fix codacy issues, erase vtk code for older versions

pygem/affine.py

@@ -4,8 +4,8 @@
 """
 import math
 import sys
-import numpy as np
 from functools import reduce
+import numpy as np
 
 
 def angles2matrix(rot_z=0, rot_y=0, rot_x=0):

pygem/freeform.py

@@ -150,19 +150,19 @@ def perform(self):
 
         # shift_mesh_points needs to be transposed to be summed with mesh_points
         # apply inverse transformation to shifted mesh points
-        new_mesh_points = self._transform_points(np.transpose(shift_mesh_points) +
-          mesh_points, inverse_transformation) + \
-           translation
+        new_mesh_points = self._transform_points(
+            np.transpose(shift_mesh_points) + mesh_points,
+            inverse_transformation) + translation
 
         # merge non-shifted mesh points with shifted ones
         self.modified_mesh_points = np.copy(self.original_mesh_points)
-        self.modified_mesh_points[(reference_frame_mesh_points[:,0] >= 0.) &
-          (reference_frame_mesh_points[:,0] <= 1.) &
-          (reference_frame_mesh_points[:,1] >= 0.) &
-          (reference_frame_mesh_points[:,1] <= 1.) &
-          (reference_frame_mesh_points[:,2] >= 0.) &
-          (reference_frame_mesh_points[:,2] <= 1.)] \
-         = new_mesh_points
+        self.modified_mesh_points[(reference_frame_mesh_points[:, 0] >= 0.)
+                                  & (reference_frame_mesh_points[:, 0] <= 1.) &
+                                  (reference_frame_mesh_points[:, 1] >= 0.) &
+                                  (reference_frame_mesh_points[:, 1] <= 1.) &
+                                  (reference_frame_mesh_points[:, 2] >= 0.) &
+                                  (reference_frame_mesh_points[:, 2] <=
+                                   1.)] = new_mesh_points
 
     @staticmethod
     def _transform_points(original_points, transformation):

pygem/idw.py

@@ -25,21 +25,18 @@
         {\\displaystyle\\sum_{j=1}^\\mathcal{N} w(\\mathrm{x},\\mathrm{x}_j)}
         u_k
 
-
     where, in general, :math:`w(\\mathrm{x}, \\mathrm{x}_i)` represents the
     weighting function:
 
     .. math::
         w(\\mathrm{x}, \\mathrm{x}_i) = \\| \\mathrm{x} - \\mathrm{x}_i \\|^{-p}
-    
+
     being :math:`\\| \\mathrm{x} - \\mathrm{x}_i \\|^{-p} \\ge 0` is the
     Euclidean distance between :math:`\\mathrm{x}` and data point
     :math:`\\mathrm{x}_i` and :math:`p` is a power parameter, typically equal to
     2.
-
 """
 import numpy as np
-
 from scipy.spatial.distance import cdist
 
 
@@ -91,7 +88,10 @@ def perform(self):
         """
 
         def distance(u, v):
-            return np.linalg.norm(u - v, self.parameters.power)
+            """
+            Norm of u - v
+            """
+            return np.linalg.norm(u - v, ord=self.parameters.power)
 
         # Compute displacement of the control points
         displ = (self.parameters.deformed_control_points -

pygem/igeshandler.py

@@ -1,7 +1,6 @@
 """
 Derived module from filehandler.py to handle iges and igs files.
 """
-
 from OCC.IGESControl import (IGESControl_Reader, IGESControl_Writer,
                              IGESControl_Controller_Init)
 from OCC.IFSelect import IFSelect_RetDone

pygem/openfhandler.py

@@ -11,8 +11,8 @@ class OpenFoamHandler(fh.FileHandler):
 
     :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 [''] since
-        openFOAM files do not have extension.
+    :cvar list extensions: extensions of the input/output files. It
+        is equal to [''] since openFOAM files do not have extension.
     """
 
     def __init__(self):
@@ -21,12 +21,13 @@ def __init__(self):
 
     def parse(self, filename):
         """
-        Method to parse the `filename`. It returns a matrix with all the coordinates.
+        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
+        :return: mesh_points: it is a `n_points`-by-3 matrix containing
+            the coordinates of the points of the mesh
         :rtype: numpy.ndarray
 
         .. todo::
@@ -58,12 +59,13 @@ def parse(self, filename):
 
     def write(self, mesh_points, filename):
         """
-        Writes a openFOAM 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 openFOAM file.
+        Writes a openFOAM 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 openFOAM file.
 
