ModelSets: The interface to models in the Toolbox

ModelSets: The interface to models in the Toolbox#

PDRT supports a variety of PDR models to be used to fit your data. These are represented in the Python class ModelSet. Broadly three classes are available:

Wolfire/Kaufman 2020 models for constant density media (metallicities Z=0.5,1) and viewing angles 0 (face-on), 30, 45, 60, 75 degrees.

Wolfire/Kaufman 2006 face-on models for constant density media (Z=0.1,1,3)

Kosma-$\tau$ 2013 models for clumpy and non-clumpy media (Z=1)

The viewing angle models calculate the emitted line intensity along a line-of-sight at angle, theta, with respect to the illuminated face of the PDR. The angle theta=0 is a line that is perpendicular to the face while the angle theta=90 is a line that is parallel to the face. The line intensity for each transition as well as the integrated far-infrared intensity is calculated as in Pabst et al. 2017, A&A, 606, A29. We make the assumption that each line of sight passes through all layers of the PDR to an optical depth of Av=7 from the face. This means that the integral along the line-of-sight as well as Av increases as 7/cos(theta), and the thickness of the PDR increases as 7*tan(theta). The user should keep in mind that this assumption may lead to unrealistically large Av that should be checked against observations if possible. The different angles and Avs are given in the fits headers as follows LOSANGLE angle in degrees with respect to illuminated face of PDR.

Note that the face-on intensity is angle averaged over intensities emitted from the PDR face as in Tielens & Hollenbach 1985, but the angle-on intensity is the intensity along the ray at the given angle.

Models are stored in FITS format as ratios of intensities as a function of radiation field and hydrogen nucleus volume density. The FITS headers list three different extinction values:

AV: optical depth in magnitudes of visual extinction of PDR along a line through the illuminated face to the deepest layers. All models are fixed at $A_V = 7$.

AVPERP: optical depth in magnitudes of visual extinction of the PDR perpendicular to Av.

AVLOS: optical depth in magnitudes of visual extinction of the PDR along the line-of-sight.

For example how to use ModelSets, see the notebook PDRT_Example_ModelSets.ipynb

Manage pre-computed PDR models

class pdrtpy.modelset.ModelSet(name, z, medium='constant density', losangle=0, mass=None, modelsetinfo=None, format='ipac', debug=False)[source]#

Bases: object

Class for computed PDR Model Sets. ModelSet provides interface to a directory containing the model FITS files and the ability to query details about.

Parameters:

namestr

Identifying name, e.g., ‘wk2006’.

zfloat

Metallicity in solar units.

mediumstr

Medium type, e.g. ‘constant density’, ‘clumpy’, ‘non-clumpy’.

losanglefloat

The line-of-sight inclination angle (aka viewing angle), losangle=0 is face-on, losangle=90 is edge-on. Valid values are 0, 30, 45, 60, 75, 90.

massfloat

Maximum clump mass (for KosmaTau models). Default: None (appropriate for Wolfire/Kaufman models).

modelsetinfostr or Table

For adding user specified ModelSet, this parameter specifies the file with information about the ModelSet. It can be a pathname to an external tabular file in an astropy-recognized format or an astropy Table object. If an external tabular file, its format should be given by the format keyword. The columns are:

['PDRcode','name', 'version','path','filename','medium','z','inc', 'mass','description']

z, ‘inc’, and mass should be numbers, the rest should be strings. The name, version, medium, z, ‘inc’, and mass columns contain the values available in the input ModelSet as described above. PDRcode is the originator of the code e.g., “KOSMA-tau”, version is the code version, path is the full-qualified pathname to the FITS files, filename is the tabular file which contains descriptions of individual FITS files. This must also be in the format specified by the format keyword. description is a description of the input ModelSet.

formatstr

If modelsetinfo is a file, give the format of file. Must be an astropy recognized Table format. e.g., ascii, ipac, votable. Default is IPAC format

