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Commit fcac44cb authored by jonas's avatar jonas
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transposing correct way fixes cmilos-fits

parent 5d76c549
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hrt_pipe_sub.py
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......@@ -465,11 +465,11 @@ def cmilos_fits(data_f, hdr_arr, wve_axis_arr, data_shape, cpos_arr, data, rte,
hdr['LAMBDA5'] = wave_axis[5]
#write out data to temp fits for cmilos-fits input
input_arr = np.transpose(sdata, axes = (3,2,1,0)) #must transpose due to cfitsio
input_arr = np.transpose(sdata, axes = (3,2,0,1)) #must transpose due to cfitsio
hdu1 = fits.PrimaryHDU(data=input_arr, header = hdr)
#mask
mask = np.ones((sdata.shape[1],sdata.shape[0])) #change this for fdt
mask = np.ones((sdata.shape[0],sdata.shape[1])) #change this for fdt
hdu2 = fits.ImageHDU(data=mask)
#write out to temp fits
......@@ -498,43 +498,29 @@ def cmilos_fits(data_f, hdr_arr, wve_axis_arr, data_shape, cpos_arr, data, rte,
#print(del_dummy)
with fits.open(out_dir+'temp_cmilos_io.fits') as hdu_list:
print(hdu_list[0].data.shape)
print(hdu_list[1].data.shape)
print(np.mean(hdu_list[0].data-input_arr))
rte_out = hdu_list[0].data
#hdu_list.writeto(out_dir+'rte_out.fits', overwrite=True)
del input_arr
# res = np.loadtxt('dummy_out.txt')
# npixels = res.shape[0]/12.
# #print(npixels)
# #print(npixels/x)
# result = np.zeros((12,y*x)).astype(float)
# rte_invs = np.zeros((12,y,x)).astype(float)
# for i in range(y*x):
# result[:,i] = res[i*12:(i+1)*12]
# result = result.reshape(12,y,x)
# result = np.einsum('ijk->ikj', result)
# rte_invs = result
# del result
# rte_invs_noth = np.copy(rte_invs)
"""
From 0 to 11
Counter (PX Id)
Iterations
Strength
Inclination
Azimuth
Eta0 parameter
Doppler width
Damping
Damping/aa
Los velocity
alfa? Counter PID?
Constant source function
Slope source function
Minimum chisqr value
"""
"""
Direct from cmilos-fits/milos.c
inv->iter = malloc(npix*sizeof(int));
inv->B = malloc(npix*sizeof(double));
inv->gm = malloc(npix*sizeof(double));
......@@ -550,64 +536,58 @@ def cmilos_fits(data_f, hdr_arr, wve_axis_arr, data_shape, cpos_arr, data, rte,
"""
# noise_in_V = np.mean(data[:,:,3,cpos_arr[0],:])
# low_values_flags = np.max(np.abs(data[:,:,3,:,scan]),axis=-1) < noise_in_V # Where values are low
"""
noise_in_V = np.mean(data[:,:,3,cpos_arr[0],:])
low_values_flags = np.max(np.abs(data[:,:,3,:,scan]),axis=-1) < noise_in_V # Where values are low
# rte_invs[2,low_values_flags] = 0
# rte_invs[3,low_values_flags] = 0
# rte_invs[4,low_values_flags] = 0
rte_out[2,low_values_flags] = 0 #not sure about 2,3,4 indexing here
rte_out[3,low_values_flags] = 0
rte_out[4,low_values_flags] = 0
"""
rte_data_products = np.zeros((6,rte_out.shape[1],rte_out.shape[2]))
# #np.savez_compressed(out_dir+'_RTE', rte_invs=rte_invs, rte_invs_noth=rte_invs_noth)
# del_dummy = subprocess.call("rm dummy_out.txt",shell=True)
# #print(del_dummy)
rte_data_products[0,:,:] = rte_out[9,:,:] + rte_out[10,:,:] #continuum
rte_data_products[1,:,:] = rte_out[1,:,:] #b mag strength
rte_data_products[2,:,:] = rte_out[2,:,:] #inclination
rte_data_products[3,:,:] = rte_out[3,:,:] #azimuth
rte_data_products[4,:,:] = rte_out[7,:,:] #vlos
rte_data_products[5,:,:] = rte_out[1,:,:]*np.cos(rte_out[2,:,:]*np.pi/180.) #blos
