remove dependency on boost::thread

[KrisThielemans]

instances of boost::thread and boost::mutex are all replaced by std versions.
This means we don't need to link with boost::thread anymore.

This should reduce boost version conflicts, such as those in #429 and #241.

[KrisThielemans]

@paskino can you test this on a machine with many cores? Travis has only 2

[KrisThielemans]

@dchansen did something very similar now in Gadgetron. He's used std::lock_guard as opposed to std::unique_lock and a different way to initialise reader_thread_, see https://github.com/gadgetron/gadgetron/blob/8ea7f911e87575f666e30bfa5ffe7269023b0480/apps/clients/gadgetron_ismrmrd_client/gadgetron_ismrmrd_client.cpp#L1193.

I guess he knows what he's doing (as opposed to me), so I suggest that we sync this PR with his code.

[codecov]

Codecov Report

Merging #430 into master will increase coverage by 3.83%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #430      +/-   ##
==========================================
+ Coverage   47.05%   50.89%   +3.83%     
==========================================
  Files           2        2              
  Lines        1883     1629     -254     
==========================================
- Hits          886      829      -57     
+ Misses        997      800     -197

Impacted Files	Coverage Δ
src/xSTIR/pSTIR/STIR.py	53.38% <0%> (+3.23%)	⬆️
src/xGadgetron/pGadgetron/Gadgetron.py	48.02% <0%> (+4.6%)	⬆️

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[KrisThielemans]

@paskino could you give this a quick spin? We need to merge this and then fix the OSX filesystem problem to get Travis Green again. (Also, it'll avoid installation problems for users of course)

[KrisThielemans]

@rijobro problems with boost::thread have disappeared on OSX Travis (of course). Still the related std::filesystem error of course

[ 86%] Linking CXX executable sirf_crop_image

Undefined symbols for architecture x86_64:
  "boost::filesystem::detail::create_directory(boost::filesystem::path const&, boost::system::error_code*)", referenced from:
      sirf::NiftiImageData<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) const in libReg.a(NiftiImageData.cpp.o)
      sirf::AffineTransformation<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const in libReg.a(AffineTransformation.cpp.o)
  "boost::filesystem::detail::status(boost::filesystem::path const&, boost::system::error_code*)", referenced from:
      sirf::NiftiImageData<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) const in libReg.a(NiftiImageData.cpp.o)
      sirf::AffineTransformation<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const in libReg.a(AffineTransformation.cpp.o)
  "boost::filesystem::path::parent_path() const", referenced from:
      sirf::NiftiImageData<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) const in libReg.a(NiftiImageData.cpp.o)
      sirf::AffineTransformation<float>::write(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) const in libReg.a(AffineTransformation.cpp.o)
ld: symbol(s) not found for architecture x86_64

As this is part of our continuing OSX problems, I strongly recommend we test this on a multi-core Linux/CentOS machine (@paskino, @rijobro ?) and merge.

[KrisThielemans]

sadly, Travis gives segfaults in the MR_PYTHON_TESTS on Linux.

Not much useful to debug it in the log file

"MR_TESTS_PYTHON" start time: Sep 29 10:55 UTC
Output:
----------------------------------------------------------
<end of output>
Test time =  10.52 sec
----------------------------------------------------------
Test Failed.

2:     Start 3: MR_TESTS_PYTHON
2: 3/5 Test #3: MR_TESTS_PYTHON ..................***Exception: SegFault 10.52 sec

travis_time:end:03417ebb:start=1569754684195916395,finish=1569754684210980875,duration=15064480,event=script

sigh

[KrisThielemans]

I'm a bit lost on this. It's the previous commit that made the linux versions crash (or something on travis itself of course, but unlikely as the previous one was 1 hour earlier and ok).

However, the only thing that that commit did was to remove linking boost files for cGadgetron, which it doesn't use anyway. Anyone any ideas?

[rijobro]

I've restarted the Travis jobs just in case it was a temporary bug on their side. If that doesn't work, we can have a re-think.

[rijobro]

This looks good to me if travis is happy

[rijobro]

seg fault in MR ctests. I suppose that implies data race?