3. SEDM Pipeline

3.1. Pipeline Overview

A new pipeline developed by Mickael Rigault has been installed for automatic reduction of SEDM data. The distribution is available on github. It generates a geometry solution from the calibration images and then automatically extracts target spectra based on the WCS solution of the guider images. Please see the documentation that accompanies the github repository. The extracted spectrum is classified using SNID and if it is a ZTF target, the ascii spectrum is uploaded to the growth marshal. The only interactive step is to generate a final report once all the extractions have been verified.

If there is a failure of the WCS solution, or if the target is particularly difficult to model with a PSF, there are ways to re-extract the spectrum. This will be described in more detail below.

3.1.1. Python Requirements

The IFU pipeline is compatible with python v2.7 and v3.6 and currently runs under the miniconda3 distribution. It requires the astroconda environment from STScI and expects the name to be ‘astroconda’:

conda create -n astroconda stsci

3.2. Automated Pipeline Operations

Now we describe the steps that the pipeline takes during the automated operations. We start with the pre-science processing that generates the nightly geometry solution and then continue with the science target processing.

3.2.1. Pre-Science Processing

Pre-science processing occurs in the afternoon and takes roughly 30 minutes to complete. In the afternoon when the UT date changes, the following steps are automatically performed:

  1. The appropriate reduced directory is created using the UT date:
    • /scr2/sedmdrp/redux/20180907 (e.g.)
  2. The required raw calibration files are linked into the directory as they are taken.
  3. Once all the bias files are acquired the master biases are generated.
  4. All subsequent calibration files are linked into the directory and then bias-subtracted and cosmic ray cleaned.
  5. Once all the calibration files are acquired a geometry solution and flat field is generated.
  6. If there is a failure in the geometry solution, geometry files from previous runs are linked in.
  7. The most recent fluxcal fits file is linked in, usually from the previous night.

You can verify the success of the geometry solution and flat field by looking at the plots generated when they are produced. One is the wavelength solution dispersion and the other is the flat field. They will be in the reduced directory and have names that start with the UT date string (20180907, e.g.).


Figure 1. Wavelength solution dispersion in Angstroms (20180907_wavesolution_dispersionmap.png).


Figure 2. Flat field (20180907_flat3d.png).

3.2.2. Science Processing

Now the SEDM is ready for science images. Near the end of astronomical twilight, science image acquisition begins. The following steps are automatically performed:

  1. All new IFU images are linked in and bias-subtracted and cosmic ray cleaned.
  2. The sky lines are used to solve for the flexure offsets for the observation.
  3. The geometry solution is used to generate a flexure-corrected cube for the observation.
  4. If the target is a standard star:
    1. no guider image is generated.
    2. the brightest spaxel is used to define the extraction region.
    3. PSF-forced spectro-photometry is performed.
    4. a fluxcal fits file is generated.
  5. If the target is a science object:
    1. a guider image is generated from all the guider frames and the WCS is solved.
    2. an extraction region in the IFU is based on the guider WCS and the target coordinates.
    3. PSF-forced spectro-photometry is performed.
    4. the most recent fluxcal file is used to calibrate the science target.
    5. the telluric absorption is corrected based on header AIRMASS.
    6. the resulting spectrum is classified using SNID
    7. the SNID results are put in the ascii spectrum header.
    8. the extraction is recorded in a file called report.txt
  6. If the target is a ZTF object:
    1. the spectrum is uploaded to the growth marshal.
    2. the marshal URL is recorded in the file report_ztf.txt

The format of the ascii spectrum that is generated is universal enough to be input to any classifier (Superfit, e.g.).

3.2.3. Quality

A quality value is assigned to each spectrum based on several criteria. In this scheme, quality values 0, 1, and 2 are considered acceptable. Any value above 2 indicates a major problem and the spectrum will neither be classified nor uploaded to the marshal. Here is the current quality scheme:

  • Quality 0: default quality (usually what standard stars have)
  • Quality 1: extraction OK
  • Quality 2: a minor problem was encountered, but won’t interfere with classification
  • Quality 3: the telescope offset placed the target outside the IFU
  • Quality 4: more than 20% of the flux is negative
  • Quality 5: the guide image astrometry failed (for science targets only)

Standard star observations never generate guider image astrometry solutions and always use the brightest spaxel to define the centroid. Therefore, standard stars should never have a quality of 5.

Quality 3 objects cannot be fixed. Quality 4 and 5 objects may possibly be fixed, but will require hand-extraction (see Adjustment below).

3.3. Interactive Processing

All target extractions should be verified and adjusted if required. Once that is done a final report is generated that sends out a summary e-mail of the night’s results. In order to do this, one has to connect to pharos.caltech.edu via a VNC connection. If the screen lock is active, just enter the password to unlock it. Below is is a figure showing the layout of the main desktop screen connected through the VNC connection.


Figure 3. Pharos sedmdrp desktop on screen 7 (5907).

The automatic pipeline script is running in the bottom right xterm window. Some status information can be gleaned from the output there. The xterm set on the left may be used by the observer to examine the files on pharos. A web browser will be set up on the secondary desktop to the right which can be selected using the chooser on the lower right. This is where you can interact with the SEDM web site and the growth marshal and other web services to look at finder charts.

