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input_file
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####################################################################################
# #
# FIT KL14 PRINCIPLE TO OBSERVED GALAXY MAPS #
# start environment with >> idl heisenberg -arg [full/absolute path of input file] #
# #
# to skip iterative diffuse filtering, start environment with: #
# >> idl heisenberg_nodf -arg [full/absolute path of input file] #
# #
# BEGIN PARAMETER FILE #
# #
####################################################################################
# FILE NAMES
datadir /full/path/of/directory/where/fits/files/are/stored/ # Full path of data directory
galaxy string_identifying_galaxy_in_ouput_filenames # Name of data set
starfile this_is_a_SF_map.fits # Name of primary stellar map
starfile2 - # Name of secondary stellar map (specifically for peak identification - only used if use_star2=1)
gasfile this_is_a_gas_map.fits # Name of primary gas map
gasfile2 - # Name of secondary gas map (specifically for peak identification - only used if use_gas2=1)
starfile3 - # Name of additional stellar map (only used if use_star3=1)
# PEAKID FILE NAMES
peaksdir /full/path/of/directory/where/peak/files/are/stored/ # Full path of the directory containing .sav file for the identified gas and stellar peaks (only used if id_peaks = 2)
peakiddir /full/path/of/directory/where/peakid/files/are/stored/ # Full path of the directory containing output files from clumpfind (files of the form star/gasfile_peaks.dat star/gasfile.fits.clf) (only used if id_peaks = 2)
starpeakidfile this_is_a_peakid_file_for_starfile_peaks.dat # Name of the peak_id .dat file for starfile (e.g. starfile_iter0_peaks.dat) (only used if id_peaks = 2)
gaspeakidfile this_is_a_peakid_file_for_gasfile_peaks.dat # Name of the peak_id .dat file for gasfile (e.g. gasfile_iter0_peaks.dat) (only used if id_peaks = 2)
intpeakidfile this_is_an_interactive_peak_ID_report.dat # Name of the interactive peakid report (e.g. galaxy_interactive_peak_ID_report.dat) (only used if id_peaks = 2)
# MASK FILE NAMES
maskdir /full/path/of/directory/where/region/files/are/stored/ # Full path of mask directory
star_ext_mask masks_external_pixels_for_SF.reg # Region file for masking areas in starfile exterior to closed shapes (only used if mask_star=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
star_int_mask masks_internal_pixels_for_SF.reg # Region file for masking areas in starfile interior to closed shapes (only used if mask_star=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
gas_ext_mask masks_external_pixels_for_gas.reg # Region file for masking areas in gasfile exterior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
gas_int_mask masks_internal_pixels_for_gas.reg # Region file for masking areas in gasfile interior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
star_ext_mask2 - # Region file for masking areas in starfile2 exterior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
star_int_mask2 - # Region file for masking areas in starfile2 interior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
gas_ext_mask2 - # Region file for masking areas in gasfile2 exterior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
gas_int_mask2 - # Region file for masking areas in gasfile2 interior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
star_ext_mask3 - # Region file for masking areas in starfile3 exterior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
star_int_mask3 - # Region file for masking areas in starfile3 interior to closed shapes (only used if mask_gas=1); should be a ds9 region file using the image coordinate system (other coordinate systems can be used if convert_masks=1, which calls ds9)
# UNFILTERED FILE NAMES
unfiltdir /full/path/of/directory/where/unfiltered/files/are/stored/ # Full path of unfiltered image directory
star_unfilt_file -
gas_unfilt_file -
# FLAGS 1 (module switches)
mask_images 1 # Mask images (on/off)
regrid 1 # Read and regrid original files and synchronise masks across all used images, i.e. pixels masked in one image will be masked in all images (on/off)
