readme init

README.md

-# HRT PIPELINE
+# SO/PHI-HRT PIPELINE
 
-# 
+Reduction software for SO/PHI-HRT instrument on the ESA Solar Orbiter
+## PHI-HRT data reduction
+1. read in science data (+scaling) open path option + open for several scans at once
+2. read in flat field (+scaling)- just accepts one flat field fits file
+3. read in dark field (+scaling)
+4. apply dark field
+5. option to clean flat field with unsharp masking (Stokes V only)
+6. normalise flat field
+7. apply flat field
+8. prefilter correction - **not implemented yet**
+9. read in field stop
+10. apply field stop
+11. demodulate with const demod matrix <br />
+        a) option to output demod to fits file <br />
+12. normalise to quiet sun
+13. calibration <br />
+        a) ghost correction - **not implemented yet** <br />
+        b) cross talk correction - **not implemented yet** <br />
+14. rte inversion with cmilos <br />
+        a) output rte data products to fits file <br />
+## SETUP
 
+1. Compile milos:
 
-Credit: SPGPylibs for the foundation, from which it was expanded upon
-        Especially the section for the RTE inversion with cmilos
+```bash
+make clean
+make
+```
+        
+2. Setup virtual environment from requirements.txt
+
+using pip
+```bash
+pip install -r requirements.txt
+```
+using conda
+```bash
+conda create --name <env_name> --file requirements.txt
+```
+2. Change fits files paths in ```run.py```
+
+3. Execute ```run.py```
+
+```bash
+python run.py
+```
+
+Authors: <br />
+
+Jonas Sinjan - Max Planck Institute for Solar System Research, Goettingen Germany
+
+Credit: <br />
+
+SPGPylibs for the foundation, from which it was expanded upon
\ No newline at end of file

hrt_pipe.py

@@ -2,10 +2,8 @@ from re import L
 import numpy as np 
 import os.path
 from astropy.io import fits
-import random, statistics
 import subprocess
 from scipy.ndimage import gaussian_filter
-import matplotlib.pyplot as plt
 import time
 
 from utils import *