BOOL=ON \
    -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" \
    -DITK_SOURCE_DIR="${srcdir}/ITK-5.2.0"

However, it seems that -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4" is not passed to ITK build stage, so itk.Image.GetTypes() shows no 3D type supported.

[hubutui]

I check ${srcdir}/ITKPythonPackage-5.2.0/_skbuild/linux-x86_64-3.9/cmake-build/ITKb/CMakeCache.txt, and found ITK_WRAP_IMAGE_DIMS:STRING=2, if I set "-DITK_WRAP_IMAGE_DIMS:STRING=2;3;4".

ITK_WRAP_IMAGE_DIMS:STRING=2 is also found in ${srcdir}/ITKPythonPackage-5.2.0/_skbuild/linux-x86_64-3.9/cmake-build/ITKb/CMakeCache.txt if I set -DITK_WRAP_IMAGE_DIMS:STRING="2;3;4".

[hubutui]

I check the build log, and log messages mentioned ITK_WRAP_IMAGE_DIMS in build stage:

-- SuperBuild - Searching for python[OK]
-- SuperBuild -   DOXYGEN_EXECUTABLE: /usr/bin/doxygen
-- ITK CMake Cache Args -   -DITK_WRAP_IMAGE_DIMS=2;3;4;-DITK_WRAP_double=ON;-DITK_WRAP_unsigned_short=ON
-- SuperBuild -
...
...
Configuring Project
  Working directory:
    /build/python-itk/src/ITKPythonPackage-5.2.0/_skbuild/linux-x86_64-3.9/cmake-build
  Command:
    cmake /build/python-itk/src/ITKPythonPackage-5.2.0 -G 'Unix Makefiles' -DCMAKE_INSTALL_PREFIX:PATH=/build/python-itk/src/ITKPythonPackage-5.2.0/_skbuild/linux-x86_64-3.9/cmake-install -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/python -DPYTHON_VERSION_STRING:STRING=3.9.3 -DPYTHON_INCLUDE_DIR:PATH=/usr/include/python3.9 -DPYTHON_LIBRARY:FILEPATH=/usr/lib/libpython3.9.so -DSKBUILD:BOOL=TRUE -DCMAKE_MODULE_PATH:PATH=/usr/lib/python3.9/site-packages/skbuild/resources/cmake -DITK_WRAP_unsigned_short:BOOL=ON -DITK_WRAP_double:BOOL=ON '-DITK_WRAP_IMAGE_DIMS:STRING=2;3;4' -DITK_SOURCE_DIR=/build/python-itk/src/ITK-5.2.0 -DCMAKE_BUILD_TYPE:STRING=Release

[hubutui]

update:
I rebuild with v5.2.0.post1, now ITK_WRAP_IMAGE_DIMS:STRING=2,3,4 is found in ${srcdir}/ITKPythonPackage-5.2.0/_skbuild/linux-x86_64-3.9/cmake-build/ITKb/CMakeCache.txt as expected. However, it seems that there is something wrong with the install step.

python setup.py install --root="${pkgdir}" --optimize=1 --skip-build

Nothing is installed except an __init__.py file.
The install tree looks like this:

.
└── usr
    └── lib
        └── python3.9
            └── site-packages
                ├── itk
                │   └── __init__.py
                └── itk-5.2.0.post1-py3.9.egg-info
                    ├── dependency_links.txt
                    ├── not-zip-safe
                    ├── PKG-INFO
                    ├── requires.txt
                    ├── SOURCES.txt
                    └── top_level.txt

check the complete build log here