Configuration¶
This page describes the configuration management scheme used within the fermiPy package and the documents the configuration parameters that can be set in the configuration file.
Class Configuration¶
Classes in the fermiPy package follow a common convention for configuring the runtime behavior of a class instance. Internally every class instance has a dictionary that defines its configuration state. Elements of the configuration dictionary can be scalars (str, int ,float) or dictionaries defining nested blocks of the configuration.
The class configuration dictionary is initialized at the time of object creation by passing a dictionary or a path to YAML configuration file to the class constructor. Keyword arguments can be optionally passed to the constructor to override configuration parameters in the input dictionary. For instance in the following example the config dictionary defines values for the parameters emin and emax. By passing a dictionary for the selection keyword argument, the value of emax in the keyword argument (10000) overrides the value of this parameter in the input dictionary.
config = {
'selection' : { 'emin' : 100,
'emax' : 1000 }
}
gta = GTAnalysis(config,selection={'emax' : 10000})
The first argument can also be the path to a YAML configuration file rather than a dictionary:
gta = GTAnalysis('config.yaml',selection={'emax' : 10000})
Configuration File¶
fermiPy uses YAML files to read and write its configuration in a persistent format. The configuration file has a hierarchical structure that organizes parameters into groups that are keyed to a section name (data, binnig, etc.).
data:
evfile : ft1.fits
scfile : ft2.fits
binning:
roiwidth : 10.0
binsz : 0.1
binsperdec : 8
The configuration file mirrors the layout of the configuration dictionary. The parameters that can be set in each section are described below.
binning¶
Options in the binning section control the spatial and spectral binning of the data.
binning:
# Binning
roiwidth : 10.0
npix : null
binsz : 0.1 # spatial bin size in deg
binsperdec : 8 # nb energy bins per decade
projtype : WCS
Option | Default | Description |
---|---|---|
binsperdec |
8 | Number of energy bins per decade. |
binsz |
0.1 | Spatial bin size in degrees. |
coordsys |
CEL | Coordinate system of the spatial projection (CEL or GAL). |
enumbins |
None | Number of energy bins. If none this will be inferred from energy range and binsperdec parameter. |
hpx_ebin |
True | Include energy binning |
hpx_order |
10 | Order of the map (int between 0 and 12, included) |
hpx_ordering_scheme |
RING | HEALPix Ordering Scheme |
npix |
None | Number of pixels. If none then this will be set from roiwidth and binsz . |
proj |
AIT | Spatial projection for WCS mode. |
projtype |
WCS | Projection mode (WCS or HPX). |
roiwidth |
10.0 | Width of the ROI in degrees. The number of pixels in each spatial dimension will be set from roiwidth / binsz (rounded up). |
components¶
The components section can be used to define analysis configurations for a sequence of independent subselections of the data. Each subselection will have its own binned likelihood instance that will be combined in a global likelihood likelihood function for the whole ROI (implemented with the SummedLikelihood class in pyLikelihood). This section is optional and when this section is empty (the default) fermiPy will construct a single likelihood with the parameters of the root analysis configuration.
The component section can be defined as either a list or dictionary of dictionary elements where each element sets analysis parameters for a different subcomponent of the analysis. Dictionary elements have the same hierarchy of parameters as the root analysis configuration. Parameters not defined in a given element will default to the values set in the root analysis configuration.
The following example illustrates how to define a Front/Back analysis with the a list of dictionaries. In this case files associated to each component will be named according to their order in the list (e.g. file_00.fits, file_01.fits, etc.).
# Component section for Front/Back analysis with list style
components:
- { selection : { evtype : 1 } } # Front
- { selection : { evtype : 2 } } # Back
This example illustrates how to define the components as a dictionary of dictionaries. In this case the files of a component will be appended with its corresponding key (e.g. file_front.fits, file_back.fits).
# Component section for Front/Back analysis with dictionary style
components:
front : { selection : { evtype : 1 } } # Front
back : { selection : { evtype : 2 } } # Back
data¶
The data section defines the input data files for the analysis (FT1,
FT2, and livetime cube). evfile
and scfile
can either be
individual files or group of files. The optional ltcube
option can
be used to choose a pre-generated livetime cube. If ltcube
is
null a livetime cube will be generated at runtime with gtltcube
.
data :
evfile : ft1.lst
scfile : ft2.fits
ltcube : null
Option | Default | Description |
---|---|---|
evfile |
None | Path to FT1 file or list of FT1 files. |
ltcube |
None | Path to livetime cube. If none a livetime cube will be generated with gtmktime . |
scfile |
None | Path to FT2 (spacecraft) file. |
extension¶
The options in extension control the default behavior of the
extension
method. For more information
about running this method see the Extension Fitting page.