Attributes:

avlos: The visual extinction along the line of sight, expressed in magnitudes.
avperp: The PDR thickness for inclined viewing angle models, expressed in visual magnitudes.
code: The PDR code that created this ModelSet, e.g.
description: The description of this model
identifiers: Table of lines and continuum that are included in ratio models of this ModelSet.
is_wk2006: Indicate this is a wk2006 model, to deal with quirks of that modelset.
is_wk2020: Indicate this is a wk2020 model, to deal with quirks of that modelset.
losangle: The inclination (viewing) angle with respect to the line of sight, in degrees.
medium: The medium type of this model, e.g.
metallicity: The metallicity of this ModelSet
name: The name of this ModelSet
supported_intensities: Table of lines and continuum that are covered by this ModelSet and have models separate from the any ratio model they might be in.
supported_ratios: The emission ratios that are covered by this ModelSet
table: The table containing details of the models in this ModelSet.
user_added_models: Show which models have been added to this ModelSet by the user
version: The version of this ModelSet
viewangle: The viewing angle (inclination) with respect to the line of sight, in degrees.
z: The metallicity of this ModelSet

Methods

`add_model`(identifier, model, title[, overwrite])	Add your own model to this ModelSet.
`all_sets`([debug])	Return a table of the names and descriptions of available ModelSets (not just this one)
`find_files`(m[, ext])	Find the valid model ratios files in this ModelSet for a given list of measurement IDs.
`find_pairs`(m)	Find the valid model ratios labels in this ModelSet for a given list of measurement IDs
`get_model`(identifier[, unit, ext])	Get a specific model by its identifier
`get_models`(identifiers[, model_type, ext])	Get the models from this ModelSet that match the input list of identifiers
`list`()	Print the names and descriptions of available ModelSets (not just this one)
`model_intensities`(m)	Return the model intensities in this ModelSet that match the input Measurement ID list.
`model_ratios`(m)	Return the model ratios that match the input Measurement ID list.
`ratiocount`(m)	The number of valid ratios in this ModelSet, given a list of observation (`Measurement`) identifiers.

Raises:

ValueError: If model set not recognized/found.

add_model(identifier, model, title, overwrite=False)[source]#

Add your own model to this ModelSet.

Parameters:

identifierstr: A Measurement ID. It can be an intensity or a ratio, e.g., “CII_158”,”CI_609/FIR”.
modelstr or Measurement: The model to add. If a string, this must be the fully-qualified path of a FITS file. If a Measurement it must have the same CTYPEs and CUNITs as the models in the ModelSet.
titlestr: A formatted string (e.g., LaTeX) describing this observation that can be used for plotting. Python r-strings are accepted, e.g., r’$^{13}$CO(3-2)’ would give $^{13}{\rm CO(3-2)}$.
overwritebool: Whether to overwrite the model if the identifier already exists in the ModelSet or has been previously added. Default: False.

static all_sets(debug=False)[source]#

Return a table of the names and descriptions of available ModelSets (not just this one)

Returns:

Table

property avlos#

The visual extinction along the line of sight, expressed in magnitudes. Returns None for non-wk2020 models.

Returns:

float or None

property avperp#

The PDR thickness for inclined viewing angle models, expressed in visual magnitudes. Returns None for face-on geometry (losangle=0) and for non-wk2020 models.

Returns:

float or None

property code#

The PDR code that created this ModelSet, e.g. ‘KOSMA-tau’

Returns:

str

property description#

The description of this model

Returns:

str

find_files(m, ext='fits')[source]#

Find the valid model ratios files in this ModelSet for a given list of measurement IDs. See id()

Parameters:

mlist: List of string Measurement IDs, e.g. [“CII_158”,”OI_145”,”FIR”].
extstr: File extension. Default: “fits”.

