PyStructure.conf

###############################
#   PyStructure Confif File   #
###############################

# meta data to be saved in the database
# name of the user for documentation
user = 'Dr. Hubble Trouble'

# arbitrary comments for documentation
comments = 'Doctor by name, trouble by nature.'

####################################
# Step 1: Define the correct Paths #
####################################

# <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/'

#####################################
# Step 2: Set the Target Resolution #
#####################################
# Set the target resolution for all data in arcseconds (if resolution set to angular)
target_res = 27.

#!!!!!!!!!!!!!Advanced------------------------------------------
NAXIS_shuff = 200
CDELT_SHUFF = 4000.  # m/s
spacing_per_beam = 2 # default, use half beam spacing

# give number (in units deg) or set to 'auto'
max_rad = 'auto' #default extension of the map in deg (increase, if your map is larger)

# 'angular': use target_res in as
# 'physical': convert target_res (in pc) to as
# 'native': use the angular resolution of the overlay image
resolution = 'angular'

# Save the convolved cubes & bands
save_fits = False

# Save the moment maps
save_mom_maps = True
save_band_maps = True

#folder to save fits files in
folder_savefits = './saved_FITS_files/'

# Define which line to use as reference line for the spectral processing
# 'first': use first line in cube_list as reference line
# '<LINE_NAME>': Use line name as reference line
# 'all': Use all lines in cube for mask
# n: (integer) use first n lines as reference. n=0 is same result as 'first'.
# 'ref+HI': Use first line and HI
ref_line = 'first'

#define upper and lower mask threshold (S/N)
SN_processing = [2,4]
strict_mask = False

# define whether input mask or fixed velocity window should be used for processing line cubes (defined in step 6)
use_input_mask = False
use_fixed_vel_mask = False

# (only relevant when use_fixed_vel_mask = True)
# Set to True to define one or more explicit noise velocity ranges in Step 6.
# Those ranges are used for the per-channel RMS estimation and its propagation
# into the moment maps, instead of the default behaviour of using all off-signal
# (mask == 0) channels.
use_noise_vel_ranges = False

# define whether masking should be adjusted to hyperfine structure lines
# <filename of hyperfine structure file>
# hfs_file = 'List_Files/hfs_lines.txt' # for usage: uncomment and set use_hfs_lines to True
use_hfs_lines = False

#define SN threshold for Mom1, Mom2 and EW calculation (for individual lines)
mom_thresh = 5
conseq_channels = 3 # needs to be integer larger or equal 3

#differentiate between 'fwhm', 'sqrt', or 'math'
# math: use mathematical definition
# sqrt: take square-root of mom2
# fwhm: convert sqrt(mom2) to fwhm
mom2_method = 'fwhm'

# Spectral smoothing
# 'default': Do not perform any spectral smoothing
# 'overlay': Perform spectral smoothing to spectral resolution of overlay cube
# n: float – convolve to spectral resolution n [km/s] !!!Not yet correctly implemented -> highly oversampled
spec_smooth = 'default'

# define the way the spectral smoothing should be performed:
# 'binned': binn channels together (to nearest integer of ratio theta_target/theta_nat)
# 'gauss': perform convolution with gaussian kernel (theta_target^2-theta_nat^2)**0.5
# !!!! Warning, gaussian smoothing seems to systematicaly underestimate the rms by 10-15%
# 'combined': do the binned smoothing first (to nearest integer ratio) and then the rest via Gauss
spec_smooth_method = 'binned'

# Define how pyStructure should be run
# - default: A file will be created and overwritten if the PyStructure code is run
# - fill: When running the PyStructure code, opens an exisitng PyStructure and completes it with additional lines
#     - optional: provide the name of the file as it appears in the Output folder adding below the following key:
#     fname_fill = '<PyStructure_file>.npy'
# - archive: each run creates a new copy, ensuring archiving of all runs (not yet implemented)
structure_creation ='default'

#####################################
# Step 3: Set Sources              #
#####################################
#can be single source (e.g. cloud or galaxy), or list of strings: sources = 'ngc5194', 'ngc5457'
sources = 'ngc5194'

#####################################
# 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/

#####################################
# Step 5: Define Cubes              #
#####################################
# 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/

#####################################
# Step 6: Define Mask               #
#####################################
# Column 1: short name of mask
# Column 2: description for database
# Column 3: extension
# Column 4: path to files

## PPV velocity mask as fits file
# Column 1: short name of mask
# Column 2: description for database
# Column 3: extension
# Column 4: path to files
# mask, input_mask, _co21_mask.fits,	data/

## Fixed velocity window
# Column 1: short name of mask
# Column 2: description for database
# Column 3: window start
# Column 4: window end
# Column 5: velocity unit
# mask, fixed_velocity_window, -100, 100, km/s

## Noise velocity range(s) for RMS estimation (only used when use_noise_vel_ranges = True)
# Add one or more lines below the fixed velocity window line.  Each line defines a
# velocity window over which the noise (RMS) is measured.  Multiple ranges are
# combined (OR logic) into a single noise mask that is applied per spatial point.
# The same five-column format as the signal window is used:
# Column 1: any short label (e.g. noise_vel)
# Column 2: description (arbitrary)
# Column 3: window start (same unit as Column 5)
# Column 4: window end   (same unit as Column 5)
# Column 5: velocity unit (must be consistent with the signal mask unit above)
#
# Example – two noise windows flanking the signal:
# noise_vel, noise_range_blue, -300, -150, km/s
# noise_vel, noise_range_red,   150,  300, km/s