diff --git a/auto/Examples/bayesian/likelihood_sampling.py b/auto/Examples/bayesian/likelihood_sampling.py index 49ccddbce6b207bafbd3529d7dbd86b16532e1da..1fa6401c3e32d614afc415eaac60cdbde15eb209 100755 --- a/auto/Examples/bayesian/likelihood_sampling.py +++ b/auto/Examples/bayesian/likelihood_sampling.py @@ -57,9 +57,12 @@ def run_simulation(points, ni_thickness, ti_thickness): if __name__ == '__main__': filepath = os.path.join(datadir, "specular/genx_alternating_layers.dat.gz") - data = ba.readData2D(filepath).npArray() - data[:, 0] *= np.pi/360 # convert incident angles from deg to rad - data[:, 2] = data[:, 1]*0.1 # arbitrary uncertainties of 10% + flags = ba.ImportSettings1D("2alpha (deg)", "#", "", 1, 2) + data = ba.readData1D(filepath, ba.csv1D, flags) + + q = data.npXcenters() + y = data.npArray() + dy = y * 0.1 # arbitrary uncertainties def log_likelihood(P): """ @@ -70,9 +73,6 @@ if __name__ == '__main__': :array yerr: the ordinate uncertainty (dR-values) :return: log-likelihood """ - q = data[:, 0] - y = data[:, 1] - dy = data[:, 2] y_sim = run_simulation(q, *P) sigma2 = dy**2 + y_sim**2 return -0.5*np.sum((y - y_sim)**2/sigma2 + np.log(sigma2)) @@ -104,14 +104,10 @@ if __name__ == '__main__': plt.show() # Plot and show MLE and data of reflectivity - plt.errorbar(data[:, 0], - data[:, 1], - data[:, 2], - marker='.', - ls='') + plt.errorbar(q, y, dy, marker='.', ls='') plt.plot( - data[:, 0], - run_simulation(data[:, 0], *flat_samples.mean(axis=0)), + q, + run_simulation(q, *flat_samples.mean(axis=0)), '-') plt.xlabel('$\\alpha$/rad') plt.ylabel('$R$') diff --git a/auto/MiniExamples/bayesian/likelihood_sampling.py b/auto/MiniExamples/bayesian/likelihood_sampling.py index 9144431229378469ed89ad12dba6bc3a0a0165be..c5094bd65147f84e277d0ac112cc5e56ae385f3d 100755 --- a/auto/MiniExamples/bayesian/likelihood_sampling.py +++ b/auto/MiniExamples/bayesian/likelihood_sampling.py @@ -57,9 +57,12 @@ def run_simulation(points, ni_thickness, ti_thickness): if __name__ == '__main__': filepath = os.path.join(datadir, "specular/genx_alternating_layers.dat.gz") - data = ba.readData2D(filepath).npArray() - data[:, 0] *= np.pi/360 # convert incident angles from deg to rad - data[:, 2] = data[:, 1]*0.1 # arbitrary uncertainties of 10% + flags = ba.ImportSettings1D("2alpha (deg)", "#", "", 1, 2) + data = ba.readData1D(filepath, ba.csv1D, flags) + + q = data.npXcenters() + y = data.npArray() + dy = y * 0.1 # arbitrary uncertainties def log_likelihood(P): """ @@ -70,9 +73,6 @@ if __name__ == '__main__': :array yerr: the ordinate uncertainty (dR-values) :return: log-likelihood """ - q = data[:, 0] - y = data[:, 1] - dy = data[:, 2] y_sim = run_simulation(q, *P) sigma2 = dy**2 + y_sim**2 return -0.5*np.sum((y - y_sim)**2/sigma2 + np.log(sigma2)) @@ -104,14 +104,10 @@ if __name__ == '__main__': # plt.show() # Plot and show MLE and data of reflectivity - plt.errorbar(data[:, 0], - data[:, 1], - data[:, 2], - marker='.', - ls='') + plt.errorbar(q, y, dy, marker='.', ls='') plt.plot( - data[:, 0], - run_simulation(data[:, 0], *flat_samples.mean(axis=0)), + q, + run_simulation(q, *flat_samples.mean(axis=0)), '-') plt.xlabel('$\\alpha$/rad') plt.ylabel('$R$') diff --git a/rawEx/bayesian/likelihood_sampling.py b/rawEx/bayesian/likelihood_sampling.py index ce7f70578fd2690e35a7b13fc586ef6ab8af96c9..be2f4332cfe7ecf3f6dd552706f20c3a571be465 100755 --- a/rawEx/bayesian/likelihood_sampling.py +++ b/rawEx/bayesian/likelihood_sampling.py @@ -57,9 +57,12 @@ def run_simulation(points, ni_thickness, ti_thickness): if __name__ == '__main__': filepath = os.path.join(datadir, "specular/genx_alternating_layers.dat.gz") - data = ba.readData2D(filepath).npArray() - data[:, 0] *= np.pi/360 # convert incident angles from deg to rad - data[:, 2] = data[:, 1]*0.1 # arbitrary uncertainties of 10% + flags = ba.ImportSettings1D("2alpha (deg)", "#", "", 1, 2) + data = ba.readData1D(filepath, ba.csv1D, flags) + + q = data.npXcenters() + y = data.npArray() + dy = y * 0.1 # arbitrary uncertainties def log_likelihood(P): """ @@ -70,9 +73,6 @@ if __name__ == '__main__': :array yerr: the ordinate uncertainty (dR-values) :return: log-likelihood """ - q = data[:, 0] - y = data[:, 1] - dy = data[:, 2] y_sim = run_simulation(q, *P) sigma2 = dy**2 + y_sim**2 return -0.5*np.sum((y - y_sim)**2/sigma2 + np.log(sigma2)) @@ -104,14 +104,10 @@ if __name__ == '__main__': <%= sm ? "# " : "" %>plt.show() # Plot and show MLE and data of reflectivity - plt.errorbar(data[:, 0], - data[:, 1], - data[:, 2], - marker='.', - ls='') + plt.errorbar(q, y, dy, marker='.', ls='') plt.plot( - data[:, 0], - run_simulation(data[:, 0], *flat_samples.mean(axis=0)), + q, + run_simulation(q, *flat_samples.mean(axis=0)), '-') plt.xlabel('$\\alpha$/rad') plt.ylabel('$R$')