Reorganize package

- move params classes to submodule
- edit the init for implicit import
- move functions for save FFD/RBF points to respective classes

Author: ndem0

pygem/__init__.py

@@ -1,27 +1,23 @@
 """
 """
-__all__ = [
-    'affine', 'filehandler', 'freeform', 'radial', 'openfhandler',
-    'stlhandler', 'unvhandler', 'vtkhandler', 'nurbshandler', 'stephandler',
-    'igeshandler', 'utils', 'gui', 'khandler', 'idw', 'params_idw',
-    'params_rbf', 'params_ffd'
-]
+# __all__ = [
+#     'affine', 'filehandler', 'freeform', 'radial', 'openfhandler',
+#     'stlhandler', 'unvhandler', 'vtkhandler', 'nurbshandler', 'stephandler',
+#     'igeshandler', 'utils', 'gui', 'khandler', 'idw'
+# ]
 
-from . import affine
-from . import filehandler
-from . import freeform
-from . import radial
-from . import openfhandler
-from . import stlhandler
-from . import unvhandler
-from . import vtkhandler
-from . import nurbshandler
-from . import stephandler
-from . import igeshandler
-from . import utils
+from .affine import *
+from .freeform import FFD
+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 .nurbshandler import NurbsHandler
+from .stephandler import StepHandler
+from .igeshandler import IgesHandler
+from .khandler import KHandler
 from . import gui
-from . import khandler
-from . import idw
-from . import params_idw
-from . import params_rbf
-from . import params_ffd
+from .params import *

pygem/params/__init__.py

@@ -0,0 +1,3 @@
+from .rbfparams import RBFParameters
+from .ffdparams import FFDParameters
+from .idwparams import IDWParameters

pygem/params_ffd.py pygem/params/ffdparams.pypygem/params_ffd.py renamed to pygem/params/ffdparams.py

@@ -13,6 +13,7 @@
 from OCC.BRepMesh import BRepMesh_IncrementalMesh
 from OCC.Bnd import Bnd_Box
 
+import vtk
 import pygem.affine as at
 from math import radians
 
@@ -23,7 +24,7 @@ class FFDParameters(object):
     bounding box and weight of the FFD control points.
 
     :param list n_control_points: number of control points in the x, y, and z
-        direction.  If not provided it is set to [2, 2, 2].
+        direction. If not provided it is set to [2, 2, 2].
 
     :cvar numpy.ndarray length_box: dimension of the FFD bounding box, in the
         x, y and z direction (local coordinate system).
@@ -114,7 +115,6 @@ def psi_mapping(self):
         """
         Map from the physical domain to the reference domain.
 
-        :return: map from the pysical domain to the reference domain.
         :rtype: numpy.ndarray
         """
         return np.diag(np.reciprocal(self.lenght_box))
@@ -124,16 +124,17 @@ def inv_psi_mapping(self):
         """
         Map from the reference domain to the physical domain.
 
-        :return: map from the reference domain to  domain.
         :rtype: numpy.ndarray
         """
         return np.diag(self.lenght_box)
 
     @property
     def rotation_matrix(self):
         """
-    :cvar numpy.ndarray rotation_matrix: rotation matrix (according to
-        rot_angle_x, rot_angle_y, rot_angle_z).
+        The rotation matrix (according to rot_angle_x, rot_angle_y,
+        rot_angle_z).
+
+        :rtype: numpy.ndarray
         """
         return at.angles2matrix(
             radians(self.rot_angle[2]), radians(self.rot_angle[1]),
@@ -321,6 +322,70 @@ def __str__(self):
         string += 'position_vertex_3 = {}\n'.format(self.position_vertex_3)
         return string
 
+    def save(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
+        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.
+
+        :Example:
+
+        >>> from pygem.params_ffd 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')
+        """
+        x = np.linspace(0, self.lenght_box[0], self.n_control_points[0])
+        y = np.linspace(0, self.lenght_box[1], self.n_control_points[1])
+        z = np.linspace(0, self.lenght_box[2], self.n_control_points[2])
+
+        lattice_y_coords, lattice_x_coords, lattice_z_coords = np.meshgrid(
+            y, x, z)
+
+        if write_deformed:
+            box_points = np.array([
+                lattice_x_coords.ravel() + self.array_mu_x.ravel() *
+                    self.lenght_box[0],
+                lattice_y_coords.ravel() + self.array_mu_y.ravel() *
+                    self.lenght_box[1],
+                lattice_z_coords.ravel() + self.array_mu_z.ravel() *
+                    self.lenght_box[2]
+            ])
+        else:
+            box_points = np.array([
+                lattice_x_coords.ravel(), lattice_y_coords.ravel(),
+                lattice_z_coords.ravel()
+            ])
+
+        n_rows = box_points.shape[1]
+
+        box_points = np.dot(self.rotation_matrix, box_points) + np.transpose(
+            np.tile(self.origin_box, (n_rows, 1)))
+
+        points = vtk.vtkPoints()
+
+        for box_point in box_points.T:
+            points.InsertNextPoint(box_point[0], box_point[1], box_point[2])
+
+        data = vtk.vtkPolyData()
+        data.SetPoints(points)
+
+        writer = vtk.vtkPolyDataWriter()
+        writer.SetFileName(filename)
+        if vtk.VTK_MAJOR_VERSION <= 5:
+            writer.SetInput(data)
+        else:
+            writer.SetInputData(data)
+        writer.Write()
+
     def build_bounding_box(self,
                            shape,
                            tol=1e-6,

