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explanatory.ini
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explanatory.ini
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*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
* cross-correlation input parameter file *
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
> This is an example of input file, it lists all
> possibilities with detailed comments.
> All the parameters are given their default values.
> You can use a more concise version, in
> which only the arguments in which you are interested would appear.
> Only lines containing an equal sign not preceded by a sharp sign "#" are
> considered by the code. Hence, do not write an equal sign within a comment,
> the whole line would be interpreted as relevant input. Input files must have
> an extension ".ini".
----------------------------
----> flags:
----------------------------
*) Flag to compute the bootstrap realization: If this flag is set to 'true', the program
will compute num_bootstrap bootstrap samples of the cross-correlation (provided
flag_compute_cross_correlation is 'true') and the bootstrap covariance matrix (provided
flag_compute_covariance is 'true'). This option is disabled if flag_load_only is set to
'true'
flag_compute_bootstrap = true
*) Flag to compute the covariance matrix: If this flag is set to 'true', the program will
compute the covariance matrix. If flag_compute_bootstrap is also set to 'true', then the
program will also compute the bootstrap covariance matrix. This option is disabled if
flag_load_only is set to 'true'
flag_compute_covariance = true
*) Flag to compute the cross-correlation: If this flag is set to 'true', the program will
compute the cross-correlation of the specified datasets (see ----> inputs). If
flag_compute_bootstrap is also set to 'true' then the program will generate num_bootstrap
bootstrap samples for the cross-correlation. This option is disabled if flag_load_only is
set to 'true'
flag_compute_cross_correlation = true
*) Flag to compute the distortion matrix: If this flag is set to 'true', the program will
compute the distortion matrix of the specified datasets (see ----> inputs). This option is
disabled if flag_load_only is set to 'true'
flag_compute_distortion = true
*) Flag to compute the plate neighbours list: If this flag is set to 'true', the program will
create a list of all the used plates and their neighbouring plates
flag_compute_plate_neighbours = false
*) Flag to compute the covariance matrix reading the pairs information from files: If this flag is
set to 'ture', the program will read the pairs information from the partial results files instead
of computing it directly. To use this flag, the code has to run with flag_compute_cross_correlation
set to 'true' and flag_write_results greater than 0 or has to have been run with this configuration
in the same output folder (see ----> output)
flag_covariance_matrix_from_file = false
*) Flag to end program after loading the datasets: If this flag is set to 'true', the program
will end after loading the required catalogs (and plotting their info if flag_plot_catalog_info
is set to 'true')
flag_load_only = false
*) Flag to plot: If this flag is set to 'true', the program will run the plotting scripts
flag_plot = true
*) Flag to plot the catalog information: If set to 'true', then the program will create the
scripts necessary to plot the right ascention-declination dispersion and the redshift histogram
for the diferent datasets
flag_plot_catalog_info = false
*) Flag to project the delta field: If set to 'true', then the program will project the delta
field. Default value is the same as flag_compute_distortion
flag_project_deltas = true
*) Verbose flag: The higher the value for this flag, the more information the program will
display on screen. Incrementing the value for this flag will
result in an equal increment on the different specific verbose flags. To avoid this specifically
add the desired values for the other verbose flags
flag_verbose = 1
*) C IV spectra verbose flag: Verbose flag for the class CIVSpectraDataset. Default is the same as
flag_verbose
flag_verbose_civ_spectra_dataset = 1
*) Compute plate neighbours verbose flag: Verbose flag for the function compute_plate_neighbours.
