Frequently Asked Questions

General Problems

The pipeline does not run and gives me an error similar to `pp_run: Command not found`. What is wrong?
There are two things to check: (1) did you properly setup the PHOTPIPEDIR environment variable (check this by typing echo $PHOTPIPEDIR in a terminal), or (2) the command pp_run uses a symbolic link to; if the former does not work, try the latter.
**Running the pipeline creates warnings (e.g., FutureWarning); what
should I do?**
Warnings are usually caused by Python module version issues and cause no harm whatsoever. In theory, there should be no warnings, but they happen occasionally. If you are haunted by some warnings, let me know and I will try to resolve the issue.
**I get an error message like `Intel MKL FATAL ERROR: Cannot load or`. What do I have to do?**
This seems to be a problems with your numpy or scipy installation. Try to install the latest versions of both packages. If you are using anaconda, try conda install -f numpy and conda install -f scipy.

pp_calibrate (Photometric Calibration)

I keep getting output like `zeropoint for image.fits: Warning: 0 reference stars after source matching for frame image.ldac`. What does it mean?
It means that none of the reference stars with measured magnitudes in your field of view could be matched with a source in your image. As a result, the magnitudes in the photometry output files are simply instrumental magnitudes, not calibrated ones. Try using a different photometric catalog in pp_calibrate(). If your field of view is small (<2 arcmin), there might just be no stars with known magnitudes in the field, in which case there is not a lot that can be done…
The pipeline fails to derive useful magnitude zeropoints from 2MASS data
This problem might be solved by installing the latest version of astropy (currently 2.0.2).

The pipeline crashes in ``pp_calibrate`` with the following error message: `IndexError: too many indices for array`. ** Well, this is embarassing… I am familiar with this problem, but I haven’t found a way to solve it, yet. The problem is that Source Extractor runs in ``pp_photometry`` to produce an array of aperture photometry results for the curve-of-growth analysis. After that, Source Extractor is supposed to run then once again using the optimum aperture radius. Sometimes, this second Source Extractor runs seems to fail, causing ``pp_calibrate`` to fail. A manual workaround is to run ``pp_photometry`` again using the ``-aprad`` option and the optimum aperture derived from the last run. Running ``pp_calibrate`` again will then succeed. - **Update: this problem should now be fixed. If you still encounter problems, please let me know!

pp_distill (Target Photometry Extraction)

Why does the target photometry vary wildly, although the magnitude zeropoints are consistent with each other?

Check the offset of the photometry position to the expected target position. If the offsets are not consistent, it is likely that PP picks up noise or nearby sources (also check the target thumbnail images). This can happen if the target is very faint (in this case, lower the snr limit in pp_photometry()), or if the snr limit and minarea paramters are picked too small and too much noise is picked up. In either case, redo the pp_photometry() step and play with the snr and minarea parameters.