Utility functions / classes (utils)

Introduction

gammapy.utils is a collection of utility functions that are used in many places or don’t fit in one of the other packages.

Since the various sub-modules of gammapy.utils are mostly unrelated, they are not imported into the top-level namespace. Here are some examples of how to import functionality from the gammapy.utils sub-modules:

from gammapy.utils.random import sample_sphere
sample_sphere(size=10)

from gammapy.utils import random
random.sample_sphere(size=10)

Time handling in Gammapy

See gammapy.utils.time.

Time format and scale

In Gammapy, astropy.time.Time objects are used to represent times:

>>> from astropy.time import Time
>>> Time(['1999-01-01T00:00:00.123456789', '2010-01-01T00:00:00'])
<Time object: scale='utc' format='isot' value=['1999-01-01T00:00:00.123' '2010-01-01T00:00:00.000']>

Note that Astropy chose format='isot' and scale='utc' as default and in Gammapy these are also the recommended format and time scale.

Warning

Actually what’s written here is not true. In CTA it hasn’t been decided if times will be in utc or tt (terrestial time) format.

Here’s a reminder that this needs to be settled / updated: https://github.com/gammapy/gammapy/issues/284

When other time formats are needed it’s easy to convert, see the time format section and table in the Astropy docs.

E.g. sometimes in astronomy the modified Julian date mjd is used and for passing times to matplotlib for plotting the plot_date format should be used:

>>> from astropy.time import Time
>>> time = Time(['1999-01-01T00:00:00.123456789', '2010-01-01T00:00:00'])
>>> time.mjd
array([ 51179.00000143,  55197.        ])
>>> time.plot_date
array([ 729755.00000143,  733773.        ])

Converting to other time scales is also easy, see the time scale section, diagram and table in the Astropy docs.

E.g. when converting celestial (RA/DEC) to horizontal (ALT/AZ) coordinates, the sidereal time is needed. This is done automatically by astropy.coordinates.AltAz when the astropy.coordinates.AltAz.obstime is set with a Time object in any scale, no need for explicit time scale transformations in Gammapy (although if you do want to explicitly compute it, it’s easy, see here).

The Fermi-LAT time systems in a nutshell page gives a good, brief explanation of the differences between the relevant time scales UT1, UTC and TT.

Mission elapsed times (MET)

[MET] time references are times representing UTC seconds after a specific origin. Each experiment may have a different MET origin that should be included in the header of the corresponding data files. For more details see Fermi-LAT time systems in a nutshell.

It’s not clear yet how to best implement METs in Gammapy, it’s one of the tasks here: https://github.com/gammapy/gammapy/issues/284

For now, we use the gammapy.time.time_ref_from_dict, gammapy.time.time_relative_to_ref and gammapy.time.absolute_time functions to convert MET floats to Time objects via the reference times stored in FITS headers.

Time differences

TODO: discuss when to use TimeDelta or Quantity or [MET] floats and where one needs to convert between those and what to watch out for.

Energy handling in Gammapy

Basics

Most objects in Astronomy require an energy axis, e.g. counts spectra or effective area tables. In general, this axis can be defined in two ways.

  • As an array of energy values. E.g. the Fermi-LAT diffuse flux is given at certain energies and those are stored in an ENERGY FITS table extension. In Gammalib this is represented by GEnergy.
  • As an array of energy bin edges. This is usually stored in EBOUNDS tables, e.g. for Fermi-LAT counts cubes. In Gammalib this is represented by GEbounds.

In Gammapy both the use cases are handled by two seperate classes: gammapy.utils.energy.Energy for energy values and gammapy.utils.energy.EnergyBounds for energy bin edges

Energy

The Energy class is a subclass of Quantity and thus has the same functionality plus some convenience functions for fits I/O

>>> from gammapy.utils.energy import Energy
>>> energy = Energy([1,2,3], 'TeV')
>>> hdu = energy.to_fits()
>>> type(hdu)
<class 'astropy.io.fits.hdu.table.BinTableHDU'>

EnergyBounds

The EnergyBounds class is a subclass of Energy. Additional functions are available e.g. to compute the bin centers

>>> from gammapy.utils.energy import EnergyBounds
>>> ebounds = EnergyBounds.equal_log_spacing(1, 10, 8, 'GeV')
>>> ebounds.size
9
>>> ebounds.nbins
8
>>> center = ebounds.log_centers
>>> center
<Energy [ 1.15478198, 1.53992653, 2.05352503, 2.73841963, 3.65174127,
          4.86967525, 6.49381632, 8.65964323] GeV>

Reference/API

gammapy.utils.energy Module

Classes

Energy Energy quantity scalar or array.
EnergyBounds EnergyBounds array.

gammapy.utils.units Module

Units and Quantity related helper functions

Functions

standardise_unit(unit) Standardise unit.

gammapy.utils.coordinates Package

Astronomical coordinate calculation utility functions.

