Setup: Input 1D spectra (plp)#

To enable error estimation, IGRINS RV cannot get RVs from the standard 1D spectra reduced by igrins plp v2.2.0. You will need the raw fits file, and to perform a specific (but semi-automated) reduction procedure.

To derive uncertainty estimates for its radial velocity measurements, IGRINS RV analyzes each observation from an exposure (a nodding sequence) separately and calculates an RV from each. When it comes to data reduction, this is done by adding the --frac-slit command flag for A0 standards and the science targets during reduction.

Running IGRINS pipeline version 2.2.0 (plp v2.2.0)#

First, open a new terminal and cd into the plp directory. Make sure you are not in ANY conda environment. All plp_main_stepXs will open/close the environment for you.

Because we are only modifying input of the recipe, the first step is to make sure that plp v2.2.0 is able to run on your machine. See https://github.com/igrins/plp/wiki/How-to-run-pipeline for more detail.

If you already have igrins plp v2.2.0 on your machine, you can just download plp_main_step1.py, plp_main_step2.py, and plp_main_step2_s.py. Put these three .py files at the same level as the igr_pipe.py.

You can follow the step by step tutorials below with example data of the GJ281 given under the ./indata/20170216

Modify the raw data and make new recipe#

  • Place your .tmp recipe file under ./recipes/[target_name]_recipes/.

The .tmp recipe file can be obtained via the simple command python igr_pipe.py prepare-recipe-logs [NIGHT] built into igrins plp IF you have the observation log under indata/[NIGHT]/IGRINS_DT_Log_[NIGHT]-1_[band].txt (For more detail, please visit How to prepare recipe logs). Without the observation log, one will need to make the .tmp recipe file manually.

An example of the .tmp recipe file:

OBJNAME, OBJTYPE, GROUP1, GROUP2, EXPTIME, RECIPE, OBSIDS, FRAMETYPES
# Available recipes : FLAT, THAR, SKY, A0V_AB, A0V_ONOFF, STELLAR_AB, STELLAR_ONOFF, EXTENDED_AB, EXTENDED_ONOFF
FLAT ON/OFF, FLAT, 11, 1, 30.000000, FLAT,11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30, OFF OFF OFF OFF OFF OFF OFF OFF OFF OFF ON ON ON ON ON ON ON ON ON ON
 , TAR, 59sky, 1, 300.000000, SKY,59, A
HR 1482, STD, 39, 1, 60.000000, A0V_AB, 39 40 41 42, A B B A
GJ 281, TAR, 60, 54, 600.000000, STELLAR_AB,60 61 62 63, A B B A

Example .tmp for GJ281 is provided under: ./recipes/GJ281_recipes/20170216.recipes.tmp

  • !!! There is a “space” in the first column of the SKY !!!

  • Run plp_main_step1.py via --> python plp_main_stepX.py [target name] [-c -h keywords]

† Example command for the example data:

~$ python plp_main_step1.py GJ\ 281 -c 4

This step will generate a new recipe file 20170216.recipes that separate the ABBA nodding into two pairs of AB and BA:

OBJNAME, OBJTYPE, GROUP1, GROUP2, EXPTIME, RECIPE, OBSIDS, FRAMETYPES
# Available recipes : FLAT, THAR, SKY, A0V_AB, A0V_ONOFF, STELLAR_AB, STELLAR_ONOFF, EXTENDED_AB, EXTENDED_ONOFF
FLAT ON/OFF, FLAT, 11, 1, 30.000000, FLAT,11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30, OFF OFF OFF OFF OFF OFF OFF OFF OFF OFF ON ON ON ON ON ON ON ON ON ON
 , TAR, 59sky, 1, 300.000000, SKY,59, A
HR 1482, STD, 39, 1, 60.000000, A0V_AB, 39 40 41 42, A B B A
GJ 281, TAR, 60, 1, 600.000000, STELLAR_AB, 60 61, A B
GJ 281, TAR, 62, 1, 600.000000, STELLAR_AB, 62 63, B A

  • There will be one [NIGHT].recipes file saved under ./recipes/[target_name]_recipes/, and it will also be copied to ./recipes_logs. The igrins plp only monitors (reads) recipes under ./recipes_logs. An example file structure:

plp(-master)
├── functions
│   ├── run_IGRINS.py
│   └── ...
│
├── recipe_logs
│   └── 20170216.recipes
│
├── recipes                  
│   ├── GJ281_recipes
│   │   ├── 20170216.recipes
│   │   └── 20170216.recipes.tmp   
│   ├── [Target]_recipes   
│   └── ... 
│
├── igr_pipe.py     
├── plp_main_step1.py
├── plp_main_step2.py
└── ...

  • Note that depending on how you setup your environment, line 10 in ./functions/run_IGRINS.py might need to be changed. The default is fh.write("source activate igr-pipe\n"), one might need to change source to conda, or change igr-pipe to their environment names.

    One or more .sh bash scripts are generated under ./run_sh/. Run them via bash GJ281_run_igrins1.sh.
    They contain commands to obtain the A and B separated spectra, e.g:

  python igr_pipe.py a0v-ab $UTDATE --basename-postfix="_A" --frac-slit="0,0.5"
  python igr_pipe.py a0v-ab $UTDATE --basename-postfix="_B" --frac-slit="0.5,1"
  python igr_pipe.py stellar-ab $UTDATE --basename-postfix="_A" --frac-slit="0,0.5"
  python igr_pipe.py stellar-ab $UTDATE --basename-postfix="_B" --frac-slit="0.5,1"

  • Tip: Open/login with muti-terminal and run bash GJ281_run_igrinsX.sh one by one in each terminal to save time.

Analyzing Multiple Observations Per Night (i.e., Multiple RVs)#

If you have intensely observed a target such that you have enough data to constitute multiple observations per night, you can change the reduction accordingly. In the ./tmp file with:

GJ 281, TAR, 60, 54, 600.000000, STELLAR_AB,60 61 62 63 64 65 66 67 68 69 70 71, A B B A A B B A A B B A

you can modify it to:

GJ 281, TAR, 60, 54, 600.000000, STELLAR_AB,60 61 62 63, A B B A
GJ 281, TAR, 64, 54, 600.000000, STELLAR_AB,64 65 66 67, A B B A
GJ 281, TAR, 68, 54, 600.000000, STELLAR_AB,68 69 70 71, A B B A

This would set up IGRINS RV to ultimately generate three RVs instead of one for the night.

  • Then you can run plp_main_step1.py normally.

Note that for the Muti-RVs Per Night analysis, the files under ./recipes/[target_name]_recipes/ are important for IGRINS RV to track the split you did in the later processing.

Getting the input data for IGRINS RV#

After seeing the IGRINS Pipeline Finished print out, we are ready for plp_main_step2.py or plp_main_step2_s.py.

  • plp_main_step2.py for normal usage

  • plp_main_step2_s.py for Muti-RVs Per Night usage

† Example command:

~$ python plp_main_step2.py GJ\ 281

Run step2 like step1, and you will get final spectra under ./final_A_B_spec/[target_name].
Now, move the entire folder plp-master/final_A_B_spec/[target_name] to ./igrins_rv-master/input/.

Voilà, you are almost ready to get RVs out from your data with IGRINS RV!
Next you need to PrepData Files (Step 0), and choose (see Setup: Stellar Templates) the stellar template you would like to use.