fermipy_diffuse.rst

fermipy.diffuse subpackage

The fermipy.diffuse sub-package is a collection of standalone utilities that allow the user to parallelize the data and template preparation for all-sky analysis.

The tools described here perform a number of functions:

• Making binned counts maps and expousre maps over the whole sky.
• Managing model components for all-sky analysis; including both diffuse emission and point source contributions. This includes make spatial-spectral templates and expected counts maps for various components.
• Building intergrated models for a collection of model components.
• Fitting those models.

Overview

This package implements an analysis pipeline prepare data and templates for analysis. This involves a lot of bookkeeping and loops over various things.It is probably easiest to first describe this with a bit of pseudo-code that represents the various analysis steps.

The various loop variables are:

• Input data files

  For practical reasons, the input photon event files (FT1) files are split into monthly files. In the binning step of the analysis we loop over those files.

• binning components

  We split the data into several "binning components" and make seperate binned counts maps for each components. A binning component is defined by energy range and data sub-selection (such as PSF event type and zenith angle cuts).

• Diffuse model components

  The set of all the model components that represent diffuse emission, such as contributions for cosmic ray interactions with

• Catalog model components

  The set of all the catalog sources (both point sources and extended source), merged into a few distinct contributions.

• Diffuse emission model definitions

  A set of user defined models that merge the various model components with specific spectral models.

 # Data Binning, prepare the analysis directories and precompute the DM spectra

 # First we loop over all the input input files and split up the
 # data by binning component and bin the data using the command
 # fermipy-split-and-bin-sg, which is equivalent to:
 for file in input_data_files:
     fermipy-split-and-bin(file)

 # Then we loop over the binning components and coadd the binned
 # data from all the input files using the command
 # fermipy-coadd-split-sf, which is equivalent to:
 for comp in binning_components:
     fermipy-coadd-split(comp)

 # We also loop over the binning components and compute the
 # exposure maps for each binning component using the command
 # fermipy-gtexpcube2-sg, which is equivalent to:
 for comp in binned_components:
     gtexpcube2(comp)

 # We loop over the diffuse components that come from GALProp
 # templates and refactor them using the command
 # fermipy-sum-ring-gasmaps-sg, which is equivalent to
 for galprop_comp in diffuse_galprop_components:
    fermipy-coadd(galprop_comp)

# We do a triple loop over all of the diffuse components, all the
# binning components and all the energy bins and convolve the
# emission template with the instrument response using the command
# fermipy-srcmaps-diffuse-sg, which is equivalent to
for diffuse_comp in diffuse_components:
    for binning_comp in binned_components:
        for energy in energy_bins:
             fermipy-srcmap-diffuse(diffuse_comp, binning_comp, energy)

# We then do a double loop over all the diffuse components and all
# the binning components and stack the template maps into single
# files using the command
# fermipy-vstack-diffuse-sg, which is equivalent to
for diffuse_comp in diffuse_components:
    for binning_comp in binned_components:
        fermipy-vstack-diffuse(diffuse_comp, binning_comp)

 # We then do a double loop over source catalogs and binning
 # components and compute the templates for each source using the
 # command
 # fermipy-srcmaps-catalog-sg, which is equivalent to
 for catalog in catalogs:
    for binning_comp in binned_components:
        fermipy-srcmaps-catalog(catalog, binning_comp)

 # We then loop over the catalog components (essentially
 # sub-sets of catalog sources that we want to merge)
 # and merge those sources into templates using the command
 # fermipy-merge-srcmaps-sg, which is equivalent to
 for catalog_comp in catalog_components:
    for binning_comp in binned_components:
        fermipy-merge-srcmaps(catalog_comp, binning_comp)

 # At this point we have a library to template maps for all the
 # emision components that we have defined.
 # Now we want to define specific models.  We do this
 # using the commands
 # fermipy-init-model and fermipy-assemble-model-sg, which is equivalent to
 for model in models:
     fermipy-assemble-model(model)

 # At this point we, for each model under consideration we have an
 # analysis directory that is set up for fermipy

Configuration

This section describes the configuration management scheme used within the fermipy.diffuse package and documents the configuration parameters that can be set in the configuration file.

Analysis classes in the dmpipe package all inherit from the fermipy.jobs.Link class, which allow user to invoke the class either interactively within python or from the unix command line.

