lsst.obs.base

The lsst.obs.base module provides the framework and common API for telescope/camera specific “obs” packages. New cameras will derive from the classes defined here. lsst.obs.base.tests provides the tests that all “obs” packages should pass.

Changes

Using lsst.obs.base

Contributing

lsst.obs.base is developed at https://github.com/lsst/obs_base. You can find Jira issues for this module under the obs_base component.

Command Line Interface

daf_butler implements a command line interface command called butler. The following subcommands are implemented by this package and available to the butler command when this package is setup.

butler

Run the command.

butler [OPTIONS] COMMAND [ARGS]...

convert

Convert one or more Butler gen 2 repositories into a gen 3 repository.

REPO is the URI or path to the gen3 repository. Will be created if it does not already exist

This is a highly simplified interface that should only be used to convert suites of gen 2 repositories that contain at most one calibration repo and has no chained reruns. Custom scripts that call ConvertRepoTask should be used on more complex suites of repositories.

butler convert [OPTIONS] REPO

Options

--gen2root <gen2root>

Required Root path of the gen 2 repo to be converted.

--skymap-name <skymap_name>

Name of the new gen3 skymap (e.g. ‘discrete/ci_hsc’).

--skymap-config <skymap_config>

Path to skymap config file defining the new gen3 skymap.

--calibs <calibs>

Path to the gen 2 calibration repo. It can be absolute or relative to gen2root.

--reruns <TEXT ...>

List of rerun paths to convert. Output collection names will be guessed, which can fail if the Gen2 repository paths do not follow a recognized convention. In this case, the command-line interface cannot be used.

-t, --transfer <transfer>

Mode to use to transfer files into the new repository.

Options:

auto | link | symlink | hardlink | copy | move | relsymlink | direct

-j, --processes <processes>

Number of processes to use.

-C, --config-file <config_file>

Path to a ConvertRepoConfig override to be included after the Instrument config overrides are applied.

-@, --options-file <options_file>

URI to YAML file containing overrides of command line options. The YAML should be organized as a hierarchy with subcommand names at the top level options for that subcommand below.

Arguments

REPO

Required argument

See ‘butler –help’ for more options.

define-visits

Define visits from exposures in the butler registry.

REPO is the URI or path to the gen3 repository. Will be created if it does not already exist

The fully-qualified name of an Instrument subclass.

The calibration collection containing the camera geometry can not be specified.

butler define-visits [OPTIONS] REPO INSTRUMENT

Options

-C, --config-file <config_file>

Path to a pex_config override to be included after the Instrument config overrides are applied.

--collections <TEXT ...>

The collections to be searched (in order) when reading datasets.

--where <where>

A string expression similar to a SQL WHERE clause.

--update-records, --no-update-records

Use this option to force updates to the visit definition record. Should only be used if you know that there has been a change to the exposure records, such as a change to the metadata translator.

--incremental, --no-incremental

Use this option to force updates to the visit definition record when multi-snap visits are being ingested incrementally and so you might encounter partial visits. Implies –update-records.

-@, --options-file <options_file>

URI to YAML file containing overrides of command line options. The YAML should be organized as a hierarchy with subcommand names at the top level options for that subcommand below.

Arguments

REPO

Required argument

INSTRUMENT

Required argument

See ‘butler –help’ for more options.

ingest-raws

Ingest raw frames into from a directory into the butler registry.

REPO is the URI or path to the gen3 repository. Will be created if it does not already exist

LOCATIONS specifies files to ingest and/or locations to search for files.

butler ingest-raws [OPTIONS] REPO LOCATIONS ...

Options

--regex <regex>

Regex string used to find files in directories listed in LOCATIONS. Searches for fits files by default.

-c, --config <TEXT=TEXT>

Config override, as a key-value pair.

-C, --config-file <config_file>

Path to a pex config override to be included after the Instrument config overrides are applied.

--output-run <output_run>

The name of the run datasets should be output to.

-t, --transfer <transfer>

The external data transfer mode.

Options:

auto | link | symlink | hardlink | copy | move | relsymlink | direct

-j, --processes <processes>

Number of processes to use.

--ingest-task <ingest_task>

The fully qualified class name of the ingest task to use.

--track-file-attrs, --no-track-file-attrs

Indicate to the datastore whether file attributes such as file size or checksum should be tracked or not. Whether this parameter is honored depends on the specific datastore implentation.

--fail-fast

Stop ingest as soon as any problem is encountered with any file. Otherwise problem files will be skipped and logged and a report issued at completion.

--update-records, --no-update-records

Use this option to force updates to the exposure records. Should only be used if you know that there has been a change to the exposure records, such as a change to the metadata translator.

