Release Notes¶

Add the option of excluding mask planes before coaddition¶

The user-configurable parameter removeMaskPlanes has been added to AssembleCoaddConfig. This is a list of mask planes which will not be propagated to the coadd; by default, the CROSSTALK and NOT_DEBLENDED mask planes are removed. [DM-4866]

Dumping task configuration parameters now includes documentation¶

That is, running ${TASK} ... --show config displays not only the names and values of the configuration but also associated documentation. [DM-3811]

Clean up interpolation tasks and implement useFallbackValueAtEdge¶

The interpImageTask in pipe_tasks has been refactored to implement a single run function for interpolation over a list of defects in an image. This run function will accept an afw image type of either MaskedImage or Exposure. A defects list can be passed in directly or the name of mask plane can be passed from which a defects list will be created. If a PSF is attached to the image, it will be used as the (required) argument for the interpolateoverDefects function in meas_algorithms used for the interpolation. Otherwise a FWHM (in pixels) can be provided or the defaultFWHM value in meas_algorithms‘ GaussianFactory is used. Note that while the PSF is a required argument for meas_algorithms‘ interpolateOverDefects function it is currently not being used, so it is not necessary to pass in an accurate PSF.

The useFallbackValueAtEdge option is now implemented. This tapers the interpolation to a fallbackValue towards the image edge. The fallbackValue can be set via config parameters to be either computed as a statistical representation of the image data (MEAN, MEDIAN, or MEANCLIP) or set by providing a specific value. Allowance for a negative fallbackValue is also controlled though a config parameter.

[DM-3677]

HSC backport: Avoid I/O race conditions config write out¶

This adds functionality to avoid potential I/O race conditions when running multiple simultaneous process. This is accomplished by writing to temporary files and then renaming them to the correct destination filename in a single operation. Also, to avoid similar race conditions in the backup file creation (e.g. config.py~1, config.py~2, …), a --no-backup-config option (to be used with --clobber-config) is added here to prevent the backup copies being made. The outcome for this option is that the config that are still recorded are for the most recent run. [DM-3911]

HSC backport: Introduce SafeClipAssembleCoaddTask which extends AssembleCoaddTask to make clipping safer¶

SafeClipAssembleCoaddTask does the following,

• build both clipped and unclipped coadds and difference them first
• detect on the difference
• identify difference footprints that overlap appreciably with only one input image
• use identified difference footprints as a mask into a final coadd
• set a “clipped” bit on the final coadd for any pixel that did not include all input frames within the valid polygons.

To support the new coadd task, the pixel flags measurement plugin has been modified to accept two new configuration parameters. These new parameters, named masksFpCenter and masksFpAnywhere, each accept a list of mask planes. When the pixel flags measurement plugin searches for mask planes to set corresponding flags, it will now additionally search the user supplied mask plane lists. The masksFpCenter parameter specifies mask planes that, if found within the center of a footprint, will have a corresponding pixel flag set. The masksFpCenter parameter specifies mask planes that, if found anywhere in a footprint, will have a corresponding pixel flag set. The masksFpAnywhere parameter now has it’s defaults set within the stack which specify the clipped mask plane created by SafeClipAssembleCoaddTask.

SafeClipAssebleCoaddTask is now the default method for building a coadd within the LSST Stack. The assembleCoadd.py CommandLineTask now supports the --legacy command line flag which will allow the original AssembleCoaddTask to be run. If the legacy task is run, the clipped mask plane must be removed from the masksFpAnywhere configuration parameter.

[DM-2915]

HSC backport: Allow for some fraction of PSF Candidates to be reserved from PSF fitting¶

This adds functionality that allows for the reservation of a fraction of the PSF Candidates from PSF fitting. The reserved fraction can then be used to test for over-fitting, do cross-validation, etc.. To support this functionality, the run methods of CalibrateTask and MeasurePsfTask now accept the additional keyword argument expId. Dummy versions of this keyword were added to the SdssCalibrateTask and CfhtCalibrateTask to maintain a consistent API. [DM-3692]

Updated pipeline configuration based on Hyper Suprime-Cam experience¶

Configuration defaults and metadata through the LSST single-processing pipeline have been updated to match the current best practice established on HSC. Major changes include:

• Support for narrow band filters;
• Updated CCD defect lists;
• Optimized (in terms of CPU time) deblender settings;
• Avoiding failure in certain corner cases (e.g. operating on zero-length arrays, taking log₁₀ of zero).

