Upload 97 files

mesh-fix-MSVC_compilation/.gitattributes

@@ -0,0 +1,5 @@
+/data/unittest/* text eol=lf
+/data/unittest/*.obj text
+/data/unittest/*.pp text
+/data/unittest/sphere.ply text
+/data/unittest/test_box.ply text

mesh-fix-MSVC_compilation/.gitignore

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+build/*
+*.pyc
+temporary_test
+dist
+MANIFEST
+*.xml
+*.egg-info
+doc/build
+.eggs
+.idea

mesh-fix-MSVC_compilation/LICENSE.txt

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+
+Max-Planck grants you a non-exclusive, non-transferable, free of charge right to
+use the *psbody-mesh package* on computers owned, leased or otherwise controlled 
+by you and/or your organization for the sole purpose of performing non-commercial 
+scientific research.
+
+Any other use, in particular any use for commercial purposes, is prohibited.
+This includes, without limitation, incorporation in a commercial product, use in
+a commercial service, or production of other artifacts for commercial purposes
+including, for example, web services, movies, television programs, or video
+games. The Model may not be reproduced, modified and/or made available in any
+form to any third party without MPG’s prior written permission. By using the
+Model, you agree not to reverse engineer it.
+
+You expressly acknowledge and agree that the Model is provided “AS IS”, may
+contain errors, and that any use of the Model is at your sole risk. MAX PLANCK
+MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE DATA, NEITHER
+EXPRESS NOR IMPLIED, AND THE ABSENCE OF ANY LEGAL OR ACTUAL DEFECTS, WHETHER
+DISCOVERABLE OR NOT. Specifically, and not to limit the foregoing, Max-Planck
+makes no representations or warranties (i) regarding the merchantability or
+fitness for a particular purpose of the Model, (ii) that the use of the Model
+will not infringe any patents, copyrights or other intellectual property rights
+of a third party, and (iii) that the use of the Model will not cause any damage
+of any kind to you or a third party.
+
+Under no circumstances shall Max-Planck be liable for any incidental, special,
+indirect or consequential damages arising out of or relating to this license,
+including but not limited to, any lost profits, business interruption, loss of
+programs or other data, or all other commercial damages or losses, even if
+advised of the possibility thereof. 

mesh-fix-MSVC_compilation/MANIFEST.in

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+recursive-include mesh/src *
+recursive-include mesh/ressources *

mesh-fix-MSVC_compilation/Makefile

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+# Makefile for mesh package
+package_name := mesh_package
+
+all:
+	@echo "\033[0;36m----- [" ${package_name} "] Installing on the local virtual environment `which python`\033[0m"
+	@pip install --upgrade -r requirements.txt && pip list
+	@pip install --no-deps --install-option="--boost-location=$$BOOST_ROOT" --verbose --no-cache-dir .
+
+import_tests:
+	@echo "\033[0;33m----- [" ${package_name} "] Performing import tests\033[0m"
+	@PSBODY_MESH_CACHE=`mktemp -d -t mesh_package.XXXXXXXXXX` python -c "from psbody.mesh.mesh import Mesh"
+	@python -c "from psbody.mesh.meshviewer import MeshViewers"
+	@echo "\033[0;33m----- [" ${package_name} "] OK import tests\033[0m"
+
+unit_tests:
+	@if test "$(USE_NOSE)" = "" ; then \
+		echo "\033[0;33m----- [" ${package_name} "] Running tests using unittest, no report file\033[0m" ; \
+		PSBODY_MESH_CACHE=`mktemp -d -t mesh_package.XXXXXXXXXX` python -m unittest -v ; \
+	else \
+		echo "\033[0;33m----- [" ${package_name} "] Running tests using nosetests\033[0m" ; \
+		pip install nose ; \
+		PSBODY_MESH_CACHE=`mktemp -d -t mesh_package.XXXXXXXXXX` nosetests -v --with-xunit; \
+	fi ;
+
+tests: import_tests unit_tests
+
+# Creating source distribution
+sdist:
+	@echo "\033[0;33m----- [" ${package_name} "] Creating the source distribution\033[0m"
+	@python setup.py sdist
+
+# Creating wheel distribution
+wheel:
+	@echo "\033[0;33m----- [" ${package_name} "] Creating the wheel distribution\033[0m"
+	@pip install wheel
+	@python setup.py --verbose build_ext --boost-location=$$BOOST_ROOT bdist_wheel
+
+# Build documentation
+documentation:
+	@echo "\033[0;33m----- [" ${package_name} "] Building Sphinx documentation\033[0m"
+	@pip install -U sphinx sphinx_bootstrap_theme
+	@cd doc && make html
+
+clean:
+	@rm -rf build
+	@rm -rf dist
+	@rm -rf psbody_mesh.egg-info
+	@rm -rf *.xml

mesh-fix-MSVC_compilation/README.md

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+Perceiving Systems Mesh Package
+===============================
+
+This package contains core functions for manipulating meshes and visualizing them.
+It requires ``Python 3.5+`` and is supported on Linux and macOS operating systems.
+
+The ``Mesh`` processing libraries support several of our projects such as
+* [CoMA: Convolutional Mesh Encoders for Generating 3D Faces](http://coma.is.tue.mpg.de/)
+* [FLAME: Learning a model of facial shape and expression from 4D scans](http://flame.is.tue.mpg.de/)
+* [MANO: Modeling and Capturing Hands and Bodies Together](http://mano.is.tue.mpg.de/)
+* [SMPL: A Skinned Multi-Person Linear Model](http://smpl.is.tue.mpg.de/)
+* [VOCA: Voice Operated Character Animation](https://github.com/TimoBolkart/voca)
+* [RingNet: 3D Face Shape and Expression Reconstruction from an Image](https://github.com/soubhiksanyal/RingNet)
+
+Requirements
+------------
+
+You first need to install the `Boost <http://www.boost.org>`_ libraries.
+You can compile your own local version. 
+
+On Windows/MSVC, you must download and compile it yourself.
+
+On Linux you can simply install it via:
+
+```
+$ sudo apt-get install libboost-dev
+```
+
+On macOS:
+
+```
+$ brew install boost
+```
+
+Installation
+------------
+
+First, create a dedicated Python virtual environment and activate it:
+
+```
+$ python3 -m venv --copies my_venv
+$ source my_venv/bin/activate
+```
+
+#### Linux/MacOS
+You should then compile and install the ``psbody-mesh`` package using the Makefile.
+If you are using the system-wide ``Boost`` libraries:
+
+```
+$ make all
+```
+
+or the libraries locally installed:
+
+```
+$ BOOST_ROOT=/path/to/boost/libraries make all
+```
+
+#### Windows 
+Since Makefile and the linux commands in it does not work on Windows, run the command below instead:
+(remember to replace <path_to_your_boost> with your path to boost)
+```
+pip install --no-deps --install-option="--boost-location=<path_to_your_boost>" --verbose --no-cache-dir .
+```
+
+Note on MeshViewer: Windows users need a special version of PyOpenGL to use the MeshViewer, because the one automatically installed via PYPI does not include the required DLL.
+
+please download the unofficial PyOpenGL wheel file from [here](https://www.lfd.uci.edu/~gohlke/pythonlibs/#pyopengl), uninstall the original version and install the new one by commands below:
+
+```
+pip uninstall pyOpenGL
+pip install <the-name-of-your-wheel-file>
+```
+
+Testing
+-------
+
+To run the tests, simply do:
+
+#### Linux/MacOS
+
+```
+$ make tests
+```
+
+#### Windows 
+
+```
+python -m unittest -v
+```
+
+Documentation
+-------------
+
+A detailed documentation can be compiled using the Makefile:
+
+```
+$ make documentation
+```
+
+License
+-------
+Please refer for LICENSE.txt for using this software. The software is compiled using CGAL sources following the license in CGAL_LICENSE.pdf
+
+Acknowledgments
+---------------
+
+We thank the external contribution from the following people:
+* [Kenneth Chaney](https://github.com/k-chaney)  ([PR #5](https://github.com/MPI-IS/mesh/pull/5))
+* [Dávid Komorowicz](https://github.com/Dawars) ([PR #8](https://github.com/MPI-IS/mesh/pull/8))

mesh-fix-MSVC_compilation/data/unittest/cylinder.obj

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+# Blender v2.61 (sub 0) OBJ File: ''
+# www.blender.org
+g Cylinder
+v 0.000000 -1.000000 -1.000000
+v 0.000000 -1.000000 1.000000
+v -0.382683 -1.000000 0.923880
+v -0.707107 -1.000000 0.707107
+v -0.923880 -1.000000 0.382684
+v -1.000000 -1.000000 -0.000000
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+v 0.000001 1.000000 -1.000000
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+v -0.923878 1.000000 -0.382686
+v -0.707105 1.000000 -0.707109
+v -0.382681 1.000000 -0.923881
+s off
+f 10 1 18
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+f 5 14 6
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+f 3 12 4
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+f 2 11 3
+f 11 12 3

mesh-fix-MSVC_compilation/data/unittest/cylinder_trans.obj

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+# Blender v2.61 (sub 0) OBJ File: ''
+# www.blender.org
+g Cylinder
+v 1.057678 -1.000000 -1.000000
+v 1.057678 -1.000000 1.000000
+v 0.674994 -1.000000 0.923880
+v 0.350571 -1.000000 0.707107
+v 0.133798 -1.000000 0.382684
+v 0.057678 -1.000000 -0.000000
+v 0.133798 -1.000000 -0.382684
+v 0.350571 -1.000000 -0.707107
+v 0.674995 -1.000000 -0.923880
+v 1.057678 1.000000 -1.000000
+v 1.057676 1.000000 1.000000
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+v 0.133799 1.000000 -0.382686
+v 0.350573 1.000000 -0.707109
+v 0.674997 1.000000 -0.923881
+s off
+f 10 1 18
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+f 5 14 6
+f 14 15 6
+f 4 13 5
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+f 3 12 4
+f 12 13 4
+f 2 11 3
+f 11 12 3

mesh-fix-MSVC_compilation/data/unittest/self_intersecting_cyl.obj

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+# Blender v2.61 (sub 0) OBJ File: ''
+# www.blender.org
+g Plane
+v 0.000000 -0.500000 -1.000000
+v 0.707107 -0.500000 -0.707107
+v 1.000000 -0.500000 0.000000
+v 0.707107 -0.500000 0.707107
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+v -0.707107 -0.500000 0.707107
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+v -0.707106 0.500000 -0.707107
+v 0.000000 -0.500000 0.000000
+v 0.000000 -0.835754 0.000000
+s off
+f 17 1 2
+f 18 10 9
+f 17 2 3
+f 18 11 10
+f 17 3 4
+f 18 12 11
+f 17 4 5
+f 18 13 12
+f 17 5 6
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+f 5 13 14 6
+f 6 14 15 7
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+f 9 1 8 16

mesh-fix-MSVC_compilation/data/unittest/sphere.obj

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+####
+#
+# OBJ File Generated by Meshlab
+#
+####
+# Object sphere.obj
+#
+# Vertices: 422
+# Faces: 840
+#
+####
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mesh-fix-MSVC_compilation/data/unittest/sphere.ply

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+3 383 352 382
+3 353 384 354
+3 384 353 383
+3 354 385 355
+3 385 354 384
+3 355 386 356
+3 386 355 385
+3 356 387 357
+3 387 356 386
+3 357 388 358
+3 388 357 387
+3 358 389 359
+3 389 358 388
+3 359 390 360
+3 390 359 389
+3 360 361 331
+3 361 360 390
+3 361 392 362
+3 392 361 391
+3 362 393 363
+3 393 362 392
+3 363 394 364
+3 394 363 393
+3 364 395 365
+3 395 364 394
+3 365 396 366
+3 396 365 395
+3 366 397 367
+3 397 366 396
+3 367 398 368
+3 398 367 397
+3 368 399 369
+3 399 368 398
+3 369 400 370
+3 400 369 399
+3 370 401 371
+3 401 370 400
+3 371 402 372
+3 402 371 401
+3 372 403 373
+3 403 372 402
+3 373 404 374
+3 404 373 403
+3 374 405 375
+3 405 374 404
+3 375 406 376
+3 406 375 405
+3 376 407 377
+3 407 376 406
+3 377 408 378
+3 408 377 407
+3 378 409 379
+3 409 378 408
+3 379 410 380
+3 410 379 409
+3 380 411 381
+3 411 380 410
+3 381 412 382
+3 412 381 411
+3 382 413 383
+3 413 382 412
+3 383 414 384
+3 414 383 413
+3 384 415 385
+3 415 384 414
+3 385 416 386
+3 416 385 415
+3 386 417 387
+3 417 386 416
+3 387 418 388
+3 418 387 417
+3 388 419 389
+3 419 388 418
+3 389 420 390
+3 420 389 419
+3 390 391 361
+3 391 390 420
+3 391 421 392
+3 392 421 393
+3 393 421 394
+3 394 421 395
+3 395 421 396
+3 396 421 397
+3 397 421 398
+3 398 421 399
+3 399 421 400
+3 400 421 401
+3 401 421 402
+3 402 421 403
+3 403 421 404
+3 404 421 405
+3 405 421 406
+3 406 421 407
+3 407 421 408
+3 408 421 409
+3 409 421 410
+3 410 421 411
+3 411 421 412
+3 412 421 413
+3 413 421 414
+3 414 421 415
+3 415 421 416
+3 416 421 417
+3 417 421 418
+3 418 421 419
+3 419 421 420
+3 420 421 391

mesh-fix-MSVC_compilation/data/unittest/test_box.obj

@@ -0,0 +1,50 @@
+####
+#
+# OBJ File Generated by Meshlab
+#
+####
+# Object test_box.obj
+#
+# Vertices: 8
+# Faces: 12
+#
+####
+vn 0.577350 0.577350 0.577350
+#landmark pospospos
+v 0.500000 0.500000 0.500000
+vn -0.333333 0.666667 0.666667
+v -0.500000 0.500000 0.500000
+vn 0.666667 -0.333333 0.666667
+v 0.500000 -0.500000 0.500000
+vn -0.666667 -0.666667 0.333333
+v -0.500000 -0.500000 0.500000
+vn 0.666667 0.666667 -0.333333
+v 0.500000 0.500000 -0.500000
+vn -0.666667 0.333333 -0.666667
+v -0.500000 0.500000 -0.500000
+vn 0.333333 -0.666667 -0.666667
+v 0.500000 -0.500000 -0.500000
+vn -0.577350 -0.577350 -0.577350
+#landmark negnegneg
+v -0.500000 -0.500000 -0.500000
+# 8 vertices, 0 vertices normals
+
+g a
+f 1//1 2//2 3//3
+f 4//4 3//3 2//2
+f 1//1 3//3 5//5
+f 7//7 5//5 3//3
+f 1//1 5//5 2//2
+f 6//6 2//2 5//5
+g b
+f 8//8 6//6 7//7
+g c
+f 5//5 7//7 6//6
+f 8//8 7//7 4//4
+f 3//3 4//4 7//7
+g b
+f 8//8 4//4 6//6
+f 2//2 6//6 4//4
+# 12 faces, 0 coords texture
+
+# End of File

mesh-fix-MSVC_compilation/data/unittest/test_box.ply

@@ -0,0 +1,29 @@
+ply
+format ascii 1.0
+element vertex 8
+property float x
+property float y
+property float z
+element face 12
+property list uchar int vertex_indices
+end_header
+0.5 0.5 0.5 
+-0.5 0.5 0.5 
+0.5 -0.5 0.5 
+-0.5 -0.5 0.5 
+0.5 0.5 -0.5 
+-0.5 0.5 -0.5 
+0.5 -0.5 -0.5 
+-0.5 -0.5 -0.5 
+3 0 1 2 
+3 3 2 1 
+3 0 2 4 
+3 6 4 2 
+3 0 4 1 
+3 5 1 4 
+3 7 5 6 
+3 4 6 5 
+3 7 6 3 
+3 2 3 6 
+3 7 3 5 
+3 1 5 3 

mesh-fix-MSVC_compilation/data/unittest/test_box.pp

@@ -0,0 +1,11 @@
+<!DOCTYPE PickedPoints>
+<PickedPoints>
+ <DocumentData>
+  <DateTime time="23:00:01" date="2012-04-10"/>
+  <User name="javier"/>
+  <DataFileName name="test_box.ply"/>
+  <templateName name=".pickPointsTemplate.pptpl"/>
+ </DocumentData>
+ <point x="0.5" y="0.5" z="0.5" active="1" name="pospospos"/>
+ <point x="-0.5" y="-0.5" z="-0.5" active="1" name="negnegneg"/>
+</PickedPoints>

mesh-fix-MSVC_compilation/data/unittest/test_doublebox.obj

@@ -0,0 +1,64 @@
+####
+#
+# OBJ File
+#
+####
+# Object test_doublebox.obj
+#
+# Vertices: 12
+# Faces: 20
+#
+####
+vn 0.577350 0.577350 0.577350
+v 0.500000 0.500000 0.500000
+vn -0.333333 0.666667 0.666667
+v -0.500000 0.500000 0.500000
+vn 0.666667 -0.333333 0.666667
+v 0.500000 -0.500000 0.500000
+vn -0.666667 -0.666667 0.333333
+v -0.500000 -0.500000 0.500000
+vn 0.666667 0.666667 -0.333333
+v 0.500000 0.500000 -0.500000
+vn -0.666667 0.333333 -0.666667
+v -0.500000 0.500000 -0.500000
+vn 0.333333 -0.666667 -0.666667
+v 0.500000 -0.500000 -0.500000
+vn -0.577350 -0.577350 -0.577350
+v -0.500000 -0.500000 -0.500000
+
+vn 0.577350 0.577350 0.577350
+v 0.500000 0.500000 1.500000
+vn -0.333333 0.666667 0.666667
+v -0.500000 0.500000 1.500000
+vn 0.666667 -0.333333 0.666667
+v 0.500000 -0.500000 1.500000
+vn -0.666667 -0.666667 0.333333
+v -0.500000 -0.500000 1.500000
+# 12 vertices, 0 vertices normals
+
+g box1
+f 1//1 3//3 5//5
+f 7//7 5//5 3//3
+f 1//1 5//5 2//2
+f 6//6 2//2 5//5
+f 8//8 6//6 7//7
+f 5//5 7//7 6//6
+f 8//8 7//7 4//4
+f 3//3 4//4 7//7
+f 8//8 4//4 6//6
+f 2//2 6//6 4//4
+g box2
+f 9//9 10//10 11//11
+f 12//12 11//11 10//10
+f 9//9 11//11 1//1
+f 3//3 1//1 11//11
+f 9//9 1//1 10//10
+f 2//2 10//10 1//1
+f 4//4 3//3 12//12
+f 11//11 12//12 3//3
+f 4//4 12//12 2//2
+f 10//10 2//2 12//12
+
+# 20 faces, 0 coords texture
+
+# End of File

mesh-fix-MSVC_compilation/doc/Makefile

@@ -0,0 +1,177 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/PSBodyMeshPackage.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/PSBodyMeshPackage.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/PSBodyMeshPackage"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/PSBodyMeshPackage"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+latexpdfja:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through platex and dvipdfmx..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

mesh-fix-MSVC_compilation/doc/make.bat

@@ -0,0 +1,242 @@
+@ECHO OFF
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set BUILDDIR=build
+set ALLSPHINXOPTS=-d %BUILDDIR%/doctrees %SPHINXOPTS% source
+set I18NSPHINXOPTS=%SPHINXOPTS% source
+if NOT "%PAPER%" == "" (
+	set ALLSPHINXOPTS=-D latex_paper_size=%PAPER% %ALLSPHINXOPTS%
+	set I18NSPHINXOPTS=-D latex_paper_size=%PAPER% %I18NSPHINXOPTS%
+)
+
+if "%1" == "" goto help
+
+if "%1" == "help" (
+	:help
+	echo.Please use `make ^<target^>` where ^<target^> is one of
+	echo.  html       to make standalone HTML files
+	echo.  dirhtml    to make HTML files named index.html in directories
+	echo.  singlehtml to make a single large HTML file
+	echo.  pickle     to make pickle files
+	echo.  json       to make JSON files
+	echo.  htmlhelp   to make HTML files and a HTML help project
+	echo.  qthelp     to make HTML files and a qthelp project
+	echo.  devhelp    to make HTML files and a Devhelp project
+	echo.  epub       to make an epub
+	echo.  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter
+	echo.  text       to make text files
+	echo.  man        to make manual pages
+	echo.  texinfo    to make Texinfo files
+	echo.  gettext    to make PO message catalogs
+	echo.  changes    to make an overview over all changed/added/deprecated items
+	echo.  xml        to make Docutils-native XML files
+	echo.  pseudoxml  to make pseudoxml-XML files for display purposes
+	echo.  linkcheck  to check all external links for integrity
+	echo.  doctest    to run all doctests embedded in the documentation if enabled
+	goto end
+)
+
+if "%1" == "clean" (
+	for /d %%i in (%BUILDDIR%\*) do rmdir /q /s %%i
+	del /q /s %BUILDDIR%\*
+	goto end
+)
+
+
+%SPHINXBUILD% 2> nul
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "html" (
+	%SPHINXBUILD% -b html %ALLSPHINXOPTS% %BUILDDIR%/html
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/html.
+	goto end
+)
+
+if "%1" == "dirhtml" (
+	%SPHINXBUILD% -b dirhtml %ALLSPHINXOPTS% %BUILDDIR%/dirhtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/dirhtml.
+	goto end
+)
+
+if "%1" == "singlehtml" (
+	%SPHINXBUILD% -b singlehtml %ALLSPHINXOPTS% %BUILDDIR%/singlehtml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The HTML pages are in %BUILDDIR%/singlehtml.
+	goto end
+)
+
+if "%1" == "pickle" (
+	%SPHINXBUILD% -b pickle %ALLSPHINXOPTS% %BUILDDIR%/pickle
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the pickle files.
+	goto end
+)
+
+if "%1" == "json" (
+	%SPHINXBUILD% -b json %ALLSPHINXOPTS% %BUILDDIR%/json
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can process the JSON files.
+	goto end
+)
+
+if "%1" == "htmlhelp" (
+	%SPHINXBUILD% -b htmlhelp %ALLSPHINXOPTS% %BUILDDIR%/htmlhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run HTML Help Workshop with the ^
+.hhp project file in %BUILDDIR%/htmlhelp.
+	goto end
+)
+
+if "%1" == "qthelp" (
+	%SPHINXBUILD% -b qthelp %ALLSPHINXOPTS% %BUILDDIR%/qthelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; now you can run "qcollectiongenerator" with the ^
+.qhcp project file in %BUILDDIR%/qthelp, like this:
+	echo.^> qcollectiongenerator %BUILDDIR%\qthelp\PSBodyMeshPackage.qhcp
+	echo.To view the help file:
+	echo.^> assistant -collectionFile %BUILDDIR%\qthelp\PSBodyMeshPackage.ghc
+	goto end
+)
+
+if "%1" == "devhelp" (
+	%SPHINXBUILD% -b devhelp %ALLSPHINXOPTS% %BUILDDIR%/devhelp
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished.
+	goto end
+)
+
+if "%1" == "epub" (
+	%SPHINXBUILD% -b epub %ALLSPHINXOPTS% %BUILDDIR%/epub
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The epub file is in %BUILDDIR%/epub.
+	goto end
+)
+
+if "%1" == "latex" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished; the LaTeX files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdf" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "latexpdfja" (
+	%SPHINXBUILD% -b latex %ALLSPHINXOPTS% %BUILDDIR%/latex
+	cd %BUILDDIR%/latex
+	make all-pdf-ja
+	cd %BUILDDIR%/..
+	echo.
+	echo.Build finished; the PDF files are in %BUILDDIR%/latex.
+	goto end
+)
+
+if "%1" == "text" (
+	%SPHINXBUILD% -b text %ALLSPHINXOPTS% %BUILDDIR%/text
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The text files are in %BUILDDIR%/text.
+	goto end
+)
+
+if "%1" == "man" (
+	%SPHINXBUILD% -b man %ALLSPHINXOPTS% %BUILDDIR%/man
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The manual pages are in %BUILDDIR%/man.
+	goto end
+)
+
+if "%1" == "texinfo" (
+	%SPHINXBUILD% -b texinfo %ALLSPHINXOPTS% %BUILDDIR%/texinfo
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The Texinfo files are in %BUILDDIR%/texinfo.
+	goto end
+)
+
+if "%1" == "gettext" (
+	%SPHINXBUILD% -b gettext %I18NSPHINXOPTS% %BUILDDIR%/locale
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The message catalogs are in %BUILDDIR%/locale.
+	goto end
+)
+
+if "%1" == "changes" (
+	%SPHINXBUILD% -b changes %ALLSPHINXOPTS% %BUILDDIR%/changes
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.The overview file is in %BUILDDIR%/changes.
+	goto end
+)
+
+if "%1" == "linkcheck" (
+	%SPHINXBUILD% -b linkcheck %ALLSPHINXOPTS% %BUILDDIR%/linkcheck
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Link check complete; look for any errors in the above output ^
+or in %BUILDDIR%/linkcheck/output.txt.
+	goto end
+)
+
+if "%1" == "doctest" (
+	%SPHINXBUILD% -b doctest %ALLSPHINXOPTS% %BUILDDIR%/doctest
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Testing of doctests in the sources finished, look at the ^
+results in %BUILDDIR%/doctest/output.txt.
+	goto end
+)
+
+if "%1" == "xml" (
+	%SPHINXBUILD% -b xml %ALLSPHINXOPTS% %BUILDDIR%/xml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The XML files are in %BUILDDIR%/xml.
+	goto end
+)
+
+if "%1" == "pseudoxml" (
+	%SPHINXBUILD% -b pseudoxml %ALLSPHINXOPTS% %BUILDDIR%/pseudoxml
+	if errorlevel 1 exit /b 1
+	echo.
+	echo.Build finished. The pseudo-XML files are in %BUILDDIR%/pseudoxml.
+	goto end
+)
+
+:end

