Merge pull request #66 from mtezzele/qc_fixes

quantified code fixes

Author: mtezzele

pygem/affine.py

@@ -8,34 +8,33 @@
 
 def angles2matrix(rot_z=0, rot_y=0, rot_x=0):
 	"""
-	This method returns the rotation matrix for given rotations around z, y and x axes. The output rotation matrix is
-	equal to the composition of the	individual rotations. Rotations are counter-clockwise.
-	The default value of the three rotations is zero.
+	This method returns the rotation matrix for given rotations around z, y and x axes.
+	The output rotation matrix is equal to the composition of the individual rotations.
+	Rotations are counter-clockwise. The default value of the three rotations is zero.
 
 	:param float rot_z: rotation angle (in radians) around z-axis.
 	:param float rot_y: rotation angle (in radians) around y-axis.
 	:param float rot_x: rotation angle (in radians) around x-axis.
 
 	:return: rot_matrix: rotation matrix for the given angles. The matrix shape is always (3, 3).
-	:rtype: numpy.ndarray		  
-		
+	:rtype: numpy.ndarray
+
 	:Example:
 
 	>>> import pygem.affine as at
 	>>> import numpy as np
 
-	>>> # Example of a rotation around x, y, z axis 
+	>>> # Example of a rotation around x, y, z axis
 	>>> rotz = 10*np.pi/180
 	>>> roty = 20*np.pi/180
 	>>> rotx = 30*np.pi/180
 	>>> rot_matrix = at.angles2matrix(rotz, roty, rotx)
-	
+
 	.. note::
 
 		- The direction of rotation is given by the right-hand rule.
 		- When applying the rotation to a vector, the vector should be column vector
 		  to the right of the rotation matrix.
-
 	"""
 	rot_matrix = []
 	if rot_z:
@@ -65,18 +64,17 @@ def to_reduced_row_echelon_form(matrix):
 
 	:return matrix: the reduced matrix.
 	:rtype: matrix
-		
-		
+
 	:Example:
 
 	>>> import pygem.affine as at
 
 	>>> matrix = [[1., 1., 1.], [1., 1., 1.], [1., 1., 1.]]
 	>>> rref_matrix = at.to_reduced_row_echelon_form(matrix)
-	
+
 	.. note::
+		
 		`matrix` will change after calling this function.
-
 	"""
 	lead = 0
 	row_count = len(matrix)
@@ -138,8 +136,8 @@ def affine_points_fit(points_start, points_end):
 	c = [[0.0 for a in range(dim)] for i in range(dim+1)]
 	for j in range(dim):
 		for k in range(dim+1):
-			for i in range(len(points_start)):
-				qt = list(points_start[i]) + [1]
+			for i, pnts_i in enumerate(points_start):
+				qt = list(pnts_i) + [1]
 				c[k][j] += qt[k] * points_end[i][j]
 
 	# Fill an an empty (dim+1) x (dim+1) matrix
@@ -152,11 +150,11 @@ def affine_points_fit(points_start, points_end):
 
 
 	# Augement Q with c and get the reduced row echelon form of the result
-	M = [Q[i] + c[i] for i in range(dim+1)]
+	affine_matrix = [Q[i] + c[i] for i in range(dim+1)]
 
-	if np.linalg.cond(M) < 1/sys.float_info.epsilon:
-		rref_M = to_reduced_row_echelon_form(M)
-		rref_M = np.array(rref_M)
+	if np.linalg.cond(affine_matrix) < 1/sys.float_info.epsilon:
+		rref_aff_matrix = to_reduced_row_echelon_form(affine_matrix)
+		rref_aff_matrix = np.array(rref_aff_matrix)
 	else:
 		raise RuntimeError("Error: singular matrix. Points are probably coplanar.")
 
@@ -173,9 +171,9 @@ def transform_vector(source):
 		destination = np.zeros(dim)
 		for i in range(dim):
 			for j in range(dim):
-				destination[j] += source[i] * rref_M[i][j+dim+1]
+				destination[j] += source[i] * rref_aff_matrix[i][j+dim+1]
 			# Add the last line of the rref
-			destination[i] += rref_M[dim][i+dim+1]
+			destination[i] += rref_aff_matrix[dim][i+dim+1]
 		return destination
 
 	return transform_vector

pygem/filehandler.py

@@ -18,7 +18,7 @@ def __init__(self):
 		self.extension = None
 
 
-	def parse(self, infile):
+	def parse(self, *args):
 		"""
 		Abstract method to parse a specific file.
 