[DM-3942]

Define polygon bounds for CCDs based on vignetted regions¶

This adds a function in ip_isr’s isrTask.py to set a “valid polygon” for a given CCD exposure as the intersection of a polygon defined in focal plane coordinates and the CCD corners. It is currently being used in obs_subaru‘s isr.py to set the polygon bounds (added in DM-2981) for a CCD exposure to include the non-vignetted regions. The settings for the vignetted region is in a separate config file so that it can be used in different places in the code. [DM-3259]

Introduce --rerun option for command line tasks¶

This new command line option streamlines the process of specifying input and output repositories for command line tasks. In its simplest form, the --rerun option is a shorthand for specifying an output repository: output is written to a location relative to the input. Thus

CmdLineTask /path/to/inputroot --rerun useroutput

is equivalent to

CmdLineTask /path/to/inputroot --output /path/to/inputroot/rerun/useroutput

Often, one task will process the output of a previous rerun. For this situation, --rerun provides a two-valued form which specifies relative locations of both input and output. In this mode,

CmdLineTask /path/to/inputroot --rerun process1:useroutput

is equivalent to

CmdLineTask /path/to/inputroot --input /path/to/inputroot/rerun/process1 --output /path/to/inputroot/rerun/useroutput

[RFC-95, DM-3371]

Introduce framework for injecting fake sources into data processing¶

A new boolean option (doFakes) and a retargetable task (fakes) have been introduced into the ProcessCcdTask. This (along with a new class called BaseFakeSourcesTask) sets up a frame work that others may use to introduce known fake sources into the data processing stream. However, this framework itself does not actually insert any fake data itself, but provides an interface others may use to define their own fake source injection task. To implement a fake injection task one must create a child class of BaseFakeSourcesTask (located in lsst.pipe.tasks.fakes) and overload the run method to do the work of injecting the sources. Each source that is injected should have a corresponding bit set in the FAKE maskplane which can be accessed with the bitmask attribute of BaseFakeSourcesTask. Once a task has been created, the config field fakes in processCcd must be retargeted to point to the user created task. Additionally, the task will not be run unless the doFakes configuration option in processCcd is set to True. However, if this variable is set to True, and the task is not retargeted processCcd will fail. [DM-3380]

Add convenience routines for working with tracts¶

Added two new data id containers:

1. PerTractCcdDataIdContainer: determines the set of tracts each visit touches and adds a data reference with those tracts for each of the visit components. This allows for the user to run a command line task forcedPhotCcd.py for a given visit without having to know which tracts overlap the visit. Note this will also be used by meas_mosaic if/when it gets incorporated into the LSST Stack.
2. TractDataIdContainer: generates a list of data references for patches within a given tract (effectively a “data reference list” that points to the entire tract). Note that, at the time of writing, this is only being used by a QA analysis script currently under development.

[DM-4373]

Warp images based on an XYTransform¶

Added the ability to warp images using a transformation defined by an lsst::afw::geom::XYTransform. [DM-4162]

Add getCoordSystem to Coord and add UNKNOWN CoordSystem enum¶

Added method getCoordSystem to lsst::afw::coord::Coord. Also added UNKNOWN=-1 as a new CoordSystem enum (the existing enums retain their existing value). DM-4606

Adapt joinMatchListWithCatalog to facilitate and simplify denormalizing a match list¶

