Extraction Configuration

This applies to both GMOS and SPRAT.

Extraction configuration (YAML)

Once the flattening is performed, the longslit spectral extraction is like any extractions from a generic spectrograph. The format of the parameter files for GMOS and SPRAT are the same. Most of the parameters can be kept constant, respective to the instrument. The file paths, which are the first few lines of the file, have to be updated for each extraction. The output data can be exported as FITS/CSV, static png/jpg/pdf image, an interactive plotly iframe, or just the JSON file for the plotly graph. The following shows the example YAML of the GMOS extraction.

folder_path: "."
output_folder_path: "20181115_gaia18cnz/output"

# Input
science_file:
  # - they have to be in a list
  - "20181115_gaia18cnz/output/N20181115S0097_flattened.fits"
  - "20181115_gaia18cnz/output/N20181115S0098_flattened.fits"
  - "20181115_gaia18cnz/output/N20181115S0101_flattened.fits"
  - "20181115_gaia18cnz/output/N20181115S0102_flattened.fits"
science_arc_file: "20181115_gaia18cnz/output/N20181115S0215_flattened.fits"

standard_file: "20180811_g191b2b/output/N20180811S0148_flattened.fits"
standard_arc_file: "20180811_g191b2b/output/N20180813S0115_flattened.fits"

# If sensitivity curve is provided, standard star extraction will be skipped
sensitivity_file:  "20180811_g191b2b/output/sensitivity_itp.npy"

# Output - they have to be lists
science_output_file:
  # - they have to be in a list
  - "20181115_gaia18cnz/output/N20181115S0097"
  - "20181115_gaia18cnz/output/N20181115S0098"
  - "20181115_gaia18cnz/output/N20181115S0101"
  - "20181115_gaia18cnz/output/N20181115S0102"
standard_output_file: "20180811_g191b2b/output/N20180811S0148"

science_output_type:
  - "fits"
  - "csv"
  - "png"
  - "iframe"
standard_output_type:
  - "fits"
  - "csv"
  - "png"
  - "iframe"

# Output
savefits: True
fits_output: 'flux_resampled+wavecal+flux+adu+adu_resampled'
fits_filename: 'reduced'
fits_stype: 'science'
fits_individual: False
fits_overwrite: False
savecsv: True
csv_output: 'flux_resampled+wavecal+flux+adu+adu_resampled'
csv_filename: 'reduced'
csv_stype: 'science'
csv_individual: False
csv_overwrite: False

# Only needed if images/iframe are being exported
width: 1920
height: 1080

It is then followed by all the extraction parameters. At the time of writing, the readnoise, gain, seeing and exptime are not read automatically from the header. In order to have a correct absolute flux calibration, the exposure time has to be filled in manually. The gain is constant for the instrument over time, so it does not need adusting unless the observatory has changed the instrument setting. While the seeing varies with time, it does not affect the extraction quality, it can slightly slow down the speed in aperture tracing, which is hardly a bottleneck process of the data extraction to begin with, so it can be left as it is. The same applies to the paramteers for the standard.

# Science traget

# TwoDSpec parameters
science_saxis: 1
science_spatial_mask: ''
science_spec_mask: ''
science_flip: True
science_cosmicray: True
science_cosmicray_sigma: 5.
science_readnoise: 0.
science_gain: 1.64
science_seeing: 1.2
science_exptime: 300
science_silence: False

Below is the rest of the configuration file.

