Install without conda

[shuocao818]

Hi, is it possible to install pyembree without using conda?
I tried python setup.py install and also I set the include path of my embree in the setup.py like this
include_path = [np.get_include(),"C:\python36\Lib\site-packages\embree-2.14.0.x64.windows\include"]
but I got an error: fatal error LNK1181: cannot open input file 'embree.lib'
so I am wondering whether conda is the only way to install it. Thanks!

[scopatz]

Yeah, you should be able to install it without conda, but you'll need to install embree seprately and then point pip/setup.py install to the location you installed embree at

[ttsesm]

@shuocao818 go into the pyembree folder and run the following command and it should work without issues:
pip install --global-option=build_ext --global-option="-IC:\Program Files\Intel\Embree v2.17.7 x64\include" --global-option="-LC:\Program Files\Intel\Embree v2.17.7 x64\lib" .

just modify your embree installation folder path.

[shuocao818]

Thank you so much!

[mikedh]

For whatever it's worth we install pyembree/embree 2.17.7 on the trimesh docker images (vanilla Python + Debian buster) using this bash script:

wget https://github.com/mikedh/trimesh/blob/master/docker/builds/embree.bash
sudo bash embree.bash

[rgs-edu]

@shuocao818 go into the pyembree folder and run the following command and it should work without issues:
pip install --global-option=build_ext --global-option="-IC:\Program Files\Intel\Embree v2.17.7 x64\include" --global-option="-LC:\Program Files\Intel\Embree v2.17.7 x64\lib" .

just modify your embree installation folder path.

After changing to embree installation path, I get the following error.

pyembree/mesh_construction.cpp:644:10: fatal error: 'embree2/rtcore.h' file not found #include "embree2/rtcore.h" ^~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. error: command 'clang' failed with exit status 1

-----edit-------
Issue is the path embree2/* doesn't exist with version upgrade and download of embree3.
To keep up with each release of embree, you will have to change those references.

[ttsesm]

@yehDilBeparwah but since you were linking to the embree v2.17.7 the folder embree2 should be there.

[Shivin302]

I installed it by going to https://github.com/mikedh/trimesh/blob/master/docker/builds/embree.bash, copying the script into a file named embree.bash, and running sudo bash embree.bash. Then, I added
export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
to my .bashrc and I can use pyembree

[adamgranthendry]

@ttsesm @Shivin302 @yeDilBeparwah @mikedh I am trying to install pyembree without conda as well. So far, my steps have been:

System: Windows 10 x64, Build 1909, Python 3.8.10

1. Install Embree v3.13.0 via the msi installer
2. Install Microsoft C++ Build Tools for Visual Studio Community 2019, including
   (a) Desktop development with C++
   (b) .NET desktop build tools
   (c) Universal Windows Platform build tools
   (d) .NET build tools
   (e) Vistual Studio extension development
3. Install the Windows 10.0.19041.685 SDK
4. Add the following to the system path:

C:\Program Files (x86)\Microsoft Visual Studio\2019\Community
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools
C:\Program Files (x86)\Microsoft Visual Studio\2019\BuildTools\VC\Tools\MSVC\14.29.30037\bin\Hostx64\x64
C:\Program Files (x86)\Windows Kits\10
C:\Program Files (x86)\Windows Kits\10\Lib\10.0.10240.0\ucrt\x64\
C:\Program Files (x86)\Windows Kits\10\Include\10.0.19041.0\

4. Install poetry via PowerShell
5. Create a poetry 1.1.7 project in a folder (%USERPROFILE%\Code\myproject) with a venv virtual environment in subfolder .venv
6. Clone the pyembree repo to %USERPROFILE%\Code\myproject\.venv\Lib\site-packages\ (creates a subfolder pyembree): git clone https://github.com/scopatz/pyembree.git
7. Open a Developer Command Prompt for VS 2019, which activates vcvarsall.bat for x64 build
8. Run the following:

set INCLUDE="C:\Program Files\Intel\Embree3\include\embree3\"
set LIB="C:\Program Files\Intel\Embree3\lib\"
cd "%USERPROFILE%\Code\myproject"
.venv\Scripts\activate.bat
cd ".venv\Lib\site-packages\pyembree"
py setup.py install

However, no matter what, I get the following output:

Warning: passing language='c++' to cythonize() is deprecated. Instead, put "# distutils: language=c++" in your .pyx or .pxd file(s)
running install
running bdist_egg
running egg_info
writing pyembree.egg-info\PKG-INFO
writing dependency_links to pyembree.egg-info\dependency_links.txt
writing top-level names to pyembree.egg-info\top_level.txt
reading manifest file 'pyembree.egg-info\SOURCES.txt'
adding license file 'LICENSE'
adding license file 'AUTHORS'
writing manifest file 'pyembree.egg-info\SOURCES.txt'
installing library code to build\bdist.win-amd64\egg
running install_lib
running build_py
running build_ext
building 'pyembree.mesh_construction' extension
error: Microsoft Visual C++ 14.0 or greater is required. Get it with "Microsoft C++ Build Tools": https://visualstudio.microsoft.com/visual-cpp-build-tools/

Any ideas what I'm doing wrong?

