5. Primitives

This section documents all the primitives available in the MAROONX Data Reduction pipeline. These primitives are organized by functionality and processing stage.

Note

This document provides detailed information about each primitive method, including parameters, return values, and usage examples.

5.1. 2D Image Processing Primitives

Note

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5.2. Echelle Extraction Primitives

5.3. Spectrum Processing Primitives

5.4. PDF Reports

Several primitives produce diagnostic PDF reports to help assess the quality of each reduction step. Reports are enabled by default via the report boolean parameter (default True) on each primitive and are written to the current working directory. All plotting functions are defined in maroonxdr/maroonx/maroonx_plots.py and use matplotlib.backends.backend_pdf.PdfPages for PDF generation.

5.4.1. Primitives That Generate Reports

5.4.1.1. `removeStrayLight`

Source: primitives_maroonx_2D.py
Output: {input}_backgroundfit.pdf (7 pages)
Pages: raw frame, orders masked, background model (1st iteration), background subtracted, masked pixels per mesh cell, correction background model, final subtracted data
Called in: makeProcessedFlat recipe
Plotting function: plot_backgroundfit()

5.4.1.2. `fitAndApplyEtalonWls`

Source: primitives_maroonx_spectrum.py
Output: spline_[symmetrical_]{input}.pdf
Content: etalon dispersion plots per fiber, wavelength solution residuals after spline fit
Called in: makeDynamicWavecal recipe
Plotting functions: MXEchelleSpectrum.plot_etalon_dispersion() (method on spectrum object) and plot_residuals()

5.4.1.3. `applyWavelengthSolution`

Source: primitives_maroonx_spectrum.py
Output: {input}_spline.pdf
Content: calibration fiber offset measurements vs wavelength, per-order fit residuals, etalon residuals per fiber
Called in: reduce recipe (ECHELLE_SPECT)
Plotting functions: plot_calibfiber_offset(), plot_etalon_residuals()

5.4.1.4. `combineFibers`

Source: primitives_maroonx_spectrum.py
Output: {input}_fiber[6|7_symmetrical].pdf
Content: one page per echelle order showing intensity comparison (fibers 2, 3, 4 + combined), sigma deviations from median, weights (1/variance), and SNR
Called in: reduce recipe (ECHELLE_SPECT)
Plotting function: plot_fiber_combination()

5.4.1.5. `barycentricCorrection`

Source: primitives_maroonx_spectrum.py
Output: {input}_exposuremeter.pdf (1 page)
Content: dual-axis time series of PC and FRD exposure meter channels with exposure boundaries and zeropoints
Called in: applyBarycentricCorrection sub-recipe
Plotting function: plot_exposuremeter()

5.4.2. Plotting Functions Reference

The following functions in maroonxdr/maroonx/maroonx_plots.py produce the figures written into the PDF reports.

Function	Description
`plot_backgroundfit()`	Returns a list of 7 Figures covering each stage of background fitting and subtraction.
`plot_residuals()`	Returns 1 Figure with 3 subplots: residuals vs wavelength, residual RMS per order, and residuals vs normalized X position.
`plot_fiber_combination()`	Returns 1 Figure with 4 subplots: intensity, sigma deviations from median, weights (1/variance), and SNR.
`plot_calibfiber_offset()`	Returns 1 Figure with 3 subplots. Supports overlay mode via the `fig` parameter to plot multiple fibers on the same axes.
`plot_etalon_residuals()`	Returns 1 Figure with 4 subplots. Supports incremental fill via the `plotnumber` and `fig` parameters.
`plot_exposuremeter()`	Returns 1 Figure with dual y-axes (PC and FRD exposure meter channels).

5.4.3. Disabling Reports

Reports can be disabled by passing report=False to any primitive. In a custom recipe this is done directly:

p.removeStrayLight(report=False)

From the command line, use the DRAGONS parameter override system:

reduce @flats.list -p removeStrayLight:report=False