Python LineList.all_transitions方法代碼示例

# 需要導入模塊: from linetools.lists.linelist import LineList [as 別名]
# 或者: from linetools.lists.linelist.LineList import all_transitions [as 別名]
def test_all_transitions():
    error_msg = 'Something is wrong in all_transitions()'
    ism = LineList('ISM')
    #check simple case
    line = 'OVI'
    ovi_transitions = ism.all_transitions(line)
    assert len(ovi_transitions) == 2, error_msg
    #print(ovi_transitions['name'])
    #check unknown
    line = 'unknown'
    out = ism.all_transitions(line)
    assert type(out) == dict, error_msg
    #check case of single transition ion
    line = 'CIII'
    out = ism.all_transitions(line)
    assert type(out) == dict, error_msg
    # wrest
    out = ism.all_transitions(1215.6700*u.AA)
    assert len(out) == 30 # 30 Lyman series transitions

# 需要導入模塊: from linetools.lists.linelist import LineList [as 別名]
# 或者: from linetools.lists.linelist.LineList import all_transitions [as 別名]
def test_all_transitions():
    error_msg = 'Something is wrong in all_transitions()'
    ism = LineList('ISM')
    #check simple case
    line = 'OVI'
    ovi_transitions = ism.all_transitions(line)
    assert len(ovi_transitions) == 2, error_msg
    #print(ovi_transitions['name'])
    #check unknown
    line = 'unknown'
    out = ism.all_transitions(line)
    assert type(out) == dict, error_msg
    #check case of single transition ion
    line = 'CIII'
    out = ism.all_transitions(line)
    assert type(out) == dict, error_msg
    #check case of transitions from excited levels
    line='FeII*'
    out = ism.all_transitions(line)
    assert len(out) == 27, "wrong line counts"
    print(out)
    # wrest
    out = ism.all_transitions(1215.6700*u.AA)
    assert len(out) == 30,"wrong line counts" # 30 Lyman series transitions
    #print('test_all_transitions() passed')
    h2 = LineList('H2')
    line = 'B19-0P(1)'
    out = h2.all_transitions(line)
    assert len(out) == 7

# 需要導入模塊: from linetools.lists.linelist import LineList [as 別名]
# 或者: from linetools.lists.linelist.LineList import all_transitions [as 別名]
class Component(object):
    def __init__(self, z, wrest, vlim=[-300.,300]*u.km/u.s,
        linelist=None):
        # Init
        self.init_wrest = wrest
        self.zcomp = z
        self.vlim = vlim
        self.attrib = {'N': 0., 'Nsig': 0., 'flagN': 0, # Column
                       'b': 0.*u.km/u.s, 'bsig': 0.*u.km/u.s,  # Doppler
                       'z': self.zcomp, 'zsig': 0.,
                       'Quality': 'None'}
        self.comment = 'None'
        #
        self.linelist = linelist
        self.lines = []
        self.init_lines()
        #
        self.name = 'z{:.5f}_{:s}'.format(
            self.zcomp,self.lines[0].data['name'].split(' ')[0])
        #
    def init_lines(self):
        '''Fill up the component lines
        '''
        if self.linelist is None:
            self.linelist = LineList('Strong')
        # Get the lines

        all_trans = self.linelist.all_transitions(self.init_wrest)
        #QtCore.pyqtRemoveInputHook()
        #xdb.set_trace()
        #QtCore.pyqtRestoreInputHook()
        if isinstance(all_trans,dict):
            all_trans = [all_trans]
        for trans in all_trans:
            self.lines.append(AbsLine(trans['wrest'],
                linelist=self.linelist))

        # Sync
        self.sync_lines()

    def sync_lines(self):
        '''Synchronize attributes of the lines
        '''
        for line in self.lines:
            line.attrib['N'] = self.attrib['N']
            line.attrib['b'] = self.attrib['b']
            line.attrib['z'] = self.attrib['z']

# 需要導入模塊: from linetools.lists.linelist import LineList [as 別名]
# 或者: from linetools.lists.linelist.LineList import all_transitions [as 別名]
    def add_abslines_from_linelist(self, llist='ISM', wvlim=None, min_Wr=None, **kwargs):
        """
        It adds associated AbsLines satisfying some conditions (see parameters below).

        Parameters
        ----------
        llist : str
            Name of the linetools.lists.linelist.LineList
            object where to look for the transition names.
            Default is 'ISM', which means the function looks
            within `list = LineList('ISM')`.
        wvlims : Quantity array, optional
            Observed wavelength limits for AbsLines to be added.
            e.g. [1200, 2000]*u.AA.
        min_Wr : Quantity, optional
            Minimum rest-frame equivalent with for AbsLines to be added.
            This is calculated in the very low optical depth regime tau0<<1,
            where Wr is independent of Doppler parameter or gamma (see eq. 9.15 of
            Draine 2011). Still, a column density attribute for the AbsComponent
            is needed.

        Returns
        -------
        Adds AbsLine objects to the AbsComponent._abslines list.

        Notes
        -----
        **kwargs are passed to AbsLine.add_absline() method.

