Add bounding box params

.travis.yml

@@ -1,6 +1,10 @@
-
+sudo: true
+dist: trusty
+
 language: python
 
+service: docker
+
 matrix:
     include:
         - os: linux
@@ -43,7 +47,7 @@ install:
         conda create --yes -n test python="2.7";
       fi
     - source activate test
-    - conda install --yes numpy scipy matplotlib pip nose vtk
+    - conda install --yes numpy scipy matplotlib pip nose vtk sip=4.18
     - conda install --yes -c https://conda.anaconda.org/dlr-sc pythonocc-core
     - pip install setuptools
     - pip install enum34
@@ -52,8 +56,12 @@ install:
     - pip install coverage
     - python setup.py install
 
-script: coverage run test.py
-
+script:
+    - coverage run test.py
+    # Docker in travis works only with linux. 
+    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
+        docker run -u root docker.io/pygemdocker/pygem:latest /bin/sh -c "cd /home/PyGeM/build/PyGeM; coverage run test.py";
+      fi
 after_success:
     - coveralls
 

README.md

@@ -57,7 +57,34 @@ To uninstall the package you have to rerun the installation and record the insta
 > python setup.py install --record installed_files.txt
 > cat installed_files.txt | xargs rm -rf
 ```
+Alternatively, a way to run the PyGeM library is to use our prebuilt and high-performance Docker images.
+Docker containers are extremely lightweight, secure, and are based on open standards that run on all major Linux distributions, macOS and Microsoft Windows platforms.
 
+Install Docker for your platform by following [these instructions](https://docs.docker.com/engine/getstarted/step_one/).
+If using the Docker Toolbox (macOS versions < 10.10 or Windows versions < 10), make sure you run all commands inside the Docker Quickstart Terminal.
+
+Now we will pull the docker.io/pygemdocker/pygem image from our cloud infrastructure:
+```bash
+>  docker pull docker.io/pygemdocker/pygem:latest
+```
+Docker will pull the latest tag of the image pygemdocker/pygem from docker.io. The download is around 3.246 GB. The  image is a great place to start experimenting with PyGeM and includes all dependencies already compiled for you.
+Once the download is complete you can start PyGeM for the first time. Just run:
+```bash
+>  docker run -ti  pygemdocker/pygem:latest
+```
+To facilitate the devoloping, using the text editor,version control and other tools already installed on your computers,
+it is possible to share files from the host into the container:
+
+```bash
+>  docker run -ti -v $(pwd):/home/PyGeM/shared  pygemdocker/pygem:latest
+```
+To allow the X11 forwarding in the container, on Linux system just run:
+
+```bash
+>  docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix  -v $(pwd):/home/PyGeM/shared  pygemdocker/pygem:latest
+```
+
+For Windows system, you need to install Cygwin/X version and running the command in Cygwin terminal. While for mac system, you need to install xquartz. 
 
 ## Documentation
 **PyGeM** uses [Sphinx](http://www.sphinx-doc.org/en/stable/) for code documentation. To build the html versions of the docs simply:

dockerfiles/Dockerfile

@@ -0,0 +1,86 @@
+FROM phusion/baseimage:0.9.19
+
+# Get Ubuntu updates
+USER root
+RUN apt-get update -q && \ 
+    apt-get upgrade -y -o Dpkg::Options::="--force-confold" && \
+    apt-get -y install sudo && \
+    apt-get -y install locales && \
+    echo "C.UTF-8 UTF-8" > /etc/locale.gen && \
