[SyneRBI/SIRF-SuperBuild] Add windows install instructions (#467)

[Biguri]

All instructions are for unix type systems.

We should add instrutions for windows

(may make a PR when I figure out how to build it)

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[Kris Thielemans]

There should be something on the wiki, but surely incomplete, as the SuperBuild started the work only a week ago or so, and things are still moving. Summary is

• install CMake very latest version
• install VS (Community Edition) or another compiler (haven't tried!)
• install Boost (I'm using 1.74.0. haven't tried with 1.75).
• run CMake, configure (either disable MATLAB or Python, don't use both), use SyneRBI/SIRF#847 for SIRF, enable USE_ITK (not default yet I think), let it find boost, generate, open project
• build with VS (don't attempt Debug mode, see SyneRBI/SIRF#42)., ignoring SyneRBI/SIRF#839)
• set your environment as in #460
• lead a happy life

You probably want to stick to STIR release_4 in the first instance due to a recent problem after @danieldeidda's calibration update (although this should not affect you).

[Biguri]

Thanks, I have indeed followed those steps, building now.
We should also document which VS versions have been tested, VS is famous for changing as much as possible between versions. I am using 2019 now.

[Biguri]

Plus, MVS doesnt come with a lot of things by default, e.g. a C++ compiler (yes, really). So we should clarify too what of MVS is needed :)

[Kris Thielemans]

it'll work with all of them of course 😉 .

[Biguri]

@KrisThielemans I am having trouble with Boost. I have it installed, but cmake refuses to let me point it out towards its location in my system, it keeps saying not found. For a test, can you let me know what folders you use for Boost_DIR, Boost_INCLUDE_DIR and Boost_SOURCE_DIR ?

[Kris Thielemans]

SyneRBI/SIRF#847 is now merged, so now it's easy :-)

[Biguri]

@KrisThielemans not sure if its easy, I was already using it and still Boost was not being detected...

[Kris Thielemans]

boost: I used the default settings for the installer, which installed it in c:\local\boost_1_74_0. CMake didn't find that by default. So I created a new variable to tell it where it is. This can be done in the GUI, or from the command line:

cd whereveryoubuild
cmake -DBOOST_ROOT:PATH=c:\local\boost_1_74_0 .

[Biguri]

Ah, yes, I was playing with that but I was getting illegal character messages. Should not that variable be part of the CMAKE (instead of user-specified)? In any case, definitely worth documenting. In which section of the readme do you want it?

[Kris Thielemans]

Sadly they've marked BOOST_ROOT as an advanced variable, so you don't get it by default. Also, CMake is changing its policy for variables called package_ROOT, see SyneRBI/SIRF#233, but we're still on the old behaviour, so it'll work for a bit longer. Their message doesn't tell you what to do though (as often the case).

Illegal characters: you can always try c:/local/boost_1_74_0. Probably safer whatever shell/cmd/powershell you're using.

Of course, we need to document it, but it first needs to work! where to document it? It's quite like that our OS specific install instructions are still on the wiki. That's what I see on https://github.com/SyneRBI/SIRF-SuperBuild/tree/master/#os-specific-information. There's the (terse!) https://github.com/SyneRBI/SIRF/wiki/SIRF-SuperBuild-on-Windows-with-Visual-Studio for instance. And the soon to be outdated https://github.com/SyneRBI/SIRF/wiki/Installation-instructions#steps-on-windows-. We did agree to move info on the wiki to markdown in the repo (and point the wiki to those pages) to reduce the amount of duplication/confusion. That's easy enough (the Github wiki uses markdown and files can be downloaded/copied). But that seems another issue that needs to be created....

[Biguri]

ah, not use to my laptop for compiling. I get the confusing error When compiling SIRF:

11>CMake Error at C:/Program Files/CMake/share/cmake-3.19/Modules/FindPackageHandleStandardArgs.cmake:218 (message):
11>  Could NOT find Boost (missing: system filesystem thread date_time chrono)
11>  (found suitable version "1.65.1", minimum required is "1.36.0")

Confusing because it found a version that seem OK, and confusing because I installed 1.75.0 (but I think SIRF-Superbuild attempts to install 1.65.1, am I right?)

I set up BOOST_ROOT to where my boost library is, but I can not configure cmake without getting whatever is in Boost_DIR removed.

[Kris Thielemans]

There was a boost 1.65.1 in INSTALL/include, probably because of attempts (not sure). We're trying again after deleting it. More tomorrow.

[Biguri]

My problem was that I was either using pre-built 1.75.0 Boost which is not supported by CMAKE (released 5 days before my CMAKE version, but too new nevertheless), or non-built 1.74.0. Installing a pre-built 1.74.0 seems to have solve the problem, but I am getting:

Severity	Code	Description	Project	File	Line	Suppression State
Error	C2039	'runtime_error': is not a member of 'std' [D:\SIRF\build\builds\SIRF\build\src\Registration\cReg\Reg.vcxproj]	SIRF	D:\SIRF\build\sources\SIRF\src\Registration\cReg\Resample.cpp	81	

I can see in here, that a solution to this is to include <stdexcept> which I added in resample.cpp.

This removes the (several) runtime_error errors, but adds

Error	C1189	#error:  WinSock.h has already been included [D:\SIRF\build\builds\SIRF\build\src\Synergistic\tests\SYN_TEST_CPLUSPLUS.vcxproj]	SIRF	C:\local\boost_1_74_0\boost\asio\detail\socket_types.hpp	24	

Internet suggests that changing the location of the include is the solution, but I don't know where to put it, if its the first line of resample.cpp the error is still there.
https://stackoverflow.com/questions/9750344/boostasio-winsock-and-winsock-2-compatibility-issue

Investigating...

[Kris Thielemans]

I strongly suspect your SIRF is out-of-date. I've fixed those 2 recently. See for instance
https://github.com/SyneRBI/SIRF/blob/2e1d74aa4d40f5edf6a441d54e60a26a55f79b71/src/Registration/cReg/Resample.cpp#L31
and SyneRBI/SIRF#847

[Biguri]

My current steps:

1. CMAKE, python38, boost (<=1.74.0)
2. Configure cmake as follows (I use the GUI):

• USE_ITK: ON
• DISABLE_Matlab: ON
• BOOST_ROOT: path_to_boost (e.g. C:\local\boost_1.74.0)
• USE_NiftyPET: OFF // requires python27
• SIRF_TAG: origin/master

3. configure/Generate
4. Open MSV19, built all (release mode)
5. Set enviroment variables:
   Kris has:
   

$install="C:\Users\krisf\Documents\devel\buildVC\SIRF-SuperBuild\INSTALL"
 $Env:Path = "${install}\bin" + ";" + $Env:Path
 $Env:Path += ";${install}\FFTW"
 $Env:Path += ";c:/local/boost_1_74_0/lib64-msvc-14.2/"
 # need to be forward slashes 
 $Env:SIRF_PATH = "C:/Users/krisf/Documents/devel/buildVC/SIRF-SuperBuild/sources/SIRF"
 $Env:PYTHONPATH = "${install}\python"
 $Env:MATLABPATH = "${install}\matlab"
 $Env:MATLABPATH+=';C:\Users\krisf\Documents\devel\buildVC\SIRF-SuperBuild\sources\SPM'
 $Env:Path += ";c\Program Files\MATLAB\R2020b\bin\win64;c:\Program Files\MATLAB\R2020b\extern\bin\win64"