mesh-fix-MSVC_compilation/doc/source/conf.py

@@ -0,0 +1,356 @@
+# -*- coding: utf-8 -*-
+#
+# PSBody Mesh Package documentation build configuration file, created by
+# sphinx-quickstart on Wed Mar 23 07:26:06 2016.
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+import sys
+import os
+import sphinx_bootstrap_theme
+
+root_source_folder = os.path.abspath(
+    os.path.join(os.path.dirname(__file__),
+                 os.pardir,
+                 os.pardir))
+sys.path.insert(0, root_source_folder)
+
+from mesh.version import __version__
+
+print(root_source_folder)
+print("version {}".format(__version__))
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+# sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir)))
+
+# -- General configuration ------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.autosummary',
+]
+
+autoclass_content = 'both'
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix of source filenames.
+source_suffix = '.rst'
+
+# The encoding of source files.
+#source_encoding = 'utf-8-sig'
+
+# The master toctree document.
+master_doc = 'index'
+
+# General information about the project.
+project = u'PSBody Mesh Package'
+copyright = u'2016, Max Planck Institute for Intelligent Systems, PSBody group'
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+
+# The short X.Y version
+version = __version__
+# The full version, including alpha/beta/rc tags
+release = __version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#language = None
+
+# There are two options for replacing |today|: either, you set today to some
+# non-false value, then it is used:
+#today = ''
+# Else, today_fmt is used as the format for a strftime call.
+#today_fmt = '%B %d, %Y'
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = []
+
+# The reST default role (used for this markup: `text`) to use for all
+# documents.
+#default_role = None
+
+# If true, '()' will be appended to :func: etc. cross-reference text.
+#add_function_parentheses = True
+
+# If true, the current module name will be prepended to all description
+# unit titles (such as .. function::).
+#add_module_names = True
+
+# If true, sectionauthor and moduleauthor directives will be shown in the
+# output. They are ignored by default.
+#show_authors = False
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+# A list of ignored prefixes for module index sorting.
+#modindex_common_prefix = []
+
+# If true, keep warnings as "system message" paragraphs in the built documents.
+#keep_warnings = False
+
+
+# -- Options for HTML output ----------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+html_theme = 'bootstrap'
+html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#html_theme_options = {}
+
+# Add any paths that contain custom themes here, relative to this directory.
+#html_theme_path = []
+
+# The name for this set of Sphinx documents.  If None, it defaults to
+# "<project> v<release> documentation".
+#html_title = None
+
+# A shorter title for the navigation bar.  Default is the same as html_title.
+#html_short_title = None
+
+# The name of an image file (relative to this directory) to place at the top
+# of the sidebar.
+#html_logo = None
+
+# The name of an image file (within the static path) to use as favicon of the
+# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
+# pixels large.
+#html_favicon = None
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Add any extra paths that contain custom files (such as robots.txt or
+# .htaccess) here, relative to this directory. These files are copied
+# directly to the root of the documentation.
+#html_extra_path = []
+
+# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
+# using the given strftime format.
+#html_last_updated_fmt = '%b %d, %Y'
+
+# If true, SmartyPants will be used to convert quotes and dashes to
+# typographically correct entities.
+#html_use_smartypants = True
+
+# Custom sidebar templates, maps document names to template names.
+#html_sidebars = {}
+
+# Additional templates that should be rendered to pages, maps page names to
+# template names.
+#html_additional_pages = {}
+
+# If false, no module index is generated.
+#html_domain_indices = True
+
+# If false, no index is generated.
+#html_use_index = True
+
+# If true, the index is split into individual pages for each letter.
+#html_split_index = False
+
+# If true, links to the reST sources are added to the pages.
+#html_show_sourcelink = True
+
+# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
+#html_show_sphinx = True
+
+# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
+#html_show_copyright = True
+
+# If true, an OpenSearch description file will be output, and all pages will
+# contain a <link> tag referring to it.  The value of this option must be the
+# base URL from which the finished HTML is served.
+#html_use_opensearch = ''
+
+# This is the file name suffix for HTML files (e.g. ".xhtml").
+#html_file_suffix = None
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'PSBodyMeshPackagedoc'
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+latex_elements = {
+# The paper size ('letterpaper' or 'a4paper').
+#'papersize': 'letterpaper',
+
+# The font size ('10pt', '11pt' or '12pt').
+#'pointsize': '10pt',
+
+# Additional stuff for the LaTeX preamble.
+#'preamble': '',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+  ('index', 'PSBodyMeshPackage.tex', u'PSBody Mesh Package Documentation',
+   u'Max Planck Institute for Intelligent Systems, PSBody group', 'manual'),
+]
+
+# The name of an image file (relative to this directory) to place at the top of
+# the title page.
+#latex_logo = None
+
+# For "manual" documents, if this is true, then toplevel headings are parts,
+# not chapters.
+#latex_use_parts = False
+
+# If true, show page references after internal links.
+#latex_show_pagerefs = False
+
+# If true, show URL addresses after external links.
+#latex_show_urls = False
+
+# Documents to append as an appendix to all manuals.
+#latex_appendices = []
+
+# If false, no module index is generated.
+#latex_domain_indices = True
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    ('index', 'psbodymeshpackage', u'PSBody Mesh Package Documentation',
+     [u'Max Planck Institute for Intelligent Systems, PSBody group'], 1)
+]
+
+# If true, show URL addresses after external links.
+#man_show_urls = False
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+  ('index', 'PSBodyMeshPackage', u'PSBody Mesh Package Documentation',
+   u'Max Planck Institute for Intelligent Systems, PSBody group', 'PSBodyMeshPackage', 'One line description of project.',
+   'Miscellaneous'),
+]
+
+# Documents to append as an appendix to all manuals.
+#texinfo_appendices = []
+
+# If false, no module index is generated.
+#texinfo_domain_indices = True
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#texinfo_show_urls = 'footnote'
+
+# If true, do not generate a @detailmenu in the "Top" node's menu.
+#texinfo_no_detailmenu = False
+
+
+# -- Options for Epub output ----------------------------------------------
+
+# Bibliographic Dublin Core info.
+epub_title = u'PSBody Mesh Package'
+epub_author = u'Max Planck Institute for Intelligent Systems, PSBody group'
+epub_publisher = u'Max Planck Institute for Intelligent Systems, PSBody group'
+epub_copyright = u'2016, Max Planck Institute for Intelligent Systems, PSBody group'
+
+# The basename for the epub file. It defaults to the project name.
+#epub_basename = u'PSBody Mesh Package'
+
+# The HTML theme for the epub output. Since the default themes are not optimized
+# for small screen space, using the same theme for HTML and epub output is
+# usually not wise. This defaults to 'epub', a theme designed to save visual
+# space.
+#epub_theme = 'epub'
+
+# The language of the text. It defaults to the language option
+# or en if the language is not set.
+#epub_language = ''
+
+# The scheme of the identifier. Typical schemes are ISBN or URL.
+#epub_scheme = ''
+
+# The unique identifier of the text. This can be a ISBN number
+# or the project homepage.
+#epub_identifier = ''
+
+# A unique identification for the text.
+#epub_uid = ''
+
+# A tuple containing the cover image and cover page html template filenames.
+#epub_cover = ()
+
+# A sequence of (type, uri, title) tuples for the guide element of content.opf.
+#epub_guide = ()
+
+# HTML files that should be inserted before the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_pre_files = []
+
+# HTML files shat should be inserted after the pages created by sphinx.
+# The format is a list of tuples containing the path and title.
+#epub_post_files = []
+
+# A list of files that should not be packed into the epub file.
+epub_exclude_files = ['search.html']
+
+# The depth of the table of contents in toc.ncx.
+#epub_tocdepth = 3
+
+# Allow duplicate toc entries.
+#epub_tocdup = True
+
+# Choose between 'default' and 'includehidden'.
+#epub_tocscope = 'default'
+
+# Fix unsupported image types using the PIL.
+#epub_fix_images = False
+
+# Scale large images.
+#epub_max_image_width = 0
+
+# How to display URL addresses: 'footnote', 'no', or 'inline'.
+#epub_show_urls = 'inline'
+
+# If false, no index is generated.
+#epub_use_index = True
+
+
+# Example configuration for intersphinx: refer to the Python standard library.
+intersphinx_mapping = {'http://docs.python.org/': None}

mesh-fix-MSVC_compilation/doc/source/index.rst

@@ -0,0 +1,163 @@
+.. PSBody Mesh Package documentation master file, created by
+   sphinx-quickstart on Wed Mar 23 07:26:06 2016.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to PSBody Mesh Package's documentation!
+===============================================
+
+This is the documentation of the Mesh package of the Body Group, Max Planck Institute
+for Intelligent Systems, Tübingen, Germany.
+
+Contents:
+
+.. toctree::
+   :maxdepth: 2
+
+   Mesh<pages/mesh>
+   Mesh Viewer<pages/mesh_viewer>
+   Geometry<pages/geometry>
+
+
+What is this package about?
+===========================
+This package contains core functions for manipulating Meshes and visualizing them.
+It requires ``Python 3.5+`` and is supported on Linux and macOS operating systems.
+
+
+Getting started
+===============
+
+Installation
+------------
+
+
+There are several places where you can download the latest release of the ``psbody-mesh`` package:
+
+* `Code Doc <https://code.is.localnet/series/3/8/>`_  , the internal documentation center of the MPI-IS
+* `GitLab <https://gitlab.tuebingen.mpg.de/ps-body/mesh>`_, the internal repository used for development
+* `GitHub <https://github.com/MPI-IS/mesh>`_ for the public release
+
+``Code Doc`` contains the wheel and source distributions, and the documentation of the **complete** package.
+
+``GitLab`` contains the source code of the **complete** package.
+
+``GitHub`` contains the source code of the public, **limited** package.
+
+
+First, create a dedicated Python virtual environment and activate it:
+
+.. code::
+
+    $ python3 -m venv --copies my_venv
+    $ source my_venv/bin/activate
+
+The easiest way to install the ``psbody-mesh`` package is to use the wheel distribution:
+
+.. code::
+
+    $ pip install psbody_mesh_*.whl
+
+.. warning::
+
+	Make sure to use to wheel corresponding to your OS and your Python version.
+
+You can also install the ``psbody-mesh`` package using the source distribution.
+For this, you first need to install the `Boost <http://www.boost.org>`_ libraries.
+You can compile your own local version or simply do:
+
+.. code::
+
+	$ sudo apt-get install libboost-dev
+
+and then install the  ``psbody-mesh`` package:
+
+.. code::
+
+	$ pip install psbody_mesh_*.tar.gz
+
+As a last option, you can also compile and install the ``psbody-mesh`` package using the Makefile.
+If you are using the system-wide ``Boost libraries``:
+
+.. code::
+
+	$ make all
+
+or the libraries locally installed:
+
+.. code::
+
+	$ BOOST_ROOT=/path/to/boost/libraries make all
+
+Testing
+-------
+
+To run the tests (only available in the **complete** package), simply do:
+
+.. code::
+
+	$ make tests
+
+Documentation
+-------------
+
+A detailed documentation can be compiled using the Makefile:
+
+.. code::
+
+	$ make documentation
+
+Loading a mesh
+--------------
+
+Loading a :py:class:`Mesh <psbody.mesh.mesh.Mesh>` class from a file is that easy:
+
+.. code::
+
+    from psbody.mesh import Mesh
+    my_mesh = Mesh(filename='mesh_filename.ply')
+
+Rendering a mesh
+----------------
+
+From a previously loaded mesh ``my_mesh``, it is possible to visualize it inside an interactive window using the
+:py:class:`MeshViewers <psbody.mesh.meshviewer.MeshViewers>` class:
+
+.. code::
+
+    from psbody.mesh import MeshViewers
+
+    # creates a grid of 2x2 mesh viewers
+    mvs = MeshViewers(shape=[2, 2])
+
+    # sets the first (top-left) mesh to my_mesh
+    mvs[0][0].set_static_meshes([my_mesh])
+
+Caching
+-------
+
+Some operations make use of caching for performance reasons. The default folder used for caching is
+
+.. code::
+
+  ~/.psbody/mesh_package_cache
+
+
+If you need to specify the cache folder, define the environment variable ``PSBODY_MESH_CACHE``
+prior to any loading of the Mesh package:
+
+.. code::
+
+  export PSBODY_MESH_CACHE="some/folder"
+  python
+  >> from psbody.mesh import Mesh
+  # now uses the specified cache
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

mesh-fix-MSVC_compilation/doc/source/pages/geometry.rst

@@ -0,0 +1,29 @@
+Geometry
+========
+
+The geometry subpackage contains some utilities on the geometric entities.
+
+.. autosummary::
+
+  psbody.mesh.geometry.triangle_area.triangle_area
+  psbody.mesh.geometry.rodrigues.rodrigues
+  psbody.mesh.geometry.barycentric_coordinates_of_projection.barycentric_coordinates_of_projection
+  psbody.mesh.geometry.cross_product.CrossProduct
+
+
+Reference
+---------
+
+.. automodule:: psbody.mesh.geometry.triangle_area
+   :members:
+
+.. automodule:: psbody.mesh.geometry.rodrigues
+   :members:
+
+.. automodule:: psbody.mesh.geometry.barycentric_coordinates_of_projection
+   :members:
+ 
+.. automodule:: psbody.mesh.geometry.cross_product
+   :members:
+ 
+ 

mesh-fix-MSVC_compilation/doc/source/pages/mesh.rst

@@ -0,0 +1,31 @@
+Mesh
+====
+
+The :py:class:`Mesh <psbody.mesh.mesh.Mesh>` class is the core class of the Mesh package.  
+
+Loading and Saving a mesh
+-------------------------
+
+The entry point for loading a mesh is :py:func:`Mesh.load_from_file <psbody.mesh.mesh.Mesh.load_from_file>`.
+
+Supported file formats:
+
+* ply
+* obj
+
+Querying meshes
+---------------
+Meshes contain functions to query their content efficiently. 
+
+Transforming meshes
+------------------- 
+
+
+Reference
+---------
+
+.. automodule:: psbody.mesh.mesh
+   :members:
+   :undoc-members:
+
+ 

mesh-fix-MSVC_compilation/doc/source/pages/mesh_viewer.rst

@@ -0,0 +1,11 @@
+Mesh viewer
+===========
+
+
+Reference
+---------
+
+.. automodule:: psbody.mesh.meshviewer
+   :members:
+   :undoc-members:
+ 

mesh-fix-MSVC_compilation/mesh/CMakeLists.txt

@@ -0,0 +1,114 @@
+# Copyright 2016, Max Planck Society.
+# Not licensed
+# author Raffi Enficiaud
+
+cmake_minimum_required (VERSION 2.8.12)
+set_property(GLOBAL PROPERTY USE_FOLDERS ON)
+
+enable_testing()
+
+project(Mesh)
+
+add_custom_target(cmake_files SOURCES 
+                    cmake/python_helper.cmake
+                    cmake/thirdparty.cmake
+                    src/hijack_python_headers.hpp)
+
+include(cmake/thirdparty.cmake)
+include(cmake/python_helper.cmake)
+
+
+include_directories(${PYTHON_INCLUDE_PATH})
+
+set(MESHPYTHON_SRC
+    __init__.py
+    mesh.py
+    meshviewer.py
+    colors.py
+    search.py
+  )
+
+# for convenience
+add_custom_target(MeshPython SOURCES ${MESHPYTHON_SRC})
+
+
+
+
+# aabb_normals
+# CGAL_NDEBUG removes calls to logging, warning and error functions that would need
+#   a link to the CGAL libraries
+# CGAL_HAS_NO_THREADS removes the thread safety of the AABB tree with the advantage
+#   of removing the dependency to boost::thread (and indirectly boost::system compiled library)
+# MESH_CGAL_AVOID_COMPILED_VERSION is a define of our own in order to hack a remaining
+#   log of error without the need to include CGAL generated libraries
+# CGAL_NO_AUTOLINK_CGA prevents autolinking on Visual
+
+set(DEFINES_MESH_EXTENSIONS_WITH_CGAL_WITHOUT_LINK
+    -DCGAL_NDEBUG=1
+    -DMESH_CGAL_AVOID_COMPILED_VERSION=1
+    -DCGAL_HAS_NO_THREADS=1
+    -DCGAL_NO_AUTOLINK_CGAL=1)
+
+python_add_library(TARGET aabb_normals SOURCES
+  src/cgal_error_emulation.hpp
+  src/AABB_n_tree.h
+  src/aabb_normals.cpp)
+set_property(TARGET aabb_normals PROPERTY FOLDER "GeometryExt/")
+target_include_directories(aabb_normals PRIVATE
+    ${libcgalroot}/include
+    ${NUMPY_INCLUDE_PATH}
+    ${Boost_INCLUDE_DIRS})
+target_compile_definitions(aabb_normals PRIVATE
+    ${DEFINES_MESH_EXTENSIONS_WITH_CGAL_WITHOUT_LINK})
+
+
+# spatial search
+python_add_library(TARGET spatialsearch SOURCES
+  src/cgal_error_emulation.hpp
+  src/nearest_point_triangle_3.h
+  src/nearest_triangle_normals.hpp
+  src/nearest_triangle.hpp
+    
+  src/spatialsearchmodule.cpp
+)
+set_property(TARGET spatialsearch PROPERTY FOLDER "GeometryExt/")
+target_include_directories(spatialsearch PRIVATE
+    ${libcgalroot}/include
+    ${NUMPY_INCLUDE_PATH}
+    ${Boost_INCLUDE_DIRS})
+target_compile_definitions(spatialsearch PRIVATE
+    ${DEFINES_MESH_EXTENSIONS_WITH_CGAL_WITHOUT_LINK})
+
+
+    
+# visibility
+python_add_library(TARGET visibility SOURCES 
+    src/py_visibility.cpp
+    src/visibility.cpp
+    )
+target_include_directories(visibility PRIVATE 
+  ${libcgalroot}/include
+  ${NUMPY_INCLUDE_PATH}
+  ${Boost_INCLUDE_DIRS})
+set_property(TARGET visibility PROPERTY FOLDER "GeometryExt/")
+target_compile_definitions(visibility PRIVATE
+    ${DEFINES_MESH_EXTENSIONS_WITH_CGAL_WITHOUT_LINK})
+
+
+# serialization extensions
+
+# plyutils
+python_add_library(TARGET plyutils SOURCES
+  src/plyutils.h
+  src/plyutils.c
+  src/rply.h
+  src/rply.c)
+set_property(TARGET plyutils PROPERTY FOLDER "SerializationExt/")
+
+# loadobj
+python_add_library(TARGET loadobj SOURCES src/py_loadobj.cpp)
+target_include_directories(loadobj PRIVATE 
+  ${NUMPY_INCLUDE_PATH}
+  ${Boost_INCLUDE_DIRS})
+set_property(TARGET loadobj PROPERTY FOLDER "SerializationExt/")
+

mesh-fix-MSVC_compilation/mesh/__init__.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+
+import os
+from os.path import abspath, dirname, expanduser, join
+
+from .mesh import Mesh
+from .meshviewer import MeshViewer, MeshViewers
+
+texture_path = abspath(join(dirname(__file__), '..', 'data', 'template', 'texture_coordinates'))
+
+if 'PSBODY_MESH_CACHE' in os.environ:
+    mesh_package_cache_folder = expanduser(os.environ['PSBODY_MESH_CACHE'])
+else:
+    mesh_package_cache_folder = expanduser('~/.psbody/mesh_package_cache')
+
+if not os.path.exists(mesh_package_cache_folder):
+    os.makedirs(mesh_package_cache_folder)

mesh-fix-MSVC_compilation/mesh/arcball.py

@@ -0,0 +1,247 @@
+#!/usr/bin/env python
+# encoding: utf-8
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+
+"""
+Math utilities, vector, matrix types and ArcBall quaternion rotation class
+==========================================================================
+
+"""
+
+import numpy as Numeric
+import copy
+from math import sqrt
+
+# //assuming IEEE-754(GLfloat), which i believe has max precision of 7 bits
+Epsilon = 1.0e-5
+
+
+class ArcBallT(object):
+    def __init__(self, NewWidth, NewHeight):
+        self.m_StVec = Vector3fT()
+        self.m_EnVec = Vector3fT()
+        self.m_AdjustWidth = 1.0
+        self.m_AdjustHeight = 1.0
+        self.setBounds(NewWidth, NewHeight)
+
+    def __str__(self):
+        str_rep = ""
+        str_rep += "StVec = " + str(self.m_StVec)
+        str_rep += "\nEnVec = " + str(self.m_EnVec)
+        str_rep += "\n scale coords %f %f" % (self.m_AdjustWidth, self.m_AdjustHeight)
+        return str_rep
+
+    def setBounds(self, NewWidth, NewHeight):
+        # //Set new bounds
+        assert (NewWidth > 1.0 and NewHeight > 1.0), "Invalid width or height for bounds."
+        # //Set adjustment factor for width/height
+        self.m_AdjustWidth = 1.0 / ((NewWidth - 1.0) * 0.5)
+        self.m_AdjustHeight = 1.0 / ((NewHeight - 1.0) * 0.5)
+
+    def _mapToSphere(self, NewPt):
+        # Given a new window coordinate, will modify NewVec in place
+        X = 0
+        Y = 1
+        Z = 2
+
+        NewVec = Vector3fT()
+        # //Copy paramter into temp point
+        TempPt = copy.copy(NewPt)
+        # //Adjust point coords and scale down to range of [-1 ... 1]
+        TempPt[X] = (NewPt[X] * self.m_AdjustWidth) - 1.0
+        TempPt[Y] = 1.0 - (NewPt[Y] * self.m_AdjustHeight)
+        # //Compute the square of the length of the vector to the point from the center
+        length = Numeric.sum(Numeric.dot(TempPt, TempPt))
+        # //If the point is mapped outside of the sphere... (length > radius squared)
+        if (length > 1.0):
+            # //Compute a normalizing factor (radius / sqrt(length))
+            norm = 1.0 / sqrt(length)
+
+            # //Return the "normalized" vector, a point on the sphere
+            NewVec[X] = TempPt[X] * norm
+            NewVec[Y] = TempPt[Y] * norm
+            NewVec[Z] = 0.0
+        else:  # //Else it's on the inside
+            # //Return a vector to a point mapped inside the sphere sqrt(radius squared - length)
+            NewVec[X] = TempPt[X]
+            NewVec[Y] = TempPt[Y]
+            NewVec[Z] = sqrt(1.0 - length)
+
+        return NewVec
+
+    def click(self, NewPt):
+        # Mouse down (Point2fT
+        self.m_StVec = self._mapToSphere(NewPt)
+        return
+
+    def drag(self, NewPt):
+        # Mouse drag, calculate rotation (Point2fT Quat4fT)
+        """ drag (Point2fT mouse_coord) -> new_quaternion_rotation_vec
+        """
+        X = 0
+        Y = 1
+        Z = 2
+        W = 3
+
+        self.m_EnVec = self._mapToSphere(NewPt)
+
+        # //Compute the vector perpendicular to the begin and end vectors
+        # Perp = Vector3fT ()
+        Perp = Vector3fCross(self.m_StVec, self.m_EnVec)
+
+        NewRot = Quat4fT()
+        # Compute the length of the perpendicular vector
+        if (Vector3fLength(Perp) > Epsilon):
+            # if its non-zero
+            # We're ok, so return the perpendicular vector as the transform after all
+            NewRot[X] = Perp[X]
+            NewRot[Y] = Perp[Y]
+            NewRot[Z] = Perp[Z]
+            # //In the quaternion values, w is cosine (theta / 2), where theta is rotation angle
+            NewRot[W] = Vector3fDot(self.m_StVec, self.m_EnVec)
+        else:
+            # if its zero
+            # The begin and end vectors coincide, so return a quaternion of zero matrix (no rotation)
+            NewRot[X] = NewRot[Y] = NewRot[Z] = NewRot[W] = 0.0
+
+        return NewRot
+
+
+def Matrix4fT():
+    return Numeric.identity(4, 'f')
+
+
+def Matrix3fT():
+    return Numeric.identity(3, 'f')
+
+
+def Quat4fT():
+    return Numeric.zeros(4, 'f')
+
+
+def Vector3fT():
+    return Numeric.zeros(3, 'f')
+
+
+def Point2fT(x=0.0, y=0.0):
+    pt = Numeric.zeros(2, 'f')
+    pt[0] = x
+    pt[1] = y
+    return pt
+
+
+def Vector3fDot(u, v):
+    # Dot product of two 3f vectors
+    dotprod = Numeric.dot(u, v)
+    return dotprod
+
+
+def Vector3fCross(u, v):
+    # Cross product of two 3f vectors
+    X = 0
+    Y = 1
+    Z = 2
+    cross = Numeric.zeros(3, 'f')
+    cross[X] = (u[Y] * v[Z]) - (u[Z] * v[Y])
+    cross[Y] = (u[Z] * v[X]) - (u[X] * v[Z])
+    cross[Z] = (u[X] * v[Y]) - (u[Y] * v[X])
+    return cross
+
+
+def Vector3fLength(u):
+    mag_squared = Numeric.sum(Numeric.dot(u, u))
+    mag = sqrt(mag_squared)
+    return mag
+
+
+def Matrix3fSetIdentity():
+    return Numeric.identity(3, 'f')
+
+
+def Matrix3fMulMatrix3f(matrix_a, matrix_b):
+    return matrix_a.dot(matrix_b)
+
+
+def Matrix4fSVD(NewObj):
+    X = 0
+    Y = 1
+    Z = 2
+    s = sqrt(((NewObj[X][X] * NewObj[X][X]) + (NewObj[X][Y] * NewObj[X][Y]) + (NewObj[X][Z] * NewObj[X][Z]) +
+              (NewObj[Y][X] * NewObj[Y][X]) + (NewObj[Y][Y] * NewObj[Y][Y]) + (NewObj[Y][Z] * NewObj[Y][Z]) +
+              (NewObj[Z][X] * NewObj[Z][X]) + (NewObj[Z][Y] * NewObj[Z][Y]) + (NewObj[Z][Z] * NewObj[Z][Z])) / 3.0)
+    return s
+
+
+def Matrix4fSetRotationScaleFromMatrix3f(NewObj, three_by_three_matrix):
+    """Modifies NewObj in-place by replacing its upper 3x3 portion from the
+    passed in 3x3 matrix.
+
+    :param NewObj: a `Matrix4fT`
+    """
+    NewObj[0:3, 0:3] = three_by_three_matrix
+    return NewObj
+
+
+def Matrix4fSetRotationFromMatrix3f(NewObj, three_by_three_matrix):
+    """
+    Sets the rotational component (upper 3x3) of this matrix to the matrix
+    values in the T precision Matrix3d argument; the other elements of
+    this matrix are unchanged; a singular value decomposition is performed
+    on this object's upper 3x3 matrix to factor out the scale, then this
+    object's upper 3x3 matrix components are replaced by the passed rotation
+    components, and then the scale is reapplied to the rotational
+    components.
+
+    :param three_by_three_matrix: T precision 3x3 matrix
+    """
+    scale = Matrix4fSVD(NewObj)
+
+    NewObj = Matrix4fSetRotationScaleFromMatrix3f(NewObj, three_by_three_matrix)
+    scaled_NewObj = NewObj * scale  # Matrix4fMulRotationScale(NewObj, scale);
+    return scaled_NewObj
+
+
+def Matrix3fSetRotationFromQuat4f(q1):
+    """Converts the H quaternion q1 into a new equivalent 3x3 rotation matrix."""
+    X = 0
+    Y = 1
+    Z = 2
+    W = 3
+
+    NewObj = Matrix3fT()
+    n = Numeric.sum(Numeric.dot(q1, q1))
+    s = 0.0
+    if (n > 0.0):
+        s = 2.0 / n
+
+    xs = q1[X] * s
+    ys = q1[Y] * s
+    zs = q1[Z] * s
+
+    wx = q1[W] * xs
+    wy = q1[W] * ys
+    wz = q1[W] * zs
+
+    xx = q1[X] * xs
+    xy = q1[X] * ys
+    xz = q1[X] * zs
+
+    yy = q1[Y] * ys
+    yz = q1[Y] * zs
+    zz = q1[Z] * zs
+
+    # This math all comes about by way of algebra, complex math, and trig identities.
+    # See Lengyel pages 88-92
+    NewObj[X][X] = 1.0 - (yy + zz)
+    NewObj[Y][X] = xy - wz
+    NewObj[Z][X] = xz + wy
+
+    NewObj[X][Y] = xy + wz
+    NewObj[Y][Y] = 1.0 - (xx + zz)
+    NewObj[Z][Y] = yz - wx
+
+    NewObj[X][Z] = xz - wy
+    NewObj[Y][Z] = yz + wx
+    NewObj[Z][Z] = 1.0 - (xx + yy)
+
+    return NewObj

mesh-fix-MSVC_compilation/mesh/cmake/python_helper.cmake

@@ -0,0 +1,74 @@
+# Copyright 2016, Max Planck Society.
+# Not licensed
+# author Raffi Enficiaud
+
+# helper file containing commands easing the declaration of python modules
+
+include(CMakeParseArguments)
+
+
+#.rst:
+# .. command:: python_add_library
+#
+#   Adds a shared library that is meant to be a python extension module.
+#   The added library links to python library and has the proper extension.
+#
+#   ::
+#
+#     python_add_library(
+#         TARGET targetname
+#         SOURCES source_list)
+#
+#   ``targetname`` name of the python extension
+#   ``source_list`` list of source files for this target.
+#
+function(python_add_library)
+
+  if("${PYTHON_MODULES_EXTENSIONS}" STREQUAL "")
+    if("${PYTHON_VERSION}" VERSION_GREATER "2.5")
+      if(UNIX OR MINGW)
+        set(PYTHON_MODULES_EXTENSIONS_TEMP ".so")
+      else()
+        set(PYTHON_MODULES_EXTENSIONS_TEMP ".pyd")
+      endif()
+    else()
+      if(APPLE)
+        set(PYTHON_MODULES_EXTENSIONS_TEMP ".so")
+      else()
+        set(PYTHON_MODULES_EXTENSIONS_TEMP ${CMAKE_SHARED_LIBRARY_SUFFIX})
+      endif()
+    endif()
+    set(PYTHON_MODULES_EXTENSIONS ${PYTHON_MODULES_EXTENSIONS_TEMP} CACHE STRING "Python modules extension for the current platform")
+  endif()
+
+  
+  set(options )
+  set(oneValueArgs TARGET)
+  set(multiValueArgs SOURCES)
+  cmake_parse_arguments(local_python_add_cmd "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})  
+
+  if("${local_python_add_cmd_TARGET}" STREQUAL "")
+    message(FATAL_ERROR "python_add_library: the TARGET should be specified")
+  endif()
+
+  if("${local_python_add_cmd_SOURCES}" STREQUAL "")
+    message(FATAL_ERROR "python_add_library: at least one source file should be specified")
+  endif()
+  
+  add_library(${local_python_add_cmd_TARGET} SHARED 
+      src/hijack_python_headers.hpp  # by default
+      "${local_python_add_cmd_SOURCES}")
+  target_include_directories(${local_python_add_cmd_TARGET} PRIVATE ${PYTHON_INCLUDE_PATH})
+  target_link_libraries(${local_python_add_cmd_TARGET} ${PYTHON_LIBRARY}) # PYTHON_LIBRARIES may contain the debug version of python, which we do not want
+  set_target_properties(${local_python_add_cmd_TARGET} 
+    PROPERTIES SUFFIX ${PYTHON_MODULES_EXTENSIONS}
+    PREFIX "")
+  
+  if(FALSE)
+  set_target_properties(${local_python_add_cmd_TARGET}
+      PROPERTIES 
+        OUTPUT_NAME_DEBUG ${local_python_add_cmd_TARGET}_d
+        )
+  endif()
+
+endfunction(python_add_library)