@@ -28,7 +28,7 @@ def parse(self, infile):
 			+ self.__class__.__name__ + ".parse")
 
 
-	def write(self, mesh_points, outfile):
+	def write(self, *args):
 		"""
 		Abstract method to write a specific file.
 
@@ -51,19 +51,21 @@ def _check_extension(self, filename):
 				It is {0!s}, instead of {1!s}.'.format(file_ext, self.extension))
 
 
-	def _check_filename_type(self, filename):
+	@staticmethod
+	def _check_filename_type(filename):
 		"""
-		This private method checks if `filename` is a string. If not it raises a TypeError.
+		This private static method checks if `filename` is a string. If not it raises a TypeError.
 
 		:param string filename: file to check.
 		"""
 		if not isinstance(filename, basestring):
 			raise TypeError('The given filename ({0!s}) must be a string'.format(filename))
 
 
-	def _check_infile_instantiation(self, infile):
+	@staticmethod
+	def _check_infile_instantiation(infile):
 		"""
-		This private method checks if the input file `infile` is instantiated. If not it means
+		This private static method checks if the input file `infile` is instantiated. If not it means
 		that nobody called the parse method, i.e. `self.infile` is None. If the check fails
 		it raises a RuntimeError.
 

pygem/freeform.py

@@ -67,8 +67,7 @@ class FFD(object):
 	>>> 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
-			
+	>>> new_mesh_points = free_form.modified_mesh_points		
     """
 	def __init__(self, ffd_parameters, original_mesh_points):
 		self.parameters = ffd_parameters
@@ -152,9 +151,10 @@ def perform(self):
 									reference_frame_mesh_points, inverse_transformation) + translation
 
 
-	def _transform_points(self, original_points, transformation):
+	@staticmethod
+	def _transform_points(original_points, transformation):
 		"""
-		This method transforms the points according to the affine transformation taken from
+		This private static method transforms the points according to the affine transformation taken from
 		affine_points_fit method.
 
 		:param numpy.ndarray original_points: coordinates of the original points.

pygem/unvhandler.py

@@ -35,27 +35,25 @@ def parse(self, filename):
 
 		self.infile = filename
 
-		input_file = open(self.infile, 'r')
-		nline = 0
-		while True:
-			line = input_file.readline()
-			nline += 1
-			if len(line) == 0:
-				break
-			if line.startswith('    -1'):
-				section_id = input_file.readline().strip()
+		with open(self.infile, 'r') as input_file:
+			nline = 0
+			while True:
+				line = input_file.readline()
 				nline += 1
-				if section_id == '2411':
-					count = 0
-					while not input_file.readline().startswith('    -1'):
-						count += 1
-					start_line = nline + 2
-					last_line = start_line + count
-				else:
-					while not input_file.readline().startswith('    -1'):
-						nline += 1
-
-		input_file.close()
+				if not line:
+					break
+				if line.startswith('    -1'):
+					section_id = input_file.readline().strip()
+					nline += 1
+					if section_id == '2411':
+						count = 0
+						while not input_file.readline().startswith('    -1'):
+							count += 1
+						start_line = nline + 2
+						last_line = start_line + count
+					else:
+						while not input_file.readline().startswith('    -1'):
+							nline += 1
 
 		n_points = count/2
 		mesh_points = np.zeros(shape=(n_points, 3))
@@ -65,7 +63,7 @@ def parse(self, filename):
 		with open(self.infile, 'r') as input_file:
 			for line in input_file:
 				nline += 1
-				if nline % 2 == 1 and nline > start_line and nline < last_line:
+				if nline % 2 == 1 and start_line < nline < last_line:
 					line = line.strip()
 					j = 0
 					for number in line.split():
@@ -100,7 +98,7 @@ def write(self, mesh_points, filename):
 		with open(self.infile, 'r') as input_file, open(self.outfile, 'w') as output_file:
 			for line in input_file:
 				nrow += 1
-				if nrow % 2 == 1 and nrow > 20 and nrow <= (20 + n_points * 2):
+				if nrow % 2 == 1 and 20 < nrow <= (20 + n_points * 2):
 					for j in range(0, 3):
 						output_file.write('   ' + str(mesh_points[i][j]))
 					output_file.write('\n')

setup.py

@@ -1,6 +1,9 @@
 from setuptools import setup
 
 def readme():
+	"""
+	This function just return the content of README.md
+	"""
 	with open('README.md') as f:
 		return f.read()