I have:

 $install="D:/SIRF/build/INSTALL"
 $Env:Path = "${install}\bin" + ";" + $Env:Path
 $Env:Path += ";${install}\FFTW"
 $Env:Path += ";c:/local/boost_1_74_0/lib64-msvc-14.2/"
 # need to be forward slashes 
 $Env:SIRF_PATH = "D:/SIRF/build/sources/SIRF"
 $Env:PYTHONPATH = "${install}\python"

6. Open powershell, run the script for env-vars.
7. Use the shell for python.

[Kris Thielemans]

I think

• step 1. Install boost via the .exe (do not use the .zip)
• step 6. Open powershell, copy-paste content of script into the terminal for env-vars

[Biguri]

@KrisThielemans indeed. For step 6, I instead save it in a .ps1 file and run it from the powershell

[Evgueni Ovtchinnikov]

Tried to build SIRF-SuperBuild afresh, got these errors:

13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(535): error C2131: expression did not evaluate to a constant [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(563): error C2131: expression did not evaluate to a constant [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(569): error C2446: ':': no conversion from 'hsize_t *' to 'int' [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(613): error C2131: expression did not evaluate to a constant [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(658): error C2131: expression did not evaluate to a constant [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(664): error C2446: ':': no conversion from 'hsize_t *' to 'int' [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(695): error C2131: expression did not evaluate to a constant [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]
13>C:\Users\wps46139\Documents\GitHub\try\build\sources\STIR\src\IO\GEHDF5Wrapper.cxx(703): error C2446: ':': no conversion from 'hsize_t *' to 'int' [C:\Users\wps46139\Documents\GitHub\try\build\builds\STIR\build\src\IO\IO.vcxproj]

Conversion from 'hsize_t *' to 'int' is not a problem, but the other errors are very puzzling given the declaration of m_max_dataset_dims:

    const int m_max_dataset_dims =5;

[Kris Thielemans]

are you using STIR master? I've fixed a similar error on release_4 (see UCL/STIR#777) and haven't merged that yet to master. can try and do it now

[Evgueni Ovtchinnikov]

I do (git fetch does not fetch).

Quick fixed m_max_dataset_dims error by

#define m_max_dataset_dims 5

and built STIR. Now going through the usual fixes in SIRF build, will comment separately.

[Evgueni Ovtchinnikov]

SIRF Windows build annoyance 1.

CMake puts this rubbish in SIRF.sln:

Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "C:", "C:", "{EDA60312-2021-3C94-8E6A-E3C505A86C58}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Users", "C:\Users", "{E760C743-ABDE-3140-8D0A-356CA064D5A8}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "wps46139", "C:\Users\wps46139", "{A05394FE-A4A1-3C77-ABAE-B9B5BC4DACC4}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Documents", "C:\Users\wps46139\Documents", "{2E5941D4-A2D2-3884-A881-A7AE1A3F4C48}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "GitHub", "C:\Users\wps46139\Documents\GitHub", "{B04EF322-7E84-36C8-8C14-1628406FBE2D}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "try", "C:\Users\wps46139\Documents\GitHub\try", "{8B5DBC82-06F0-3331-8977-CC29F738067C}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "build", "C:\Users\wps46139\Documents\GitHub\try\build", "{A24ECC70-224F-329F-9016-0C2910523406}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "INSTALL", "C:\Users\wps46139\Documents\GitHub\try\build\INSTALL", "{80639F0D-8C7C-3029-8E40-92043AA82323}"
EndProject
Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "bin", "C:\Users\wps46139\Documents\GitHub\try\build\INSTALL\bin", "{B99B5A13-953C-3B24-9BCD-C9C7FC2D246F}"
EndProject

which creates spurious projects C, Users etc. So, each time the build of SIRF runs CMake, I have to remove this rubbish manually using a text editor.

[Evgueni Ovtchinnikov]

SIRF Windows build annoyance 2.

SIRF projects _pygadgetron, _pyreg, _pysirf, _pystir, MR_TESTS_CPLUSPLUS, REG_TEST_CPLUSPLUS, SYN_TEST_CPLUSPLUS, cstir_tests, sirf_affine_to_disp, sirf_change_datatype, sirf_convert_image_type, sirf_crop_image, sirf_do_images_match, sirf_flip_or_mirror_image, sirf_inverse_transform, sirf_nifti_maths, sirf_print_nifti_info, sirf_registration, sirf_resample, sirf_tensor_split_join and test_conv_img have extra dependency on hdf5.lib without path (in addition to one with the proper path), which I have to remove manually each time the SIRF build runs CMake.

[Kris Thielemans]

@evgueni-ovtchinnikov can you please confirm your CMake version? It needs to be 3.19.2... (some fixes coming in 3.19.3 and hopefully final ones in 3.20.0...)

@AnderBiguri and I are using VS 2019, but that shouldn't matter.

the point is obviously that none of these edits should be necessary! If you have to make them, then I would stop right trying to fix them manually.

[Evgueni Ovtchinnikov]

I was using 3.13.3 - will upgrade now.

[Kris Thielemans]

UCL/STIR#797 to update master is created but will probably only be merged tomorrow.

[Evgueni Ovtchinnikov]

same story with CMake 3.19.3

[Kris Thielemans]

I am completely baffled. Why would CMake generate wrong project files on your computer and not ours? It makes no sense to me. Sigh.

Possibly you could post your CMakeCache.txt? (Ideally the one from the SuperBuild directory and the one it generates in builds/SIRF/build).

[Evgueni Ovtchinnikov]

CMakeCache.txt in folder build:

# This is the CMakeCache file.
# For build in directory: c:/Users/wps46139/Documents/GitHub/try/build
# It was generated by CMake: C:/Program Files/CMake/bin/cmake.exe
# You can edit this file to change values found and used by cmake.
# If you do not want to change any of the values, simply exit the editor.
# If you do want to change a value, simply edit, save, and exit the editor.
# The syntax for the file is as follows:
# KEY:TYPE=VALUE
# KEY is the name of a variable in the cache.
# TYPE is a hint to GUIs for the type of VALUE, DO NOT EDIT TYPE!.
# VALUE is the current value for the KEY.

########################
# EXTERNAL cache entries
########################

//ON
ACE_TAG:STRING=origin/master

//ON
ACE_URL:STRING=https://github.com/paskino/libace-conda

//Build CCPi CIL Modules and ASTRA engine
BUILD_CIL:BOOL=OFF

//Build CCPi CIL Modules
BUILD_CIL_LITE:BOOL=OFF

//Build Gadgetron
BUILD_Gadgetron:BOOL=OFF

//Build NIFTYREG
BUILD_NIFTYREG:BOOL=ON

//Build SIRF
BUILD_SIRF:BOOL=ON

//Build SIRF-Contribs
BUILD_SIRF_Contribs:BOOL=ON

//Build SIRFS's registration functionality
BUILD_SIRF_Registration:BOOL=ON

//Build SPM. Only SPM12 tested
BUILD_SPM:BOOL=ON

//Build STIR
BUILD_STIR:BOOL=ON

//Build tests for ITK
BUILD_TESTING_ITK:BOOL=OFF

//Build tests for JSON
BUILD_TESTING_JSON:BOOL=OFF

//Build tests for SIRF
BUILD_TESTING_SIRF:BOOL=ON

//Build tests for STIR
BUILD_TESTING_STIR:BOOL=OFF

//Build pet_rd_tools
BUILD_pet_rd_tools:BOOL=OFF

//Build siemens_to_ismrmrd
BUILD_siemens_to_ismrmrd:BOOL=OFF

//The directory containing a CMake configuration file for Boost.
Boost_DIR:PATH=Boost_DIR-NOTFOUND