mesh-fix-MSVC_compilation/mesh/cmake/thirdparty.cmake

@@ -0,0 +1,107 @@
+# Copyright 2016, Max Planck Society.
+# Not licensed
+# author Raffi Enficiaud
+
+# this file contains all the necessary to link against thirdparty libraries
+
+# location of the stored thirdparty archives
+set(thirdparty_dir ${CMAKE_SOURCE_DIR}/thirdparty)
+
+# the location where the archives will be deflated, to avoid pollution
+# of the source tree
+set(thirdparties_deflate_directory ${CMAKE_BINARY_DIR}/external_libs_deflate)
+if(NOT EXISTS ${thirdparties_deflate_directory})
+  file(MAKE_DIRECTORY ${thirdparties_deflate_directory})
+endif()
+
+# this module may be used to find system installed libraries on Linux
+if(UNIX AND NOT APPLE)
+  find_package(PkgConfig)
+endif()
+
+
+# Python libraries, required
+find_package(PythonLibs REQUIRED)
+find_package(PythonInterp REQUIRED)
+
+# numpy
+execute_process(
+  COMMAND ${PYTHON_EXECUTABLE} -c "import numpy; print(numpy.get_include())"
+  OUTPUT_VARIABLE NUMPY_INCLUDE_PATH
+  ERROR_VARIABLE  NUMPY_ERROR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  )
+if(NOT (NUMPY_ERROR STREQUAL "") OR (NUMPY_INCLUDE_PATH STREQUAL ""))
+  message(FATAL_ERROR "[numpy] the following error occured: ${NUMPY_ERROR} - Consider setting PYTHON_ROOT in the environment")
+endif()
+message(STATUS "[numpy] found headers in ${NUMPY_INCLUDE_PATH}")
+
+
+# cgal
+set(CGAL_MAJOR_VERSION 4)
+set(CGAL_MINOR_VERSION 7)
+set(CGAL_VERSION ${CGAL_MAJOR_VERSION}.${CGAL_MINOR_VERSION})
+set(LIBCGAL CGAL-${CGAL_MAJOR_VERSION}.${CGAL_MINOR_VERSION})
+set(libcgalroot ${thirdparties_deflate_directory}/${LIBCGAL})
+
+if(NOT EXISTS ${libcgalroot})
+  message(STATUS "Untarring ${LIBCGAL}")
+  execute_process(
+    COMMAND ${CMAKE_COMMAND} -E tar xzf ${thirdparty_dir}/${LIBCGAL}.tar.gz
+    WORKING_DIRECTORY ${thirdparties_deflate_directory})
+endif()
+
+if(NOT EXISTS ${libcgalroot}/include/CGAL/compiler_config.h)
+  message(STATUS "[CGAL] creating empty configuration file for header only compilation")
+  file(WRITE 
+       ${libcgalroot}/include/CGAL/compiler_config.h
+       "// automatically generated by mesh cmake")
+endif()
+
+
+
+# boost (needed by CGAL)
+if(NOT BOOST_ROOT)
+  message(STATUS "[BOOST] Boost root not configured, taking the system boost version")
+  set(MESH_BOOST_FROM_SYSTEM TRUE)
+else()
+  message(STATUS "[BOOST] Boost root directory set to ${BOOST_ROOT}")
+  set(MESH_BOOST_FROM_SYSTEM FALSE)
+endif()
+
+if(UNIX AND NOT APPLE AND NOT MESH_BOOST_FROM_SYSTEM)
+  message(WARNING "[BOOST] you are setting a different boost than the one provided by the system. This option should be taken with care.")
+endif()
+
+set(Boost_ADDITIONAL_VERSIONS   
+    "1.54" "1.54.0" "1.55" "1.55.0" "1.56" "1.56.0" "1.57.0" "1.58" "1.58.0" "1.59" "1.59.0"
+    "1.60" "1.60.0" "1.61" "1.61.0")
+
+
+add_definitions(-DBOOST_ALL_NO_LIB)   # disable auto link
+set(Boost_USE_STATIC_LIBS OFF)        # linking with static library version (not used because of the header only)
+if(NOT Boost_USE_STATIC_LIBS)
+  # link against dynamic libraries
+  add_definitions(-DBOOST_ALL_DYN_LINK)
+endif()
+
+# if we are using the system version, we do not want to have the exact version embedded in the rpath/ldd
+if(MESH_BOOST_FROM_SYSTEM)
+  set(Boost_REALPATH OFF)
+else()
+  set(Boost_REALPATH ON)
+endif()
+
+set(Boost_USE_MULTITHREADED ON)
+set(Boost_DEBUG ON)
+set(Boost_DETAILED_FAILURE_MSG ON)
+if(DEFINED BOOST_ROOT)
+  set(Boost_NO_SYSTEM_PATHS ON)
+else()
+  set(Boost_NO_SYSTEM_PATHS OFF)
+endif()
+set(Boost_NO_BOOST_CMAKE ON)
+
+# only the header locations
+find_package(Boost 1.59)
+

mesh-fix-MSVC_compilation/mesh/colors.py

@@ -0,0 +1,790 @@
+#!/usr/bin/env python
+# encoding: utf-8
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2012-05-12.
+
+"""
+Colors utilities
+================
+
+
+"""
+
+import re
+import numpy as np
+
+
+def main():
+    """Generates code for name_to_rgb dict, assuming an rgb.txt file available (in X11 format)."""
+    with open('rgb.txt') as fp:
+
+        line = fp.readline()
+        while line:
+            reg = re.match('\s*(\d+)\s*(\d+)\s*(\d+)\s*(\w.*\w).*', line)
+            if reg:
+                r = int(reg.group(1)) / 255.
+                g = int(reg.group(2)) / 255.
+                b = int(reg.group(3)) / 255.
+                d = reg.group(4)
+                print("'%s': np.array([%.2f, %.2f, %.2f])," % (d, r, g, b))
+            line = fp.readline()
+
+
+name_to_rgb = {
+    'snow': np.array([1.00, 0.98, 0.98]),
+    'ghost white': np.array([0.97, 0.97, 1.00]),
+    'GhostWhite': np.array([0.97, 0.97, 1.00]),
+    'white smoke': np.array([0.96, 0.96, 0.96]),
+    'WhiteSmoke': np.array([0.96, 0.96, 0.96]),
+    'gainsboro': np.array([0.86, 0.86, 0.86]),
+    'floral white': np.array([1.00, 0.98, 0.94]),
+    'FloralWhite': np.array([1.00, 0.98, 0.94]),
+    'old lace': np.array([0.99, 0.96, 0.90]),
+    'OldLace': np.array([0.99, 0.96, 0.90]),
+    'linen': np.array([0.98, 0.94, 0.90]),
+    'antique white': np.array([0.98, 0.92, 0.84]),
+    'AntiqueWhite': np.array([0.98, 0.92, 0.84]),
+    'papaya whip': np.array([1.00, 0.94, 0.84]),
+    'PapayaWhip': np.array([1.00, 0.94, 0.84]),
+    'blanched almond': np.array([1.00, 0.92, 0.80]),
+    'BlanchedAlmond': np.array([1.00, 0.92, 0.80]),
+    'bisque': np.array([1.00, 0.89, 0.77]),
+    'peach puff': np.array([1.00, 0.85, 0.73]),
+    'PeachPuff': np.array([1.00, 0.85, 0.73]),
+    'navajo white': np.array([1.00, 0.87, 0.68]),
+    'NavajoWhite': np.array([1.00, 0.87, 0.68]),
+    'moccasin': np.array([1.00, 0.89, 0.71]),
+    'cornsilk': np.array([1.00, 0.97, 0.86]),
+    'ivory': np.array([1.00, 1.00, 0.94]),
+    'lemon chiffon': np.array([1.00, 0.98, 0.80]),
+    'LemonChiffon': np.array([1.00, 0.98, 0.80]),
+    'seashell': np.array([1.00, 0.96, 0.93]),
+    'honeydew': np.array([0.94, 1.00, 0.94]),
+    'mint cream': np.array([0.96, 1.00, 0.98]),
+    'MintCream': np.array([0.96, 1.00, 0.98]),
+    'azure': np.array([0.94, 1.00, 1.00]),
+    'alice blue': np.array([0.94, 0.97, 1.00]),
+    'AliceBlue': np.array([0.94, 0.97, 1.00]),
+    'lavender': np.array([0.90, 0.90, 0.98]),
+    'lavender blush': np.array([1.00, 0.94, 0.96]),
+    'LavenderBlush': np.array([1.00, 0.94, 0.96]),
+    'misty rose': np.array([1.00, 0.89, 0.88]),
+    'MistyRose': np.array([1.00, 0.89, 0.88]),
+    'white': np.array([1.00, 1.00, 1.00]),
+    'black': np.array([0.00, 0.00, 0.00]),
+    'dark slate gray': np.array([0.18, 0.31, 0.31]),
+    'DarkSlateGray': np.array([0.18, 0.31, 0.31]),
+    'dark slate grey': np.array([0.18, 0.31, 0.31]),
+    'DarkSlateGrey': np.array([0.18, 0.31, 0.31]),
+    'dim gray': np.array([0.41, 0.41, 0.41]),
+    'DimGray': np.array([0.41, 0.41, 0.41]),
+    'dim grey': np.array([0.41, 0.41, 0.41]),
+    'DimGrey': np.array([0.41, 0.41, 0.41]),
+    'slate gray': np.array([0.44, 0.50, 0.56]),
+    'SlateGray': np.array([0.44, 0.50, 0.56]),
+    'slate grey': np.array([0.44, 0.50, 0.56]),
+    'SlateGrey': np.array([0.44, 0.50, 0.56]),
+    'light slate gray': np.array([0.47, 0.53, 0.60]),
+    'LightSlateGray': np.array([0.47, 0.53, 0.60]),
+    'light slate grey': np.array([0.47, 0.53, 0.60]),
+    'LightSlateGrey': np.array([0.47, 0.53, 0.60]),
+    'gray': np.array([0.75, 0.75, 0.75]),
+    'grey': np.array([0.75, 0.75, 0.75]),
+    'light grey': np.array([0.83, 0.83, 0.83]),
+    'LightGrey': np.array([0.83, 0.83, 0.83]),
+    'light gray': np.array([0.83, 0.83, 0.83]),
+    'LightGray': np.array([0.83, 0.83, 0.83]),
+    'midnight blue': np.array([0.10, 0.10, 0.44]),
+    'MidnightBlue': np.array([0.10, 0.10, 0.44]),
+    'navy': np.array([0.00, 0.00, 0.50]),
+    'navy blue': np.array([0.00, 0.00, 0.50]),
+    'NavyBlue': np.array([0.00, 0.00, 0.50]),
+    'cornflower blue': np.array([0.39, 0.58, 0.93]),
+    'CornflowerBlue': np.array([0.39, 0.58, 0.93]),
+    'dark slate blue': np.array([0.28, 0.24, 0.55]),
+    'DarkSlateBlue': np.array([0.28, 0.24, 0.55]),
+    'slate blue': np.array([0.42, 0.35, 0.80]),
+    'SlateBlue': np.array([0.42, 0.35, 0.80]),
+    'medium slate blue': np.array([0.48, 0.41, 0.93]),
+    'MediumSlateBlue': np.array([0.48, 0.41, 0.93]),
+    'light slate blue': np.array([0.52, 0.44, 1.00]),
+    'LightSlateBlue': np.array([0.52, 0.44, 1.00]),
+    'medium blue': np.array([0.00, 0.00, 0.80]),
+    'MediumBlue': np.array([0.00, 0.00, 0.80]),
+    'royal blue': np.array([0.25, 0.41, 0.88]),
+    'RoyalBlue': np.array([0.25, 0.41, 0.88]),
+    'blue': np.array([0.00, 0.00, 1.00]),
+    'dodger blue': np.array([0.12, 0.56, 1.00]),
+    'DodgerBlue': np.array([0.12, 0.56, 1.00]),
+    'deep sky blue': np.array([0.00, 0.75, 1.00]),
+    'DeepSkyBlue': np.array([0.00, 0.75, 1.00]),
+    'sky blue': np.array([0.53, 0.81, 0.92]),
+    'SkyBlue': np.array([0.53, 0.81, 0.92]),
+    'light sky blue': np.array([0.53, 0.81, 0.98]),
+    'LightSkyBlue': np.array([0.53, 0.81, 0.98]),
+    'steel blue': np.array([0.27, 0.51, 0.71]),
+    'SteelBlue': np.array([0.27, 0.51, 0.71]),
+    'light steel blue': np.array([0.69, 0.77, 0.87]),
+    'LightSteelBlue': np.array([0.69, 0.77, 0.87]),
+    'light blue': np.array([0.68, 0.85, 0.90]),
+    'LightBlue': np.array([0.68, 0.85, 0.90]),
+    'powder blue': np.array([0.69, 0.88, 0.90]),
+    'PowderBlue': np.array([0.69, 0.88, 0.90]),
+    'pale turquoise': np.array([0.69, 0.93, 0.93]),
+    'PaleTurquoise': np.array([0.69, 0.93, 0.93]),
+    'dark turquoise': np.array([0.00, 0.81, 0.82]),
+    'DarkTurquoise': np.array([0.00, 0.81, 0.82]),
+    'medium turquoise': np.array([0.28, 0.82, 0.80]),
+    'MediumTurquoise': np.array([0.28, 0.82, 0.80]),
+    'turquoise': np.array([0.25, 0.88, 0.82]),
+    'cyan': np.array([0.00, 1.00, 1.00]),
+    'light cyan': np.array([0.88, 1.00, 1.00]),
+    'LightCyan': np.array([0.88, 1.00, 1.00]),
+    'cadet blue': np.array([0.37, 0.62, 0.63]),
+    'CadetBlue': np.array([0.37, 0.62, 0.63]),
+    'medium aquamarine': np.array([0.40, 0.80, 0.67]),
+    'MediumAquamarine': np.array([0.40, 0.80, 0.67]),
+    'aquamarine': np.array([0.50, 1.00, 0.83]),
+    'dark green': np.array([0.00, 0.39, 0.00]),
+    'DarkGreen': np.array([0.00, 0.39, 0.00]),
+    'dark olive green': np.array([0.33, 0.42, 0.18]),
+    'DarkOliveGreen': np.array([0.33, 0.42, 0.18]),
+    'dark sea green': np.array([0.56, 0.74, 0.56]),
+    'DarkSeaGreen': np.array([0.56, 0.74, 0.56]),
+    'sea green': np.array([0.18, 0.55, 0.34]),
+    'SeaGreen': np.array([0.18, 0.55, 0.34]),
+    'medium sea green': np.array([0.24, 0.70, 0.44]),
+    'MediumSeaGreen': np.array([0.24, 0.70, 0.44]),
+    'light sea green': np.array([0.13, 0.70, 0.67]),
+    'LightSeaGreen': np.array([0.13, 0.70, 0.67]),
+    'pale green': np.array([0.60, 0.98, 0.60]),
+    'PaleGreen': np.array([0.60, 0.98, 0.60]),
+    'spring green': np.array([0.00, 1.00, 0.50]),
+    'SpringGreen': np.array([0.00, 1.00, 0.50]),
+    'lawn green': np.array([0.49, 0.99, 0.00]),
+    'LawnGreen': np.array([0.49, 0.99, 0.00]),
+    'green': np.array([0.00, 1.00, 0.00]),
+    'chartreuse': np.array([0.50, 1.00, 0.00]),
+    'medium spring green': np.array([0.00, 0.98, 0.60]),
+    'MediumSpringGreen': np.array([0.00, 0.98, 0.60]),
+    'green yellow': np.array([0.68, 1.00, 0.18]),
+    'GreenYellow': np.array([0.68, 1.00, 0.18]),
+    'lime green': np.array([0.20, 0.80, 0.20]),
+    'LimeGreen': np.array([0.20, 0.80, 0.20]),
+    'yellow green': np.array([0.60, 0.80, 0.20]),
+    'YellowGreen': np.array([0.60, 0.80, 0.20]),
+    'forest green': np.array([0.13, 0.55, 0.13]),
+    'ForestGreen': np.array([0.13, 0.55, 0.13]),
+    'olive drab': np.array([0.42, 0.56, 0.14]),
+    'OliveDrab': np.array([0.42, 0.56, 0.14]),
+    'dark khaki': np.array([0.74, 0.72, 0.42]),
+    'DarkKhaki': np.array([0.74, 0.72, 0.42]),
+    'khaki': np.array([0.94, 0.90, 0.55]),
+    'pale goldenrod': np.array([0.93, 0.91, 0.67]),
+    'PaleGoldenrod': np.array([0.93, 0.91, 0.67]),
+    'light goldenrod yellow': np.array([0.98, 0.98, 0.82]),
+    'LightGoldenrodYellow': np.array([0.98, 0.98, 0.82]),
+    'light yellow': np.array([1.00, 1.00, 0.88]),
+    'LightYellow': np.array([1.00, 1.00, 0.88]),
+    'yellow': np.array([1.00, 1.00, 0.00]),
+    'gold': np.array([1.00, 0.84, 0.00]),
+    'light goldenrod': np.array([0.93, 0.87, 0.51]),
+    'LightGoldenrod': np.array([0.93, 0.87, 0.51]),
+    'goldenrod': np.array([0.85, 0.65, 0.13]),
+    'dark goldenrod': np.array([0.72, 0.53, 0.04]),
+    'DarkGoldenrod': np.array([0.72, 0.53, 0.04]),
+    'rosy brown': np.array([0.74, 0.56, 0.56]),
+    'RosyBrown': np.array([0.74, 0.56, 0.56]),
+    'indian red': np.array([0.80, 0.36, 0.36]),
+    'IndianRed': np.array([0.80, 0.36, 0.36]),
+    'saddle brown': np.array([0.55, 0.27, 0.07]),
+    'SaddleBrown': np.array([0.55, 0.27, 0.07]),
+    'sienna': np.array([0.63, 0.32, 0.18]),
+    'peru': np.array([0.80, 0.52, 0.25]),
+    'burlywood': np.array([0.87, 0.72, 0.53]),
+    'beige': np.array([0.96, 0.96, 0.86]),
+    'wheat': np.array([0.96, 0.87, 0.70]),
+    'sandy brown': np.array([0.96, 0.64, 0.38]),
+    'SandyBrown': np.array([0.96, 0.64, 0.38]),
+    'tan': np.array([0.82, 0.71, 0.55]),
+    'chocolate': np.array([0.82, 0.41, 0.12]),
+    'firebrick': np.array([0.70, 0.13, 0.13]),
+    'brown': np.array([0.65, 0.16, 0.16]),
+    'dark salmon': np.array([0.91, 0.59, 0.48]),
+    'DarkSalmon': np.array([0.91, 0.59, 0.48]),
+    'salmon': np.array([0.98, 0.50, 0.45]),
+    'light salmon': np.array([1.00, 0.63, 0.48]),
+    'LightSalmon': np.array([1.00, 0.63, 0.48]),
+    'orange': np.array([1.00, 0.65, 0.00]),
+    'dark orange': np.array([1.00, 0.55, 0.00]),
+    'DarkOrange': np.array([1.00, 0.55, 0.00]),
+    'coral': np.array([1.00, 0.50, 0.31]),
+    'light coral': np.array([0.94, 0.50, 0.50]),
+    'LightCoral': np.array([0.94, 0.50, 0.50]),
+    'tomato': np.array([1.00, 0.39, 0.28]),
+    'orange red': np.array([1.00, 0.27, 0.00]),
+    'OrangeRed': np.array([1.00, 0.27, 0.00]),
+    'red': np.array([1.00, 0.00, 0.00]),
+    'hot pink': np.array([1.00, 0.41, 0.71]),
+    'HotPink': np.array([1.00, 0.41, 0.71]),
+    'deep pink': np.array([1.00, 0.08, 0.58]),
+    'DeepPink': np.array([1.00, 0.08, 0.58]),
+    'pink': np.array([1.00, 0.75, 0.80]),
+    'light pink': np.array([1.00, 0.71, 0.76]),
+    'LightPink': np.array([1.00, 0.71, 0.76]),
+    'pale violet red': np.array([0.86, 0.44, 0.58]),
+    'PaleVioletRed': np.array([0.86, 0.44, 0.58]),
+    'maroon': np.array([0.69, 0.19, 0.38]),
+    'medium violet red': np.array([0.78, 0.08, 0.52]),
+    'MediumVioletRed': np.array([0.78, 0.08, 0.52]),
+    'violet red': np.array([0.82, 0.13, 0.56]),
+    'VioletRed': np.array([0.82, 0.13, 0.56]),
+    'magenta': np.array([1.00, 0.00, 1.00]),
+    'violet': np.array([0.93, 0.51, 0.93]),
+    'plum': np.array([0.87, 0.63, 0.87]),
+    'orchid': np.array([0.85, 0.44, 0.84]),
+    'medium orchid': np.array([0.73, 0.33, 0.83]),
+    'MediumOrchid': np.array([0.73, 0.33, 0.83]),
+    'dark orchid': np.array([0.60, 0.20, 0.80]),
+    'DarkOrchid': np.array([0.60, 0.20, 0.80]),
+    'dark violet': np.array([0.58, 0.00, 0.83]),
+    'DarkViolet': np.array([0.58, 0.00, 0.83]),
+    'blue violet': np.array([0.54, 0.17, 0.89]),
+    'BlueViolet': np.array([0.54, 0.17, 0.89]),
+    'purple': np.array([0.63, 0.13, 0.94]),
+    'medium purple': np.array([0.58, 0.44, 0.86]),
+    'MediumPurple': np.array([0.58, 0.44, 0.86]),
+    'thistle': np.array([0.85, 0.75, 0.85]),
+    'snow1': np.array([1.00, 0.98, 0.98]),
+    'snow2': np.array([0.93, 0.91, 0.91]),
+    'snow3': np.array([0.80, 0.79, 0.79]),
+    'snow4': np.array([0.55, 0.54, 0.54]),
+    'seashell1': np.array([1.00, 0.96, 0.93]),
+    'seashell2': np.array([0.93, 0.90, 0.87]),
+    'seashell3': np.array([0.80, 0.77, 0.75]),
+    'seashell4': np.array([0.55, 0.53, 0.51]),
+    'AntiqueWhite1': np.array([1.00, 0.94, 0.86]),
+    'AntiqueWhite2': np.array([0.93, 0.87, 0.80]),
+    'AntiqueWhite3': np.array([0.80, 0.75, 0.69]),
+    'AntiqueWhite4': np.array([0.55, 0.51, 0.47]),
+    'bisque1': np.array([1.00, 0.89, 0.77]),
+    'bisque2': np.array([0.93, 0.84, 0.72]),
+    'bisque3': np.array([0.80, 0.72, 0.62]),
+    'bisque4': np.array([0.55, 0.49, 0.42]),
+    'PeachPuff1': np.array([1.00, 0.85, 0.73]),
+    'PeachPuff2': np.array([0.93, 0.80, 0.68]),
+    'PeachPuff3': np.array([0.80, 0.69, 0.58]),
+    'PeachPuff4': np.array([0.55, 0.47, 0.40]),
+    'NavajoWhite1': np.array([1.00, 0.87, 0.68]),
+    'NavajoWhite2': np.array([0.93, 0.81, 0.63]),
+    'NavajoWhite3': np.array([0.80, 0.70, 0.55]),
+    'NavajoWhite4': np.array([0.55, 0.47, 0.37]),
+    'LemonChiffon1': np.array([1.00, 0.98, 0.80]),
+    'LemonChiffon2': np.array([0.93, 0.91, 0.75]),
+    'LemonChiffon3': np.array([0.80, 0.79, 0.65]),
+    'LemonChiffon4': np.array([0.55, 0.54, 0.44]),
+    'cornsilk1': np.array([1.00, 0.97, 0.86]),
+    'cornsilk2': np.array([0.93, 0.91, 0.80]),
+    'cornsilk3': np.array([0.80, 0.78, 0.69]),
+    'cornsilk4': np.array([0.55, 0.53, 0.47]),
+    'ivory1': np.array([1.00, 1.00, 0.94]),
+    'ivory2': np.array([0.93, 0.93, 0.88]),
+    'ivory3': np.array([0.80, 0.80, 0.76]),
+    'ivory4': np.array([0.55, 0.55, 0.51]),
+    'honeydew1': np.array([0.94, 1.00, 0.94]),
+    'honeydew2': np.array([0.88, 0.93, 0.88]),
+    'honeydew3': np.array([0.76, 0.80, 0.76]),
+    'honeydew4': np.array([0.51, 0.55, 0.51]),
+    'LavenderBlush1': np.array([1.00, 0.94, 0.96]),
+    'LavenderBlush2': np.array([0.93, 0.88, 0.90]),
+    'LavenderBlush3': np.array([0.80, 0.76, 0.77]),
+    'LavenderBlush4': np.array([0.55, 0.51, 0.53]),
+    'MistyRose1': np.array([1.00, 0.89, 0.88]),
+    'MistyRose2': np.array([0.93, 0.84, 0.82]),
+    'MistyRose3': np.array([0.80, 0.72, 0.71]),
+    'MistyRose4': np.array([0.55, 0.49, 0.48]),
+    'azure1': np.array([0.94, 1.00, 1.00]),
+    'azure2': np.array([0.88, 0.93, 0.93]),
+    'azure3': np.array([0.76, 0.80, 0.80]),
+    'azure4': np.array([0.51, 0.55, 0.55]),
+    'SlateBlue1': np.array([0.51, 0.44, 1.00]),
+    'SlateBlue2': np.array([0.48, 0.40, 0.93]),
+    'SlateBlue3': np.array([0.41, 0.35, 0.80]),
+    'SlateBlue4': np.array([0.28, 0.24, 0.55]),
+    'RoyalBlue1': np.array([0.28, 0.46, 1.00]),
+    'RoyalBlue2': np.array([0.26, 0.43, 0.93]),
+    'RoyalBlue3': np.array([0.23, 0.37, 0.80]),
+    'RoyalBlue4': np.array([0.15, 0.25, 0.55]),
+    'blue1': np.array([0.00, 0.00, 1.00]),
+    'blue2': np.array([0.00, 0.00, 0.93]),
+    'blue3': np.array([0.00, 0.00, 0.80]),
+    'blue4': np.array([0.00, 0.00, 0.55]),
+    'DodgerBlue1': np.array([0.12, 0.56, 1.00]),
+    'DodgerBlue2': np.array([0.11, 0.53, 0.93]),
+    'DodgerBlue3': np.array([0.09, 0.45, 0.80]),
+    'DodgerBlue4': np.array([0.06, 0.31, 0.55]),
+    'SteelBlue1': np.array([0.39, 0.72, 1.00]),
+    'SteelBlue2': np.array([0.36, 0.67, 0.93]),
+    'SteelBlue3': np.array([0.31, 0.58, 0.80]),
+    'SteelBlue4': np.array([0.21, 0.39, 0.55]),
+    'DeepSkyBlue1': np.array([0.00, 0.75, 1.00]),
+    'DeepSkyBlue2': np.array([0.00, 0.70, 0.93]),
+    'DeepSkyBlue3': np.array([0.00, 0.60, 0.80]),
+    'DeepSkyBlue4': np.array([0.00, 0.41, 0.55]),
+    'SkyBlue1': np.array([0.53, 0.81, 1.00]),
+    'SkyBlue2': np.array([0.49, 0.75, 0.93]),
+    'SkyBlue3': np.array([0.42, 0.65, 0.80]),
+    'SkyBlue4': np.array([0.29, 0.44, 0.55]),
+    'LightSkyBlue1': np.array([0.69, 0.89, 1.00]),
+    'LightSkyBlue2': np.array([0.64, 0.83, 0.93]),
+    'LightSkyBlue3': np.array([0.55, 0.71, 0.80]),
+    'LightSkyBlue4': np.array([0.38, 0.48, 0.55]),
+    'SlateGray1': np.array([0.78, 0.89, 1.00]),
+    'SlateGray2': np.array([0.73, 0.83, 0.93]),
+    'SlateGray3': np.array([0.62, 0.71, 0.80]),
+    'SlateGray4': np.array([0.42, 0.48, 0.55]),
+    'LightSteelBlue1': np.array([0.79, 0.88, 1.00]),
+    'LightSteelBlue2': np.array([0.74, 0.82, 0.93]),
+    'LightSteelBlue3': np.array([0.64, 0.71, 0.80]),
+    'LightSteelBlue4': np.array([0.43, 0.48, 0.55]),
+    'LightBlue1': np.array([0.75, 0.94, 1.00]),
+    'LightBlue2': np.array([0.70, 0.87, 0.93]),
+    'LightBlue3': np.array([0.60, 0.75, 0.80]),
+    'LightBlue4': np.array([0.41, 0.51, 0.55]),
+    'LightCyan1': np.array([0.88, 1.00, 1.00]),
+    'LightCyan2': np.array([0.82, 0.93, 0.93]),
+    'LightCyan3': np.array([0.71, 0.80, 0.80]),
+    'LightCyan4': np.array([0.48, 0.55, 0.55]),
+    'PaleTurquoise1': np.array([0.73, 1.00, 1.00]),
+    'PaleTurquoise2': np.array([0.68, 0.93, 0.93]),
+    'PaleTurquoise3': np.array([0.59, 0.80, 0.80]),
+    'PaleTurquoise4': np.array([0.40, 0.55, 0.55]),
+    'CadetBlue1': np.array([0.60, 0.96, 1.00]),
+    'CadetBlue2': np.array([0.56, 0.90, 0.93]),
+    'CadetBlue3': np.array([0.48, 0.77, 0.80]),
+    'CadetBlue4': np.array([0.33, 0.53, 0.55]),
+    'turquoise1': np.array([0.00, 0.96, 1.00]),
+    'turquoise2': np.array([0.00, 0.90, 0.93]),
+    'turquoise3': np.array([0.00, 0.77, 0.80]),
+    'turquoise4': np.array([0.00, 0.53, 0.55]),
+    'cyan1': np.array([0.00, 1.00, 1.00]),
+    'cyan2': np.array([0.00, 0.93, 0.93]),
+    'cyan3': np.array([0.00, 0.80, 0.80]),
+    'cyan4': np.array([0.00, 0.55, 0.55]),
+    'DarkSlateGray1': np.array([0.59, 1.00, 1.00]),
+    'DarkSlateGray2': np.array([0.55, 0.93, 0.93]),
+    'DarkSlateGray3': np.array([0.47, 0.80, 0.80]),
+    'DarkSlateGray4': np.array([0.32, 0.55, 0.55]),
+    'aquamarine1': np.array([0.50, 1.00, 0.83]),
+    'aquamarine2': np.array([0.46, 0.93, 0.78]),
+    'aquamarine3': np.array([0.40, 0.80, 0.67]),
+    'aquamarine4': np.array([0.27, 0.55, 0.45]),
+    'DarkSeaGreen1': np.array([0.76, 1.00, 0.76]),
+    'DarkSeaGreen2': np.array([0.71, 0.93, 0.71]),
+    'DarkSeaGreen3': np.array([0.61, 0.80, 0.61]),
+    'DarkSeaGreen4': np.array([0.41, 0.55, 0.41]),
+    'SeaGreen1': np.array([0.33, 1.00, 0.62]),
+    'SeaGreen2': np.array([0.31, 0.93, 0.58]),
+    'SeaGreen3': np.array([0.26, 0.80, 0.50]),
+    'SeaGreen4': np.array([0.18, 0.55, 0.34]),
+    'PaleGreen1': np.array([0.60, 1.00, 0.60]),
+    'PaleGreen2': np.array([0.56, 0.93, 0.56]),
+    'PaleGreen3': np.array([0.49, 0.80, 0.49]),
+    'PaleGreen4': np.array([0.33, 0.55, 0.33]),
+    'SpringGreen1': np.array([0.00, 1.00, 0.50]),
+    'SpringGreen2': np.array([0.00, 0.93, 0.46]),
+    'SpringGreen3': np.array([0.00, 0.80, 0.40]),
+    'SpringGreen4': np.array([0.00, 0.55, 0.27]),
+    'green1': np.array([0.00, 1.00, 0.00]),
+    'green2': np.array([0.00, 0.93, 0.00]),
+    'green3': np.array([0.00, 0.80, 0.00]),
+    'green4': np.array([0.00, 0.55, 0.00]),
+    'chartreuse1': np.array([0.50, 1.00, 0.00]),
+    'chartreuse2': np.array([0.46, 0.93, 0.00]),
+    'chartreuse3': np.array([0.40, 0.80, 0.00]),
+    'chartreuse4': np.array([0.27, 0.55, 0.00]),
+    'OliveDrab1': np.array([0.75, 1.00, 0.24]),
+    'OliveDrab2': np.array([0.70, 0.93, 0.23]),
+    'OliveDrab3': np.array([0.60, 0.80, 0.20]),
+    'OliveDrab4': np.array([0.41, 0.55, 0.13]),
+    'DarkOliveGreen1': np.array([0.79, 1.00, 0.44]),
+    'DarkOliveGreen2': np.array([0.74, 0.93, 0.41]),
+    'DarkOliveGreen3': np.array([0.64, 0.80, 0.35]),
+    'DarkOliveGreen4': np.array([0.43, 0.55, 0.24]),
+    'khaki1': np.array([1.00, 0.96, 0.56]),
+    'khaki2': np.array([0.93, 0.90, 0.52]),
+    'khaki3': np.array([0.80, 0.78, 0.45]),
+    'khaki4': np.array([0.55, 0.53, 0.31]),
+    'LightGoldenrod1': np.array([1.00, 0.93, 0.55]),
+    'LightGoldenrod2': np.array([0.93, 0.86, 0.51]),
+    'LightGoldenrod3': np.array([0.80, 0.75, 0.44]),
+    'LightGoldenrod4': np.array([0.55, 0.51, 0.30]),
+    'LightYellow1': np.array([1.00, 1.00, 0.88]),
+    'LightYellow2': np.array([0.93, 0.93, 0.82]),
+    'LightYellow3': np.array([0.80, 0.80, 0.71]),
+    'LightYellow4': np.array([0.55, 0.55, 0.48]),
+    'yellow1': np.array([1.00, 1.00, 0.00]),
+    'yellow2': np.array([0.93, 0.93, 0.00]),
+    'yellow3': np.array([0.80, 0.80, 0.00]),
+    'yellow4': np.array([0.55, 0.55, 0.00]),
+    'gold1': np.array([1.00, 0.84, 0.00]),
+    'gold2': np.array([0.93, 0.79, 0.00]),
+    'gold3': np.array([0.80, 0.68, 0.00]),
+    'gold4': np.array([0.55, 0.46, 0.00]),
+    'goldenrod1': np.array([1.00, 0.76, 0.15]),
+    'goldenrod2': np.array([0.93, 0.71, 0.13]),
+    'goldenrod3': np.array([0.80, 0.61, 0.11]),
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+    'gray98': np.array([0.98, 0.98, 0.98]),
+    'grey98': np.array([0.98, 0.98, 0.98]),
+    'gray99': np.array([0.99, 0.99, 0.99]),
+    'grey99': np.array([0.99, 0.99, 0.99]),
+    'gray100': np.array([1.00, 1.00, 1.00]),
+    'grey100': np.array([1.00, 1.00, 1.00]),
+    'dark grey': np.array([0.66, 0.66, 0.66]),
+    'DarkGrey': np.array([0.66, 0.66, 0.66]),
+    'dark gray': np.array([0.66, 0.66, 0.66]),
+    'DarkGray': np.array([0.66, 0.66, 0.66]),
+    'dark blue': np.array([0.00, 0.00, 0.55]),
+    'DarkBlue': np.array([0.00, 0.00, 0.55]),
+    'dark cyan': np.array([0.00, 0.55, 0.55]),
+    'DarkCyan': np.array([0.00, 0.55, 0.55]),
+    'dark magenta': np.array([0.55, 0.00, 0.55]),
+    'DarkMagenta': np.array([0.55, 0.00, 0.55]),
+    'dark red': np.array([0.55, 0.00, 0.00]),
+    'DarkRed': np.array([0.55, 0.00, 0.00]),
+    'light green': np.array([0.56, 0.93, 0.56]),
+    'LightGreen': np.array([0.56, 0.93, 0.56])
+}
+
+
+if __name__ == '__main__':
+    main()