Functions

angle_to_radius(angle, distance) Radius (pc), distance(kpc), angle(deg)
cartesian(r, theta) Convert polar coordinates to cartesian coordinates.
flux_to_luminosity(flux, distance) Distance is assumed to be in kpc
galactic(x, y, z[, obs_pos]) Compute galactic coordinates lon, lat (deg) and distance (kpc) for given position in cartesian coordinates (kpc)
luminosity_to_flux(luminosity, distance) Distance is assumed to be in kpc
minimum_separation(lon1, lat1, lon2, lat2) Compute minimum distance of each (lon1, lat1) to any (lon2, lat2).
motion_since_birth(v, age, theta, phi) Compute motion of a object with given velocity, direction and age.
pair_correlation(lon, lat, theta_bins) Compute pair correlation function for points on the sphere.
polar(x, y) Convert cartesian coordinates to polar coordinates.
radius_to_angle(radius, distance) Radius (pc), distance(kpc), angle(deg)
velocity_glon_glat(x, y, z, vx, vy, vz) Compute projected angular velocity in galactic coordinates.

Variables

D_SUN_TO_GALACTIC_CENTER A Quantity represents a number with some associated unit.

gammapy.utils.table Module

Table helper utilities.

Functions

table_standardise_units_copy(table) Standardise units for all columns in a table in a copy.
table_standardise_units_inplace(table) Standardise units for all columns in a table in place.
table_row_to_dict(row[, make_quantity]) Make one source data dict.
table_from_row_data(rows, **kwargs) Helper function to create table objects from row data.

gammapy.utils.fits Module

Gammapy FITS utilities

FITS tables

In Gammapy we use the nice astropy.table.Table class a lot to represent all kinds of data (e.g. event lists, spectral points, light curves, source catalogs). The most common format to store tables is FITS. In this section we show examples and mention some limitations of Table FITS I/O.

Also, note that if you have the choice, you might want to use a better format than FITS to store tables. All of these are nice and have very good support in Astropy: ECSV, HDF5, ASDF.

In Astropy, there is the Table class with a nice data model and API. Let’s make an example table object that has some metadata on the table and columns of different types:

>>> from astropy.table import Table, Column
>>> table = Table(meta={'version': 42})
>>> table['a'] = [1, 2]
>>> table['b'] = Column([1, 2], unit='m', description='Velocity')
>>> table['c'] = ['x', 'yy']
>>> table
<Table length=2>
  a     b    c
        m
int64 int64 str2
----- ----- ----
    1     1    x
    2     2   yy
>>> table.info()
<Table length=2>
name dtype unit description
---- ----- ---- -----------
   a int64
   b int64    m    Velocity
   c  str2

Writing and reading the table to FITS is easy:

>>> table.write('table.fits')
>>> table2 = Table.read('table.fits')

and works very nicely, column units and description round-trip:

>>> table2
<Table length=2>
  a      b      c
         m
int64 float64 bytes2
----- ------- ------
    1     1.0      x
    2     2.0     yy
>>> table2.info()
<Table length=2>
name  dtype  unit description
---- ------- ---- -----------
   a   int64
   b float64    m    Velocity
   c  bytes2

This is with Astropy 3.0. In older versions of Astropy this didn’t use to work, namely column description was lost.

Looking at the FITS header and table2.meta, one can see that they are cheating a bit, storing table meta in COMMENT:

>>> fits.open('table.fits')[1].header
XTENSION= 'BINTABLE'           / binary table extension
BITPIX  =                    8 / array data type
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   18 / length of dimension 1
NAXIS2  =                    2 / length of dimension 2
PCOUNT  =                    0 / number of group parameters
GCOUNT  =                    1 / number of groups
TFIELDS =                    3 / number of table fields
TTYPE1  = 'a       '
TFORM1  = 'K       '
TTYPE2  = 'b       '
TFORM2  = 'K       '
TUNIT2  = 'm       '
TTYPE3  = 'c       '
TFORM3  = '2A      '
VERSION =                   42
COMMENT --BEGIN-ASTROPY-SERIALIZED-COLUMNS--
COMMENT datatype:
COMMENT - {name: a, datatype: int64}
COMMENT - {name: b, unit: m, datatype: int64, description: Velocity}
COMMENT - {name: c, datatype: string}
COMMENT meta:
COMMENT   __serialized_columns__: {}
COMMENT --END-ASTROPY-SERIALIZED-COLUMNS--
>>> table2.meta
OrderedDict([('VERSION', 42),
             ('comments',
              ['--BEGIN-ASTROPY-SERIALIZED-COLUMNS--',
               'datatype:',
               '- {name: a, datatype: int64}',
               '- {name: b, unit: m, datatype: int64, description: Velocity}',
               '- {name: c, datatype: string}',
               'meta:',
               '  __serialized_columns__: {}',
               '--END-ASTROPY-SERIALIZED-COLUMNS--'])])

