Whitespace removal.

gprMax/fractals.py

@@ -58,7 +58,7 @@ class FractalSurface(object):
 
     def generate_fractal_surface(self, G):
         """Generate a 2D array with a fractal distribution.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -135,7 +135,7 @@ class FractalVolume(object):
 
     def generate_fractal_volume(self, G):
         """Generate a 3D volume with a fractal distribution.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -216,11 +216,11 @@ class Grass(object):
 
     def calculate_blade_geometry(self, blade, height):
         """Calculates the x and y coordinates for a given height of grass blade.
-            
+
         Args:
             blade (int): Numeric ID of grass blade.
             height (float): Height of grass blade.
-        
+
         Returns:
             x, y (float): x and y coordinates of grass blade.
         """
@@ -234,11 +234,11 @@ class Grass(object):
 
     def calculate_root_geometry(self, root, depth):
         """Calculates the x and y coordinates for a given depth of grass root.
-            
+
         Args:
             root (int): Numeric ID of grass root.
             depth (float): Depth of grass root.
-        
+
         Returns:
             x, y (float): x and y coordinates of grass root.
         """

gprMax/input_cmd_funcs.py

@@ -137,7 +137,7 @@ def geometry_view(xs, ys, zs, xf, yf, zf, dx, dy, dz, filename, type='n'):
         dx, dy, dz (float): Spatial discretisation of geometry view.
         filename (str): Filename where geometry file information will be stored.
         type (str): Can be either n (normal) or f (fine) which specifies whether to output the geometry information on a per-cell basis (n) or a per-cell-edge basis (f).
-        
+
     Returns:
         s, f, d (tuple): 3 namedtuple Coordinate for the start, finish coordinates and spatial discretisation
     """
@@ -157,7 +157,7 @@ def snapshot(xs, ys, zs, xf, yf, zf, dx, dy, dz, time, filename):
         dx, dy, dz (float): Spatial discretisation of geometry view.
         time (float): Time in seconds (float) or the iteration number (integer) which denote the point in time at which the snapshot will be taken.
         filename (str): Filename where geometry file information will be stored.
-        
+
     Returns:
         s, f, d (tuple): 3 namedtuple Coordinate for the start, finish coordinates and spatial discretisation
     """
@@ -181,7 +181,7 @@ def edge(xs, ys, zs, xf, yf, zf, material):
     Args:
         xs, ys, zs, xf, yf, zf (float): Start and finish coordinates.
         material (str): Material identifier.
-        
+
     Returns:
         s, f (tuple): 2 namedtuple Coordinate for the start and finish coordinates
     """
@@ -198,7 +198,7 @@ def plate(xs, ys, zs, xf, yf, zf, material):
     Args:
         xs, ys, zs, xf, yf, zf (float): Start and finish coordinates.
         material (str): Material identifier(s).
-        
+
     Returns:
         s, f (tuple): 2 namedtuple Coordinate for the start and finish coordinates
     """
@@ -216,7 +216,7 @@ def triangle(x1, y1, z1, x2, y2, z2, x3, y3, z3, thickness, material):
         x1, y1, z1, x2, y2, z2, x3, y3, z3 (float): Coordinates of the vertices.
         thickness (float): Thickness for a triangular prism, or zero for a triangular patch.
         material (str): Material identifier(s).
-        
+
     Returns:
         v1, v2, v3 (tuple): 3 namedtuple Coordinate for the vertices
     """
@@ -304,7 +304,7 @@ def excitation_file(file1):
 