-@, --options-file <options_file>

URI to YAML file containing overrides of command line options. The YAML should be organized as a hierarchy with subcommand names at the top level options for that subcommand below.

Arguments

REPO

Required argument

LOCATIONS

Required argument(s)

See ‘butler –help’ for more options.

write-curated-calibrations

Add an instrument’s curated calibrations to the data repository.

REPO is the URI or path to the gen3 repository. Will be created if it does not already exist

The fully-qualified name of an Instrument subclass.

LBL: One or more extra strings to include in the collection name (see –label).

butler write-curated-calibrations [OPTIONS] REPO INSTRUMENT  ...

Options

--collection <collection>

Name of the calibration collection that associates datasets with validity ranges.

--label <labels>

Extra strings to include (with automatic delimiters) in all RUN collection names, as well as the calibration collection name if it is not provided via –collection. May be provided as a positional argument instead of or in addition to this option, as long as at least one label is provided. Positional-argument labels appear before those provided by this option.

--prefix <prefix>

Prefix for the collection name. Default is the instrument name. This is ignored if –collection is passed.

-@, --options-file <options_file>

URI to YAML file containing overrides of command line options. The YAML should be organized as a hierarchy with subcommand names at the top level options for that subcommand below.

Arguments

REPO

Required argument

INSTRUMENT

Required argument

LBL

Optional argument(s)

See ‘butler –help’ for more options.

Python API reference

lsst.obs.base Package

Functions

bboxFromIraf(irafBBoxStr)

Return a Box2I corresponding to an IRAF-style BBOX.

createInitialSkyWcs(visitInfo, detector[, flipX])

Create a SkyWcs from the visit information and detector geometry.

createInitialSkyWcsFromBoresight(boresight, ...)

Create a SkyWcs from the telescope boresight and detector geometry.

loadCamera(butler, dataId, *[, collections])

Attempt to load versioned camera geometry from a butler, but fall back to obtaining a nominal camera from the Instrument class if that fails.

makeExposureRecordFromObsInfo(obsInfo, ...)

Construct an exposure DimensionRecord from astro_metadata_translator.ObservationInfo.

makeTransferChoiceField([doc, default])

Create a Config field with options for transferring data between repos.

Classes

DefineVisitsConfig(*args, **kw)

Configure visit definition.

DefineVisitsTask(config, *, butler, **kwargs)

Driver Task for defining visits (and their spatial regions) in Gen3 Butler repositories.

FilterDefinition(physical_filter[, band, ...])

The definition of an instrument's filter bandpass.

FilterDefinitionCollection(*filters)

An order-preserving collection of multiple FilterDefinition.

FitsRawFormatterBase(*args, **kwargs)

Abstract base class for reading and writing raw data to and from FITS files.

GroupExposuresConfig(*args, **kw)

Configure exposure grouping.

GroupExposuresTask(config, **kwargs)

Abstract base class for the subtask of DefineVisitsTask that is responsible for grouping exposures into visits.

InitialSkyWcsError

For handling failures when creating a SkyWcs from a camera geometry and boresight.

Instrument([collection_prefix])

Rubin-specified base for instrument-specific logic for the Gen3 Butler.

MakeRawVisitInfoViaObsInfo([log, doStripHeader])

Base class functor to make a VisitInfo from the FITS header of a raw image using ObservationInfo translators.

RawIngestConfig(*args, **kw)

Configuration class for RawIngestTask.

RawIngestTask(config, *, butler, on_success, ...)

Driver Task for ingesting raw data into Gen3 Butler repositories.

VisitDefinitionData(instrument, id, name, ...)

Struct representing a group of exposures that will be used to define a visit.

VisitSystem(value[, names, module, ...])

Enumeration used to label different visit systems.

