From cef86633c9cdb1611f2fcd3e344b259813eb0dc3 Mon Sep 17 00:00:00 2001
From: Craig Warren <craig_warren@me.com>
Date: Tue, 19 Jan 2016 16:29:59 +0000
Subject: [PATCH] Removed modules related to old version of gprMax.

---
 tools/inputfile_new2old.py  | 298 ------------------------------------
 tools/outputfile_old2new.py | 159 -------------------
 2 files changed, 457 deletions(-)
 delete mode 100644 tools/inputfile_new2old.py
 delete mode 100644 tools/outputfile_old2new.py

diff --git a/tools/inputfile_new2old.py b/tools/inputfile_new2old.py
deleted file mode 100644
index 60de90d8..00000000
--- a/tools/inputfile_new2old.py
+++ /dev/null
@@ -1,298 +0,0 @@
-# Copyright (C) 2015-2016: The University of Edinburgh
-#                 Authors: Craig Warren and Antonis Giannopoulos
-#
-# This file is part of gprMax.
-#
-# 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/>.
-
-import argparse, os, sys
-import numpy as np
-
-from gprMax.exceptions import CmdInputError
-
-"""Converts new to old style input files."""
-
-# Parse command line arguments
-parser = argparse.ArgumentParser(description='Converts new style input file to old style input file.', usage='cd gprMax; python -m tools.inputfile_old2new inputfile')
-parser.add_argument('inputfile', help='name of input file including path')
-args = parser.parse_args()
-
-inputfile = args.inputfile
-
-with open(inputfile, 'r') as f:
-    # Strip out any newline characters and comments that must begin with double hashes
-    inputlines = [line.rstrip() for line in f]
-
-# New file name base
-try:
-    newfile = inputfile.split('.')[0]
-except:
-    pass
-newfile += '_oldstyle'
-
-print("Attempting to convert inputfile '{}' to use old syntax...\n".format(inputfile))
-
-newcommands = ['#add_dispersion_lorentz', '#add_dispersion_drude', '#fractal_box', '#soil_peplinski', '#python', '#end_python', '#add_surface_roughness', '#add_surface_water', '#add_grass', '#magnetic_dipole', '#pml_cfs', '#cylindrical_sector', '#time_step_limit_type']
-materials = {}
-debyes = []
-waveforms = []
-badwaveforms = ['gaussiandotdot', 'ricker']
-hertziandipoles = []
-voltagesources = []
-analysiscmds = []
-ompthreadscheck = False
-pmlcheck = False
-messagescheck = False
-
-lindex = 0
-while(lindex < len(inputlines)):
-    
-    if inputlines[lindex].startswith('#') and not inputlines[lindex].startswith('##'):
-        cmd = inputlines[lindex].split(':')
-        cmdname = cmd[0].lower()
-        params = cmd[1].split()
-
-        if cmdname == '#domain':
-            domain = (float(params[0]), float(params[1]), float(params[2]))
-            lindex += 1
-
-        elif cmdname == '#dx_dy_dz':
-            dx_dy_dz = (float(params[0]), float(params[1]), float(params[2]))
-            lindex += 1
-        
-        elif cmdname == '#time_window':
-            if '.' in params[0] or 'e' in params[0].lower():
-                timewindow = float(params[0])
-            else:
-                timewindow = int(params[0])
-            lindex += 1
-        
-        elif cmdname == '#messages':
-            messagescheck = True
-
-        elif cmdname == '#voltage_source':
-            voltagesources.append(inputlines[lindex])
-            inputlines.pop(lindex)
-
-        elif cmdname == '#hertzian_dipole':
-            hertziandipoles.append(inputlines[lindex])
-            inputlines.pop(lindex)
-
-        elif cmdname == '#rx':
-            analysiscmds.append(inputlines[lindex])
-            inputlines.pop(lindex)
-
-        elif cmdname == '#waveform':
-            waveforms.append(inputlines[lindex])
-            inputlines.pop(lindex)
-
-        elif cmdname == '#material':
-            materials[lindex] = inputlines[lindex]
-            lindex += 1
-        
-        elif cmdname == '#add_dispersion_debye':
