correac/morpholopy

MorpholoPy

Python package that calculates the following morphological parameters :

kappa_co (see e.g. https://arxiv.org/pdf/1704.06283.pdf), specific angular momentum and axial ratios (see e.g https://arxiv.org/pdf/1805.03210.pdf ) for stars and HI+H2 gas. It also calculates HI+H2 surface densities and makes particle projections of the ten most massive galaxies in the simulations.

Morphology outputs figures and tables in a html format.

Requirements

The morpholopy package requires:

• python3.6 or above
• see requirements.txt

Usage

To run the script in the single-run mode use

 python3 morpholopy.py -d run_directory \
                       -s snapshot_name \
                       -c catalogue_name \
                       -n name_of_the_run \
                       -g number_of_individual_galaxies_to_show \
                       -o path_to_output_directory \
                       -m minimal_stellar_mass_for_galaxies_to_be_analysed

To run the script in the comparison mode use

 python3 morpholopy.py -d directory_of_run1 directory_of_run2 \
                       -s snapshot_name_run1 snapshot_name_run2 \
                       -c catalogue_name_run1 catalogue_name_run2 \
                       -n name_of_the_run1 name_of_the_run2 \
                       -g number_of_individual_galaxies_to_show \
                       -o path_to_output_directory \
                       -m minimal_stellar_mass_for_galaxies_to_be_analysed

morpholopy's Issues

Update the molecular surface density over neutral surface density plots

We should also update the molecular surface density over neutral surface density plots. This is what @sylviaploeckinger has been working on.

Using star-gas smoothing in stellar mass maps

morpholopy/morpholopy/particles.py

Line 66 in 0d46597

stars_data[:,7] = data.stars.smoothing_lengths[mask_stars].value * siminfo.a * 1e3 #kpc

This is not so physically relevant for the stellar mass distributions, could instead use a fixed smoothing, e.g:

baryon_maxsoft = float(data.metadata.parameters["Gravity:max_physical_baryon_softening"])*1000. #kpc                                                                                                                                      
stars_data[:,7] = 2*baryon_maxsoft*np.ones(stars_mass.size)

Stellar and gas component maps are calculated incorrectly

The stellar and gas component maps should be calculated with a good backend of swiftsimio instead of what is done currently using py-sphviewer.

Improve comparison option for new plots

The plots I have recently added are not yet behaving very well when the pipeline is used to compare runs. Currently, all plots are just multiplied even those where the data from different snapshots can be over-plotted.

I would also suggest to only show the combined plots (i.e. not the plots for individual galaxies) when runs are compared. We do not match haloes and comparing individual galaxies by their halo id might be misleading. This is especially the case when comparing different box sized.

Use the correct backends for plots

Currently, the code uses the histogram backend for most of the code, so this should be updated that we can use the subsampled backends instead of these.

Use the same angular momentum vector for all surface density plots

[I'll drop this here so that I do not forget.] Currently the new surface density plots for the HI-H2 transition do not use the same angular momentum vector for the projections as the other plots (e.g the KS plots) (see discussion in #12). They are calculated in a very similar way, but the mask is slightly different and for consistency it would be good if they would use the same projections.