     Args:
         file1 (str): filename
-        
+
     Returns:
         file1 (str): filename
     """
@@ -321,7 +321,7 @@ def waveform(shape, amplitude, frequency, identifier):
         amplitude (float): is the amplitude of the waveform.
         frequency (float): is the frequency of the waveform in Hertz.
         identifier (str): is an identifier for the waveform used to assign it to a source.
-        
+
     Returns:
         identifier (str): is an identifier for the waveform used to assign it to a source.
     """
@@ -339,7 +339,7 @@ def hertzian_dipole(polarization, f1, f2, f3, identifier, t0=None, t_remove=None
         identifier (str): is the identifier of the waveform that should be used with the source.
         t0 (float): is an optinal argument for the time delay in starting the source.
         t_remove (float): is a time to remove the source.
-        
+
     Returns:
         coordinates (tuple): namedtuple Coordinate of the source location
     """
@@ -357,7 +357,7 @@ def rx(x, y, z, identifier=None, to_save=None):
         x, y, z (float): are the coordinates (x,y,z) of the receiver in the model.
         identifier (str): is the optional identifier of the receiver
         to_save (list):  is a list of outputs with this receiver. It can be any selection from 'Ex', 'Ey', 'Ez', 'Hx', 'Hy', 'Hz', 'Ix', 'Iy', or 'Iz'.
-        
+
     Returns:
         coordinates (tuple): namedtuple Coordinate of the receiver location
     """
@@ -372,7 +372,7 @@ def src_steps(dx=0, dy=0, dz=0):
 
     Args:
         dx, dy, dz (float): are the increments in (x, y, z) to move all simple sources or all receivers.
-        
+
     Returns:
         coordinates (tuple): namedtuple Coordinate of the increments
     """
@@ -388,7 +388,7 @@ def rx_steps(dx=0, dy=0, dz=0):
 
     Args:
         dx, dy, dz (float): are the increments in (x, y, z) to move all simple sources or all receivers.
-        
+
     Returns:
         coordinates (tuple): namedtuple Coordinate of the increments
     """

gprMax/input_cmds_file.py

@@ -25,11 +25,11 @@ from gprMax.exceptions import CmdInputError
 
 def process_python_include_code(inputfile, usernamespace):
     """Looks for and processes any Python code found in the input file. It will ignore any lines that are comments, i.e. begin with a double hash (##), and any blank lines. It will also ignore any lines that do not begin with a hash (#) after it has processed Python commands. It will also process any include commands and insert the contents of the included file at that location.
-        
+
     Args:
         inputfile (str): Name of the input file to open.
         usernamespace (dict): Namespace that can be accessed by user in any Python code blocks in input file.
-        
+
     Returns:
         processedlines (list): Input commands after Python processing.
     """
@@ -118,7 +118,7 @@ def process_python_include_code(inputfile, usernamespace):
 
 def write_processed_file(inputfile, modelrun, numbermodelruns, processedlines):
     """Writes an input file after any Python code and include commands in the original input file have been processed.
-        
+
     Args:
         inputfile (str): Name of the input file to open.
         modelrun (int): Current model run number.
@@ -140,11 +140,11 @@ def write_processed_file(inputfile, modelrun, numbermodelruns, processedlines):
 
 def check_cmd_names(processedlines, checkessential=True):
     """Checks the validity of commands, i.e. are they gprMax commands, and that all essential commands are present.
-        
+
     Args:
         processedlines (list): Input commands after Python processing.
         checkessential (boolean): Perform check to see that all essential commands are present.
-        
+
     Returns:
         singlecmds (dict): Commands that can only occur once in the model.
         multiplecmds (dict): Commands that can have multiple instances in the model.

gprMax/input_cmds_geometry.py

@@ -33,10 +33,10 @@ from gprMax.utilities import round_value
 
 def process_geometrycmds(geometry, G):
     """This function checks the validity of command parameters, creates instances of classes of parameters, and calls functions to directly set arrays solid, rigid and ID.
-        
+
     Args:
         geometry (list): Geometry commands in the model
-        
+
     """
 
     for object in geometry:

gprMax/input_cmds_singleuse.py

@@ -30,7 +30,7 @@ from gprMax.waveforms import Waveform
 
 def process_singlecmds(singlecmds, G):
     """Checks the validity of command parameters and creates instances of classes of parameters.
-        
+
     Args:
         singlecmds (dict): Commands that can only occur once in the model.
         G (class): Grid class instance - holds essential parameters describing the model.