In the top-right Xterm window, the observer interacts with the pipeline as described below. Be sure to cd into the current directory, which is the UT date formatted as YYYYMMDD (20180907, e.g., which would be found in /scr2/sedmdrp/redux/20180907).

3.3.1. Verification

The automated pipeline generates verification plots as each image is processed. These are PNG image files that start with verify_. You can display all of them using the display command from ImageMagick like this:

display verify_*.png &

Figures 4 - 6 show the three types of verification plots. For all three types, the acquisition finder chart is shown in the upper right and the IFU spaxel plot is in the upper left. The PSF extraction results are shown in the lower left in three plots showing the Data, Model, and Residual. Finally, in the lower right, is shown some form of the extracted spectrum. For a standard star, it will show the calibration check plot comparing the reference spectrum to the observed spectrum (see Figure 4).


Figure 4. Verification plot for standard star BD+33d2642

For a science target that has a successful classification from SNID, it will show the SNID template match plot (see Figure 5).


Figure 5. Verification plot for successfully typed science target ZTF18abosrco

For a science target for which SNID fails to find a classification, it will show only the extracted spectrum (see Figure 6).


Figure 6. Verification plot for unsuccessfuly typed science target ZTF18absqitc

The first step of verification is to compare the B&W finder (upper right) with the IFU extraction region (upper left). The red right-angle in the B&W finder indicates the location of the target. If the IFU extraction region indicated by black dots contains the object and the centroid, indicated by either a red X or a red circle is reasonably close to the target, then this is probably a good extraction. Next, examine the PSF fit and residual plots in the lower left. If the model looks reasonably close to the data and the residuals look like the model accounted for most of the target’s flux, then the extraction was successful. This is also bolstered if the spectrum looks good and is either a good match to a SNID template, or to a reference spectrum, or seems to have good signal-to-noise.

If you want further verification of the target, you will need to move to the desktop to the right (using the chooser in the lower right, or by moving the mouse the the right edge of the desktop). There you can open a web browser, if needed, and log into the ZTF marshal, the TNS website, or any other web-based source of finder charts for the target.

3.3.2. Adjustment

There are three types of adjustment that can be made. The first two types, fixing the centroid and adjusting the extraction region, will completely replace the original spectrum. The object adjusted in these two ways will still need to be re-classified, re-reported on the slack channel (pysedm-report), and re-uploaded to the growth marshal (if the target is a ZTF object). This is now done automagically with a script called redex that is available on pharos in the sedmdrp account.

NOTE: if the target was given the quality value of 5 (guide image astrometry failed), then you must identify the target by hand and reset the centroid appropriately.

The third type of adjustment, using an aperture instead of a psf, creates new files and requires more bookkeeping and is therefore, not recommended unless specifically required. Redex Script

There is a script available that performs many of the bookkeeping tasks required by re-extraction. It is called redex and can be used as follows:

redex <timestr> [<X Y>],

where <timestr> is the UT time stamp for the specific observation, and <X Y> are replaced by the corrected centroid values as determined from the IFU spaxel plot. The <timestr> is formatted:


and is shown in the title of the verification plot. The <X Y> values are optional, and if not included will invoke the --display option for extract_star.py. The script does the following:

  1. re-run extract_star.py with the appropriate parameters,
  2. completely replace the spectrum file for the object,
  3. re-generate the extraction plots,
  4. remove any old classification files generated by SNID,
  5. re-run SNID on the new spectrum,
  6. re-generate the verification plot,
  7. re-generate the pysedm_report plot,
  8. push this plot to the SEDM-P60 slack channel pysedm-report
    1. (if you add --noslack to command line, this won’t happen),
  9. remove the marshal upload lock file (*.upl), if it is a ZTF object.

It will not upload the new spectrum to the marshal, so you will need to re-run make ztfupload after you have adjusted all the objects that require it. Adjust Centroid

This is the simplest adjustment to make. It will arise in some cases if the WCS solution of the guider images failed (Quality 5). This is indicated in the IFU spaxel plot when the centroid is plotted a red circle instead of a red X. When the WCS solution fails, the extraction is defined by the brightest pixel. This is fine for standard stars, but does not always work for science targets. Sometimes even successful WCS solutions will define the centroid in the wrong place. Let the finder chart in the verification plot and any other finders from the web be your guide.

It is also possible that a target that is strongly influenced by a neighbor (host galaxy, nearby star) can be fixed by just moving the centroid, and hence moving the extraction region, off of the offending neighbor.

To make this adjustment, you simply need to pass the new centroid to the redex script. Use the IFU spaxel plot to determine the new centroid for the target. Then enter the command:

redex <timestr> <X Y>,

using the parameters described above. Here is an example:

redex 10_55_22 0 -5.

You can use display on the new verification plot to see the results of your re-extraction. You can re-load the verification plot in the display window by right-clicking and selecting ‘Former’ and then right-clicking and selecting ‘Next’.