//Path to a file.
Boost_INCLUDE_DIR:PATH=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1

//Source directory for Boost
Boost_SOURCE_DIR:PATH=C:/Users/wps46139/Documents/GitHub/try/build/sources/Boost

//ON
CCPi-Astra_TAG:STRING=v20.04

//ON
CCPi-Astra_URL:STRING=https://github.com/vais-ral/CCPi-Astra.git

//ON
CCPi-FrameworkPlugins_TAG:STRING=v20.04

//ON
CCPi-FrameworkPlugins_URL:STRING=https://github.com/vais-ral/CCPi-FrameworkPlugins.git

//ON
CCPi-Framework_TAG:STRING=v20.04

//ON
CCPi-Framework_URL:STRING=https://github.com/vais-ral/CCPi-Framework.git

//ON
CCPi-Regularisation-Toolkit_TAG:STRING=v20.04

//ON
CCPi-Regularisation-Toolkit_URL:STRING=https://github.com/vais-ral/CCPi-Regularisation-Toolkit.git

//Path to a program.
CMAKE_AR:FILEPATH=C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/x86_amd64/lib.exe

//Choose the type of build, options are: None Debug Release RelWithDebInfo
// MinSizeRel.
CMAKE_BUILD_TYPE:STRING=Release

//Semicolon separated list of supported configuration types, only
// supports Debug, Release, MinSizeRel, and RelWithDebInfo, anything
// else will be ignored.
CMAKE_CONFIGURATION_TYPES:STRING=Debug;Release;MinSizeRel;RelWithDebInfo

//Flags used by the CXX compiler during all build types.
CMAKE_CXX_FLAGS:STRING=/DWIN32 /D_WINDOWS /W3 /GR /EHsc

//Flags used by the CXX compiler during DEBUG builds.
CMAKE_CXX_FLAGS_DEBUG:STRING=/MDd /Zi /Ob0 /Od /RTC1

//Flags used by the CXX compiler during MINSIZEREL builds.
CMAKE_CXX_FLAGS_MINSIZEREL:STRING=/MD /O1 /Ob1 /DNDEBUG

//Flags used by the CXX compiler during RELEASE builds.
CMAKE_CXX_FLAGS_RELEASE:STRING=/MD /O2 /Ob2 /DNDEBUG

//Flags used by the CXX compiler during RELWITHDEBINFO builds.
CMAKE_CXX_FLAGS_RELWITHDEBINFO:STRING=/MD /Zi /O2 /Ob1 /DNDEBUG

//Libraries linked by default with all C++ applications.
CMAKE_CXX_STANDARD_LIBRARIES:STRING=kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib

//Flags used by the C compiler during all build types.
CMAKE_C_FLAGS:STRING=/DWIN32 /D_WINDOWS /W3

//Flags used by the C compiler during DEBUG builds.
CMAKE_C_FLAGS_DEBUG:STRING=/MDd /Zi /Ob0 /Od /RTC1

//Flags used by the C compiler during MINSIZEREL builds.
CMAKE_C_FLAGS_MINSIZEREL:STRING=/MD /O1 /Ob1 /DNDEBUG

//Flags used by the C compiler during RELEASE builds.
CMAKE_C_FLAGS_RELEASE:STRING=/MD /O2 /Ob2 /DNDEBUG

//Flags used by the C compiler during RELWITHDEBINFO builds.
CMAKE_C_FLAGS_RELWITHDEBINFO:STRING=/MD /Zi /O2 /Ob1 /DNDEBUG

//Libraries linked by default with all C applications.
CMAKE_C_STANDARD_LIBRARIES:STRING=kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib

//Flags used by the linker during all build types.
CMAKE_EXE_LINKER_FLAGS:STRING=/machine:x64

//Flags used by the linker during DEBUG builds.
CMAKE_EXE_LINKER_FLAGS_DEBUG:STRING=/debug /INCREMENTAL

//Flags used by the linker during MINSIZEREL builds.
CMAKE_EXE_LINKER_FLAGS_MINSIZEREL:STRING=/INCREMENTAL:NO

//Flags used by the linker during RELEASE builds.
CMAKE_EXE_LINKER_FLAGS_RELEASE:STRING=/INCREMENTAL:NO

//Flags used by the linker during RELWITHDEBINFO builds.
CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO:STRING=/debug /INCREMENTAL

//Prefix for path for installation
CMAKE_INSTALL_PREFIX:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL

//Path to a program.
CMAKE_LINKER:FILEPATH=C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/x86_amd64/link.exe

//Flags used by the linker during the creation of modules during
// all build types.
CMAKE_MODULE_LINKER_FLAGS:STRING=/machine:x64

//Flags used by the linker during the creation of modules during
// DEBUG builds.
CMAKE_MODULE_LINKER_FLAGS_DEBUG:STRING=/debug /INCREMENTAL

//Flags used by the linker during the creation of modules during
// MINSIZEREL builds.
CMAKE_MODULE_LINKER_FLAGS_MINSIZEREL:STRING=/INCREMENTAL:NO

//Flags used by the linker during the creation of modules during
// RELEASE builds.
CMAKE_MODULE_LINKER_FLAGS_RELEASE:STRING=/INCREMENTAL:NO

//Flags used by the linker during the creation of modules during
// RELWITHDEBINFO builds.
CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO:STRING=/debug /INCREMENTAL

//Path to a program.
CMAKE_MT:FILEPATH=CMAKE_MT-NOTFOUND

//Value Computed by CMake
CMAKE_PROJECT_DESCRIPTION:STATIC=

//Value Computed by CMake
CMAKE_PROJECT_HOMEPAGE_URL:STATIC=

//Value Computed by CMake
CMAKE_PROJECT_NAME:STATIC=SuperBuild_SyneRBI

//RC compiler
CMAKE_RC_COMPILER:FILEPATH=rc

//Flags for Windows Resource Compiler during all build types.
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CMAKE_RC_FLAGS_MINSIZEREL:STRING=

//Flags for Windows Resource Compiler during RELEASE builds.
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//Flags for Windows Resource Compiler during RELWITHDEBINFO builds.
CMAKE_RC_FLAGS_RELWITHDEBINFO:STRING=

//Flags used by the linker during the creation of shared libraries
// during all build types.
CMAKE_SHARED_LINKER_FLAGS:STRING=/machine:x64

//Flags used by the linker during the creation of shared libraries
// during DEBUG builds.
CMAKE_SHARED_LINKER_FLAGS_DEBUG:STRING=/debug /INCREMENTAL

//Flags used by the linker during the creation of shared libraries
// during MINSIZEREL builds.
CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL:STRING=/INCREMENTAL:NO

//Flags used by the linker during the creation of shared libraries
// during RELEASE builds.
CMAKE_SHARED_LINKER_FLAGS_RELEASE:STRING=/INCREMENTAL:NO

//Flags used by the linker during the creation of shared libraries
// during RELWITHDEBINFO builds.
CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO:STRING=/debug /INCREMENTAL

