Merge pull request #72 from mtezzele/doc

fixed doc, renamed utilities and minor fixes

Author: mtezzele

pygem/__init__.py

@@ -1,5 +1,5 @@
 
-__all__ = ['affine', 'filehandler', 'freeform', 'openfhandler', 'params', 'stlhandler', 'unvhandler', 'vtkhandler', 'igeshandler', 'utilities']
+__all__ = ['affine', 'filehandler', 'freeform', 'openfhandler', 'params', 'stlhandler', 'unvhandler', 'vtkhandler', 'igeshandler', 'utils']
 
 from . import affine
 from . import freeform
@@ -10,4 +10,4 @@
 from . import unvhandler
 from . import vtkhandler
 from . import igeshandler
-from . import utilities
+from . import utils

pygem/filehandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Base module with the base class for reading and writing different CAD files.
 """
 import os
 

pygem/igeshandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Derived module from filehandler.py to handle iges and igs files.
 """
 import os
 import numpy as np
@@ -52,6 +52,8 @@ def parse(self, filename):
 		"""
 		Method to parse the file `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

pygem/openfhandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Derived module from filehandler.py to handle OpenFOAM files.
 """
 import numpy as np
 import pygem.filehandler as fh
@@ -23,6 +23,8 @@ 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

pygem/stlhandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Derived module from filehandler.py to handle STereoLithography files.
 """
 import numpy as np
 from mpl_toolkits import mplot3d
@@ -25,6 +25,8 @@ 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
@@ -55,8 +57,6 @@ def write(self, mesh_points, filename, write_bin=False):
 			the coordinates of the points of the mesh.
 		:param string filename: name of the output file.
 		:param boolean write_bin: flag to write in the binary format. Default is False.
-
-		.. todo:: DOCS
 		"""
 		self._check_filename_type(filename)
 		self._check_extension(filename)

pygem/unvhandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Derived module from filehandler.py to handle Universal (unv) files.
 """
 import numpy as np
 import pygem.filehandler as fh
@@ -21,14 +21,13 @@ def __init__(self):
 	def parse(self, filename):
 		"""
 		Method to parse the file `filename`. It returns a matrix with all the coordinates.
+		It reads only the section 2411 of the unv files and it assumes there are only triangles.
 
+		: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
+			the points of the mesh.
 		:rtype: numpy.ndarray
-
-		.. todo::
-
-			- specify when it works
 		"""
 		self._check_filename_type(filename)
 		self._check_extension(filename)
@@ -83,8 +82,6 @@ def write(self, mesh_points, filename):
 		: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)

pygem/utilities.py pygem/utils.pypygem/utilities.py renamed to pygem/utils.py

@@ -1,86 +1,82 @@
 """
 Auxiliary utilities for PyGeM.
 """
-
 import vtk
-import vtk.util.numpy_support as ns
 import numpy as np
 
 # TODO: add the connectivity to the ffd control points to visualize the lattice.
 
-
-
 def write_bounding_box(parameters, outfile, 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 flag is set to original (default) the method writes out the undeformed lattice, 
-	if it is set to modified it writes out the deformed lattice.
-	
+	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 FFDParameters parameters: parameters of the Free Form Deformation.
 	:param string outfile: name of the output file.
-	:param bool write_deformed: flag to write the original or modified FFD control lattice. 
-		The default is set to deformed.
-		
+	:param bool write_deformed: flag to write the original or modified FFD control lattice.
+		The default is set to True.
+
 	:Example:
-	
-	>>> import pygem.utilities as util
+
+	>>> 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')
-	>>> util.write_bounding_box(params, 'tests/test_datasets/box_test_sphere.vtk')
+	>>> ut.write_bounding_box(params, 'tests/test_datasets/box_test_sphere.vtk')
 	"""
-
 	aux_x = np.linspace(0, parameters.lenght_box_x, parameters.n_control_points[0])
 	aux_y = np.linspace(0, parameters.lenght_box_y, parameters.n_control_points[1])
 	aux_z = np.linspace(0, parameters.lenght_box_z, parameters.n_control_points[2])
 	lattice_y_coords, lattice_x_coords, lattice_z_coords = np.meshgrid(aux_y, aux_x, aux_z)
 
-	if write_deformed == False:
-		box_points = np.array([lattice_x_coords.ravel(), lattice_y_coords.ravel(), lattice_z_coords.ravel()])
-	if write_deformed == True:
-		box_points = np.array([lattice_x_coords.ravel() + parameters.array_mu_x.ravel()*parameters.lenght_box_x, \
-		lattice_y_coords.ravel()  + parameters.array_mu_y.ravel()*parameters.lenght_box_y, \
-		lattice_z_coords.ravel()  + parameters.array_mu_z.ravel()*parameters.lenght_box_z])
-		
+	if write_deformed:
+		box_points = np.array([lattice_x_coords.ravel() + parameters.array_mu_x.ravel() * parameters.lenght_box_x,\
+			lattice_y_coords.ravel() + parameters.array_mu_y.ravel() * parameters.lenght_box_y, \
+			lattice_z_coords.ravel() + parameters.array_mu_z.ravel() * parameters.lenght_box_z])
+	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(parameters.rotation_matrix, box_points) + \
+		np.transpose(np.tile(parameters.origin_box, (n_rows, 1)))
 