mesh-fix-MSVC_compilation/mesh/errors.py

@@ -0,0 +1,15 @@
+# Copyright (c) 2017 Max Planck Society. All rights reserved.
+
+"""
+Error heirarchy for Mesh class
+"""
+
+
+class MeshError(Exception):
+    """Base error class for Mesh-related errors"""
+    pass
+
+
+class SerializationError(MeshError):
+    """Mesh reading or writing errors"""
+    pass

mesh-fix-MSVC_compilation/mesh/fonts.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+# encoding: utf-8
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+
+import os
+import numpy as np
+from OpenGL.GL import glPixelStorei, \
+    glGenTextures, \
+    glBindTexture, \
+    glGenerateMipmap, \
+    glHint, \
+    glTexImage2D
+from OpenGL.GL import GL_UNPACK_ALIGNMENT, \
+    GL_TEXTURE_2D, \
+    GL_RGB, \
+    GL_BGR, \
+    GL_GENERATE_MIPMAP_HINT, \
+    GL_NICEST, \
+    GL_UNSIGNED_BYTE
+
+
+def get_image_with_text(text, fgcolor, bgcolor):
+    if not hasattr(get_image_with_text, 'cache'):
+        get_image_with_text.cache = {}
+
+    import zlib
+    uid = str(zlib.crc32(text)) + str(zlib.crc32(np.array(fgcolor))) + str(zlib.crc32(np.array(bgcolor)))
+    if uid not in get_image_with_text.cache:
+        from PIL import ImageFont
+        from PIL import Image
+        from PIL import ImageDraw
+
+        font = ImageFont.truetype("/Library/Fonts/Courier New.ttf", 30)
+
+        imsize = (256, 256)
+
+        bgarray = np.asarray(np.zeros((imsize[0], imsize[1], 3)), np.uint8)
+        bgarray[:, :, 0] += bgcolor[0]
+        bgarray[:, :, 1] += bgcolor[1]
+        bgarray[:, :, 2] += bgcolor[2]
+        img = Image.fromarray(bgarray)
+        draw = ImageDraw.Draw(img)
+        w, h = draw.textsize(text, font=font)
+        text_pos = ((imsize[0] - w) / 2, (imsize[1] - h) / 2)
+        draw.text(text_pos, text, fill=fgcolor, font=font)
+        get_image_with_text.cache[uid] = np.array(img.getdata()).reshape(img.size[0], img.size[1], 3) * 255
+    return get_image_with_text.cache[uid]
+
+
+def get_textureid_with_text(text, fgcolor, bgcolor):
+    if not hasattr(get_textureid_with_text, 'cache'):
+        get_textureid_with_text.cache = {}
+
+    import zlib
+    uid = str(zlib.crc32(text)) + str(zlib.crc32(np.array(fgcolor))) + str(zlib.crc32(np.array(bgcolor)))
+    if uid not in get_textureid_with_text.cache:
+        from PIL import ImageFont
+        from PIL import Image
+        from PIL import ImageDraw
+
+        font = ImageFont.truetype(os.path.join(os.path.dirname(__file__),
+                                               "ressources",
+                                               "Arial.ttf"),
+                                  100)
+
+        imsize = (128, 128)
+
+        bgarray = np.asarray(np.zeros((imsize[0], imsize[1], 3)), np.uint8)
+        bgarray[:, :, 0] += bgcolor[0]
+        bgarray[:, :, 1] += bgcolor[1]
+        bgarray[:, :, 2] += bgcolor[2]
+        img = Image.fromarray(bgarray)
+        draw = ImageDraw.Draw(img)
+        w, h = draw.textsize(text, font=font)
+        text_pos = ((imsize[0] - w) / 2, (imsize[1] - h) / 2)
+        draw.text(text_pos, text, fill=tuple(np.asarray(fgcolor, np.uint8)), font=font)
+        texture_data = np.asarray(np.array(img.getdata()).reshape(img.size[0], img.size[1], 3) * 255, np.uint8)
+
+        textureID = glGenTextures(1)
+        glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
+        glBindTexture(GL_TEXTURE_2D, textureID)
+        glTexImage2D(GL_TEXTURE_2D, 0, GL_RGB, texture_data.shape[1], texture_data.shape[0], 0, GL_BGR, GL_UNSIGNED_BYTE, texture_data.flatten())
+        glHint(GL_GENERATE_MIPMAP_HINT, GL_NICEST)  # must be GL_FASTEST, GL_NICEST or GL_DONT_CARE
+        glGenerateMipmap(GL_TEXTURE_2D)
+        get_textureid_with_text.cache[uid] = textureID
+
+    return get_textureid_with_text.cache[uid]

mesh-fix-MSVC_compilation/mesh/geometry/__init__.py

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2016 Max Planck Society. All rights reserved.

mesh-fix-MSVC_compilation/mesh/geometry/barycentric_coordinates_of_projection.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+
+from numpy import cross, sum, isscalar, spacing, vstack
+
+
+def barycentric_coordinates_of_projection(p, q, u, v):
+    """Given a point, gives projected coords of that point to a triangle
+    in barycentric coordinates.
+
+    See
+
+        **Heidrich**, Computing the Barycentric Coordinates of a Projected Point, JGT 05
+        at http://www.cs.ubc.ca/~heidrich/Papers/JGT.05.pdf
+
+    :param p: point to project
+    :param q: a vertex of the triangle to project into
+    :param u,v: edges of the the triangle such that it has vertices ``q``, ``q+u``, ``q+v``
+
+    :returns: barycentric coordinates of ``p``'s projection in triangle defined by ``q``, ``u``, ``v``
+            vectorized so ``p``, ``q``, ``u``, ``v`` can all be ``3xN``
+    """
+
+    p = p.T
+    q = q.T
+    u = u.T
+    v = v.T
+
+    n = cross(u, v, axis=0)
+    s = sum(n * n, axis=0)
+
+    # If the triangle edges are collinear, cross-product is zero,
+    # which makes "s" 0, which gives us divide by zero. So we
+    # make the arbitrary choice to set s to epsv (=numpy.spacing(1)),
+    # the closest thing to zero
+    if isscalar(s):
+        s = s if s else spacing(1)
+    else:
+        s[s == 0] = spacing(1)
+
+    oneOver4ASquared = 1.0 / s
+    w = p - q
+    b2 = sum(cross(u, w, axis=0) * n, axis=0) * oneOver4ASquared
+    b1 = sum(cross(w, v, axis=0) * n, axis=0) * oneOver4ASquared
+    b = vstack((1 - b1 - b2, b1, b2))
+
+    return b.T

mesh-fix-MSVC_compilation/mesh/geometry/cross_product.py

@@ -0,0 +1,37 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2012-07-20.
+
+import numpy as np
+
+
+def CrossProduct(a, b):
+    """Computes the cross product of 2 vectors"""
+    a = a.reshape(-1, 3)
+    b = b.reshape(-1, 3)
+
+    a1 = a[:, 0]
+    a2 = a[:, 1]
+    a3 = a[:, 2]
+
+    Ax = np.zeros((len(a1), 3, 3))
+    Ax[:, 0, 1] = -a3
+    Ax[:, 0, 2] = +a2
+    Ax[:, 1, 0] = +a3
+    Ax[:, 1, 2] = -a1
+    Ax[:, 2, 0] = -a2
+    Ax[:, 2, 1] = +a1
+
+    return _call_einsum_matvec(Ax, b)
+
+
+def _call_einsum_matvec(m, righthand):
+    r = righthand.reshape(m.shape[0], 3)
+    return np.einsum('ijk,ik->ij', m, r).flatten()
+
+
+def _call_einsum_matmat(m, righthand):
+    r = righthand.reshape(m.shape[0], 3, -1)
+    return np.einsum('ijk,ikm->ijm', m, r).reshape(-1, r.shape[2])

mesh-fix-MSVC_compilation/mesh/geometry/rodrigues.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2012-07-22.
+
+import numpy as np
+
+
+def rodrigues(r, calculate_jacobian=True):
+    """Computes the Rodrigues transform and its derivative
+
+    :param r: either a 3-vector representing the rotation parameter, or a full rotation matrix
+    :param calculate_jacobian: indicates if the Jacobian of the transform is also required
+    :returns: If `calculate_jacobian` is `True`, the Jacobian is given as the second element of the returned tuple.
+    """
+
+    r = np.array(r, dtype=np.double)
+    eps = np.finfo(np.double).eps
+
+    if np.all(r.shape == (3, 1)) or np.all(r.shape == (1, 3)) or np.all(r.shape == (3,)):
+        r = r.flatten()
+        theta = np.linalg.norm(r)
+        if theta < eps:
+            r_out = np.eye(3)
+            if calculate_jacobian:
+                jac = np.zeros((3, 9))
+                jac[0, 5] = jac[1, 6] = jac[2, 1] = -1
+                jac[0, 7] = jac[1, 2] = jac[2, 3] = 1
+
+        else:
+            c = np.cos(theta)
+            s = np.sin(theta)
+            c1 = 1. - c
+            itheta = 1.0 if theta == 0.0 else 1.0 / theta
+            r *= itheta
+            I = np.eye(3)
+            rrt = np.array([r * r[0], r * r[1], r * r[2]])
+            _r_x_ = np.array([[0, -r[2], r[1]], [r[2], 0, -r[0]], [-r[1], r[0], 0]])
+            r_out = c * I + c1 * rrt + s * _r_x_
+            if calculate_jacobian:
+                drrt = np.array([[r[0] + r[0], r[1], r[2], r[1], 0, 0, r[2], 0, 0],
+                                 [0, r[0], 0, r[0], r[1] + r[1], r[2], 0, r[2], 0],
+                                 [0, 0, r[0], 0, 0, r[1], r[0], r[1], r[2] + r[2]]])
+                d_r_x_ = np.array([[0, 0, 0, 0, 0, -1, 0, 1, 0],
+                                   [0, 0, 1, 0, 0, 0, -1, 0, 0],
+                                   [0, -1, 0, 1, 0, 0, 0, 0, 0]])
+                I = np.array([I.flatten(), I.flatten(), I.flatten()])
+                ri = np.array([[r[0]], [r[1]], [r[2]]])
+                a0 = -s * ri
+                a1 = (s - 2 * c1 * itheta) * ri
+                a2 = np.ones((3, 1)) * c1 * itheta
+                a3 = (c - s * itheta) * ri
+                a4 = np.ones((3, 1)) * s * itheta
+                jac = a0 * I + a1 * rrt.flatten() + a2 * drrt + a3 * _r_x_.flatten() + a4 * d_r_x_
+    elif np.all(r.shape == (3, 3)):
+        u, d, v = np.linalg.svd(r)
+        r = np.dot(u, v)
+        rx = r[2, 1] - r[1, 2]
+        ry = r[0, 2] - r[2, 0]
+        rz = r[1, 0] - r[0, 1]
+        s = np.linalg.norm(np.array([rx, ry, rz])) * np.sqrt(0.25)
+        c = np.clip((np.sum(np.diag(r)) - 1) * 0.5, -1, 1)
+        theta = np.arccos(c)
+        if s < 1e-5:
+            if c > 0:
+                r_out = np.zeros((3, 1))
+            else:
+                rx, ry, rz = np.clip(np.sqrt((np.diag(r) + 1) * 0.5), 0, np.inf)
+                if r[0, 1] < 0:
+                    ry = -ry
+                if r[0, 2] < 0:
+                    rz = -rz
+                if np.abs(rx) < np.abs(ry) and np.abs(rx) < np.abs(rz) and ((r[1, 2] > 0) != (ry * rz > 0)):
+                    rz = -rz
+
+                r_out = np.array([[rx, ry, rz]]).T
+                theta /= np.linalg.norm(r_out)
+                r_out *= theta
+            if calculate_jacobian:
+                jac = np.zeros((9, 3))
+                if c > 0:
+                    jac[1, 2] = jac[5, 0] = jac[6, 1] = -0.5
+                    jac[2, 1] = jac[3, 2] = jac[7, 0] = 0.5
+        else:
+            vth = 1.0 / (2.0 * s)
+            if calculate_jacobian:
+                dtheta_dtr = -1. / s
+                dvth_dtheta = -vth * c / s
+                d1 = 0.5 * dvth_dtheta * dtheta_dtr
+                d2 = 0.5 * dtheta_dtr
+                dvardR = np.array([
+                    [0, 0, 0, 0, 0, 1, 0, -1, 0],
+                    [0, 0, -1, 0, 0, 0, 1, 0, 0],
+                    [0, 1, 0, -1, 0, 0, 0, 0, 0],
+                    [d1, 0, 0, 0, d1, 0, 0, 0, d1],
+                    [d2, 0, 0, 0, d2, 0, 0, 0, d2]])
+                dvar2dvar = np.array([
+                    [vth, 0, 0, rx, 0],
+                    [0, vth, 0, ry, 0],
+                    [0, 0, vth, rz, 0],
+                    [0, 0, 0, 0, 1]])
+                domegadvar2 = np.array([
+                    [theta, 0, 0, rx * vth],
+                    [0, theta, 0, ry * vth],
+                    [0, 0, theta, rz * vth]])
+                jac = np.dot(np.dot(domegadvar2, dvar2dvar), dvardR)
+                for ii in range(3):
+                    jac[ii] = jac[ii].reshape((3, 3)).T.flatten()
+                jac = jac.T
+            vth *= theta
+            r_out = np.array([[rx, ry, rz]]).T * vth
+    else:
+        raise Exception("rodrigues: input matrix must be 1x3, 3x1 or 3x3.")
+    if calculate_jacobian:
+        return r_out, jac
+    else:
+        return r_out
+
+
+def rodrigues2rotmat(r):
+    # R = np.zeros((3, 3))
+    r_skew = np.array([[0, -r[2], r[1]], [r[2], 0, -r[0]], [-r[1], r[0], 0]])
+    theta = np.linalg.norm(r)
+    return np.identity(3) + np.sin(theta) * r_skew + (1 - np.cos(theta)) * r_skew.dot(r_skew)

mesh-fix-MSVC_compilation/mesh/geometry/tri_normals.py

@@ -0,0 +1,72 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2012-07-22.
+
+
+"""
+tri_normals.py
+
+"""
+
+from ..utils import col
+from .cross_product import CrossProduct
+
+import numpy as np
+
+
+def TriNormals(v, f):
+    return NormalizedNx3(TriNormalsScaled(v, f))
+
+
+def TriNormalsScaled(v, f):
+    return CrossProduct(TriEdges(v, f, 1, 0), TriEdges(v, f, 2, 0))
+
+
+def NormalizedNx3(v):
+    ss = np.sum(v.reshape(-1, 3) ** 2, axis=1)
+    ss[ss == 0] = 1
+    s = np.sqrt(ss)
+
+    return (v.reshape(-1, 3) / col(s)).flatten()
+
+
+def TriEdges(v, f, cplus, cminus):
+    assert(cplus >= 0 and cplus <= 2 and cminus >= 0 and cminus <= 2)
+    return _edges_for(v, f, cplus, cminus)
+
+
+def _edges_for(v, f, cplus, cminus):
+    return (
+        v.reshape(-1, 3)[f[:, cplus], :] -
+        v.reshape(-1, 3)[f[:, cminus], :]).ravel()
+
+
+def TriToScaledNormal(x, tri):
+
+    v = x.reshape(-1, 3)
+
+    def v_xyz(iV):
+        return v[tri[:, iV], :]
+
+    return np.cross(v_xyz(1) - v_xyz(0), v_xyz(2) - v_xyz(0))
+
+
+def _bsxfun(oper, a, b):
+    if a.shape[0] == b.shape[0] or a.shape[1] == b.shape[1]:
+        return oper(a, b)
+    elif min(a.shape) == 1 and min(b.shape) == 1:
+        if a.shape[0] == 1:
+            return oper(np.tile(a, (b.shape[0], 1)), b)
+        else:
+            return oper(np.tile(a, (1, b.shape[1], b)))
+    else:
+        raise '_bsxfun failure'
+
+
+def NormalizeRows(x):
+
+    s = (np.sqrt(np.sum(x ** 2, axis=1))).flatten()
+    s[s == 0] = 1
+    return _bsxfun(np.divide, x, col(s))

mesh-fix-MSVC_compilation/mesh/geometry/triangle_area.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+
+from .tri_normals import TriToScaledNormal
+import numpy as np
+
+
+def triangle_area(v, f):
+    """Computes the area associated to a set of triangles"""
+    return (np.sqrt(np.sum(TriToScaledNormal(v, f) ** 2, axis=1)) / 2.).flatten()

mesh-fix-MSVC_compilation/mesh/geometry/vert_normals.py

@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2013-03-12.
+
+
+import scipy.sparse as sp
+import numpy as np
+from .tri_normals import NormalizedNx3, TriNormalsScaled
+from ..utils import col
+
+
+def MatVecMult(mtx, vec):
+    return mtx.dot(col(vec)).flatten()
+
+
+def VertNormals(v, f):
+    return NormalizedNx3(VertNormalsScaled(v, f))
+
+
+def VertNormalsScaled(v, f):
+    IS = f.flatten()
+    JS = np.array([range(f.shape[0])] * 3).T.flatten()
+    data = np.ones(len(JS))
+
+    IS = np.concatenate((IS * 3, IS * 3 + 1, IS * 3 + 2))
+    JS = np.concatenate((JS * 3, JS * 3 + 1, JS * 3 + 2))  # is this right?
+    data = np.concatenate((data, data, data))
+
+    faces_by_vertex = sp.csc_matrix((data, (IS, JS)), shape=(v.size, f.size))
+
+    # faces_by_vertex should be 3 x wider...?
+    return NormalizedNx3(MatVecMult(faces_by_vertex, TriNormalsScaled(v, f)))

mesh-fix-MSVC_compilation/mesh/landmarks.py

@@ -0,0 +1,102 @@
+#!/usr/bin/env python
+# encoding: utf-8
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2013-02-20.
+
+
+import numpy as np
+
+"""
+landmarks.py
+
+"""
+
+
+def landm_xyz_linear_transform(self, ordering=None):
+    from .utils import col, sparse
+
+    landmark_order = ordering if ordering else self.landm_names
+    # construct a sparse matrix that converts between the landmark pts and all vertices, with height (# landmarks * 3) and width (# vertices * 3)
+    if hasattr(self, 'landm_regressors'):
+        landmark_coefficients = np.hstack([self.landm_regressors[name][1] for name in landmark_order])
+        landmark_indices = np.hstack([self.landm_regressors[name][0] for name in landmark_order])
+        column_indices = np.hstack([col(3 * landmark_indices + i) for i in range(3)]).flatten()
+        row_indices = np.hstack([[3 * index, 3 * index + 1, 3 * index + 2] * len(self.landm_regressors[landmark_order[index]][0]) for index in np.arange(len(landmark_order))])
+        values = np.hstack([col(landmark_coefficients) for i in range(3)]).flatten()
+        return sparse(row_indices, column_indices, values, 3 * len(landmark_order), 3 * self.v.shape[0])
+    elif hasattr(self, 'landm'):
+        landmark_indices = np.array([self.landm[name] for name in landmark_order])
+        column_indices = np.hstack(([col(3 * landmark_indices + i) for i in range(3)])).flatten()
+        row_indices = np.arange(3 * len(landmark_order))
+        return sparse(row_indices, column_indices, np.ones(len(column_indices)), 3 * len(landmark_order), 3 * self.v.shape[0])
+    else:
+        return np.zeros((0, 0))
+
+
+@property
+def landm_xyz(self, ordering=None):
+    landmark_order = ordering if ordering else self.landm_names
+    landmark_vertex_locations = (self.landm_xyz_linear_transform(landmark_order) * self.v.flatten()).reshape(-1, 3) if landmark_order else np.zeros((0, 0))
+    if landmark_order:
+        return dict([(landmark_order[i], xyz) for i, xyz in enumerate(landmark_vertex_locations)])
+    return {}
+
+
+def recompute_landmark_indices(self, landmark_fname=None, safe_mode=True):
+    filtered_landmarks = dict(
+        filter(
+            lambda e, : e[1] != [0.0, 0.0, 0.0],
+            self.landm_raw_xyz.items()
+        ) if (landmark_fname and safe_mode) else self.landm_raw_xyz.items())
+    if len(filtered_landmarks) != len(self.landm_raw_xyz):
+        print("WARNING: %d landmarks in file %s are positioned at (0.0, 0.0, 0.0) and were ignored" % (len(self.landm_raw_xyz) - len(filtered_landmarks), landmark_fname))
+
+    self.landm = {}
+    self.landm_regressors = {}
+    if filtered_landmarks:
+        landmark_names = list(filtered_landmarks.keys())
+        closest_vertices, _ = self.closest_vertices(np.array(list(filtered_landmarks.values())))
+        self.landm = dict(zip(landmark_names, closest_vertices))
+        if len(self.f):
+            face_indices, closest_points = self.closest_faces_and_points(np.array(list(filtered_landmarks.values())))
+            vertex_indices, coefficients = self.barycentric_coordinates_for_points(closest_points, face_indices)
+            self.landm_regressors = dict([(name, (vertex_indices[i], coefficients[i])) for i, name in enumerate(landmark_names)])
+        else:
+            self.landm_regressors = dict([(name, (np.array([closest_vertices[i]]), np.array([1.0]))) for i, name in enumerate(landmark_names)])
+
+
+def set_landmarks_from_xyz(self, landm_raw_xyz):
+    self.landm_raw_xyz = landm_raw_xyz if hasattr(landm_raw_xyz, 'keys') else dict((str(i), l) for i, l in enumerate(landm_raw_xyz))
+    self.recompute_landmark_indices()
+
+
+def is_vertex(x):
+    return hasattr(x, "__len__") and len(x) == 3
+
+
+def is_index(x):
+    return isinstance(x, (int, np.int32, np.int64))
+
+
+def set_landmarks_from_raw(self, landmarks):
+    '''
+    can accept:
+    {'name1': [float, float, float], 'name2': [float, float, float], ...}
+    {'name1': np.array([float, float, float]), 'name2': np.array([float, float, float]), ...}
+    [[float,float,float],[float,float,float], ...]
+    np.array([[float,float,float],[float,float,float], ...])
+    [np.array([float,float,float]),np.array([float,float,float]), ...]
+    {'name1': int, 'name2': int, ...}
+    [int,int,int]
+    np.array([int,int,int])
+    '''
+    landmarks = landmarks if hasattr(landmarks, 'keys') else dict((str(i), l) for i, l in enumerate(landmarks))
+
+    if all(is_vertex(x) for x in landmarks.values()):
+        landmarks = dict((i, np.array(l)) for i, l in landmarks.items())
+        self.set_landmarks_from_xyz(landmarks)
+    elif all(is_index(x) for x in landmarks.values()):
+        self.landm = landmarks
+        self.recompute_landmark_xyz()
+    else:
+        raise Exception("Can't parse landmarks")

mesh-fix-MSVC_compilation/mesh/lines.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+# encoding: utf-8
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+
+import numpy as np
+from . import colors
+
+
+class Lines(object):
+    """Collection of 3D lines
+
+    Attributes:
+        v: Vx3 array of vertices
+        e: Ex2 array of edges
+    """
+
+    def __init__(self, v, e, vc=None, ec=None):
+
+        self.v = np.array(v)
+        self.e = np.array(e)
+
+        if vc is not None:
+            self.set_vertex_colors(vc)
+
+        if ec is not None:
+            self.set_edge_colors(ec)
+
+    def colors_like(self, color, arr):
+        from .utils import row, col
+        if isinstance(color, str):
+            color = colors.name_to_rgb[color]
+        elif isinstance(color, list):
+            color = np.array(color)
+
+        if color.shape == (arr.shape[0],):
+            def jet(v):
+                fourValue = 4 * v
+                red = min(fourValue - 1.5, -fourValue + 4.5)
+                green = min(fourValue - 0.5, -fourValue + 3.5)
+                blue = min(fourValue + 0.5, -fourValue + 2.5)
+                result = np.array([red, green, blue])
+                result[result > 1.0] = 1.0
+                result[result < 0.0] = 0.0
+                return row(result)
+            color = col(color)
+            color = np.concatenate([jet(color[i]) for i in xrange(color.size)], axis=0)
+
+        return np.ones((arr.shape[0], 3)) * color
+
+    def set_vertex_colors(self, vc):
+        self.vc = self.colors_like(vc, self.v)
+
+    def set_edge_colors(self, ec):
+        self.ec = self.colors_like(ec, self.e)
+
+    def write_obj(self, filename):
+        with open(filename, 'w') as fi:
+            for r in self.v:
+                fi.write('v %f %f %f\n' % (r[0], r[1], r[2]))
+            for e in self.e:
+                fi.write('l %d %d\n' % (e[0] + 1, e[1] + 1))