The match lists created when performing image calibration (astrometry and photometry) are normalized (i.e. stripped down to a list of the matched reference and source ids and their distance) prior to being persisted. The ability to denormalize a match catalog is very useful (for post QA analysis, for example). This can now be done using the joinMatchListWithCatalog function in meas_algorithms‘s LoadReferenceObjectsTask. It has been moved from meas_astrom‘s ANetBasicAstrometryTask so that it can be easily accessed (requiring only that a reference object loader be initiated) and to allow it to work with any kind of reference catalog (i.e. other than a_net). [DM-3633]

Add a script for visualizing skymaps and CCDs¶

The skymap package now contains the script showVisitSkyMap.py which provides a convenient way of visualizing the tracts, patches and CCDs contained in a set of visits. [DM-4095]

Add functions to generate “unpacked matches” to and from a catalog¶

Functions have been added to lsst::afw::catalogMatches to provide the ability to convert a match list into a catalog and vice versa (this can be useful for post-processing analyses; QA analysis, for example). [DM-4729]

Add a measurement algorithm which records the focal plane coordinates of sources¶

The SingleFrameFPPositionPlugin measurement plugin, available in meas_base, records the positions of source centroids in focal plane coordinates (which may be convenient for plotting). This plugin is not enabled by default, but may be switched on by requesting base_FPPosition in measurement configuration. [DM-4234]

Add a measurement algorithm which records the Jacobian at the positions of sources¶

The SingleFrameJacobianPlugin calculates the ratio between the nominal Jacobian determinant at the source centroid (as determined by a user-specified pixel scale) and the actual Jacobian determinant as derived from the astrometric solution. This plugin is not enabled by default, but may be switched on by requesting base_Jacobian in measurement configuration. [DM-4234]

Add a measurement algorithm which records the number of input images contributing to a coadd sources¶

When run on a source detected on a coadd, SingleFrameInputCountPlugin records the number of input images which were stacked to create the coadd at the position corresponding to the source centroid. The plugin is referred to as base_CountInputs, and is enabled by default when performing measurement on coadded images. It is not appropriate to enable this plugin when processing single visit (i.e., not coadded) images. [DM-4235]

Add a measurement algorithm which records the variance at the positions of sources¶

The SingleFrameVariancePlugin records the median variance in the background around the position of the source being measured. The plugin is referred to as base_Variance and is enabled by default when performing single frame measurement. [DM-4235, DM-5427]

Add a measurement algorithm which records source flux in an aperture scaled to the PSF¶

The ScaledApertureFluxAlgorithm measures the flux in a circular aperture with radius scaled to some user-specified multiple of the PSF FWHM. This plugin is not enabled by default, but may be switched on by requesting the base_ScaledApertureFlux in measurement configuration. [DM-3257]

Add a measurement algorithm which quantifies the amount of “blendedness” of an object¶

The BlendednessAlgorithm measures the amount to which an object is blended. Both the flux and shape of each child object are compared to measurements at the same point on the full image. The size of the weight function used on both images is determined from the child object. The blendedness metric implemented is defined as 1-childFlux/parentFlux. The plugin is referred to as base_Blendedness and is not enabled by default. [DM-4847]

Add a “simple” shape measurement algorithm¶

The SimpleShape algorithm, provided in the meas_extensions_simpleShape package, computes the non-adaptive elliptical Gaussian-weighted moments of an image. The plugin is referred to as ext_simpleShape_SimpleShape and is not enabled by default. [DM-5284]

Add Hirata-Seljak-Mandelbaum shape measurement algorithms¶

The meas_extensions_shapeHSM package has been added to the distribution. This provides a series of measurement algorithms based on the work by Hirata and Seljak (2003) and Mandelbaum et al (2005). Please cite those works if publishing results based on this code. These algorithms are disabled by default; they can be enabled by requesting ext_shapeHSM_HsmShapeBj, ext_shapeHSM_HsmShapeLinear, ext_shapeHSM_HsmShapeKsb, ext_shapeHSM_HsmShapeRegauss, ext_shapeHSM_HsmSourceMoments and/or ext_shapeHSM_HsmPsfMoments in the measurement configuration. [DM-2141, DM-3384, DM-4780]

