Merge pull request #151 from mtezzele/doc

fix documentation and tests for save_points

Author: mtezzele

.travis.yml

@@ -50,7 +50,7 @@ install:
       fi
     - source activate test
     - pip install numpy scipy matplotlib vtk nose
-    - conda install --yes -c https://conda.anaconda.org/dlr-sc pythonocc-core==0.17
+    - conda install --yes -c conda-forge -c dlr-sc -c pythonocc -c oce pythonocc-core==0.17.3 python=2
     - pip install setuptools
     - pip install coveralls
     - pip install coverage

README.md

@@ -48,13 +48,13 @@ See the [**Examples**](#examples) section below and the [**Tutorials**](tutorial
 
 
 ## Dependencies and installation
-**PyGeM** requires `numpy`, `scipy`, `matplotlib`, `vtk`, `sphinx` (for the documentation) and `nose` (for local test). They can be easily installed via `pip`. 
+**PyGeM** requires `numpy`, `scipy`, `matplotlib`, `vtk`, `numpy-stl`, `sphinx` (for the documentation) and `nose` (for local test). They can be easily installed via `pip`. The code is compatible with Python 2.7.
 Moreover **PyGeM** depends on `OCC`. These requirements cannot be satisfied through `pip`.
 Please see the table below for instructions on how to satisfy the requirements.
 
-| Package | Version  | Comment                                                                    |
-|---------|----------|----------------------------------------------------------------------------|
-| OCC     | == 0.17  | See pythonocc.org or github.com.tpaviot/pythonocc-core for instructions or `conda install -c https://conda.anaconda.org/dlr-sc pythonocc-core==0.17` |
+| Package | Version     | Comment                                                                    |
+|---------|-------------|----------------------------------------------------------------------------|
+| OCC     | ==0.17.3    | See pythonocc.org or github.com.tpaviot/pythonocc-core for instructions or `conda install -c conda-forge -c dlr-sc -c pythonocc -c oce pythonocc-core==0.17.3 python=2` |
 
 
 The official distribution is on GitHub, and you can clone the repository using

pygem/freeform.py

@@ -10,28 +10,28 @@
     consists in three different step:
     
     - Mapping the physical domain to the reference one with map
-    :math:`\\boldsymbol{\psi}`.  In the code it is named *transformation*.
-      
+      :math:`\\boldsymbol{\\psi}`.  In the code it is named *transformation*.
+
     - Moving some control points to deform the lattice with :math:`\\hat{T}`.
-    The movement of the control points is basically the weight (or displacement)
-    :math:`\\boldsymbol{\mu}` we set in the *parameters file*.
-      
+      The movement of the control points is basically the weight (or displacement)
+      :math:`\\boldsymbol{\\mu}` we set in the *parameters file*.
+
     - Mapping back to the physical domain with map
-    :math:`\\boldsymbol{\psi}^-1`.  In the code it is named
-    *inverse_transformation*.
-      
+      :math:`\\boldsymbol{\\psi}^{-1}`.  In the code it is named
+      *inverse_transformation*.
+
     FFD map (:math:`T`) is the composition of the three maps, that is
-    
+
     .. math:: T(\\cdot, \\boldsymbol{\\mu}) = (\\Psi^{-1} \\circ \\hat{T} \\circ
             \\Psi) (\\cdot, \\boldsymbol{\\mu})
-            
+
     In this way, every point inside the FFD box changes it position according to
-    
-    .. math:: \\boldsymbol{P} = \\boldsymbol{\psi}^-1 \\left( \\sum_{l=0} ^L
-            \\sum_{m=0} ^M \\sum_{n=0} ^N
+
+    .. math:: \\boldsymbol{P} = \\boldsymbol{\\psi}^{-1} \\left( \\sum_{l=0}^L
+            \\sum_{m=0}^M \\sum_{n=0}^N
             \\mathsf{b}_{lmn}(\\boldsymbol{\\psi}(\\boldsymbol{P}_0))
             \\boldsymbol{\\mu}_{lmn} \\right)
-        
+
     where :math:`\\mathsf{b}_{lmn}` are Bernstein polynomials.  We improve the
     traditional version by allowing a rotation of the FFD lattice in order to
     give more flexibility to the tool.
@@ -56,21 +56,21 @@ class FFD(object):
 
     :cvar FFDParameters parameters: parameters of the Free Form Deformation.
     :cvar numpy.ndarray original_mesh_points: coordinates of the original points
-        of the mesh.  The shape is `n_points`-by-3.
+        of the mesh. The shape is `n_points`-by-3.
     :cvar numpy.ndarray modified_mesh_points: coordinates of the points of the
-        deformed mesh.  The shape is `n_points`-by-3.
+        deformed mesh. The shape is `n_points`-by-3.
 