smoothen 1 # Create smoothened maps for each aperture size (on/off)
sensitivity 1 # Fit Gaussians to pixel intensity PDFs to determine sensitivity limits (on/off)
id_peaks 1 # [0] Reused identified peaks from a previous run with files in the default locations (should not be used for iterative runs) [1, DEFAULT] Identify peaks and save their locations [2] Reuse identified peaks from a previous run, with files in the locations specified by peaksdir and peakiddir
calc_ap_flux 1 # Calculate the enclosed flux for each peak and aperture size (on/off)
generate_plot 1 # Generate output plots and save to PostScript files (on/off)
get_distances 1 # Calculate distances between all peak pairs (on/off)
calc_obs 1 # Monte-Carlo sample peaks, get observed tuning fork (on/off)
calc_fit 1 # Fit KL14 principle model (on/off)
diffuse_frac 1 # Calculate diffuse fraction in images (on/off)
derive_phys 1 # Calculate derived physical quantities (on/off)
write_output 1 # Write results to output files (on/off)
cleanup 2 # [0] Keep auxiliary files to allow any of the above flags to be set to 0 for future runs; [1, DEFAULT] Delete auxiliary files after confirmation prompt; [2] WARNING: Automatically delete auxiliary files
autoexit 0 # Exit IDL automatically upon successful run completion (on/off)
# FLAGS 2 (use ancillary files)
use_star2 0 # Use different map for identifying stellar peaks and use the original for performing the flux calculation (on/off)
use_gas2 0 # Use different map for identifying gas peaks and use the original for performing the flux calculation (on/off)
use_star3 0 # Use an additional stellar tracer map to mask pixels based on their flux ratios (on/off; e.g. Hα/FUV)
# FLAGS 3 (masking-related options)
mstar_ext 1 # Mask areas in starfile exterior to regions described in star_ext_mask (on/off)
mstar_int 1 # Mask areas in starfile interior to regions described in star_int_mask (on/off)
mgas_ext 1 # Mask areas in gasfile exterior to regions described in gas_ext_mask (on/off)
mgas_int 1 # Mask areas in gasfile interior to regions described in gas_int_mask (on/off)
mstar_ext2 0 # Mask areas in starfile2 exterior to regions described in star_ext_mask2 (on/off)
mstar_int2 0 # Mask areas in starfile2 interior to regions described in star_int_mask2 (on/off)
mgas_ext2 0 # Mask areas in gasfile2 exterior to regions described in gas_ext_mask2 (on/off)
mgas_int2 0 # Mask areas in gasfile2 interior to regions described in gas_int_mask2 (on/off)
mstar_ext3 0 # Mask areas in starfile3 exterior to regions described in star_ext_mask3 (on/off)
mstar_int3 0 # Mask areas in starfile3 interior to regions described in star_int_mask3 (on/off)
convert_masks 0 # Convert masks from other ds9 region coordinate systems to image coordinates (requires command line version of ds9) (on/off)
cut_radius 1 # Mask maps outside a specified radial interval within the galaxy (on/off)
# FLAGS 4 (choose analysis options)
set_centre 1 # [0] Pixel coordinates of galaxy centre are set to the central pixel of starfile; [1, DEFAULT] Specify pixel coordinates of galaxy centre under INPUT PARAMETERS 1 (basic map analysis)
tophat 1 # [0] Use Gaussian kernel to smoothen maps to larger aperture sizes; [1, DEFAULT] Use tophat kernel to smoothen maps to larger aperture sizes
loglevels 1 # [0] Linear equal-spacing of peak identification contour levels; [1, DEFAULT] Logarithmic equal-spacing of peak identification contour levels
peak_find_tui 0 # [0, DEFAULT] select peaks only using INPUT PARAMETERS 3 (peak identification) without user interactivity; [1] use INPUT PARAMETERS 3 (peak identification) for initial peak finding and then enter interactive peak finding Text User Interface (TUI)
flux_weight 0 # [0, DEFAULT] Peak positions correspond to brightest pixel in peak area; [1] Peak positions correspond to flux-weighted mean position of peak area
calc_ap_area 1 # Calculate the area of apertures used based on number of unmasked pixels within the target aperture defined under INPUT PARAMETERS 2 (apertures) (on/off)