Add option to temporarily remove an interpolated background prior to detection¶

This has the potential for removing a large number of junk detections around bright objects due to noise fluctuations in the elevated local background. The extra subtracted interpolated background is added back in after detection. Currently, the default setting for the config parameter doTempLocalBackround is set to False. [DM-4821]

Add function to average coordinates¶

Added function lsst.afw.coord.averageCoord, which will return an average coordinate (accounting for spherical geometry) given a list of input coordinates. [DM-4933]

Integrate support for Hyper Suprime-Cam¶

The obs_subaru camera package, which enables the stack to operate on data taken with the Suprime-Cam and Hyper Suprime-Cam instruments on Subaru, has been modernized, resolving build and test issues and integrating it with LSST’s continuous integration system. It will now be included as part of the lsst_distrib release. Note, though, that usage of Suprime-Cam with the stack is unsupported and unmaintained at present. [DM-3518, DONE DM-4358, DM-5007]

Reimplement PSF Shapelet approximations for CModel¶

A new algorithm for computing multi-shapelet approximations (DoubleShapeletPsfApprox) has been added to meas_modelfit. This is simpler and more robust than the old algorithm, which has been renamed to GeneralShapeletPsfApprox. The new algorithm is recommended for production use, and is now the default. [DM-5197]

Propagate flags from individual visits to coadds¶

A task has been added which can propagate flags from individual visit catalogs to coadd catalogs. This is useful, for example, to track which stars in the coadd were used for measuring PSFs on the individual visits. [DM-4878, DM-5084]

Prototype Brighter-Fatter correction¶

Code for correcting for the Brighter-Fatter effect on CCDs is now available in the stack. It is enabled using the doBrighterFatter configuration option to IsrTask. It requires a pre-generated correction kernel. Calculation of this kernel is not currently performed within the stack: a prototype exists, and will be merged to the Calibration Products Pipeline in a future cycle. [DM-4837, DM-5082, DM-5130]

Aperture correction on coadd measurements¶

Aperture corrections are now enabled for measurements performed on coadds. [DM-5086]

Return grown Footprints from detection¶

By default, Footprints returned by SourceDetectionTask are now grown by a multiple of the PSF size. [DM-4410]

Enable measurement of “sky objects” in coadd processing¶

Sky objects correspond to source properties measured at positions when no objects have been detected. This enables us to better characterize the depth of the survey. This functionality is enabled by default; it can be disabled by setting nSkySourcesPerPatch to zero in the configuration of MergeDetectionsTask. [DM-4840, DM-5288]

Specification of output directory is now mandatory¶

When running a command line task which produces output it is now mandatory to specify an output directory (previously, if no output location was specified, data products were written back to the input repository). Output locations may be specified with the --rerun or --output command line options. More information is available on community.lsst.org. [DM-4236]

Bright object masks¶

Given an input catalog listing the known positions and sizes of bright objects, a bit is set in the mask plane for every pixel lying within the object’s footprint. [DM-4831]

CModel fitting improvements¶

CModel is a model fitting approach in which a pure exponential and pure de Vaucouleur are each fit separately, and then their linear combination is fit while the ellipse parameters are held fixed. Improvements in this release make CModel fitting faster and improves results on objects which are detected with an unphysically large likelihood radius. This has been achieved in three ways:

• The initial approximate exponential fit that is used to determine the starting parameters and pixel region to use for the exp and dev fit now uses per-pixel variances;
• The method used to determine the pixel region used in fitting has been adjusted to make smarter choices, using fewer pixels on average for all objects and many fewer pixels for unphysically large objects;
• A new semi-empirical Bayesian prior on radius and ellipticity based on COSMOS distributions has been introduced.