-	box_points = np.dot(parameters.rotation_matrix,box_points) + np.transpose(np.tile(parameters.origin_box, (n_rows,1)))
-	
 	_write_vtk_box(box_points, outfile)
-	
-	
+
+
 def _write_vtk_box(box_points, filename):
 	"""
-	Method that writes a vtk file containing FFD control points.
-	
+	Private method that writes a vtk file containing FFD control points.
+
 	:param numpy.ndarray box_points: coordinates of the FFD control points.
 	:param string filename: name of the output file.
 	"""
 	# setup points and vertices
 	points = vtk.vtkPoints()
 	vertices = vtk.vtkCellArray()
-	
+
 	for index in range(0, box_points.shape[1]):
-		id = points.InsertNextPoint(box_points[0, index], box_points[1, index], box_points[2, index])
+		ind = points.InsertNextPoint(box_points[0, index], box_points[1, index], box_points[2, index])
 		vertices.InsertNextCell(1)
-		vertices.InsertCellPoint(id)
-		
+		vertices.InsertCellPoint(ind)
+
 	polydata = vtk.vtkPolyData()
 	polydata.SetPoints(points)
 	polydata.SetVerts(vertices)
-	
 	polydata.Modified()
+
 	writer = vtk.vtkDataSetWriter()
 	writer.SetFileName(filename)
-	
+
 	if vtk.VTK_MAJOR_VERSION <= 5:
 		polydata.Update()
 		writer.SetInput(polydata)
 	else:
 		writer.SetInputData(polydata)
-		
+
 	writer.Write()
 

pygem/vtkhandler.py

@@ -1,5 +1,5 @@
 """
-Utilities for reading and writing different CAD files.
+Derived module from filehandler.py to handle vtk files.
 """
 import numpy as np
 import matplotlib.pyplot as plt
@@ -25,6 +25,8 @@ def parse(self, filename):
 		"""
 		Method to parse the file `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

tests/test_utilities.py tests/test_utils.pytests/test_utilities.py renamed to tests/test_utils.py

@@ -1,39 +1,38 @@
 
 from unittest import TestCase
 import unittest
-import pygem.utilities as util
+import pygem.utils as ut
 import pygem.params as pars
 import numpy as np
 import filecmp
 import os
+import vtk
 
 
 class TestVtkHandler(TestCase):
 
 
-	def test_utilities_write_original_box(self):
+	def test_utils_write_original_box(self):
 		params = pars.FFDParameters()
 		params.read_parameters(filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
 
 		outfilename = 'tests/test_datasets/box_test_sphere.vtk'
 
-		util.write_bounding_box(params, outfilename, False)
+		ut.write_bounding_box(params, outfilename, False)
 		os.remove(outfilename)
 
 
-	def test_utilities_write_modified_box(self):
+	def test_utils_write_modified_box(self):
 		params = pars.FFDParameters()
 		params.read_parameters(filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
 
 		outfilename = 'tests/test_datasets/box_test_sphere.vtk'
 
-		util.write_bounding_box(params, outfilename)
+		ut.write_bounding_box(params, outfilename)
 		os.remove(outfilename)
 
 
-	def test_utilities_check_vtk_original_box(self):
-		import vtk
-		
+	def test_utils_check_vtk_original_box(self):
 		params = pars.FFDParameters()
 		params.read_parameters(filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
 
@@ -43,15 +42,13 @@ def test_utilities_check_vtk_original_box(self):
 		else:
 			outfilename_expected = 'tests/test_datasets/box_test_sphere_true_version6.vtk'
 
-		util.write_bounding_box(params, outfilename, False)
+		ut.write_bounding_box(params, outfilename, False)
 
 		self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
 		os.remove(outfilename)
 
 
-	def test_utilities_check_vtk_modified_box(self):
-		import vtk
-		
+	def test_utils_check_vtk_modified_box(self):
 		params = pars.FFDParameters()
 		params.read_parameters(filename='tests/test_datasets/parameters_test_ffd_sphere.prm')
 
@@ -61,7 +58,7 @@ def test_utilities_check_vtk_modified_box(self):
 		else:
 			outfilename_expected = 'tests/test_datasets/box_modified_test_sphere_true_version6.vtk'
 
-		util.write_bounding_box(params, outfilename)
+		ut.write_bounding_box(params, outfilename)
 
 		self.assertTrue(filecmp.cmp(outfilename, outfilename_expected))
 		os.remove(outfilename)