//If set, runtime paths are not added when installing shared libraries,
// but are added when building.
CMAKE_SKIP_INSTALL_RPATH:BOOL=OFF

//If set, runtime paths are not added when using shared libraries.
CMAKE_SKIP_RPATH:BOOL=OFF

//Flags used by the linker during the creation of static libraries
// during all build types.
CMAKE_STATIC_LINKER_FLAGS:STRING=/machine:x64

//Flags used by the linker during the creation of static libraries
// during DEBUG builds.
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//Flags used by the linker during the creation of static libraries
// during MINSIZEREL builds.
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// during RELEASE builds.
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//Flags used by the linker during the creation of static libraries
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CMAKE_VERBOSE_MAKEFILE:BOOL=OFF

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//Value Computed by CMake
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//Value Computed by CMake
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//Build SyneRBI and the projects it depends on via SuperBuild.cmake.
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//Build using an external version of ISMRMRD
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//Build using an external version of NIFTYREG
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//Build using an external version of SIRF
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//Build using an external version of STIR
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//Build using an external version of SWIG
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//Build using an external version of siemens_to_ismrmrd
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//ON
astra-toolbox_TAG:STRING=origin/master

//ON
astra-toolbox_URL:STRING=https://github.com/astra-toolbox/astra-toolbox

//ON
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//ON
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//ON
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//ON
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[Biguri]

@evgueni-ovtchinnikov not sure if this changes anything, but I needed to create a new variable BOOST_ROOT: C:/local/boost_1.74.0 (in my case that path) to make the thing compile, otherwise it would not find boost. I can see it in my Cmake-cache.txt, but not in yours.

[Evgueni Ovtchinnikov]

CMakeCache.txt in folder builds\SIRF\build:

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//No help, variable specified on the command line.
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//The directory containing a CMake configuration file for VTK.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Path to a library.
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//Dependencies for the target
cgadgetron_LIB_DEPENDS:STATIC=general;iutilities;general;csirf;general;Boost::system;general;Boost::filesystem;general;Boost::thread;general;Boost::date_time;general;Boost::chrono;general;ISMRMRD::ISMRMRD;general;C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW/libfftw3f-3.lib;

//Dependencies for the target
csirf_LIB_DEPENDS:STATIC=general;iutilities;general;csyn;

//Dependencies for the target
cstir_LIB_DEPENDS:STATIC=general;csirf;general;iutilities;general;analytic_FBP3DRP;analytic_FBP2D;iterative_OSMAPOSL;iterative_KOSMAPOSL;iterative_OSSPS;scatter_buildblock;modelling_buildblock;listmode_buildblock;recon_buildblock;display;IO;data_buildblock;numerics_buildblock;buildblock;spatial_transformation_buildblock;Shape_buildblock;eval_buildblock;numerics_buildblock;modelling_buildblock;listmode_buildblock;IO;modelling_buildblock;IO;buildblock;general;Boost::system;general;Boost::filesystem;general;Boost::thread;general;Boost::date_time;general;Boost::chrono;

//Dependencies for the target
csyn_LIB_DEPENDS:STATIC=general;cgadgetron;general;cstir;general;Reg;

//Path to a library.
reg_nifti_full_path:FILEPATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/reg_nifti.lib

//Path to a library.
reg_png_full_path:FILEPATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/reg_png.lib

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_Boost_COMPONENTS_SEARCHED:INTERNAL=atomic;chrono;date_time;filesystem;system;thread
//Last used Boost_INCLUDE_DIR value.
_Boost_INCLUDE_DIR_LAST:INTERNAL=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1
//Last used Boost_LIBRARY_DIR_DEBUG value.
_Boost_LIBRARY_DIR_DEBUG_LAST:INTERNAL=C:/Boost/lib
//Last used Boost_LIBRARY_DIR_RELEASE value.
_Boost_LIBRARY_DIR_RELEASE_LAST:INTERNAL=C:/Boost/lib
//Last used Boost_NAMESPACE value.
_Boost_NAMESPACE_LAST:INTERNAL=boost
//Last used Boost_USE_MULTITHREADED value.
_Boost_USE_MULTITHREADED_LAST:INTERNAL=TRUE

[Evgueni Ovtchinnikov]

@AnderBiguri: thanks for trying to help, but I do not seem to have any problems with Boost, only with the VS project generated by CMake.

[Kris Thielemans]

@evgueni-ovtchinnikov could you edit the posts above and remove the explicit text and just drag the file in instead? It makes things a bit easier to scroll through.

[Kris Thielemans]

I do not seem to have any problems with Boost, only with the VS project generated by CMake.

ok. I believe that CMake looks in c:\boost but not in c:\local\boost, which is why you don't need it. Nevertheless, it's weird to have

Boost_INCLUDE_DIR:PATH=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1

with libraries in c:\boost. It'd feel a bit safer to have them all be from the same location. I guess it found stuff from a previous attempt in your normal build. However, they same to all be 1.65.1, so more than likely no problem.

[Kris Thielemans]

One difference between @evgueni-ovtchinnikov build\SIF\build\CMakeCache.txt is that it sets

//The directory containing a CMake configuration file for HDF5.
HDF5_DIR:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/cmake

//No help, variable specified on the command line.
HDF5_INCLUDE_DIRS:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include

//No help, variable specified on the command line.
HDF5_ROOT:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL

for me, HDF5_DIRS is ..NOT-FOUND and I then have

//Path to a library.
HDF5_hdf5_LIBRARY_RELEASE:FILEPATH=C:/Users/krisf/Documents/devel/buildVC/SIRF-SuperBuild/INSTALL/lib/hdf5.lib

This means that for @evgueni-ovtchinnikov , CMake found ...\INSTALL\cmake\hdf5-config.cmake (exported when building HDF5), while for me it didn't. The consequence of this is that CMake goes through to 2 different paths, where for @evgueni-ovtchinnikov it uses the exported targets (created by HDF5) while for me it uses the libraries (found by FindHDF5.cmake). (Read up on CONFIG vs MODULE mode in find_package here.)

@evgueni-ovtchinnikov did you set HDF5_DIRS? (probably not but checking). Could you post a file with the output of a CMake Configure of the SuperBuild and also when you tell CMake to load the binary-dir ...\builds\SIRF\build (it'll find the corresponding source dir, so no need to set that) and then press Configure. (or do it from the cmdline).

[Biguri]

Mine is also

//The directory containing a CMake configuration file for HDF5.
HDF5_DIR:PATH=D:/SIRF/build/INSTALL/cmake

Have not touched anything HDF5 related on configuring CMAKE flags.

[Evgueni Ovtchinnikov]

@KrisThielemans: no I did not set anything, just disabled MATLAB and set SIRF and STIR tags to master.

CMake output is:

Selecting Windows SDK version  to target Windows 10.0.10586.
The C compiler identification is MSVC 19.0.24215.1
The CXX compiler identification is MSVC 19.0.24215.1
Detecting C compiler ABI info
Detecting C compiler ABI info - done
Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/x86_amd64/cl.exe - skipped
Detecting C compile features
Detecting C compile features - done
Detecting CXX compiler ABI info
Detecting CXX compiler ABI info - done
Check for working CXX compiler: C:/Program Files (x86)/Microsoft Visual Studio 14.0/VC/bin/x86_amd64/cl.exe - skipped
Detecting CXX compile features
Detecting CXX compile features - done
Found PYTHON_EXECUTABLE=C:/Python/Python36/python.exe
Python version 3.6
Found PYTHON_INCLUDE_DIRS=C:/Python/Python36/include
Found PYTHON_LIBRARIES=C:/Python/Python36/libs/python36.lib
Python libraries found
SIRF and/or STIR Python modules will be installed in C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/python
Matlab support disabled
Found OpenMP_C: -openmp (found version "2.0") 
Found OpenMP_CXX: -openmp (found version "2.0") 
Found OpenMP: TRUE (found version "2.0")  
OpenMP found, support enabled
SuperBuild - First pass
Matlab_ROOT_DIR=C:/Program Files/MATLAB/R2019b
STIR_DIR=
NIFTYREG_DIR=
STIR_EXTRA_CMAKE_ARGS=
Adding project STIR
SuperBuild - First pass - done
SuperBuild - SyneRBI => Requires SIRF, STIR, NIFTYREG, SIRF-Contribs, 
Matlab_ROOT_DIR=C:/Program Files/MATLAB/R2019b
STIR_DIR=
NIFTYREG_DIR=
SuperBuild -   SIRF => Requires Boost, HDF5, ISMRMRD, FFTW3, SWIG, NIFTYREG, STIR, SPM, 
SuperBuild -     Boost[OK]
Found Boost: C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1 (found suitable version "1.65.1", minimum required is "1.58.0")  
USING the system Boost, using Boost_CMAKE_ARGS=-DBOOST_INCLUDEDIR:PATH=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1
SuperBuild -     HDF5[OK]
Adding project HDF5
HDF5_DOWNLOAD_VERSION=1.10.1
HDF5_CMAKE_ARGS=-DHDF5_ROOT:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL;-DHDF5_INCLUDE_DIRS:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include;-DHDF5_FIND_DEBUG:BOOL=ON
SuperBuild -     ISMRMRD => Requires HDF5[INCLUDED], Boost[INCLUDED], FFTW3, 
SuperBuild -       FFTW3[OK]
Adding project FFTW3
FFTW3_CMAKE_ARGS=-DFFTW3_INCLUDE_DIR:PATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW/;-DFFTW3F_LIBRARY:FILEPATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW/libfftw3f-3.lib;-DFFTW3_LIBRARY:FILEPATH=C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW/libfftw3-3.lib
SuperBuild -     ISMRMRD[OK]
Adding project ISMRMRD
Will perform git checkout for ISMRMRD...
SuperBuild -     SWIG[OK]
Adding project SWIG
SuperBuild -     NIFTYREG[OK]
NIFTYREG_EXTRA_CMAKE_ARGS=
Adding project NIFTYREG
Will perform git checkout for NIFTYREG...
STIR_EXTRA_CMAKE_ARGS=
Adding project STIR
SuperBuild -     STIR => Requires Boost[INCLUDED], ITK, JSON, HDF5[INCLUDED], 
SuperBuild -       ITK => Requires HDF5[INCLUDED], 
SuperBuild -       ITK[OK]
Adding project ITK
Will perform git checkout for ITK...
SuperBuild -       JSON[OK]
JSON_EXTRA_CMAKE_ARGS=
Adding project JSON
Will perform git checkout for JSON...
SuperBuild -     STIR[OK]
Will perform git checkout for STIR...
SuperBuild -     SPM[OK]
Adding project SPM
Will perform git checkout for SPM...
SuperBuild -   SIRF[OK]
SIRF_EXTRA_CMAKE_ARGS=
Adding project SIRF
HDF5_ROOT in External_SIRF: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL
Will perform git checkout for SIRF...
SuperBuild -   SIRF-Contribs[OK]
SIRF-Contribs_EXTRA_CMAKE_ARGS=
Adding project SIRF-Contribs
Will perform git checkout for SIRF-Contribs...
SuperBuild - SyneRBI[OK]

Boost_CMAKE_ARGS= -DBOOST_INCLUDEDIR:PATH=C:/Users/wps46139/Documents/GitHub/build/SIRF-SuperBuild/INSTALL/include/boost-1_65_1
ISMRMRD_DIR = C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/cmake/ISMRMRD
STIR_DIR = C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/cmake
HDF5_ROOT = C:/Users/wps46139/Documents/GitHub/try/build/INSTALL
GTEST_ROOT = 
Matlab_ROOT_DIR = C:/Program Files/MATLAB/R2019b
PYTHON_EXECUTABLE=C:/Python/Python36/python.exe
PYTHON_LIBRARIES=C:/Python/Python36/libs/python36.lib
PYTHON_INCLUDE_DIRS=C:/Python/Python36/include
Configuring done
Generating done

[Evgueni Ovtchinnikov]

tell CMake to load the binary-dir ...\builds\SIRF\build

Selecting Windows SDK version  to target Windows 10.0.10586.
Python libraries found
SIRF Python modules will be installed in C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/python
Matlab support disabled
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/iUtilities/CMakeLists.txt:50 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/CMakeFindDependencyMacro.cmake:47 (find_package):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable HDF5_ROOT is set to:

    C:/Users/wps46139/Documents/GitHub/try/build/INSTALL

  For compatibility, CMake is ignoring the variable.
Call Stack (most recent call first):
  C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/cmake/ISMRMRD/ISMRMRDConfig.cmake:72 (find_dependency)
  src/CMakeLists.txt:32 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

Found HDF5 at C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/cmake via NO_MODULE. Now trying to extract locations etc.
Trying to get properties of target hdf5::hdf5-shared
Found imported configurations: RELEASE
Start search through imported configurations in the following order: Release;RELWITHDEBINFO;RELEASE;DEBUG;RELEASE
Selected imported configuration: RELEASE
Found HDF5: hdf5::hdf5-shared (found version "1.10.1") found components: C 
HDF5_DIR: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/cmake
HDF5_DEFINITIONS: 
HDF5_INCLUDE_DIRS: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include
HDF5_LIBRARIES: hdf5::hdf5-shared
HDF5_HL_LIBRARIES: 
HDF5_C_DEFINITIONS: 
HDF5_C_INCLUDE_DIR: 
HDF5_C_INCLUDE_DIRS: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include
HDF5_C_LIBRARY: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/hdf5.lib
HDF5_C_LIBRARIES: hdf5::hdf5-shared
HDF5_C_HL_LIBRARY: 
HDF5_C_HL_LIBRARIES: 
FFTW3 WINDOWS libraries: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW/libfftw3f-3.lib
Install FFTW3 libraries from C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/FFTW 
Install boost shared libraries from C:/Boost/lib 
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/xGadgetron/pGadgetron/CMakeLists.txt:38 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

Matlab not enabled, so SPM cannot be enabled
VTK found: 0
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/Registration/pReg/CMakeLists.txt:40 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

