Guide
The configure File
Here we go through the configuration file step-by-step and explain the necessary user input.
Step 1
In the first step, the user need to specify some of the key paths as well as the overlay 3D cube to be used.
####################################
# Step 1: Define the correct Paths #
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# <path to directory with the data files>
data_dir = "data/"
# <filename of geometry file>
geom_file = "List_Files/geometry.txt"
# <filename of overlay or mask> #should be stored in data_dir
overlay_file = "_12co21.fits"
# <Output Directory for Dictionaries>
out_dic = "Output/"
geom_fileThe geometry file contains information on the source properties (see The geometry file for more details).overlay_fileThe FITS file extension of the overlay 3D data cube to be used. The overlay is used to define the spatial extend of the hexagonal grid.
Note
All data filenames must have the following convention:
<source_name><file_extension>
For example: ngc5194_co21.fits, where ngc5194 is the source name and _co21.fits the file extension.
The geometry.txt file must contain the source name.
Step 2
In the next step, the targeted angular resolution needs to be provided. By default, this needs to be given in arcsec.
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# Step 2: Set the Target Resolution #
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# Set the target resolution for all data in arcseconds (if resolution set to angular)
target_res = 27.
Step 3
In this step, you need to define the source or list of sources. Note that all datafiles must start with the source name as specified in this step.
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# Step 3: Set Sources #
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#can be single source (e.g. cloud or galaxy), or list of strings: sources = "ngc5194", "ngc5457"
sources = "ngc5194"
Step 4
In this step, we define the list of 2D data we want to include in the PyStructure. It is not required to include any 2D data.
#####################################
# Step 4: Define Bands #
#####################################
# Column 1: short name of band
# Column 2: description for database
# Column 3: units
# Column 4: extension
# Column 5: path to files
# Column 6: extension to uc file
spire250, SPIRE250, MJy/sr, _spire250_gauss21.fits, ./data/, _spire250_gauss21_unc.fits
Note
If no uncertainty file extist, simply write not_included for the uncertainty file extension.
Step 5
The final step consists of specifying the list of 3D data cubes. Here at least one data cube must be provided.
#####################################
# Step 5: Define Cubes #
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# Column 1: short name of cube
# Column 2: description for database
# Column 3: units
# Column 4: extension
# Column 5: path to files
# Column 6 optional: extension, if 2D map provided
# Column 7 optional: extension err, if 2D map provided
12co21, 12CO2-1, K, _12co21.fits, data/
12co10, 12CO1-0, K, _12co10.fits, data/
Important
By default, the first cube specified in this list will be used as prior line to define a spectral and spatial mask over which the 3D data cubes will be postprocessed to determine the moment-0 and peak temperature maps. It is therefore adviced to select the brightest line as the first entry.
Additional Files
The geometry file
The geometry.txt file is a crucial component of the PyStructure. Here, the source properties need to be defined.
# column 1: name
# column 2: R.A. center [decimal degrees J2000]
# column 3: Dec. center [decimal degrees J2000]
# column 4: distance [Mpc]
# column 5: uncertainty in distance
# column 6: inclination [deg] (LEDA)
# column 7: uncertainty in inclination
# column 8: position angle [deg] (LEDA)
# column 9: uncertainty in position angle
# column 10: radius 25th magnitude isophote [arcmin]
# column 11: uncertainty in radius 25th
# column 12: ref for position angle
# Attach comments with #
# Distances and uncertainties from Brent Groves' NED querying program.
# Inclinations and PA from Maria's compilation
# Radius from Leda
#-------------------------------------------------------------
# !!!Make sure columns separated by only one tab!!!
#-------------------------------------------------------------
M82 148.969687 69.679383 3.5 0.2 77.0 NaN 62 NaN 5.60 0.1
ngc0628 24.1739458 15.7836619 9.0 0.14 7.0 NaN 20.0 NaN 5.00 0.05
ngc2903 143.042125 21.500833 8.7 0.9 65.0 NaN 204.0 NaN 6.01 0.05
The name of the source needs to match the source name of the data files
The source properties are tailored to match usefull properties characterizing nearby galaxies. Therefore, parameters, such as inclination or position angle, might not be meaningfull if you work on other types of sources (e.g. Galactic clouds). In this case, it is adviced to enter
0orNaNinstead.