        """
        # get the transitions from LineList
        llist = LineList(llist)
        name = ions.ion_name(self.Zion, nspace=0)
        transitions = llist.all_transitions(name)
        # unify output to be always QTable
        if isinstance(transitions, dict):
            transitions = llist.from_dict_to_qtable(transitions)

        # check wvlims
        if wvlim is not None:
            cond = (transitions['wrest']*(1+self.zcomp) >= wvlim[0]) & \
                   (transitions['wrest']*(1+self.zcomp) <= wvlim[1])
            transitions = transitions[cond]

        # check outputs
        if len(transitions) == 0:
            warnings.warn("No transitions satisfying the criteria found. Doing nothing.")
            return

        # loop over the transitions when more than one found
        for transition in transitions:
            iline = AbsLine(transition['name'], z=self.zcomp)
            iline.limits.set(self.vlim)
            iline.attrib['coord'] = self.coord
            iline.attrib['logN'] = self.logN
            iline.attrib['sig_logN'] = self.sig_logN
            iline.attrib['flag_N'] = self.flag_N
            iline.attrib['N'] = 10**iline.attrib['logN'] / (u.cm * u.cm)
            iline.attrib['sig_N'] = 10**iline.attrib['sig_logN'] / (u.cm * u.cm)

            for key in self.attrib.keys():
                iline.attrib[key] = self.attrib[key]

            if min_Wr is not None:
                # check logN is defined
                logN = self.logN
                if logN == 0:
                    warnings.warn("AbsComponent does not have logN defined. Appending AbsLines "
                                 "regardless of min_Wr.")
                else:
                    N = 10**logN / (u.cm*u.cm)
                    Wr_iline = iline.get_Wr_from_N(N=N)  # valid for the tau0<<1 regime.
                    if Wr_iline < min_Wr:  # do not append
                        continue
            # add the absline
            self.add_absline(iline)

# 需要導入模塊: from linetools.lists.linelist import LineList [as 別名]
# 或者: from linetools.lists.linelist.LineList import all_transitions [as 別名]
    def add_abslines_from_linelist(self, llist='ISM', init_name=None, wvlim=None, min_Wr=None, **kwargs):
        """
        It adds associated AbsLines satisfying some conditions (see parameters below).

        Parameters
        ----------
        llist : str, optional
            Name of the linetools.lists.linelist.LineList
            object where to look for the transition names.
            Default is 'ISM', which means the function looks
            within `list = LineList('ISM')`.
        init_name : str, optional
            Name of the initial transition used to define the AbsComponent
        wvlim : Quantity array, optional
            Observed wavelength limits for AbsLines to be added.
            e.g. [1200, 2000]*u.AA.
        min_Wr : Quantity, optional
            Minimum rest-frame equivalent with for AbsLines to be added.
            This is calculated in the very low optical depth regime tau0<<1,
            where Wr is independent of Doppler parameter or gamma (see eq. 9.15 of
            Draine 2011). Still, a column density attribute for the AbsComponent
            is needed.

        Returns
        -------
        Adds AbsLine objects to the AbsComponent._abslines list.

        Notes
        -----
        **kwargs are passed to AbsLine.add_absline() method.

        """
        from linetools.lists import utils as ltlu

        # get the transitions from LineList
        llist = LineList(llist)
        if init_name is None:  # we have to guess it
            if (self.Zion) == (-1, -1):  # molecules
                # init_name must be in self.attrib (this is a patch)
                init_name = self.attrib['init_name']
            else:  # atoms
                init_name = ions.ion_to_name(self.Zion, nspace=0)
        transitions = llist.all_transitions(init_name)

        # unify output to be a Table
        if isinstance(transitions, dict):
            transitions = ltlu.from_dict_to_table(transitions)

        # check wvlims
        if wvlim is not None:
            # Deal with units
            wrest = transitions['wrest'].data * transitions['wrest'].unit
            # Logic
            cond = (wrest*(1+self.zcomp) >= wvlim[0]) & \
                   (wrest*(1+self.zcomp) <= wvlim[1])
            transitions = transitions[cond]

        # check outputs
        if len(transitions) == 0:
            warnings.warn("No transitions satisfying the criteria found. Doing nothing.")
            return

        # loop over the transitions when more than one found
        for transition in transitions:
            iline = AbsLine(transition['name'], z=self.zcomp, linelist=llist)
            iline.limits.set(self.vlim)
            iline.attrib['coord'] = self.coord
            iline.attrib['logN'] = self.logN
            iline.attrib['sig_logN'] = self.sig_logN
            iline.attrib['flag_N'] = self.flag_N
            iline.attrib['N'] = 10**iline.attrib['logN'] / (u.cm * u.cm)
            iline.attrib['sig_N'] = 10**iline.attrib['sig_logN'] / (u.cm * u.cm)

            for key in self.attrib.keys():
                iline.attrib[key] = self.attrib[key]

            if min_Wr is not None:
                # check logN is defined
                if self.logN == 0:
                    pass
                else:
                    N = 10.**self.logN / u.cm**2
                    Wr_iline = iline.get_Wr_from_N(N=N)  # valid for the tau0<<1 regime.
                    if Wr_iline < min_Wr:  # do not append
                        continue
            # add the absline
            self.add_absline(iline)