From the command line

$ fermipy-srcmaps-diffuse-sg --comp config/binning.yaml --data config/dataset_source.yaml --library models/library.yaml

From python there are a number of ways to do it, we recommend this:

from fermipy.diffuse.gt_srcmap_partial import SrcmapsDiffuse_SG
link = SrcmapsDiffuse_SG( )
link.update_args(dict(comp='config/binning.yaml', data='config/dataset_source.yaml',library='models/library.yaml'))
link.run()

Top Level Configuration

We use a yaml file to define the top-level analysis parameters.

 # The binning components
 comp : config/binning.yaml
 # The dataset
 data : config/dataset_source.yaml
 # Library with the fitting components
 library : models/library.yaml
 # Yaml file with the list of models to prepare
 models : models/modellist.yaml
 # Input FT1 file
 ft1file : P8_P305_8years_source_zmax105.lst
 # HEALPix order for counts cubes
 hpx_order_ccube : 9
 # HEALPix order for exposure cubes
 hpx_order_expcube : 6
 # HEALPix order fitting models
 hpx_order_fitting : 7
 # Build the XML files for the diffuse emission model components
 make_diffuse_comp_xml : True
 # Build the XML files for the catalog source model components
 make_catalog_comp_xml : True
 # Name of the directory for the merged GALProp gasmaps
 merged_gasmap_dir : merged_gasmap
 # Number of catalog sources per batch job
 catalog_nsrc : 500

Binning Configuration

We use a yaml file to define the binning components.

coordsys : 'GAL'
E0:
    log_emin : 1.5
    log_emax : 2.0
    enumbins : 2
    zmax : 80.
    psf_types :
        PSF3 :
            hpx_order : 5
E1:
    log_emin : 2.0
    log_emax : 2.5
    enumbins : 2
    zmax : 90.
    psf_types :
        PSF23 :
            hpx_order : 6
E2:
    log_emin : 2.5
    log_emax : 3.0
    enumbins : 3
    zmax : 100.
    psf_types :
        PSF123 :
            hpx_order : 8
E3:
    log_emin : 3.0
    log_emax : 6.0
    enumbins : 9
    zmax : 105.
    psf_types :
        PSF0123 :
           hpx_order : 9

• coordsys : 'GAL' or 'CEL'

  Coordinate system to use

• log_emin, log_emax: float

  Energy bin boundries in log10(MeV)

• enumbins: int

  Number of energy bins for this binning component

• zmax : float

  Maximum zenith angle (in degrees) for this binning component

• psf_types: dict

  Sub-dictionary of binning components by PSF event type, PSF3 means PSF event type 3 events only. PSF0123 means all four PSF event types.

• hpx_order: int

  HEALPix order to use for binning. The more familiar nside parameter is nside = 2**order

Dataset Configuration

We use a yaml file to define the data set we are using. The example below specifies using a pre-defined 8 year dataset, selecting the "SOURCE" event class and using the V2 version of the corresponding IRFs (specifically P8R3_SOURCE_V2).

 basedir : '/gpfs/slac/kipac/fs1/u/dmcat/data/flight/diffuse_dev'
 data_pass : 'P8'
 data_ver : 'P305'
 evclass : 'source'
 data_time : '8years'
 irf_ver : 'V2'

The basedir parameter should point at the analysis directory. For the most part the other parameter are using to make the names of the various files produced by the pipeline. The evclass parameter defines the event selection, and the IRF version is defined by a combination of the data_ver, evclass and irf_ver parameters.

GALProp Rings Configuration

We use a yaml file to define the how we combine GALProp emission templates. The example below specifies how to construct as series of 'merged_CO' rings by combining GALProp intensity template predictions.

 galprop_run : 56_LRYusifovXCO5z6R30_QRPD_150_rc_Rs8
 ring_limits : [1, 2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 15]
 diffuse_comp_dict :
     merged_CO : ['pi0_decay_H2R', 'bremss_H2R']
 remove_rings : ['merged_CO_7']

• galprop_run : string

  Define the GALProp run to use for this component. This is used to make the filenames for input template maps.

• ring_limits : list of int

  This specfies how to combine the GALProp rings into a smaller set of rings.

