.. _outputs: Eureka! Outputs =============== Stage 2 through Stage 6 of ``Eureka!`` can be configured to output plots of the pipeline's interim results as well as the data required to run further stages. .. _s2-out: Stage 2 Outputs --------------- If ``skip_extract_1d`` is set in the Stage 2 ECF, the 1-dimensional spectrum will not be extracted, and no plots will be made. Otherwise, Stage 2 will extract the 1-dimensional spectrum from the calibrated images, and will plot the spectrum. .. figure:: ../media/S2_out/fig2101_file1_x1dints.png :alt: Stage 2 1-dimensional spectrum plot Fig 2101: 1-Dimensional Spectrum Plot .. _s3-out: Stage 3 Outputs --------------- In Stage 3 through Stage 5, output plots are controlled with the ``isplots_SX`` parameter. The resulting plots are cumulative: setting ``isplots_S3 = 5`` will also create the plots specified in ``isplots_S3 = 3`` and ``isplots_S3 = 1``. In Stage 3: - If ``isplots_S3`` = 1: ``Eureka!`` will plot the 2-dimensional, non-drift-corrected light curve, as well as variations in the source position and width on the detector. .. figure:: ../media/S3_out/fig3101-2D_LC.png :alt: Stage 3 2-dimensional spectrum plot Fig 3101: 2-Dimensional Spectrum Plot with a linear wavelength x-axis .. figure:: ../media/S3_out/fig3102-2D_LC.png :alt: Stage 3 2-dimensional spectrum plot Fig 3102: 2-Dimensional Spectrum Plot with a linear detector pixel x-axis .. figure:: ../media/S3_out/fig3103_file0_int00_source_pos.png :alt: Stage 3 source position fit Fig 3103: Source Position Fit Plot .. figure:: ../media/S3_out/fig3104_DriftYPos.png :alt: Stage 3 y drift Fig 3104: Variations in the spatial-axis position .. figure:: ../media/S3_out/fig3105_DriftYWidth.png :alt: Stage 3 y PSF width changes Fig 3105: Variations in the spatial-axis PSF width .. figure:: ../media/S3_out/fig3106_Drift2D.png :alt: Stage 3 2D drift fit Fig 3106: 2D drift fit (currently only produced for WFC3) .. figure:: ../media/S3_out/fig3107_file0_Curvature.png :alt: Stage 3 trace curvature Fig 3107: Measured, smoothed, and integer-rounded position of trace - If ``isplots_S3`` = 3: ``Eureka!`` will plot the results of the background and optimal spectral extraction steps for each exposure in the observation as well as the cleaned median frame. .. figure:: ../media/S3_out/fig3301_file0_int001_ImageAndBackground.png :alt: Stage 3 background subtracted flux plot Fig 3301: Background Subtracted Flux Plot .. figure:: ../media/S3_out/fig3302_file0_int001_Spectrum.png :alt: Stage 3 1-dimensional spectrum plot Fig 3302: 1-Dimensional Spectrum Plot .. figure:: ../media/S3_out/fig3303_file0_int001_Profile.png :alt: Stage 3 weighting profile Fig 3303: Weighting Profile Plot .. figure:: ../media/S3_out/fig3304_file0_ResidualBG.png :alt: Stage 3 residual background Fig 3304: Residual Background Plot .. figure:: ../media/S3_out/fig3308_file0_MedianFrame.png :alt: Stage 3 clean median frame plot Fig 3308: Clean Median Frame Plot - If ``isplots_S3`` = 5: ``Eureka!`` will plot the Subdata plots from the optimal spectral extraction step. .. figure:: ../media/S3_out/fig3501_file0_int001_col0117_subdata.png :alt: Stage 3 subdata plot Fig 3501: Spectral Extraction Subdata Plot .. figure:: ../media/S3_out/fig3507a_file0_int011_tilt_events.png :alt: Stage 3 tilt event plots Fig 3507a: Tilt event frame plot. Figures 3507b and 3507c are GIF versions of this figure, b is at the segment level and c is over all segments .. _s4-out: Stage 4 Outputs --------------- In Stage 4: - If ``isplots_S4`` = 1: ``Eureka!`` will plot the spectral drift per exposure, the drift-corrected 2-dimensional lightcurve with extracted bins overlaid, and the 1D light curves. .. figure:: ../media/S4_out/fig4101_2D_LC.png :alt: Stage 4 2-dimensional spectrum Fig 4101: 2-Dimensional Spectrum with a linear wavelength x-axis. .. figure:: ../media/S4_out/fig4102_ch0_1D_LC.png :alt: Stage 4 1-dimensional binned spectrum Fig 4102: 1-Dimensional Binned Spectrum .. figure:: ../media/S4_out/fig4103_DriftXPos.png :alt: Stage 4 spectral drift plot Fig 4103: Spectral Drift Plot - If ``isplots_S4`` = 3: ``Eureka!