Using the Data class

Getting the Data class

The ACID_code.Data class stores the data for all calculations done in ACID, including the final resulting profiles. It is used to work seamlessly with the ACID_code.Acid, ACID_code.LSD, and ACID_code.Result classes to get configuration and store data. The most useful examples of the usage of the class are shown below if desired by the user.

Remember that all attributes and methods of Data can be found in the ACID_code.Data API.

from astropy.io import fits
import ACID_code as acid

spec_file = fits.open('sample_spec_1.fits')
wavelength = spec_file[0].data   # Wavelengths in Angstroms
spectrum = spec_file[1].data     # Spectral Flux
error = spec_file[2].data        # Spectral Flux Errors
sn = spec_file[3].data           # SN of Spectrum
linelist = 'example_linelist.txt' # Insert path to line list

Acid = acid.Acid(velocities=velocities, linelist=linelist)
result = Acid.ACID(wavelength, spectrum, error, sn, nsteps=5000)

data = result.data  # Acid and Result share the Data class, so this is the same as Acid.data

Plotting

You can plot any of the three pre-mcmc set of plots with the following. See the API for the full list of optional inputs to each method.

# Plot the initial continuum fit
data.plot_continuum_fit("initial")

# Plot the continuum fit after masking
data.plot_continuum_fit("masked")

# Plot the residual mask results
data.plot_residual_masking()

Getting run times

You can also extract run times:

print(data.initialisation_time)  # time taken for initialization
print(data.mcmc_time)  # time taken for MCMC sampling
print(data.get_profiles_time)  # time taken to get profiles
print(data.full_run_time)  # total time for the full run

Saving and Loading

You can also save and load the data class using its method (It’s not recommended to directly pickle yourself, see “Saving the Result” in Results and Plotting for an explanation why).

data.save("data.pkl")
new_data = acid.Data.load("data.pkl")

The loaded data can now be directly input into Acid to load the previous configuration and results.

# Load into a new Acid instance
Acid = acid.Acid(data=new_data)

# Or load into a Results instance (note that the sampler will not be available)
result = acid.Result(new_data)

# Or see the next section on DataLists for putting Data instances into lists for running Acid on echelle spectra