clean run.py

hrt_pipe.py

@@ -80,21 +80,23 @@ def phihrt_pipe(data_f,dark_f,flat_f,norm_f = True, clean_f = False, sigma = 59,
     '''
     PHI-HRT data reduction pipeline
     1. read in science data (+scaling) open path option + open for several scans at once
-    2. read in flat field - just one, so any averaging must be done before
-    3. option to clean flat field with unsharp masking
-    4. read in dark field
-    5. apply dark field
+    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
     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
+        a) option to output demod to fits file
     12. normalise to quiet sun
     13. calibration
         a) ghost correction - not implemented yet
         b) cross talk correction - not implemented yet
     14. rte inversion with cmilos
+        a) output rte data products to fits file
 
     Parameters
     ----------
@@ -133,10 +135,8 @@ def phihrt_pipe(data_f,dark_f,flat_f,norm_f = True, clean_f = False, sigma = 59,
         correct the ghost in bottom left corner
     ItoQUV: bool, DEFAULT: False 
         apply I -> Q,U,V correction
-    rte: bool, DEFAULT: False 
-        invert using cmilos
-    out_rte_file: bool, DEFAULT: False
-        output of rte result to fits file
+    rte: str, DEFAULT: False 
+        invert using cmilos, options: 'RTE' for Milne Eddington Inversion, 'CE' for Classical Estimates, 'CE+RTE' for combined
     
     Returns
     -------

run.py

 from hrt_pipe import phihrt_pipe
 
-sciencedata_fits_filenames = ['solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.fits']
-flatfield_fits_filename = 'solo_L0_phi-hrt-flat_0667134081_V202103221851C_0162201100.fits'
-darkfield_fits_filename = 'solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
+sciencedata_fits_filenames = ['../fits_files/solo_L0_phi-hrt-ilam_0667414748_V202103221851C_0142230201.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'
 
-folder = '../fits_files/'
-
-if folder != None:
-
-    def add_folder_to_file_path(folder, filename_list):
-        return [folder + i for i in filename_list]
-
-    sciencedata_fits_filenames = add_folder_to_file_path(folder, sciencedata_fits_filenames)
-    flatfield_fits_filename = folder + flatfield_fits_filename
-    darkfield_fits_filename = folder + darkfield_fits_filename
-
-data = phihrt_pipe(sciencedata_fits_filenames, darkfield_fits_filename, flatfield_fits_filename, norm_stokes = True, clean_f = True, out_demod_file = True, out_dir = './', rte = 'RTE')
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+data = phihrt_pipe(sciencedata_fits_filenames, darkfield_fits_filename, flatfield_fits_filename, norm_stokes = True, 
+                    clean_f = True, out_demod_file = True, out_dir = './', rte = 'RTE')
\ No newline at end of file