-            debyes.append(inputlines[lindex])
-            inputlines.pop(lindex)
-
-        elif cmdname == '#triangle':
-            # Syntax of command: #triangle: x1 y1 z1 x2 y2 z2 x3 y3 z3 thickness ID
-            if float(params[9]) == 0:
-                replacement = '#triangle: {} {} {} {} {} {} {} {} {} {}'.format(params[0], params[1], params[2], params[3], params[4], params[5], params[6], params[7], params[8], params[10])
-            else:
-                replacement = '#wedge: {} {} {} {} {} {} {} {} {} {} {}'.format(params[0], params[1], params[2], params[3], params[4], params[5], params[6], params[7], params[8], params[9], params[10])
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            inputlines.insert(lindex, replacement)
-            lindex += 1
-
-        elif cmdname == '#cylinder':
-            # Syntax of command: #cylinder: x1 y1 z1 x2 y2 z2 radius ID
-            replacement = '#cylinder_new: {} {} {} {} {} {} {} {}'.format(params[0], params[1], params[2], params[3], params[4], params[5], params[6], params[7])
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            inputlines.insert(lindex, replacement)
-            lindex += 1
-
-        elif cmdname == '#pml_cells':
-            pmlcheck = True
-            # Syntax of command: #pml_cells: xminus yminus zminus xplus yplus zplus or #pml_cells: i1 (assumes latter behaviour)
-            replacement = '#pml_layers: {}'.format(params[0])
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            inputlines.insert(lindex, replacement)
-            lindex += 1
-        
-        elif cmdname == '#num_threads':
-            ompthreadscheck = True
-            # Set number of threads to number of physical CPU cores, i.e. avoid hyperthreading with OpenMP for now
-            if sys.platform == 'darwin':
-                nthreads = int(os.popen('sysctl hw.physicalcpu').readlines()[0].split(':')[1].strip())
-            elif sys.platform == 'win32':
-                # Consider using wmi tools to check hyperthreading on Windows
-                nthreads = os.cpu_count()
-            elif 'linux' in sys.platform:
-                lscpu = os.popen('lscpu').readlines()
-                cpusockets = [item for item in lscpu if item.startswith('Socket(s)')]
-                cpusockets = int(cpusockets[0].split(':')[1].strip())
-                corespersocket = [item for item in lscpu if item.startswith('Core(s) per socket')]
-                corespersocket = int(corespersocket[0].split(':')[1].strip())
-                nthreads = cpusockets * corespersocket
-            else:
-                nthreads = os.cpu_count()
-            # Syntax of command: #num_threads: nthreads
-            replacement = '#num_of_procs: {}'.format(nthreads)
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            analysiscmds.append(replacement)
-            lindex += 1
-
-        elif cmdname == '#snapshot':
-            # Syntax of command: #snapshot: x1 y1 z1 x2 y2 z2 dx dy dz time filename
-            replacement = '#snapshot: {} {} {} {} {} {} {} {} {} {} {} v'.format(params[0], params[1], params[2], params[3], params[4], params[5], params[6], params[7], params[8], params[9], params[10])
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            analysiscmds.append(replacement)
-            lindex += 1
-
-        elif cmdname == '#geometry_view':
-            # Syntax of command: #geometry_vtk: x1 y1 z1 x2 y2 z2 dx dy dz filename type
-            replacement = '#geometry_vtk: {} {} {} {} {} {} {} {} {} {} {}'.format(params[0], params[1], params[2], params[3], params[4], params[5], params[6], params[7], params[8], params[9], params[10])
-            print("Command '{}', replaced with '{}'".format(inputlines[lindex], replacement))
-            inputlines.pop(lindex)