# Aperture Tracing
science_aptrace_nspec: 1
science_aptrace_nwindow: 25
science_aptrace_spec_sep: 5
science_aptrace_resample_factor: 10
science_aptrace_rescale: False
science_aptrace_scaling_min: 0.995
science_aptrace_scaling_max: 1.005
science_aptrace_scaling_step: 0.001
science_aptrace_percentile: 5
science_aptrace_tol: 3
science_aptrace_polydeg: 3
science_aptrace_ap_faint: 10
science_aptrace_display: False
science_aptrace_renderer: "default"
science_aptrace_jsonstring: False
science_aptrace_iframe: False
science_aptrace_open_iframe: False
# Aperture Extraction
science_apextract_apwidth: 10
science_apextract_skysep: 5
science_apextract_skywidth: 5
science_apextract_skydeg: 1
science_apextract_optimal: True
science_apextract_display: False
science_apextract_renderer: "default"
science_apextract_jsonstring: False
science_apextract_iframe: False
science_apextract_open_iframe: False
# WavelengthCalibration
science_silence: False
science_pixel_list: ~
# Provide polyfit coefficients
science_polyfit: False
science_polyfit_coeff: [0., 0., 0., 0., 0.]
science_polyfit_type: ['poly']
# Extract Arc spectrum
science_arc_spec_display: False
science_arc_spec_jsonstring: False
science_arc_spec_renderer: 'default'
science_arc_spec_iframe: False
science_arc_spec_open_iframe: False
# Find arc lines
science_findarc_background: 1000.
science_findarc_percentile: ~
science_findarc_prominence: 0.
science_findarc_distance: 5.
science_findarc_refine: True
science_findarc_refine_window_width: 5
science_findarc_display: False
science_findarc_jsonstring: False
science_findarc_renderer: 'default'
science_findarc_iframe: False
science_findarc_open_iframe: False
# Calibrator parameters
science_wavecal_min_wavelength: 5000
science_wavecal_max_wavelength: 9500
science_wavecal_plotting_library: 'plotly'
science_wavecal_log_level: 'info'
# Calibrator Fit constraints
science_constraints_num_slopes: 10000
science_constraints_range_tolerance: 500
science_constraints_fit_tolerance: 10.
science_constraints_polydeg: 4
science_constraints_candidate_thresh: 15.
science_constraints_linearity_thresh: 1.5
science_constraints_ransac_thresh: 3
science_constraints_num_candidates: 25
science_constraints_xbins: 200
science_constraints_ybins: 200
science_constraints_brute_force: False
science_constraints_polyfit_type: 'poly'
science_constraints_spec_id: ~
# Atlas
science_atlas_elements: ['Cu', 'Ar']
science_atlas_min_atlas_wavelength: 0
science_atlas_max_atlas_wavelength: 15000
science_atlas_min_intensity: 0
science_atlas_min_distance: 0
science_atlas_vacuum: False
science_atlas_pressure: ~
science_atlas_temperature: ~
science_atlas_relative_humidity: ~
science_atlas_constrain_poly: False
science_atlas_spec_id: ~
# User-supplied Atlas, the following OVERRIDES the Atlas config set above
science_atlas_user_supplied: True
science_atlas_user_wavelengths: [
                4703.632, 4728.19041, 4766.19677, 4807.36348, 4849.16386, 4881.22627, 4890.40721, 4906.12088, 4934.58593, 4966.46490,
                5018.56194, 5063.44827, 5163.723, 5189.191, 5497.401,
                5560.246, 5608.290, 5913.723,
                6754.698, 6873.185, 6967.352,
                7032.190, 7069.167, 7149.012, 7274.940, 7386.014,
                7505.935, 7516.721, 7637.208, 7725.887, 7893.246, 7950.362,
                8105.921, 8117.542, 8266.794, 8410.521, 8426.963,
                8523.783, 8670.325,
                9125.471, 9197.161, 9227.03, 9356.787,
                9660.435, 9787.186
            ]
science_atlas_user_elements: ['CuAr']
science_atlas_user_vacuum: True
science_atlas_user_pressure: ~
science_atlas_user_temperature: ~
science_atlas_user_relative_humidity: ~
science_atlas_user_constrain_poly: False
science_atlas_user_spec_id: ~