-        :param numpy.ndarray mesh_points: it is a `n_points`-by-3 matrix containing
-            the coordinates of the points of the mesh.
+        :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
@@ -82,8 +84,8 @@ def write(self, mesh_points, filename):
             for line in input_file:
                 nrow += 1
                 if 20 < nrow < 21 + n_points:
-                    output_file.write('(' + str(mesh_points[i][0]) + ' ' + str(mesh_points[i][1]) + \
-                       ' ' + str(mesh_points[i][2]) +')')
+                    output_file.write('(' + str(mesh_points[i][0]) + ' ' + str(
+                        mesh_points[i][1]) + ' ' + str(mesh_points[i][2]) + ')')
                     output_file.write('\n')
                     i += 1
                 else:

pygem/params/__init__.py

@@ -1,3 +1,6 @@
+"""
+params init
+"""
 from .rbfparams import RBFParameters
 from .ffdparams import FFDParameters
 from .idwparams import IDWParameters

pygem/params/ffdparams.py

@@ -1,21 +1,18 @@
 """
-Utilities for reading and writing parameters files to perform the desired
+Utilities for reading and writing parameters files to perform FFD
 geometrical morphing.
 """
 try:
     import configparser as configparser
 except ImportError:
     import ConfigParser as configparser
 import os
-
 import numpy as np
+from OCC.Bnd import Bnd_Box
 from OCC.BRepBndLib import brepbndlib_Add
 from OCC.BRepMesh import BRepMesh_IncrementalMesh
-from OCC.Bnd import Bnd_Box
-
 import vtk
 import pygem.affine as at
-from math import radians
 
 
 class FFDParameters(object):
@@ -44,7 +41,7 @@ class FFDParameters(object):
     :Example: from file
 
     >>> import pygem.params as ffdp
-    >>> 
+    >>>
     >>> # Reading an existing file
     >>> params1 = ffdp.FFDParameters()
     >>> params1.read_parameters(
@@ -115,8 +112,8 @@ def rotation_matrix(self):
         :rtype: numpy.ndarray
         """
         return at.angles2matrix(
-            radians(self.rot_angle[2]), radians(self.rot_angle[1]),
-            radians(self.rot_angle[0]))
+            np.radians(self.rot_angle[2]), np.radians(self.rot_angle[1]),
+            np.radians(self.rot_angle[0]))
 
     @property
     def position_vertices(self):
@@ -213,69 +210,99 @@ def write_parameters(self, filename='parameters.prm'):
         output_string += 'n control points z: ' + str(
             self.n_control_points[2]) + '\n'
 
-        output_string += '\n# box lenght indicates the length of the FFD bounding box along the three canonical directions (x, y, z).\n'
+        output_string += '\n# box lenght indicates the length of the FFD '
+        output_string += 'bounding box along the three canonical directions (x, y, z).\n'
+
         output_string += '# It uses the local coordinate system.\n'
-        output_string += '# For example to create a 2 x 1.5 x 3 meters box use the following: lenght box: 2.0, 1.5, 3.0\n'
+        output_string += '# For example to create a 2 x 1.5 x 3 meters box '
+        output_string += 'use the following: lenght box: 2.0, 1.5, 3.0\n'
+
         output_string += 'box lenght x: ' + str(self.lenght_box[0]) + '\n'
         output_string += 'box lenght y: ' + str(self.lenght_box[1]) + '\n'
         output_string += 'box lenght z: ' + str(self.lenght_box[2]) + '\n'
 
-        output_string += '\n# box origin indicates the x, y, and z coordinates of the origin of the FFD bounding box. That is center of\n'
-        output_string += '# rotation of the bounding box. It corresponds to the point coordinates with position [0][0][0].\n'
+        output_string += '\n# box origin indicates the x, y, and z coordinates of '
+        output_string += 'the origin of the FFD bounding box. That is center of\n'
+
+        output_string += '# rotation of the bounding box. It corresponds to '
+        output_string += 'the point coordinates with position [0][0][0].\n'
+
         output_string += '# See section "Parameters weights" for more details.\n'
-        output_string += '# For example, if the origin is equal to 0., 0., 0., use the following: origin box: 0., 0., 0.\n'
+        output_string += '# For example, if the origin is equal to 0., 0., 0., use '
+        output_string += 'the following: origin box: 0., 0., 0.\n'
+
         output_string += 'box origin x: ' + str(self.origin_box[0]) + '\n'
         output_string += 'box origin y: ' + str(self.origin_box[1]) + '\n'
         output_string += 'box origin z: ' + str(self.origin_box[2]) + '\n'
 