[adamgranthendry]

Is part of my issue that I'm using Embree 3 and not Embree 2?

[adamgranthendry]

Installation Instructions

Tested on:

OS: Windows 10 x64 Professional, Build 1909
Python: 3.8.5 x64
Date: 31-JULY-2021

Steps

1. Install Microsoft Visual Studio 2017 Build Tools and the Windows 10 SDK. These are required for building cython code.

(NOTE: FYI, Microsoft Visual Studio version numbers are not the same as Microsoft Visual C++ Compiler versions. MSVCv14X x64/x86 build tools are required for Python 3.8. Installing the Visual Studio 2017 Build Tools with the Windows 10 SDK. If you wish to install Visual Studio 2017, select the Desktop development with C++ Workload and make sure the required Windows 10 SDK build tool is selected under Individual Components. Refer to the Python Wiki for the right build tool versions to install).

2. Install vcpkg in C:\vcpkg and add the path to your System Environment Variables. Be sure to bootstrap and integrate vcpkg:

cd C:\vcpkg
git clone https://github.com/Microsoft/vcpkg.git
bootstrap-vcpkg.bat
vcpkg integrate install

Alternatively, you can download and install the embree-2.17.7.x64.msi Installer on Embree's GitHub page (to learn more about Embree, visit their website).

3. Install embree2 64-bit. If using vcpkg, this is done from the command-line as:

vcpkg install embree2:x64-windows

NOTE: To date, pyembree relies on Embree 2 and has not been updated version 3. The above command will install version 2.17.7, which is the required version.

4. Create your project folder and initialize a virtual environment with venv. In this example, Python 3.8.5 x64-bit is chosen, simply as it is the Python version used in Miniconda py38_4.9.2. (It may work for Python 3.6 and 3.7, but at the time of this writing, one should not go to higher than 3.8)

5. Install the following packages:

py -m pip install numpy cython wheel setuptools pyvista pykdtree rtree trimesh

6. Navigate to <virtual environment folder>\Lib\site-packages and clone the pyembree repo:

git clone https://github.com/scopatz/pyembree.git

and remove the underlying .git subfolder.

7. Move into pyembree folder and modify the setup.py file to:

import os
from setuptools import find_packages, setup

import numpy as np
from Cython.Build import cythonize
from Cython.Distutils import build_ext


include_path = [
    np.get_include(),
]

ext_modules = cythonize("pyembree/*.pyx", language_level=3, include_path=include_path)

for ext in ext_modules:
    ext.include_dirs = include_path
    ext.libraries = [
        "pyembree/embree2/lib/embree",
        "pyembree/embree2/lib/tbb",
        "pyembree/embree2/lib/tbbmalloc",
    ]

setup(
    name="pyembree",
    version="0.1.6",
    cmdclass={"build_ext": build_ext},
    ext_modules=ext_modules,
    zip_safe=False,
    packages=find_packages(),
    include_package_data=True,
    package_data={"pyembree": ["*.cpp", "*.dll"]},
)

8. Move into the pyembree subfolder. Copy the folder C:\vcpkg\installed\x64-windows\include\embree2 into this folder (if you installed from the .msi, this will be the folder C:\Program Files\Intel\Embree v2.17.7 x64\include\embree2). In addition, copy the libraries from C:\vcpkg\installed\x64-windows\lib into this embree2 folder (if you installed from the .msi, this will be the folder C:\Program Files\Intel\Embree v2.17.7 x64\lib\). You only need the (static) libraries

embree.lib
tbb.lib
tbbmalloc.lib

and dynamic libraries

embree.dll
tbb.dll
tbbmalloc.dll

9. Add the following line to the top of every *.pyx and *.pxd file in pyembree:

# distutils: language=c++

and change every relative import of an rtcore module to an absolute import in each file. For example, change:

cimport rtcore as rtc

to

cimport pyembree.rtcore as rtc

10. Create the following MANIFEST.in file in the top-level pyembree folder:

include *.h *.pxd *.dll
recursive-include embree2 *.h *.isph
recursive-include embree2/lib *.lib

