readme update + rm incorrect cont pos shift print - kll run

README.md

@@ -39,7 +39,7 @@ using conda
 ```bash
 conda create --name <env_name> --file requirements.txt
 ```
-2. Change fits files paths in ```run.py```
+2. Change fits files paths, desired processing steps and output directory in ```run.py```
 
 3. Execute ```run.py```
 

hrt_pipe.py

@@ -208,10 +208,12 @@ def phihrt_pipe(data_f,dark_f,flat_f,norm_f = True, clean_f = False, sigma = 59,
         first_cpos = cpos_arr[0]
         result = all(c_position == first_cpos for c_position in cpos_arr)
         if (result):
-            print("All the scans have the same continuum wavelength position, shifting all to 0th index if not already there")
+            print("All the scans have the same continuum wavelength position")
 
         else:
-            print("The scans have different continuum_wavelength postitions! \n Attempting to shift all to the 0th index")
+            print("The scans have different continuum_wavelength postitions! Please fix \n Ending Process")
+
+            exit()
 
         data = np.stack(data_arr, axis = -1)
         data = np.moveaxis(data, 0,-2) #so that it is [y,x,24,scans]

run.py

 from hrt_pipe import phihrt_pipe
 
 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'
+flatfield_fits_filename = '../fits_files/solo_L0_phi-hrt-flat_20210321T210847_V202106071514C_0163211100.fits'
 darkfield_fits_filename = '../fits_files/solo_L0_phi-fdt-ilam_20200228T155100_V202002281636_0022210004_000.fits'
 
 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
+                    clean_f = True, out_demod_file = True, out_dir = '../hrt_pipe_results/kll/', rte = 'False')
\ No newline at end of file