Returns:

iterator: An iterator of model ratio files for the given list of Measurement IDs.

find_pairs(m)[source]#

Find the valid model ratios labels in this ModelSet for a given list of measurement IDs

Parameters:

mlist: List of string Measurement IDs, e.g. [“CII_158”,”OI_145”,”FIR”].

Returns:

iterator: An iterator of model ratio labels for the given list of measurement IDs.

get_model(identifier, unit=None, ext='fits')[source]#

Get a specific model by its identifier

Parameters:

identifierstr: A Measurement ID. It can be an intensity or a ratio, e.g., “CII_158”,”CI_609/FIR”.

Returns:

Measurement: The model matching the identifier.

Raises:

KeyError: If identifier not found in this ModelSet.

get_models(identifiers, model_type='ratio', ext='fits')[source]#

Get the models from this ModelSet that match the input list of identifiers

Parameters:

identifierslist: List of string Measurement IDs, e.g., [“CII_158”,”OI_145”,”CS_21”].
model_typestr: Indicates which type of model is requested: one of ‘ratio’ or ‘intensity’.

Returns:

list: The matching models as a list of Measurement.

Raises:

KeyError: If identifiers not found in this ModelSet.

property identifiers#

Table of lines and continuum that are included in ratio models of this ModelSet. Only lines and continuum that are part of ratios are included in this list. For a separate list of line and continuum intensity models see supported_intensities().

Returns:

astropy.table.Table

property is_wk2006#

Indicate this is a wk2006 model, to deal with quirks of that modelset.

Returns:

bool: True if it is.

property is_wk2020#

Indicate this is a wk2020 model, to deal with quirks of that modelset.

Returns:

bool: True if it is.

static list()[source]#: Print the names and descriptions of available ModelSets (not just this one)

property losangle#

The inclination (viewing) angle with respect to the line of sight, in degrees. A value of 0 means face-on.

Returns:

float

property medium#

The medium type of this model, e.g. ‘constant density’, ‘clumpy’, ‘non-clumpy’

Returns:

str

property metallicity#

The metallicity of this ModelSet

Returns:

float

model_intensities(m)[source]#

Return the model intensities in this ModelSet that match the input Measurement ID list. This method will return the intersection of the input list and the list of supported lines.

Parameters:

mlist: List of string Measurement IDs, e.g., [“CII_158”,”OI_145”,”CS_21”].

Returns:

list: List of string identifiers of intensity IDs, e.g., [‘CII_158’,’OI_145’].

model_ratios(m)[source]#

Return the model ratios that match the input Measurement ID list. You must provide at least 2 Measurements IDs

Parameters:

mlist: List of string Measurement IDs, e.g., [“CII_158”,”OI_145”,”FIR”].

Returns:

list: List of string identifiers of ratio IDs, e.g., [‘OI_145/CII_158’, ‘OI_145+CII_158/FIR’].

property name#

The name of this ModelSet

Returns:

str

ratiocount(m)[source]#

The number of valid ratios in this ModelSet, given a list of observation (Measurement) identifiers.

Parameters:

mlist: List of string Measurement IDs, e.g. [“CII_158”,”OI_145”,”FIR”].

Returns:

int: The number of model ratios found for the given list of measurement IDs.

property supported_intensities#

Table of lines and continuum that are covered by this ModelSet and have models separate from the any ratio model they might be in.

Returns:

astropy.table.Table

property supported_ratios#

The emission ratios that are covered by this ModelSet

Returns:

astropy.table.Table

property table#

The table containing details of the models in this ModelSet.

Returns:

astropy.table.Table

property user_added_models#

Show which models have been added to this ModelSet by the user

Returns:

list

property version#

The version of this ModelSet

Returns:

str

property viewangle#

The viewing angle (inclination) with respect to the line of sight, in degrees. A value of 0 means face-on.

Returns:

float

property z#

The metallicity of this ModelSet

Returns:

float

ModelSets: The interface to models in the Toolbox

Contents

ModelSets: The interface to models in the Toolbox#