gprMax/materials.py

@@ -69,7 +69,7 @@ class Material(object):
 
     def calculate_update_coeffsH(self, G):
         """Calculates the magnetic update coefficients of the material.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -85,7 +85,7 @@ class Material(object):
     # Calculate electric update coefficients
     def calculate_update_coeffsE(self, G):
         """Calculates the electric update coefficients of the material.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -167,7 +167,7 @@ class PeplinskiSoil(object):
 
     def calculate_debye_properties(self, nbins, G):
         """Calculates the real and imaginery part of a Debye model for the soil as well as a conductivity. It uses a semi-empirical model (http://dx.doi.org/10.1109/36.387598).
-            
+
         Args:
             nbins (int): Number of bins to use to create the different materials.
             G (class): Grid class instance - holds essential parameters describing the model.

gprMax/optimisation_taguchi.py

@@ -30,7 +30,7 @@ from gprMax.gprMax import run_std_sim, run_mpi_sim
 
 def run_opt_sim(args, numbermodelruns, inputfile, usernamespace):
     """Run a simulation using Taguchi's optmisation process.
-        
+
     Args:
         args (dict): Namespace with command line arguments
         numbermodelruns (int): Total number of model runs.
@@ -159,11 +159,11 @@ def run_opt_sim(args, numbermodelruns, inputfile, usernamespace):
 
 def taguchi_code_blocks(inputfile, taguchinamespace):
     """Looks for and processes a Taguchi code block (containing Python code) in the input file. It will ignore any lines that are comments, i.e. begin with a double hash (##), and any blank lines.
-        
+
     Args:
         inputfile (str): Name of the input file to open.
         taguchinamespace (dict): Namespace that can be accessed by user a Taguchi code block in input file.
-        
+
     Returns:
         processedlines (list): Input commands after Python processing.
     """
@@ -205,10 +205,10 @@ def taguchi_code_blocks(inputfile, taguchinamespace):
 
 def construct_OA(optparams):
     """Load an orthogonal array (OA) from a numpy file. Configure and return OA and properties of OA.
-        
+
     Args:
         optparams (dict): Dictionary containing name of parameters to optimise and their initial ranges
-        
+
     Returns:
         OA (array): Orthogonal array
         N (int): Number of experiments in OA
@@ -292,7 +292,7 @@ def construct_OA(optparams):
 
 def calculate_ranges_experiments(optparams, optparamsinit, levels, levelsopt, levelsdiff, OA, N, k, s, i):
     """Calculate values for parameters to optimise for a set of experiments.
-        
+
     Args:
         optparams (dict): Ordered dictionary containing name of parameters to optimise and their values
         optparamsinit (list): Initial ranges for parameters to optimise
@@ -304,7 +304,7 @@ def calculate_ranges_experiments(optparams, optparamsinit, levels, levelsopt, le
         k (int): Number of parameters to optimise in OA
         s (int): Number of levels in OA
         i (int): Iteration number
-        
+
     Returns:
         optparams (dict): Ordered dictionary containing name of parameters to optimise and their values
         levels (array): Lower, central, and upper values for each parameter
@@ -359,7 +359,7 @@ def calculate_ranges_experiments(optparams, optparamsinit, levels, levelsopt, le
 
 def calculate_optimal_levels(optparams, levels, levelsopt, fitnessvalues, OA, N, k):
     """Calculate optimal levels from results of fitness metric by building a response table.
-        
+
     Args:
         optparams (dict): Ordered dictionary containing name of parameters to optimise and their values
         levels (array): Lower, central, and upper values for each parameter
@@ -368,7 +368,7 @@ def calculate_optimal_levels(optparams, levels, levelsopt, fitnessvalues, OA, N,
         OA (array): Orthogonal array
         N (int): Number of experiments in OA
         k (int): Number of parameters to optimise in OA
-        
+
     Returns:
         optparams (dict): Ordered dictionary containing name of parameters to optimise and their values
         levelsopt (array): Optimal level for each parameter from previous iteration
@@ -417,7 +417,7 @@ def calculate_optimal_levels(optparams, levels, levelsopt, fitnessvalues, OA, N,
 
