Config key

This file defines the spectral “products” and array “configurations” that to be processed and combined by the pipeline. Here, the user provides detailed parameters for each product and config.

This file should be space or tab delimited. Each entry should have 3 columns, as described below.

Column Definitions

Column 1: Type of field

This must be one of the following:

line_product: a spectral line imaging product (e.g., co21_2p5kms)
cont_product: a continuum imaging product (e.g., cont)
interf_config: a configuration containing only interferometric data (e.g., 12m)
feather_config: a configuration combining single dish and interferometric data (e.g., 7m+tp)

Column 2: Name

This can be anything, but should not have any spaces or _ characters to avoid confusion.

Column 3: Pameters

This is evaluated as a literal dictionary (i.e., the line is fed to python). Please avoid spaces and follow the fields required below.

Note

Configuration definitions can repeat multiple lines, in which case the dictionary parameters are accumulated across all lines. Don’t repeat parameters, but if you do then in theory the later lines will overwrite the earlier ones.

Parameter options

`line_product`

This defines a spectral line product, which will be produced by clean using specmode=’cube’. The name can be anything, it does not have to be the line name, e.g., lowresco is fine.

Parameters:

line_tag: this is the line tag we use in our pipeline and should agree with the line names in our utilsLines.py module. If this is missing, then you should add the line to your utilsLines module (and file an issue).
channel_kms: this is the target channel width of our output image cubes in units of km/s. Depending on the chosen regridding algorithm this may be the exact channel width or an approximate target.
exclude_freq_ranges_ghz: given as a list of list, this gives a set [low, high] frequency range in GHz to avoid when using uvcontsub. e.g. 'exclude_freq_ranges_ghz':[[1.40,1.42]]. This is useful when multiple targets emit in the same transition along a line-of-sight (e.g., Galactic and extragalactic 21-cm HI).
flag_edge_fraction (optional): float between 0.0 and 0.5 This is an input to avoid using the edges of a SPW for fitting the continuum in uvcontsub.
lines_to_flag : these are the spectral line families (for groups of lines) or spectral line tags (for individual lines) to exclude (at the velocity and bandwidth of the source) from continuum imaging. They need to be known by our utilsLines.py.

`cont_product`

This defines a continuum product, which will be produced by clean using specmode=’mfs’. The name can be anything, e.g., 850umcont.

Parameters:

freq_ranges_ghz: These are given as a list of lists, and define a [low, high] frequency range in GHz for the continuum imaging.
lines_to_flag : these are the spectral line families (for groups of lines) or spectral line tags (for individual lines) to exclude (at the velocity and bandwidth of the source) from continuum imaging. They need to be known by our utilsLines.py.

`interf_config`

This defines an interferometric configuration, which is a collection of data from interferometric arrays. These will eventually be combined into a single visibility file and imaged together. The name can be anything, e.g., BCD or 12m+7m. Note that these cover both individual interferometric configurations (e.g. 12m), as well as more complicated joint array combinations (e.g. 12m+7m).

Parameters:

array_tags: defines a list of array tags to be concatenated into this config. These array tags are assigned to each measurement set in the ms_key, which lists the visibility data. Thus, they only mean anything inasmuch as they agree with those defined in that file. The natural mapping is, e.g., VLA config, ALMA array, and maybe a code roughly indicating the ALMA subarray (e.g., 12mext). This is fundamentally up to the user to decide. Despite the names used by PHANGS-ALMA (12m, 7m) the pipeline does NOT attempt to detect and assign data to arrays on its own.
clean_scales_arcsec: These are the scales used for multiscale cleaning of data from this array. The units are arcseconds.
requires: By default, we require ALL arrays that make up the configuration, but this can be changed to an OR if you only need one of a certain combination, e.g. {'requires':['12m_1|12m_2']} requires only one of 12m_1 or 12m_2 to be present. If an array is not in the requires list, then it is assumed to be required.

`feather_config`

This defines a “feather configuration,” which is a combination of an interferometric configuration and total power data. The name can be anything, e.g., BCD+tp or 12m+7m+tp.

Parameters:

interf_config: each feather config needs to map back to an interferometric config. This mapping is used to carry out the feathering process. This field defines the interf_config corresponding to this feather config. When data from that interf_config is feathered it produces data labeled with this feather_config.

`singledish_config`

This controls how the singledish data is processed, and is required if running the SingleDishPipeline.

Parameters:

bl_order: Baseline order for line fitting. Can probably leave as 1.
chan_dv_kms: Velocity resolution for the final cube. This should be set to the resolution you plan to image your interferometric cubes at.
do_plots: Whether to produce diagnostic plots during the singledish processing.

Example config key file

##########################################################################
# CONFIG_DEFINITIONS KEY
##########################################################################

# This file defines the file defines the spectral "products" and array
# "configurations" that to be processed and combined by the
# pipeline. Here, the user provides detailed parameters for each
# product and config. The file has three columns:

# Column 1: type of field (see below)

# Column 2: name (this can be anything, it will appear in file names
# and be used by the handlers and keys)

# Column 3: parameters (write as literal dictionaries with no spaces)

# ------------------------------------------------------------------------
# Column 1 : "type of field"
# ------------------------------------------------------------------------

# This must be one of the following:

# "line_product" : a spectral line imaging product (e.g., "lowresCO21")

# "cont_product" : a continuum imaging product (e.g., "mmcont")

# "interf_config" : a configuration containing only interferometric data (e.g., "VLAC")

# "feather_config" : a configuration combining single dish and
#  interferometric data (e.g., "7m+tp")

# ------------------------------------------------------------------------
# Column 2 : "name"
# ------------------------------------------------------------------------

# This can be anything, but should not have any spaces or _ characters
# to avoid confusion.

# ------------------------------------------------------------------------
# Column 3 : "parameters"
# ------------------------------------------------------------------------

# This is evaluated as a literal dictionary (i.e., the line is fed to
# python). Please avoid spaces and follow the fields required below.

# N.B. Configuration definitions can repeat multiple lines, in which
# case the dictionary parameters are accumulated across all
# lines. Don't repeat parameters, but if you do then in theory the
# later lines will overwrite the earlier ones.

##########################################################################

# ------------------------------------------------------------------------
# line_product : a spectral line data product
# ------------------------------------------------------------------------

# This defines a spectral line product, which will be produced by
# clean using specmode='cube'. The name can be anything, it does not
# have to be the line name, e.g., "lowresco" is fine.

# The parameters need to include:

# 'line_tag' : this is the line tag we use in our pipeline and should
# agree with the line names in our "utilsLines.py" module. If this is
# missing, then you should add the line to your utilsLines module (and
# maybe file an issue).

# 'channel_kms', this is the target channel width of our output image
# cubes in units of km/s. Depending on the chosen regridding algorithm
# this may be the exact channel width or an approximate target.

# 'exclude_freq_ranges_ghz': given as a list of list, this gives a set
# [low, high] frequency range in GHz to avoid when using uvcontsub.
# e.g. 'exclude_freq_ranges_ghz':[[1.40,1.42]].
# This is useful when multiple targets emit in the same transition along
# a line-of-sight (e.g., Galactic and extragalactic 21-cm HI).

# flag_edge_fraction: float between 0.0 and 0.5
# This is an optional input to avoid using the edges of a SPW for
# fitting the continuum in uvcontsub

# ------------------------------------------------------------------------
# cont_product : a continuum data product
# ------------------------------------------------------------------------

# This defines a continuum product, which will be produced by clean
# using specmode='mfs'. The name can be anything, e.g., '850umcont'.

# These parameters need to be included (use [] for none):

# 'lines_to_flag' : these are the spectral line families (for groups
# of lines) or spectral line tags (for individual lines) to exclude
# (at the velocity and bandwidth of the source) from continuum
# imaging. They need to be known by our utilsLines.py. If they are not
# known, then you can add them to your version.

# ------------------------------------------------------------------------
# interferometry configuation
# ------------------------------------------------------------------------

# This defines an interferometric configuration, which is a collection
# of data from interferometric arrays. These will eventually be
# combined into a single visibility file and imaged together. The name
# can be anything, e.g., 'BCD' or '12m+7m'.

# These parameters need to be included:

# 'array_tags' : defines a list of "array_tag"s to be concatenated
# into this config. These array tags are assigned to each measurement
# set in the "ms_file_key.txt", which lists the visibility data. Thus,
# they only mean anything inasmuch as they agree with those defined in
# that file. The natural mapping is, e.g., VLA config, ALMA array, and
# maybe a code roughly indicating the ALMA subarray (e.g.,
# "12mext"). This is fundamentally up to the user to decide. Despite
# the names used by PHANGS-ALMA (12m, 7m) the pipeline does NOT
# attempt to detect and assign data to arrays on its own.

# 'clean_scales_arcsec' : These are the scales used for multiscale
# cleaning of data from this array. The units are arcseconds.

# ------------------------------------------------------------------------
# feathering configuation (combining single dish and interferometry data)
# ------------------------------------------------------------------------

# This defines a "feather configuration," which is a combination of an
# interferometric configuration and total power data. The name can be
# anything, e.g., 'BCD+tp' or '12m+7m+tp'.

# These parameters need to be included:

# 'interf_config' : each feather config needs to map back to an
# interferometric config. This mapping is used to carry out the
# feathering process. This field defines the interf_config
# corresponding to this feather config. When data from that
# interf_config is feathered it produces data labeled with this
# feather_config.

##########################################################################

# DELETE AFTER HERE FOR NEW PROJECT, FULL PHANGS-ALMA CASE FOLLOWS

line_product    co21      {'line_tag':'co21','channel_kms':2.6,'statwt_edge_kms':50.0}
line_product    co21      {'fitorder':0,'combinespw':False,'lines_to_flag':['co21']}
line_product    13co21    {'line_tag':'13co21','channel_kms':2.6,'statwt_edge_kms':50.0}
line_product    13co21    {'fitorder':0,'combinespw':False,'lines_to_flag':['13co21','c18o21']}
line_product    c18o21    {'line_tag':'c18o21','channel_kms':6.0,'statwt_edge_kms':100.0}
line_product    c18o21    {'fitorder':0,'combinespw':False,'lines_to_flag':['c18o21','13co21']}

cont_product    cont      {'freq_ranges_ghz':[[214.87,216.83],[217.51,219.36],[229.49,230.40],[230.62,232.58]],'lines_to_flag':['co','13co','c18o','hcn','hcop']}

interf_config   12m       {'array_tags':['12m']}
interf_config   12m       {'clean_scales_arcsec':[0,1,2.5,5.0]}

interf_config   12m+7m    {'array_tags':['12m','7m']}
interf_config   12m+7m    {'clean_scales_arcsec':[0,1,2.5,5.0,10.0]}

interf_config   7m        {'array_tags':['7m']}
interf_config   7m        {'clean_scales_arcsec':[0,5.0,10.0]}

feather_config  12m+7m+tp   {'interf_config':'12m+7m'}

feather_config  7m+tp       {'interf_config':'7m'}

Config key

Column Definitions

Column 1: Type of field

Column 2: Name

Column 3: Pameters

Parameter options

line_product

cont_product

interf_config

feather_config

singledish_config

Example config key file

`line_product`

`cont_product`

`interf_config`

`feather_config`

`singledish_config`