Default is the same as flag_verbose
flag_verbose_compute_plate_neighbours = 1
*) Correlation plate verbose flag: Verbose flag for the class CorrelationPlate. Default is the same
as flag_verbose
flag_verbose_correlation_plate = 1
*) Correlation results verbose flag: Verbose flag for the class CorrelationResults. Default is the
same as flag_verbose
flag_verbose_correlation_results = 1
*) Covariance matrix verbose flag: Verbose flag for the class CovarianceMatrix. Default is the same
as flag_verbose
flag_verbose_covariance_matrix = 1
*) Covariance plate verbose flag: Verbose flag for the class CovariancePlate. Default is the same
as flag_verbose
flag_verbose_covariance_plate = 1
*) DLA dataset verbose flag: Verbose flag fot the class DLADataset. Default is the same as
flag_verbose
flag_verbose_dla_dataset = 1
*) Distortion matrix verbose flag: Verbose flag for the class DistortionMatrix. Default is the same
as flag_verbose
flag_verbose_distortion_matrix = 1
*) Distortion plate verbose flag: Verbose flag for the class DistortionPlate. Default is the same as
flag_verbose
flag_verbose_distortion_plate = 1
*) Lya spectra dataset verbose flag: Verbose flag for the class LyaSpectraDataset. Default is the same
as flag_verbose
flag_verbose_lya_spectra_dataset = 1
*) Main verbose flag: Verbose flag for the main program. Default is the same as flag_verbose
flag_verbose_main = 1
*) Pair dataset verbose flag: Verbose flag for the class PairDataset. Default is the same as
flag_verbose
flag_verbose_pair_dataset = 1
*) Plate neighbours verbose flag: Verbose flag for the class PlateNeighbours. Default is the same as
flag_verbose
flag_verbose_plate_neighbours = 1
*) Quasar dataset verbose flag: Verbose flag for the class QuasarDataset. Default is the same as
flag_verbose
flag_verbose_quasar_dataset = 1
*) Write partial results: When this flag is greater than zero, then the program will
save partial results information in the results directory (see ----> outputs).
The amount of information saved depends on the value of the flag. Note that the code will
become much more slower for values greater than zero.
flag_write_partial_results = 0
----------------------------
----> inputs:
----------------------------
*) Directory where the input files are located. If one of the inputs is located on another path
the full adress can be specified for each of the inputs individually.
input = ../catalogues/
*) Object catalog filename. If the full address is not specified, the value of input will be added
at the beginning
dataset1 = DR12Q.fits
*) Object catalog name
dataset1_name = DR12Q
*) Type of objects (quasar, dla, ...)
dataset1_type = quasar
*) Spectra catalog filename. If the full address is not specified, the value of input will be added
at the beginning
dataset2 = DR11Q_spectra_forest_list.ls
*) Spectra catalog name
dataset2_name = DR11LyaF
*) Type of spectra (lya, civ, ...)
dataset2_type = lya
*) Plate neighbours filename. If flag_compute_plate_neighbours is set to 'true', the file will be
overwritten by the program. If the full address is not specified, the value of input will be added
at the beginning
plate_neighbours = plate_neighbours.dat
*) Number of plates to ignore at the beginning of the computation. This is thought to be used in
conjunction with flag_write_results > 0 to resum an interrupted computation. If the number is
greater than zero, then the program will not overwrite the partial results files
(see ----> outputs) but will append to it. Note that the resulting cross-correlation measurement
will not include the specified number of plates. Once the computation is complete, then the
program should be rerun with flag_write_results = 0
skip_plates = 0
*) Total number of plates
num_plates = 2044
*) Directory where the spectrum files are located. If the full address is not specified, the value
of input will be added at the beginning
lya_spectra_dir = spectrum_fits_files/
----------------------------
----> outputs:
----------------------------
*) Directory where all the results will be stored
output = output/
*) Base name for all the results files. Unless specifically specified it will be automatically
set to dataset1_name + "-" + dataset2_name (see ----> inputs)
output_base_name = DR12Q-DR11LyaF