rte_data_products *= field_stop[np.newaxis,start_row:start_row + data.shape[0],start_col:start_col + data.shape[1]] #field stop, set outside to 0
if out_rte_filename is None:
filename_root = str(file_path.split('.fits')[0][-10:])
else:
if isinstance(out_rte_filename, list):
filename_root = out_rte_filename[scan]
elif isinstance(out_rte_filename, str):
filename_root = out_rte_filename
else:
filename_root = str(file_path.split('.fits')[0][-10:])
print(f"out_rte_filename neither string nor list, reverting to default: {filename_root}")
with fits.open(file_path) as hdu_list:
hdu_list[0].hdr = hdr
hdu_list[0].data = rte_data_products
hdu_list.writeto(out_dir+filename_root+'_rte_data_products.fits', overwrite=True)
with fits.open(file_path) as hdu_list:
hdu_list[0].hdr = hdr
hdu_list[0].data = rte_data_products[5,:,:]
hdu_list.writeto(out_dir+filename_root+'_blos_rte.fits', overwrite=True)
# rte_data_products = np.zeros((6,rte_invs_noth.shape[1],rte_invs_noth.shape[2]))
# rte_data_products[0,:,:] = rte_invs_noth[9,:,:] + rte_invs_noth[10,:,:] #continuum
# rte_data_products[1,:,:] = rte_invs_noth[2,:,:] #b mag strength
# rte_data_products[2,:,:] = rte_invs_noth[3,:,:] #inclination
# rte_data_products[3,:,:] = rte_invs_noth[4,:,:] #azimuth
# rte_data_products[4,:,:] = rte_invs_noth[8,:,:] #vlos
# rte_data_products[5,:,:] = rte_invs_noth[2,:,:]*np.cos(rte_invs_noth[3,:,:]*np.pi/180.) #blos
# rte_data_products *= field_stop[np.newaxis,start_row:start_row + data.shape[0],start_col:start_col + data.shape[1]] #field stop, set outside to 0
# if out_rte_filename is None:
# filename_root = str(file_path.split('.fits')[0][-10:])
# else:
# if isinstance(out_rte_filename, list):
# filename_root = out_rte_filename[scan]
# elif isinstance(out_rte_filename, str):
# filename_root = out_rte_filename
# else:
# filename_root = str(file_path.split('.fits')[0][-10:])
# print(f"out_rte_filename neither string nor list, reverting to default: {filename_root}")
# with fits.open(file_path) as hdu_list:
# hdu_list[0].hdr = hdr
# hdu_list[0].data = rte_data_products
# hdu_list.writeto(out_dir+filename_root+'_rte_data_products.fits', overwrite=True)
# with fits.open(file_path) as hdu_list:
# hdu_list[0].hdr = hdr
# hdu_list[0].data = rte_data_products[5,:,:]
# hdu_list.writeto(out_dir+filename_root+'_blos_rte.fits', overwrite=True)
# with fits.open(file_path) as hdu_list:
# hdu_list[0].hdr = hdr
# hdu_list[0].data = rte_data_products[4,:,:]
# hdu_list.writeto(out_dir+filename_root+'_vlos_rte.fits', overwrite=True)
# with fits.open(file_path) as hdu_list:
# hdu_list[0].hdr = hdr
# hdu_list[0].data = rte_data_products[0,:,:]
# hdu_list.writeto(out_dir+filename_root+'_Icont_rte.fits', overwrite=True)
with fits.open(file_path) as hdu_list:
hdu_list[0].hdr = hdr
hdu_list[0].data = rte_data_products[4,:,:]
hdu_list.writeto(out_dir+filename_root+'_vlos_rte.fits', overwrite=True)
with fits.open(file_path) as hdu_list:
hdu_list[0].hdr = hdr
hdu_list[0].data = rte_data_products[0,:,:]
hdu_list.writeto(out_dir+filename_root+'_Icont_rte.fits', overwrite=True)
printc('--------------------------------------------------------------',bcolors.OKGREEN)
printc(f"------------- CMILOS RTE Run Time: {np.round(time.time() - start_time,3)} seconds ",bcolors.OKGREEN)
......
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