mesh-fix-MSVC_compilation/mesh/mesh.py

@@ -0,0 +1,492 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+
+"""
+Mesh module
+-----------
+
+"""
+
+
+import os
+from functools import reduce
+
+import numpy as np
+
+from . import colors
+from . import search
+
+try:
+    from .serialization import serialization
+except ImportError:
+    pass
+
+from . import landmarks
+from . import texture
+from . import processing
+
+
+__all__ = ["Mesh"]
+
+
+class Mesh(object):
+    """3d Triangulated Mesh class
+
+    Attributes:
+        v: Vx3 array of vertices
+        f: Fx3 array of faces
+
+    Optional attributes:
+        fc: Fx3 array of face colors
+        vc: Vx3 array of vertex colors
+        vn: Vx3 array of vertex normals
+        segm: dictionary of part names to triangle indices
+
+    """
+    def __init__(self,
+                 v=None,
+                 f=None,
+                 segm=None,
+                 filename=None,
+                 ppfilename=None,
+                 lmrkfilename=None,
+                 basename=None,
+                 vc=None,
+                 fc=None,
+                 vscale=None,
+                 landmarks=None):
+        """
+        :param v: vertices
+        :param f: faces
+        :param filename: a filename from which a mesh is loaded
+        """
+
+        if filename is not None:
+            self.load_from_file(filename)
+            if hasattr(self, 'f'):
+                self.f = np.require(self.f, dtype=np.uint32)
+            self.v = np.require(self.v, dtype=np.float64)
+            self.filename = filename
+            if vscale is not None:
+                self.v *= vscale
+        if v is not None:
+            self.v = np.array(v, dtype=np.float64)
+            if vscale is not None:
+                self.v *= vscale
+        if f is not None:
+            self.f = np.require(f, dtype=np.uint32)
+
+        self.basename = basename
+        if self.basename is None and filename is not None:
+            self.basename = os.path.splitext(os.path.basename(filename))[0]
+
+        if segm is not None:
+            self.segm = segm
+        if landmarks is not None:
+            self.set_landmark_indices_from_any(landmarks)
+        if ppfilename is not None:
+            self.set_landmark_indices_from_ppfile(ppfilename)
+        if lmrkfilename is not None:
+            self.set_landmark_indices_from_lmrkfile(lmrkfilename)
+
+        if vc is not None:
+            self.set_vertex_colors(vc)
+
+        if fc is not None:
+            self.set_face_colors(fc)
+
+    def __del__(self):
+        if hasattr(self, 'textureID'):
+            from OpenGL.GL import glDeleteTextures
+            glDeleteTextures([self.textureID])
+
+    def edges_as_lines(self, copy_vertices=False):
+        from .lines import Lines
+        edges = self.f[:, [0, 1, 1, 2, 2, 0]].flatten().reshape(-1, 2)
+        verts = self.v.copy() if copy_vertices else self.v
+        return Lines(v=verts, e=edges)
+
+    def show(self, mv=None, meshes=[], lines=[]):
+        from .meshviewer import MeshViewer
+        from .utils import row
+
+        if mv is None:
+            mv = MeshViewer(keepalive=True)
+
+        if hasattr(self, 'landm'):
+            from .sphere import Sphere
+            sphere = Sphere(np.zeros((3)), 1.).to_mesh()
+            scalefactor = 1e-2 * np.max(np.max(self.v) - np.min(self.v)) / np.max(np.max(sphere.v) - np.min(sphere.v))
+            sphere.v = sphere.v * scalefactor
+            spheres = [Mesh(vc='SteelBlue', f=sphere.f, v=sphere.v + row(np.array(self.landm_raw_xyz[k]))) for k in self.landm.keys()]
+            mv.set_dynamic_meshes([self] + spheres + meshes, blocking=True)
+        else:
+            mv.set_dynamic_meshes([self] + meshes, blocking=True)
+        mv.set_dynamic_lines(lines)
+        return mv
+
+    def colors_like(self, color, arr=None):
+        from .utils import row, col
+
+        if arr is None:
+            arr = np.zeros(self.v.shape)
+
+        # if arr is single-dim, reshape it
+        if arr.ndim == 1 or arr.shape[1] == 1:
+            arr = arr.reshape(-1, 3)
+
+        if isinstance(color, str):
+            color = colors.name_to_rgb[color]
+        elif isinstance(color, list):
+            color = np.array(color)
+
+        if color.shape[0] == arr.shape[0] and color.shape[0] == color.size:
+            def jet(v):
+                fourValue = 4 * v
+                red = min(fourValue - 1.5, -fourValue + 4.5)
+                green = min(fourValue - 0.5, -fourValue + 3.5)
+                blue = min(fourValue + 0.5, -fourValue + 2.5)
+                result = np.array([red, green, blue])
+                result[result > 1.0] = 1.0
+                result[result < 0.0] = 0.0
+                return row(result)
+            color = col(color)
+            color = np.concatenate([jet(color[i]) for i in range(color.size)], axis=0)
+
+        return np.ones_like(arr) * color
+
+    def set_vertex_colors(self, vc, vertex_indices=None):
+        if vertex_indices is not None:
+            self.vc[vertex_indices] = self.colors_like(vc, self.v[vertex_indices])
+        else:
+            self.vc = self.colors_like(vc, self.v)
+        return self
+
+    def set_vertex_colors_from_weights(self, weights, scale_to_range_1=True, color=True):
+        # from numpy import ones_like
+        if weights is None:
+            return self
+        if scale_to_range_1:
+            weights = weights - np.min(weights)
+            weights = (1.0 - 0.0) * weights / np.max(weights) + 0.0
+        if color:
+            from matplotlib import cm
+            self.vc = cm.jet(weights)[:, :3]
+        else:
+            self.vc = np.tile(np.reshape(weights, (len(weights), 1)), (1, 3))  # *ones_like(self.v)
+        return self
+
+    def scale_vertex_colors(self, weights, w_min=0.0, w_max=1.0):
+        if weights is None:
+            return self
+        weights = weights - np.min(weights)
+        weights = (w_max - w_min) * weights / np.max(weights) + w_min
+        self.vc = (weights * self.vc.T).T if weights is not None else self.vc
+        return self
+
+    def set_face_colors(self, fc):
+        self.fc = self.colors_like(fc, self.f)
+        return self
+
+    def faces_by_vertex(self, as_sparse_matrix=False):
+        import scipy.sparse as sp
+        if not as_sparse_matrix:
+            faces_by_vertex = [[] for i in range(len(self.v))]
+            for i, face in enumerate(self.f):
+                faces_by_vertex[face[0]].append(i)
+                faces_by_vertex[face[1]].append(i)
+                faces_by_vertex[face[2]].append(i)
+        else:
+            row = self.f.flatten()
+            col = np.array([range(self.f.shape[0])] * 3).T.flatten()
+            data = np.ones(len(col))
+            faces_by_vertex = sp.csr_matrix((data, (row, col)), shape=(self.v.shape[0], self.f.shape[0]))
+        return faces_by_vertex
+
+    def estimate_vertex_normals(self, face_to_verts_sparse_matrix=None):
+        from .geometry.tri_normals import TriNormalsScaled
+
+        face_normals = TriNormalsScaled(self.v, self.f).reshape(-1, 3)
+        ftov = face_to_verts_sparse_matrix if face_to_verts_sparse_matrix else self.faces_by_vertex(as_sparse_matrix=True)
+        non_scaled_normals = ftov * face_normals
+        norms = (np.sum(non_scaled_normals ** 2.0, axis=1) ** 0.5).T
+        norms[norms == 0] = 1.0
+        return (non_scaled_normals.T / norms).T
+
+    def barycentric_coordinates_for_points(self, points, face_indices):
+        from .geometry.barycentric_coordinates_of_projection import barycentric_coordinates_of_projection
+        vertex_indices = self.f[face_indices.flatten(), :]
+        tri_vertices = np.array([self.v[vertex_indices[:, 0]], self.v[vertex_indices[:, 1]], self.v[vertex_indices[:, 2]]])
+        return vertex_indices, barycentric_coordinates_of_projection(points, tri_vertices[0, :], tri_vertices[1, :] - tri_vertices[0, :], tri_vertices[2, :] - tri_vertices[0, :])
+
+    def transfer_segm(self, mesh, exclude_empty_parts=True):
+        self.segm = {}
+        if hasattr(mesh, 'segm'):
+            face_centers = np.array([self.v[face, :].mean(axis=0) for face in self.f])
+            (closest_faces, closest_points) = mesh.closest_faces_and_points(face_centers)
+            mesh_parts_by_face = mesh.parts_by_face()
+            parts_by_face = [mesh_parts_by_face[face] for face in closest_faces.flatten()]
+            self.segm = dict([(part, []) for part in mesh.segm.keys()])
+            for face, part in enumerate(parts_by_face):
+                self.segm[part].append(face)
+            for part in self.segm.keys():
+                self.segm[part].sort()
+                if exclude_empty_parts and not self.segm[part]:
+                    del self.segm[part]
+
+    @property
+    def verts_by_segm(self):
+        return dict((segment, sorted(set(self.f[indices].flatten()))) for segment, indices in self.segm.items())
+
+    def parts_by_face(self):
+        segments_by_face = [''] * len(self.f)
+        for part in self.segm.keys():
+            for face in self.segm[part]:
+                segments_by_face[face] = part
+        return segments_by_face
+
+    def verts_in_common(self, segments):
+        """
+        returns array of all vertex indices common to each segment in segments"""
+        return sorted(reduce(lambda s0, s1: s0.intersection(s1),
+                             [set(self.verts_by_segm[segm]) for segm in segments]))
+        # # indices of vertices in the faces of the first segment
+        # indices = self.verts_by_segm[segments[0]]
+        # for segment in segments[1:] :
+        #    indices = sorted([index for index in self.verts_by_segm[segment] if index in indices]) # Intersect current segment with current indices
+        # return sorted(set(indices))
+
+    @property
+    def joint_names(self):
+        return self.joint_regressors.keys()
+
+    @property
+    def joint_xyz(self):
+        joint_locations = {}
+        for name in self.joint_names:
+            joint_locations[name] = self.joint_regressors[name]['offset'] + \
+                np.sum(self.v[self.joint_regressors[name]['v_indices']].T * self.joint_regressors[name]['coeff'], axis=1)
+        return joint_locations
+
+    # creates joint_regressors from a list of joint names and a per joint list of vertex indices (e.g. a ring of vertices)
+    # For the regression coefficients, all vertices for a given joint are given equal weight
+    def set_joints(self, joint_names, vertex_indices):
+        self.joint_regressors = {}
+        for name, indices in zip(joint_names, vertex_indices):
+            self.joint_regressors[name] = {'v_indices': indices,
+                                           'coeff': [1.0 / len(indices)] * len(indices),
+                                           'offset': np.array([0., 0., 0.])}
+
+    def vertex_visibility(self, camera, normal_threshold=None, omni_directional_camera=False, binary_visiblity=True):
+
+        vis, n_dot_cam = self.vertex_visibility_and_normals(camera, omni_directional_camera)
+
+        if normal_threshold is not None:
+            vis = np.logical_and(vis, n_dot_cam > normal_threshold)
+
+        return np.squeeze(vis) if binary_visiblity else np.squeeze(vis * n_dot_cam)
+
+    def vertex_visibility_and_normals(self, camera, omni_directional_camera=False):
+        from .visibility import visibility_compute
+        arguments = {'v': self.v,
+                     'f': self.f,
+                     'cams': np.array([camera.origin.flatten()])}
+
+        if not omni_directional_camera:
+            arguments['sensors'] = np.array([camera.sensor_axis.flatten()])
+
+        arguments['n'] = self.vn if hasattr(self, 'vn') else self.estimate_vertex_normals()
+
+        return(visibility_compute(**arguments))
+
+    def visibile_mesh(self, camera=[0.0, 0.0, 0.0]):
+        vis = self.vertex_visibility(camera)
+        faces_to_keep = filter(lambda face: vis[face[0]] * vis[face[1]] * vis[face[2]], self.f)
+        vertex_indices_to_keep = np.nonzero(vis)[0]
+        vertices_to_keep = self.v[vertex_indices_to_keep]
+        old_to_new_indices = np.zeros(len(vis))
+        old_to_new_indices[vertex_indices_to_keep] = range(len(vertex_indices_to_keep))
+        return Mesh(v=vertices_to_keep, f=np.array([old_to_new_indices[face] for face in faces_to_keep]))
+
+    def estimate_circumference(self, plane_normal, plane_distance, partNamesAllowed=None, want_edges=False):
+        raise Exception('estimate_circumference function has moved to body.mesh.metrics.circumferences')
+
+    # ######################################################
+    # Processing
+    def reset_normals(self, face_to_verts_sparse_matrix=None, reset_face_normals=False):
+        return processing.reset_normals(self, face_to_verts_sparse_matrix, reset_face_normals)
+
+    def reset_face_normals(self):
+        return processing.reset_face_normals(self)
+
+    def uniquified_mesh(self):
+        """This function returns a copy of the mesh in which vertices are copied such that
+        each vertex appears in only one face, and hence has only one texture"""
+        return processing.uniquified_mesh(self)
+
+    def keep_vertices(self, keep_list):
+        return processing.keep_vertices(self, keep_list)
+
+    def remove_vertices(self, v_list):
+        return self.keep_vertices(np.setdiff1d(np.arange(self.v.shape[0]), v_list))
+
+    def point_cloud(self):
+        return Mesh(v=self.v, f=[], vc=self.vc) if hasattr(self, 'vc') else Mesh(v=self.v, f=[])
+
+    def remove_faces(self, face_indices_to_remove):
+        return processing.remove_faces(self, face_indices_to_remove)
+
+    def scale_vertices(self, scale_factor):
+        return processing.scale_vertices(self, scale_factor)
+
+    def rotate_vertices(self, rotation):
+        return processing.rotate_vertices(self, rotation)
+
+    def translate_vertices(self, translation):
+        return processing.translate_vertices(self, translation)
+
+    def flip_faces(self):
+        return processing.flip_faces(self)
+
+    def simplified(self, factor=None, n_verts_desired=None):
+        from .topology import qslim_decimator
+        return qslim_decimator(self, factor, n_verts_desired)
+
+    def subdivide_triangles(self):
+        return processing.subdivide_triangles(self)
+
+    def concatenate_mesh(self, mesh):
+        return processing.concatenate_mesh(self, mesh)
+
+    # new_ordering specifies the new index of each vertex. If new_ordering[i] = j,
+    # vertex i should now be the j^th vertex. As such, each entry in new_ordering should be unique.
+    def reorder_vertices(self, new_ordering, new_normal_ordering=None):
+        processing.reorder_vertices(self, new_ordering, new_normal_ordering)
+
+    # ######################################################
+    # Landmark methods
+
+    @property
+    def landm_names(self):
+        names = []
+        if hasattr(self, 'landm_regressors') or hasattr(self, 'landm'):
+            names = self.landm_regressors.keys() if hasattr(self, 'landm_regressors') else self.landm.keys()
+        return list(names)
+
+    @property
+    def landm_xyz(self, ordering=None):
+        landmark_order = ordering if ordering else self.landm_names
+        landmark_vertex_locations = (self.landm_xyz_linear_transform(landmark_order) * self.v.flatten()).reshape(-1, 3) if landmark_order else np.zeros((0, 0))
+        return dict([(landmark_order[i], xyz) for i, xyz in enumerate(landmark_vertex_locations)]) if landmark_order else {}
+
+    def set_landmarks_from_xyz(self, landm_raw_xyz):
+        self.landm_raw_xyz = landm_raw_xyz if hasattr(landm_raw_xyz, 'keys') else dict((str(i), l) for i, l in enumerate(landm_raw_xyz))
+        self.recompute_landmark_indices()
+
+    def landm_xyz_linear_transform(self, ordering=None):
+        return landmarks.landm_xyz_linear_transform(self, ordering)
+
+    def recompute_landmark_xyz(self):
+        self.landm_raw_xyz = dict((name, self.v[ind]) for name, ind in self.landm.items())
+
+    def recompute_landmark_indices(self, landmark_fname=None, safe_mode=True):
+        landmarks.recompute_landmark_indices(self, landmark_fname, safe_mode)
+
+    def set_landmarks_from_regressors(self, regressors):
+        self.landm_regressors = regressors
+
+    def set_landmark_indices_from_any(self, landmark_file_or_values):
+        serialization.set_landmark_indices_from_any(self, landmark_file_or_values)
+
+    def set_landmarks_from_raw(self, landmark_file_or_values):
+        landmarks.set_landmarks_from_raw(self, landmark_file_or_values)
+
+    #######################################################
+    # Texture methods
+
+    @property
+    def texture_image(self):
+        if not hasattr(self, '_texture_image'):
+            self.reload_texture_image()
+        return self._texture_image
+
+    def set_texture_image(self, path_to_texture):
+        self.texture_filepath = path_to_texture
+
+    def texture_coordinates_by_vertex(self):
+        return texture.texture_coordinates_by_vertex(self)
+
+    def reload_texture_image(self):
+        texture.reload_texture_image(self)
+
+    def transfer_texture(self, mesh_with_texture):
+        texture.transfer_texture(self, mesh_with_texture)
+
+    def load_texture(self, texture_version):
+        texture.load_texture(self, texture_version)
+
+    def texture_rgb(self, texture_coordinate):
+        return texture.texture_rgb(self, texture_coordinate)
+
+    def texture_rgb_vec(self, texture_coordinates):
+        return texture.texture_rgb_vec(self, texture_coordinates)
+
+    #######################################################
+    # Search methods
+
+    def compute_aabb_tree(self):
+        return search.AabbTree(self)
+
+    def compute_aabb_normals_tree(self):
+        return search.AabbNormalsTree(self)
+
+    def compute_closest_point_tree(self, use_cgal=False):
+        return search.CGALClosestPointTree(self) if use_cgal else search.ClosestPointTree(self)
+
+    def closest_vertices(self, vertices, use_cgal=False):
+        return self.compute_closest_point_tree(use_cgal).nearest(vertices)
+
+    def closest_points(self, vertices):
+        return self.closest_faces_and_points(vertices)[1]
+
+    def closest_faces_and_points(self, vertices):
+        return self.compute_aabb_tree().nearest(vertices)
+
+    #######################################################
+    # Serialization methods
+
+    def load_from_file(self, filename):
+        serialization.load_from_file(self, filename)
+
+    def load_from_ply(self, filename):
+        serialization.load_from_ply(self, filename)
+
+    def load_from_obj(self, filename):
+        serialization.load_from_obj(self, filename)
+
+    def write_json(self, filename, header="", footer="", name="", include_faces=True, texture_mode=True):
+        serialization.write_json(self, filename, header, footer, name, include_faces, texture_mode)
+
+    def write_three_json(self, filename, name=""):
+        serialization.write_three_json(self, filename, name)
+
+    def write_ply(self, filename, flip_faces=False, ascii=False, little_endian=True, comments=[]):
+        serialization.write_ply(self, filename, flip_faces, ascii, little_endian, comments)
+
+    def write_mtl(self, path, material_name, texture_name):
+        """Serializes a material attributes file"""
+        serialization.write_mtl(self, path, material_name, texture_name)
+
+    def write_obj(self, filename, flip_faces=False, group=False, comments=None):
+        serialization.write_obj(self, filename, flip_faces, group, comments)
+
+    def load_from_obj_cpp(self, filename):
+        serialization.load_from_obj_cpp(self, filename)
+
+    def set_landmark_indices_from_ppfile(self, ppfilename):
+        serialization.set_landmark_indices_from_ppfile(self, ppfilename)
+
+    def set_landmark_indices_from_lmrkfile(self, lmrkfilename):
+        serialization.set_landmark_indices_from_lmrkfile(self, lmrkfilename)