     :Example:
 
-    >>> import pygem.freeform as ffd
-    >>> import pygem.params as ffdp
-    >>> import numpy as np
-    >>> ffd_parameters = ffdp.FFDParameters()
-    >>> ffd_parameters.read_parameters('tests/test_datasets/parameters_test_ffd_sphere.prm')
-    >>> original_mesh_points = np.load('tests/test_datasets/meshpoints_sphere_orig.npy')
-    >>> free_form = ffd.FFD(ffd_parameters, original_mesh_points)
-    >>> free_form.perform()
-    >>> new_mesh_points = free_form.modified_mesh_points
+        >>> import pygem.freeform as ffd
+        >>> import pygem.params as ffdp
+        >>> import numpy as np
+        >>> ffd_params = ffdp.FFDParameters()
+        >>> ffd_params.read_parameters('tests/test_datasets/parameters_test_ffd_sphere.prm')
+        >>> original_mesh_points = np.load('tests/test_datasets/meshpoints_sphere_orig.npy')
+        >>> free_form = ffd.FFD(ffd_params, original_mesh_points)
+        >>> free_form.perform()
+        >>> new_mesh_points = free_form.modified_mesh_points
     """
 
     def __init__(self, ffd_parameters, original_mesh_points):

pygem/idw.py

@@ -17,7 +17,7 @@
 
     The interpolation value :math:`u` of a given point :math:`\\mathrm{x}`
     from a set of samples :math:`u_k = u(\\mathrm{x}_k)`, with
-    :math:`k = 1,2,\dotsc,\\mathcal{N}`, is given by:
+    :math:`k = 1,2,\\dotsc,\\mathcal{N}`, is given by:
 
     .. math::
         u(\\mathrm{x}) = \\displaystyle\\sum_{k=1}^\\mathcal{N}

pygem/params/ffdparams.py

@@ -40,33 +40,33 @@ class FFDParameters(object):
 
     :Example: from file
 
-    >>> import pygem.params as ffdp
-    >>>
-    >>> # Reading an existing file
-    >>> params1 = ffdp.FFDParameters()
-    >>> params1.read_parameters(
-    >>>     filename='tests/test_datasets/parameters_test_ffd_identity.prm')
-    >>> 
-    >>> # Creating a default parameters file with the right dimensions (if the
-    >>> # file does not exists it is created with that name). So it is possible
-    >>> # to manually edit it and read it again.
-    >>> params2 = ffdp.FFDParameters(n_control_points=[2, 3, 2])
-    >>> params2.read_parameters(filename='parameters_test.prm')
-    >>> 
-    >>> # Creating bounding box of the given shape
-    >>> from OCC.IGESControl import IGESControl_Reader
-    >>> params3 = ffdp.FFDParameters()
-    >>> reader = IGESControl_Reader()
-    >>> reader.ReadFile('tests/test_datasets/test_pipe.igs')
-    >>> reader.TransferRoots()
-    >>> shape = reader.Shape()
-    >>> params3.build_bounding_box(shape)
+        >>> import pygem.params as ffdp
+        >>>
+        >>> # Reading an existing file
+        >>> params1 = ffdp.FFDParameters()
+        >>> params1.read_parameters(
+        >>>     filename='tests/test_datasets/parameters_test_ffd_identity.prm')
+        >>> 
+        >>> # Creating a default parameters file with the right dimensions (if the
+        >>> # file does not exists it is created with that name). So it is possible
+        >>> # to manually edit it and read it again.
+        >>> params2 = ffdp.FFDParameters(n_control_points=[2, 3, 2])
+        >>> params2.read_parameters(filename='parameters_test.prm')
+        >>> 
+        >>> # Creating bounding box of the given shape
+        >>> from OCC.IGESControl import IGESControl_Reader
+        >>> params3 = ffdp.FFDParameters()
+        >>> reader = IGESControl_Reader()
+        >>> reader.ReadFile('tests/test_datasets/test_pipe.igs')
+        >>> reader.TransferRoots()
+        >>> shape = reader.Shape()
+        >>> params3.build_bounding_box(shape)
 
     .. note::
         Four vertex (non coplanar) are sufficient to uniquely identify a
         parallelepiped.
         If the four vertex are coplanar, an assert is thrown when
-        affine_points_fit is used.
+        `affine_points_fit is used.
 
     """
 
@@ -339,21 +339,21 @@ def save_points(self, filename, write_deformed=True):
         Method that writes a vtk file containing the FFD lattice. This method
         allows to visualize where the FFD control points are located before the
         geometrical morphing. If the `write_deformed` flag is set to True the
-        method writes out the deformed lattice, otherwise it writes one the
+        method writes out the deformed lattice, otherwise it writes the
         original undeformed lattice.
 
         :param str filename: name of the output file.
         :param bool write_deformed: flag to write the original or modified FFD
-            control lattice.  The default is set to True.
+            control lattice. The default is True.
 