11. At the end, your folder should look like this:

<virtual environment folder>\Lib\site-packages\pyembree
│   .authors.yml
│   .gitignore
│   .mailmap
│   .travis-install.sh
│   .travis.yml
│   AUTHORS
│   CHANGELOG.rst
│   LICENSE
│   MANIFEST.in
│   README.rst
│   rever.xsh
│   setup.py
│   
├───examples
│       attenuate.py
│       intersection.py
│       
├───news
│       TEMPLATE.rst
│       
├───pyembree
│   │   embree.dll
│   │   mesh_construction.h
│   │   mesh_construction.pyx
│   │   rtcore.pxd
│   │   rtcore.pyx
│   │   rtcore_geometry.pxd
│   │   rtcore_geometry_user.pxd
│   │   rtcore_ray.pxd
│   │   rtcore_scene.pxd
│   │   rtcore_scene.pyx
│   │   tbb.dll
│   │   tbbmalloc.dll
│   │   triangles.pyx
│   │   __init__.pxd
│   │   __init__.py
│   │
│   └───embree2
│       │   rtcore.h
│       │   rtcore.isph
│       │   rtcore_builder.h
│       │   rtcore_geometry.h
│       │   rtcore_geometry.isph
│       │   rtcore_geometry_user.h
│       │   rtcore_geometry_user.isph
│       │   rtcore_ray.h
│       │   rtcore_ray.isph
│       │   rtcore_scene.h
│       │   rtcore_scene.isph
│       │   rtcore_version.h
│       │
│       └───lib
│               embree.lib
│               tbb.lib
│               tbbmalloc.lib
│
├───recipes
│   └───pyembree
│           build.sh
│           meta.yaml
│
└───tests
        test_intersection.py

12. Build pyembree by running the following from the top-level pyembree folder (TIP: To help debug errors, pipe stderr to a local file errors.txt that you can look at):

py setup.py build_ext -i 2> errors.txt

13. Test that everything is working correctly by opening a python terminal in your virtual environment and running

>>> import pyembree
>>> from pyembree import rtcore_scene
>>>

If you get no errors, then pyembree has been installed correctly. You can also create a .egg and install the library with

py setup.py install

The setup.py we created will copy the dlls and cpp files to the correct folder.

14. As an last optional step, create a main.py in your virtual environment and copy and paste the code from Project to Finite Plane. If it runs without errors in 1-2 seconds, then pyembree is working properly with trimesh for vectorized ray tracing (NOTE: trimesh will work without pyembree, but it will be very slow. It should not take a long time to run this example code if pyembree is properly installed. trimesh resorts back to trimesh.ray.ray_triangle.RayMeshIntersector if it cannot import pyembree (see pyembree ray casting acceleration #875), so you won't see any errors; just slow running code):

import numpy as np
from pykdtree.kdtree import KDTree

import pyvista as pv
from pyvista import examples

# Load data
data = examples.load_random_hills()
data.translate((10, 10, 10))

# Create triangular plane (vertices [10, 0, 0], [0, 10, 0], [0, 0, 10])
size = 10
vertices = np.array([[size, 0, 0], [0, size, 0], [0, 0, size]])
face = np.array([3, 0, 1, 2])

planes = pv.PolyData(vertices, face)

# Subdivide plane so we have multiple points to project to
planes = planes.subdivide(8)

# Get origins and normals
origins = planes.cell_centers().points
normals = planes.compute_normals(cell_normals=True, point_normals=False)["Normals"]

# Vectorized Ray trace
points, pt_inds, cell_inds = data.multi_ray_trace(
    origins, normals
)  # Must have rtree, trimesh, and pyembree installed

# Filter based on distance threshold, if desired (mimics VTK ray_trace behavior)
# threshold = 10  # Some threshold distance
# distances = np.linalg.norm(origins[inds] - points, ord=2, axis=1)
# inds = inds[distances <= threshold]

tree = KDTree(data.points.astype(np.double))
_, data_inds = tree.query(points)

elevations = data.point_arrays["Elevation"][data_inds]

# Mask points on planes
planes.cell_arrays["Elevation"] = np.zeros((planes.n_cells,))
planes.cell_arrays["Elevation"][pt_inds] = elevations
planes.set_active_scalars("Elevation")  # Probably not necessary, but just in case

# Create axes
axis_length = 20
tip_length = 0.25 / axis_length * 3
tip_radius = 0.1 / axis_length * 3
shaft_radius = 0.05 / axis_length * 3
x_axis = pv.Arrow(
    direction=(axis_length, 0, 0),
    tip_length=tip_length,
    tip_radius=tip_radius,
    shaft_radius=shaft_radius,
    scale="auto",
)
y_axis = pv.Arrow(
    direction=(0, axis_length, 0),
    tip_length=tip_length,
    tip_radius=tip_radius,
    shaft_radius=shaft_radius,
    scale="auto",
)
z_axis = pv.Arrow(
    direction=(0, 0, axis_length),
    tip_length=tip_length,
    tip_radius=tip_radius,
    shaft_radius=shaft_radius,
    scale="auto",
)
x_label = pv.PolyData([axis_length, 0, 0])
y_label = pv.PolyData([0, axis_length, 0])
z_label = pv.PolyData([0, 0, axis_length])
x_label.point_arrays["label"] = [
    "x",
]
y_label.point_arrays["label"] = [
    "y",
]
z_label.point_arrays["label"] = [
    "z",
]

# Plot results
p = pv.Plotter()
p.add_mesh(x_axis, color="r")
p.add_point_labels(x_label, "label", show_points=False, font_size=24)
p.add_mesh(y_axis, color="r")
p.add_point_labels(y_label, "label", show_points=False, font_size=24)
p.add_mesh(z_axis, color="r")
p.add_point_labels(z_label, "label", show_points=False, font_size=24)
p.add_mesh(data)
p.add_mesh(planes)
p.show()