Remote observation of cometary atmospheres produces a measurement of the cometary emissions integrated along the line of sight. This integration is the so-called Abel transform of the local emission rate. The observation is generally interpreted under the hypothesis of spherical symmetry of the coma. Under that hypothesis, the Abel transform can be inverted. We derive a numerical inversion method adapted to cometary atmospheres using both analytical results and least squares fitting techniques. This method, derived under the usual hypothesis of spherical symmetry, allows us to retrieve the radial distribution of the emission rate of any unabsorbed emission, which is the fundamental, physically meaningful quantity governing the observation. A Tikhonov regularization technique is also applied to reduce the possibly deleterious effects of the noise present in the observation and to warrant that the problem remains well posed. Standard error propagation techniques are included in order to estimate the uncertainties affecting the retrieved emission rate. Several theoretical tests of the inversion techniques are carried out to show its validity and robustness. In particular, we show that the Abel inversion of real data is only weakly sensitive to an offset applied to the input flux, which implies that the method, applied to the study of a cometary atmosphere, is only weakly dependent on uncertainties on the sky background which has to be subtracted from the raw observations of the coma. We apply the method to observations of three different comets observed using the TRAPPIST telescope: 103P/ Hartley 2, F6/ Lemmon and A1/ Siding Spring. We show that the method retrieves realistic emission rates, and that characteristic lengths and production rates can be derived from the emission rate for both CN and C2 molecules. We show that the retrieved characteristic lengths can differ from those obtained from a direct least squares fitting over the observed flux of radiation, and that discrepancies can be reconciled for by correcting this flux by an offset (to which the inverse Abel transform is nearly not sensitive). The A1/Siding Spring observations were obtained very shortly after the comet produced an outburst, and we show that the emission rate derived from the observed flux of CN emission at 387nm and from the C2 emission at 514.1nm both present an easily-identifiable shoulder that corresponds to the separation between pre- and post-outburst gas. As a general result, we show that diagnosing properties and features of the coma using the emission rate is easier than directly using the observed flux, because the Abel transform produces a smoothing that blurs the signatures left by features present in the coma. We also determine the parameters of a Haser model fitting the inverted data and fitting the line-of-sight integrated observation, for which we provide the exact analytical expression of the line-of-sight integration of the Haser model.
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