You may also want to display the new extraction plots. Find the appropriate psf profile plot file (starts with psfprofile_ and ends with .png). Use the display command to check if your improved centroid had the effect you wanted. You can also check the extracted spectrum in the same way. Find the spectrum plot file (starts with spec_forcepsf_ and ends with .png) and display it. As a final check, you can display the new IFU spaxel plot (starts with ifu_spaxels_ and ends with .png). This plot will now have a black cross where your adjusted centroid falls on the spaxels.


Figure 7. Adjusted centroid indicated by black cross.

It is fine to tweak the centroid and re-extract the spectrum more than once. It’s important to get a good extraction and this sometimes takes more than one adjustment to the centroid. If you think you might be doing this, please use the --noslack parameter until you have the correct centroid.

NOTE: passing the centroid to the redex script will remove the quality 5 condition.

NOTE: there is nothing in the verification plot for this object to indicate that it needs adjustment. This was done just to demonstrate the procedure. Adjust Extraction Region

This is also a fairly easy adjustment to make. If the extraction region includes a neighbor that strongly influences the psf model, and just moving the centroid doesn’t fix it, you can use the redex script to invoke the –display parameter of the extract_star.py program to re-draw the region. To do this enter the command without centroid values:

redex <timestr>,

which will bring up a display window showing the IFU spaxel plot with the region and the right is the spaxel map where you can re-draw the region.


Figure 8. extract_star.py with the --display parameter and a hand-drawn extraction region.

Just hit the shift key and draw a region (by left clicking and dragging the mouse) around your target that does not include the offending neighbor. Once you release the left mouse button, the selected region will be shown on the plot (see Figure 8). If you want to try again, hit the <ESC> key, which will reset the region, and try again. If you want to use a new centroid, just double-click on the location of the new centroid. This will be required, if the target was assigned a quality of 5 (guider image astrometry failed). Once you are happy with the centroid and region, close the plot. This is done by using the menu at the upper left corner of the window and selecting Close. The extraction will proceed once the window is closed.

If you want to abort the re-extraction, choose the Destroy option on the menu and it will halt the re-extraction.

Here is the command that produced Figure 8:

redex 10_55_22.

As with fixing the centroid, the spectrum file and all the plots will be replaced. Use the same method described above to verify that your new region achieved what you wanted.

NOTE: if the target was assigned a quality of 5, you will have to double-click on the target to reset the centroid. If you do not, the target will still have a quality of 5 and won’t be classified or uploaded. Fix A Cosmic Ray

Using the --display parameter also allows you to find and avoid spaxels that are corrupted by a cosmic ray. After the redex command is entered (without centroid values), you can click on individual spaxels until you see the one that is heavily influenced by the cosmic ray. Then, hit the shift key and draw your extraction region so as to exclude the offending spaxel. You may have to expand the window to more accurately draw the region. Adjust Extraction Method

This is a more challenging adjustment to make. As of now, the two previous adjustments seem to be able to fix nearly every situation. If you need to perform an aperture extraction, please contact the SEDM team and we can instruct you how to do this.

3.3.3. Re-Classify

NOTE: This is now handled automatically by the redex script.

If you have re-extracted an object that was previously classified by SNID, it’s a good idea to remove the old template match plot. If you don’t, this plot may be taken as the correct classification of the object. To find the old template plot, look for a file that starts with spec_ and includes your target name and ends with .png. The template match file will have a classification type in the filename. Look for Ia, Ib, QSO, e.g., in the file name just after the target name and delete that plot file.

Once that is done, you can re-classify the spectrum. This is done by entering:

make classify

in the terminal.

3.3.4. Re-Report

NOTE: This is now handled automatically by the redex script, unless you use --noslack on the command line.

After re-classification, you should send a new report to the SEDM slack channel pysedm-report with the updated extraction. To do this you enter the command:

pysedm_report.py <UTdate> --contains <timestr> --slack,

where <UTdate> and <timestr> have the same meaning as before. Here is an example of this command:

pysedm_report.py 20180907 --contains 10_11_12 --slack.

This pushes a new report onto the slack channel. If you have access to the channel, it is good to make a short comment there that indicates why you have re-extracted.

3.3.5. Re-Upload

NOTE: This will need to be performed, if you adjusted any ZTF targets.

If the target you are working on is a ZTF target, then you will want to push your new results to the growth marshal. If the old spectrum has been replaced, then you will need to delete the corresponding *.upl file. These files keep track of what has already been uploaded to the marshal. Therefore, any new version will not upload unless that file is deleted. This file will have the same root as the new text spectrum file, but will end with .upl. This file is automatically deleted if you ran the redex script. Once it has been deleted, just enter the command:

make ztfupload

and this will re-upload the text spectrum to the marshal.

If you have an account on the marshal and if the original spectrum was from a bad extraction, then you should log onto the marshal, navigate to the target that was re-extracted and delete the old spectrum.

3.3.6. Final Report

The last step at the end of the night is to generate the final report which sends a night summary e-mail report out the to the SEDM team. To initiate this final step, please enter:

make finalreport

It is a good idea to check this e-mail (if you are on the list) and make sure all of the links work and that the correct extractions are displayed.

Congratulations! You are done, for now…

Last updated on 25 Jan 2019