def __init__(self):
if 'CLOUDY_EXE' in os.environ:
self.cloudy_exe = os.environ['CLOUDY_EXE']
else:
self.cloudy_exe = 'cloudy.exe'
self.cloudy_dict = {
'10.00': '/usr/local/Cloudy/c10.00/cloudy.exe',
'13.03': '/usr/local/Cloudy/c13.03/source/cloudy.exe',
'17.00': '/usr/local/Cloudy/c17.00/source/cloudy.exe',
'17.01': '/usr/local/Cloudy/c17.01/source/cloudy.exe',
'17.02': '/usr/local/Cloudy/c17.02/source/cloudy.exe'
}
self.INSTALLED = {}
try:
try:
from matplotlib.tri.triangulation import Triangulation
except:
from matplotlib.delaunay import Triangulation
self.INSTALLED['Triangulation'] = True
except:
self.INSTALLED['Triangulation'] = False
_Config.log_.warn(
'pyCloudy works better with matplotlib Triangulation',
calling='pyCloudy config')
try:
import matplotlib.pyplot as plt
self.INSTALLED['plt'] = True
except:
self.INSTALLED['plt'] = False
try:
import pyneb as pn
self.INSTALLED['PyNeb'] = True
except:
self.INSTALLED['PyNeb'] = False
_Config.log_.warn('pyCloudy works better with PyNeb',
calling='pyCloudy config')
try:
from scipy.integrate import cumtrapz
from scipy.interpolate import interp1d
self.INSTALLED['scipy'] = True
except:
self.INSTALLED['scipy'] = False
_Config.log_.warn('pyCloudy works better with scipy',
calling='pyCloudy config')
try:
from PIL import Image
self.INSTALLED['Image'] = True
except:
self.INSTALLED['Image'] = False
_Config.log_.warn(
'pyCloudy needs PIL or Pillow for 3 colors images',
calling='pyCloudy config')
try:
import MySQLdb
self.INSTALLED['MySQL'] = True
except:
self.INSTALLED['MySQL'] = False
try:
import pymysql
self.INSTALLED['PyMySQL'] = True
except:
self.INSTALLED['PyMySQL'] = False
try:
import pandas
self.INSTALLED['pandas'] = True
except:
self.INSTALLED['pandas'] = False
try:
import pyfits
self.INSTALLED['pyfits'] = True
self.INSTALLED['pyfits from astropy'] = False
except:
self.INSTALLED['pyfits'] = False
try:
import astropy.io.fits as pyfits
self.INSTALLED['pyfits from astropy'] = True
except:
self.INSTALLED['pyfits from astropy'] = False
try:
from numpy.version import version as numpy_version
if [int(n) for n in (numpy_version.split('.')[:3])] > [1, 5, 1]:
self.INSTALLED['np.genfromtxt new'] = True
except:
try:
test_str = ['#one\t two\t three', '1\t 2\t 3']
test_res = np.genfromtxt(test_str,
names=True,
comments=';',
delimiter='\t')
if test_res.dtype.fields is None:
self.INSTALLED['np.genfromtxt new'] = False
else:
self.INSTALLED['np.genfromtxt new'] = True
except:
self.INSTALLED['np.genfromtxt new'] = False
if not self.INSTALLED['np.genfromtxt new']:
_Config.log_.warn('pyCloudy works better with numpy >= 1.6.0',
calling='pyCloudy config')
try:
import multiprocessing as mp
self.INSTALLED['mp'] = True
self.Nprocs = mp.cpu_count()
except:
self.INSTALLED['mp'] = False
self.log_.message('multiprocessing not available',
calling=self.calling)
self.Nprocs = 1
try:
import numexpr as ne
self.INSTALLED['numexpr'] = True
except:
self.INSTALLED['numexpr'] = False
self.SAVE_LIST = [['radius', '.rad'], ['continuum', '.cont'],
['physical conditions', '.phy'],
['overview', '.ovr'], ['heating', '.heat'],
['cooling', '.cool'], ['optical depth', '.opd']]
self.SAVE_LIST_GRAINS = [['grain temperature', '.gtemp'],
['grain abundances', '.gabund'],
['grain D/G ratio', '.gdgrat']]
self.SAVE_LIST_ELEMS = [['hydrogen', '.ele_H'], ['helium', '.ele_He'],
['carbon', '.ele_C'], ['nitrogen', '.ele_N'],
['oxygen', '.ele_O'], ['argon', '.ele_Ar'],
['neon', '.ele_Ne'], ['sulphur', '.ele_S'],
['chlorin', '.ele_Cl'], ['iron', '.ele_Fe'],
['silicon', '.ele_Si']]
self.def_c13c17()
calc_emiss_o_ii_rl, calc_emiss_ne_ii_rl, \
calc_abund_he_i_rl, calc_abund_he_ii_rl, \
calc_abund_c_ii_rl, calc_abund_c_iii_rl, \
calc_abund_n_ii_rl, calc_abund_n_iii_rl, \
calc_abund_o_ii_rl, calc_abund_ne_ii_rl, \
redlaw, redlaw_gal, redlaw_gal2, \
redlaw_ccm, redlaw_jbk, redlaw_fm, \
redlaw_smc, redlaw_lmc, \
deredden_flux, deredden_relflux
from .version import __version__
import sys
from numpy.version import version as numpy_version
if sys.version_info[0:2] < (2, 6):
log_.warn(
'pyequib requires Python version >= 2.6, but it is version {0}'.format(
sys.version_info),
calling='pyequib')
try:
if [int(n) for n in (numpy_version.split('.')[:3])] < [1, 5, 1]:
log_.warn(
'pyequib Numpy version >= 1.5.1, but it is version {0}'.format(
numpy_version),
calling='pyequib')
except:
log_.warn(
'Cannot find Numpy version {0}, report the bug'.format(numpy_version),
calling='pyemcee')
# 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 this program. If not, see <http://www.gnu.org/licenses/>.
from collections import namedtuple
from enum import Enum
from abc import ABCMeta, abstractmethod
import warnings
import numpy as np
from numpy.version import version as npver
npv = tuple(int(x) for x in npver.split('.'))
class namedarray:
"""Class representing a set of field names such that any list or array of numbers can be casted into a :class:`numpy.recarray`"""
def __init__(self, field_names):
""":param field_names: List of field names
:type field_names: list"""
if isinstance(field_names, str):
self._fields = [field_name.strip() for field_name in field_names.split(',')]
else:
self._fields = field_names[:]
self._nfields = len(self._fields)
self.dtype = np.dtype([(field_name, float) for field_name in self._fields])
def __repr__(self):