# Fit
science_fit_sample_size: 5
science_fit_top_n: 10
science_fit_max_tries: 20000
science_fit_progress: True
science_fit_coeff: ~
science_fit_linear: True
science_fit_weighted: True
science_fit_filter_close: False
science_fit_display: False
science_fit_savefig: False
science_fit_filename: ~
science_fit_spec_id: ~
# Refine Fit 1st pass
science_refinefit1: False
science_refinefit1_polyfit_coeff: ~
science_refinefit1_n_delta: 2
science_refinefit1_refine: True
science_refinefit1_tolerance: 10.
science_refinefit1_method: 'Nelder-Mead'
science_refinefit1_convergence: 1.0e-6
science_refinefit1_robust_refit: True
science_refinefit1_polydeg: ~
science_refinefit1_display: False
science_refinefit1_savefig: False
science_refinefit1_filename: ~
science_refinefit1_spec_id: ~
# Refine Fit 2nd pass
science_refinefit2: False
science_refinefit2_polyfit_coeff: ~
science_refinefit2_n_delta: ~
science_refinefit2_refine: True
science_refinefit2_tolerance: 5.
science_refinefit2_method: 'Nelder-Mead'
science_refinefit2_convergence: 1.0e-6
science_refinefit2_robust_refit: True
science_refinefit2_polydeg: ~
science_refinefit2_display: False
science_refinefit2_savefig: False
science_refinefit2_filename: ~
science_refinefit2_spec_id: ~

