Repository Structure

In the package

PACMAN/src/pacman

All code PACMAN needs to run and templates for the pcf and fit_par files are stored here. The scripts here use other python code from PACMAN/src/pacman/lib.
- PACMAN/src/pacman/lib
This directory contains auxiliary scripts for the stages. E.g., PACMAN/src/pacman/lib/plots.py creates and saves plots.
- PACMAN/src/pacman/data
  - PACMAN/src/pacman/data/bandpass
  This directory contains the throughput for the G102 and the G141 grisms. These files will be used in Stage 03 to create the reference spectrum.
  - PACMAN/src/pacman/data/flats
  The flats (for the G102 and G141 grisms) are used to find the locations of bad pixels.
  - PACMAN/src/pacman/data/stellar_models
  This directory tells PACMAN which stellar models are available to download. PACMAN can download three different stellar models: Kurucz stellar models 1993, Castelli and Kurucz stellar models 2004 and Phoenix models by Allard and collaborators. These models will be used in Stage 03 to create the reference spectrum. More on this at the walkthrough of Stage 03 using GJ1214 data as an example.
  - PACMAN/src/pacman/data/pacman_run_files
  Note
  
  These three files have to be copied over to the run directory where the analysis will be run from! You find more information about that in Before Running.
  - -> PACMAN/src/pacman/data/pacman_run_files/run_pacman.py
  This python script runs PACMAN. If the user did not install PACMAN properly as explained in the installation walkthrough (not recommended) they might have to add a path to the sys.path.append pointing to the PACMAN directory:
```
sys.path.append('/home/zieba/Desktop/Projects/Open_source/PACMAN/')
```
  The path in sys.path.append has to be changed to the location of PACMAN on the user’s device.
  
  Note
  
  The path should point to /PACMAN/ and not to /PACMAN/src/pacman/.
  - -> PACMAN/src/pacman/data/pacman_run_files/obs_par.pcf
  The PACMAN control file (pcf): the user sets parameters related to the analysis. E.g., which plots should be saved, the path to the data directory and others. A thorough explanation of all the parameters in the pcf can be found on the PCF page.
  - -> PACMAN/src/pacman/data/pacman_run_files/fit_par.txt
  The fit_par.txt file is used in Stage 30 to fit the light curve. The user defines here which fit parameters should be fixed, shared across visits, and sets other information like priors.

Nomenclature

An example for a directory structure:

user
└── Desktop
    └── Projects
        └── Observations
            └── Hubble
                └── GJ1214_13021  (="run directory")
                    ├── pacman_run_files
                    │   ├── run_pacman.py
                    │   ├── obs_par.pcf
                    │   └── fit_par.txt
                    ├── stage00
                    ├── stage01
                    ├── stage02
                    ├── stage03
                    ├── stage10
                    ├── stage20
                    ├── stage21
                    └── stage30
        └── Data
            └── GJ1214_Hubble13021  (="data directory")
                ├── ibxy06d0q_ima.fits
                ├── ...
                └── ibxy07ryq_ima.fits

run directory:

Example: /home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021.

This is the top-level directory for one PACMAN analysis. It contains the pacman_run_files directory and one output directory for each PACMAN stage.
pacman_run_files directory:

Example: /home/zieba/Desktop/Projects/Observations/Hubble/GJ1214_13021/pacman_run_files.

This directory contains the files used to configure and start a PACMAN run:
- run_pacman.py
- obs_par.pcf
- fit_par.txt
To run PACMAN, navigate into this directory and execute:
```
python run_pacman.py
```
The settings in obs_par.pcf and fit_par.txt are read from this directory.
stage directories:

PACMAN stores outputs in stage-specific directories:
- stage00
- stage01
- stage02
- stage03
- stage10
- stage20
- stage21
- stage30
Each stage directory can contain one or more timestamped run directories. The name of each run directory is a combination of the stage name and the time at which the stage was started:
```
s00_run_YYYY-MM-DD_HH-MM-SS
```
For example:
```
stage00
└── s00_run_2022-03-04_15-10-29
```
When a later stage is run, by default, PACMAN uses the most recent run directory from the previous stage unless the user specifies a different input path.
data directory:

Example: /home/zieba/Desktop/Data/GJ1214_Hubble13021.

This directory contains the FITS files that will be reduced and analyzed.
pipeline directory:

Example: /home/zieba/Desktop/Projects/Open_Source/PACMAN/src.

This is the installed PACMAN source code directory. Users normally do not need to edit files in this directory during an analysis.