Getting started¶
This step-by-step guide is intended to assist in manually reducing EXES data. A more general introduction to the Redux GUI and reduction algorithms can be found in the EXES Redux User’s Manual.
Cross-dispersed data¶
Overall process: get the order spacing right, get the slit rotation right, get the extraction right, get the central wavelength right, get the dispersion right.
Load in the data (File -> Open New Reduction).
If there is more than one science file, you may want to select just one to start with, along with the flat, until you are sure you have the correct distortion parameters (step 2-3).
If RAW files are available, load those instead of the truly raw files. If not, you may want to generate them for all science files first (by running Load Data), then start again with the RAW files.
Step to: Make Flat.
Verify that the step completed successfully (no ERROR messages in the terminal).
Verify the spacing between orders.
Measure the actual spacing in the image (use d in ximgtool and right-click to draw a horizontal line), and verify that it roughly matches the predicted spacing (printed to the terminal).
Verify that the calculated spacing matches the predicted order spacing.
Verify that the orders look roughly rectilinear.
If any of these checks fail: Undo the Make Flat step (or Reset).
If the predicted spacing seems off, it can be fixed by changing XDFL. Edit Param for the Load Data step to enter a new value. The value used in the first run should have been printed to the terminal. Increasing XDFL will increase the predicted spacing.
The predicted spacing does not have to match the actual spacing exactly. It just needs to be close enough for the optimization algorithm to find the right value.
Typical values for XDFL are about 85-110. If you find you have to use values far outside that range, something else is probably wrong.
If the calculated spacing or the rotation of the orders seems off, it is likely that the edge detection routine failed. Edit Param for the Make Flat step, select Debug, and run again. Debugging will stop the reduction with an error message and display some useful images. Buffer 1 is the undistorted flat, Buffer 2 is the edge-enhanced image, Buffer 3 is the FFT of that image, Buffer 4 is the region of the FFT near where a peak is predicted (in the first and second harmonics of the FFT), and Buffer 5 is the calculated illumination mask. If the edge detection is working correctly, there will be a clear peak in at least one of the stamps in Buffer 4, and the illumination mask in Buffer 5 will match the undistorted flat. If this is not the case, try a different Edge enhancement method in the Make Flat parameters and run again. Which method works best sometimes depends on the illumination characteristics of the particular flat being reduced.
If you can’t get the edge detection algorithm to work at all, it may be that the flat just doesn’t have obvious enough edges. You may be able to get close to a good correction by deselecting Optimize rotation angle, and editing the Starting rotation angle and/or Predicted spacing by hand.
If the order spacing and rotation look okay, but the pipeline reports that it couldn’t find the order edges, try increasing the Threshold factor to make the inter-order spacing a little wider.
When you have a reasonable undistorted flat, turn off Debug and run the step once more.
Step to: Undistort.
Check that the distortion correction looks okay, and there are no bad nod pairs. Use Display -> Quick Look to step through each input file. Use Buffer -> Cycle Frames to step through each nod pair in the file.
If emission or absorption features appear tilted across the orders, you may need to modify the slit rotation. Reset the reduction and Edit Param for Load Data to change the slit rotation. Increasing the slit rotation angle rotates the lines clockwise.
To get the slit rotation exactly right, it may be helpful to extract sky spectra at the top and bottom of the order and compare features in the extracted apertures. To do this, Edit Param for Subtract Nods to skip nod subtraction, and for Find Objects and Set Apertures to set manual apertures, then Step to: Extract Spectra. Reset, edit Slit Rotation, and re-reduce as necessary.
If there are bad nod pairs (eg. if the observation was aborted), note the file number and frame number. Edit Param for Coadd Pairs and enter any frames that need to be excluded in Exclude Pairs. Files are separated by semi-colons, frames are separated by commas. For example, to exclude the first frame from the first file, and the last frame from last file in a 3-file, 6-nod sequence, enter 1;;6.
Step to: Make Profiles. Step to: Set Apertures.
Check that the apertures have been correctly set.
Use Display -> Quick Look to check each image; look for light blue lines over the center of each aperture in the image. Look for a green overlay over most of the source in the spatial profile. If the apertures are badly placed, Undo.
If the objects look misidentified, set them by hand by using Fix or Guess parameters in Find Objects.
If the apertures look wrong, set them by hand using the Override parameters in Set Apertures.
Step to: Extract Spectra. Verify the spectra from all apertures/files look about the same. If not, some non-standard extraction parameters may need to be used (eg. turn off bad pixel correction, use median spatial profile, set background regions, etc.).
A single file is usually loaded into xvspec. More can be added in for direct comparison using Add Spectra. They can also be viewed/combined in the separate tool called xcombspec.
Step to: Merge Orders. Click Cancel in the Refine Wavecal GUI. Compare the atmospheric transmission in the Transmission pane in xvspec to the merged spectrum to identify an atmospheric feature. It can be overplotted on the data with Plot -> Overplot -> Transmission.
The wavenumber of the feature can be measured by selecting Transmission, clicking on the plot, typing f over the new window, and clicking on the left, then the right, side of the feature. The centroid of the feature will be reported in the bar at the top of the window.
Measure the wavenumber of the corresponding feature in the science spectrum by clicking Flux and repeating the above process to centroid the line. The initial central wavenumber is sometimes very far off, which can make identification of a corresponding feature difficult.
