FAQ / Known Issues

This page contains a list of Frequently Asked Questions, and known issues related the operations of the pipeline that are not likely to be fixed in the short term. Only issues which will not be fixed with a new release of the pipeline within around a month will be added to this list. Wherever possible, a link to relevant GitHub issues will be provided.

Frequently Asked Questions

Why are my output cubes reduced with this pipeline slightly offset from cubes made with the IDL pipeline?

This version of the pipeline includes functionality that the IDL pipeline did not, notably an air-to-vacuum wavelength correction, and a barycentric wavelength correction. These, predictably, result in small but noticable offsets between new and old cubes.

What are all of these output files?

Please reference the Data Products page for information on what files are produced by the pipeline.

I think I might be missing some calibration files, but I’m not sure. How do I check?

There is a script installed with the pipeline called check_cals that can help you here. It scans a data directory and pipeline config, and outputs a report about what calibrations it matched with what science frames. If any are missing, it tells you which, and how many are needed. More details can be found here.

Known Issues

Pipeline Ingests Blue Files as Red, and Vice Versa

There is a known bug in the Keck DRP framework that prevents two instances of the DRP from running at the same time. This can be inconvenient, as this means you cannot reduce red and blue side data at the same time on the same machine. Until this bug gets fixed, the only solution is to run through your data first for one set of blue/red data, then the other.

Firefox/geckodriver cannot be found

Error message:

RuntimeError: Neither firefox and geckodriver nor a variant of chromium browser and chromedriver are available on system PATH. You can install the former with 'conda install -c conda-forge firefox geckodriver'.

This issue has been submitted by a small number of users. This error is thrown by our plotting library, bokeh, when it can’t automatically find the path to a driver needed to generate plots. The following describes a one-off workaround.

These instructions assume you are using conda to manage your environment.

If you installed the pipeline with pip, uninstall with pip uninstall kcwidrp
Install the pipeline following the Installing for Development instructions on the Installing KCWI_DRP page.

Install the following two packages:

pip install selenium
pip install geckodriver

Open KCWI_DRP/kcwidrp/core/kcwi_plotting.py in a text editor
Add the following import at the top of the file:
```
from selenium import webdriver
```
Find your firefox installation by executing which firefox from the command line. Make note of the output. It should look something like /PATH/TO/CONDA/envs/kcwidrp/bin/firefox

Replace the function save_plot with the following:

def save_plot(fig, filename=None):
    if filename is None:
        fnam = os.path.join('plots', 'kcwi_drp_plot.png')
    else:
        fnam = os.path.join('plots', filename)

    options = webdriver.FirefoxOptions()

    options.add_argument("--headless")
    options.add_argument("--hide-scrollbars")
    options.add_argument("--force-device-scale-factor=1")
    options.add_argument("--force-color-profile=srgb")
    driver = webdriver.Firefox(firefox_binary="[YOUR/PATH/HERE]",
                                firefox_options=options)
    export_png(fig, filename=fnam, webdriver=driver)
    driver.close()
    logger.info(">>> Saving to %s" % fnam)

where [YOUR/PATH/HERE] is replaced by the path found in the previous step

Navigate to the KCWI_DRP directory, and run:
```
python setup.py install
```

Massive Slowdown When Calculating Central Dispersion

This issue does not throw an error, but can be identified by the logs as it happens. The logs will look something like

2021-06-08 18:49:51:KCWI:INFO: Using TAPERFRAC = 0.200
Bar#:   4, Cdisp: 0.2392
Bar#:   0, Cdisp: 0.2391
Bar#:   8, Cdisp: 0.2393
Bar#:  12, Cdisp: 0.2393
...
Bar#: 119, Cdisp: 0.2397

This step typically takes anywhere from 30 seconds to several minutes, depending on the resources available to your computer. However, sometimes this step takes upwards of 20 minutes, even on a powerful machine. This appears to be caused by a conflict in thread allocation between various packages used by the pipeline, although the specifics remain unknown.

To fix the issue, you need to specify how threads are allocated directly. This can be done directly from the command line by typing the following lines into your terminal:

export MKL_NUM_THREADS=16
export NUMEXPR_NUM_THREADS=1
export OMP_NUM_THREADS=1

This will not persist between terminal sessions, so you should add it to your .bashrc file.

PyQt5

Some users have reported an issue where PyQt5 is required to run the DRP, which looks like

Failed to import any Qt binding

If this is the case, run

pip install pyqt5

and the issue should be fixed.