Merge branch 'master' into version2

Author: ndem0

.travis.yml

@@ -25,11 +25,11 @@ before_install:
     # We do this conditionally because it saves us some downloading if the
     # version is the same.
     - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then
-        wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
       else
         brew update;
         brew install python;
-        wget https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh -O miniconda.sh;
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
       fi
     - chmod +x miniconda.sh
     - bash miniconda.sh -b -p $HOME/miniconda

README.md

@@ -16,6 +16,9 @@
     <a href="https://www.codacy.com/app/mathLab/PyGeM?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=mathLab/PyGeM&amp;utm_campaign=Badge_Grade" target="_blank">
         <img alt="Codacy Badge" src="https://api.codacy.com/project/badge/Grade/7299abd9d61c4aa586903d80cea01c82">
     </a>
+    <a href="https://registry.hub.docker.com/r/sissamathlab/pygem">	
+	<img alt="Docker Pulls" src="https://img.shields.io/docker/pulls/sissamathlab/pygem">
+	</a>
 </p>
 
 [PyGeM](http://mathlab.github.io/PyGeM/) (Python Geometrical Morphing) is a python package that allows you to deform a given geometry or mesh with different deformation techniques such as FFD, RBF and IDW.
@@ -38,7 +41,7 @@
 **PyGeM** is a python package using **Free Form Deformation**, **Radial Basis Functions** and **Inverse Distance Weighting** to parametrize and morph complex geometries.  It is ideally suited for actual industrial problems, since it allows to handle:
 
 - Computer Aided Design files (in .iges, .step, and .stl formats)
-- Mesh files (in .unv and OpenFOAM formats)
+- Mesh files (in .unv, Elmer, and OpenFOAM formats)
 - Output files (in .vtk format)
 - LS-Dyna Keyword files (.k format)
 
@@ -83,25 +86,25 @@ Docker containers are extremely lightweight, secure, and are based on open stand
 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:
+Now we will pull the sissamathlab/pygem image from our cloud infrastructure:
 ```bash
->  docker pull docker.io/pygemdocker/pygem:latest
+>  docker pull sissamathlab/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
+>  docker run -ti  sissamathlab/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
+>  docker run -ti -v $(pwd):/home/PyGeM/shared  sissamathlab/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 $(pwd):/home/PyGeM/shared  pygemdocker/pygem:latest
+>  docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix  -v $(pwd):/home/PyGeM/shared  sissamathlab/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. 

dockerfiles/Dockerfile

@@ -25,9 +25,6 @@ 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
@@ -50,7 +47,7 @@ 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  && \
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh  && \
     chmod +x miniconda.sh && \
     bash miniconda.sh -b -p /usr/local/miniconda && \
     rm /tmp/*
@@ -63,7 +60,7 @@ 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";
+    conda create --yes -n test python="3.7";
 
 RUN /bin/bash -c 'source  activate test'  
 # The default sip version has api that is not compatible with qt4.
@@ -82,5 +79,3 @@ RUN cd $HOME  && \
     python setup.py install
 
 USER PyGeM
-
-

dockerfiles/set-home-permissions.sh

@@ -2,7 +2,7 @@
 PyGeM init
 """
 # __all__ = [
-#     'affine', 'filehandler', 'freeform', 'radial', 'openfhandler',
+#     'affine', 'filehandler', 'freeform', 'radial', 'openfhandler', 'elmerhandler',
 #     'stlhandler', 'unvhandler', 'vtkhandler', 'nurbshandler', 'stephandler',
 #     'igeshandler', 'utils', 'gui', 'khandler', 'idw'
 # ]
@@ -25,17 +25,4 @@ def get_current_year():
 from .ffd import FFD
 from .rbf import RBF
 from .idw import IDW
-from .rbf_factory import RBFFactory
-
-"""
-"""
-#from .radial import RBF
-#from .idw import IDW
-#from .filehandler import FileHandler
-#from .openfhandler import OpenFoamHandler
-#from .stlhandler import StlHandler
-#from .unvhandler import UnvHandler
-#from .vtkhandler import VtkHandler
-#from .khandler import KHandler
-#from .mdpahandler import MdpaHandler
-#from .params import *
+from .rbf_factory import RBFFactory

pygem/__init__.py

@@ -0,0 +1,97 @@
+"""
+Derived module from filehandler.py to handle ElmerFEM files.
+"""
+import numpy as np
+import pygem.filehandler as fh
+
+
+class ElmerHandler(fh.FileHandler):
+    """
+    Elmer mesh file handler class.
+
+    :cvar string infile: name of the input file to be processed.
+    :cvar string outfile: name of the output file where to write in.
+    :cvar list extensions: extensions of the input/output files. It
+        is equal to ['.node'] since elmer files do not have extension.
+    """
+
+    def __init__(self):
+        super(ElmerHandler, self).__init__()
+        self.extensions = ['.nodes']
+
+    def parse(self, filename):
+        """
+        Method to parse the `filename`. It returns a matrix with all
+        the coordinates.
+
+        :param string filename: name of the input file.
+        
+        :return: mesh_points: it is a `n_points`-by-3 matrix containing
+            the coordinates of the points of the mesh
+        :rtype: numpy.ndarray
+
+        .. todo::
+
+            - specify when it works
+        """
+        self._check_filename_type(filename)
+        self._check_extension(filename)
+
+        self.infile = filename
+
+        i = 0
+        n_points = 0
+        with open(self.infile, 'r') as input_file:
+            for line in input_file:
+                n_points += 1
+            mesh_points = np.zeros(shape=(n_points, 3))
+
+        with open(self.infile, 'r') as input_file:
+            
+            i = 0
+            for line in input_file:
+                numbers = line.split() #[n1 p x y z] -> [x y z]
+                del numbers[0:2] 
+
+                j = 0
+                for number in numbers:
+
+                    mesh_points[i][j] = float(number)
+                    j += 1
+                i += 1
+
+        return mesh_points
+
+    def write(self, mesh_points, filename):
+        """
+        Writes a elmer file, called filename, copying all the
+        lines from self.filename but the coordinates. mesh_points
+        is a matrix that contains the new coordinates to write in
+        the elmer file.
+
+        :param numpy.ndarray mesh_points: it is a `n_points`-by-3
+            matrix containing the coordinates of the points of the mesh.
+        :param string filename: name of the output file.
+
+        .. todo:: DOCS
+        """
+        self._check_filename_type(filename)
+        self._check_extension(filename)
+        self._check_infile_instantiation()
+        self.outfile = filename
+
+        n_points = mesh_points.shape[0]
+        i = 0
+        with open(self.infile, 'r') as input_file, open(self.outfile,
+                                                        'w') as output_file:
+            for line in input_file:
+                numbers = line.split() #[n1 p x y z]
+
+                output_file.write(numbers[0] + ' ' +numbers[1] + ' ' \
+                    + str(mesh_points[i][0]) + ' ' + str(mesh_points[i][1]) \
+                    + ' ' + str(mesh_points[i][2]))
+                i += 1
+
+                if i != n_points:
+                    output_file.write('\n')
+