`` will plot the cross-correlated reference spectrum with the current spectrum for each integration, and the cross-correlation strength for each integration. .. figure:: ../media/S4_out/fig4301_int00_CC_Spec.png :alt: Stage 4 cross correlated reference spectrum Fig 4301: Cross-Correlated Reference Spectrum .. figure:: ../media/S4_out/fig4302_int00_CC_Vals.png :alt: Stage 4 cross correlation strength Fig 4302: Cross-Correlation Strength .. _s5-out: Stage 5 Outputs --------------- In Stage 5: - If ``isplots_S5`` = 1: ``Eureka!`` will plot the fitted lightcurve model over the data in each channel. If fitting with a GP, an additional figure will be made showing the GP component. If fitting a sinusoid_pc model, another zoomed-in figure with binned data will be made to emphasize the phase variations. Finally, an additional plot compares the fits from different fitters. .. figure:: ../media/S5_out/fig5101_ch0_lc_emcee.png :alt: Stage 5 fit data and lightcurve Fig 5101: Fitted Lightcurve, Model, and Residual Plot .. figure:: ../media/S5_out/fig5102_ch0_lc_GP_emcee.png :alt: Stage 5 GP plot Fig 5102: Fitted Lightcurve, GP Model, and Residual Plot .. figure:: ../media/S5_out/fig5103_ch0_all_fits.png :alt: Stage 5 All fits comparison Fig 5103: Comparison of Different Fitters Fig 5104: *(Demo figure to come)* Zoomed-in Figure Emphasizing Phase Variations Using Temporally Binned Data. - If ``isplots_S5`` = 3: ``Eureka!`` will plot an RMS deviation plot for each channel to help check for correlated noise, plot the normalized residual distribution, and plot the fitting chains for each channel. If fitting a sinusoid_pc model, another zoomed-in figure with binned data in front of the unbinned data will be made to emphasize the phase variations. .. figure:: ../media/S5_out/fig5301_ch0_allanplot_emcee.png :alt: Stage 5 RMS deviation plot Fig 5301: RMS Deviation Plot .. figure:: ../media/S5_out/fig5302_ch0_res_distri_emcee.png :alt: Stage 5 residual distribution Fig 5302: Residual Distribution .. figure:: ../media/S5_out/fig5303_ch0_burninchain.png :alt: Stage 5 fitting chains .. figure:: ../media/S5_out/fig5303_ch0_chain.png :alt: Stage 5 fitting chains Figs 5303: Fitting Chains. Only made for ``emcee`` runs. Two version of the plot will be saved, one including the burn in steps and one without the burn in steps. Fig 5304: *(Demo figure to come)* Zoomed-in Figure Emphasizing Phase Variations Using Temporally Binned Data Over Unbinned Data. - If ``isplots_S5`` = 5, and if ``emcee`` or ``dynesty`` were used as the fitter: ``Eureka!`` will plot a corner plot for each channel. .. figure:: ../media/S5_out/fig5501_ch0_corner_emcee.png :alt: Stage 5 corner plot Fig 5501: Corner Plot .. _s6-out: Stage 6 Outputs --------------- In Stage 6: - If ``isplots_S6`` = 1: ``Eureka!`` will plot the transmission or emission spectrum, depending on the setting of ``y_unit``. If a model is provided, it will be plotted on the same figure along with points binned from that model to the resolution of the data. .. figure:: ../media/S6_out/fig6101_transmission.png :alt: Stage 6 transmission spectrum. Fig 6101: Transmission Spectrum. .. figure:: ../media/S6_out/fig6101_emission.png :alt: Stage 6 emission spectrum. Fig 6101: Emission Spectrum. - If ``isplots_S6`` = 3: ``Eureka!`` will make another transmission plot (if ``y_unit`` is transmission type) with a second y-axis which is in units of atmospheric scale height. .. figure:: ../media/S6_out/fig6301_transmission.png :alt: Stage 6 transmission spectrum with a second y-axis in units of atmospheric scale height. Fig 6301: Transmission Spectrum with Double y-axis.