def test_abs_file_path():
assert abs_file_path('sample') == join(abspath(curdir), 'sample')
if platform == 'win32':
assert abs_file_path(join('~', 'sample')) == \
join(environ['HOMEDRIVE'], environ['HOMEPATH'], 'sample')
else:
assert abs_file_path(join('~', 'sample')) == \
join(environ['HOME'], 'sample')
environ['__TESTING__'] = 'SILLY'
assert abs_file_path(join(environ['__TESTING__'], 'sample')) == \
join(abspath(curdir), 'SILLY', 'sample')
assert abs_file_path(join(environ['HOME'], 'sample'), env=True) == \
join('$HOME', 'sample')
def read_input(input_file):
'''Defines what to expect from the input file and then
reads it in.'''
# Creates an input reader instance
reader = InputReader(default=SUPPRESS)
# Rate parameter, either rate or lifetime, not both
rate = reader.add_mutually_exclusive_group(required=True)
# The units are s, ns, ps, or fs. The default is ps.
rate.add_line_key('lifetime', type=float,
glob={'len' : '?',
'type' : ('ps', 'fs', 'ns', 's'),
'default' : 'ps'})
rate.add_line_key('rate', type=float,
glob={'len' : '?',
'type' : ('thz', 'phz', 'ghz', 'hz'),
'default' : 'thz'})
# The range of the X-axis
reader.add_line_key('xlim', type=[int, int], default=(1900, 2000))
reader.add_boolean_key('reverse', action=True, default=False)
# Read in the raw data.
reader.add_line_key('raw', type=[], glob={'len':'*', 'join':True, },
default=None, case=True)
# Read in the peak data. The wavenumber and height is required.
# The Lorentzian and Gaussian widths are defaulted to 10 if not given.
floatkw = {'type' : float, 'default' : 10.0}
reader.add_line_key('peak', required=True, repeat=True, type=[float,float],
keywords={'g':floatkw, 'l':floatkw,
'num' : {'type':int,'default':-1}})
# Read the exchange information.
reader.add_line_key('exchange', repeat=True, type=[int, int],
glob={'type' : float,
'default' : 1.0,
'len' : '?'})
reader.add_boolean_key('nosym', action=False, default=True,
dest='symmetric_exchange')
# Actually read the input file
args = reader.read_input(input_file)
# Make sure the filename was given correctly and read in data
if args.raw:
args.add('rawName', args.raw)
args.raw = loadtxt(abs_file_path(args.raw))
# Make the output file path absolute if given
args.data = abs_file_path(args.data) if 'data' in args else ''
if 'save_plot_script' in args:
args.save_plot_script = abs_file_path(args.save_plot_script)
else:
args.save_plot_script = ''
# Adjust the input rate or lifetime to wavenumbers
if 'lifetime' in args:
convert = { 'ps' : 1E-12, 'ns' : 1E-9, 'fs' : 1E-15, 's' : 1 }
args.add('k', 1 / ( convert[args.lifetime[1]] * args.lifetime[0] ))
else:
convert = { 'thz' : 1E12, 'ghz' : 1E9, 'phz' : 1E15, 'hz' : 1 }
args.add('k', convert[args.rate[1]] * args.rate[0])
args.k *= HZ2WAVENUM / ( 2 * pi )
# Parse the vibrational input
num, vib, Gamma_Lorentz, Gamma_Gauss, heights, rel_rates, num_given = (
[], [], [], [], [], [], [])
for peak in args.peak:
# Vibration #
num.append(peak[2]['num'])
num_given.append(False if peak[2]['num'] < 0 else True)
# Angular frequency
vib.append(peak[0])
# Relative peak heights
heights.append(peak[1])
# Default Gaussian or Lorentzian width or relative rate
Gamma_Lorentz.append(peak[2]['l'])
Gamma_Gauss.append(peak[2]['g'])
# Either all or none of the numbers must be given explicitly
if not (all(num_given) or not any(num_given)):
raise ReaderError('All or none of the peaks must '
'be given numbers explicitly')
# If the numbers were give, make sure there are no duplicates
if all(num_given):
if len(num) != len(set(num)):
raise ReaderError('Duplicate peaks cannot be given')
# If none were given, number automatically
else:
num = range(1, len(num)+1, 1)
args.add('num', array(num))
args.add('vib', array(vib))
args.add('heights', array(heights))
args.add('Gamma_Lorentz', array(Gamma_Lorentz))
args.add('Gamma_Gauss', array(Gamma_Gauss))
# Set up the exchanges
# Make sure the each exchange number appears in num.
num = set(num)
ex = []
rates = []
string = 'Requested peak {0} in exchange does not exist'
if 'exchange' in args:
for exchange in args.exchange:
p1 = exchange[0]
if p1 not in num:
raise ReaderError(string.format(p1))
p2 = exchange[1]
if p2 not in num:
raise ReaderError(string.format(p2))
if p1 == p2 and args.symmetric_exchange:
raise ReaderError('Self exchange is not allowed')
rate = exchange[2]
# Offset the peak number by one to match python indicies
ex.append([p1-1, p2-1])
rates.append(rate)
else:
ex = []
rates = []
args.add('exchanges', array(ex, dtype=int))
args.add('exchange_rates', array(rates))
# Make sure the xlimits are ascending
try:
range_check(args.xlim[0], args.xlim[1])
except ValueError:
raise ReaderError('In xrange, the low value must '
'less than the high value')
return args