tstar_incl 0 # [0, DEFAULT] Reference time-scale tstariso does not include the overlap phase (tstar=tstariso+tover); [1] tstariso includes the overlap phase (tstar=tstariso)
peak_prof 2 # [0] Model independent regions as points; [1] Model independent regions as constant-surface density discs; [2, DEFAULT] Model independent regions as two-dimensional Gaussians
map_units 1 # [0] Unknown, do not calculate derived quantities; [1, DEFAULT] star=SFR and gas=gas; [2] star=gas1 and gas=gas2; [3] star=SFR1 and gas=SFR2
star_tot_mode 0 # [0, DEFAULT] Use sfr/gas mass total for the stellar map calculated on the input map [1] use values of sfr/gas mass specified with the parameter star_tot_val
gas_tot_mode 0 # [0, DEFAULT] Use sfr/gas mass total for the gas map calculated on the input map [1] use values of sfr/gas mass specified with the parameter gas_tot_val
use_X11 1 # [0] Not allowed to create X11 windows; [1] Allowed to create X11 windows
log10_output 1 # [0] Values of output parameters in output file: galaxy_output.dat are written as naturally formatted double precision floating point numbers. This is recommended when running in iterative mode. [1] Values of output parameters in output file: galaxy_output.dat are written with as log10(value)
# INPUT PARAMETERS 1 (basic map analysis)
distance 840000. # Distance to galaxy in pc
inclination 0. # Inclination angle in degrees
posangle 0. # Position angle in degrees
centrex 701 # Index of pixel x-axis coordinate of galaxy centre in starfile (important: start counting at zero on the left-hand side of the image)
centrey 701 # Index of pixel y-axis coordinate of galaxy centre in starfile (important: start counting at zero on the bottom side of the image)
minradius 0. # Minimum radius for analysis in pc
maxradius 10000. # Maximum radius for analysis in pc
Fs1_Fs2_min 15. # Minimum primary-to-secondary star formation tracer flux ratio for including pixels (only if use_star3=1)
max_sample 10 # Maximum number of pixels per map resolution FWHM
astr_tolerance 1.e-6 # allowable tolerance in decimal degrees between astrometric position of image pixels of different images (e.g. 0.9" = 2.5e-4 decimal degrees)
nbins 20 # Number of bins used during sensitivity limit calculation to sample the intensity PDFs and fit Gaussians
# INPUT PARAMETERS 2 (apertures)
lapmin 25. # Minimum aperture size (i.e. diameter) in pc to create smoothened maps for
lapmax 6400. # Maximum aperture size (i.e. diameter) in pc to create smoothened maps for
naperture 9 # Number of aperture sizes
peak_res 1 # Minimum aperture size used in fitting the KL14 principle model, also index of aperture size at which peaks are identified (start counting at 0) - is set to map resolution if originally chosen to be smaller
max_res 8 # Maximum aperture size used in fitting the KL14 principle model, also index of aperture size at which fluxes best reflect galactic averages (start counting at 0)
# INPUT PARAMETERS 3 (peak identification)
npixmin 20 # Minimum number of pixels for a valid peak (use npixmin=1 to allow points)
nsigma 5 # Multiple of the sensitivity limit needed for a valid peak
logrange_s 2. # Logarithmic range covered by flux contour levels for stellar peak identification, counting down from stellar flux maximum
logspacing_s 0.5 # Logarithmic interval between flux contour levels for stellar peak identification
logrange_g 2. # Logarithmic range covered by flux contour levels for gas peak identification, counting down from gas flux maximum
logspacing_g 0.5 # Logarithmic interval between flux contour levels for gas peak identification
nlinlevel_s 11 # Number of flux contour levels for stellar peak identification between zero and stellar flux maximum (only if loglevels=0)
nlinlevel_g 11 # Number of flux contour levels for gas peak identification between zero and gas flux maximum (only if loglevels=0)
# INPUT PARAMETERS 4 (timeline)
tstariso 1. # Reference time-scale spanned by star formation tracer in Myr
tstariso_errmin 0. # Downward standard error of the reference time-scale in Myr
tstariso_errmax 0. # Upward standard error of the reference time-scale in Myr
