Ctrl+K

. include:: ../../references.txt

PIG 25 - Metadata container for Gammapy#

  • Author: Régis Terrier

  • Created: April 14th, 2023

  • Accepted: July 10th, 2023

  • Status: Accepted

  • Discussion: GH 4491

Abstract#

Metadata handling is crucial to correctly store information that are not directly data but are still required for processing, post-processing and serialization. They are fundamental for reproducibility.

Introduction#

As of version 1.0, Gammapy has very little support for metadata. Existing features are heterogeneous, hardly configurable and appear sporadically in the code, mostly in containers. At the DL3 level, EventList metadata is carried by its Table.meta dictionary. It is extracted from the file FITS header which follows the GADF specifications. Similarly, Observation contains an obs_info dictionary that is build from the header as well. After data reduction, Dataset contains a meta_table which consists in a selection of Observation.obs_info entries (one table row per observation). During Dataset stacking the meta_table are stacked. The Datasets collection also aggregates the meta_table of its members. After estimation, the FluxPoints don’t contain any specific meta information.

The algorithm classes (Makers and Estimators) don’t contain any meta information so far. This might be an issue since some information could be transferred on their various products as well.

A minimal information that needs to be present on every Gammapy product and serialized in various formats is the CREATOR which is the software and software version used, as well as the DATE when the object was created, and possibly the ORIGIN (the user, the consortium that has produced the object). The Gammapy version number is important to ensure reproducibility and compatibility.

An Observation also needs some information to ensure correct handling of data. For instance, the telescope name, the sub-array used, the observation mode, the telescope location etc.

A practical and systematic solution must be implemented in Gammapy. This PIG discusses the approach and proposes a solution for this. It does not discuss the metadata model, i.e. what information has to be stored on which data product. It proposes a basic concept and a possible implementation of a metadata container object that fulfill the requirements.

Requirements#

The Gammapy metadata solution should:

  • offer flexibility regarding the content of the data model, e.g.:

    • it should allow optional entries

    • it should be configurable to allow for specific data models

  • have a systematic validation of its content

  • allow for serialization to various formats, e.g.:

    • export specific keywords to fits headers depending on the data format

    • export content to yaml

  • allow hierarchical content to allow easy propagation of metadata content along the analysis flow

  • be easily sub-scriptable to allow for specialized metadata containers for the various objects in Gammapy.

In the following, we propose a plausible solution fulfilling these requirements based on the the pydantic package BaseModel class.

Metadata API#

All Gammapy classes containing metadata should store them in a meta attribute.

Type validation#

The API should support simple validation on input, even for non standard types such as astropy or Gammapy objects.

# direct assignment
>>> meta.zenith_angle = Angle(30, "deg")
# or via a string representation
>>> meta.zenith_angle = "30 deg"
# input validation
>>> meta.zenith_angle = 2*u.TeV
ValidationError: 1 validation error for MetaData zenith_angle
# attribute type is astropy Angle
>>> print(meta.zenith_angle)
30d00m00s

Hierarchy#

The API should allow hierarchical structure with metadata classes having other metadata objects as attributes. See the following example:

class CreatorMedadata:
    creator : str
    date : datetime
    origin : str

class ObservationMetadata:
    obs_id : str
    creator : CreatorMetadata

Serialization#

The metadata classes should have a to_dict() or dict() method to convert their content to a dictionary.

Conversion to various output formats should be supported with specific methods such as to_yaml() of to_header() to export the content in the form of a FITS header, when possible.

Because we expect the number of data formats will increase over the years, specific Reader and Writer functions or classes could be defined to support e.g. reading and writing to gadf DL3 format.

Proposed solution#

pydantic#

The pydantic package has been built to perform data validation and settings management using Python type annotations. It enforces type hints at runtime, and provides user friendly errors when data is invalid.

It offers nice features such as:

  • it can be extended to custom data types (e.g. a Quantity or a Map) with a simple decorator based scheme to define validators.

  • it supports recursive models

The package now extremely widely used in the python ecosystem with more than 50 millions monthly Pypi downloads. Its long-term viability does not appear problematic.

Gammapy already uses pydantic for its high level analysis configuration class.