# Standard traget

# TwoDSpec parameters
standard_saxis: 1
standard_spatial_mask: ''
standard_spec_mask: ''
standard_flip: True
standard_cosmicray: True
standard_cosmicray_sigma: 5.
standard_readnoise: ~
standard_gain: ~
standard_seeing: ~
standard_exptime: ~
standard_silence: False
# TwoDSpec header keywords (NOT used if the values are provided above)
standard_readnoise_keyword: ~
standard_gain_keyword: ~
standard_seeing_keyword: ~
standard_exptime_keyword: ~
# Aperture Tracing
standard_aptrace_nspec: 1
standard_aptrace_nwindow: 25
standard_aptrace_spec_sep: 5
standard_aptrace_resample_factor: 10
standard_aptrace_rescale: False
standard_aptrace_scaling_min: 0.995
standard_aptrace_scaling_max: 1.005
standard_aptrace_scaling_step: 0.001
standard_aptrace_percentile: 5
standard_aptrace_tol: 3
standard_aptrace_polydeg: 3
standard_aptrace_ap_faint: 10
standard_aptrace_display: False
standard_aptrace_renderer: "default"
standard_aptrace_jsonstring: False
standard_aptrace_iframe: False
standard_aptrace_open_iframe: False
# Aperture Extraction
standard_apextract_apwidth: 15
standard_apextract_skysep: 5
standard_apextract_skywidth: 5
standard_apextract_skydeg: 1
standard_apextract_optimal: True
standard_apextract_display: False
standard_apextract_renderer: "default"
standard_apextract_jsonstring: False
standard_apextract_iframe: False
standard_apextract_open_iframe: False
# WavelengthCalibration
standard_silence: False
standard_pixel_list: ~
# Provide polyfit coefficients
standard_polyfit: False
standard_polyfit_coeff: [0., 0., 0., 0., 0.]
standard_polyfit_type: ['poly']
# Extract Arc spectrum
standard_arc_spec_display: False
standard_arc_spec_jsonstring: False
standard_arc_spec_renderer: 'default'
standard_arc_spec_iframe: False
standard_arc_spec_open_iframe: False
# Find arc lines
standard_findarc_background: 1000.
standard_findarc_percentile: ~
standard_findarc_prominence: 0.
standard_findarc_distance: 5.
standard_findarc_refine: True
standard_findarc_refine_window_width: 5
standard_findarc_display: False
standard_findarc_jsonstring: False
standard_findarc_renderer: 'default'
standard_findarc_iframe: False
standard_findarc_open_iframe: False
# Calibrator parameters
standard_wavecal_min_wavelength: 5000
standard_wavecal_max_wavelength: 9500
standard_wavecal_plotting_library: 'plotly'
standard_wavecal_log_level: 'info'
# Calibrator Fit constraints
standard_constraints_num_slopes: 10000
standard_constraints_range_tolerance: 500
standard_constraints_fit_tolerance: 10.
standard_constraints_polydeg: 4
standard_constraints_candidate_thresh: 15.
standard_constraints_linearity_thresh: 1.5
standard_constraints_ransac_thresh: 3
standard_constraints_num_candidates: 25
standard_constraints_xbins: 200
standard_constraints_ybins: 200
standard_constraints_brute_force: False
standard_constraints_polyfit_type: 'poly'
standard_constraints_spec_id: ~
# Atlas
standard_atlas_elements: ['Cu', 'Ar']
standard_atlas_min_atlas_wavelength: 0
standard_atlas_max_atlas_wavelength: 15000
standard_atlas_min_intensity: 0
standard_atlas_min_distance: 0
standard_atlas_vacuum: False
standard_atlas_pressure: ~
standard_atlas_temperature: ~
standard_atlas_relative_humidity: ~
standard_atlas_constrain_poly: False
standard_atlas_spec_id: ~
# User-supplied Atlas, the following OVERRIDES the Atlas config set above
standard_atlas_user_supplied: True
standard_atlas_user_wavelengths: [
                4703.632, 4728.19041, 4766.19677, 4807.36348, 4849.16386, 4881.22627, 4890.40721, 4906.12088, 4934.58593, 4966.46490,
                5018.56194, 5063.44827, 5163.723, 5189.191, 5497.401,
                5560.246, 5608.290, 5913.723,
                6754.698, 6873.185, 6967.352,
                7032.190, 7069.167, 7149.012, 7274.940, 7386.014,
                7505.935, 7516.721, 7637.208, 7725.887, 7893.246, 7950.362,
                8105.921, 8117.542, 8266.794, 8410.521, 8426.963,
                8523.783, 8670.325,
                9125.471, 9197.161, 9227.03, 9356.787,
                9660.435, 9787.186
            ]
standard_atlas_user_elements: ['CuAr']
standard_atlas_user_vacuum: True
standard_atlas_user_pressure: ~
standard_atlas_user_temperature: ~
standard_atlas_user_relative_humidity: ~
standard_atlas_user_constrain_poly: False
standard_atlas_user_spec_id: ~
# Fit
standard_fit_sample_size: 5
standard_fit_top_n: 20
standard_fit_max_tries: 20000
standard_fit_progress: True
standard_fit_coeff: ~
standard_fit_linear: True
standard_fit_weighted: True
standard_fit_filter_close: False
standard_fit_display: False
standard_fit_savefig: False
standard_fit_filename: ~
standard_fit_spec_id: ~
# Refine Fit 1st pass
standard_refinefit1: True
standard_refinefit1_polyfit_coeff: ~
standard_refinefit1_n_delta: 2
standard_refinefit1_refine: True
standard_refinefit1_tolerance: 10.
standard_refinefit1_method: 'Nelder-Mead'
standard_refinefit1_convergence: 1.0e-6
standard_refinefit1_robust_refit: True
standard_refinefit1_polydeg: ~
standard_refinefit1_display: False
standard_refinefit1_savefig: False
standard_refinefit1_filename: ~
standard_refinefit1_spec_id: ~
# Refine Fit 2nd pass
standard_refinefit2: True
standard_refinefit2_polyfit_coeff: ~
standard_refinefit2_n_delta: ~
standard_refinefit2_refine: True
standard_refinefit2_tolerance: 5.
standard_refinefit2_method: 'Nelder-Mead'
standard_refinefit2_convergence: 1.0e-6
standard_refinefit2_robust_refit: True
standard_refinefit2_polydeg: ~
standard_refinefit2_display: False
standard_refinefit2_savefig: False
standard_refinefit2_filename: ~
standard_refinefit2_spec_id: ~

# Choose Flux Calibration
fluxcal_target: 'LTT7987'
fluxcal_library: 'esoxshooter'
fluxcal_ftype: 'flux'
fluxcal_cutoff: 0.4
fluxcal_display: True
fluxcal_renderer: 'default'
fluxcal_jsonstring: False
fluxcal_iframe: True
fluxcal_open_iframe: True
# Compute sensitivity curve
sensecurve_kind: 3
sensecurve_smooth: False
sensecurve_slength: 5
sensecurve_sorder: 3
sensecurve_mask_range:
  - [6860, 6960]
  - [7150, 7410]
  - [7580, 7720]
sensecurve_display: False
sensecurve_renderer: 'default'
sensecurve_jsonstring: False
sensecurve_iframe: False
sensecurve_open_iframe: False