diff --git a/README.md b/README.md index 811ca90..32318c3 100644 --- a/README.md +++ b/README.md @@ -40,8 +40,9 @@ If you use this software, or part it, please reference the code from the Astroph - [Vigan & N'Diaye, 2018, ascl:1806.003](https://ui.adsabs.harvard.edu/abs/2018ascl.soft06003V/abstract) -Authors -------- +Authors and contributors +------------------------ - Arthur Vigan, [arthur.vigan@lam.fr](mailto:arthur.vigan@lam.fr) - Mamadou N'Diaye, [mamadou.ndiaye@oca.eu](mailto:mamadou.ndiaye@oca.eu) +- Raphaël Pourcelot, [raphael.pourcelot@oca.eu](mailto:raphael.pourcelot@oca.eu) diff --git a/examples/advanced_pyzelda_analysis.py b/examples/advanced_pyzelda_analysis.py new file mode 100644 index 0000000..093ab76 --- /dev/null +++ b/examples/advanced_pyzelda_analysis.py @@ -0,0 +1,101 @@ +import matplotlib.pyplot as plt +import matplotlib.gridspec as gridspec +import numpy as np + +import pyzelda.zelda as zelda +import pyzelda.ztools as ztools +import pyzelda.utils.aperture as aperture +import pyzelda.utils.zernike as zernike +import pyzelda.utils.mft as mft + +from pathlib import Path + +#%% parameters + +# path = Path('/Users/mndiaye/Dropbox/python/zelda/pyZELDA/') +path = Path('/Users/avigan/Work/GitHub/pyZELDA/data/') +# path = Path('D:/Programmes/GitHub/pyZELDA/') + +wave = 1.642e-6 + +z = zelda.Sensor('CLASSIC') + +#%%################################ +# Creation of apodized pupil data # +################################### + +# Aberration: astigmatism +basis = np.nan_to_num(zernike.zernike_basis(nterms=5, npix=z.pupil_diameter))*1e-9 +aberration = 20*basis[4] +gaussian_std = 1 + +# Gaussian apodized entrance pupil +x_vals = np.arange(z.pupil_diameter) +xx, yy = np.meshgrid(x_vals, x_vals) +cx, cy = x_vals[z.pupil_diameter//2], x_vals[z.pupil_diameter//2] +r = np.sqrt((xx-cx)**2+(yy-cy)**2) +r = r/r[0, z.pupil_diameter//2] + +apodizer = np.exp(-(r**2)/2/gaussian_std**2) + +#%%############################# +# Simulation of the wavefront. # +################################ + +# Clear pupil image +clear_pupil = abs(apodizer)**2 + +zelda_pupil = ztools.propagate_opd_map(aberration, z.mask_diameter, z.mask_depth, z.mask_substrate, + z.mask_Fratio, z.pupil_diameter, apodizer, wave) + +#%%######################### +# Wavefront reconstruction # +############################ + +# Standard analysis +z_opd_standard = z.analyze(clear_pupil, zelda_pupil, wave) + +# Advanced analysis +pupil_roi = aperture.disc(z.pupil_diameter, z.pupil_diameter, diameter=True, cpix=False) +z_opd_advanced = z.analyze(clear_pupil, zelda_pupil, wave, + use_arbitrary_amplitude=True, + refwave_from_clear=True, + cpix=False, pupil_roi=pupil_roi) + +#%% plot + +fig = plt.figure(0, figsize=(24, 4)) +plt.clf() + +gs = gridspec.GridSpec(ncols=7, nrows=1, figure=fig, width_ratios=[.1,1,1,1,1,1,.1]) + +ax = fig.add_subplot(gs[0,1]) +mappable = ax.imshow(clear_pupil, aspect='equal', vmin=0, vmax=1) +ax.set_title('Clear pupil') + +ax = fig.add_subplot(gs[0,0]) +cbar1 = fig.colorbar(mappable=mappable, cax=ax) +cbar1.set_label('Normalized