ITK support in STIR enabled.
HDF5 support in STIR enabled.
Found HDF5 at C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/cmake via NO_MODULE. Now trying to extract locations etc.
Trying to get properties of target hdf5::hdf5-shared
Found imported configurations: RELEASE
Start search through imported configurations in the following order: Release;RELWITHDEBINFO;RELEASE;DEBUG;RELEASE
Selected imported configuration: RELEASE
Found HDF5: hdf5::hdf5-shared (found suitable version "1.10.1", minimum required is "1.10.1")  
HDF5_DIR: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/cmake
HDF5_DEFINITIONS: 
HDF5_INCLUDE_DIRS: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include
HDF5_LIBRARIES: hdf5::hdf5-shared
HDF5_HL_LIBRARIES: 
HDF5_C_DEFINITIONS: 
HDF5_C_INCLUDE_DIR: 
HDF5_C_INCLUDE_DIRS: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/include
HDF5_C_LIBRARY: C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/lib/hdf5.lib
HDF5_C_LIBRARIES: hdf5::hdf5-shared
HDF5_C_HL_LIBRARY: 
HDF5_C_HL_LIBRARIES: 
=============================
STIR version: 5.0.0-prealpha
=============================
STIR not built with NiftyPET.
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/xSTIR/pSTIR/CMakeLists.txt:39 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

Registration, ISMRMRD and STIR (with ITK) have been built. Building synergistic code.
Downloading (if not already done)...
		Path:     C:/Users/wps46139/Documents/GitHub/try/build/sources/SIRF/data/examples/MR/zenodo/SIRF_recon.h5
		URL:      https://zenodo.org/record/3571228/files/SIRF_recon.h5?download=1
		MD5:      0d69892502d3a5cd220716a717cc2c26
Downloading (if not already done)...
		Path:     C:/Users/wps46139/Documents/GitHub/try/build/sources/SIRF/data/examples/MR/zenodo/dicom_as_nifti.nii
		URL:      https://zenodo.org/record/3571228/files/dicom_as_nifti.nii?download=1
		MD5:      c5f5b519e5c032560ead912713479b53
Registration, ISMRMRD and STIR (with ITK) have been built.
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/common/CMakeLists.txt:59 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

python alias:pGadgetron<-sirf.Gadgetron
python alias:pSTIR<-sirf.STIR
python alias:pUtilities<-sirf.Utilities
python alias:pygadgetron<-sirf.pygadgetron
python alias:pystir<-sirf.pystir
python alias:pyiutilities<-sirf.pyiutilities
python alias:pReg<-sirf.Reg
python alias:pyreg<-sirf.pyreg
setup.py:C:/Users/wps46139/Documents/GitHub/try/build/INSTALL/python/setup.py
Configuring done
Generating done

[Biguri]

My current situation is that it sometimes compiles, sometimes it does not, and I have no idea when does one and when does the other. I have clean and rebuilt the entire thing several times, always following my instructions,

I get errors that SIRF can't find the python38.lib, but I can see the python variables all directly referring to the correct location of python. So no idea why the errors are there.

The \build\builds\SIRF\build CMAKE configuration fails, with the following output:

Selecting Windows SDK version 10.0.18362.0 to target Windows 10.0.19041.
Found PythonLibs: optimized;optimized;debug;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib (found version "3.8.2") 
Python libraries found
SIRF Python modules will be installed in D:/SIRF/build/INSTALL/python
Matlab support disabled
Found PythonLibs: optimized;optimized;optimized;optimized;optimized;debug;optimized;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib;debug;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib (found version "3.8.2") 
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/iUtilities/CMakeLists.txt:50 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier "debug"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "debug" is followed by specifier "optimized"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/iUtilities/CMakeLists.txt:52 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

Gadgetron support disabled.
Matlab not enabled, so SPM cannot be enabled
VTK found: 0
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/Registration/pReg/CMakeLists.txt:40 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier "debug"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "debug" is followed by specifier "optimized"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/Registration/pReg/CMakeLists.txt:42 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

ITK support in STIR enabled.
CMake Warning (dev) at D:/SIRF/build/INSTALL/lib/cmake/ITK-4.13/Modules/ITKHDF5.cmake:15 (find_package):
  Policy CMP0074 is not set: find_package uses <PackageName>_ROOT variables.
  Run "cmake --help-policy CMP0074" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  CMake variable HDF5_ROOT is set to:

    D:/SIRF/build/INSTALL

  For compatibility, CMake is ignoring the variable.
Call Stack (most recent call first):
  D:/SIRF/build/INSTALL/lib/cmake/ITK-4.13/ITKModuleAPI.cmake:71 (include)
  D:/SIRF/build/INSTALL/lib/cmake/ITK-4.13/ITKModuleAPI.cmake:26 (itk_module_load)
  D:/SIRF/build/INSTALL/lib/cmake/ITK-4.13/ITKModuleAPI.cmake:124 (_itk_module_config_recurse)
  D:/SIRF/build/INSTALL/lib/cmake/ITK-4.13/ITKConfig.cmake:82 (itk_module_config)
  D:/SIRF/build/INSTALL/lib/cmake/STIRConfig.cmake:83 (find_package)
  src/CMakeLists.txt:84 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

HDF5 support in STIR enabled.
Found HDF5 at D:/SIRF/build/INSTALL/cmake via NO_MODULE. Now trying to extract locations etc.
Trying to get properties of target hdf5::hdf5-shared
Found imported configurations: RELEASE
Start search through imported configurations in the following order: Release;RELWITHDEBINFO;RELEASE;DEBUG;RELEASE
Selected imported configuration: RELEASE
HDF5_DIR: D:/SIRF/build/INSTALL/cmake
HDF5_DEFINITIONS: 
HDF5_INCLUDE_DIRS: D:/SIRF/build/INSTALL/include
HDF5_LIBRARIES: hdf5::hdf5-shared
HDF5_HL_LIBRARIES: 
HDF5_C_DEFINITIONS: 
HDF5_C_INCLUDE_DIR: 
HDF5_C_INCLUDE_DIRS: D:/SIRF/build/INSTALL/include
HDF5_C_LIBRARY: D:/SIRF/build/INSTALL/lib/hdf5.lib
HDF5_C_LIBRARIES: hdf5::hdf5-shared
HDF5_C_HL_LIBRARY: 
HDF5_C_HL_LIBRARIES: 
=============================
STIR version: 4.1.0-prealpha
=============================
STIR not built with NiftyPET.
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/xSTIR/pSTIR/CMakeLists.txt:39 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier "debug"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "debug" is followed by specifier "optimized"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/xSTIR/pSTIR/CMakeLists.txt:41 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

One or more of the following components are missing: Registration, ISMRMRD and STIR (with ITK). Synergistic code will not be built.
ISMRMRD missing.
Either Registration or ISMRMRD or STIR (with ITK) have not been built.
CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:513 (message):
  Policy CMP0086 is not set: UseSWIG honors SWIG_MODULE_NAME via -module
  flag.  Run "cmake --help-policy CMP0086" for policy details.  Use the
  cmake_policy command to set the policy and suppress this warning.

Call Stack (most recent call first):
  C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:764 (SWIG_ADD_SOURCE_TO_MODULE)
  src/common/CMakeLists.txt:59 (SWIG_ADD_LIBRARY)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier
  "optimized" instead of a library name.  The first specifier will be
  ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "optimized" is followed by specifier "debug"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake/share/cmake-3.19/Modules/UseSWIG.cmake:901 (target_link_libraries):
  Link library type specifier "debug" is followed by specifier "optimized"
  instead of a library name.  The first specifier will be ignored.
Call Stack (most recent call first):
  src/common/CMakeLists.txt:61 (SWIG_LINK_LIBRARIES)
This warning is for project developers.  Use -Wno-dev to suppress it.

python alias:pGadgetron<-sirf.Gadgetron
python alias:pSTIR<-sirf.STIR
python alias:pUtilities<-sirf.Utilities
python alias:pygadgetron<-sirf.pygadgetron
python alias:pystir<-sirf.pystir
python alias:pyiutilities<-sirf.pyiutilities
python alias:pReg<-sirf.Reg
python alias:pyreg<-sirf.pyreg
setup.py:D:/SIRF/build/INSTALL/python/setup.py
Configuring done

[Biguri]

The above CMake seems to suggest that its finding

C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib
but the errors I get are because It does not find
C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38.lib

At the superbuild level, both of those are properly linked, but maybe at SIRF only the debug one is passed, yet it tries to use the other one. Investigating.

