From 8b91290c543128e8cb06c9b69a11188b74451c7b Mon Sep 17 00:00:00 2001 From: Thibault Barnouin Date: Wed, 10 May 2023 13:27:08 +0200 Subject: [PATCH] debug for input target to None --- src/FOC_reduction.py | 40 +++++++++++++++++++++------------------- src/lib/query.py | 13 ++++++++----- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/src/FOC_reduction.py b/src/FOC_reduction.py index d93c1d9..d50016d 100755 --- a/src/FOC_reduction.py +++ b/src/FOC_reduction.py @@ -56,7 +56,7 @@ def main(target=None, proposal_id=None, infiles=None): # Final crop crop = False #Crop to desired ROI - final_display = False #Whether to display all polarization map outputs + final_display = True #Whether to display all polarization map outputs # Polarization map output SNRp_cut = 3. #P measurments with SNR>3 @@ -70,8 +70,10 @@ def main(target=None, proposal_id=None, infiles=None): # Get data from fits files and translate to flux in erg/cm²/s/Angstrom. if not infiles is None: products = [np.array([["/".join(filepath.split('/')[:-1]),filepath.split('/')[-1]] for filepath in infiles],dtype=str)] + if target is None: + target = input("Target name:\n>") else: - products = retrieve_products(target,proposal_id) + target, products = retrieve_products(target,proposal_id) data_folder = products[0][0,0] try: plots_folder = data_folder.replace("data","plots") @@ -92,7 +94,7 @@ def main(target=None, proposal_id=None, infiles=None): # Estimate error from data background, estimated from sub-image of desired sub_shape. background = None - data_array, error_array, headers, background = proj_red.get_error(data_array, headers, error_array, sub_type=error_sub_type, subtract_error=subtract_error, display=display_error, savename=figname+"_errors", plots_folder=plots_folder, return_background=True) + data_array, error_array, headers, background = proj_red.get_error(data_array, headers, error_array, sub_type=error_sub_type, subtract_error=subtract_error, display=display_error, savename="_".join([figname,"_errors"]), plots_folder=plots_folder, return_background=True) # Align and rescale images with oversampling. data_array, error_array, headers, data_mask = proj_red.align_data(data_array, headers, error_array=error_array, background=background, upsample_factor=10, ref_center=align_center, return_shifts=False) @@ -109,7 +111,7 @@ def main(target=None, proposal_id=None, infiles=None): #Plot array for checking output if display_data and px_scale.lower() not in ['full','integrate']: - proj_plots.plot_obs(data_array, headers, vmin=data_array[data_array>0.].min()*headers[0]['photflam'], vmax=data_array[data_array>0.].max()*headers[0]['photflam'], savename=figname+"_center_"+align_center, plots_folder=plots_folder) + proj_plots.plot_obs(data_array, headers, vmin=data_array[data_array>0.].min()*headers[0]['photflam'], vmax=data_array[data_array>0.].max()*headers[0]['photflam'], savename="_".join([figname,"center",align_center]), plots_folder=plots_folder) background = np.array([np.array(bkg).reshape(1,1) for bkg in background]) background_error = np.array([np.array(np.sqrt((bkg-background[np.array([h['filtnam1']==head['filtnam1'] for h in headers],dtype=bool)].mean())**2/np.sum([h['filtnam1']==head['filtnam1'] for h in headers]))).reshape(1,1) for bkg,head in zip(background,headers)]) @@ -135,16 +137,16 @@ def main(target=None, proposal_id=None, infiles=None): ## Step 4: # Save image to FITS. - Stokes_test = proj_fits.save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P, s_P_P, PA, s_PA, s_PA_P, headers, data_mask, figname+figtype, data_folder=data_folder, return_hdul=True) + Stokes_test = proj_fits.save_Stokes(I_stokes, Q_stokes, U_stokes, Stokes_cov, P, debiased_P, s_P, s_P_P, PA, s_PA, s_PA_P, headers, data_mask, "_".join([figname,figtype]), data_folder=data_folder, return_hdul=True) data_mask = Stokes_test[-1].data.astype(bool) ## Step 5: # crop to desired region of interest (roi) if crop: - figtype += "_crop" + figtype += "crop" stokescrop = proj_plots.crop_Stokes(deepcopy(Stokes_test)) stokescrop.crop() - stokescrop.writeto(data_folder+figname+figtype+".fits") + stokescrop.writeto("/".join([data_folder,"_".join([figname,figtype+".fits"])])) Stokes_test, data_mask = stokescrop.hdul_crop, stokescrop.data_mask print("F_int({0:.0f} Angs) = ({1} ± {2})e{3} ergs.cm^-2.s^-1.Angs^-1".format(headers[0]['photplam'],*proj_plots.sci_not(Stokes_test[0].data[data_mask].sum()*headers[0]['photflam'],np.sqrt(Stokes_test[3].data[0,0][data_mask].sum())*headers[0]['photflam'],2,out=int))) @@ -156,17 +158,17 @@ def main(target=None, proposal_id=None, infiles=None): print("PA_bkg = {0:.1f} ± {1:.1f} °".format(PA_bkg[0,0],np.ceil(s_PA_bkg[0,0]*10.)/10.)) # Plot polarization map (Background is either total Flux, Polarization degree or Polarization degree error). if px_scale.lower() not in ['full','integrate'] and final_display: - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype, plots_folder=plots_folder) - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_I", plots_folder=plots_folder, display='Intensity') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_P_flux", plots_folder=plots_folder, display='Pol_Flux') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_P", plots_folder=plots_folder, display='Pol_deg') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_PA", plots_folder=plots_folder, display='Pol_ang') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_I_err", plots_folder=plots_folder, display='I_err') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_P_err", plots_folder=plots_folder, display='Pol_deg_err') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_SNRi", plots_folder=plots_folder, display='SNRi') - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename=figname+figtype+"_SNRp", plots_folder=plots_folder, display='SNRp') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype]), plots_folder=plots_folder) + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"I"]), plots_folder=plots_folder, display='Intensity') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"P_flux"]), plots_folder=plots_folder, display='Pol_Flux') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"P"]), plots_folder=plots_folder, display='Pol_deg') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"PA"]), plots_folder=plots_folder, display='Pol_ang') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"I_err"]), plots_folder=plots_folder, display='I_err') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"P_err"]), plots_folder=plots_folder, display='Pol_deg_err') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"SNRi"]), plots_folder=plots_folder, display='SNRi') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, step_vec=step_vec, vec_scale=vec_scale, savename="_".join([figname,figtype,"SNRp"]), plots_folder=plots_folder, display='SNRp') elif final_display: - proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename=figname+figtype, plots_folder=plots_folder, display='integrate') + proj_plots.polarization_map(deepcopy(Stokes_test), data_mask, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut, savename="_".join([figname,figtype]), plots_folder=plots_folder, display='integrate') elif px_scale.lower() not in ['full', 'integrate']: pol_map = proj_plots.pol_map(Stokes_test, SNRp_cut=SNRp_cut, SNRi_cut=SNRi_cut) @@ -184,5 +186,5 @@ if __name__ == "__main__": parser.add_argument('-f','--files', metavar='path', required=False, nargs='*', help='the full or relative path to the data products', default=None) args = parser.parse_args() - prodpaths = main(target=args.target, proposal_id=args.proposal_id, infiles=args.files) - print(prodpaths) \ No newline at end of file + exitcode = main(target=args.target, proposal_id=args.proposal_id, infiles=args.files) + print("Finished with ExitCode: ",exitcode) \ No newline at end of file diff --git a/src/lib/query.py b/src/lib/query.py index d0133ca..24e86ff 100644 --- a/src/lib/query.py +++ b/src/lib/query.py @@ -5,7 +5,7 @@ from astropy.table import unique import numpy as np -def get_product_list(target, proposal_id=None): +def get_product_list(target=None, proposal_id=None): """ Retrieve products list for a given target from the MAST archive """ @@ -37,6 +37,9 @@ def get_product_list(target, proposal_id=None): 'Proposal ID', 'PI last name'] + if target is None: + target = input("Target name:\n>") + # Use query_object method to resolve the object name into coordinates results = mission.query_object( target, @@ -97,14 +100,14 @@ def get_product_list(target, proposal_id=None): calib_level=[2], description="DADS C0F file - Calibrated exposure WFPC/WFPC2/FOC/FOS/GHRS/HSP") - return products + return target, products -def retrieve_products(target, proposal_id=None): +def retrieve_products(target=None, proposal_id=None): """ Given a target name and a proposal_id, create the local directories and retrieve the fits files from the MAST Archive """ - products = get_product_list(target=target,proposal_id=proposal_id) + target, products = get_product_list(target=target,proposal_id=proposal_id) prodpaths = [] data_dir = path_join("../data", target) out = "" @@ -123,7 +126,7 @@ def retrieve_products(target, proposal_id=None): filepaths.append([obs_dir,file]) prodpaths.append(np.array(filepaths,dtype=str)) - return prodpaths + return target, prodpaths if __name__ == "__main__":