cfitsio reads different order than astropy

hrt_pipe.py

@@ -76,7 +76,7 @@ def demod_hrt(data,pmp_temp):
 def phihrt_pipe(data_f, dark_f = '', flat_f = '', scale_data = True, bit_flat = True, norm_f = True, clean_f = False, 
                 sigma = 59, flat_states = 24, prefilter_f = None,flat_c = True, dark_c = True, fs_c = True,
                 demod = True, norm_stokes = True, out_dir = './',  out_demod_file = False,  out_demod_filename = None,
-                ItoQUV = False, ctalk_params = None, rte = False, out_rte_filename = None, pmilos = True):
+                ItoQUV = False, ctalk_params = None, rte = False, out_rte_filename = None, p_milos = True):
 
     '''
     PHI-HRT data reduction pipeline
@@ -148,7 +148,7 @@ def phihrt_pipe(data_f, dark_f = '', flat_f = '', scale_data = True, bit_flat =
         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
-    pmilos: bool, DEFAULT = True
+    p_milos: bool, DEFAULT = True
         if True, will execute the RTE inversion using the parallel version of the CMILOS code on 16 processors
     
     Returns
@@ -876,7 +876,7 @@ def phihrt_pipe(data_f, dark_f = '', flat_f = '', scale_data = True, bit_flat =
 
     if rte == 'RTE' or rte == 'CE' or rte == 'CE+RTE':
 
-        if pmilos:
+        if p_milos:
 
             try:
                 pmilos(data_f, wve_axis_arr, data_shape, cpos_arr, data, rte, field_stop, start_row, start_col, out_rte_filename, out_dir)

run.py

@@ -50,7 +50,7 @@ out_names = ['0024160031000_test_rte']#, '0024160032000_noflat', '0024160033000_
 phihrt_pipe(sciencedata_fits_filenames, flat_f = flatfield_fits_filename, dark_f = darkfield_fits_filename, scale_data = False, 
             bit_flat = True, norm_f = True, clean_f = False, sigma = 59, flat_states = 24, norm_stokes = True, prefilter_f = None, 
             dark_c = True, flat_c = True, fs_c = True, demod = True, ctalk_params = c_talk_params, ItoQUV = False, out_demod_file = True, 
-            out_demod_filename = out_names, out_dir = '/data/slam/home/sinjan/hrt_pipe_results/april_2020/', rte = 'RTE', out_rte_filename='', pmilos = False) 
+            out_demod_filename = out_names, out_dir = '/data/slam/home/sinjan/hrt_pipe_results/april_2020_pmilos/', rte = 'RTE', out_rte_filename=None, p_milos = True) 
 """
  Input Parameters:
 ----------

utils.py

@@ -312,13 +312,15 @@ def pmilos(data_f, wve_axis_arr, data_shape, cpos_arr, data, rte, field_stop, st
 
         #write wavelengths to wavelength.fits file for the settings
 
-        wave_input = np.zeros((6,2))
-        wave_input[:,0] = int(1)
-        wave_input[:,1] = wave_axis
+        wave_input = np.zeros((2,6)) #cfitsio reads dimensions in opposite order
+        wave_input[0,:] = 1
+        wave_input[1,:] = wave_axis
+
+        print(wave_axis)
 
         hdr = fits.Header()
 
-        primary_hdu = fits.PrimaryH0DU(wave_input, header = hdr)
+        primary_hdu = fits.PrimaryHDU(wave_input, header = hdr)
         hdul = fits.HDUList([primary_hdu])
         hdul.writeto(f'./P-MILOS/run/wavelength_tmp.fits', overwrite=True)
 
@@ -342,26 +344,32 @@ def pmilos(data_f, wve_axis_arr, data_shape, cpos_arr, data, rte, field_stop, st
 
         cwd = os.getcwd()
         os.chdir("./P-MILOS/run/")
-        cmd = "mpiexec -np 16 ../pmilos.x pmilos.minit" #PMILOS_LOC+"./milos"
+        cmd = "mpiexec -np 10 ../pmilos.x pmilos.minit" #PMILOS_LOC+"./milos"
 
         if rte == 'RTE':
-            cmd = "mpiexec -np 16 ../pmilos.x pmilos.minit"
+            cmd = "mpiexec -np 10 ../pmilos.x pmilos.minit"
             
         if rte == 'CE':
-            cmd = "mpiexec -np 16 ../pmilos.x pmilos_ce.minit"
+            cmd = "mpiexec -np 10 ../pmilos.x pmilos_ce.minit"
 
         if rte == 'CE+RTE':
             print("CE+RTE not possible on PMILOS, performing RTE instead")
-            cmd = "mpiexec -np 16 ../pmilos.x pmilos.minit"
+            cmd = "mpiexec -np 10 ../pmilos.x pmilos.minit"
 
         rte_on = subprocess.call(cmd,shell=True)
 
         os.chdir(cwd)
 
-        with fits.open('./P-MILOS/run/results/inv_input_tmp_mod.fits') as hdu_list:
+        if rte == 'CE':
+            out_file = 'inv_input_tmp_mod_ce.fits'
+
+        else:
+            out_file = 'inv_input_tmp_mod.fits'
+
+        with fits.open(f'./P-MILOS/run/results/{out_file}') as hdu_list:
             result = hdu_list[0].data
 
-        del_dummy = subprocess.call("rm ./P-MILOS/run/results/inv_input_tmp_mod.fits",shell=True) #must delete the output file
+        del_dummy = subprocess.call(f"rm ./P-MILOS/run/results/{out_file}.fits",shell=True) #must delete the output file
       
         #result has dimensions [rows,cols,13]