• diffuse_comp_dict : dict

  This specifies how to make GALProp components into merged components for the diffuse analysis

• remove_rings: list of str

  This allow use to remove certain rings from the model

Catalog Component Configuration

We use a yaml file to define the how we split up the catalog source components. The example below specifies using the FL8Y source list, and to split out the faint sources (i.e., those with the Signif_Avg value less that 100.), and the extended source, and to keep all the remaining sources (i.e., the bright, pointlike, sources) as individual sources.

 catalog_name : FL8Y
 catalog_file : /nfs/slac/kipac/fs1/u/dmcat/ancil/catalogs/official/4FGLp/gll_psc_8year_v4.fit
 catalog_extdir : /nfs/slac/kipac/fs1/u/dmcat/ancil/catalogs/official/extended/Extended_archive_v18
 catalog_type : FL8Y
 rules_dict :
     faint :
         cuts :
             - { cut_var: Signif_Avg, max_val : 100. }
             - mask_extended
     extended :
         cuts :
             - select_extended
     remainder :
         merge : False

Model Component Library

We use a yaml file to define a "library" of model components. The comprises a set of named emission components, and a set one or more versions for each named component. Here is an example library defintion file.

 # Catalog Components
 FL8Y :
     model_type : catalog
     versions : [v00]
 # Diffuse Components
 galprop_rings :
     model_type : galprop_rings
     versions : [p8-ref_IC_thin, p8-ref_HI_150, p8-ref_CO_300_mom, p8-ref_dnm_300hp]
 dnm_merged:
     model_type : MapCubeSource
    versions : ['like_4y_300K']
 gll-iem :
     model_type : MapCubeSource
     versions : [v06]
 loopI :
     model_type : MapCubeSource
     versions : [haslam]
 bubbles :
     model_type : MapCubeSource
     versions : [v00, v01]
 iso_map :
     model_type : MapCubeSource
     versions : [P8R3_SOURCE_V2]
 patches :
     model_type : MapCubeSource
     versions : [v09]
     selection_dependent : True
     no_psf : True
     edisp_disable : True
 unresolved :
     model_type : MapCubeSource
     versions : [strong]
 sun-ic :
     model_type : MapCubeSource
     versions : [v2r0, P8R3-v2r0]
     moving : True
     edisp_disable : True
 sun-disk :
     model_type : MapCubeSource
     versions : [v3r1, P8R3-v3r1]
     moving : True
     edisp_disable : True
 moon :
     model_type : MapCubeSource
     versions : [v3r2, P8R3-v3r2]
     moving : True
     edisp_disable : True

• model_type: 'MapCubeSource' or 'catalog' or 'galprop_rings' or 'SpatialMap'

  Specifies how this model should be constructed. See more below in the versions parameters.

• versions: list of str

  Specifies different versions of this model component. How this string is used depend on the model type. for 'MapCubeSource' and 'SpatialMap' sources it is used to construct the expected filename for the intensity template. For 'catalog' and 'galprop_rings' it is used to construct the filename for the yaml file that defines the sub-components for that component.

• moving: bool If true, then will use source-specific livetime cubes to constuct source templates for each zenith angle cut.
• selection_dependent : bool If true, then will used different source templates for each binning component.
• no_psf : bool Turns of PSF convolution for this source. Useful for data-driven components.
• edisp_disable : bool Turns off energy dispersion for the source. Useful for data-driven components.

Spectral Model Configuration

We use a yaml file to define the spectral models and default parameters. This file is simply a dictionary mapping names to sub-dictionaries defining spectral models and default model parameters.

Model Defintion

We use a yaml file to define each overall model, which combine library components and spectral models.