tgasmini 0.1 # Minimum value of tgas considered during fitting process in Myr
tgasmaxi 1000. # Maximum value of tgas considered during fitting process in Myr
tovermini 0.01 # Minimum value of tover considered during fitting process in Myr
# INPUT PARAMETERS 5 (fitting)
nmc 1000 # Number of Monte-Carlo peak drawing experiments to be executed and averaged over during fitting process
ndepth 4 # Maximum number of free parameter array refinement loops for obtaining best-fitting value
ntry 101 # Size of each free parameter array to obtain the best-fitting value
nphysmc 1000000 # Number of Monte-Carlo experiments for error propagation of derived physical quantities
# INPUT PARAMETERS 6 (Fourier filtering for diffuse emission fraction calculation)
use_unfilt_ims 0 # Calculate the diffuse fraction of [0] starfile and gasfile, the images used for the fitting process [1] star_unfilt_file and gas_unfilt_file, pass-through images (in the case of iterative diffuse filtering to calculate diffuse fraction of the unfiltered images)
diffuse_quant 1 # Calculate the diffuse fraction of [0] flux, [1] power
f_filter_type 2 # Filter type choice for Fourier filtering: [0] butterworth filter [1] gaussian filter [2] ideal filter (Only relevant if diffuse_quant = 0 [flux], but a dummy value should be supplied anyway)
bw_order 2 # The order of the butterworth filter (Must be an integer. Only relevant if f_filter_type = 0 [butterworth] and diffuse_quant = 0 [flux], but a dummy value should be supplied anyway)
filter_len_conv 1.0 # conversion factor for Fourier filtering cut_length (cut_length = lambda * filter_len_conv)
emfrac_cor_mode 0 # Apply corrections to measured fgmc and fcl [0] apply no correction [1] apply correction for flux loss from signal regions [2] #!#DEPRECIATED#!# apply correction for the filling factor, zeta, only [3] #!#DEPRECIATED#!# apply both corrections (flux loss from signal regions and filling factor, zeta) [4] apply the correction for overlap between regions calculated from peak distances [5] apply both corrections (flux loss from signal regions and overlap between regions calculated from peak distances)
rpeak_cor_mode 0 # [0] use measured r_peaks [1] use supplied values of rpeaks_cor_val and rpeakg_cor_val
rpeaks_cor_val 1.0 # value of r_peak_star to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
rpeaks_cor_emin 0.5 # downwards error of r_peak_star to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
rpeaks_cor_emax 0.5 # upwards error of r_peak_star to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
rpeakg_cor_val 1.0 # value of r_peak_gas to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
rpeakg_cor_emin 0.5 # downwards error of r_peak_gas to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
rpeakg_cor_emax 0.5 # upwards error of r_peak_gas to use when correcting for flux_loss. Only used if emfrac_cor_mode = 1 or 3 and rpeak_cor_mode = 2
# INPUT PARAMETERS 7 (conversions and constants to calculate derived quantities)
convstar -3.69206 # Log of multiplication factor to convert the pixel value in starfile to a SFR in Msun/yr (if maptypes=1 or maptypes=3) or to a gas mass in Msun (if maptypes=2)
convstar_rerr 0. # Relative error (sigma_x/x) of convstar
convgas 2.30794 # Log of multiplication factor to convert the pixel value in gasfile to a gas mass in Msun (if maptypes=1 or maptypes=2) or to a SFR in Msun/yr (if maptypes=3)
convgas_rerr 0. # Relative error (sigma_x/x) of convgas
convstar3 0. # Log of multiplication factor to convert the pixel value in starfile3 to a SFR in Msun/yr
convstar3_rerr 0. # Relative error (sigma_x/x) of convstar3
lighttomass 0.002 # Light-to-mass ratio of a desired feedback mechanism in m^2 s^-3 (default 0.002 is SNe)
momratetomass 5.e-10 # Momentum output rate per unit mass of a desired feedback mechanism in m s^-2 (default 5.e-10 is SNe+winds)
star_tot_val 1.0 # Input value of the total sfr/gas mass of the star map (only used if star_tot_mode = 1). Note that this should be the total SFR (including diffuse emission) in oder to calculate the correct depletion time and derived quantities.
