rm run.py from tracking

run.py

-from hrt_pipe import phihrt_pipe
-import numpy as np
-
-sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_20210421T120003_V202106080929C_0144210101.fits', 'solo_L0_phi-hrt-ilam_20210424T120003_V202106141014C_0144240101.fits',
-  'solo_L0_phi-hrt-ilam_20210425T120002_V202106141020C_0144250101.fits', 'solo_L0_phi-hrt-ilam_20210426T120002_V202106162118C_0144260101.fits',
-  'solo_L0_phi-hrt-ilam_20210427T120002_V202106162052C_0144270101.fits', 'solo_L0_phi-hrt-ilam_20210427T120002_V202106171444C_0144270101.fits', 
-  'solo_L0_phi-hrt-ilam_20210427T120002_V202106171517C_0144270101.fits'] 
-
-flatfield_fits_filename = '../fits_files/solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
-darkfield_fits_filename = '../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
-
-sciencedata_fits_filenames = ['../fits_files/' + i for i in sciencedata_fits_filenames]
-
-prefilter_f = '../fits_files/fitted_prefilter.fits'
-
-#######################################################################################################
-#
-# The fitted prefilter can be downloaded from: 
-# http://www2.mps.mpg.de/data/outgoing/hirzberger/solo/RSCW3_helioseismology_test/fitted_prefilter.fits
-# OR from BOB: /www/docs/data/outgoing/hirzberger/solo/RSCW3_helioseismology_test/fitted_prefilter.fits
-#
-#######################################################################################################
-
-c_talk_params = np.zeros((2,3))
-
-q_slope = 0.0038
-u_slope = -0.0077
-v_slope = -0.0009
-
-q_int = -0.0056 #the offset, normalised to I_c
-u_int = 0.0031
-v_int = -0.0002 
-
-c_talk_params[0,0] = q_slope
-c_talk_params[0,1] = u_slope
-c_talk_params[0,2] = v_slope
-
-c_talk_params[1,0] = q_int
-c_talk_params[1,1] = u_int
-c_talk_params[1,2] = v_int
-
-phihrt_pipe(sciencedata_fits_filenames, flat_f = flatfield_fits_filename, dark_f = darkfield_fits_filename, scale_data = True, norm_f = True, clean_f = True, 
-            sigma = 59, flat_states = 24, norm_stokes = True, prefilter_f = prefilter_f, dark_c = True, flat_c = True, 
-            fs_c = True, demod = True, ctalk_params = c_talk_params, ItoQUV = True, out_demod_file = True, 
-            out_dir = '/path/to/files', rte = 'RTE', out_rte_filename='your_desired_rte_filename') 
-"""
- Input Parameters:
-----------
-data_f : list or string
-    list containing paths to fits files of the raw HRT data OR string of path to one file  
-
-dark_f : string, DEFAULT ''
-    Fits file of a dark file (ONLY ONE FILE)
-
-flat_f : string, DEFAULT ''
-    Fits file of a HRT flatfield (ONLY ONE FILE)
-
-** Options:
-read_scale_data: bool, DEFAULT True
-    reads in science data and performs appropriate scaling
-
-norm_f: bool, DEFAULT: True
-    to normalise the flat fields before applying
-
-clean_f: bool, DEFAULT: False
-    clean the flat field with unsharp masking
-
-sigma: int, DEFAULT: 59
-    sigma of the gaussian convolution used for unsharp masking if clean_f == True 
-
-flat_states: int, DEFAULT: 24
-    Number of flat fields to be applied, options are 4 (one for each pol state), 6 (one for each wavelength), 24 (one for each image)
-
-prefilter_f: str, DEFAULT None
-    file path location to prefilter fits file, apply prefilter correction
-
-flat_c: bool, DEFAULT: True
-    apply flat field correction
-
-dark_c: bool, DEFAULT: True
-    apply dark field correction
-
-field_stop: bool, DEFAULT True
-    apply HRT field stop
-
-demod: bool, DEFAULT: True
-    apply demodulate to the stokes
-
-norm_stokes: bool, DEFAULT: True
-    normalise the stokes vector to the quiet sun (I_continuum)
-
-out_dir : string, DEFUALT: './'
-    directory for the output files
-
-out_demod_file: bool, DEFAULT: False
-    output file with the stokes vectors to fits file
-
-correct_ghost: bool, DEFAULT: False 
-    correct the ghost in bottom left corner
-
-ItoQUV: bool, DEFAULT: False 
-    apply I -> Q,U,V correction
-
-ctalk_params: numpy arr, DEFAULT: None 
-    cross talk parameters for ItoQUV, (2,3) numpy array required: first axis: Slope, Offset (Normalised to I_c) - second axis:  Q,U,V
-
-rte: str, DEFAULT: False 
-    invert using cmilos, options: 'RTE' for Milne Eddington Inversion, 'CE' for Classical Estimates, 'CE+RTE' for combined
-
-out_rte_filename: str, DEFAULT = ''
-    if '', takes last 10 characters of input scan filename (assumes its a DID), change if want other name
-"""
\ No newline at end of file