 library : models/library.yaml
 spectral_models : models/spectral_models.yaml
 sources :
     galprop_rings_p8-ref_IC_thin :
         model_type : galprop_rings
         version : p8-ref_IC_150
         SpectrumType :
             default : Constant_Correction
     galprop_rings-p8-ref_HI_300:
         model_type : galprop_rings
         version : p8-ref_HI_300
         SpectrumType :
             default : Powerlaw_Correction
             merged_HI_2_p8-ref_HI_300 : BinByBin_5
             merged_HI_3_p8-ref_HI_300 : BinByBin_5
             merged_HI_4_p8-ref_HI_300 : BinByBin_9
             merged_HI_5_p8-ref_HI_300 : BinByBin_9
             merged_HI_6_p8-ref_HI_300 : BinByBin_9
             merged_HI_8_p8-ref_HI_300 : BinByBin_5
             merged_HI_9_p8-ref_HI_300 : BinByBin_5
     galprop_rings-p8-ref_CO_300:
         model_type : galprop_rings
         version : p8-ref_CO_300_mom
         SpectrumType :
             default : Powerlaw_Correction
             merged_CO_2_p8-ref_CO_300_mom : BinByBin_5
             merged_CO_3_p8-ref_CO_300_mom : BinByBin_5
             merged_CO_4_p8-ref_CO_300_mom : BinByBin_9
             merged_CO_5_p8-ref_CO_300_mom : BinByBin_9
             merged_CO_6_p8-ref_CO_300_mom : BinByBin_9
             merged_CO_8_p8-ref_CO_300_mom : BinByBin_5
             merged_CO_9_p8-ref_CO_300_mom : BinByBin_5
     dnm_merged :
         version : like_4y_300K
         SpectrumType : BinByBin_5
     iso_map :
         version : P8R3_SOURCE_V2
         SpectrumType : Iso
     sun-disk :
         version : v3r1
         SpectrumType : Constant_Correction
         edisp_disable : True
     sun-ic :
         version : v2r0
         SpectrumType : Constant_Correction
         edisp_disable : True
     moon :
         version : v3r2
         SpectrumType : Constant_Correction
         edisp_disable : True
     patches :
         version : v09
         SpectrumType : Patches
         edisp_disable : True
     unresolved :
         version : strong
         SpectrumType : Constant_Correction
     FL8Y :
         model_type : Catalog
         version : v00
         SpectrumType :
             default : Constant_Correction
             FL8Y_v00_remain : Catalog
             FL8Y_v00_faint : BinByBin_9

• model_type: 'MapCubeSource' or 'catalog' or 'galprop_rings' or 'SpatialMap'

  Specifies how this model should be constructed. See more below.

• version: str

  Specifies version of this model component.

• edisp_disable : bool Turns off energy dispersion for the source. Useful for data-driven components. Needed for model XML file construction.
• SpectrumType: str or dictionary This specifies the Spectrum type to use for this model component. For 'catalog' and 'galprop_rings' model types it can be a dictionary mapping model sub-components to spectrum types. Note that the spectrum types should be defined in the spectral model configuration described above.

Examples

Module contents

.. automodule:: fermipy.diffuse
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Configuration, binning, default options, etc...

.. automodule:: fermipy.diffuse.binning
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.. automodule:: fermipy.diffuse.defaults
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.. automodule:: fermipy.diffuse.name_policy
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Utilities and tools

.. automodule:: fermipy.diffuse.spectral
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.. automodule:: fermipy.diffuse.timefilter
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.. automodule:: fermipy.diffuse.source_factory
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.. automodule:: fermipy.diffuse.utils
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Helper classes to manage model building

.. autoclass:: fermipy.diffuse.model_component.ModelComponentInfo
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.. autoclass:: fermipy.diffuse.model_component.CatalogInfo
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.. autoclass:: fermipy.diffuse.model_component.GalpropMergedRingInfo
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.. autoclass:: fermipy.diffuse.model_component.ModelComponentInfo
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.. autoclass:: fermipy.diffuse.model_component.IsoComponentInfo
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.. autoclass:: fermipy.diffuse.model_component.PointSourceInfo
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.. autoclass:: fermipy.diffuse.model_component.CompositeSourceInfo
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.. autoclass:: fermipy.diffuse.model_component.CatalogSourcesInfo
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.. autoclass:: fermipy.diffuse.diffuse_src_manager.GalpropMapManager
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.. autoclass:: fermipy.diffuse.diffuse_src_manager.DiffuseModelManager
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.. autoclass:: fermipy.diffuse.catalog_src_manager.CatalogSourceManager
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.. autoclass:: fermipy.diffuse.model_manager.ModelComponent
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.. autoclass:: fermipy.diffuse.model_manager.ModelInfo
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.. autoclass:: fermipy.diffuse.model_manager.ModelManager
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Trivial Link Sub-classes

