Stage 0: Data Handling
Prefer Jupyter notebooks? A .ipynb of this tutorial is also available on GitHub!
The first stage of any data reduction project is to download the data. HUSTLE-tools Stage 0 handles downloading and organizing the data for your program ID, visit number, and target of interest. The only engagement required from you is to supply the .hustle configuration file and identify the target star in the direct image. This tutorial will walk you through this process.
1. Creating the Stage 0 configuration file
The first step is to create the configuration file that will guide the execution of Stage 0. Create a folder to store the configuration file in, e.g. configs/. Then create configs/stage_0_input_config.hustle and populate it with the following template:
# HUSTLE-tools config file for launching Stage 0: Data Handling
# Setup for Stage 0
toplevel_dir './files' # Directory where you want your files to be stored after Stage 0 has run. This is where /specimages, /directimages, /visitfiles, and /miscfiles will be stored.
verbose 2 # Int from 0 to 2. 0 = print nothing. 1 = print some statements. 2 = print every action.
show_plots 2 # Int from 0 to 2. 0 = show nothing. 1 = show some plots. 2 = show all plots.
save_plots 2 # Int from 0 to 2. 0 = save nothing. 1 = save some plots. 2 = save all plots.
# Step 1: Download files from MAST
do_download True # Bool. Whether to perform this step.
programID '12345' # ID of the observing program you want to query data from. On MAST, referred to as "proposal_ID".
target_name 'PLANET-B' # Name of the target object you want to query data from. On MAST, referred to as "target_name".
token None # str or None. If you are downloading proprietary data, please visit https://auth.mast.stsci.edu/token?suggested_name=Astroquery&suggested_scope=mast:exclusive_access to obtain an authentication token and enter it as a '' string here.
extensions ['_flt.fits', '_jit.fits'] # lst of str or None. File extensions you want to download. If None, take all file extensions. Otherwise, take only the files specified. _flt.fits are required. _jit.fits are recommended if you want to use jitter decorrelation to detrend systematics.
# Step 2: Organizing files
do_organize True # Bool. Whether to perform this step.
visit_number '00' # The visit number you want to operate on.
filesfrom_dir None # None or str. If you downloaded data in Step 1, leave this as None. If you have pre-downloaded data, please place all of it in filesfrom_dir. Don't sort it into sub-folders; HUSTLE-tools won't be able to find them if they are inside sub-folders!
# Step 3: Locating the target star
do_locate True # Bool. Whether to perform this step.
location None # None or tuple of float. Prior to running Stage 0, this will be None. After running Stage 0, a copy of this .hustle file will be made with this information included.
# Step 4: Quality quicklook
do_quicklook True # Bool. Whether to perform this step.
traces_included ('+1',) # List of str. Which traces are included in the white light curve plot included in the quicklook.
# ENDPARSE
Let’s break down each of these steps to make sure we understand what we can tune in this stage.
Setup for Stage 0
You can customize the toplevel_dir folder to be any name you like as long as you use the same folder name for all stages. The verbose, show_plots, and save_plots keys respectively control the level of detail in the statements printed by the pipeline while it executes, the number of plots opened in the terminal or .ipynb notebook cell you are running the script in, and the number of plots saved out to .png or .gif files to be reviewed at any time after execution.
Step 1: Download files from MAST
If you have not pre-downloaded the data for your program, then set do_download to True. If you are unsure of your obsevation’s programID and/or target_name, you can head to https://www.stsci.edu/hst/observing/program-information and search for your program by proposal ID and/or PI/Co-I name. If your data is protected by a proprietary period, you can visit https://auth.mast.stsci.edu/token?suggested_name=Astroquery&suggested_scope=mast:exclusive_access to acquire an authentication token, which you supply as a string encased in ‘’ marks to the token variable. The extensions variable controls which file extensions you want to acquire. The minimum recommended case includes all images, while additional extensions may be useful to acquire e.g. telescope telemetry data.
Step 2: Organizing files
If you have not pre-downloaded the data, or if you have pre-downloaded the data but they are not yet organized, then set do_organize to True. This step will sort your files by orbit number, visit number, and file contents. Specify the visit_number variable as a two-character string to select which visit in the observation corresponds to your target. As before, you can find the visit number by heading to https://www.stsci.edu/hst/observing/program-information and searching for your program by proposal ID and/or PI/Co-I name. If you have pre-downloaded your data, store all of it in the folder specified in the filesfrom_dir variable.
Step 3: Locating the target star
Set do_locate to True to prompt the pipeline to present the direct image so that you can locate the target star within this frame. This is the only step of the pipeline which requires user input, but it is necessary to ensure successful wavelength calibration in Stage 2. If you have already located the coordinates of the target star, you can set do_locate to False and simply supply the coordinates as a tuple of floats to the location variable. Otherwise, a copy of this configuration file will be output after execution which will update the location variable to the coordinates selected during the do_locate step.
