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Merge pull request #38 from LSSTDESC/fitchromaticpsf1d
Fitchromaticpsf1d
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,138 @@ | ||
| import matplotlib.pyplot as plt | ||
| from mpl_toolkits.axes_grid1 import make_axes_locatable | ||
| import numpy as np | ||
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| from spectractor import parameters | ||
| from spectractor.config import set_logger | ||
| from spectractor.simulation.simulator import SimulatorInit, SpectrumSimulation | ||
| from spectractor.simulation.atmosphere import Atmosphere, AtmosphereGrid | ||
| from spectractor.fit.fitter import FitWorkspace | ||
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| class SpectrumFitWorkspace(FitWorkspace): | ||
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| def __init__(self, file_name, atmgrid_file_name="", nwalkers=18, nsteps=1000, burnin=100, nbins=10, | ||
| verbose=0, plot=False, live_fit=False, truth=None): | ||
| FitWorkspace.__init__(self, file_name, nwalkers, nsteps, burnin, nbins, verbose, plot, live_fit, truth=truth) | ||
| self.my_logger = set_logger(self.__class__.__name__) | ||
| self.spectrum, self.telescope, self.disperser, self.target = SimulatorInit(file_name) | ||
| self.airmass = self.spectrum.header['AIRMASS'] | ||
| self.pressure = self.spectrum.header['OUTPRESS'] | ||
| self.temperature = self.spectrum.header['OUTTEMP'] | ||
| if atmgrid_file_name == "": | ||
| self.atmosphere = Atmosphere(self.airmass, self.pressure, self.temperature) | ||
| else: | ||
| self.use_grid = True | ||
| self.atmosphere = AtmosphereGrid(file_name, atmgrid_file_name) | ||
| if parameters.VERBOSE: | ||
| self.my_logger.info(f'\n\tUse atmospheric grid models from file {atmgrid_file_name}. ') | ||
| self.lambdas = self.spectrum.lambdas | ||
| self.data = self.spectrum.data | ||
| self.err = self.spectrum.err | ||
| self.A1 = 1.0 | ||
| self.A2 = 0.05 | ||
| self.ozone = 300. | ||
| self.pwv = 3 | ||
| self.aerosols = 0.03 | ||
| self.reso = 1.5 | ||
| self.D = self.spectrum.header['D2CCD'] | ||
| self.shift = self.spectrum.header['PIXSHIFT'] | ||
| self.p = np.array([self.A1, self.A2, self.ozone, self.pwv, self.aerosols, self.reso, self.D, self.shift]) | ||
| self.ndim = len(self.p) | ||
| self.input_labels = ["A1", "A2", "ozone", "PWV", "VAOD", "reso [pix]", r"D_CCD [mm]", | ||
| r"alpha_pix [pix]"] | ||
| self.axis_names = ["$A_1$", "$A_2$", "ozone", "PWV", "VAOD", "reso [pix]", r"$D_{CCD}$ [mm]", | ||
| r"$\alpha_{\mathrm{pix}}$ [pix]"] | ||
| self.bounds = [(0, 2), (0, 0.5), (0, 800), (0, 10), (0, 1), (1, 10), (50, 60), (-20, 20)] | ||
| if atmgrid_filename != "": | ||
| self.bounds[2] = (min(self.atmosphere.OZ_Points), max(self.atmosphere.OZ_Points)) | ||
| self.bounds[3] = (min(self.atmosphere.PWV_Points), max(self.atmosphere.PWV_Points)) | ||
| self.bounds[4] = (min(self.atmosphere.AER_Points), max(self.atmosphere.AER_Points)) | ||
| self.nwalkers = max(2 * self.ndim, nwalkers) | ||
| self.simulation = SpectrumSimulation(self.spectrum, self.atmosphere, self.telescope, self.disperser) | ||
| self.get_truth() | ||
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| def get_truth(self): | ||
| if 'A1' in list(self.spectrum.header.keys()): | ||
| A1_truth = self.spectrum.header['A1'] | ||
| A2_truth = self.spectrum.header['A2'] | ||
| ozone_truth = self.spectrum.header['OZONE'] | ||
| pwv_truth = self.spectrum.header['PWV'] | ||
| aerosols_truth = self.spectrum.header['VAOD'] | ||
| reso_truth = self.spectrum.header['RESO'] | ||
| D_truth = self.spectrum.header['D2CCD'] | ||
| shift_truth = self.spectrum.header['X0SHIFT'] | ||