Option | Default | Description |
---|---|---|
fix_background |
False | Fix any background parameters that are currently free in the model when performing the likelihood scan over extension. |
save_model_map |
False | |
save_templates |
False | |
spatial_model |
GaussianSource | Spatial model use for extension test. |
update |
False | Update the source model with the best-fit spatial extension. |
width |
None | Parameter vector for scan over spatial extent. If none then the parameter vector will be set from width_min , width_max , and width_nstep . |
width_max |
1.0 | Maximum value in degrees for the likelihood scan over spatial extent. |
width_min |
0.01 | Minimum value in degrees for the likelihood scan over spatial extent. |
width_nstep |
21 | Number of steps for the spatial likelihood scan. |
fileio¶
The fileio section collects options related to file bookkeeping.
The outdir
option sets the root directory of the analysis instance
where all output files will be written. If outdir
is null then the
output directory will be automatically set to the directory in which
the configuration file is located. Enabling the usescratch
option
will stage all output data files to a temporary scratch directory
created under scratchdir
.
fileio:
outdir : null
logfile : null
usescratch : False
scratchdir : '/scratch'
Option | Default | Description |
---|---|---|
logfile |
None | Path to log file. If None then log will be written to fermipy.log. |
outdir |
None | Path of the output directory. If none this will default to the directory containing the configuration file. |
savefits |
True | Save intermediate FITS files. |
scratchdir |
/scratch | Path to the scratch directory. |
usescratch |
False | Run analysis in a temporary directory under scratchdir . |
workdir |
None | Override the working directory. |
gtlike¶
Options in the gtlike section control the setup of the likelihood
analysis include the IRF name (irfs
).
Option | Default | Description |
---|---|---|
bexpmap |
None | |
convolve |
True | |
edisp |
True | Enable the correction for energy dispersion. |
edisp_disable |
None | Provide a list of sources for which the edisp correction should be disabled. |
irfs |
None | Set the IRF string. |
minbinsz |
0.05 | Set the minimum bin size used for resampling diffuse maps. |
resample |
True | |
rfactor |
2 | |
srcmap |
None |
model¶
The model section collects options that control the inclusion of
point-source and diffuse components in the model. galdiff
and
isodiff
set the templates for the Galactic IEM and isotropic
diffuse respectively. catalogs
defines a list of catalogs that
will be merged to form a master analysis catalog from which sources
will be drawn. Valid entries in this list can be FITS files or XML
model files. sources
can be used to insert additional
point-source or extended components beyond those defined in the master
catalog. src_radius
and src_roiwidth
set the maximum distance
from the ROI center at which sources in the master catalog will be
included in the ROI model.
model :
# Diffuse components
galdiff : '$FERMI_DIR/refdata/fermi/galdiffuse/gll_iem_v06.fits'
isodiff : '$FERMI_DIR/refdata/fermi/galdiffuse/iso_P8R2_SOURCE_V6_v06.txt'
# List of catalogs to be used in the model.
catalogs :
- '3FGL'
- 'extra_sources.xml'
sources :
- { 'name' : 'SourceA', 'ra' : 60.0, 'dec' : 30.0, 'SpectrumType' : PowerLaw }
- { 'name' : 'SourceB', 'ra' : 58.0, 'dec' : 35.0, 'SpectrumType' : PowerLaw }
# Include catalog sources within this distance from the ROI center
src_radius : null
# Include catalog sources within a box of width roisrc.
src_roiwidth : 15.0
Option | Default | Description |
---|---|---|
assoc_xmatch_columns |
[‘3FGL_Name’] | Choose a set of association columns on which to cross-match catalogs. |
catalogs |
None | |
diffuse |
None | |
extdir |
Extended_archive_v15 | |
extract_diffuse |
False | Extract a copy of all mapcube components centered on the ROI. |
galdiff |
None | Set the galactic IEM mapcube. |
isodiff |
None | Set the isotropic template. |
limbdiff |
None | |
merge_sources |
True | Merge properties of sources that appear in multiple source catalogs. If merge_sources=false then subsequent sources with the same name will be ignored. |
sources |
None | |
src_radius |
None | Set the maximum distance for inclusion of sources in the ROI model. Selects all sources within a circle of this radius centered on the ROI. If none then no selection is applied. This selection will be ORed with sources passing the cut on src_roiwidth. |
src_radius_roi |
None | Half-width of the ROI selection. This parameter can be used in lieu of src_roiwidth. |
src_roiwidth |
None | Select sources within a box of RxR centered on the ROI. If none then no cut is applied. |
optimizer¶
Option | Default | Description |
---|---|---|
min_fit_quality |
3 | Set the minimum fit quality. |
optimizer |
MINUIT | Set the optimization algorithm to use when maximizing the likelihood function. |
retries |
3 | Set the number of times to retry the fit when the fit quality is less than min_fit_quality . |
tol |
0.0001 | Set the optimizer tolerance. |
verbosity |
0 |
plotting¶
Option | Default | Description |
---|---|---|
catalogs |
None | |
cmap |
ds9_b | Set the colormap for 2D plots. |
erange |
None | |
format |
png | |
graticule_radii |
None | Define a list of radii at which circular graticules will be drawn. |
label_ts_threshold |
0.0 | TS threshold for labeling sources in sky maps. If None then no sources will be labeled. |
sed¶
The options in the sed section controls the default behavior of the
sed
method. For more information
about running this method see the SED Analysis page.