Step 4: Quality quicklook
If you want to save a “quicklook” gif that presents all of the data frames in succession as well as simple diagnostics of the image and trace flux, simply set do_quicklook to True. You can use the traces_included variable to include flux from the +1 trace, the -1 trace, or both.
Running Stage 0
Now that you understand what each variable does, edit your config file as you like. With the configuration file created and stored in configs/stage_0_input_config.hustle, create a simple .py or .ipynb script with the following contents:
from hustle_tools import run_pipeline
config_files_dir = "configs"
stages = (0,)
run_pipeline(config_files_dir, stages)
Then execute this script to run Stage 0! The output in your cell should look similar to the output shown below, where we have used HST-GO 17183 (PI: Hannah Wakeford), visit 12, target WASP-127 as an example:
Querying MAST for files under program ID 17183, target WASP-127...
Found 169 files related to program ID 17183, target WASP-127.
Creating directory output to store your files in...
Downloaded data will be stored in directory output.
Examining 251 queried data products for files in visit number 12...
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COMPLETE : None
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Downloading file number 11 from mast:HST/product/iexr12f6q_spt.fits...
INFO: Found cached file output/iexr12f6q_spt.fits with expected size 103680. [astroquery.query]
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Downloading file number 12 from mast:HST/product/iexr12f6q_spt.fits...
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Downloading file number 14 from mast:HST/product/iexr12f6q_flt.fits...
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COMPLETE : None
Downloading file number 15 from mast:HST/product/iexr12f6q_flt.fits...
INFO: Found cached file output/iexr12f6q_flt.fits with expected size 12758400. [astroquery.query]
COMPLETE : None
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Downloading file number 163 from mast:HST/product/iexr12051_spt.fits...
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Downloading file number 168 from mast:HST/product/iexr12041_spt.fits...
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Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_f300x_iexr12f6_flt.fits...
Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_f300x_iexr12f6_flt.fits...
Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_g280_iexr12f7_flt.fits...
Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_g280_iexr12fm_flt.fits...
Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_g280_iexr12ir_flt.fits...
Skipping over file at mast:HST/product/hst_17183_12_wfc3_uvis_g280_iexr12gl_flt.fits...
Downloaded 169 queried files that had visit number 12.
Collecting and categorizing files from output...
Collected spec, direct, and misc files.
Detected 5 orbits and created new filenames to update.
Renaming spec and misc files.
Detected 5 orbits and created new filenames to update.
Renaming spec and misc files.
Renamed all files to follow or##fm### (for spec frames) or or##dr### (for direct frames) convention.
Moving 158 listed files to target directory output/specimages...
All files listed moved into output/specimages.
Moving 2 listed files to target directory output/directimages...
All files listed moved into output/directimages.
Moving 0 listed files to target directory output/visitfiles...
All files listed moved into output/visitfiles.
Moving 5 listed files to target directory output/miscfiles...
All files listed moved into output/miscfiles.
All spec, direct, and misc files moved.
Please input your best guess for the x position of the source star: 975
Please input your best guess for the y position of the source star: 160
Located 1 possible sources.
Please select the source from this list:
0 (np.float64(974.8154860553503), np.float64(160.15959552212985))
0
Enter 0 to keep this source,
1 to search again,
2 to update the search parameters and then search again,
or 3 to select manually: 0
Source selected: 974.8154860553503 160.15959552212985
Writing config file for Stage 0...
Config file written.
Parsing files for quicklookup... Progress:: 100%|██████████████████████████████████████████████████████████████████████████████████| 158/158 [00:01<00:00, 93.41it/s]
MovieWriter ffmpeg unavailable; using Pillow instead.
Assessing Stage 0’s success
Stage 0 is the simplest stage that has very few diagnostics to look over.
Diagnostic 1: toplevel_dir directory structure
Stage 0 will create a toplevel_dir populated with the specimages, directimages, jitterfiles, visitfiles, miscfiles, and outputs subfolders, as shown:
The toplevel_dir filetree with expected subfolders; here, toplevel_dir has been named ‘output’.
Diagnostic 2: updated location variable
The output toplevel_dir/outputs/stage_0 folder will contain a near-copy of the input Stage 0 .hustle configuration file. If you set do_locate to True, then the only change will be an updated location variable matching the location you found when running Stage 0.
Diagnostic 3: quicklookup.gif and image files contain expected observations
You should check to confirm that the output toplevel_dir/specimages and toplevel_dir/directimages folders contain the expected number of *flt.fits files. To confirm the contents of the spectroscopic image files, check the quicklookup.gif to ensure that it (1) has as many frames as there are *flt.fits files in toplevel_dir/specimages, and (2) has a trace flux time series (bottom right plot) matching the event you expected to observe. We show an example direct image and frame from the quicklookup.gif below from HUSTLE program observations of a transit of WASP-127b from visit 12 of HST-GO 17183 (PI: Hannah Wakeford):
F300X image of the target star in visit 12 of HST-GO-17183, with target star in the yellow circle.
Last frame of quicklookup.gif file from visit 12 of HST-GO 17183, with a clear transit visible in the bottom right plot.