TODO: we’ll have to see how to handle this, i.e. if we want that behaviour or not, and how to get consistent output accross Astropy versions. See https://github.com/astropy/astropy/issues/7364

Let’s make sure for the following examples we have a clean table.meta like we did at the start:

>>> table.meta.pop('comments', None)

If you want to avoid writing to disk, the way to directly convert between Table and BinTableHDU is like this:

>>> hdu = fits.BinTableHDU(table)

This calls astropy.io.fits.table_to_hdu in BinTableHDU.__init__, i.e. if you don’t pass extra options, this is equivalent to

>>> hdu = fits.table_to_hdu(table)

However, in this case, the column metadata that is serialised is doesn’t include the column description. TODO: how to get consistent behaviour and FITS headers?

>>> hdu.header
XTENSION= 'BINTABLE'           / binary table extension
BITPIX  =                    8 / array data type
NAXIS   =                    2 / number of array dimensions
NAXIS1  =                   18 / length of dimension 1
NAXIS2  =                    2 / length of dimension 2
PCOUNT  =                    0 / number of group parameters
GCOUNT  =                    1 / number of groups
TFIELDS =                    3 / number of table fields
VERSION =                   42
TTYPE1  = 'a       '
TFORM1  = 'K       '
TTYPE2  = 'b       '
TFORM2  = 'K       '
TUNIT2  = 'm       '
TTYPE3  = 'c       '
TFORM3  = '2A      '

Somewhat surprisingly, Table(hdu) doesn’t work and there is no hdu_to_table function; instead you have to call Table.read if you want to convert in the other direction:

>>> table2 = Table.read(hdu)
>>> table2.info()
<Table length=2>
name dtype unit
---- ----- ----
   a int64
   b int64    m
   c  str2

Another trick worth knowing about is how to read and write multiple tables to one FITS file. There is support in the Table API to read any HDU from a FITS file with multiple HDUs via the hdu option to Table.read; you can pass an integer HDU index or an HDU extension name string (see FITS).

For writing (or if you prefer also for reading) multiple tables, you should use the in-memory conversion to HDU objects and the HDUList like this:

hdu_list = fits.HDUList([
    fits.PrimaryHDU(),
    fits.BinTableHDU(table, name='spam'),
    fits.BinTableHDU(table, name='ham'),
])
hdu_list.info()
hdu_list.writeto('tables.fits')

For further information on Astropy, see the Astropy docs at Data Tables (astropy.table) and FITS.

We will have to see if / what we need here in gammapy.utils.fits as a stable and nice interface on top of what Astropy provides.

Functions

energy_axis_to_ebounds(energy) Convert EnergyBounds to OGIP EBOUNDS extension.

Classes

SmartHDUList(hdu_list) A FITS HDU list wrapper with some sugar.

gammapy.utils.root Package

Utility functions to work with ROOT and rootpy.

Functions

TH2_to_FITS(hist[, flipx]) Convert ROOT 2D histogram to FITS format.
TH2_to_FITS_data(hist[, flipx]) Convert TH2 bin values into a numpy array.
TH2_to_FITS_header(hist[, flipx]) Create FITS header for a given ROOT histogram.
graph1d_to_table(graph) Convert ROOT TGraph to an astropy Table.
hist1d_to_table(hist) Convert 1D ROOT histogram into astropy table.

gammapy.utils.random Module

Random sampling for some common distributions

Functions

get_random_state(init) Get a numpy.random.RandomState instance.
sample_sphere(size[, lon_range, lat_range, …]) Sample random points on the sphere.
sample_sphere_distance([distance_min, …]) Sample random distances if the 3-dim space density is constant.
sample_powerlaw(x_min, x_max, gamma[, size, …]) Sample random values from a power law distribution.

gammapy.utils.distributions Package

Utility functions / classes for working with distributions (e.g. probability density functions)

Functions

density(func) Returns the radial surface density of a given one dimensional PDF.
draw(low, high, size, dist[, random_state]) Allows drawing of random numbers from any distribution.
normalize(func, x_min, x_max) Normalize a 1D function over a given range.
pdf(func) Returns the one dimensional PDF of a given radial surface density.