-            inputlines.insert(lindex, replacement)
-            lindex += 1
-
-        elif cmdname in newcommands:
-            print("Command '{}' cannot be used in the old version of gprMax.".format(inputlines[lindex]))
-            inputlines.pop(lindex)
-
-        else:
-            lindex += 1
-
-    else:
-        lindex +=1
-
-# If messages not found set to on
-if not messagescheck:
-    cmd = '#messages: y'
-    print("Command '{}' added.".format(cmd))
-    inputlines.append(cmd)
-
-# Detect number of CPUs/cores on machine and set OpenMP threads if not already set
-if not ompthreadscheck:
-    # Set number of threads to number of physical CPU cores, i.e. avoid hyperthreading with OpenMP for now
-    if sys.platform == 'darwin':
-        nthreads = int(os.popen('sysctl hw.physicalcpu').readlines()[0].split(':')[1].strip())
-    elif sys.platform == 'win32':
-        # Consider using wmi tools to check hyperthreading on Windows
-        nthreads = os.cpu_count()
-    elif 'linux' in sys.platform:
-        lscpu = os.popen('lscpu').readlines()
-        cpusockets = [item for item in lscpu if item.startswith('Socket(s)')]
-        cpusockets = int(cpusockets[0].split(':')[1].strip())
-        corespersocket = [item for item in lscpu if item.startswith('Core(s) per socket')]
-        corespersocket = int(corespersocket[0].split(':')[1].strip())
-        nthreads = cpusockets * corespersocket
-    else:
-        nthreads = os.cpu_count()
-    cmd = '#num_of_procs: {}'.format(nthreads)
-    print("Command '{}' added.".format(cmd))
-    inputlines.append(cmd)
-
-# Add the default PML if not already set
-if not pmlcheck:
-    cmd1 = '#abc_type: pml'
-    cmd2 = '#pml_layers: 10'
-    print("Commands '{}' and '{}' added.".format(cmd1, cmd2))
-    inputlines.append(cmd1)
-    inputlines.append(cmd2)
-
-# Process materials
-for position, material in materials.items():
-    params = material.split()
-    debye = next((debye for debye in debyes if debye.split()[-1] == params[5]), None)
-    if debye:
-        if len(debye.split()) > 5:
-            raise CmdInputError("Command '{}' cannot be used in the old version of gprMax as it only supports materials with a single Debye pole.".format(''.join(debye)))
-        medium = '#medium: {} {} {} {} {} {} {}'.format(float(params[1]) + float(debye.split()[2]), params[1], float(debye.split()[3]), params[2], params[3], params[4], params[5])
-        print("Commands '{}' and '{}', replaced with '{}'".format(material, debye, medium))
-    else:
-        medium = '#medium: {} 0 0 {} {} {} {}'.format(params[1], params[2], params[3], params[4], params[5])
-        print("Command '{}', replaced with '{}'".format(material, medium))
-    inputlines[position] = medium
-
-
-# Create #analysis block
-outputfile = newfile.split(os.sep)
-analysis = '#analysis: 1 {} b'.format(outputfile[-1] + '.out')
-analysiscmds.insert(0, analysis)
-
-
-# Convert #hertzian_dipole and #waveform to #tx and #hertzian_dipole
-for source in hertziandipoles:
-    params = source.split()
-    if len(params) > 6:
-        ID = params[7]
-        tx = '#tx: {} {} {} {} {} {} {}'.format(params[1], params[2], params[3], params[4], ID, params[5], params[6])
-    else:
-        ID = params[5]
-        tx = '#tx: {} {} {} {} {} {} {}'.format(params[1], params[2], params[3], params[4], ID, 0, timewindow)
-
-    waveform = next(waveform for waveform in waveforms if waveform.split()[4] == ID)
-    waveformparams = waveform.split()
-    if waveformparams[1] is badwaveforms:
-        raise CmdInputError("Waveform types {} are not compatible between new and old versions of gprMax.".format(''.join(badwaveforms)))
-    elif waveformparams[1] == 'gaussiandotnorm':
-        waveformparams[1] = 'ricker'
