rassine

Rolling Alpha Shape for a Spectral Improved Normalisation Estimator (RASSINE)

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   { }    .' O'.     / o .-. O \     /  .--`\
   { }   / .-. o\   /O  /   \  o\   /O /    ^  (RASSSSSSINE)
    \ `-` /   \ O`-'o  /     \  O`-`o /
jgs  `-.-`     '.____.'       `.____.'

Authors: Michael Cretignier, Jeremie Francfort and Denis Rosset

usage: rassine [--config CONFIG] [--root ROOT]
               [--pickle-protocol PICKLE_PROTOCOL]
               [--logging-level LOGGING_LEVEL] [-s INPUT_SPECTRUM]
               [-I INPUT_TABLE] [-i INPUT_FOLDER] [-o OUTPUT_FOLDER]
               [--output-pattern OUTPUT_PATTERN] [-l INPUT_ANCHOR_PICKLE]
               [--output-anchor-ini OUTPUT_ANCHOR_INI]
               [--output-plot-folder OUTPUT_PLOT_FOLDER]
               [--output-plot-pattern OUTPUT_PLOT_PATTERN] [-p PAR_STRETCHING]
               [--par-vicinity PAR_VICINITY]
               [--par-smoothing-box PAR_SMOOTHING_BOX]
               [--par-smoothing-kernel {rectangular,gaussian,savgol,erf,hat_exp}]
               [--par-fwhm PAR_FWHM] [--CCF-mask CCF_MASK] [-r PAR_R]
               [-R PAR_RMAX] [--par-reg-nu PAR_REG_NU]
               [--mask-telluric MASK_TELLURIC]
               [--synthetic-spectrum {true,false}]
               [--interpolation {cubic,literal}]
               [--denoising-dist DENOISING_DIST]
               [--count-cut-lim COUNT_CUT_LIM] [--count-out-lim COUNT_OUT_LIM]
               [--random-seed RANDOM_SEED]
               input_indices

Named Arguments

--config

Use the specified configuration files.

Files can be separated by commas/the command can be invoked multiple times.

--pickle-protocol

Pickle protocol version to use

--logging-level

Logging level to use

-s, --input-spectrum

Path of the spectrum pickle

Either a path to a spectrum pickle needs to be provided, or one needs to provide the –input-table, –input-folder and inputs (positional) arguments

Note that input_spectrum is a path relative to “root” and “input_folder”

-I, --input-table

Table of stacked spectra from which to read the individual file names

-i, --input-folder

Relative path to the folder containing the stacked spectra

input_indices

Indices of spectrum to process

If provided, then input_table and input_folder must be provided If not provided, then input_spectrum must be provided

--output-pattern

Pattern to use for the RASSINE output filename

The “{}” part will be replaced by the input filename stem

-l, --input-anchor-pickle

Put a RASSINE output file that will fix the value of the 7 parameters to the same value than in the anchor file

--output-anchor-ini

Optional INI output anchor file that can be used as an input configuration file

Only valid if input_spectrum is used and not the multi-spectrum reduction

--output-plot-folder

Where to put the output plot, if empty no plot is produced

The plot name will be derived from the spectrum name, with a “_output.png” suffix

--output-plot-pattern

Pattern to use for the RASSINE output filename

The “{}” part will be replaced by the input filename stem

-p, --par-stretching

Scaling of the flux axis compared to the wavelength axis. The format of the automatic mode is’auto x’ with x a 1 decimal positive float number. x = 0.0 means high tension, whereas x = 1.0 mean low tension.

PARAMETER 1

--par-vicinity

half-window size to find a local maxima

--par-smoothing-box

half-window of the box used to smooth (1 => no smoothing, ‘auto’ available)

PARAMETER 2

--par-smoothing-kernel

Possible choices: rectangular, gaussian, savgol, erf, hat_exp

To use the automatic mode which apply a Fourier filtering use ‘erf ‘ or ‘hat exp’ kernel and ‘auto’ in par smoothing box. Else, use ‘rectangular’, ‘gaussian’, ‘savgol’. Developers advise the ‘savgol’ kernel except if the user is dealing with spectra spanning low and high SNR range.

--par-fwhm

FWHM of the CCF of the spectrum in km/s. The user can let ‘auto’ to let RASSINE determine this value by itself.

PARAMETER 3

--CCF-mask

CCF mask used to determine the FWHM. RASSINE construct its own mask by default. The user can specify its own mask which should be placed in the CCF MASK directory. Only needed if par_fwhm is in ‘auto’

-r, --par-R

Minimum radius of the rolling pin in angstrom and in the extreme blue (‘auto’ available)

PARAMETER 4

-R, --par-Rmax

Maximum radius of the rolling pin in angstrom in the extreme blue (‘auto’ available)

PARAMETER 5

--par-reg-nu

Penality-radius law

poly_d (d the degree of the polynome x**d) or sigmoid_c_s where c is the center and s the steepness

PARAMETER 6

--mask-telluric

a list of left and right borders to eliminate from the mask of the CCF only if CCF = ‘master’ and par_fwhm = ‘auto’

--synthetic-spectrum

Possible choices: true, false

True if working with a noisy-free synthetic spectra in order to inject a small noise for numerical stability

--interpolation

Possible choices: cubic, literal

Define the interpolation for the continuum displayed in the subproducts

note that at the end a cubic and linear interpolation are saved in ‘output’ regardless this value

--denoising-dist

Half window of the area used to average the number of point around the local max for the continuum

--count-cut-lim

Number of border cut in automatic mode (put at least 3 if Automatic mode)

--count-out-lim

Number of outliers clipping in automatic mode (put at least 1 if Automatic mode)

--random-seed

Random seed, derived from spectrum name if empty

required arguments

--root

Root path of the data, used as a base for other relative paths

-o, --output-folder

Directory where output files are written