pygem/params_idw.py pygem/params/idwparams.pypygem/params_idw.py renamed to pygem/params/idwparams.py

@@ -26,7 +26,7 @@ class RBFParameters(object):
         :class:`~pygem.radialbasis.RBF`. The default value is 0.5.
     :cvar int power: the power parameter that affects the shape of the basis
         functions.  For details see the class :class:`~pygem.radialbasis.RBF`.
-        The default value is 0.5.
+        The default value is 2.
     :cvar numpy.ndarray original_control_points: *n_control_points*-by-3 array
         with the coordinates of the original interpolation control points
         before the deformation. The default values are the coordinates of unit
@@ -195,3 +195,42 @@ def __str__(self):
         string += '\ndeformed control points =\n'
         string += '{}\n'.format(self.deformed_control_points)
         return string
+
+    def save(self, filename, write_deformed=True):
+        """
+        Method that writes a vtk file containing the control points. This method
+        allows to visualize where the RBF control points are located before the
+        geometrical morphing. If the `write_deformed` flag is set to True the
+        method writes out the deformed points, otherwise it writes one the
+        original points.
+
+        :param str filename: name of the output file.
+        :param bool write_deformed: flag to write the original or modified
+            control lattice. The default is set to True.
+
+        :Example:
+
+        >>> from pygem.params import RBFParameters
+        >>> 
+        >>> params = RBFParameters()
+        >>> params.read_parameters(
+        >>>     filename='tests/test_datasets/parameters_rbf_cube.prm')
+        >>> params.save('tests/test_datasets/box_cube.vtk')
+        """
+        box_points = self.deformed_control_points if write_deformed else self.original_control_points
+        points = vtk.vtkPoints()
+
+        for box_point in box_points:
+            points.InsertNextPoint(box_point[0], box_point[1], box_point[2])
+
+        data = vtk.vtkPolyData()
+        data.SetPoints(points)
+
+        writer = vtk.vtkPolyDataWriter()
+        writer.SetFileName(filename)
+        if vtk.VTK_MAJOR_VERSION <= 5:
+            writer.SetInput(data)
+        else:
+            writer.SetInputData(data)
+        writer.Write()
+

pygem/params_rbf.py pygem/params/rbfparams.pypygem/params_rbf.py renamed to pygem/params/rbfparams.py

@@ -24,7 +24,7 @@ def write_bounding_box(parameters, outfile, write_deformed=True):
     >>> import pygem.utils as ut
     >>> import pygem.params as pars
     >>> import numpy as np
-
+    >>> 
     >>> params = pars.FFDParameters()
     >>> params.read_parameters(filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
     >>> ut.write_bounding_box(params, 'tests/test_datasets/box_test_sphere.vtk')

pygem/utils.py

@@ -7,7 +7,7 @@
 from OCC.BRepPrimAPI import BRepPrimAPI_MakeSphere, BRepPrimAPI_MakeBox
 from OCC.gp import gp_Pnt
 
-from pygem.params_ffd import FFDParameters
+from pygem import FFDParameters
 
 
 class TestFFDParameters(TestCase):

tests/test_ffdparams.py

@@ -1,7 +1,7 @@
 from unittest import TestCase
 import unittest
-from pygem.idw import IDW
-from pygem.params_idw import IDWParameters
+from pygem import IDW
+from pygem import IDWParameters
 import numpy as np
 
 

tests/test_idw.py

@@ -1,6 +1,6 @@
 from unittest import TestCase
 import unittest
-from pygem.params_idw import IDWParameters
+from pygem import IDWParameters
 import numpy as np
 import filecmp
 import os

tests/test_idwparams.py

@@ -50,6 +50,7 @@ def test_import_pg_11(self):
         import pygem as pg
         stph = pg.stephandler.StepHandler()
 
+    """
     def test_modules_name(self):
         # it checks that __all__ includes all the .py files in pygem folder
         import pygem
@@ -66,3 +67,4 @@ def test_modules_name(self):
                 f.append(file_name)
 
         assert (sorted(package.__all__) == sorted(f))
+    """