*) Directory where the partial results will be stored. If the full address is not specified, the value
of output will be added at the beginning
results = partial_results/
----------------------------
----> bin settings:
----------------------------
*) Maximum angular distance at which two plates are considered as neighbours (in radians)
neighbours_max_distance = 0.06981317007977318 # (2 degrees)
*) Maximum value for parallel separation (in Mpc/h)
max_pi = 50.0
*) Step in parallel separation (in Mpc/h). Cannot be used simultaneously with num_pi_bins
step_pi = 5.0
*) Number of parallel separation bins. Cannot be used simultaneously with step_pi
#num_pi_bins = 20
*) Maximum value for perpendicular separation (in Mpc/h)
max_sigma = 50.0
*) Step in perpendicular separation (in Mpc/h) Cannot be used simultaneously with num_sigma_bins
step_sigma = 5.0
*) Number of perpendicular separation bins. Cannot be used simultaneously with step_sigma
num_sigma_bins = 10
----------------------------
----> bootstrap settings
----------------------------
*) Number of bootstrap realizations
num_bootstrap = 10000
*) Directory where the bootstrap results will be saved. If the full full address is not
specified, the value of results will be added at the beginning (see ----> outputs)
bootstrap_results = bootstrap_realizations/
----------------------------
----> lya autocorrelation settings
----------------------------
*) Lyman alpha auto-correlation measurement. If the full address is not specified, the value
of input will be added at the beginning (see ----> inputs)
lya_auto_correlation = PalanqueDelabrouille_1DPk-Fft.out
*) Lyman alpha bins width (in km/s)
lya_pixel_width = 210
*) Maximum pixel separation (in number of pixels) for the contribution of the lyman alpha
autocorrelation to contribute to the covariance matrix
pixels_separation = 5
*) PSF of the Lyman alpha auto-correlation measurement (in km/s)
sigma_psf = 70
----------------------------
----> fiducial model
----------------------------
*) Hubble constant (in km/s/Mpc). Cannot be used simultaneously with h
H0 = 67.74
*) reduced Hubble constant (in km/s/Mpc). Cannot be used simultaneously with H0
#h = 0.6774
*) Omega matter
wm = 0.3089
----------------------------
----> line and redshift settings:
----------------------------
*) lyman-alpha wavelength (in Angstroms)
lya_wl = 1215.67
*) Minimum redshift required to accept a quasar. Quasars present in the catalogue
with lower redshift values will be ignored
z_min = 2.0
*) Maximum redshift required to accept a quasar. Quasars present in the catalogue
with higher redshift values will be ignored
z_max = 3.5
*) Minimum redshift value considered for the interpolation grid (This will be used
in conjunction with the fidutial model to compute the distances to the objects)
z_min_interpolation = 1.5
*) Maximum redshift value considered for the interpolation grid (This will be used
in conjunction with the fidutial model to compute the distances to the objects)
z_max_interpolation = 4.0
*) Number of points the interpolation grid will have (This will be used in
conjunction with the fidutial model to compute the distances to the objects)
num_points_interpolation = 30000
*) Maximum value for Log10 of HI column density (cm^-2) required to accept a DLA. DLAs
present in the catalogue with higher values will be ignored
nhi_max = 22
*) Minimum value for Log10 of HI column density (cm^-2) required to accept a DLA. DLAs
present in the catalogue with lower values will be ignored
nhi_min = 20
*) Minimum continuum to noise ratio to accept a DLA. DLAs present in the catalogue with
lower values will be ignored
cnr_min = 3
*) Minimum quasar restframe wavelength at which the DLA is found to accept a DLA (in angs).
DLAs present in the catalogue observed at lower quasar restframe wavelengths will be ignored.
rf_wl_min = 1026.0
// Maximum quasar restframe wavelength at which the DLA is found to accept a DLA (in angs).
DLAs present in the catalogue observed at higher quasar restframe wavelengths will be ignored.
rf_wl_max = 1195.395
// Forbidden interval in the quasar interval wavelength at which the DLA is found (in angs).
DLAs present in the catalogue observed with quasar restframe wavelength in this interval will
be ignored
rf_wl_forbidden_interval = (1005.0, 1037.0)