Classes

GeneralRandom(pdf, min_range, max_range[, …]) Fast random number generation with an arbitrary pdf of a continuous variable x.
GeneralRandomArray(pdf) Draw random indices from a discrete probability distribution given by a numpy array.

gammapy.utils.scripts Module

Utils to create scripts and command-line tools

Functions

get_parser([function, description]) Make an ArgumentParser how we like it.
get_installed_scripts() Get list of installed scripts via pkg-resources.
get_all_main_functions() Get a dict with all scripts (used for testing).
set_up_logging_from_args(args) Set up logging from command line arguments.
read_yaml(filename[, logger]) Read YAML file
write_yaml(dictionary, filename[, logger]) Write YAML file.
make_path(path) Expand environment variables on Path construction.
recursive_merge_dicts(a, b) Recursively merge two dictionaries.

Classes

GammapyFormatter(prog[, indent_increment, …]) ArgumentParser formatter_class argument.

gammapy.utils.testing Module

Utilities for testing

Functions

requires_dependency(name) Decorator to declare required dependencies for tests.
requires_data(name) Decorator to declare required data for tests.
assert_wcs_allclose(wcs1, wcs2) Assert all-close for WCS
assert_skycoord_allclose(actual, desired) Assert all-close for SkyCoord.
assert_time_allclose(actual, desired) Assert that two astropy.time.Time objects are almost the same.

gammapy.utils.wcs Module

WCS related utility functions.

Functions

linear_wcs_to_arrays(wcs, nbins_x, nbins_y) Make a 2D linear binning from a WCS object.
linear_arrays_to_wcs(name_x, name_y, …) Make a 2D linear WCS object from arrays of bin edges.
get_wcs_ctype(wcs) Get celestial coordinate type of WCS instance.
get_resampled_wcs(wcs, factor, downsampled) Get resampled WCS object.

gammapy.utils.nddata Module

Utility functions and classes for n-dimensional data and axes.

Functions

sqrt_space(start, stop, num) Return numbers spaced evenly on a square root scale.

Classes

NDDataArray(axes[, data, meta, interp_kwargs]) ND Data Array Base class
DataAxis(nodes[, name, interpolation_mode]) Data axis to be used with NDDataArray
BinnedDataAxis(lo, hi, **kwargs) Data axis for binned data

gammapy.utils.time Module

Time related utility functions.

Functions

time_ref_from_dict(meta[, format, scale]) Calculate the time reference from metadata.
time_ref_to_dict(time[, scale]) TODO: document and test.
time_relative_to_ref(time, meta) Convert a time using an existing reference.
absolute_time(time_delta, meta) Convert a MET into human readable date and time.

gammapy.utils.modeling Module

Model classes to generate XML.

This is prototype code.

The goal was to be able to save gamma-cat in XML format for the CTA data challenge GPS sky model.

TODO (needs a bit of experimentation / discussion / thought and a few days of coding):

  • add repr to all classes
  • integrate this the existing Gammapy model classes to make analysis possible.
  • don’t couple this to gamma-cat. Gamma-cat should change to create model classes that support XML I/O.
  • sub-class Astropy Parameter and ParameterSet classes instead of starting from scratch?
  • implement spatial and spectral mode registries instead of if-elif set on type to make SourceLibrary extensible.
  • write test and docs
  • Once modeling setup OK, ask new people to add missing models (see Gammalib, Fermi ST, naima, Sherpa, HESS) (it’s one of the simplest and nicest things to get started with)

For XML model format definitions, see here:

Classes

Parameter(name, value[, unit, parmin, …]) Class representing model parameters.
ParameterList(parameters[, covariance]) List of Parameter
SourceLibrary(source_list)
SourceModel(source_name, source_type, …) TODO: having “source_type” separate, but often inferred from the spatial model is weird.
SpectralModel(parameters) Spectral model abstract base class.
SpectralModelPowerLaw(parameters)
SpectralModelPowerLaw2(parameters)
SpectralModelExpCutoff(parameters)
SpatialModel(parameters) Spatial model abstract base class
SpatialModelPoint(parameters)
SpatialModelGauss(parameters)
SpatialModelShell(parameters)
UnknownModelError Error when encountering unknown model types.

gammapy.utils.fitting Package

Fitting utility functions.

Functions

fit_minuit(parameters, function) iminuit optimization