Undo. Step to: Refine Wavecal. Identify the feature in the spectrum (click on the order, centroid the line, click Add from Plot in the little GUI window), then edit the wavelength to the measured wavelength from the Transmission spectrum. Click Done.
Click Reset. The calculated wavenumber will now be used to update the distortion/dispersion parameters. Step to: Refine Wavecal to redo the full reduction.
Verify that the distortion correction still looks right.
Verify that the identified feature now has the correct wavenumber. If the central wavelength was far off, you may have to Refine it, and repeat the reduction again.
If there are overlapping orders, the dispersion may need to be tuned to get the lines to appear at the same wavelength in each order.
The separate tool xmergeorders can be used to check the overlapping regions.
For cross-dispersed spectra, the dispersion is tuned with the HRFL parameter. Reducing HRFL decreases the wavenumber of the left end of the spectrum (eg. if a feature at the left end of Order 2 is to the right of a feature at the right end of Order 1, decreasing HRFL slightly may fix it). To edit HRFL, Reset the reduction, Edit Param for Load Data, and repeat from step 7. Changing HRFL will change the wavelength calibration, which changes the distortion correction, so the wavecal will have to be Refined, and possibly Refined again.
Typical values for HRFL are about 85-110, as for XDFL.
Step to: Merge Orders.
For spectra with overlap regions, verify that the final spectrum looks right, eg. that there are not discontinuous jumps, or excessively noisy overlap regions. If there are, Undo and Edit Param for Merge Orders. Try higher or lower values for the Selection threshold. Spectra can also be merged by hand using the xmergeorders tool.
Finally: save the reduction parameters for the observation, using Parameters -> Save Current Parameters. These parameters serve as a record of the manual reduction, and can later be directly loaded into either the GUI or the automatic pipeline to repeat the same reduction.
Long-slit data¶
Overall process: Same as for cross-dispersed data, except that there is no order spacing to worry about in the distortion correction, and no order merging in the final product.
Load in the data (File -> Open New Reduction).
Step to: Undistort.
Check that the distortion correction looks okay, and there are no bad nod pairs. Use Display -> Quick Look to step through each input file. Use Buffer -> Cycle Frames to step through each nod pair in the file.
If emission or absorption features appear tilted across the order, you may need to modify the slit rotation. Reset the reduction and Edit Param for Load Data to change the slit rotation. Decreasing the slit rotation angle rotates the lines clockwise.
To get the slit rotation exactly right, it may be helpful to extract sky apertures at the top and bottom of the order and compare features in the extracted apertures. To do this, Edit Param for Subtract Nods to skip nod subtraction, and for Find Objects and Set Apertures to set manual apertures, then Step to: Extract Spectra. Reset, edit Slit Rotation, and re-reduce as necessary.
If there are bad nod pairs (eg. if the observation was aborted), note the file number and frame number. Edit Param for Coadd Pairs and enter any frames that need to be excluded in Exclude Pairs. Files are separated by semi-colons, frames are separated by commas. For example, to exclude the first frame from the first file, and the last frame from last file in a 3-file, 6-nod sequence, enter 1;;6.
Step to: Make Profiles. Step to: Set Apertures.
Check that the apertures have been correctly set.
Use Display -> Quick Look to check each image; look for light blue lines over the center of each aperture in the image. Look for a green overlay over most of the source in the spatial profile. If the apertures or objects are bad, Undo.
If the objects look misidentified, set them by hand by using Fix or Guess parameters in Find Objects.
If the apertures look wrong, set them by hand using the Override paramters in Set Apertures.
Step to: Extract Spectra. Verify the spectra from all apertures/files look about the same. If not, some non-standard extraction parameters may need to be used (eg. turn off bad pixel correction, use median spatial profile, set background regions, etc.).
A single file is usually loaded into xvspec. More can be added in for direct comparison using Add Spectra. They can also be viewed/combined in the separate tool called xcombspec.
Step to: Refine Wavecal. Compare the atmospheric transmission in the Transmission pane in xvspec to the combined spectrum to identify an atmospheric feature. It can be overplotted on the data with Plot -> Overplot -> Transmission.
The wavenumber of the feature can be measured by selecting Transmission, clicking on the plot, typing f over the new window, and clicking on either side of the feature. The centroid of the feature will be reported in the top of the window.
Select the corresponding feature in the science spectrum by clicking Flux and repeating the above process to centroid the line. Click Add from Plot in the little GUI window, then edit the wavelength to the measured wavelength from the Transmission spectrum. Click Done.
Click Reset. The calculated wavenumber will now be used to modify the distortion/dispersion parameters. Step to: Refine Wavecal to redo the full reduction.
Verify that the identified feature now has the correct wavenumber. If the initial central wavelength was far off, you may have to Refine it, and repeat the reduction again.
The dispersion may need to be tuned to get the lines to appear at the correct wavelengths all the way across the spectrum.
For long-slit spectra, the dispersion is tuned with the XDFL parameter. Reducing XDFL decreases the wavenumber of the left end of the spectrum and increases the wavenumber of the right end, when the central wavelength is correctly identified. To edit XDFL, Reset the reduction, Edit Param for Load Data, and repeat from step 6. Changing XDFL will change the wavelength calibration, which changes the distortion correction, so the wavecal will have to be Refined, and possibly Refined again.
Finally: save the reduction parameters for the observation, using Parameters -> Save Current Parameters. These parameters serve as a record of the manual reduction, and can later be directly loaded into either the GUI or the automatic pipeline to repeat the same reduction.