intensity') + +ax = fig.add_subplot(gs[0,2]) +ax.imshow(zelda_pupil, aspect='equal', vmin=0, vmax=1) +ax.set_title('ZELDA pupil') + +ax = fig.add_subplot(gs[0,3]) +ax.imshow(aberration*1e9, aspect='equal', vmin=-40, vmax=40, cmap='magma') +ax.set_title('Introduced aberration (nm)') + +ax = fig.add_subplot(gs[0,4]) +cax = ax.imshow(z_opd_standard, aspect='equal', vmin=-40, vmax=40, cmap='magma') +ax.set_title('Reconstructed aberration - standard') + +ax = fig.add_subplot(gs[0,5]) +cax = ax.imshow(z_opd_advanced, aspect='equal', vmin=-40, vmax=40, cmap='magma') +ax.set_title('Reconstructed aberration - advanced') + +ax = fig.add_subplot(gs[0,6]) +cbar = fig.colorbar(mappable=cax, cax=ax) +cbar.set_label('OPD [nm]') + +plt.tight_layout() +plt.show() diff --git a/examples/simple_zelda_analysis.py b/examples/simple_zelda_analysis.py index a6563b2..f56386f 100644 --- a/examples/simple_zelda_analysis.py +++ b/examples/simple_zelda_analysis.py @@ -7,6 +7,8 @@ from pathlib import Path +#%% parameters + # path = Path('/Users/mndiaye/Dropbox/python/zelda/pyZELDA/') path = Path('/Users/avigan/Work/GitHub/pyZELDA/data/') # path = Path('D:/Programmes/GitHub/pyZELDA/') @@ -26,35 +28,37 @@ dark_file = 'SPHERE_GEN_IRDIS057_0003' pupil_tel = True -# ZELDA analysis +#%% ZELDA analysis z = zelda.Sensor('SPHERE-IRDIS', pupil_telescope=pupil_tel) clear_pupil, zelda_pupil, center = z.read_files(path, clear_pupil_files, zelda_pupil_files, dark_file, - collapse_clear=True, collapse_zelda=True) + collapse_clear=True, collapse_zelda=False) opd_map = z.analyze(clear_pupil, zelda_pupil, wave=wave) +if opd_map.ndim == 3: + opd_map = opd_map.mean(axis=0) # decomposition on Zernike polynomials -basis, coeff, opd_zern = ztools.zernike_expand(opd_map.mean(axis=0), 20) +basis, coeff, opd_zern = ztools.zernike_expand(opd_map, 20) -# plot +#%% plot fig = plt.figure(0, figsize=(16, 4)) plt.clf() ax = fig.add_subplot(141) -ax.imshow(clear_pupil.mean(axis=0), aspect='equal', vmin=0, vmax=15000, origin=1) +ax.imshow(clear_pupil.mean(axis=0), aspect='equal', vmin=0, vmax=2000) ax.set_title('Clear pupil') ax = fig.add_subplot(142) -ax.imshow(zelda_pupil.mean(axis=0), aspect='equal', vmin=0, vmax=15000, origin=1) +ax.imshow(zelda_pupil.mean(axis=0), aspect='equal', vmin=0, vmax=2000) ax.set_title('ZELDA pupil') ax = fig.add_subplot(143) -ax.imshow(opd_map.mean(axis=0), aspect='equal', vmin=-150, vmax=150, cmap='magma', origin=1) +ax.imshow(opd_map, aspect='equal', vmin=-150, vmax=150, cmap='magma') ax.set_title('OPD map') ax = fig.add_subplot(144) -cax = ax.imshow(opd_zern.mean(axis=0), aspect='equal', vmin=-150, vmax=150, cmap='magma', origin=1) +cax = ax.imshow(opd_zern.mean(axis=0), aspect='equal', vmin=-150, vmax=150, cmap='magma') ax.set_title('Zernike projected OPD map') cbar = fig.colorbar(cax) diff --git a/pyzelda/.idea/workspace.xml b/pyzelda/.idea/workspace.xml new file mode 100644 index 0000000..148ddf8 --- /dev/null +++ b/pyzelda/.idea/workspace.xml @@ -0,0 +1,69 @@ + + + + + + + + + + + + + + + + + + + +