star_tot_err 0.1 # Error on the input value of the total sfr/gas mass of the star map (only used if star_tot_mode = 1)
gas_tot_val 1.0e9 # input value of the total sfr/gas mass of the gas map (only used if gas_tot_mode = 1). Note that this should be the total gas mass of the galaxy minus the removed diffuse emission in order to calculate the correct depletion time and derived quantities.
gas_tot_err 1.0e8 # Error on the input value of the total sfr/gas mass of the gas map (only used if star_tot_mode = 1)
# INPUT PARAMETERS 8 (sensitivity)
use_stds 0 # [0] calculate standard deviations of images [1] Use supplied standard deviation measurements
std_star 0.1 # The measured standard deviation of starfile
std_star3 0.1 # The measured standard deviation of starfile3 (only used if use_star3 = 1)
std_gas 0.1 # The measured standard deviation of gasfile
# INPUT PARAMETERS 9 (noise threshold)
use_noisecut 1 # [0, DEFAULT] only mask negative values remaining in image after filtering [1] mask values below the noise threshold remaining in image after filtering
noisethresh_s 20.0 # Level to cut the noise in the star map after filtering
noisethresh_g 20.0 # Level to cut the noise in the gas map after filtering
# INPUT PARAMETERS 10 (Fourier diffuse removal iteration) # note that these parameters are ignored if the call sequence idl heisenberg_nodf -arg [full/absolute path of input file] is used. They are only used if the call sequence idl heisenberg -arg [full/absolute path of input file] is used.
use_guess 0 # [0] Do not Filter images before the first Heisenberg run and ignore parameter: "initial_guess" [1] Filter images with initial guess of lambda before the first Heisenberg run
initial_guess 200 # Length in pc of the initial estimate of lambda with which to filter the images
iter_criterion 0.05 # Fractional difference between lambda and previous lambda value(s) that triggers an end to the iteration process.
iter_crit_len 2 # Number of previous runs of Heisenberg over which iter_criterion must be true, i.e. if iter_crit_len = 1 then the current value of lambda is compared to the previous value of lambda, if iter_crit_len = 2 then then the current value of lambda is compared to the previous value of lambda and the value of lambda prior to the previous value
iter_nmax 10 # Maximum number of Heisenberg runs allowed in the iteration process. If iter_criterion is not reached before this number of runs the programme will exit anyway.
iter_filter 2 # Filter type choice for iterative Fourier filtering: [0] butterworth filter [1] gaussian filter [2] ideal filter
iter_bwo 2 # The order of the butterworth filter for iterative Fourier filtering (Must be an integer. Only relevant if iter_filter = 0 [butterworth], but a dummy value should be supplied anyway)
iter_len_conv 2.0 # conversion factor for iterative Fourier filtering cut_length (cut_length = lambda * filter_len_conv)
iter_rpeak_mode 0 # [0] use mode specified by rpeak_cor_mode [1] use rpeak values from iter0
iter_tot_mode_s 0 # [0, DEFAULT] Use the sfr/gas mass total for the stellar map calculated on the input map of each iteration [1] Use the sfr/gas mass total for the stellar map calculated on the initial iteration for all subsequent iterations [2] Use the sfr/gas mass total for the stellar map specified by the parameter star_tot_val for all iterations
iter_tot_mode_g 0 # [0, DEFAULT] Use the sfr/gas mass total for the gas map calculated on the input map of each iteration [1] Use the sfr/gas mass total for the gas map calculated on the initial iteration for all subsequent iterations [2] Use the sfr/gas mass total for the gas map specified by the parameter star_tot_val for all iterations
iter_autoexit 0 # Exit IDL automatically upon successful iteration run completion (on/off)
use_nice 0 # (on/off) Use the "nice" command when spawning Heisenberg runs to the terminal to adjust the process priority. Note that this may not work depending on the system configuration
nice_value 0 # Value of the priority adjustment must be an integer between -20 (the highest) to 19 (the lowest). (Note this varies according to the implementation of nice)
################################################
# #
# END PARAMETER FILE #
# #
################################################