 def plot_optimisation_history(fitnessvalueshist, optparamshist, optparamsinit):
     """Plot the history of fitness values and each optimised parameter values for the optimisation.
-        
+
     Args:
         fitnessvalueshist (list): History of fitness values
         optparamshist (dict): Name of parameters to optimise and history of their values

gprMax/pml.py

@@ -66,7 +66,7 @@ class CFS(object):
 
     def calculate_sigmamax(self, direction, er, mr, G):
         """Calculates an optimum value for sigma max based on underlying material properties.
-            
+
         Args:
             direction (str): Direction of PML slab
             er (float): Average permittivity of underlying material.
@@ -87,12 +87,12 @@ class CFS(object):
 
     def scaling_polynomial(self, order, Evalues, Hvalues):
         """Applies the polynomial to be used for the scaling profile for electric and magnetic PML updates.
-            
+
         Args:
             order (int): Order of polynomial for scaling profile.
             Evalues (float): numpy array holding scaling profile values for electric PML update.
             Hvalues (float): numpy array holding scaling profile values for magnetic PML update.
-            
+
         Returns:
             Evalues (float): numpy array holding scaling profile values for electric PML update.
             Hvalues (float): numpy array holding scaling profile values for magnetic PML update.
@@ -105,11 +105,11 @@ class CFS(object):
 
     def calculate_values(self, thickness, parameter):
         """Calculates values for electric and magnetic PML updates based on profile type and minimum and maximum values.
-            
+
         Args:
             thickness (int): Thickness of PML in cells.
             parameter (CFSParameter): Instance of CFSParameter
-            
+
         Returns:
             Evalues (float): numpy array holding profile value for electric PML update.
             Hvalues (float): numpy array holding profile value for magnetic PML update.
@@ -194,7 +194,7 @@ class PML(object):
 
     def calculate_update_coeffs(self, er, mr, G):
         """Calculates electric and magnetic update coefficients for the PML.
-            
+
         Args:
             er (float): Average permittivity of underlying material
             mr (float): Average permeability of underlying material

gprMax/snapshots.py

@@ -67,7 +67,7 @@ class Snapshot(object):
 
     def prepare_vtk_imagedata(self, modelrun, numbermodelruns, G):
         """Prepares a VTK ImageData (.vti) file for a snapshot.
-            
+
         Args:
             modelrun (int): Current model run number.
             numbermodelruns (int): Total number of model runs.
@@ -112,7 +112,7 @@ class Snapshot(object):
 
     def write_vtk_imagedata(self, Ex, Ey, Ez, Hx, Hy, Hz, G):
         """Writes electric and magnetic field values to VTK ImageData (.vti) file.
-            
+
         Args:
             Ex, Ey, Ez, Hx, Hy, Hz (memory view): Electric and magnetic field values.
             G (class): Grid class instance - holds essential parameters describing the model.

gprMax/sources.py

@@ -51,7 +51,7 @@ class VoltageSource(Source):
 
     def update_electric(self, abstime, updatecoeffsE, ID, Ex, Ey, Ez, G):
         """Updates electric field values for a voltage source.
-            
+
         Args:
             abstime (float): Absolute time.
             updatecoeffsE (memory view): numpy array of electric field update coefficients.
@@ -91,7 +91,7 @@ class VoltageSource(Source):
 
     def create_material(self, G):
         """Create a new material at the voltage source location that adds the voltage source conductivity to the underlying parameters.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -129,7 +129,7 @@ class HertzianDipole(Source):
 
     def update_electric(self, abstime, updatecoeffsE, ID, Ex, Ey, Ez, G):
         """Updates electric field values for a Hertzian dipole.
-            
+
         Args:
             abstime (float): Absolute time.
             updatecoeffsE (memory view): numpy array of electric field update coefficients.
@@ -167,7 +167,7 @@ class MagneticDipole(Source):
 
     def update_magnetic(self, abstime, updatecoeffsH, ID, Hx, Hy, Hz, G):
         """Updates magnetic field values for a magnetic dipole.
-            
+
         Args:
             abstime (float): Absolute time.
             updatecoeffsH (memory view): numpy array of magnetic field update coefficients.
@@ -231,7 +231,7 @@ class TransmissionLine(Source):
 
     def calculate_incident_V_I(self, G):
         """Calculates the incident voltage and current with a long length transmission line not connected to the main grid from: http://dx.doi.org/10.1002/mop.10415
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -250,7 +250,7 @@ class TransmissionLine(Source):
 
     def update_abc(self, G):
         """Updates absorbing boundary condition at end of the transmission line.
-            
+
         Args:
             G (class): Grid class instance - holds essential parameters describing the model.
         """
@@ -263,7 +263,7 @@ class TransmissionLine(Source):
 
     def update_voltage(self, time, G):
         """Updates voltage values along the transmission line.
-            
+
         Args:
             time (float): Absolute time.
             G (class): Grid class instance - holds essential parameters describing the model.
@@ -281,7 +281,7 @@ class TransmissionLine(Source):
 
     def update_current(self, time, G):
         """Updates current values along the transmission line.
-            
+
         Args:
             time (float): Absolute time.
             G (class): Grid class instance - holds essential parameters describing the model.
@@ -296,7 +296,7 @@ class TransmissionLine(Source):
 
     def update_electric(self, abstime, Ex, Ey, Ez, G):
         """Updates electric field value in the main grid from voltage value in the transmission line.
-            
+
         Args:
             abstime (float): Absolute time.
             Ex, Ey, Ez (memory view): numpy array of electric field values.
@@ -323,7 +323,7 @@ class TransmissionLine(Source):
 
     def update_magnetic(self, abstime, Hx, Hy, Hz, G):
         """Updates current value in transmission line from magnetic field values in the main grid.
-            
+
         Args:
             abstime (float): Absolute time.
             Hx, Hy, Hz (memory view): numpy array of magnetic field values.

gprMax/utilities.py

@@ -22,7 +22,7 @@ import decimal as d
 
 def logo(version):
     """Print gprMax logo, version, and licencing/copyright information.
-        
+
     Args:
         version (str): Version number.
     """
@@ -30,17 +30,17 @@ def logo(version):
     licenseinfo = """
 Copyright (C) 2015-2016: The University of Edinburgh
                 Authors: Craig Warren and Antonis Giannopoulos
-        
+
 gprMax is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
-                    
+
 gprMax is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 GNU General Public License for more details.
-                                    
+
 You should have received a copy of the GNU General Public License
 along with gprMax.  If not, see <http://www.gnu.org/licenses/>."""
 
@@ -65,7 +65,7 @@ along with gprMax.  If not, see <http://www.gnu.org/licenses/>."""
 
 def update_progress(progress):
     """Displays or updates a console progress bar.
-        
+
     Args:
         progress (float): Number between zero and one to signify progress.
     """
@@ -80,11 +80,11 @@ def update_progress(progress):
 
 def round_value(value, decimalplaces=0):
     """Rounding function.
-        
+
     Args:
         value (float): Number to round.
         decimalplaces (int): Number of decimal places of float to represent rounded value.
-        
+
     Returns:
         rounded (int/float): Rounded value.
     """
@@ -103,11 +103,11 @@ def round_value(value, decimalplaces=0):
 
 def human_size(size, a_kilobyte_is_1024_bytes=True):
     """Convert a file size to human-readable form.
-        
+
     Args:
         size (int): file size in bytes
         a_kilobyte_is_1024_bytes (boolean) - true for multiples of 1024, false for multiples of 1000
-        
+
     Returns:
         Human-readable (string).
     """

gprMax/waveforms.py

@@ -35,11 +35,11 @@ class Waveform(object):
 
     def calculate_value(self, time, dt):
         """Calculates value of the waveform at a specific time.
-            
+
         Args:
             time (float): Absolute time.
             dt (float): Absolute time discretisation.
-            
+
         Returns:
             waveform (float): Calculated value for waveform.
         """