.. autoclass:: fermipy.diffuse.job_library.Gtlink_select
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_bin
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_expcube2
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_scrmaps
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_ltsum
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_mktime
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.. autoclass:: fermipy.diffuse.job_library.Gtlink_ltcube
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.. autoclass:: fermipy.diffuse.solar.Gtlink_expcube2_wcs
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.. autoclass:: fermipy.diffuse.solar.Gtlink_exphpsun
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.. autoclass:: fermipy.diffuse.solar.Gtlink_suntemp
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.. autoclass:: fermipy.diffuse.job_library.Link_FermipyCoadd
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.. autoclass:: fermipy.diffuse.job_library.Link_FermipyGatherSrcmaps
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.. autoclass:: fermipy.diffuse.job_library.Link_FermipyVstack
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.. autoclass:: fermipy.diffuse.job_library.Link_FermipyHealview
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Standalone Analysis Links

.. autoclass:: fermipy.diffuse.gt_merge_srcmaps.GtMergeSrcmaps
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.. autoclass:: fermipy.diffuse.gt_srcmap_partial.GtSrcmapsDiffuse
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.. autoclass:: fermipy.diffuse.gt_srcmaps_catalog.GtSrcmapsCatalog
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.. autoclass:: fermipy.diffuse.gt_assemble_model.InitModel
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.. autoclass:: fermipy.diffuse.gt_assemble_model.AssembleModel
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.. autoclass:: fermipy.diffuse.residual_cr.ResidualCR
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Batch job dispatch classes

.. autoclass:: fermipy.diffuse.job_library.Gtexpcube2_SG
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.. autoclass:: fermipy.diffuse.job_library.Gtltsum_SG
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.. autoclass:: fermipy.diffuse.solar.Gtexpcube2wcs_SG
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.. autoclass:: fermipy.diffuse.solar.Gtexphpsun_SG
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.. autoclass:: fermipy.diffuse.solar.Gtsuntemp_SG
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.. autoclass:: fermipy.diffuse.gt_coadd_split.CoaddSplit_SG
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.. autoclass:: fermipy.diffuse.job_library.GatherSrcmaps_SG
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.. autoclass:: fermipy.diffuse.job_library.Vstack_SG
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.. autoclass:: fermipy.diffuse.job_library.Healview_SG
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.. autoclass:: fermipy.diffuse.job_library.SumRings_SG
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.. autoclass:: fermipy.diffuse.job_library.SumRings_SG
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.. autoclass:: fermipy.diffuse.residual_cr.ResidualCR_SG
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.. autoclass:: fermipy.diffuse.gt_merge_srcmaps.MergeSrcmaps_SG
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.. autoclass:: fermipy.diffuse.gt_srcmap_partial.SrcmapsDiffuse_SG
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.. autoclass:: fermipy.diffuse.gt_srcmaps_catalog.SrcmapsCatalog_SG
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.. autoclass:: fermipy.diffuse.gt_assemble_model.AssembleModel_SG
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.. autoclass:: fermipy.diffuse.residual_cr.ResidualCR_SG
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.. autoclass:: fermipy.diffuse.gt_split_and_bin.SplitAndBin_SG
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.. autoclass:: fermipy.diffuse.gt_split_and_mktime.SplitAndMktime_SG
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Analysis chain classes

.. autoclass:: fermipy.diffuse.gt_coadd_split.CoaddSplit
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.. autoclass:: fermipy.diffuse.gt_split_and_bin.SplitAndBin
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.. autoclass:: fermipy.diffuse.gt_split_and_bin.SplitAndBinChain
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.. autoclass:: fermipy.diffuse.gt_split_and_mktime.SplitAndMktime
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.. autoclass:: fermipy.diffuse.gt_split_and_mktime.SplitAndMktimeChain
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.. autoclass:: fermipy.diffuse.diffuse_analysis.DiffuseCompChain
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.. autoclass:: fermipy.diffuse.diffuse_analysis.CatalogCompChain
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.. autoclass:: fermipy.diffuse.gt_assemble_model.AssembleModelChain
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.. autoclass:: fermipy.diffuse.diffuse_analysis.DiffuseAnalysisChain
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    :undoc-members:
    :show-inheritance:

.. autoclass:: fermipy.diffuse.residual_cr.ResidualCRChain
    :members:
    :undoc-members:
    :show-inheritance:

.. autoclass:: fermipy.diffuse.solar.SunMoonChain
    :members:
    :undoc-members:
    :show-inheritance: