New issue 1232: Absorption Spectrum Error (Gizmo file type)? https://bitbucket.org/yt_analysis/yt/issues/1232/absorption-spectrum-error-g...

Anonymous:

I tried using the cookbook code for creating an absorption spectrum (http://yt-project.org/docs/dev/cookbook/cosmological_analysis.html#creating-...) for a Gizmo type cosmological simulation file. I created a light ray successfully, create and absorption spectrum via sp = AbsorptionSpectrum(900.0, 1400.0, 50000), and add a HI line to the spectrum, following the cookbook. But whenever I get to the line:

wavelength, flux = sp.make_spectrum('lightray.h5', output_file='spectrum.h5', line_list_file='lines.txt', use_peculiar_velocity=True)

I get the following error:

absorption_spectrum.pyc in _add_lines_to_spectrum(self, field_data, use_peculiar_velocity, output_absorbers_file, subgrid_resolution, observing_redshift, njobs): 444 # edges (ie the wings), then widen the wavelength 445 # window and repeat process. --> 446 if (vtau[0] < min_tau and vtau[-1] < min_tau): 447 break 448 window_width_in_bins *= 2

IndexError: index 0 is out of bounds for axis 0 with size 0

I've looked at the source code but I can't figure out what's causing the problem. If I do not try to add any lines to my absorption spectrum at all, then it doesn't error. But since I'm following the cookbook code, I'm not sure what could be going wrong...

Help?

Thanks, Kyle Stewart