mesh-fix-MSVC_compilation/mesh/meshviewer.py

@@ -0,0 +1,1238 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2012 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2012-05-11.
+
+"""
+Mesh visualization and related classes
+--------------------------------------
+
+This module contains the core visualization tools for meshes. The backend used for visualization
+is OpenGL.
+
+The module itself can be run like the following
+
+.. code::
+
+  python -m psbody.mesh.meshviewer arguments
+
+The following commands are used
+
+* ``arguments=TEST_FOR_OPENGL`` a basic OpenGL support is run. This is usually performed
+  on a forked python process. In case OpenGL is not supported, a `DummyClass``
+  mesh viewer is returned.
+* ``arguments=title nb_x_axis nb_y_axis width height`` a new window is created
+
+.. autosummary::
+
+  MeshViewer
+  MeshViewers
+  MeshViewerLocal
+  test_for_opengl
+
+"""
+
+import sys
+import os.path
+import time
+import copy
+import numpy as np
+import traceback
+from multiprocessing import freeze_support
+
+import zmq
+import re
+import subprocess
+import tempfile
+
+# this is way too verbose, organize imports better
+from OpenGL.GL import glPixelStorei, glMatrixMode, glHint, glTexParameterf, glDisableClientState
+from OpenGL.GL import glBindTexture, glEnableClientState, glPointSize, glEnable
+from OpenGL.GL import glColor3f, glDisable, glBegin, glEnd, glClearColor, glClearDepth
+from OpenGL.GL import glNormalPointer, glLineWidth, glTexCoord2f, glTexCoordPointer
+from OpenGL.GL import glViewport, glLightModeli, glLoadIdentity, glTranslatef, glPushMatrix
+from OpenGL.GL import glLoadMatrixf, glPopMatrix, glMultMatrixf, glDrawElementsui, glTexEnvf, glGetDoublev
+from OpenGL.GL import glGenTextures, glTexImage2D, glFrustum, glGenerateMipmap
+from OpenGL.GL import glBlendFunc, glVertex3f, glVertexPointer, glVertexPointerf, glColorPointerf, glColorPointer
+from OpenGL.GL import glGetFloatv, glGetIntegerv, glReadPixels
+from OpenGL.GL import glClear, glFlush, glDepthFunc, glShadeModel
+from OpenGL.GL import GL_TRUE, GL_FLOAT, GL_POINTS, GL_COLOR_ARRAY, GL_NORMAL_ARRAY, GL_LINE_SMOOTH, GL_MODELVIEW_MATRIX
+from OpenGL.GL import GL_BLEND, GL_TEXTURE_2D, GL_TEXTURE_ENV_MODE, GL_TEXTURE_MAG_FILTER, GL_SMOOTH
+from OpenGL.GL import GL_TEXTURE_MIN_FILTER, GL_VIEWPORT, GL_LINEAR, GL_COLOR_MATERIAL, GL_LIGHT0, GL_NORMALIZE
+from OpenGL.GL import GL_PROJECTION, GL_MODELVIEW, GL_VERTEX_SHADER, GL_LIGHTING, GL_TEXTURE_COORD_ARRAY
+from OpenGL.GL import GL_TEXTURE_ENV, GL_TRIANGLES, GL_LINEAR_MIPMAP_LINEAR, GL_COLOR_CLEAR_VALUE
+from OpenGL.GL import GL_FRAGMENT_SHADER, GL_NEAREST, GL_UNPACK_ALIGNMENT, GL_RGB, GL_BGR, GL_DECAL, GL_MODULATE
+from OpenGL.GL import GL_UNSIGNED_BYTE, GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA, GL_QUADS, GL_POLYGON, GL_VERTEX_ARRAY, GL_DEPTH_COMPONENT
+from OpenGL.GL import GL_LIGHT_MODEL_TWO_SIDE, GL_GENERATE_MIPMAP_HINT, GL_NICEST, GL_LINES, GL_PROJECTION_MATRIX
+from OpenGL.GL import GL_COLOR_BUFFER_BIT, GL_DEPTH_BUFFER_BIT, GL_LEQUAL, GL_DEPTH_TEST, GL_PERSPECTIVE_CORRECTION_HINT
+from OpenGL.GL import shaders
+
+from OpenGL.GLUT import glutInit, glutDisplayFunc, glutInitDisplayMode, glutInitWindowSize, glutGet, GLUT_WINDOW_WIDTH, GLUT_WINDOW_HEIGHT
+from OpenGL.GLUT import glutMainLoop, glutPostRedisplay, glutInitWindowPosition, glutCreateWindow, glutTimerFunc, glutSetWindowTitle
+from OpenGL.GLUT import glutReshapeFunc, glutKeyboardFunc, glutMouseFunc, glutMotionFunc, glutSwapBuffers
+from OpenGL.GLUT import GLUT_RGBA, GLUT_DOUBLE, GLUT_ALPHA, GLUT_DEPTH
+from OpenGL.GLUT import GLUT_LEFT_BUTTON, GLUT_DOWN, GLUT_UP, GLUT_RIGHT_BUTTON, GLUT_MIDDLE_BUTTON
+from OpenGL.GLU import gluPerspective, gluUnProject
+
+import OpenGL.arrays.vbo
+
+# if this file is processed/run as a python script/standalone, especially from the
+# internal command
+if __package__ is not None:
+    from .mesh import Mesh
+    from .geometry.tri_normals import TriNormals
+    from .arcball import ArcBallT, Matrix3fT, Matrix4fT, Point2fT, \
+        Matrix3fMulMatrix3f, Matrix3fSetRotationFromQuat4f, Matrix4fSetRotationFromMatrix3f
+
+    from .fonts import get_textureid_with_text
+
+# this block is below the previous one to make my linter happy
+if __package__ is None:
+    print("this file cannot be executed as a standalone python module")
+    print("python -m psbody.mesh.%s arguments" % (os.path.splitext(os.path.basename(__file__))[0]))
+    sys.exit(-1)
+
+
+def _run_self(args, stdin=None, stdout=None, stderr=None):
+    """Executes this same script module with the given arguments (forking without subprocess dependencies)"""
+    return subprocess.Popen([sys.executable] +
+                            ['-m'] + ['%s.%s' % (__package__, os.path.splitext(os.path.basename(__file__))[0])] +
+                            args,
+                            stdin=stdin,
+                            stdout=stdout,  # if stdout is not None else subprocess.PIPE,
+                            stderr=stderr)
+
+
+def _test_for_opengl():
+    try:
+        # from OpenGL.GLUT import glutInit
+        glutInit()
+    except Exception as e:
+        print(e, file=sys.stderr)
+        print('failure')
+    else:
+        print('success')
+
+
+test_for_opengl_cached = None
+
+
+def test_for_opengl():
+    """Tests if opengl is supported.
+
+    .. note:: the result of the test is cached
+
+    """
+
+    global test_for_opengl_cached
+    if test_for_opengl_cached is None:
+
+        with open(os.devnull) as dev_null, \
+            tempfile.TemporaryFile() as out, \
+            tempfile.TemporaryFile() as err:
+
+                p = _run_self(["TEST_FOR_OPENGL"],
+                              stdin=dev_null,
+                              stdout=out,
+                              stderr=err)
+                p.wait()
+
+                out.seek(0)
+                err.seek(0)
+
+                line = ''.join(out.read().decode())
+                test_for_opengl_cached = 'success' in line
+                if not test_for_opengl_cached:
+                    print('OpenGL test failed: ')
+                    print('\tstdout:', line)
+                    print('\tstderr:', '\n'.join(err.read().decode()))
+
+    return test_for_opengl_cached
+
+
+class Dummy(object):
+
+    def __getattr__(self, name):
+        return Dummy()
+
+    def __call__(self, *args, **kwargs):
+        return Dummy()
+
+    def __getitem__(self, key):
+        return Dummy()
+
+    def __setitem__(self, key, value):
+        pass
+
+
+def MeshViewer(titlebar='Mesh Viewer',
+               static_meshes=None,
+               static_lines=None,
+               uid=None,
+               autorecenter=True,
+               shape=(1, 1),
+               keepalive=False,
+               window_width=1280,
+               window_height=960,
+               snapshot_camera=None):
+    """Allows visual inspection of geometric primitives.
+
+    Write-only Attributes:
+
+    :param titlebar: string printed in the window titlebar
+    :param static_meshes: list of Mesh objects to be displayed
+    :param static_lines: list of Lines objects to be displayed
+
+    .. note:: `static_meshes` is meant for Meshes that are updated infrequently,
+              `and dynamic_meshes` is for Meshes that are updated frequently
+              (same for `dynamic_lines` vs. `static_lines`).
+              They may be treated differently for performance reasons.
+
+    """
+
+    if not test_for_opengl():
+        return Dummy()
+
+    mv = MeshViewerLocal(shape=(1, 1),
+                         uid=uid,
+                         titlebar=titlebar,
+                         keepalive=keepalive,
+                         window_width=window_width,
+                         window_height=window_height)
+    result = mv.get_subwindows()[0][0]
+    result.snapshot_camera = snapshot_camera
+    if static_meshes:
+        result.static_meshes = static_meshes
+    if static_lines:
+        result.static_lines = static_lines
+    result.autorecenter = autorecenter
+
+    return result
+
+
+def MeshViewers(shape=(1, 1),
+                titlebar="Mesh Viewers",
+                keepalive=False,
+                window_width=1280,
+                window_height=960):
+    """Allows subplot-style inspection of primitives in multiple subwindows.
+
+    :param shape: a tuple indicating the number of vertical and horizontal windows requested
+    :param titlebar: the title appearing on the created window
+
+
+    Returns: a list of lists of MeshViewer objects: one per window requested.
+    """
+
+    if not test_for_opengl():
+        return Dummy()
+
+    mv = MeshViewerLocal(shape=shape,
+                         titlebar=titlebar,
+                         uid=None,
+                         keepalive=keepalive,
+                         window_width=window_width,
+                         window_height=window_height)
+    return mv.get_subwindows()
+
+
+class MeshSubwindow(object):
+
+    def __init__(self, parent_window, which_window):
+        self.parent_window = parent_window
+        self.which_window = which_window
+
+    def set_dynamic_meshes(self, list_of_meshes, blocking=False):
+        self.parent_window.set_dynamic_meshes(list_of_meshes, blocking, self.which_window)
+
+    def set_static_meshes(self, list_of_meshes, blocking=False):
+        self.parent_window.set_static_meshes(list_of_meshes, blocking, self.which_window)
+
+    # list_of_model_names_and_parameters should be of form [{'name': scape_model_name, 'parameters': scape_model_parameters}]
+    # here scape_model_name is the filepath of the scape model.
+    def set_dynamic_models(self, list_of_model_names_and_parameters, blocking=False):
+        self.parent_window.set_dynamic_models(list_of_model_names_and_parameters, blocking, self.which_window)
+
+    def set_dynamic_lines(self, list_of_lines, blocking=False):
+        self.parent_window.set_dynamic_lines(list_of_lines, blocking, self.which_window)
+
+    def set_static_lines(self, list_of_lines, blocking=False):
+        self.parent_window.set_static_lines(list_of_lines, blocking=blocking, which_window=self.which_window)
+
+    def set_titlebar(self, titlebar, blocking=False):
+        self.parent_window.set_titlebar(titlebar, blocking, which_window=self.which_window)
+
+    def set_lighting_on(self, lighting_on, blocking=True):
+        self.parent_window.set_lighting_on(lighting_on, blocking=blocking, which_window=self.which_window)
+
+    def set_autorecenter(self, autorecenter, blocking=False):
+        self.parent_window.set_autorecenter(autorecenter, blocking=blocking, which_window=self.which_window)
+
+    def set_background_color(self, background_color, blocking=False):
+        self.parent_window.set_background_color(background_color, blocking=blocking, which_window=self.which_window)
+
+    def save_snapshot(self, path, blocking=False):
+        self.parent_window.save_snapshot(path, blocking=blocking, which_window=self.which_window)
+
+    def get_event(self):
+        return self.parent_window.get_event()
+
+    def get_keypress(self):
+        return self.parent_window.get_keypress()['key']
+
+    def get_mouseclick(self):
+        return self.parent_window.get_mouseclick()
+
+    def close(self):
+        self.parent_window.p.terminate()
+
+    background_color = property(fset=set_background_color, doc="Background color, as 3-element numpy array where 0 <= color <= 1.0.")
+    dynamic_meshes = property(fset=set_dynamic_meshes, doc="List of meshes for dynamic display.")
+    static_meshes = property(fset=set_static_meshes, doc="List of meshes for static display.")
+    dynamic_models = property(fset=set_dynamic_models, doc="List of model names and parameters for dynamic display.")
+    dynamic_lines = property(fset=set_dynamic_lines, doc="List of Lines for dynamic display.")
+    static_lines = property(fset=set_static_lines, doc="List of Lines for static display.")
+    titlebar = property(fset=set_titlebar, doc="Titlebar string.")
+    lighting_on = property(fset=set_lighting_on, doc="Titlebar string.")
+
+
+class MeshViewerLocal(object):
+    """Proxy viewer instance for visual inspection of geometric primitives.
+
+    The lass forks another python process holding the display. It communicates
+    the commands with the remote instance seemlessly.
+
+    Write-only attributes:
+
+    :param titlebar: string printed in the window titlebar
+    :param dynamic_meshes: list of Mesh objects to be displayed
+    :param static_meshes: list of Mesh objects to be displayed
+    :param dynamic_lines: list of Lines objects to be displayed
+    :param static_lines: list of Lines objects to be displayed
+
+    .. note::
+
+      `static_meshes` is meant for Meshes that are
+      updated infrequently, and dynamic_meshes is for Meshes
+      that are updated frequently (same for dynamic_lines vs
+      static_lines). They may be treated differently for
+      performance reasons.
+
+    """
+
+    managed = {}
+
+    def __new__(cls, titlebar, uid, shape, keepalive, window_width, window_height):
+        assert(uid is None or isinstance(uid, str))
+
+        if uid == 'stack':
+            uid = ''.join(traceback.format_list(traceback.extract_stack()))
+        if uid and uid in MeshViewer.managed.keys():
+            return MeshViewer.managed[uid]
+
+        result = super(MeshViewerLocal, cls).__new__(cls)
+
+        result.client = zmq.Context.instance().socket(zmq.PUSH)
+        result.client.linger = 0
+
+        with open(os.devnull) as dev_null, \
+            tempfile.TemporaryFile() as err:
+
+                result.p = _run_self([titlebar, str(shape[0]), str(shape[1]), str(window_width), str(window_height)],
+                                     stdin=dev_null,
+                                     stdout=subprocess.PIPE,
+                                     stderr=err)
+
+                line = result.p.stdout.readline().decode()
+                result.p.stdout.close()
+                current_port = re.match('<PORT>(.*?)</PORT>', line)
+                if not current_port:
+                    raise Exception("MeshViewer remote appears to have failed to launch")
+                current_port = int(current_port.group(1))
+                result.client.connect('tcp://127.0.0.1:%d' % (current_port))
+
+                if uid:
+                    MeshViewerLocal.managed[uid] = result
+                result.shape = shape
+                result.keepalive = keepalive
+                return result
+
+    def get_subwindows(self):
+        return [[MeshSubwindow(parent_window=self, which_window=(r, c)) for c in range(self.shape[1])] for r in range(self.shape[0])]
+
+    @staticmethod
+    def _sanitize_meshes(list_of_meshes):
+        lm = []
+
+        # have to copy the meshes for now, because some contain CPython members,
+        # before pushing them on the queue
+        for m in list_of_meshes:
+            if hasattr(m, 'fc'):
+                lm.append(Mesh(v=m.v, f=m.f, fc=m.fc))
+            elif hasattr(m, 'vc'):
+                lm.append(Mesh(v=m.v, f=m.f, vc=m.vc))
+            else:
+                lm.append(Mesh(v=m.v, f=m.f if hasattr(m, 'f') else []))
+
+            if hasattr(m, 'vn'):
+                lm[-1].vn = m.vn
+            if hasattr(m, 'fn'):
+                lm[-1].fn = m.fn
+
+            if hasattr(m, 'v_to_text'):
+                lm[-1].v_to_text = m.v_to_text
+            if hasattr(m, 'texture_filepath') and hasattr(m, 'vt') and hasattr(m, 'ft'):
+                lm[-1].texture_filepath = m.texture_filepath
+                lm[-1].vt = m.vt
+                lm[-1].ft = m.ft
+
+        return lm
+
+    def _send_pyobj(self, label, obj, blocking, which_window):
+        if blocking:
+            context = zmq.Context.instance()
+            server = context.socket(zmq.PULL)
+            server.linger = 0
+            port = server.bind_to_random_port('tcp://127.0.0.1',
+                                              min_port=49152,
+                                              max_port=65535,
+                                              max_tries=100000)
+            # sending with blocking'
+            self.client.send_pyobj({'label': label,
+                                    'obj': obj,
+                                    'port': port,
+                                    'which_window': which_window})
+            task_completion_time = server.recv_pyobj()
+            # task completion time was %.2fs in other process' % (task_completion_time,)
+            server.close()
+        else:
+            # sending nonblocking
+            self.client.send_pyobj({'label': label,
+                                    'obj': obj,
+                                    'which_window': which_window})
+
+    def set_dynamic_meshes(self, list_of_meshes, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('dynamic_meshes', self._sanitize_meshes(list_of_meshes), blocking, which_window)
+
+    def set_static_meshes(self, list_of_meshes, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('static_meshes', self._sanitize_meshes(list_of_meshes), blocking, which_window)
+
+    # list_of_model_names_and_parameters should be of form [{'name': scape_model_name, 'parameters': scape_model_parameters}]
+    # here scape_model_name is the filepath of the scape model.
+    def set_dynamic_models(self, list_of_model_names_and_parameters, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('dynamic_models', list_of_model_names_and_parameters, blocking, which_window)
+
+    def set_dynamic_lines(self, list_of_lines, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('dynamic_lines', list_of_lines, blocking, which_window)
+
+    def set_static_lines(self, list_of_lines, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('static_lines', list_of_lines, blocking, which_window)
+
+    def set_titlebar(self, titlebar, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('titlebar', titlebar, blocking, which_window)
+
+    def set_lighting_on(self, lighting_on, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('lighting_on', lighting_on, blocking, which_window)
+
+    def set_autorecenter(self, autorecenter, blocking=False, which_window=(0, 0)):
+        self._send_pyobj('autorecenter', autorecenter, blocking, which_window)
+
+    def set_background_color(self, background_color, blocking=False, which_window=(0, 0)):
+        assert(isinstance(background_color, np.ndarray))
+        assert(background_color.size == 3)
+        self._send_pyobj('background_color', background_color.flatten(), blocking, which_window)
+
+    def get_keypress(self):
+        return self.get_ui_event('get_keypress')
+
+    def get_mouseclick(self):
+        """Returns a mouse click event.
+
+        .. note::
+
+          the call is blocking the caller until an event is received
+        """
+        return self.get_ui_event('get_mouseclick')
+
+    def get_event(self):
+        return self.get_ui_event('get_event')
+
+    def get_ui_event(self, event_id):
+        context = zmq.Context.instance()
+        server = context.socket(zmq.PULL)
+        server.linger = 0
+        port = server.bind_to_random_port('tcp://127.0.0.1',
+                                          min_port=49152,
+                                          max_port=65535,
+                                          max_tries=100000)
+        self._send_pyobj(event_id, port, blocking=True, which_window=(0, 0))
+        result = server.recv_pyobj()
+        server.close()
+        return result
+
+    background_color = property(fset=set_background_color,
+                                doc="Background color, as 3-element numpy array where 0 <= color <= 1.0.")
+
+    dynamic_meshes = property(fset=set_dynamic_meshes,
+                              doc="List of meshes for dynamic display.")
+    static_meshes = property(fset=set_static_meshes,
+                             doc="List of meshes for static display.")
+    dynamic_models = property(fset=set_dynamic_models,
+                              doc="List of model names and parameters for dynamic display.")
+
+    dynamic_lines = property(fset=set_dynamic_lines,
+                             doc="List of Lines for dynamic display.")
+    static_lines = property(fset=set_static_lines,
+                            doc="List of Lines for static display.")
+
+    titlebar = property(fset=set_titlebar,
+                        doc="Titlebar string.")
+
+    def save_snapshot(self, path, blocking=False, which_window=(0, 0)):
+        """Saves a snapshot of the current window into the specified file
+
+        :param path: filename to which the current window content will be saved
+        """
+        self._send_pyobj('save_snapshot', path, blocking, which_window)
+
+    def __del__(self):
+        if not self.keepalive:
+            self.p.terminate()
+
+
+class MeshViewerSingle(object):
+
+    def __init__(self, x1_pct, y1_pct, width_pct, height_pct):
+        assert(width_pct <= 1)
+        assert(height_pct <= 1)
+        self.dynamic_meshes = []
+        self.static_meshes = []
+        self.dynamic_models = []
+        self.dynamic_lines = []
+        self.static_lines = []
+        self.lighting_on = True
+        self.scape_models = {}
+        self.x1_pct = x1_pct
+        self.y1_pct = y1_pct
+        self.width_pct = width_pct
+        self.height_pct = height_pct
+        self.autorecenter = True
+
+    def get_dimensions(self):
+        d = {}
+        d['window_width'] = glutGet(GLUT_WINDOW_WIDTH)
+        d['window_height'] = glutGet(GLUT_WINDOW_HEIGHT)
+        d['subwindow_width'] = self.width_pct * d['window_width']
+        d['subwindow_height'] = self.height_pct * d['window_height']
+        d['subwindow_origin_x'] = self.x1_pct * d['window_width']
+        d['subwindow_origin_y'] = self.y1_pct * d['window_height']
+        return d
+
+    def on_draw(self, transform, want_camera=False):
+
+        d = self.get_dimensions()
+
+        glViewport(
+            int(d['subwindow_origin_x']),
+            int(d['subwindow_origin_y']),
+            int(d['subwindow_width']),
+            int(d['subwindow_height']))
+
+        glMatrixMode(GL_PROJECTION)
+        glLoadIdentity()
+
+        fov_degrees = 45.
+        near = 1.0
+        far = 100.
+        ratio = float(d['subwindow_width']) / float(d['subwindow_height'])
+        if d['subwindow_width'] < d['subwindow_height']:
+            xt = np.tan(fov_degrees * np.pi / 180. / 2.0) * near
+            yt = xt / ratio
+            glFrustum(-xt, xt, -yt, yt, near, far)
+        else:
+            gluPerspective(fov_degrees, ratio, near, far)
+
+        glMatrixMode(GL_MODELVIEW)
+        glLoadIdentity()
+        glLightModeli(GL_LIGHT_MODEL_TWO_SIDE, GL_TRUE)
+
+        glTranslatef(0.0, 0.0, -6.0)
+#        glTranslatef(0.0,0.0,-3.5)
+
+        glPushMatrix()
+        glMultMatrixf(transform)
+        glColor3f(1.0, 0.75, 0.75)
+
+        if self.autorecenter:
+            camera = self.draw_primitives_recentered(want_camera=want_camera)
+        else:
+            if hasattr(self, 'current_center') and hasattr(self, 'current_scalefactor'):
+                camera = self.draw_primitives(scalefactor=self.current_scalefactor, center=self.current_center)
+            else:
+                camera = self.draw_primitives(want_camera=want_camera)
+
+        glPopMatrix()
+
+        if want_camera:
+            return camera
+
+    def draw_primitives_recentered(self, want_camera=False):
+        return self.draw_primitives(recenter=True, want_camera=want_camera)
+
+    @staticmethod
+    def set_shaders(m):
+        VERTEX_SHADER = shaders.compileShader("""void main() {
+                    gl_Position = gl_ModelViewProjectionMatrix * gl_Vertex;
+                }""", GL_VERTEX_SHADER)
+        FRAGMENT_SHADER = shaders.compileShader("""void main() {
+                    gl_FragColor = vec4( 0, 1, 0, 1 );
+                }""", GL_FRAGMENT_SHADER)
+        m.shaders = shaders.compileProgram(VERTEX_SHADER, FRAGMENT_SHADER)
+
+    @staticmethod
+    def set_texture(m):
+        texture_data = np.array(m.texture_image, dtype='int8')
+        m.textureID = glGenTextures(1)
+        glPixelStorei(GL_UNPACK_ALIGNMENT, 1)
+        glBindTexture(GL_TEXTURE_2D, m.textureID)
+        glTexImage2D(GL_TEXTURE_2D, 0, GL_RGB, texture_data.shape[1], texture_data.shape[0], 0, GL_BGR, GL_UNSIGNED_BYTE, texture_data.flatten())
+        glHint(GL_GENERATE_MIPMAP_HINT, GL_NICEST)  # must be GL_FASTEST, GL_NICEST or GL_DONT_CARE
+        glGenerateMipmap(GL_TEXTURE_2D)
+
+    @staticmethod
+    def draw_mesh(m, lighting_on):
+
+        # Supply vertices
+        glEnableClientState(GL_VERTEX_ARRAY)
+        m.vbo['v'].bind()
+        glVertexPointer(3, GL_FLOAT, 0, m.vbo['v'])
+        m.vbo['v'].unbind()
+
+        # Supply normals
+        if 'vn' in m.vbo.keys():
+            glEnableClientState(GL_NORMAL_ARRAY)
+            m.vbo['vn'].bind()
+            glNormalPointer(GL_FLOAT, 0, m.vbo['vn'])
+            m.vbo['vn'].unbind()
+        else:
+            glDisableClientState(GL_NORMAL_ARRAY)
+
+        # Supply colors
+        if 'vc' in m.vbo.keys():
+            glEnableClientState(GL_COLOR_ARRAY)
+            m.vbo['vc'].bind()
+            glColorPointer(3, GL_FLOAT, 0, m.vbo['vc'])
+            m.vbo['vc'].unbind()
+        else:
+            glDisableClientState(GL_COLOR_ARRAY)
+
+        if ('vt' in m.vbo.keys()) and hasattr(m, 'textureID'):
+            glEnable(GL_TEXTURE_2D)
+            glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_NEAREST)
+            glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_NEAREST)
+            glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE)
+            glBindTexture(GL_TEXTURE_2D, m.textureID)
+
+            glEnableClientState(GL_TEXTURE_COORD_ARRAY)
+            m.vbo['vt'].bind()
+            glTexCoordPointer(2, GL_FLOAT, 0, m.vbo['vt'])
+            m.vbo['vt'].unbind()
+        else:
+            glDisable(GL_TEXTURE_2D)
+            glDisableClientState(GL_TEXTURE_COORD_ARRAY)
+
+        # Draw
+        if len(m.f) > 0:
+            # ie if it is triangulated
+            if lighting_on:
+                glEnable(GL_LIGHTING)
+            else:
+                glDisable(GL_LIGHTING)
+            glDrawElementsui(GL_TRIANGLES, np.arange(m.f.size, dtype=np.uint32))
+        else:
+            # not triangulated, so disable lighting
+            glDisable(GL_LIGHTING)
+            glPointSize(2)
+            glDrawElementsui(GL_POINTS, np.arange(len(m.v), dtype=np.uint32))
+        if hasattr(m, 'v_to_text'):
+
+            glEnable(GL_TEXTURE_2D)
+            glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR)
+            glTexParameterf(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR_MIPMAP_LINEAR)
+            glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_DECAL)
+
+            # glEnable(GL_TEXTURE_GEN_S)
+            # glEnable(GL_TEXTURE_GEN_T)
+            # glTexGeni(GL_S, GL_TEXTURE_GEN_MODE, GL_OBJECT_LINEAR)
+            # glTexGeni(GL_T, GL_TEXTURE_GEN_MODE, GL_OBJECT_LINEAR)
+
+            bgcolor = np.array(glGetDoublev(GL_COLOR_CLEAR_VALUE))
+            fgcolor = 1. - bgcolor
+
+            from .lines import Lines
+            sc = float(np.max(np.max(m.v, axis=0) - np.min(m.v, axis=0))) / 10.
+
+            cur_mtx = np.linalg.pinv(glGetFloatv(GL_MODELVIEW_MATRIX).T)
+            xdir = cur_mtx[:3, 0]
+            ydir = cur_mtx[:3, 1]
+
+            glEnable(GL_LINE_SMOOTH)
+            glEnable(GL_BLEND)
+            glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA)
+
+            for vidx, text in m.v_to_text.items():
+                pos0 = m.v[vidx].copy()
+                pos1 = m.v[vidx].copy()
+                if hasattr(m, 'vn'):
+                    pos1 += m.vn[vidx] * sc
+                glLineWidth(5.0)
+                ln = Lines(v=np.vstack((pos0, pos1)), e=np.array([[0, 1]]))
+                glEnable(GL_LIGHTING)
+                glColor3f(1. - 0.8, 1. - 0.8, 1. - 1.00)
+                MeshViewerSingle.draw_lines(ln)
+
+                glDisable(GL_LIGHTING)
+
+                texture_id = get_textureid_with_text(text, bgcolor, fgcolor)
+                glBindTexture(GL_TEXTURE_2D, texture_id)
+
+                glPushMatrix()
+                glTranslatef(pos1[0], pos1[1], pos1[2])
+
+                dx = xdir * .10
+                dy = ydir * .10
+                if False:
+                    glBegin(GL_QUADS)
+
+                    glTexCoord2f(1., 0.)
+                    glVertex3f(*(+dx + dy))
+
+                    glTexCoord2f(1., 1.)
+                    glVertex3f(*(+dx - dy))
+
+                    glTexCoord2f(0., 1.)
+                    glVertex3f(*(-dx - dy))
+
+                    glTexCoord2f(0., 0.)
+                    glVertex3f(*(-dx + dy))
+
+                    # gluSphere(quadratic,0.05,32,32)
+                    glEnd()
+                else:
+                    glBegin(GL_POLYGON)
+
+                    for r in np.arange(0, np.pi * 2., .01):
+                        glTexCoord2f(np.cos(r) / 2. + .5, np.sin(r) / 2. + .5)
+                        glVertex3f(*(dx * np.cos(r) + -dy * np.sin(r)))
+
+                    glEnd()
+                glPopMatrix()
+
+                #
+                # glColor3f(bgcolor[0], bgcolor[1], bgcolor[2])
+                # glRasterPos3f(pos1[0], pos1[1], pos1[2])
+                # # print pos0
+                # # print pos1
+                #
+                #
+                # for t in text:
+                #     GLUT.glutBitmapCharacter(GLUT.GLUT_BITMAP_HELVETICA_18, ord(t))
+
+    @staticmethod
+    def draw_lines(ls):
+        glDisableClientState(GL_NORMAL_ARRAY)
+        glEnableClientState(GL_VERTEX_ARRAY)
+        glLineWidth(3.0)
+        allpts = ls.v[ls.e.flatten()].astype(np.float32)
+        glVertexPointerf(allpts)
+        if hasattr(ls, 'vc') or hasattr(ls, 'ec'):
+            glEnableClientState(GL_COLOR_ARRAY)
+            if hasattr(ls, 'vc'):
+                glColorPointerf(ls.vc[ls.e.flatten()].astype(np.float32))
+            else:
+                clrs = np.ones((ls.e.shape[0] * 2, 3)) * np.repeat(ls.ec, 2, axis=0)
+                glColorPointerf(clrs)
+        else:
+            glDisableClientState(GL_COLOR_ARRAY)
+
+        glDisable(GL_LIGHTING)
+        glDrawElementsui(GL_LINES, np.arange(len(allpts), dtype=np.uint32))
+
+    def draw_primitives(self,
+                        scalefactor=1.0,
+                        center=[0.0, 0.0, 0.0],
+                        recenter=False,
+                        want_camera=False):
+
+        # measure the bounding box of all our primitives, so that we can
+        # recenter them in our field of view
+        if recenter:
+            all_meshes = self.static_meshes + self.dynamic_meshes
+            all_lines = self.static_lines + self.dynamic_lines
+
+            if (len(all_meshes) + len(all_lines)) == 0:
+                if want_camera:
+                    return {'modelview_matrix': glGetDoublev(GL_MODELVIEW_MATRIX),
+                            'projection_matrix': glGetDoublev(GL_PROJECTION_MATRIX),
+                            'viewport': glGetIntegerv(GL_VIEWPORT)
+                            }
+                else:
+                    return None
+
+            for m in all_meshes:
+                m.v = m.v.reshape((-1, 3))
+
+            all_verts = np.concatenate(
+                [m.v[m.f.flatten() if len(m.f) > 0 else np.arange(len(m.v))] for m in all_meshes] +
+                [l.v[l.e.flatten()] for l in all_lines],
+                axis=0)
+
+            maximum = np.max(all_verts, axis=0)
+            minimum = np.min(all_verts, axis=0)
+            center = (maximum + minimum) / 2.
+            scalefactor = (maximum - minimum) / 4.
+            scalefactor = np.max(scalefactor)
+        else:
+            center = np.array(center)
+#            for mesh in self.dynamic_meshes :
+#                if mesh.f : mesh.reset_normals()
+            all_meshes = self.static_meshes + self.dynamic_meshes
+            all_lines = self.static_lines + self.dynamic_lines
+        self.current_center = center
+        self.current_scalefactor = scalefactor
+
+        glMatrixMode(GL_MODELVIEW)
+        glPushMatrix()
+        # uncomment to add a default rotation (useful when automatically snapshoting kinect data
+        # glRotate(220, 0.0, 1.0, 0.0)
+
+        tf = np.identity(4, 'f') / scalefactor
+        tf[:3, 3] = -center / scalefactor
+        tf[3, 3] = 1
+        cur_mtx = glGetFloatv(GL_MODELVIEW_MATRIX).T
+
+        glLoadMatrixf(cur_mtx.dot(tf).T)
+
+        if want_camera:
+            result = {'modelview_matrix': glGetDoublev(GL_MODELVIEW_MATRIX),
+                      'projection_matrix': glGetDoublev(GL_PROJECTION_MATRIX),
+                      'viewport': glGetIntegerv(GL_VIEWPORT)
+                      }
+        else:
+            result = None
+
+        for m in all_meshes:
+            if not hasattr(m, 'vbo'):
+                # Precompute vertex vbo
+                fidxs = m.f.flatten() if len(m.f) > 0 else np.arange(len(m.v))
+                allpts = m.v[fidxs].astype(np.float32).flatten()
+                vbo = OpenGL.arrays.vbo.VBO(allpts)
+                m.vbo = {'v': vbo}
+
+                # Precompute normals vbo
+                if hasattr(m, 'vn'):
+                    ns = m.vn.astype(np.float32)
+                    ns = ns[m.f.flatten(), :]
+                    m.vbo['vn'] = OpenGL.arrays.vbo.VBO(ns.flatten())
+                elif hasattr(m, 'f') and m.f.size > 0:
+                    ns = TriNormals(m.v, m.f).reshape(-1, 3)
+                    ns = np.tile(ns, (1, 3)).reshape(-1, 3).astype(np.float32)
+                    m.vbo['vn'] = OpenGL.arrays.vbo.VBO(ns.flatten())
+
+                # Precompute texture vbo
+                if hasattr(m, 'ft') and (m.ft.size > 0):
+                    ftidxs = m.ft.flatten()
+                    data = m.vt[ftidxs].astype(np.float32)[:, 0:2]
+                    data[:, 1] = 1.0 - 1.0 * data[:, 1]
+                    m.vbo['vt'] = OpenGL.arrays.vbo.VBO(data)
+
+                # Precompute color vbo
+                if hasattr(m, 'vc'):
+                    data = m.vc[fidxs].astype(np.float32)
+                    m.vbo['vc'] = OpenGL.arrays.vbo.VBO(data)
+                elif hasattr(m, 'fc'):
+                    data = np.tile(m.fc, (1, 3)).reshape(-1, 3).astype(np.float32)
+                    m.vbo['vc'] = OpenGL.arrays.vbo.VBO(data)
+
+        for e in all_lines:
+            self.draw_lines(e)
+
+        for m in all_meshes:
+            if hasattr(m, 'texture_image') and not hasattr(m, 'textureID'):
+                self.set_texture(m)
+            self.draw_mesh(m, self.lighting_on)
+
+        glMatrixMode(GL_MODELVIEW)
+        glPopMatrix()
+
+        return result
+
+
+class MeshViewerRemote(object):
+
+    def __init__(self,
+                 titlebar='Mesh Viewer',
+                 subwins_vert=1,
+                 subwins_horz=1,
+                 width=100,
+                 height=100):
+
+        context = zmq.Context.instance()
+        self.server = context.socket(zmq.PULL)
+        self.server.linger = 0
+
+        # Find a port to use. The standard set of "private" ports is 49152 through 65535, as seen in...
+        # http://en.wikipedia.org/wiki/Port_(computer_networking)
+        port = self.server.bind_to_random_port('tcp://127.0.0.1',
+                                               min_port=49152,
+                                               max_port=65535,
+                                               max_tries=100000)
+
+        # Print out our port so that our client can connect to us with it. Flush stdout immediately; otherwise
+        # our client could wait forever.
+        print('<PORT>%d</PORT>\n' % (port,))
+        sys.stdout.flush()
+
+        self.arcball = ArcBallT(width, height)
+        self.transform = Matrix4fT()
+        self.lastrot = Matrix3fT()
+        self.thisrot = Matrix3fT()
+        self.isdragging = False
+        self.need_redraw = True
+
+        self.mesh_viewers = [[MeshViewerSingle(float(c) / (subwins_horz),
+                                               float(r) / (subwins_vert),
+                                               1. / subwins_horz,
+                                               1. / subwins_vert) for c in range(subwins_horz)] for r in range(subwins_vert)]
+
+        self.tm_for_fps = 0.
+        self.titlebar = titlebar
+        self.activate(width, height)
+
+    def snapshot(self, path):
+        """
+        Takes a snapshot of the meshviewer window and saves it to disc.
+
+        :param path: path to save the snapshot at.
+
+        .. note:: Requires the Pillow package to be installed.
+
+        """
+        from PIL import Image
+        from OpenGL.GLU import GLubyte
+
+        self.on_draw()
+
+        x = 0
+        y = 0
+        width = glutGet(GLUT_WINDOW_WIDTH)
+        height = glutGet(GLUT_WINDOW_HEIGHT)
+
+        data = (GLubyte * (3 * width * height))(0)
+        glReadPixels(x, y, width, height, GL_RGB, GL_UNSIGNED_BYTE, data)
+        image = Image.frombytes(mode="RGB", size=(width, height), data=data)
+        image = image.transpose(Image.FLIP_TOP_BOTTOM)
+
+        # Save image to disk
+        image.save(path)
+
+    def activate(self, width, height):
+        glutInit(['mesh_viewer'])
+        glutInitDisplayMode(GLUT_RGBA | GLUT_DOUBLE | GLUT_ALPHA | GLUT_DEPTH)
+        glutInitWindowSize(width, height)
+        glutInitWindowPosition(0, 0)
+        self.root_window_id = glutCreateWindow(self.titlebar)
+        glutDisplayFunc(self.on_draw)
+
+        glutTimerFunc(100, self.checkQueue, 0)
+        glutReshapeFunc(self.on_resize_window)
+
+        glutKeyboardFunc(self.on_keypress)
+        glutMouseFunc(self.on_click)
+        glutMotionFunc(self.on_drag)
+
+        # for r, lst in enumerate(self.mesh_viewers):
+        #     for c, mv in enumerate(lst):
+        #         mv.glut_window_id = glutCreateSubWindow(self.root_window_id, c*width/len(lst), r*height/len(self.mesh_viewers), width/len(lst), height/len(self.mesh_viewers))
+
+        glutDisplayFunc(self.on_draw)
+        self.init_opengl()
+
+        glutMainLoop()  # won't return until process is killed
+
+    def on_drag(self, cursor_x, cursor_y):
+        """ Mouse cursor is moving
+            Glut calls this function (when mouse button is down)
+            and pases the mouse cursor postion in window coords as the mouse moves.
+        """
+        from .geometry.rodrigues import rodrigues
+        if (self.isdragging):
+            mouse_pt = Point2fT(cursor_x, cursor_y)
+            ThisQuat = self.arcball.drag(mouse_pt)  # // Update End Vector And Get Rotation As Quaternion
+            self.thisrot = Matrix3fSetRotationFromQuat4f(ThisQuat)  # // Convert Quaternion Into Matrix3fT
+            # Use correct Linear Algebra matrix multiplication C = A * B
+            self.thisrot = Matrix3fMulMatrix3f(self.lastrot, self.thisrot)  # // Accumulate Last Rotation Into This One
+
+            # make sure it is a rotation
+            self.thisrot = rodrigues(rodrigues(self.thisrot)[0])[0]
+            self.transform = Matrix4fSetRotationFromMatrix3f(self.transform, self.thisrot)  # // Set Our Final Transform's Rotation From This One
+            glutPostRedisplay()
+        return
+
+    # The function called whenever a key is pressed. Note the use of Python tuples to pass in: (key, x, y)
+    def on_keypress(self, *args):
+        key = args[0]
+        if hasattr(self, 'event_port'):
+            self.keypress_port = self.event_port
+            del self.event_port
+        if hasattr(self, 'keypress_port'):
+            client = zmq.Context.instance().socket(zmq.PUSH)
+            client.connect('tcp://127.0.0.1:%d' % (self.keypress_port))
+            client.send_pyobj({'event_type': 'keyboard', 'key': key})
+            del self.keypress_port
+
+    def on_click(self, button, button_state, cursor_x, cursor_y):
+        """ Mouse button clicked.
+            Glut calls this function when a mouse button is
+            clicked or released.
+        """
+
+        self.isdragging = False
+        # if (button == GLUT_RIGHT_BUTTON and button_state == GLUT_UP):
+        #     # Right button click
+        #     self.lastrot = Matrix3fSetIdentity ();                         # // Reset Rotation
+        #     self.thisrot = Matrix3fSetIdentity ();                         # // Reset Rotation
+        #     self.transform = Matrix4fSetRotationFromMatrix3f (self.transform, self.thisrot); # // Reset Rotation
+        if (button == GLUT_LEFT_BUTTON and button_state == GLUT_UP):
+            # Left button released
+            self.lastrot = copy.copy(self.thisrot)  # Set Last Static Rotation To Last Dynamic One
+
+        elif (button == GLUT_LEFT_BUTTON and button_state == GLUT_DOWN):
+            # Left button clicked down
+            self.lastrot = copy.copy(self.thisrot)  # Set Last Static Rotation To Last Dynamic One
+            self.isdragging = True  # // Prepare For Dragging
+            mouse_pt = Point2fT(cursor_x, cursor_y)
+            self.arcball.click(mouse_pt)  # Update Start Vector And Prepare For Dragging
+
+        elif (button == GLUT_RIGHT_BUTTON and button_state == GLUT_DOWN):
+            # If a mouse click location was requested, return it to caller
+            if hasattr(self, 'event_port'):
+                self.mouseclick_port = self.event_port
+                del self.event_port
+            if hasattr(self, 'mouseclick_port'):
+                self.send_mouseclick_to_caller(cursor_x, cursor_y)
+
+        elif (button == GLUT_MIDDLE_BUTTON and button_state == GLUT_DOWN):
+            # If a mouse click location was requested, return it to caller
+            if hasattr(self, 'event_port'):
+                self.mouseclick_port = self.event_port
+                del self.event_port
+            if hasattr(self, 'mouseclick_port'):
+                self.send_mouseclick_to_caller(cursor_x, cursor_y, button='middle')
+
+        glutPostRedisplay()
+
+    def send_mouseclick_to_caller(self,
+                                  cursor_x,
+                                  cursor_y,
+                                  button='right'):
+
+        client = zmq.Context.instance().socket(zmq.PUSH)
+        client.connect('tcp://127.0.0.1:%d' % (self.mouseclick_port))
+        cameras = self.on_draw(want_cameras=True)
+
+        window_height = glutGet(GLUT_WINDOW_HEIGHT)
+        depth_value = glReadPixels(cursor_x, window_height - cursor_y, 1, 1, GL_DEPTH_COMPONENT, GL_FLOAT)
+
+        pyobj = {
+            'event_type': 'mouse_click_%sbutton' % button,
+            'u': None, 'v': None,
+            'x': None, 'y': None, 'z': None,
+            'subwindow_row': None,
+            'subwindow_col': None
+        }
+
+        for subwin_row, camera_list in enumerate(cameras):
+            for subwin_col, camera in enumerate(camera_list):
+
+                # test for out-of-bounds
+                if cursor_x < camera['viewport'][0]:
+                    continue
+                if cursor_x > (camera['viewport'][0] + camera['viewport'][2]):
+                    continue
+                if window_height - cursor_y < camera['viewport'][1]:
+                    continue
+                if window_height - cursor_y > (camera['viewport'][1] + camera['viewport'][3]):
+                    continue
+
+                xx, yy, zz = gluUnProject(
+                    cursor_x, window_height - cursor_y, depth_value,
+                    camera['modelview_matrix'],
+                    camera['projection_matrix'],
+                    camera['viewport'])
+
+                pyobj = {
+                    'event_type': 'mouse_click_%sbutton' % button,
+                    'u': cursor_x - camera['viewport'][0], 'v': window_height - cursor_y - camera['viewport'][1],
+                    'x': xx, 'y': yy, 'z': zz,
+                    'which_subwindow': (subwin_row, subwin_col)
+                }
+
+        client.send_pyobj(pyobj)
+        del self.mouseclick_port
+
+    def on_draw(self, want_cameras=False):
+        # sys.stderr.write('fps: %.2e\n' % (1. / (time.time() - self.tm_for_fps)))
+        self.tm_for_fps = time.time()
+        glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT)
+        cameras = []
+        for mvl in self.mesh_viewers:
+            cameras.append([])
+            for mv in mvl:
+                cameras[-1].append(mv.on_draw(self.transform, want_cameras))
+        glFlush()  # Flush The GL Rendering Pipeline
+        glutSwapBuffers()
+        self.need_redraw = False
+        if want_cameras:
+            return cameras
+
+    def on_resize_window(self, Width, Height):
+        """Reshape The Window When It's Moved Or Resized"""
+        self.arcball.setBounds(Width, Height)  # //*NEW* Update mouse bounds for arcball
+        return
+
+    def handle_request(self, request):
+        label = request['label']
+        obj = request['obj']
+        w = request['which_window']
+        mv = self.mesh_viewers[w[0]][w[1]]
+
+        # Handle each type of request.
+        # Some requests require a redraw, and
+        # some don't.
+        if label == 'dynamic_meshes':
+            mv.dynamic_meshes = obj
+            self.need_redraw = True
+        elif label == 'dynamic_models':
+            mv.dynamic_models = obj
+            self.need_redraw = True
+        elif label == 'static_meshes':
+            mv.static_meshes = obj
+            self.need_redraw = True
+        elif label == 'dynamic_lines':
+            mv.dynamic_lines = obj
+            self.need_redraw = True
+        elif label == 'static_lines':
+            mv.static_lines = obj
+            self.need_redraw = True
+        elif label == 'autorecenter':
+            mv.autorecenter = obj
+            self.need_redraw = True
+        elif label == 'titlebar':
+            assert(isinstance(obj, str))
+            self.titlebar = obj
+            glutSetWindowTitle(obj)
+        elif label == 'lighting_on':
+            mv.lighting_on = obj
+            self.need_redraw = True
+        elif label == 'background_color':
+            glClearColor(obj[0], obj[1], obj[2], 1.0)
+            self.need_redraw = True
+        elif label == 'save_snapshot':  # redraws for itself
+            assert(isinstance(obj, str))
+            self.snapshot(obj)
+        elif label == 'get_keypress':
+            self.keypress_port = obj
+        elif label == 'get_mouseclick':
+            self.mouseclick_port = obj
+        elif label == 'get_event':
+            self.event_port = obj
+        else:
+            return False  # can't handle this request string
+
+        return True  # handled the request string
+
+    def checkQueue(self, unused_timer_id):
+        glutTimerFunc(20, self.checkQueue, 0)
+
+        # if True: # spinning
+        #     w_whole_window = glutGet(GLUT_WINDOW_WIDTH)
+        #     h_whole_window = glutGet(GLUT_WINDOW_HEIGHT)
+        #     center_x = w_whole_window/2
+        #     center_y = h_whole_window/2
+        #     self.on_click(GLUT_LEFT_BUTTON, GLUT_DOWN, center_x, center_y)
+        #     self.on_drag(center_x+2, center_y)
+
+        try:
+            request = self.server.recv_pyobj(zmq.NOBLOCK)
+        except zmq.ZMQError as e:
+            if e.errno != zmq.EAGAIN:
+                raise  # something wrong besides empty queue
+            return  # empty queue, no problem
+
+        if not request:
+            return
+
+        while (request):
+            task_completion_time = time.time()
+            if not self.handle_request(request):
+                raise Exception('Unknown command string: %s' % (request['label']))
+            task_completion_time = time.time() - task_completion_time
+
+            if 'port' in request:  # caller wants confirmation
+                port = request['port']
+                client = zmq.Context.instance().socket(zmq.PUSH)
+                client.connect('tcp://127.0.0.1:%d' % (port))
+                client.send_pyobj(task_completion_time)
+            try:
+                request = self.server.recv_pyobj(zmq.NOBLOCK)
+            except zmq.ZMQError as e:
+                if e.errno != zmq.EAGAIN:
+                    raise
+                request = None
+
+        if self.need_redraw:
+            glutPostRedisplay()
+
+    def init_opengl(self):
+        """A general OpenGL initialization function.  Sets all of the initial parameters.
+
+        We call this right after our OpenGL window is created.
+        """
+
+        glClearColor(0.0, 0.0, 0.0, 1.0)  # This Will Clear The Background Color To Black
+        glClearDepth(1.0)  # Enables Clearing Of The Depth Buffer
+        glDepthFunc(GL_LEQUAL)  # The Type Of Depth Test To Do
+        glEnable(GL_DEPTH_TEST)  # Enables Depth Testing
+        glShadeModel(GL_SMOOTH)
+        glHint(GL_PERSPECTIVE_CORRECTION_HINT, GL_NICEST)  # Really Nice Perspective Calculations
+
+        glEnable(GL_LIGHT0)
+        glEnable(GL_LIGHTING)
+
+        glEnable(GL_COLOR_MATERIAL)
+        glEnable(GL_NORMALIZE)  # important since we rescale the modelview matrix
+
+        return True
+
+
+if __name__ == '__main__':
+
+    # Windows specific: see http://docs.python.org/2/library/multiprocessing.html#multiprocessing.freeze_support
+    freeze_support()
+
+    if len(sys.argv) == 2 and sys.argv[1] == 'TEST_FOR_OPENGL':
+        _test_for_opengl()
+
+    elif len(sys.argv) > 2:
+        m = MeshViewerRemote(titlebar=sys.argv[1],
+                             subwins_vert=int(sys.argv[2]),
+                             subwins_horz=int(sys.argv[3]),
+                             width=int(sys.argv[4]),
+                             height=int(sys.argv[5]))
+
+    else:
+        print("#" * 10)
+        print('Usage:')
+        print("python -m %s.%s arguments" % (__package__, os.path.splitext(os.path.basename(__file__))[0]))

mesh-fix-MSVC_compilation/mesh/processing.py

@@ -0,0 +1,186 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2013-02-20.
+
+
+"""
+Mesh processing backend
+=======================
+
+"""
+
+import numpy as np
+
+
+def reset_normals(self, face_to_verts_sparse_matrix=None, reset_face_normals=False):
+    self.vn = self.estimate_vertex_normals(face_to_verts_sparse_matrix=None)
+    if reset_face_normals:
+        self.fn = self.f.copy()
+    return self
+
+
+def reset_face_normals(self):
+    if not hasattr(self, 'vn'):
+        self.reset_normals()
+    self.fn = self.f
+    return self
+
+
+def uniquified_mesh(self):
+    """This function returns a copy of the mesh in which vertices are copied such that
+    each vertex appears in only one face, and hence has only one texture"""
+    from mesh import Mesh
+    new_mesh = Mesh(v=self.v[self.f.flatten()], f=np.array(range(len(self.f.flatten()))).reshape(-1, 3))
+
+    if not hasattr(self, 'vn'):
+        self.reset_normals()
+    new_mesh.vn = self.vn[self.f.flatten()]
+
+    if hasattr(self, 'vt'):
+        new_mesh.vt = self.vt[self.ft.flatten()]
+        new_mesh.ft = new_mesh.f.copy()
+    return new_mesh
+
+
+def keep_vertices(self, keep_list):
+    trans = dict((v, i) for i, v in enumerate(keep_list))
+    trans_f = np.array([trans[v] if v in trans else -1 for row in self.f for v in row], dtype=np.uint32).reshape(-1, 3)
+    if hasattr(self, 'vn') and self.vn.shape[0] == self.vn.shape[0]:
+        self.vn = self.vn.reshape(-1, 3)[keep_list]
+    if hasattr(self, 'vc') and self.vc.shape[0] == self.v.shape[0]:
+        self.vc = self.vc.reshape(-1, 3)[keep_list]
+    if hasattr(self, 'landm_raw_xyz'):
+        self.recompute_landmark_indices()
+
+    self.v = self.v.reshape(-1, 3)[keep_list]
+    self.f = trans_f[(trans_f != np.uint32(-1)).all(axis=1)]
+    return self
+
+
+def point_cloud(self):
+    from .mesh import Mesh
+    return Mesh(v=self.v, f=[], vc=self.vc) if hasattr(self, 'vc') else Mesh(v=self.v, f=[])
+
+
+def remove_faces(self, face_indices_to_remove):
+
+    def arr_replace(arr_in, lookup_dict):
+        arr_out = arr_in.copy()
+        for k, v in lookup_dict.iteritems():
+            arr_out[arr_in == k] = v
+        return arr_out
+
+    f = np.delete(self.f, face_indices_to_remove, 0)
+    v2keep = np.unique(f)
+    self.v = self.v[v2keep]
+    self.f = arr_replace(f, dict((v, i) for i, v in enumerate(v2keep)))
+
+    if hasattr(self, 'fc'):
+        self.fc = np.delete(self.fc, face_indices_to_remove, 0)
+    if hasattr(self, 'vn') and self.vn.shape[0] == self.vn.shape[0]:
+        self.vn = self.vn.reshape(-1, 3)[v2keep]
+    if hasattr(self, 'vc') and self.vc.shape[0] == self.v.shape[0]:
+        self.vc = self.vc.reshape(-1, 3)[v2keep]
+    if hasattr(self, 'landm_raw_xyz'):
+        self.recompute_landmark_indices()
+
+    if hasattr(self, 'ft'):
+        ft = np.delete(self.ft, face_indices_to_remove, 0)
+        vt2keep = np.unique(ft)
+        self.vt = self.vt[vt2keep]
+        self.ft = arr_replace(ft, dict((v, i) for i, v in enumerate(vt2keep)))
+
+    return self
+
+
+def flip_faces(self):
+    self.f = self.f.copy()
+    for i in range(len(self.f)):
+        self.f[i] = self.f[i][::-1]
+    if hasattr(self, 'ft'):
+        for i in range(len(self.f)):
+            self.ft[i] = self.ft[i][::-1]
+    return self
+
+
+def scale_vertices(self, scale_factor):
+    self.v *= scale_factor
+    return self
+
+
+def rotate_vertices(self, rotation_matrix):
+    import cv2
+    rotation_matrix = np.matrix(cv2.Rodrigues(np.array(rotation_matrix))[0] if (np.array(rotation_matrix).shape != (3, 3)) else rotation_matrix)
+    self.v = np.array(self.v * rotation_matrix.T)
+    return self
+
+
+def translate_vertices(self, translation):
+    self.v += translation
+    return self
+
+
+def subdivide_triangles(self):
+    new_faces = []
+    new_vertices = self.v.copy()
+    for face in self.f:
+        face_vertices = np.array([self.v[face[0], :], self.v[face[1], :], self.v[face[2], :]])
+        new_vertex = np.mean(face_vertices, axis=0)
+        new_vertices = np.vstack([new_vertices, new_vertex])
+        new_vertex_index = len(new_vertices) - 1
+        if len(new_faces):
+            new_faces = np.vstack([new_faces, [face[0], face[1], new_vertex_index], [face[1], face[2], new_vertex_index], [face[2], face[0], new_vertex_index]])
+        else:
+            new_faces = np.array([[face[0], face[1], new_vertex_index], [face[1], face[2], new_vertex_index], [face[2], face[0], new_vertex_index]])
+    self.v = new_vertices
+    self.f = new_faces
+
+    if hasattr(self, 'vt'):
+        new_ft = []
+        new_texture_coordinates = self.vt.copy()
+        for face_texture in self.ft:
+            face_texture_coordinates = np.array([self.vt[face_texture[0], :], self.vt[face_texture[1], :], self.vt[face_texture[2], :]])
+            new_texture_coordinate = np.mean(face_texture_coordinates, axis=0)
+            new_texture_coordinates = np.vstack([new_texture_coordinates, new_texture_coordinate])
+            new_texture_index = len(new_texture_coordinates) - 1
+            if len(new_ft):
+                new_ft = np.vstack([new_ft, [face_texture[0], face_texture[1], new_texture_index], [face_texture[1], face_texture[2], new_texture_index], [face_texture[2], face_texture[0], new_texture_index]])
+            else:
+                new_ft = np.array([[face_texture[0], face_texture[1], new_texture_index], [face_texture[1], face_texture[2], new_texture_index], [face_texture[2], face_texture[0], new_texture_index]])
+        self.vt = new_texture_coordinates
+        self.ft = new_ft
+    return self
+
+
+def concatenate_mesh(self, mesh):
+    if len(self.v) == 0:
+        self.f = mesh.f.copy()
+        self.v = mesh.v.copy()
+        self.vc = mesh.vc.copy() if hasattr(mesh, 'vc') else None
+    elif len(mesh.v):
+        self.f = np.concatenate([self.f, mesh.f.copy() + len(self.v)])
+        self.v = np.concatenate([self.v, mesh.v])
+        self.vc = np.concatenate([self.vc, mesh.vc]) if (hasattr(mesh, 'vc') and hasattr(self, 'vc')) else None
+    return self
+
+
+# new_ordering specifies the new index of each vertex. If new_ordering[i] = j,
+# vertex i should now be the j^th vertex. As such, each entry in new_ordering should be unique.
+def reorder_vertices(self, new_ordering, new_normal_ordering=None):
+    if new_normal_ordering is None:
+        new_normal_ordering = new_ordering
+    inverse_ordering = np.zeros(len(new_ordering), dtype=int)
+    for i, j in enumerate(new_ordering):
+        inverse_ordering[j] = i
+    inverse_normal_ordering = np.zeros(len(new_normal_ordering), dtype=int)
+    for i, j in enumerate(new_normal_ordering):
+        inverse_normal_ordering[j] = i
+    self.v = self.v[inverse_ordering]
+    if hasattr(self, 'vn'):
+        self.vn = self.vn[inverse_normal_ordering]
+    for i in range(len(self.f)):
+        self.f[i] = np.array([new_ordering[vertex_index] for vertex_index in self.f[i]])
+        if hasattr(self, 'fn'):
+            self.fn[i] = np.array([new_normal_ordering[normal_index] for normal_index in self.fn[i]])

mesh-fix-MSVC_compilation/mesh/search.py

@@ -0,0 +1,100 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Created by Matthew Loper on 2013-02-20.
+# Copyright (c) 2013 MPI. All rights reserved.
+
+"""
+Searching and lookup of geometric entities
+==========================================
+
+"""
+
+
+import numpy as np
+
+__all__ = ['AabbTree', 'AabbNormalsTree', 'ClosestPointTree', 'CGALClosestPointTree']
+
+
+class AabbTree(object):
+    """Encapsulates an AABB (Axis Aligned Bounding Box) Tree"""
+    def __init__(self, m):
+        from . import spatialsearch
+        # this shit return NULL
+        self.cpp_handle = spatialsearch.aabbtree_compute(m.v.astype(np.float64).copy(order='C'), m.f.astype(np.uint32).copy(order='C'))
+
+    def nearest(self, v_samples, nearest_part=False):
+        "nearest_part tells you whether the closest point in triangle abc is in the interior (0), on an edge (ab:1,bc:2,ca:3), or a vertex (a:4,b:5,c:6)"
+        from . import spatialsearch
+        f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
+        return (f_idxs, f_part, v) if nearest_part else (f_idxs, v)
+
+    def nearest_alongnormal(self, points, normals):
+        from . import spatialsearch
+        distances, f_idxs, v = spatialsearch.aabbtree_nearest_alongnormal(self.cpp_handle,
+                                                                          points.astype(np.float64),
+                                                                          normals.astype(np.float64))
+        return (distances, f_idxs, v)
+
+    def intersections_indices(self, q_v, q_f):
+        '''
+            Given a set of query vertices and faces, the function computes which intersect the mesh
+            A list with the indices in q_f is returned
+            @param q_v The query vertices (array of 3xN float values)
+            @param q_f The query faces (array 3xF integer values)
+        '''
+        import spatialsearch
+        return spatialsearch.aabbtree_intersections_indices(self.cpp_handle,
+                                                            q_v.astype(np.float64),
+                                                            q_f.astype(np.uint32))
+
+
+class ClosestPointTree(object):
+    """Provides nearest neighbor search for a cloud of vertices (i.e. triangles are not used)"""
+    def __init__(self, m):
+        from scipy.spatial import KDTree
+        self.v = m.v
+        self.kdtree = KDTree(self.v)
+
+    def nearest(self, v_samples):
+        (distances, indices) = zip(*[self.kdtree.query(v) for v in v_samples])
+        return (indices, distances)
+
+    def nearest_vertices(self, v_samples):
+        (distances, indices) = zip(*[self.kdtree.query(v) for v in v_samples])
+        return self.v[indices]
+
+
+class CGALClosestPointTree(object):
+    """Encapsulates an AABB (Axis Aligned Bounding Box) Tree """
+    def __init__(self, m):
+        from . import spatialsearch
+        self.v = m.v
+        n = m.v.shape[0]
+        faces = np.vstack([np.array(range(n)), np.array(range(n)) + n, np.array(range(n)) + 2 * n]).T
+        eps = 0.000000000001
+        self.cpp_handle = spatialsearch.aabbtree_compute(np.vstack([m.v + eps * np.array([1.0, 0.0, 0.0]), m.v + eps * np.array([0.0, 1.0, 0.0]), m.v - eps * np.array([1.0, 1.0, 0.0])]).astype(np.float64).copy(order='C'), faces.astype(np.uint32).copy(order='C'))
+
+    def nearest(self, v_samples):
+        from . import spatialsearch
+        f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
+        return (f_idxs.flatten(), (np.sum(((self.v[f_idxs.flatten()] - v_samples) ** 2.0), axis=1) ** 0.5).flatten())
+
+    def nearest_vertices(self, v_samples):
+        from . import spatialsearch
+        f_idxs, f_part, v = spatialsearch.aabbtree_nearest(self.cpp_handle, np.array(v_samples, dtype=np.float64, order='C'))
+        return self.v[f_idxs.flatten()]
+
+
+class AabbNormalsTree(object):
+    def __init__(self, m):
+        # the weight of the normals cosine is proportional to the std of the vertices
+        # the best point can be translated up to 2*eps because of the normals
+        from . import aabb_normals
+        eps = 0.1  # np.std(m.v)#0
+        self.tree_handle = aabb_normals.aabbtree_n_compute(m.v, m.f.astype(np.uint32).copy(), eps)
+
+    def nearest(self, v_samples, n_samples):
+        from . import aabb_normals
+        closest_tri, closest_p = aabb_normals.aabbtree_n_nearest(self.tree_handle, v_samples, n_samples)
+        return (closest_tri, closest_p)

mesh-fix-MSVC_compilation/mesh/serialization/__init__.py

@@ -0,0 +1,4 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2016 Max Planck Society. All rights reserved.

mesh-fix-MSVC_compilation/mesh/serialization/serialization.py

@@ -0,0 +1,443 @@
+#!/usr/bin/env python
+# encoding: utf-8
+
+# Copyright (c) 2013 Max Planck Society. All rights reserved.
+# Created by Matthew Loper on 2013-02-20.
+
+import re
+import os
+import sys
+import numpy as np
+
+from ..errors import SerializationError
+
+"""
+serialization.py
+
+
+"""
+
+__all__ = ['load_from_obj', 'load_from_obj_cpp', 'write_obj', 'write_mtl',
+           'write_json', 'write_three_json',
+           'set_landmark_indices_from_ppfile', 'set_landmark_indices_from_lmrkfile',
+           'load_from_ply', 'load_from_file']
+
+# import os.path
+
+
+def load_from_obj(self, filename):
+    v = []
+    f = []
+    ft = []
+    fn = []
+    vt = []
+    vn = []
+    vc = []
+    segm = dict()
+    landm_raw_xyz = dict()
+    currSegm = ''
+    currLandm = ''
+    with open(filename, 'r', buffering=2 ** 10) as fp:
+        for line in fp:
+            line = line.split()
+            if len(line) > 0:
+                if line[0] == 'v':
+                    v.append([float(x) for x in line[1:4]])
+                    if len(line) == 7:
+                        vc.append([float(x) for x in line[4:]])
+                    if currLandm:
+                        landm_raw_xyz[currLandm] = v[-1]
+                        currLandm = ''
+                elif line[0] == 'vt':
+                    vt.append([float(x) for x in line[1:]])
+                elif line[0] == 'vn':
+                    vn.append([float(x) for x in line[1:]])
+                elif line[0] == 'f':
+                    faces = [x.split('/') for x in line[1:]]
+                    for iV in range(1, len(faces) - 1):  # trivially triangulate faces
+                        f.append([int(faces[0][0]), int(faces[iV][0]), int(faces[iV + 1][0])])
+                        if (len(faces[0]) > 1) and faces[0][1]:
+                            ft.append([int(faces[0][1]), int(faces[iV][1]), int(faces[iV + 1][1])])
+                        if (len(faces[0]) > 2) and faces[0][2]:
+                            fn.append([int(faces[0][2]), int(faces[iV][2]), int(faces[iV + 1][2])])
+                        if currSegm:
+                            segm[currSegm].append(len(f) - 1)
+                elif line[0] == 'g':
+                    currSegm = line[1]
+                    if currSegm not in segm.keys():
+                        segm[currSegm] = []
+                elif line[0] == '#landmark':
+                    currLandm = line[1]
+                elif line[0] == 'mtllib':
+                    self.materials_filepath = os.path.join(os.path.dirname(filename), line[1])
+                    self.materials_file = open(self.materials_filepath, 'r').readlines()
+
+    self.v = np.array(v)
+    self.f = np.array(f) - 1
+    if vt:
+        self.vt = np.array(vt)
+    if vn:
+        self.vn = np.array(vn)
+    if vc:
+        self.vc = np.array(vc)
+    if ft:
+        self.ft = np.array(ft) - 1
+    if fn:
+        self.fn = np.array(fn) - 1
+    self.segm = segm
+    self.landm_raw_xyz = landm_raw_xyz
+    self.recompute_landmark_indices()
+
+    if hasattr(self, 'materials_file'):
+        for line in self.materials_file:
+            if line and line.split() and line.split()[0] == 'map_Ka':
+                self.texture_filepath = os.path.abspath(os.path.join(os.path.dirname(filename), line.split()[1]))
+
+
+def load_from_obj_cpp(self, filename):
+    from .loadobj import loadobj
+    if sys.version_info[:2] == (2, 6):
+        from OrderedDict import OrderedDict
+    else:
+        from collections import OrderedDict
+
+    v, vt, vn, f, ft, fn, mtl_path, landm, segm = loadobj(filename)
+    if v.size != 0:
+        self.v = v
+    if f.size != 0:
+        self.f = f
+    if vn.size != 0:
+        self.vn = vn
+    if vt.size != 0:
+        self.vt = vt
+    if fn.size != 0:
+        self.fn = fn
+    if ft.size != 0:
+        self.ft = ft
+    if segm:
+        self.segm = OrderedDict([(k, v if type(v) is list else v.tolist()) for k, v in segm.items()])
+    if mtl_path:
+        try:
+            self.materials_filepath = os.path.join(os.path.dirname(filename), mtl_path.strip())
+            self.materials_file = file(self.materials_filepath, 'r').readlines()
+        except:
+            self.materials_filepath = None
+    if hasattr(self, 'materials_file'):
+        for line in self.materials_file:
+            if line and line.split() and line.split()[0] == 'map_Ka':
+                self.texture_filepath = os.path.abspath(os.path.join(os.path.dirname(filename), line.split()[1]))
+    if landm:
+        self.landm = landm
+        self.recompute_landmark_xyz()
+
+
+def write_obj(self, filename, flip_faces=False, group=False, comments=None):
+    if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
+        os.makedirs(os.path.dirname(filename))
+
+    ff = -1 if flip_faces else 1
+
+    def write_face_to_obj_file(face_index, obj_file):
+        vertex_indices = self.f[face_index][::ff] + 1
+
+        if hasattr(self, 'ft'):
+            texture_indices = self.ft[face_index][::ff] + 1
+            if not hasattr(self, 'fn'):
+                self.reset_face_normals()
+            normal_indices = self.fn[face_index][::ff] + 1
+            obj_file.write('f %d/%d/%d %d/%d/%d  %d/%d/%d\n' % tuple(
+                np.array([vertex_indices, texture_indices, normal_indices]).T.flatten()))
+        elif hasattr(self, 'fn'):
+            normal_indices = self.fn[face_index][::ff] + 1
+            obj_file.write('f %d//%d %d//%d  %d//%d\n' % tuple(np.array([vertex_indices, normal_indices]).T.flatten()))
+        else:
+            obj_file.write('f %d %d %d\n' % tuple(vertex_indices))
+
+    with open(filename, 'w') as fi:
+        if comments is not None:
+            if isinstance(comments, str):
+                comments = [comments]
+            for comment in comments:
+                for line in comment.split("\n"):
+                    fi.write("# %s\n" % line)
+
+        if hasattr(self, 'texture_filepath'):
+            outfolder = os.path.dirname(filename)
+            outbase = os.path.splitext(os.path.basename(filename))[0]
+            mtlpath = outbase + '.mtl'
+            fi.write('mtllib %s\n' % mtlpath)
+            from shutil import copyfile
+            texture_name = outbase + os.path.splitext(self.texture_filepath)[1]
+            if os.path.abspath(self.texture_filepath) != os.path.abspath(os.path.join(outfolder, texture_name)):
+                copyfile(self.texture_filepath, os.path.join(outfolder, texture_name))
+            self.write_mtl(os.path.join(outfolder, mtlpath), outbase, texture_name)
+
+        for r in self.v:
+            fi.write('v %f %f %f\n' % (r[0], r[1], r[2]))
+
+        if hasattr(self, 'fn') and hasattr(self, 'vn'):
+            for r in self.vn:
+                fi.write('vn %f %f %f\n' % (r[0], r[1], r[2]))
+
+        if hasattr(self, 'ft'):
+            for r in self.vt:
+                if len(r) == 3:
+                    fi.write('vt %f %f %f\n' % (r[0], r[1], r[2]))
+                else:
+                    fi.write('vt %f %f\n' % (r[0], r[1]))
+        if hasattr(self, 'segm') and self.segm and not group:
+            for p in self.segm.keys():
+                fi.write('g %s\n' % p)
+                for face_index in self.segm[p]:
+                    write_face_to_obj_file(face_index, fi)
+        else:
+            if hasattr(self, 'f'):
+                for face_index in range(len(self.f)):
+                    write_face_to_obj_file(face_index, fi)
+
+
+def write_mtl(self, path, material_name, texture_name):
+    """Material attribute file serialization"""
+    with open(path, 'w') as f:
+        f.write('newmtl %s\n' % material_name)
+        # copied from another obj, no idea about what it does
+        f.write('ka 0.329412 0.223529 0.027451\n')
+        f.write('kd 0.780392 0.568627 0.113725\n')
+        f.write('ks 0.992157 0.941176 0.807843\n')
+        f.write('illum 0\n')
+        f.write('map_Ka %s\n' % texture_name)
+        f.write('map_Kd %s\n' % texture_name)
+        f.write('map_Ks %s\n' % texture_name)
+
+
+def write_ply(self, filename, flip_faces=False, ascii=False, little_endian=True, comments=[]):
+    from psbody.mesh.serialization import plyutils
+
+    if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
+        os.makedirs(os.path.dirname(filename))
+
+    ff = -1 if flip_faces else 1
+
+    if isinstance(comments, str):
+        comments = [comments]
+    comments = filter(lambda c: len(c) > 0, sum(map(lambda c: c.split("\n"), comments), []))
+
+    plyutils.write(list([list(x) for x in self.v]),
+                   list([list(x[::ff]) for x in self.f] if hasattr(self, 'f') else []),
+                   list([list((x * 255).astype(int)) for x in ([] if not hasattr(self, 'vc') else self.vc)]),
+                   filename, ascii, little_endian, list(comments),
+                   list([list(x) for x in ([] if not hasattr(self, 'vn') else self.vn)]))
+
+
+def write_three_json(self, filename, name=""):
+    import json
+
+    if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
+        os.makedirs(os.path.dirname(filename))
+
+    name = name if name else self.basename
+    name = name if name else os.path.splitext(os.path.basename(filename))[0]
+
+    metadata = {"formatVersion": 3.1,
+                "sourceFile": "%s.obj" % name,
+                "generatedBy": "korper",
+                "vertices": len(self.v),
+                "faces": len(self.f),
+                "normals": len(self.vn),
+                "colors": 0,
+                "uvs": len(self.vt),
+                "materials": 1
+                }
+    materials = [{"DbgColor": 15658734,
+                  "DbgIndex": 0,
+                  "DbgName": "defaultMat",
+                  "colorAmbient": [0.0, 0.0, 0.0],
+                  "colorDiffuse": [0.64, 0.64, 0.64],
+                  "colorSpecular": [0.5, 0.5, 0.5],
+                  "illumination": 2,
+                  "opticalDensity": 1.0,
+                  "specularCoef": 96.078431,
+                  "transparency": 1.0
+                  }]
+
+    mesh_data = {"metadata": metadata,
+                 'scale': 0.35,
+                 "materials": materials,
+                 "morphTargets": [],
+                 "morphColors": [],
+                 "colors": []}
+    mesh_data["vertices"] = self.v.flatten().tolist()
+    mesh_data["normals"] = self.vn.flatten().tolist()
+    mesh_data["uvs"] = [np.array([[vt[0], vt[1]] for vt in self.vt]).flatten().tolist()]
+    mesh_data["faces"] = np.array([[42, self.f[i][0], self.f[i][1], self.f[i][2], 0, self.ft[i][0], self.ft[i][1],
+                                    self.ft[i][2], self.fn[i][0], self.fn[i][1], self.fn[i][2]] for i in
+                                   range(len(self.f))]).flatten().tolist()
+
+    json_or_js_file = open(filename, 'w')
+    json_or_js_file.write(json.dumps(mesh_data, indent=4))
+    json_or_js_file.close()
+
+
+def write_json(self, filename, header="", footer="", name="", include_faces=True, texture_mode=True):
+    import json
+
+    if os.path.dirname(filename) and not os.path.exists(os.path.dirname(filename)):
+        os.makedirs(os.path.dirname(filename))
+
+    name = name if name else self.basename
+    name = name if name else os.path.splitext(os.path.basename(filename))[0]
+
+    if texture_mode:
+        vertex_texture_pairs = {}
+        for face_index in range(len(self.f)):
+            for i in [0, 1, 2]:
+                v_index = self.f[face_index][i]
+                t_index = self.ft[face_index][i]
+                vertex_texture_pairs[(v_index, t_index)] = []
+        for face_index in range(len(self.f)):
+            for i in [0, 1, 2]:
+                v_index = self.f[face_index][i]
+                t_index = self.ft[face_index][i]
+                vertex_texture_pairs[(v_index, t_index)].append((face_index, i))
+        mesh_data = {'name': name,
+                     'vertices': [],
+                     'textures': []
+                     }
+        for v_index, t_index, faces_entries in vertex_texture_pairs.items():
+            mesh_data['vertices'].append()
+
+            if include_faces:
+                mesh_data['faces'] = list([[int(np.asscalar(i)) for i in list(x)] for x in self.f])
+
+    else:
+        mesh_data = {'name': name,
+                     'vertices': list([list(x) for x in self.v])
+                     }
+        if include_faces:
+            mesh_data['faces'] = list([[int(np.asscalar(i)) for i in list(x)] for x in self.f])
+
+    json_or_js_file = open(filename, 'w')
+    if os.path.basename(filename).endswith('js'):
+        json_or_js_file.write(header + '\nmesh = ') if header else json_or_js_file.write('var mesh = ')
+        json_or_js_file.write(json.dumps(mesh_data, indent=4))
+        json_or_js_file.write(footer)
+    else:
+        json_or_js_file.write(json.dumps(mesh_data, indent=4))
+    json_or_js_file.close()
+
+
+def set_landmark_indices_from_ppfile(self, ppfilename):
+    from xml.etree import ElementTree
+    tree = ElementTree.parse(ppfilename)
+
+    def get_xyz(e):
+        try:
+            return [float(e.attrib['x']), float(e.attrib['y']), float(e.attrib['z'])]
+        except:  # may happen if landmarks are just spaces
+            return [0, 0, 0]
+
+    self.landm_raw_xyz = dict((e.attrib['name'], get_xyz(e)) for e in tree.iter() if e.tag == 'point')
+    self.recompute_landmark_indices(ppfilename)
+
+
+def set_landmark_indices_from_lmrkfile(self, lmrkfilename):
+    with open(lmrkfilename, 'r') as lmrkfile:
+        self.landm_raw_xyz = {}
+
+        for line in lmrkfile.readlines():
+            if not line.strip():
+                continue
+            command = line.split()[0]
+            data = [float(x) for x in line.split()[1:]]
+
+            if command == '_scale':
+                selfscale_factor = np.matrix(data)
+            elif command == '_translate':
+                self.caesar_translation_vector = np.matrix(data)
+            elif command == '_rotation':
+                self.caesar_rotation_matrix = np.matrix(data).reshape(3, 3)
+            else:
+                self.landm_raw_xyz[command] = [data[1], data[2], data[0]]
+        self.recompute_landmark_indices(lmrkfilename)
+
+
+def _is_lmrkfile(filename):
+    is_lmrk = re.compile('^_scale\s[-\d\.]+\s+_translate(\s[-\d\.]+){3}\s+_rotation(\s[-\d\.]+){9}\s+')
+    with open(filename) as f:
+        data = f.read()
+        res = is_lmrk.match(data)
+    return res
+
+
+def set_landmark_indices_from_any(self, landmarks):
+    '''
+    Sets landmarks given any of:
+     - ppfile
+     - ldmk file
+     - dict of {name:inds} (i.e. mesh.landm)
+     - dict of {name:xyz} (i.e. mesh.landm_xyz)
+     - pkl, json, yaml file containing either of the above dicts
+    '''
+    import json
+    import pickle
+
+    try:
+        path_exists = os.path.exists(landmarks)
+    except:
+        path_exists = False
+    if path_exists:
+        if re.search(".ya{0,1}ml$", landmarks):
+            import yaml
+            with open(landmarks) as f:
+                self.set_landmarks_from_raw(yaml.load(f, Loader=yaml.FullLoader))
+        elif re.search(".json$", landmarks):
+            with open(landmarks) as f:
+                self.set_landmarks_from_raw(json.load(f))
+        elif re.search(".pkl$", landmarks):
+            with open(landmarks, "rb") as f:
+                self.set_landmarks_from_raw(pickle.load(f))
+        elif _is_lmrkfile(landmarks):
+            self.set_landmark_indices_from_lmrkfile(landmarks)
+        else:
+            try:
+                self.set_landmark_indices_from_ppfile(landmarks)
+            except:
+                raise Exception("Landmark file %s is of unknown format" % landmarks)
+    else:
+        self.set_landmarks_from_raw(landmarks)
+
+
+def load_from_file(self, filename, use_cpp=True):
+    if re.search(".ply$", filename):
+        self.load_from_ply(filename)
+    elif re.search(".obj$", filename):
+        # XXX experimental cpp obj loader, if problems, switch back to
+        if use_cpp:
+            self.load_from_obj_cpp(filename)
+        else:
+            self.load_from_obj(filename)
+
+    elif re.search(".bsf$", filename):
+        self.load_from_bsf(filename)
+    else:
+        raise NotImplementedError("Unknown mesh file format.")
+
+
+def load_from_ply(self, filename):
+    from os.path import abspath, dirname, join
+
+    test_data_folder = abspath(join(dirname(__file__), '..', 'data', 'unittest'))
+
+    from psbody.mesh.serialization import plyutils
+    try:
+        res = plyutils.read(filename)
+    except plyutils.error as e:
+        raise SerializationError(e)
+
+    self.v = np.array(res['pts']).T.copy()
+    self.f = np.array(res['tri']).T.copy()
+
+    if 'color' in res:
+        self.set_vertex_colors(np.array(res['color']).T.copy() / 255)
+    if 'normals' in res:
+        self.vn = np.array(res['normals']).T.copy()

mesh-fix-MSVC_compilation/mesh/sphere.py

@@ -0,0 +1,74 @@
+import numpy as np
+from .mesh import Mesh
+from .colors import name_to_rgb
+
+
+__all__ = ['Sphere']
+
+
+class Sphere(object):
+    def __init__(self, center, radius):
+        if(center.flatten().shape != (3,)):
+            raise Exception("Center should have size(1,3) instead of %s" % center.shape)
+        self.center = center.flatten()
+        self.radius = radius
+
+    def __str__(self):
+        return "%s:%s" % (self.center, self.radius)
+
+    def to_mesh(self, color=name_to_rgb['red']):
+        v = np.array([[0.0000, -1.000, 0.0000], [0.7236, -0.447, 0.5257],
+                      [-0.278, -0.447, 0.8506], [-0.894, -0.447, 0.0000],
+                      [-0.278, -0.447, -0.850], [0.7236, -0.447, -0.525],
+                      [0.2765, 0.4472, 0.8506], [-0.723, 0.4472, 0.5257],
+                      [-0.720, 0.4472, -0.525], [0.2763, 0.4472, -0.850],
+                      [0.8945, 0.4472, 0.0000], [0.0000, 1.0000, 0.0000],
+                      [-0.165, -0.850, 0.4999], [0.4253, -0.850, 0.3090],
+                      [0.2629, -0.525, 0.8090], [0.4253, -0.850, -0.309],
+                      [0.8508, -0.525, 0.0000], [-0.525, -0.850, 0.0000],
+                      [-0.688, -0.525, 0.4999], [-0.162, -0.850, -0.499],
+                      [-0.688, -0.525, -0.499], [0.2628, -0.525, -0.809],
+                      [0.9518, 0.0000, -0.309], [0.9510, 0.0000, 0.3090],
+                      [0.5876, 0.0000, 0.8090], [0.0000, 0.0000, 1.0000],
+                      [-0.588, 0.0000, 0.8090], [-0.951, 0.0000, 0.3090],
+                      [-0.955, 0.0000, -0.309], [-0.587, 0.0000, -0.809],
+                      [0.0000, 0.0000, -1.000], [0.5877, 0.0000, -0.809],
+                      [0.6889, 0.5257, 0.4999], [-0.262, 0.5257, 0.8090],
+                      [-0.854, 0.5257, 0.0000], [-0.262, 0.5257, -0.809],
+                      [0.6889, 0.5257, -0.499], [0.5257, 0.8506, 0.0000],
+                      [0.1626, 0.8506, 0.4999], [-0.425, 0.8506, 0.3090],
+                      [-0.422, 0.8506, -0.309], [0.1624, 0.8506, -0.499]])
+
+        f = np.array([[15, 3, 13], [13, 14, 15], [2, 15, 14], [13, 1, 14], [17, 2, 14], [14, 16, 17],
+                      [6, 17, 16], [14, 1, 16], [19, 4, 18], [18, 13, 19], [3, 19, 13], [18, 1, 13],
+                      [21, 5, 20], [20, 18, 21], [4, 21, 18], [20, 1, 18], [22, 6, 16], [16, 20, 22],
+                      [5, 22, 20], [16, 1, 20], [24, 2, 17], [17, 23, 24], [11, 24, 23], [23, 17, 6],
+                      [26, 3, 15], [15, 25, 26], [7, 26, 25], [25, 15, 2], [28, 4, 19], [19, 27, 28],
+                      [8, 28, 27], [27, 19, 3], [30, 5, 21], [21, 29, 30], [9, 30, 29], [29, 21, 4],
+                      [32, 6, 22], [22, 31, 32], [10, 32, 31], [31, 22, 5], [33, 7, 25], [25, 24, 33],
+                      [11, 33, 24], [24, 25, 2], [34, 8, 27], [27, 26, 34], [7, 34, 26], [26, 27, 3],
+                      [35, 9, 29], [29, 28, 35], [8, 35, 28], [28, 29, 4], [36, 10, 31], [31, 30, 36],
+                      [9, 36, 30], [30, 31, 5], [37, 11, 23], [23, 32, 37], [10, 37, 32], [32, 23, 6],
+                      [39, 7, 33], [33, 38, 39], [12, 39, 38], [38, 33, 11], [40, 8, 34], [34, 39, 40],
+                      [12, 40, 39], [39, 34, 7], [41, 9, 35], [35, 40, 41], [12, 41, 40], [40, 35, 8],
+                      [42, 10, 36], [36, 41, 42], [12, 42, 41], [41, 36, 9], [38, 11, 37], [37, 42, 38],
+                      [12, 38, 42], [42, 37, 10]]) - 1
+
+        return Mesh(v=v * self.radius + self.center, f=f, vc=np.tile(color, (v.shape[0], 1)))
+
+    def has_inside(self, point):
+        return np.linalg.norm(point - self.center) <= self.radius
+
+    def intersects(self, sphere):
+        return np.linalg.norm(sphere.center - self.center) < (self.radius + sphere.radius)
+
+    def intersection_vol(self, sphere):
+        if not self.intersects(sphere):
+            return 0
+        d = np.linalg.norm(sphere.center - self.center)
+        R, r = (self.radius, sphere.radius) if (self.radius > sphere.radius) else (sphere.radius, self.radius)
+        if R >= (d + r):
+            return (4 * np.pi * (r ** 3)) / 3
+
+        # http://mathworld.wolfram.com/Sphere-SphereIntersection.html
+        return (np.pi * (R + r - d) ** 2 * (d ** 2 + 2 * d * r - 3 * r * r + 2 * d * R + 6 * r * R - 3 * R * R)) / (12 * d)

mesh-fix-MSVC_compilation/mesh/src/AABB_n_tree.h

@@ -0,0 +1,355 @@
+// Author(s) : Javier Romero
+
+#ifndef AABB_N_TREE_H
+#define AABB_N_TREE_H
+
+#include <vector>
+
+#define CGAL_CFG_NO_CPP0X_VARIADIC_TEMPLATES 1
+#include <CGAL/AABB_tree.h>
+#include <CGAL/AABB_traits.h>
+#include <CGAL/internal/AABB_tree/nearest_point_triangle_3.h>
+#include <CGAL/Simple_cartesian.h>
+#include <CGAL/AABB_triangle_primitive.h>
+
+#include <CGAL/intersections.h>
+#include <CGAL/Bbox_3.h>
+
+#include <boost/cstdint.hpp>
+#include <boost/array.hpp>
+
+
+typedef CGAL::Simple_cartesian<double> K;
+using boost::uint32_t;
+using boost::uint64_t;
+using boost::array;
+using std::vector;
+
+typedef K::Point_3 Point;
+typedef K::Segment_3 Segment;
+typedef K::Triangle_3 Triangle;
+typedef K::Vector_3 Normal;
+typedef std::pair<Point,Normal> Point_Normal;
+
+typedef std::vector<Triangle>::iterator Iterator;
+typedef CGAL::AABB_triangle_primitive<K,Iterator> Primitive;
+
+
+namespace CGAL {
+    template<typename FT>
+    FT dist_point_normal(const Point_Normal& a, const Point_Normal& b, FT eps){
+        return (sqrt(squared_distance(a.first, b.first)) + eps*(1 - a.second*b.second));
+    }
+
+    // Adaptation of nearest_point_3 to take into account normals
+    // product with weight eps
+    template<typename FT>
+    Point_Normal nearest_pointnormal_3(const Point_Normal& origin,
+                                       const Triangle& triangle,
+                                       const Point_Normal& bound,
+                                       const FT eps,
+                                       const K& k){
+        // compute normal penalties
+        const FT dist_n_bound = eps*(1 - origin.second*bound.second);
+        //const Normal tri_n = unit_normal(triangle[0],triangle[1],triangle[2]);
+        Normal tri_n = triangle.supporting_plane().orthogonal_direction().vector();
+        tri_n = tri_n / sqrt(tri_n.squared_length());
+        const FT dist_n_triangle = eps*(1 - origin.second*tri_n);
+
+        // Distance from origin to bound
+        const FT dist_bound = sqrt(squared_distance(origin.first,bound.first)) + dist_n_bound;
+
+        // since dist_n_triangle < dist_triangle
+        if (dist_n_triangle > dist_bound)
+            return bound;
+
+        // Project origin on triangle supporting plane
+        const Point_Normal proj = std::make_pair(triangle.supporting_plane().projection(origin.first), tri_n);
+
+        const FT dist_proj = sqrt(squared_distance(origin.first,proj.first)) + dist_n_triangle;
+
+        Point moved_point;
+        // If point is projected outside, return bound
+        if ( dist_proj > dist_bound)
+            return bound;
+        // If proj is inside triangle, total dist is dist_proj
+        else if ( CGAL::internal::is_inside_triangle_3<K>(proj.first,triangle,moved_point,k) )
+            return proj;
+        // Else return the constructed point (nearest point of triangle from proj)
+        // if it is closest to origin than bound
+        else{
+            const FT dist_moved = sqrt(squared_distance(origin.first, moved_point)) + dist_n_triangle;
+            return (dist_moved > dist_bound) ? bound : std::make_pair(moved_point, tri_n);
+        }
+    }
+
+    // extends AABB_Traits with classes handling points with normals
+    template <typename GeomTraits, typename AABB_primitive>
+        class AABB_n_traits:public AABB_traits<GeomTraits,AABB_primitive>{
+
+    public:
+
+        typedef Point_Normal PointNormal;
+        typedef AABB_n_traits<GeomTraits, AABB_primitive> AT;
+
+        class Do_intersect{
+        public:
+            template<typename Query>
+                bool operator()(const Query& q, const CGAL::Bbox_3& bbox) const{
+                return CGAL::do_intersect(q, bbox);
+            }
+
+            template<typename Query>
+                bool operator()(const Query& q, const AABB_primitive& pr) const{
+                return GeomTraits().do_intersect_3_object()(q, pr.datum());
+            }
+
+            bool operator()(const typename GeomTraits::Triangle_3& q, const AABB_primitive& pr) const{
+
+                // if any point is the same, don't consider it'
+                if(q[0] == pr.datum()[0] || q[0] == pr.datum()[1] ||q[0] == pr.datum()[2] ||
+                   q[1] == pr.datum()[0] || q[1] == pr.datum()[1] ||q[1] == pr.datum()[2] ||
+                   q[2] == pr.datum()[0] || q[2] == pr.datum()[1] ||q[2] == pr.datum()[2])
+                    return false;
+                else
+                    return CGAL::do_intersect(q, pr.datum());
+            }
+        };
+
+        class Closest_point {
+            typedef typename AT::Point_3 Point;
+            typedef typename AT::PointNormal PointNormal;
+            typedef typename AT::Primitive Primitive;
+            typedef typename AT::FT FT;
+
+        public:
+
+            // for intersection: return the closest point on
+            // triangle pr or bound to pn
+            PointNormal operator()(const PointNormal& pn, const Primitive& pr,
+                                   const PointNormal& bound, FT eps) const {
+                return nearest_pointnormal_3(pn, pr.datum(), bound, eps, K());
+            }
+
+        };
+
+        class Compare_distance {
+            typedef typename AT::Point_3 Point;
+            typedef typename AT::PointNormal PointNormal;
+            typedef typename AT::FT FT;
+            typedef typename AT::Primitive Primitive;
+        public:
+
+            // create a sphere that contains all possible results
+            // (all points closer than current result) and
+            // check if pr intersects
+            template <class Solid>
+                CGAL::Comparison_result operator()(const PointNormal& p, const Solid& pr, const PointNormal& bound, FT eps) const
+                {
+                    // d_q = ||q - p|| + eps(1 - n_q*n_p) > ||q-p||
+                    // d_q < d_b -> ||q-p|| < d_b
+                    // a sphere containing all q such that ||q-p|| < d_b
+                    // contains all q such that d_q < d_b
+                    FT safe_dist = dist_point_normal(p,bound,eps);
+                    return GeomTraits().do_intersect_3_object()
+                        (GeomTraits().construct_sphere_3_object()
+                         (p.first, safe_dist*safe_dist), pr)?
+                        CGAL::SMALLER : CGAL::LARGER;
+                }
+        };
+
+        Closest_point closest_point_object() {return Closest_point();}
+        Compare_distance compare_distance_object() {return Compare_distance();}
+        Do_intersect do_intersect_object() {return Do_intersect();}
+
+    };// end of AABB_n_traits
+
+
+    /**
+     * @class Do_intersect_noself_traits
+     */
+    template<typename AABBTraits, typename Query>
+        class Do_intersect_noself_traits
+    {
+        typedef typename AABBTraits::FT FT;
+        typedef typename AABBTraits::Point_3 Point;
+        typedef typename AABBTraits::Primitive Primitive;
+        typedef typename AABBTraits::Bounding_box Bounding_box;
+        typedef typename AABBTraits::Primitive::Id Primitive_id;
+        typedef typename AABBTraits::Point_and_primitive_id Point_and_primitive_id;
+        typedef typename AABBTraits::Object_and_primitive_id Object_and_primitive_id;
+        typedef ::CGAL::AABB_node<AABBTraits> Node;
+        typedef typename ::CGAL::AABB_tree<AABBTraits>::size_type size_type;
+
+    public:
+    Do_intersect_noself_traits()
+        : m_is_found(false)
+            {}
+
+        bool go_further() const { return !m_is_found; }
+
+        void intersection(const Query& query, const Primitive& primitive)
+        {
+            if( AABBTraits().do_intersect_object()(query, primitive) )
+                m_is_found = true;
+        }
+
+        bool do_intersect(const Query& query, const Node& node) const
+        {
+            return AABBTraits().do_intersect_object()(query, node.bbox());
+        }
+
+        bool is_intersection_found() const { return m_is_found; }
+
+    private:
+        bool m_is_found;
+    };
+
+    /**
+     * @class Projection_n_traits
+     */
+    template <typename AABBTraits>
+        class Projection_n_traits
+        {
+            typedef typename AABBTraits::FT FT;
+            typedef typename AABBTraits::Point_3 Point;
+            typedef typename AABBTraits::PointNormal PointNormal;
+            typedef typename AABBTraits::Primitive Primitive;
+            typedef typename AABBTraits::Bounding_box Bounding_box;
+            typedef typename AABBTraits::Primitive::Id Primitive_id;
+            typedef typename AABBTraits::Point_and_primitive_id Point_and_primitive_id;
+            typedef typename AABBTraits::Object_and_primitive_id Object_and_primitive_id;
+            typedef ::CGAL::AABB_node<AABBTraits> Node;
+
+        public:
+        Projection_n_traits(const PointNormal& hint,
+                              const typename Primitive::Id& hint_primitive,
+                              const FT eps)
+            : m_closest_point(hint), m_closest_primitive(hint_primitive), eps(eps) {}
+
+            bool go_further() const { return true; }
+
+            void intersection(const PointNormal& query, const Primitive& primitive)
+            {
+                PointNormal new_closest_point = AABBTraits().closest_point_object()
+                    (query, primitive, m_closest_point, eps);
+                if(new_closest_point.first != m_closest_point.first)
+                    {
+                        m_closest_primitive = primitive.id();
+                        m_closest_point = new_closest_point; // this effectively shrinks the sphere
+                    }
+            }
+
+            bool do_intersect(const PointNormal& query, const Node& node) const
+            {
+                return AABBTraits().compare_distance_object()
+                    (query, node.bbox(), m_closest_point, eps) == CGAL::SMALLER;
+            }
+
+            Point closest_point() const { return m_closest_point.first; }
+            Point_and_primitive_id closest_point_and_primitive() const
+            {
+                return Point_and_primitive_id(m_closest_point.first, m_closest_primitive);
+            }
+
+        private:
+            PointNormal m_closest_point;
+            typename Primitive::Id m_closest_primitive;
+            const FT eps;
+        };
+
+    // Class that extends AABB tree with PointNormal Search
+    template <typename AABBTraits>
+        class AABB_n_tree:public AABB_tree<AABBTraits>{
+    public:
+        typedef typename AABBTraits::Point_3 Point;
+        typedef typename AABBTraits::PointNormal PointNormal;
+        typedef typename AABBTraits::Point_and_primitive_id Point_and_primitive_id;
+
+        AABB_n_tree():AABB_tree<AABBTraits>(){}
+
+        template<typename ConstPrimitiveIterator>
+            AABB_n_tree(ConstPrimitiveIterator first, ConstPrimitiveIterator beyond,
+                        typename AABBTraits::FT eps):
+        AABB_tree<AABBTraits>(first, beyond), eps(eps){}
+
+        // XXX The hint is random; that is slow and could be closer (euclideanly) than the best point
+        Point_and_primitive_id closest_point_and_primitive(const PointNormal& query) const{
+            // return closest_point_and_primitive(query,best_hint(query.first));
+            return closest_point_and_primitive(query,this->any_reference_point_and_id());
+        }
+
+        Point_and_primitive_id closest_point_and_primitive(const PointNormal& query,
+                                                           const Point_and_primitive_id& hint) const{
+
+            Normal hint_n = (*hint.second).supporting_plane().orthogonal_direction().vector();
+            PointNormal hint_pn = std::make_pair(hint.first, hint_n/sqrt(hint_n.squared_length()));
+            //            hint_pn = std::make_pair(Point(10000,10000,10000),Normal(0,0,1));
+            Projection_n_traits<AABBTraits> projection_traits(hint_pn, hint.second, eps);
+            this->traversal(query, projection_traits);
+            return projection_traits.closest_point_and_primitive();
+        }
+
+        template<typename Query>
+        bool do_intersect(const Query& query) const
+        {
+            //using namespace CGAL::internal::AABB_tree;
+            Do_intersect_noself_traits<AABBTraits, Query> traversal_traits;
+            this->traversal(query, traversal_traits);
+            return traversal_traits.is_intersection_found();
+        }
+
+        typename AABBTraits::FT eps;
+   };
+}
+
+typedef CGAL::AABB_n_traits<K, Primitive> AABB_n_triangle_traits;
+typedef AABB_n_triangle_traits::Point_and_primitive_id Point_and_Primitive_id;
+typedef CGAL::AABB_n_tree<AABB_n_triangle_traits> Tree;
+
+struct TreeAndTri {
+    TreeAndTri(const array<uint32_t, 3>* p_mesh_tri,
+               const array<double, 3>* p_mesh_points,
+               const double eps,
+               const size_t T,
+               const size_t P)
+    {
+        std::vector<K::Point_3> mesh_points;
+        mesh_points.reserve(P);
+        for(size_t pp=0; pp<P; ++pp){
+            mesh_points.push_back(K::Point_3(p_mesh_points[pp][0],
+                                             p_mesh_points[pp][1],
+                                             p_mesh_points[pp][2]));
+        }
+
+        triangles.reserve(T);
+        for(size_t tt=0; tt<T; ++tt) {
+            triangles.push_back(K::Triangle_3(mesh_points[p_mesh_tri[tt][0]],
+                                              mesh_points[p_mesh_tri[tt][1]],
+                                              mesh_points[p_mesh_tri[tt][2]]));
+        }
+
+        tree.eps = eps;
+        tree.rebuild(triangles.begin(), triangles.end());
+        //        tree.accelerate_distance_queries();
+    }
+
+    vector<K::Triangle_3> triangles;
+    Tree tree;
+};
+
+template<typename T>
+boost::uint64_t wrapPointer(T *ptr) {
+    return reinterpret_cast<uint64_t>(ptr);
+}
+template<typename T>
+T* unwrapPointer(uint64_t ptr) {
+    return reinterpret_cast<T*>(ptr);
+}
+
+#endif // AABB_N_TREE_H
+
+/***EMACS SETTINGS***/
+/* Local Variables: */
+/* tab-width: 2     */
+/* End:             */