[Biguri]

So, in SIRF CMake variables, my PYTHON_LIBRARY is optimized instead of C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38.lib That is the issue I am having.

No idea how that got there though.

[Kris Thielemans]

hi, can we please note post all this output directly? It's useful to have it all, but post only relevant bits in the box.

[Kris Thielemans]

Found PythonLibs: optimized;optimized;debug;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib (found version "3.8.2") 

is very wrong. CMake doc says

A debug, optimized, or general keyword immediately followed by another . The item following such a keyword will be used only for the corresponding build configuration

you're therefore missing the actual libs in between the optimized keywords. hence it fails. The question is why this happens. So I'm afraid we need to see the SuperBuild output (as an attachment) and in particular what it passes as PYTHON_* keywords to the SIRF Cmake.

[Biguri]

@KrisThielemans thats the thing, In the superbuild, the python part reads:

PYTHON_LIBRARIES=optimized;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38.lib;debug;C:/Users/Ander/AppData/Local/Programs/Python/Python38/libs/python38_d.lib

Which is correct. I don't fully understand how things move from the SuperBuild to the SIRF CMAKE stuff, where should I look ?

CMake_output.txt

[Biguri]

You're therefore missing the actual libs in between the optimized keywords. hence it fails.

To be more specific: the path is being replaced by the keyword optimized. Its repeated twice. Its not that its missing, its that its value is optimized (instead of the path), as I mentioned before.

[Kris Thielemans]

where should I look ?

https://github.com/SyneRBI/SIRF-SuperBuild/blob/199921c3305a1acd1c95d8de4ebfdcdd00be286b/SuperBuild/External_SIRF.cmake#L96-L98

We should not be setting PYTHON_LIBRARY. This should be a file, while PYTHON_LIBRARIES isn't. This is a SIRF-SuperBuild bug. Please create an issue.

[Biguri]

What should it be? Just PATH is not correct either. STRING? I can test and make a PR.

[Kris Thielemans]

will have to check the CMake doc for how to set it. more than likely cannot be done.

I think this is here to work around issues on OSX (probably put in by @rijobro). Anyway, all this discussion should be in the new issue.

[Kris Thielemans]

For now you can just delete all lines in the External*.cmake that set -DPYTHON_LIBRARY:FILEPATH

[Biguri]

@KrisThielemans that was my issue, I can no import sirf python packages.

[Kris Thielemans]

I hope you meant "I can now import sirf.Utilities"...

For the STIR import, I strongly suspect that your path doesn't have the DLLs that are needed. Continuing along the HDF5 line of suspects (even though your previous problem wasn't), you should have hdf5_cpp.dll in your INSTALL\bin, AND your PATH has to include it.

[Biguri]

@KrisThielemans of course yes, I meant that.

I do have hdf5_cpp.dll and D:\SIRF> Get-ChildITem Env:Path returns:

Name                           Value
----                           -----
Path                           D:/SIRF/build/INSTALL/bin;   (etc)

[Kris Thielemans]

right. not HDF5 then...

we have to find what it's missing then. Looks like we need dumpbin or dependency walker, see https://stackoverflow.com/a/64620736/15030207

[Kris Thielemans]

here's what I got

PS ...\INSTALL\python\sirf>  &"C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.28.29333\bin\Hostx86\x86\dumpbin.exe" /dependents _pystir.pyd
Microsoft (R) COFF/PE Dumper Version 14.28.29336.0
Copyright (C) Microsoft Corporation.  All rights reserved.


Dump of file _pystir.pyd

File Type: DLL

  Image has the following dependencies:

    python38.dll
    hdf5_cpp.dll
    hdf5.dll
    KERNEL32.dll
    MSVCP140.dll
    VCOMP140.DLL
    VCRUNTIME140.dll
    VCRUNTIME140_1.dll
    api-ms-win-crt-math-l1-1-0.dll
    api-ms-win-crt-stdio-l1-1-0.dll
    api-ms-win-crt-string-l1-1-0.dll
    api-ms-win-crt-heap-l1-1-0.dll
    api-ms-win-crt-runtime-l1-1-0.dll
    api-ms-win-crt-filesystem-l1-1-0.dll
    api-ms-win-crt-time-l1-1-0.dll
    api-ms-win-crt-utility-l1-1-0.dll
    api-ms-win-crt-convert-l1-1-0.dll
    api-ms-win-crt-locale-l1-1-0.dll
    api-ms-win-crt-environment-l1-1-0.dll

  Summary

        1000 .00cfg
       18000 .data
        7000 .idata
       1E000 .pdata
       AE000 .rdata
        7000 .reloc
        1000 .rsrc
      326000 .text
        1000 .tls

You can find the location of dumpbin but opening a "VS 2019 command prompt" (via Start) and doing where dumpbin

[Kris Thielemans]

oops, the above was for _pystir.pyd. For _pysirf.pyd the relevant bit is

   python38.dll
    ismrmrd.dll
    libfftw3f-3.dll
    boost_thread-vc142-mt-x64-1_74.dll
    hdf5_cpp.dll
    hdf5.dll
    boost_filesystem-vc142-mt-x64-1_74.dll
    KERNEL32.dll
    MSVCP140.dll
    VCOMP140.DLL
    WS2_32.dll
    VCRUNTIME140.dll
    VCRUNTIME140_1.dll

[Biguri]

I dont have libfftw3f-3.dll

[Kris Thielemans]

I think your path is not correct. that directory should have been added, see #467 (comment). Check if it is. I believe that you either copy-paste the content, or do . ./script (see https://superuser.com/a/71490)

[Biguri]

@KrisThielemans I simply have not show the entire path in the comment because its my personal laptop and I have tons of things in Path, but its there.

