Code clean up
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@ -1,54 +1,54 @@
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import xml.etree.ElementTree as eT
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import xml.etree.ElementTree as eT
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import numpy as np
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import numpy as np
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import quantities as pq
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import astropy.units as u
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import os
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import os
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import logging
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import logging
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import sys
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from esbo_etc.lib.helpers import error
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class Entry(object):
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class Entry(object):
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"""
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"""
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A class used to represent a configuration entry.
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A class used to represent a configuration entry.
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Copied from ExoSim (https://github.com/ExoSim/ExoSimPublic)
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"""
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"""
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val = None
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attrib = None
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xml_entry = None
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def __call__(self):
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def __call__(self):
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return self.val
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return self.val if hasattr(self, "val") else None
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def parse(self, xml):
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def parse(self, xml):
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"""
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"""
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Parse a XML tree element
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Parse attributes of a XML element
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:param xml: XML element tree to parse
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:param xml: XML element to parse the attributes from
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"""
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"""
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self.attrib = xml.attrib
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# Copy the XML attributes to object attributes
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for attr in self.attrib.keys():
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for attrib in xml.attrib.keys():
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setattr(self, attr, self.attrib[attr])
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setattr(self, attrib, xml.attrib[attrib])
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# Convert to python datatype and apply the corresponding unit (if applicable)
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if hasattr(self, 'units'):
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if hasattr(self, 'units'):
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try:
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try:
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self.val = pq.Quantity(list(map(float, self.val.split(','))),
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self.val = u.Quantity(list(map(float, self.val.split(','))),
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self.units).simplified
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self.units)
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if self.units == 'deg':
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# if self.units == 'deg':
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self.val = [x * pq.rad for x in self.val] # workaround for qt unit conversion
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# self.val = [val * pq.rad for val in self.val] # workaround for qt unit conversion
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if len(self.val) == 1:
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if len(self.val) == 1:
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self.val = self.val[0]
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self.val = self.val[0]
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except (ValueError, LookupError):
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except (ValueError, LookupError):
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logging.error('unable to convert units in entry [tag, units, value]: ',
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error("unable to convert units in entry '" + xml.tag + "': " + self.val + " " + self.units, exit_=False)
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xml.tag, self.units, self.val)
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elif hasattr(self, "val") and self.val.lower() in ["false", "true"]:
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self.val = (self.val.lower() == "true")
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class Configuration(object):
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class Configuration(object):
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"""
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"""
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A Class to parse the XML configuration file.
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A Class to parse the XML configuration file.
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Adapted from ExoSim (https://github.com/ExoSim/ExoSimPublic)
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Attributes
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Attributes
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----------
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----------
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conf : str
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conf : Entry
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Parsed XML tree
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Parsed configuration file as Entry-tree
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"""
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"""
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conf = None
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conf = None
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@ -63,83 +63,74 @@ class Configuration(object):
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default_path : str
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default_path : str
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default path to use for relative paths
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default path to use for relative paths
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"""
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"""
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if not os.path.exists(filename):
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logging.error("Configuration file '" + filename + "' doesn't exist.")
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sys.exit(1)
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# Check if configuration file exists
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if not os.path.exists(filename):
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error("Configuration file '" + filename + "' doesn't exist.")
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# Read configuration file
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logging.info("Reading configuration from file '" + filename + "'.")
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logging.info("Reading configuration from file '" + filename + "'.")
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self.conf = self.parser(eT.parse(filename).getroot())
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self.conf = self.parser(eT.parse(filename).getroot())
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if default_path:
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setattr(self.conf, "__path__", default_path)
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elif hasattr(self.conf.common, "ConfigPath"):
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setattr(self.conf, "__path__",
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os.path.expanduser(self.conf.common.ConfigPath().replace('__path__', os.getcwd())))
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else:
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logging.error("Path to config files not defined")
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self.validate_options()
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self.calc_metaoptions()
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self.calc_metaoptions()
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def parser(self, root):
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def parser(self, parent):
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"""
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"""
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Parse a XML configuration file.
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Parse a XML element tree to an Entry-tree
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Parameters
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Parameters
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----------
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----------
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root : ElementTree
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parent : ElementTree
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The XML tree to be parsed
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The parent XML tree to be parsed
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Returns
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Returns
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-------
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-------
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obj : Entry
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obj : Entry
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The parsed XML tree
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The parsed XML tree
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"""
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"""
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# Initialize empty Entry object
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obj = Entry()
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obj = Entry()
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for ch in root:
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for child in parent:
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retval = self.parser(ch)
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# recursively parse children of child element
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retval.parse(ch)
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parsed_child = self.parser(child)
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# parse attributes of child element
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parsed_child.parse(child)
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if hasattr(obj, ch.tag):
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# Add or append the parsed child to the prepared Entry object
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if isinstance(getattr(obj, ch.tag), list):
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if hasattr(obj, child.tag):
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getattr(obj, ch.tag).append(retval)
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if isinstance(getattr(obj, child.tag), list):
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getattr(obj, child.tag).append(parsed_child)
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else:
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else:
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setattr(obj, ch.tag, [getattr(obj, ch.tag), retval])
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setattr(obj, child.tag, [getattr(obj, child.tag), parsed_child])
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else:
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else:
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setattr(obj, ch.tag, retval)
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setattr(obj, child.tag, parsed_child)
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return obj
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return obj
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def validate_options(self):
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self.validate_is_list()
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self.validate_True_False_spelling()
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def validate_is_list(self):
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if not isinstance(self.conf.common_optics.optical_component, list):
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self.conf.common_optics.optical_component = [self.conf.common_optics.optical_component]
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if not isinstance(self.conf.instrument, list):
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self.conf.instrument = [self.conf.instrument]
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def validate_True_False_spelling(self):
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accepted_values = ['True', 'False']
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test_cases = [
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'noise/EnableJitter',
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'noise/EnableShotNoise',
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'noise/EnableReadoutNoise',
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]
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for item in test_cases:
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if hasattr(self.conf, item.split('/')[0]):
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if not self.conf.__getattribute__(item.split('/')[0]).__dict__[item.split('/')[1]]() in accepted_values:
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raise ValueError("Accepted values for [%s] are 'True' or 'False'" % item)
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def calc_metaoptions(self):
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def calc_metaoptions(self):
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"""
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Calculate additional attributes e.g. the wavelength grid
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Returns
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-------
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"""
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self.calc_metaoption_wl_delta()
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self.calc_metaoption_wl_delta()
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def calc_metaoption_wl_delta(self):
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def calc_metaoption_wl_delta(self):
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wl_delta = self.conf.common.wl_min() / self.conf.common.logbinres()
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"""
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setattr(self.conf.common, 'common_wl', (np.arange(self.conf.common.wl_min(),
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Calculate the wavelength grid used for the calculations.
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self.conf.common.wl_max(),
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Returns
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wl_delta) * wl_delta.units).rescale(pq.um))
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-------
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"""
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if hasattr(self.conf.common, "wl_delta"):
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wl_delta = self.conf.common.wl_delta()
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else:
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wl_delta = self.conf.common.wl_min() / self.conf.common.res()
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setattr(self.conf.common, 'wl_bins', np.arange(self.conf.common.wl_min().to(u.micron).value,
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self.conf.common.wl_max().to(u.micron).value,
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wl_delta.to(u.micron).value) * u.micron)
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if __name__ == "__main__":
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if __name__ == "__main__":
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