Class Inheritance Diagram

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"FilterDefinitionCollection" [URL="../../../py-api/lsst.obs.base.FilterDefinitionCollection.html#lsst.obs.base.FilterDefinitionCollection",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="An order-preserving collection of multiple `FilterDefinition`."]; "Sequence" -> "FilterDefinitionCollection" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FitsImageFormatterBase" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="Base class formatter for image-like storage classes stored via FITS."]; "FormatterV2" -> "FitsImageFormatterBase" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FitsRawFormatterBase" [URL="../../../py-api/lsst.obs.base.FitsRawFormatterBase.html#lsst.obs.base.FitsRawFormatterBase",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Abstract base class for reading and writing raw data to and from"]; "FitsImageFormatterBase" -> "FitsRawFormatterBase" [arrowsize=0.5,style="setlinewidth(0.5)"]; "FormatterV2" [URL="../../../py-api/lsst.daf.butler.FormatterV2.html#lsst.daf.butler.FormatterV2",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Interface for reading and writing datasets using URIs."]; "GroupExposuresConfig" [URL="../../../py-api/lsst.obs.base.GroupExposuresConfig.html#lsst.obs.base.GroupExposuresConfig",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Configure exposure grouping."]; "Config" -> "GroupExposuresConfig" [arrowsize=0.5,style="setlinewidth(0.5)"]; "GroupExposuresTask" [URL="../../../py-api/lsst.obs.base.GroupExposuresTask.html#lsst.obs.base.GroupExposuresTask",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Abstract base class for the subtask of `DefineVisitsTask` that is"]; "Task" -> "GroupExposuresTask" [arrowsize=0.5,style="setlinewidth(0.5)"]; "InitialSkyWcsError" [URL="../../../py-api/lsst.obs.base.InitialSkyWcsError.html#lsst.obs.base.InitialSkyWcsError",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="For handling failures when creating a SkyWcs from a camera geometry and"]; "Instrument" [URL="../../../py-api/lsst.obs.base.Instrument.html#lsst.obs.base.Instrument",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Rubin-specified base for instrument-specific logic for the Gen3 Butler."]; "Instrument" -> "Instrument" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Instrument" [URL="../../../py-api/lsst.pipe.base.Instrument.html#lsst.pipe.base.Instrument",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class for instrument-specific logic for the Gen3 Butler."]; "Iterable" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled"]; "MakeRawVisitInfoViaObsInfo" [URL="../../../py-api/lsst.obs.base.MakeRawVisitInfoViaObsInfo.html#lsst.obs.base.MakeRawVisitInfoViaObsInfo",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class functor to make a VisitInfo from the FITS header of a"]; "RawIngestConfig" [URL="../../../py-api/lsst.obs.base.RawIngestConfig.html#lsst.obs.base.RawIngestConfig",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Configuration class for RawIngestTask."]; "Config" -> "RawIngestConfig" [arrowsize=0.5,style="setlinewidth(0.5)"]; "RawIngestTask" [URL="../../../py-api/lsst.obs.base.RawIngestTask.html#lsst.obs.base.RawIngestTask",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Driver Task for ingesting raw data into Gen3 Butler repositories."]; "Task" -> "RawIngestTask" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Reversible" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled"]; "Iterable" -> "Reversible" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Sequence" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",tooltip="All the operations on a read-only sequence."]; "Reversible" -> "Sequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Collection" -> "Sequence" [arrowsize=0.5,style="setlinewidth(0.5)"]; "Sized" [fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled"]; "Task" [URL="../../../py-api/lsst.pipe.base.Task.html#lsst.pipe.base.Task",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Base class for data processing tasks."]; "VisitDefinitionData" [URL="../../../py-api/lsst.obs.base.VisitDefinitionData.html#lsst.obs.base.VisitDefinitionData",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Struct representing a group of exposures that will be used to define a"]; "VisitSystem" [URL="../../../py-api/lsst.obs.base.VisitSystem.html#lsst.obs.base.VisitSystem",fillcolor=white,fontname="Vera Sans, DejaVu Sans, Liberation Sans, Arial, Helvetica, sans",fontsize=10,height=0.25,shape=box,style="setlinewidth(0.5),filled",target="_top",tooltip="Enumeration used to label different visit systems."]; "Enum" -> "VisitSystem" [arrowsize=0.5,style="setlinewidth(0.5)"]; }

lsst.obs.base.tests Module

Functions

make_ramp_array(bbox, pedestal)

Make a 2-d ramp array.

make_ramp_exposure_trimmed(detector[, dtype])

Create a trimmed, assembled exposure with different ramps for each amplifier region.

make_ramp_exposure_untrimmed(detector[, dtype])

Create an untrimmed, assembled exposure with different ramps for each sub-amplifier region.

Classes

ObsTests()

Aggregator class for all of the obs_* test classes.

Class Inheritance Diagram

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lsst.obs.base.formatters.fitsExposure Module

Functions

standardizeAmplifierParameters(parameters, ...)

Preprocess the Exposure storage class's "amp" and "detector" parameters.

Classes

FitsExposureFormatter(file_descriptor, *, ref)

Concrete formatter for reading/writing Exposure from/to FITS.

FitsImageFormatter(file_descriptor, *, ref)

Concrete formatter for reading/writing Image from/to FITS.

FitsMaskFormatter(file_descriptor, *, ref[, ...])

Concrete formatter for reading/writing Mask from/to FITS.

FitsMaskedImageFormatter(file_descriptor, *, ref)

Concrete formatter for reading/writing MaskedImage from/to FITS.

Class Inheritance Diagram

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lsst.obs.base.formatters.fitsGeneric Module

Classes

FitsGenericFormatter(file_descriptor, *, ref)

Interface for reading and writing objects that support the standard afw I/O readFits/writeFits methods.

Class Inheritance Diagram

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