When giving the list of parameters through a file, cigale did not compute properly what parameter changed between to successive models.

With the new sanity check of the input parameters, cigale did not handle the fact that the redshift could be given in the parameters file. Now this is handled properly.

A significant fraction of the total run time is spent computing integrals (e.g. fluxes in passbands). We can make the integration faster by rewriting the trapezoidal rule in terms of np.dot(). This allows to offload the computation to optimised libraries. The end result is that the integration is twice as fast, with a gain of ~10-15% on the total run time.

Computers are much better at multiplying than at dividing. Therefore to correct the emission for redshifting we multiply by 1/(1+z) rather than dividing by 1+z.

The absorption of the Lyman continuum from old stars tended to be overestimated leading to some “negative fluxes” for the Lyman continuum.

In rare circumstances requiring a specific distribution of redshifts the integration of the spectrum in some filters was not done correctly, inducing relative errors of ~10¯⁵-10¯⁶.

To compute the stellar spectrum of the young component, do not pass the full SFH with the old part set to 0. Rather, only pass the corresponding part of the SFH. This nearly doubles the computing speed of the stellar spectrum.

We do not store the time grid in the SED anymore given that we assume it starts at 0 Myr with steps of 1 Myr, we can easily reconstruct to save it if needed. It should save a little bit of memory and it should go a little bit faster.

In the output the sfh.age parameter would correspond to the input value minus 1. Now both values are consistent with one another.

The optionally saved spectra in the pdf_analysis and savefluxes modules were saved in the VO-table format. The most important downside is that it is very slow to write to, which proves to be a major bottleneck in the computing speed. To overcome this issue, we rather save the spectra using the FITS formation. Instead of having one file containing the spectra (including the various components) and the SFH in a single file, now we have one file for the spectra and one file for the SFH.

Pratical implementation of the validation of the parameters. The patch is quite long as it has a direct effect on the structure of the configuration dictionary. The validation has the advantage of automatically convert the parameters to the right type. Therefore rather than building a dictionary ourselves, we rather use the ready-made dictionary from ConfigObj. Because the names of the sections are not the same, quite a bit of code had to be adapted. Finally, note that the validation file containing the specification of each variable, pcigale.ini.spec, is created while building the pcigale.ini file. Also because it is needed to convert the data to the right type, one cannot run cigale without a correct validation file.

If the list of analysed/saved physical properties is left empty in pcigale.ini, savefluxes saved all physical properties. This has been moved to the Configuration class and easily extended to the pdf_analysis module.

When the redshifts are not indicated in pcigale.ini, compute them from the input flux file when the configuration dictionary is returned rather than in the analysis module, which should not have to change the configuration.

Implement an _init_code function so the initialisation of the module is separated from the processing of the SED. Because the initialisation can be slow, this should yield a speed-up when applying the module on different SED.

Clarify the description of the module parameters to ensure that the time grid is correctly formatted and add a test to ensure this.

Be more resilient by converting the array of SFR to float. This avoids a possible crash down the road when doing an in-place assignment of an integer with a float.

In the sfhfromfile module, an extraneous offset in the column index made that it took the previous column as the SFR rather than the selected column.

Correct the mass-dependent physical quantities for the difference between the redshift of the model and the redshift of the observation. Because the former is rounded to 2 decimal places, there can be a redshift difference of 0.005 (if CIGALE computes the list of redshifts itself). This can lead to differences of more than 0.35 dex at z=0.01 for instance.

Move most of the computation to _init_code() to make the sfhdelayed module consister with other modules.

We need to start the age grid at 0 rather than 1. Otherwise when we do not normalise the SFH, the scale would be wrong, with the SFR at the first time step being sfr0×exp(-1/tau_main) rather than sfr0.

Normalise the attenuation curves so that their E(B-V) corresponds to the E(B-V) requested by the user.

Merge the output files into one. The parameters estimated from the PDF are prefixed with 'bayes' and those from the best fit with 'best'.

In the presence of upper limits, correct the scaling factor of the models to the observations before computing the χ², not after.

When estimating a parameter in log, these were not scaled appropriately and taken in log when saving the related PDF

When estimating a parameter in log, these were not scaled appropriately and taken in log when saving the related χ²

Médéric Boquien authored Dec 07, 2015 and Yannick Roehlly committed Dec 07, 2015

The detection of the '_log' suffix in variables and its removal to compute the models was overzealous. Fix this.

Revert the commit to re-apply it using git-flow hotfix.

This reverts commit d8fab1df.

The detection of the '_log' suffix in variables and its removal to compute the models was overzealous. Fix this.