| self.truth = (A1_truth, A2_truth, ozone_truth, pwv_truth, aerosols_truth, | ||
| reso_truth, D_truth, shift_truth) | ||
| else: | ||
| self.truth = None | ||
|
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| def plot_spectrum_comparison_simple(self, ax, title='', extent=None, size=0.4): | ||
| lambdas = self.spectrum.lambdas | ||
| sub = np.where((lambdas > parameters.LAMBDA_MIN) & (lambdas < parameters.LAMBDA_MAX)) | ||
| if extent is not None: | ||
| sub = np.where((lambdas > extent[0]) & (lambdas < extent[1])) | ||
| self.spectrum.plot_spectrum_simple(ax, lambdas=lambdas) | ||
| p0 = ax.plot(lambdas, self.model(lambdas), label='model') | ||
| ax.fill_between(lambdas, self.model - self.model_err, | ||
| self.model(lambdas) + self.model_err, alpha=0.3, color=p0[0].get_color()) | ||
| # ax.plot(self.lambdas, self.model_noconv, label='before conv') | ||
| if title != '': | ||
| ax.set_title(title, fontsize=10) | ||
| ax.legend() | ||
| divider = make_axes_locatable(ax) | ||
| ax2 = divider.append_axes("bottom", size=size, pad=0) | ||
| ax.figure.add_axes(ax2) | ||
| residuals = (self.spectrum.data - self.model(lambdas)) / self.model(lambdas) | ||
| residuals_err = self.spectrum.err / self.model(lambdas) | ||
| ax2.errorbar(lambdas, residuals, yerr=residuals_err, fmt='ro', markersize=2) | ||
| ax2.axhline(0, color=p0[0].get_color()) | ||
| ax2.grid(True) | ||
| residuals_model = self.model_err / self.model(lambdas) | ||
| ax2.fill_between(lambdas, -residuals_model, residuals_model, alpha=0.3, color=p0[0].get_color()) | ||
| std = np.std(residuals[sub]) | ||
| ax2.set_ylim([-2. * std, 2. * std]) | ||
| ax2.set_xlabel(ax.get_xlabel()) | ||
| ax2.set_ylabel('(data-fit)/fit') | ||
| ax2.set_xlim((lambdas[sub][0], lambdas[sub][-1])) | ||
| ax.set_xlim((lambdas[sub][0], lambdas[sub][-1])) | ||
| ax.set_ylim((0.9 * np.min(self.spectrum.data[sub]), 1.1 * np.max(self.spectrum.data[sub]))) | ||
| ax.set_xticks(ax2.get_xticks()[1:-1]) | ||
| ax.get_yaxis().set_label_coords(-0.15, 0.6) | ||
| ax2.get_yaxis().set_label_coords(-0.15, 0.5) | ||
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| def simulate(self, A1, A2, ozone, pwv, aerosols, reso, D, shift): | ||
| lambdas, model, model_err = self.simulation.simulate(A1, A2, ozone, pwv, aerosols, reso, D, shift) | ||
| # if self.live_fit: | ||
| # self.plot_fit() | ||
| self.model = model | ||
| self.model_err = model_err | ||
| return model, model_err | ||
|
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||
| def plot_fit(self): | ||
| fig = plt.figure(figsize=(12, 6)) | ||
| ax1 = plt.subplot(222) | ||
| ax2 = plt.subplot(224) | ||
| ax3 = plt.subplot(121) | ||
| A1, A2, ozone, pwv, aerosols, reso, D, shift = self.p | ||
| self.title = f'A1={A1:.3f}, A2={A2:.3f}, PWV={pwv:.3f}, OZ={ozone:.3g}, VAOD={aerosols:.3f},\n ' \ | ||
| f'reso={reso:.2f}pix, D={D:.2f}mm, shift={shift:.2f}pix ' | ||
| # main plot | ||
| self.plot_spectrum_comparison_simple(ax3, title=self.title, size=0.8) | ||
| # zoom O2 | ||
| self.plot_spectrum_comparison_simple(ax2, extent=[730, 800], title='Zoom $O_2$', size=0.8) | ||
| # zoom H2O | ||
| self.plot_spectrum_comparison_simple(ax1, extent=[870, 1000], title='Zoom $H_2 O$', size=0.8) | ||
| fig.tight_layout() | ||
| if self.live_fit: | ||
| plt.draw() | ||
| plt.pause(1e-8) | ||
| plt.close() | ||
| else: | ||
| if parameters.DISPLAY and parameters.VERBOSE: | ||
| plt.show() | ||
| if parameters.SAVE: | ||
| figname = self.filename.replace('.fits', '_bestfit.pdf') | ||
| self.my_logger.info(f'Save figure {figname}.') | ||
| fig.savefig(figname, dpi=100, bbox_inches='tight') | ||
|
|
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