         :Example:
 
-        >>> from pygem.params import FFDParameters
-        >>> 
-        >>> params = FFDParameters()
-        >>> params.read_parameters(
-        >>>     filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
-        >>> params.save('tests/test_datasets/box_test_sphere.vtk')
+            >>> from pygem.params import FFDParameters
+            >>> 
+            >>> params = FFDParameters()
+            >>> params.read_parameters(
+            >>>     filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
+            >>> params.save_points('tests/test_datasets/box_test_sphere.vtk')
 
         .. note::
             In order to visualize the points in Paraview, please select the

pygem/params/rbfparams.py

@@ -208,12 +208,12 @@ def save_points(self, filename, write_deformed=True):
 
         :Example:
 
-        >>> from pygem.params import RBFParameters
-        >>>
-        >>> params = RBFParameters()
-        >>> params.read_parameters(
-        >>>     filename='tests/test_datasets/parameters_rbf_cube.prm')
-        >>> params.save_points('tests/test_datasets/box_cube.vtk')
+            >>> from pygem.params import RBFParameters
+            >>>
+            >>> params = RBFParameters()
+            >>> params.read_parameters(
+            >>>     filename='tests/test_datasets/parameters_rbf_cube.prm')
+            >>> params.save_points('tests/test_datasets/box_cube.vtk')
 
         .. note::
             In order to visualize the points in Paraview, please select the

pygem/radial.py

@@ -83,23 +83,23 @@ class RBF(object):
 
     :Example:
 
-    >>> import pygem.radial as rbf
-    >>> import pygem.params as rbfp
-    >>> import numpy as np
-    >>> rbf_parameters = rbfp.RBFParameters()
-    >>> fname = 'tests/test_datasets/parameters_rbf_cube.prm'
-    >>> rbf_parameters.read_parameters(fname)
-    >>> nx, ny, nz = (20, 20, 20)
-    >>> mesh = np.zeros((nx * ny * nz, 3))
-    >>> xv = np.linspace(0, 1, nx)
-    >>> yv = np.linspace(0, 1, ny)
-    >>> zv = np.linspace(0, 1, nz)
-    >>> z, y, x = np.meshgrid(zv, yv, xv)
-    >>> mesh = np.array([x.ravel(), y.ravel(), z.ravel()])
-    >>> original_mesh_points = mesh.T
-    >>> radial_trans = rbf.RBF(rbf_parameters, original_mesh_points)
-    >>> radial_trans.perform()
-    >>> new_mesh_points = radial_trans.modified_mesh_points
+        >>> import pygem.radial as rbf
+        >>> import pygem.params as rbfp
+        >>> import numpy as np
+        >>> rbf_parameters = rbfp.RBFParameters()
+        >>> fname = 'tests/test_datasets/parameters_rbf_cube.prm'
+        >>> rbf_parameters.read_parameters(fname)
+        >>> nx, ny, nz = (20, 20, 20)
+        >>> mesh = np.zeros((nx * ny * nz, 3))
+        >>> xv = np.linspace(0, 1, nx)
+        >>> yv = np.linspace(0, 1, ny)
+        >>> zv = np.linspace(0, 1, nz)
+        >>> z, y, x = np.meshgrid(zv, yv, xv)
+        >>> mesh = np.array([x.ravel(), y.ravel(), z.ravel()])
+        >>> original_mesh_points = mesh.T
+        >>> radial_trans = rbf.RBF(rbf_parameters, original_mesh_points)
+        >>> radial_trans.perform()
+        >>> new_mesh_points = radial_trans.modified_mesh_points
     """
 
     def __init__(self, rbf_parameters, original_mesh_points):

tests/test_datasets/box_test_cube.vtk

@@ -0,0 +1,8 @@
+# vtk DataFile Version 4.2
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+-0.1 0 0 0 0 1 0 1 0 
+1 0 0 0 1 1 1 0 1 
+1 1 0 1 1 1 

tests/test_datasets/box_test_cube_deformed.vtk

@@ -0,0 +1,8 @@
+# vtk DataFile Version 4.2
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 8 float
+0.1 0.2 0.3 0 0 1 0 1 0 
+1 0 0 0 0.8 1 1 0 1 
+1 1 0 1.2 1.2 1.2 

tests/test_datasets/box_test_sphere.vtk

@@ -0,0 +1,10 @@
+# vtk DataFile Version 4.2
+vtk output
+ASCII
+DATASET POLYDATA
+POINTS 12 float
+-20 -55 -45 -4.37166 -55 43.6327 -42.9398 31.9333 -40.9551 
+-27.3115 31.9333 47.6776 1.40315 -49.1766 -48.774 17.0315 -49.1766 39.8587 
+-21.5367 37.7568 -44.729 -5.90834 37.7568 43.9037 22.8063 -43.3531 -52.5479 
+38.4346 -43.3531 36.0848 -0.133524 43.5802 -48.503 15.4948 43.5802 40.1297 
+