There are several other options available such as traitlets. The latter also allows the addition of user-defined TraitType.

the base class#

A typical base class for all Gammapy metadata could structured following the structure below:

class MetaDataBaseModel(BaseModel):
    class Config:
        arbitrary_types_allowed = True
        validate_all = True
        validate_assignment = True
        extra = "allow"

    def to_header(self):
        hdr_dict = {}
        for key, item in self.dict().items():
            hdr_dict[key.upper()] = item.__str__()
        return hdr_dict

    @classmethod
    def from_header(cls, hdr):
        kwargs = {}
        for key in cls.__fields__.keys():
            kwargs[key] = hdr.get(key.upper(), None)
        return cls(**kwargs)

The model Config defined allows:

  • using any type input and not only simple Annotation types (arbitrary_types_allowed = True)

  • Setting the validate_assignment to True ensures that validation is performed when a value is assigned to the attribute.

  • extra = "allow" accepts additional attributes not defined in the metadata class.

arbitrary type input and validation#

By providing a validation method, it is possible to validate non-standard objects. The validator decorator provided by pydantic makes it easy. As shown below:

class ArbitraryTypeMetaData(MetaDataBaseModel):
    # allow string defining angle or Angle object
    zenith_angle : Optional[Union[str, Angle]]
    pointing_altaz : Union[]

    # allow observatory name or astropy EarthLocation object
    location : Optional[Union[str, EarthLocation]]

    @validator('location')
    def validate_location(cls, v):
        if isinstance(v, str) and v in observatory_locations.keys():
            return observatory_locations[v]
        elif isinstance(v, EarthLocation):
            return v
        else:
            raise ValueError("Incorrect location value")

    @validator('zenith_angle')
    def validate_zenith_angle(cls, v):
        return Angle(v)

Alternatives#

Another option could be to use traitlets, but this would require creating dedicated types for non-supported types (e.g. SkyCoord). Additional functionalities such as observer would not be very useful here.

Proposed metadata classes#

Here we list the expected metadata classes that we expect. All classes will inherit from a parent MetaDataBase that will provide most base properties to the daughter classes.

We provide the list of classes by subpackage

data#

  • EventListMetaData

  • ObservationMetaData

  • DataStoreMetaData

  • PointingMetaData

  • GTIMetaData

IRF#

Here we should distinguish between actual IRFs and reduced modeling-ready IRFs such as kernels and IRF maps.

  • IRFMetaData : A single generic class could be used for all actual IRFs.

Makers#

It is unclear whether stateless algorithm classes such as Maker actually need meta information beyond their actual attributes. They will have to create or update meta information of the Dataset they create or modify. For now, we don’t propose any metadata for Maker objects.

Datasets#

The Dataset already contains some meta information with the meta_table which contains a small subset of information from the observations that where used to build the object.

The new metadata might replace the current meta_table. The metadata should support stacking, in particular some of the fields might be lists of entries which require validation.

  • MapDatasetMetaData

  • FluxPointsDatasetMetaData : the metadata class for the FluxPointsDataset.

  • DatasetsMetaData

Modeling#

Similarly to Makers, it is unclear the Fit class needs specific metadata as it is not serialized.

Because they are serialized, Model and Models objects should have a minimal meta.

  • ModelsMetadata

  • ModelMetaData

Estimators#

Again, the stateless Estimator algorithms do not need a meta attribute. They need to build the meta information of the products they create, transferring some metadata from the parent Datasets.

  • FluxMapsMetaData

  • FluxPointsMetaData

Metadata generation and propagation along the dataflow#

DL3 products should come with their pre-defined metadata (unless generated by Gammapy for instance during event simulations). But all all other data levels will have metadata generated by Gammapy. Algorithm classes (Makers, Estimators) produce new data containers (DL4 and DL5), they will generate new metadata to be stored on the container and will propagate some of the metadata from the lower level products they manipulate. What metadata will be passed or discarded, how metadata will be restructured in this process (i.e. how propagation and reduction will be performed) is beyond the scope of this PIG. For now, the important point is that metadata handling becomes a task of algorithm classes. The actual definition of the metadata classes will have to support the propagation and reduction process. An obvious case is Dataset stacking. The associated meta class will have to support the stacking mechanism.

Decision#

The PIG is accepted. Some of the proposed API will have to evolve a bit after the release of pydantic v2.

On this page
Show Source