+    locale-gen && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Set locale environment
+ENV LC_ALL=C.UTF-8 \
+    LANG=C.UTF-8 \
+    LANGUAGE=C.UTF-8
+
+# OpenBLAS threads should be 1 to ensure performance
+RUN echo 1 > /etc/container_environment/OPENBLAS_NUM_THREADS && \
+    echo 0 > /etc/container_environment/OPENBLAS_VERBOSE
+
+
+# Set up user so that we do not run as root
+RUN useradd -m -s /bin/bash -G sudo,docker_env PyGeM && \
+    echo "PyGeM:docker" | chpasswd && \
+    echo "PyGeM ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+RUN touch /etc/service/syslog-forwarder/down
+COPY set-home-permissions.sh /etc/my_init.d/set-home-permissions.sh
+RUN chmod +x /etc/my_init.d/set-home-permissions.sh
+
+USER PyGeM
+ENV HOME /home/PyGeM
+RUN touch $HOME/.sudo_as_admin_successful && \
+    mkdir $HOME/shared && \
+    mkdir $HOME/build
+VOLUME /home/PyGeM/shared
+
+WORKDIR /home/PyGeM
+ENTRYPOINT ["sudo","/sbin/my_init","--quiet","--","sudo","-u","PyGeM","/bin/bash","-l","-c"]
+CMD ["/bin/bash","-i"]
+
+# utilities and libraries
+USER root
+RUN apt-get update -y; apt-get install -y --force-yes --fix-missing --no-install-recommends curl git unzip tree subversion vim cmake bison g++ gfortran openmpi-bin pkg-config wget libpcre3-dev bison flex swig libglu1-mesa pyqt4-dev-tools    
+RUN apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+RUN id PyGeM
+RUN chown -R PyGeM:PyGeM $HOME
+
+RUN cd /tmp  && \
+    wget https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh  && \
+    chmod +x miniconda.sh && \
+    bash miniconda.sh -b -p /usr/local/miniconda && \
+    rm /tmp/*
+ENV PATH=/usr/local/miniconda/bin:$PATH
+
+RUN echo "PATH=/usr/local/miniconda/bin:$PATH" >> ~/.profile
+RUN /bin/bash -c 'source  ~/.profile'
+
+RUN  hash -r  && \
+    conda config --set always_yes yes --set changeps1 no  && \
+    conda update -q conda  
+RUN  conda info -a  && \
+    conda create --yes -n test python="2.7";
+
+RUN /bin/bash -c 'source  activate test'  
+# The default sip version has api that is not compatible with qt4.
+RUN    conda install --yes numpy scipy matplotlib pip nose vtk sip=4.18 
+RUN    conda install --yes -c https://conda.anaconda.org/dlr-sc pythonocc-core  &&\
+    pip install setuptools && \
+    pip install enum34 && \
+    pip install numpy-stl && \
+    pip install coveralls && \
+    pip install coverage
+
+RUN cd $HOME  && \
+    cd build && \
+    git clone https://github.com/mathLab/PyGeM.git  && \ 
+    cd PyGeM && \
+    python setup.py install
+
+USER PyGeM
+
+

dockerfiles/set-home-permissions.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+# User can pass e.g. --env HOST_UID=1003 so that UID in the container matches
+# with the UID on the host. This is useful for Linux users, Mac and Windows
+# already do transparent mapping of shared volumes.
+if [ "$HOST_UID" ]; then
+    usermod -u $HOST_UID PyGeM
+fi
+if [ "$HOST_GID" ]; then
+    groupmod -g $HOST_GID PyGeM
+fi
+# This makes sure that all files in /home/fenics are accessible by the user
+# fenics. We exclude the folder ~/shared to reduce IO out to the host. Docker
+# for Mac, Docker for Windows and the UID/GID trick above should mean that file
+# permissions work seamlessly now.
+cd /home/PyGeM
+find . -maxdepth 1 | grep -v "./shared" | xargs chown -R PyGeM:PyGeM
+

pygem/params.py

@@ -1,9 +1,14 @@
 """
 Utilities for reading and writing parameters files to perform the desired geometrical morphing.
 """
-import os
 import ConfigParser
+import os
+
 import numpy as np
+from OCC.BRepBndLib import brepbndlib_Add
+from OCC.BRepMesh import BRepMesh_IncrementalMesh
+from OCC.Bnd import Bnd_Box
+
 import pygem.affine as at
 
 
@@ -294,6 +299,79 @@ def print_info(self):
 		print '\nposition_vertex_3 ='
 		print self.position_vertex_3
 
+	def build_bounding_box(self, shape, tol=1e-6, triangualte=False, triangulate_tol=1e-1):
+		min_xyz, max_xyz = self._calculate_bb_dimension(shape, tol, triangualte, triangulate_tol)
+		self.origin_box = min_xyz
+		self._set_box_dimensions(min_xyz, max_xyz)
+		self._set_position_of_vertices()
+		self._set_mapping()
+		self._set_transformation_params_to_zero()
+
+	def _set_box_origin(self, xyz):
+		self.origin_box = xyz
+
+	def _set_box_dimensions(self, min_xyz, max_xyz):
+		"""
+		Dimensions of the cage are set as distance from the origin (minimum) of the cage to
+		the maximal point in each dimension.
+		:return:
+		"""
+		dims = [max_xyz[i] - min_xyz[i] for i in range(3)]
+		self.lenght_box_x = dims[0]
+		self.lenght_box_y = dims[1]
+		self.lenght_box_z = dims[2]
+
+	def _set_position_of_vertices(self):
+		"""
+		Vertices of the control box around the object are set in this method.
+		Four vertex (non coplanar) are sufficient to uniquely identify a parallelepiped -- the
+		second half of the box is created as a mirror reflection of the first four vertices.
+		:return:
+		"""
+		origin_array = np.array(self.origin_box)
+		dim = [self.lenght_box_x, self.lenght_box_y, self.lenght_box_z]
+		self.position_vertex_0 = origin_array
+		self.position_vertex_1 = origin_array + np.array([dim[0], .0, .0])
+		self.position_vertex_2 = origin_array + np.array([.0, dim[1], .0])
+		self.position_vertex_3 = origin_array + np.array([.0, .0, dim[2]])
+
+	def _set_mapping(self):
+		dim = [self.lenght_box_x, self.lenght_box_y, self.lenght_box_z]
+		self.psi_mapping = np.diag([1. / dim[i] for i in range(3)])
+		self.inv_psi_mapping = np.diag(dim)
+
+	def _set_transformation_params_to_zero(self):
+		ctrl_pnts = self.n_control_points
+		self.array_mu_x = np.zeros(ctrl_pnts)
+		self.array_mu_y = np.zeros(ctrl_pnts)
+		self.array_mu_z = np.zeros(ctrl_pnts)
+
+	def _calculate_bb_dimension(self, shape, tol=1e-6, triangualte=False, triangulate_tol=1e-1):
+		""" return the bounding box of the TopoDS_Shape `shape`
+		Parameters
+		----------
+		shape : TopoDS_Shape or a subclass such as TopoDS_Face
+			the shape to compute the bounding box from
+		tol: float
+			tolerance of the computed boundingbox
+		triangualte : bool
+			if True only the dimensions of the bb will take into account every part of the shape (also not 'visible')
+			if False only the 'visible' part is taken into account
+			*** Explanation: every UV-Surface has to be rectangular. When a solid is created surfaces are trimmed.
+			*** the trimmed part, however, is still saved inside a file. It is just 'invisible' when drawn in a program
+		Returns
+		-------
+			tuple: consisting of two tuples: first one has coords of minimum, the second one coords of maximum
+		"""
+		bbox = Bnd_Box()
+		bbox.SetGap(tol)
+		if triangualte:
+			BRepMesh_IncrementalMesh(shape, triangulate_tol)
+		brepbndlib_Add(shape, bbox, triangualte)
+		xmin, ymin, zmin, xmax, ymax, zmax = bbox.Get()
+		xyz_min = np.array([xmin, ymin, zmin])
+		xyz_max = np.array([xmax, ymax, zmax])
+		return xyz_min, xyz_max
 
 
 class RBFParameters(object):