D:/SIRF/build/INSTALL/bin;C:\Program Files (x86)\Common Files\Oracle\Java\javapath;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.2\bin;C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v10.2\libnvvp;C:\Program Files (x86)\Intel\iCLS Client\;C:\Program Files\Intel\iCLS Client\;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files\Intel\Intel(R) Management Engine Components\DAL;C:\Program Files (x86)\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\Intel\Intel(R) Management Engine Components\IPT;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\Program Files\Git\cmd;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Program Files\Microsoft SQL Server\110\Tools\Binn\;C:\WINDOWS\System32\OpenSSH\;C:\Program Files (x86)\NVIDIA Corporation\PhysX\Common;C:\Program Files\NVIDIA Corporation\NVIDIA NvDLISR;C:\Program Files\NVIDIA Corporation\Nsight Compute 2019.5.0\;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.24.28314\bin\Hostx64\x64\cl.exe;C:\Program Files\PuTTY\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0\;C:\WINDOWS\System32\OpenSSH\;D:\MATLAB_software\runtime\win64;D:\MATLAB_software\bin;C:\Program Files\CMake\bin;C:\Users\Ander\AppData\Local\Programs\Python\Python38\Scripts\;C:\Users\Ander\AppData\Local\Programs\Python\Python38\;C:\Users\Ander\AppData\Local\Microsoft\WindowsApps;C:\Users\Ander\AppData\Roaming\Dashlane\5.3.1.13504\bin\Firefox_Extension\{442718d9-475e-452a-b3e1-fb1ee16b8e9f}\components;C:\Users\Ander\AppData\Roaming\Dashlane\5.3.1.13504\ucrt;C:\Users\Ander\AppData\Local\atom\bin;C:\Users\Ander\AppData\Local\Microsoft\WindowsApps;C:\Program Files\MiKTeX 2.9\miktex\bin\x64\;C:\Users\Ander\AppData\Roaming\MiKTeX\2.9\miktex\bin\x64\;C:\Users\Ander\AppData\Local\Programs\Microsoft VS Code\bin;;D:/SIRF/build/INSTALL\FFTW;c:/local/boost_1_74_0/lib64-msvc-14.2/

[Kris Thielemans]

D:/SIRF/build/INSTALL\FFTW makes forward and backslashes. that isn't going to work probably

[Biguri]

@KrisThielemans tried that already, nothing changes. Also I removed the extra ;

[Kris Thielemans]

all of them should be \ really. Also the first entry is wrong.

[Biguri]

@KrisThielemans can you clarify why its wrong? the / you mean?

[Kris Thielemans]

yes, I do mean D:\SIRF\build\INSTALL\FFTW etc. if that isn't it, then I don't know...

[Biguri]

Just to add info:

my current dumpbin looks like this:

 &"C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.28.29333\bin\Hostx86\x86\dumpbin.exe" /dependents _pysirf.pyd

File Type: DLL

  Image has the following dependencies:

    python38.dll
    ismrmrd.dll
    boost_thread-vc141-mt-x64-1_74.dll
    hdf5_cpp.dll
    hdf5.dll
    ITKIOBruker-4.13.dll
    ITKIOHDF5-4.13.dll
    ITKIOLSM-4.13.dll
    ITKIOMINC-4.13.dll
    ITKIOMRC-4.13.dll
    ITKIOBMP-4.13.dll
    ITKIOBioRad-4.13.dll
    ITKIOGDCM-4.13.dll
    ITKIOGE-4.13.dll
    ITKIOGIPL-4.13.dll
    ITKIOJPEG-4.13.dll
    ITKIOTIFF-4.13.dll
    ITKIOMeta-4.13.dll
    WSOCK32.dll
    ITKIONIFTI-4.13.dll
    ITKIONRRD-4.13.dll
    ITKIOPNG-4.13.dll
    ITKIOStimulate-4.13.dll
    ITKIOVTK-4.13.dll
    ITKIOImageBase-4.13.dll
    ITKCommon-4.13.dll
    WS2_32.dll
    boost_filesystem-vc141-mt-x64-1_74.dll
    KERNEL32.dll
    MSVCP140.dll
    VCOMP140.DLL
    VCRUNTIME140.dll
    VCRUNTIME140_1.dll
    api-ms-win-crt-stdio-l1-1-0.dll
    api-ms-win-crt-string-l1-1-0.dll
    api-ms-win-crt-heap-l1-1-0.dll
    api-ms-win-crt-runtime-l1-1-0.dll
    api-ms-win-crt-filesystem-l1-1-0.dll
    api-ms-win-crt-math-l1-1-0.dll
    api-ms-win-crt-time-l1-1-0.dll
    api-ms-win-crt-utility-l1-1-0.dll
    api-ms-win-crt-locale-l1-1-0.dll
    api-ms-win-crt-convert-l1-1-0.dll
    api-ms-win-crt-environment-l1-1-0.dll

  Summary

       13000 .data
       14000 .pdata
       84000 .rdata
        4000 .reloc
        1000 .rsrc
      228000 .text

Adding all the DLLs and libs into the /libs folder does not change any of the behaviors described until now.

Also, I can see in the SIRF (not superbuild) CMAKE parameters, the following correct values:

[Kris Thielemans]

Sorry, can you remind me what the current problem is. Is it still the one from above

ImportError: DLL load failed while importing _pysirf: The specified module could not be found.

You could give http://dependencywalker.com/ a go.

[Biguri]

Yes it is. I will give that a go. Still usnure why I dont see FFTW in the dumpbin .... Will report back.

[Evgueni Ovtchinnikov]

SIRF Windows build annoyance 2 (extra dependency on hdf5.lib without path in addition to one with the proper path) disappeared!

My deep gratitude to whoever fixed this!

[Kris Thielemans]

SIRF Windows build annoyance 2

what about annoyance 1? And does your Python now finally run?

[Evgueni Ovtchinnikov]

Annoyance 1 is still there, but it is much less annoying as it takes less than half a minute to edit VS solution file.

Python still crashes on reading MR acquisition data.

[Kris Thielemans]

interesting, I see the same "annoyance 1" mess in my SIRF.sln, but VS didn't complain about it. Nevertheless, it shouldn't be there. Could be the same as #410

[Kris Thielemans]

As it isn't in other solutions, I guess this is a SIRF Bug

[Evgueni Ovtchinnikov]

My VS does not complain either - I only noticed something was wrong when I could not find one of my projects (VS Solution Explorer apparently has a limit for the number of projects it can show).

There must be a mistake in SIRF CMake files, and I spent quite a lot of time last couple of weeks trying to find it, but did not succeed. One thing that is obvious is that those spurious projects names are part of the path to INSTALL\bin.

[Kris Thielemans]

Possible lines for conda (with conda-forge channel enabled)

conda install hdf5 numpy boost-cpp swig fftw nlohmann_json

could use it to install cmake and even a C++ compiler i guess. If you install CMake with its own installer, make sure you tick the box "add to user path").

Then in powershell

git clone https://github.com/SyneRBI/SIRF-SuperBuild.git
mkdir build
cd build
cmake ../SIRF-SuperBuild -DUSE_SYSTEM_HDF5:BOOL=ON -DUSE_SYSTEM_SWIG:BOOL=ON -DUSE_SYSTEM_FFTW3:BOOL=ON -DUSE_SYSTEM_JSON:BOOL=ON -DUSE_ITK:BOOL=OFF

Then fine-tune the configuration (either with the CMake GUI or ccmake if present in conda). Possibly it doesn't find boost files, in which case you'd have to set BOOST_ROOT (see above)

Note, I think with Conda we have to not use ITK at the moment due to the problem I saw
conda-forge/stir-feedstock#33 (comment)
but I suppose you could try with ITK and let us know.

Then build, which you could do from the Visual Studio project or

cmake . --build -C Release

Then set your environment as in #460

[Kris Thielemans]

Just trying again with USE_SYSTEM_HDF5=OFF and other default settings, I have to set

• ITK_USE_SYSTEM_HDF5=OFF as the default HDF5 library is too old and ITK complains about backwards compatibility.
• USE_ROOT=OFF as ROOT compilation fails with missing zconf.h

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[Kris Thielemans]

Closed #467 as completed.

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[Kris Thielemans]

I've created SyneRBI/SIRF#1127 for "annoyance 1".
I believe things mentioned above have either been resolved or have now their own issues (which is probably best anyway!).

So I'll close this.

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