Option | Default | Description |
---|---|---|
bin_index |
2.0 | Spectral index that will be use when fitting the energy distribution within an energy bin. |
cov_scale |
3.0 | |
fix_background |
True | Fix background parameters when fitting the source flux in each energy bin. |
ul_confidence |
0.95 | Confidence level for upper limit calculation. |
use_local_index |
False | Use a power-law approximation to the shape of the global spectrum in each bin. If this is false then a constant index set to bin_index will be used. |
selection¶
The selection section collects parameters related to the data selection and target definition. The majority of the parameters in this section are arguments to gtselect and gtmktime. The ROI center can be set with the target parameter by providing the name of a source defined in one of the input catalogs (defined in the model section). Alternatively the ROI center can be defined by giving explicit sky coordinates with ra and dec or glon and glat.
selection:
# gtselect parameters
emin : 100
emax : 100000
zmax : 90
evclass : 128
evtype : 3
tmin : 239557414
tmax : 428903014
# gtmktime parameters
filter : 'DATA_QUAL>0 && LAT_CONFIG==1'
roicut : 'no'
# Set the ROI center to the coordinates of this source
target : 'mkn421'
Option | Default | Description |
---|---|---|
convtype |
None | Conversion type selection. |
dec |
None | |
emax |
None | Maximum Energy (MeV) |
emin |
None | Minimum Energy (MeV) |
evclass |
None | Event class selection. |
evtype |
None | Event type selection. |
filter |
None | Filter string for gtmktime selection. |
glat |
None | |
glon |
None | |
logemax |
None | Maximum Energy (log10(MeV)) |
logemin |
None | Minimum Energy (log10(MeV)) |
ra |
None | |
radius |
None | Radius of data selection. If none this will be automatically set from the ROI size. |
roicut |
no | |
target |
None | Choose an object on which to center the ROI. This option takes precendence over ra/dec or glon/glat. |
tmax |
None | Maximum time (MET). |
tmin |
None | Minimum time (MET). |
zmax |
None | Maximum zenith angle. |
sourcefind¶
Option | Default | Description |
---|---|---|
max_iter |
3 | Set the number of search iterations. |
min_separation |
1.0 | Set the minimum separation in deg for sources added in each iteration. |
model |
None | Set the source model dictionary. By default the test source will be a PointSource with an Index 2 power-law specturm. |
sources_per_iter |
3 | |
sqrt_ts_threshold |
5.0 | Set the threshold on sqrt(TS). |
tsmap_fitter |
tsmap | Set the method for generating the TS map. |
tsmap¶
Option | Default | Description |
---|---|---|
erange |
None | Lower and upper energy bounds in log10(E/MeV). By default the calculation will be performed over the full analysis energy range. |
max_kernel_radius |
3.0 | |
model |
None | Dictionary defining the properties of the test source. |
multithread |
False |
tscube¶
Option | Default | Description |
---|---|---|
cov_scale |
-1.0 | Scale factor to apply to broadband fitting cov. matrix in bin-by-bin fits ( < 0 -> fixed ) |
cov_scale_bb |
-1.0 | Scale factor to apply to global fitting cov. matrix in broadband fits. ( < 0 -> no prior ) |
do_sed |
True | Compute the energy bin-by-bin fits |
max_iter |
30 | Maximum number of iterations for the Newtons method fitter. |
model |
None | Dictionary defining the properties of the test source. By default the test source will be a PointSource with an Index 2 power-law specturm. |
nnorm |
10 | Number of points in the likelihood v. normalization scan |
norm_sigma |
5.0 | Number of sigma to use for the scan range |
remake_test_source |
False | If true, recomputes the test source image (otherwise just shifts it) |
st_scan_level |
0 | Level to which to do ST-based fitting (for testing) |
tol |
0.001 | Critetia for fit convergence (estimated vertical distance to min < tol ) |
tol_type |
0 | Absoulte (0) or relative (1) criteria for convergence. |