-    hertzian = '#hertzian_dipole: {} {} {} {}'.format(waveformparams[2], waveformparams[3], waveformparams[1], waveformparams[4])
-
-    print("Commands '{}' and '{}', replaced with '{}' and '{}'".format(source, waveform, tx, hertzian))
-    inputlines.append(hertzian)
-    analysiscmds.append(tx)
-
-
-# Convert #voltage_source and #waveform to #tx and #voltage_source
-for source in voltagesources:
-    params = source.split()
-    if len(params) > 7:
-        ID = params[8]
-        tx = '#tx: {} {} {} {} {} {} {}'.format(params[1], params[2], params[3], params[4], ID, params[6], params[7])
-    else:
-        ID = params[6]
-        tx = '#tx: {} {} {} {} {} {} {}'.format(params[1], params[2], params[3], params[4], ID, 0, timewindow)
-    
-    waveform = next(waveform for waveform in waveforms if waveform.split()[4] == ID)
-    waveformparams = waveform.split()
-    if waveformparams[1] is badwaveforms:
-        raise CmdInputError("Waveform types {} are not compatible between new and old versions of gprMax.".format(''.join(badwaveforms)))
-    elif waveformparams[1] == 'gaussiandotnorm':
-        waveformparams[1] = 'ricker'
-    voltagesource = '#voltage_source: {} {} {} {} {}'.format(waveformparams[2], waveformparams[3], waveformparams[1], params[5], waveformparams[4])
-
-    print("Commands '{}' and '{}', replaced with '{}' and '{}'".format(source, waveform, tx, voltagesource))
-    inputlines.append(voltagesource)
-    analysiscmds.append(tx)
-
-inputlines += analysiscmds
-inputlines.append('#end_analysis:')
-
-
-# Write new input file
-newinputfile = newfile + '.in'
-
-with open(newinputfile, 'w') as f:
-    for line in inputlines:
-        f.write('{}\n'.format(line))
-
-print("\nWritten new input file: '{}'".format(newinputfile))
diff --git a/tools/outputfile_old2new.py b/tools/outputfile_old2new.py
deleted file mode 100644
index aa530996..00000000
--- a/tools/outputfile_old2new.py
+++ /dev/null
@@ -1,159 +0,0 @@
-# Copyright (C) 2015-2016: The University of Edinburgh
-#                 Authors: Craig Warren and Antonis Giannopoulos
-#
-# This file is part of gprMax.
-#
-# 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/>.
-
-import os, struct, argparse
-import numpy as np
-
-from gprMax.grid import FDTDGrid
-from gprMax.receivers import Rx
-from gprMax.fields_output import prepare_output_file, write_output
-
-"""Converts old output file to new HDF5 format."""
-
-# Parse command line arguments
-parser = argparse.ArgumentParser(description='Converts old output file to new HDF5 format.', usage='cd gprMax; python -m tools.outputfile_old2new outputfile')
-parser.add_argument('outputfile', help='name of output file including path')
-args = parser.parse_args()
-
-outputfile = args.outputfile
-G = FDTDGrid()
-
-print("Reading: '{}'".format(outputfile))
-
-with open(outputfile, 'rb') as f:
-    # Get information from file header
-    f.read(2)
-    filetype, = struct.unpack('h', f.read(2))
-    myshort, = struct.unpack('h', f.read(2))
-    myfloat, = struct.unpack('h', f.read(2))
-    titlelength, = struct.unpack('h', f.read(2))
-    sourcelength, = struct.unpack('h', f.read(2))
-    medialength, = struct.unpack('h', f.read(2))
-    reserved, = struct.unpack('h', f.read(2))
-    G.title = ''
-    for c in range(titlelength):
-        tmp, = struct.unpack('c', f.read(1))
-        G.title += tmp.decode('utf-8')
-    G.iterations, = struct.unpack('f', f.read(4))
-    G.iterations = int(G.iterations)
-    G.dx, = struct.unpack('f', f.read(4))
-    G.dy, = struct.unpack('f', f.read(4))
-    G.dz, = struct.unpack('f', f.read(4))
-    G.dt, = struct.unpack('f', f.read(4))
-    nsteps, = struct.unpack('h', f.read(2))
-    G.srcstepx, = struct.unpack('h', f.read(2))
-    G.srcstepy, = struct.unpack('h', f.read(2))
-    G.srcstepz, = struct.unpack('h', f.read(2))
-    G.rxstepx, = struct.unpack('h', f.read(2))