-        output_string += '\n# rotation angle indicates the rotation angle around the x, y, and z axis of the FFD bounding box in degrees.\n'
+        output_string += '\n# rotation angle indicates the rotation angle '
+        output_string += 'around the x, y, and z axis of the FFD bounding box in degrees.\n'
+
         output_string += '# The rotation is done with respect to the box origin.\n'
-        output_string += '# For example, to rotate the box by 2 deg along the z direction, use the following: rotation angle: 0., 0., 2.\n'
+        output_string += '# For example, to rotate the box by 2 deg along the z '
+        output_string += 'direction, use the following: rotation angle: 0., 0., 2.\n'
+
         output_string += 'rotation angle x: ' + str(self.rot_angle[0]) + '\n'
         output_string += 'rotation angle y: ' + str(self.rot_angle[1]) + '\n'
         output_string += 'rotation angle z: ' + str(self.rot_angle[2]) + '\n'
 
         output_string += '\n\n[Parameters weights]\n'
-        output_string += '# This section describes the weights of the FFD control points.\n'
+        output_string += '# This section describes the weights of the FFD '
+        output_string += 'control points.\n'
+
         output_string += '# We adopt the following convention:\n'
-        output_string += '# For example with a 2x2x2 grid of control points we have to fill a 2x2x2 matrix of weights.\n'
-        output_string += '# If a weight is equal to zero you can discard the line since the default is zero.\n'
+        output_string += '# For example with a 2x2x2 grid of control points we '
+        output_string += 'have to fill a 2x2x2 matrix of weights.\n'
+
+        output_string += '# If a weight is equal to zero you can discard the line '
+        output_string += 'since the default is zero.\n'
+
         output_string += '#\n'
         output_string += '# | x index | y index | z index | weight |\n'
         output_string += '#  --------------------------------------\n'
         output_string += '# |    0    |    0    |    0    |  1.0   |\n'
-        output_string += '# |    0    |    1    |    1    |  0.0   | --> you can erase this line without effects\n'
+        output_string += '# |    0    |    1    |    1    |  0.0   | --> you '
+        output_string += 'can erase this line without effects\n'
         output_string += '# |    0    |    1    |    0    | -2.1   |\n'
         output_string += '# |    0    |    0    |    1    |  3.4   |\n'
 
-        output_string += '\n# parameter x collects the displacements along x, normalized with the box lenght x.'
+        output_string += '\n# parameter x collects the displacements along x, '
+        output_string += 'normalized with the box lenght x.'
+
         output_string += '\nparameter x:'
         offset = 1
         for i in range(0, self.n_control_points[0]):
             for j in range(0, self.n_control_points[1]):
                 for k in range(0, self.n_control_points[2]):
-                    output_string += offset * ' ' + str(i) + '   ' + str(j) + '   ' + str(k) + \
-                        '   ' + str(self.array_mu_x[i][j][k]) + '\n'
+                    output_string += offset * ' ' + str(i) + '   ' + str(
+                        j) + '   ' + str(k) + '   ' + str(
+                            self.array_mu_x[i][j][k]) + '\n'
                     offset = 13
 
-        output_string += '\n# parameter y collects the displacements along y, normalized with the box lenght y.'
+        output_string += '\n# parameter y collects the displacements along y, '
+        output_string += 'normalized with the box lenght y.'
+
         output_string += '\nparameter y:'
         offset = 1
         for i in range(0, self.n_control_points[0]):
             for j in range(0, self.n_control_points[1]):
                 for k in range(0, self.n_control_points[2]):
-                    output_string += offset * ' ' + str(i) + '   ' + str(j) + '   ' + str(k) + \
-                        '   ' + str(self.array_mu_y[i][j][k]) + '\n'
+                    output_string += offset * ' ' + str(i) + '   ' + str(
+                        j) + '   ' + str(k) + '   ' + str(
+                            self.array_mu_y[i][j][k]) + '\n'
                     offset = 13
 
-        output_string += '\n# parameter z collects the displacements along z, normalized with the box lenght z.'
+        output_string += '\n# parameter z collects the displacements along z, '
+        output_string += 'normalized with the box lenght z.'
+
         output_string += '\nparameter z:'
         offset = 1
         for i in range(0, self.n_control_points[0]):
             for j in range(0, self.n_control_points[1]):
                 for k in range(0, self.n_control_points[2]):
-                    output_string += offset * ' ' + str(i) + '   ' + str(j) + '   ' + str(k) + \
-                        '   ' + str(self.array_mu_z[i][j][k]) + '\n'
+                    output_string += offset * ' ' + str(i) + '   ' + str(
+                        j) + '   ' + str(k) + '   ' + str(
+                            self.array_mu_z[i][j][k]) + '\n'
                     offset = 13
 
         with open(filename, 'w') as f:

pygem/params/idwparams.py

@@ -1,5 +1,9 @@
-import numpy as np
+"""
+Utilities for reading and writing parameters files to perform IDW
+geometrical morphing.
+"""
 import os
+import numpy as np
 try:
     import configparser as configparser
 except ImportError: