slicer fails using numpy on OSX

[nicexe]

the test fails with

$ python3 photonslicer.py -s STLs\legocog.stl -g True -f False
/Users/nicexe/.pyxbld/temp.macosx-10.14-x86_64-3.7/pyrex/rleEncode.c:593:10: fatal error: 'numpy/arrayobject.h' file not found
#include "numpy/arrayobject.h"
         ^~~~~~~~~~~~~~~~~~~~~
1 error generated.
Traceback (most recent call last):
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py", line 118, in _compile
    extra_postargs)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py", line 909, in spawn
    spawn(cmd, dry_run=self.dry_run)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py", line 36, in spawn
    _spawn_posix(cmd, search_path, dry_run=dry_run)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/spawn.py", line 159, in _spawn_posix
    % (cmd, exit_status))
distutils.errors.DistutilsExecError: command 'clang' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 215, in load_module
    inplace=build_inplace, language_level=language_level)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 191, in build_module
    reload_support=pyxargs.reload_support)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
    dist.run_commands()
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
    _build_ext.build_ext.run(self)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/usr/local/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
    self.build_extension(ext)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
    depends=ext.depends)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py", line 574, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile
    raise CompileError(msg)
distutils.errors.CompileError: command 'clang' failed with exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "photonslicer.py", line 31, in <module>
    from Stl2Slices import *
  File "/Users/nicexe/Downloads/Slicer-master/Stl2Slices.py", line 15, in <module>
    import rleEncode
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 462, in load_module
    language_level=self.language_level)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 231, in load_module
    raise exc.with_traceback(tb)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 215, in load_module
    inplace=build_inplace, language_level=language_level)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyximport.py", line 191, in build_module
    reload_support=pyxargs.reload_support)
  File "/usr/local/lib/python3.7/site-packages/pyximport/pyxbuild.py", line 102, in pyx_to_dll
    dist.run_commands()
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/usr/local/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run
    _build_ext.build_ext.run(self)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 340, in run
    self.build_extensions()
  File "/usr/local/lib/python3.7/site-packages/Cython/Distutils/old_build_ext.py", line 194, in build_extensions
    self.build_extension(ext)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/command/build_ext.py", line 534, in build_extension
    depends=ext.depends)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/ccompiler.py", line 574, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/usr/local/Cellar/python/3.7.3/Frameworks/Python.framework/Versions/3.7/lib/python3.7/distutils/unixccompiler.py", line 120, in _compile
    raise CompileError(msg)
ImportError: Building module rleEncode failed: ["distutils.errors.CompileError: command 'clang' failed with exit status 1\n"]
$

I tried installing numpy with brew, uninstalled and then tried installing it with pip but no luck. The error messages remain the same

[aotd1]

@nicexe, I faced the same issue and make a small fix, you can try to switch to my branch and test it.

[shonrs]

This seems to be a common issue with using numpy installed from brew. My solution:

Install numpy first, then install cython
Find location of numpy headers

python3
import numpy as np
np.get_include()
export CFLAGS "-I /location/of/numpy/from/np.get $CFLAGS"
export CPPFLAGS "-I /location/of/numpy/from/np.get $CPPFLAGS"

This only needs to be done the before first time you try to run PhotonSlicer.py