-    G.rxstepy, = struct.unpack('h', f.read(2))
-    G.rxstepz, = struct.unpack('h', f.read(2))
-    ntx, = struct.unpack('h', f.read(2))
-    nrx, = struct.unpack('h', f.read(2))
-    nrxbox, = struct.unpack('h', f.read(2))
-
-    # Display some basic information
-    print('Model title: {}'.format(G.title))
-    print('Spatial discretisation: {:.3f} x {:.3f} x {:.3f} m'.format(G.dx, G.dy, G.dz))
-    print('Time step: {:.3e} secs'.format(G.dt))
-    print('Time window: {:.3e} secs ({} iterations)'.format(G.iterations * G.dt, G.iterations))
-
-    # txs
-    for tx in range(ntx):
-        polarisation, = struct.unpack('c', f.read(1))
-        x, = struct.unpack('h', f.read(2))
-        y, = struct.unpack('h', f.read(2))
-        z, = struct.unpack('h', f.read(2))
-        for c in range(sourcelength):
-            tmp, = struct.unpack('c', f.read(1))
-        start, = struct.unpack('f', f.read(4))
-        stop, = struct.unpack('f', f.read(4))
-        # Only want transmitter position information so store in a Rx class for ease
-        t = Rx(positionx=x, positiony=y, positionz=z)
-        G.txs.append(t)
-
-    # rxs
-    for r in range(nrx):
-        x, = struct.unpack('h', f.read(2))
-        y, = struct.unpack('h', f.read(2))
-        z, = struct.unpack('h', f.read(2))
-        r = Rx(positionx=x, positiony=y, positionz=z)
-        G.rxs.append(r)
-
-    # rxboxes
-    for rxbox in range(nrxbox):
-        nrxs, = struct.unpack('h', f.read(2))
-        for rx in range(nrxs):
-            x, = struct.unpack('h', f.read(2))
-            y, = struct.unpack('h', f.read(2))
-            z, = struct.unpack('h', f.read(2))
-            r = Rx(positionx=x, positiony=y, positionz=z)
-            G.rxs.append(r)
-
-    # Fields
-    fieldsdata = np.fromfile(f, dtype=np.float32)
-    ex = np.reshape(fieldsdata[0::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    ey = np.reshape(fieldsdata[1::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    ez = np.reshape(fieldsdata[2::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    hx = np.reshape(fieldsdata[3::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    hy = np.reshape(fieldsdata[4::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    hz = np.reshape(fieldsdata[5::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    ix = np.reshape(fieldsdata[6::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    iy = np.reshape(fieldsdata[7::9], (len(G.rxs), G.iterations, nsteps), order='F')
-    iz = np.reshape(fieldsdata[8::9], (len(G.rxs), G.iterations, nsteps), order='F')
-
-    if nsteps == 1:
-        ex = np.transpose(ex)
-        ey = np.transpose(ey)
-        ez = np.transpose(ez)
-        hx = np.transpose(hx)
-        hy = np.transpose(hy)
-        hz = np.transpose(hz)
-        ix = np.transpose(ix)
-        iy = np.transpose(iy)
-        iz = np.transpose(iz)
-    else:
-        for i in range(len(G.rxs)):
-            ex[:,i,:] = ex[i,:,:]
-            ey[:,i,:] = ey[i,:,:]
-            ez[:,i,:] = ez[i,:,:]
-            hx[:,i,:] = hx[i,:,:]
-            hy[:,i,:] = hy[i,:,:]
-            hz[:,i,:] = hz[i,:,:]
-            ix[:,i,:] = ix[i,:,:]
-            iy[:,i,:] = iy[i,:,:]
-            iz[:,i,:] = iz[i,:,:]
-
-    # Remove any singleton dimensions
-    ex = np.squeeze(ex)
-    ey = np.squeeze(ey)
-    ez = np.squeeze(ez)
-    hx = np.squeeze(hx)
-    hy = np.squeeze(hy)
-    hz = np.squeeze(hz)
-    ix = np.squeeze(ix)
-    iy = np.squeeze(iy)
-    iz = np.squeeze(iz)
-
-# Create new HDF5 outputfile
-newoutputfile = os.path.splitext(outputfile)
-newoutputfile = newoutputfile[0] + '_hdf5.out'
-f = prepare_output_file(newoutputfile, G)
-write_output(f, np.s_[:], ex, ey, ez, hx, hy, hz, G)
-
-print("Written: '{}'".format(newoutputfile))
-