[DM-4768]

Astropy Table views into LSST Catalog objects¶

Astropy Table views into LSST catalog objects can now be created. These views share underlying data buffers (aside from flag fields), making them read-write, but rows and columns added on either side will not be visible in the other. Two equivalent interfaces are available:

astropy_table = lsst_catalog.asAstropy()

and (in Astropy >= v1.2):

astropy_table = astropy.table.Table(lsst_catalog)

QTable objects can also be used, resulting in columns that use Astropy’s units package to enforce unit correctness. These interfaces have multiple options to control the details of the view, including how to handle columns that require copies; see the Python on-line help for asAstropy for more information.

While LSST’s catalog objects have features that make them particularly useful in building pipelines, Astropy’s are much more appropriate for most analysis tasks, and we strongly recommend using them for any analysis tasks that need to add columns to tables or combine columns from multiple tables.

[DM-5641, DM-5642, DM-5643]

Add an “afterburner” measurement facility¶

This new functionality makes it possible to register plugins to calculate quantities based on the results of pixel measurement algorithms. This might include, for example, star-galaxy separation or applying aperture corrections. Afterburners of this type are run after measurement plugins, and do not have access to pixel data. [DM-4887]

Tasks can now be kept in registries¶

Related sets of tasks should now be kept in a registry as per RFC-183, with a common abstract base class.

Tasks can now use an lsst.pex.config.RegistryField config field to specify a subtask if that subtask is in a registry (DM-6074). The task is built and used the same way as if it was specified in an lsst.pex.config.ConfigurableField, but retargeting and overriding config parameters is different. See task documentation for more information. See also How to Write a Task for guidelines for choosing between using lsst.pex.config.RegistryField and lsst.pex.config.ConfigurableField to hold a subtask.

PSF determiners are now tasks that inherit from an abstract base class lsst.meas.algorithms.PsfDeterminerTask (DM-6077). However, the effect on existing code was negligible because they were already configurables used from a registry. The way you retarget PSF determiners and override their config parameters remains unchanged.

Reimplemented the registry for star selectors that was lost in DM-5532: lsst.meas.algorithms.starSelectorRegistry (DM-6474)

One backwards incompatible change: in [DM-6474] MeasurePsfTask and MeasureApCorrTask both now specify their star selectors using an lsst.pex.config.RegistryField. This means the format for retargeting star selectors and overriding their config parameters has changed. The config override files in the various obs_ packages are updated accordingly.

New test utilities in afw: BoxGrid and makeRampImage¶

lsst.afw.geom.testUtils.BoxGrid divides a bounding box into nCol x nRow equal sized sub-boxes (as equal sized as possible for integer boxes that do not divide evenly) that tile the larger box and have the same type.

lsst.afw.image.testUtils.makeRampImage makes an image (ImageX where X is any available type) with values that increase linearly between specified limits (linearly to the extent possible, for integer images).

[DM-5462]

Correcting non-linearity¶

Introduced a standard way to correct non-linearity (linearize data) as part of Instrument Signature Removal (ISR). Linearization is performed by new functors in ip_isr:

• LinearizeBase is an abstract base class. It is called with an image and the detector information and the correction is performed in place (like all other ISR corrections in IsrTask).
• LinearizeSquared performs a simple square correction: corrImage = uncorrImage + c0*uncorrImage^2 where c0 is the first coefficient in in the linearity coefficients of the amp into catalog. This is the model used by obs_subaru for SuprimeCam and HSC.
• LinearizeLookupTable uses a lookup table to determine an offset (read the code doc string for details). The lookup table is saved with the linearizer, but the linearizer also performs a sanity check against the provided detector when called.
• You can easily add other linearizers as desired.
• Each linearizer has a class variable LinearizationType, a string whose value should be used as the linearization type in the amplifier info catalog. The linearizer checks this value when performing linearization.

All detector in a camera must use the same type of linearizer. However linearization can easily be disabled on a detector-by-detector basis by setting linearity type to lsst.afw.cameraGeom.NullLinearityType. For a camera that does not need linearization, do this for all detectors.

Linearizers are obtained from the butler, like any other calibration product.

• For LinearizeSquared and other linearizers that get coefficients from the amplifier info catalog, only one instance is needed for all detectors. In that case the simplest technique is to define map_linearize and bypass_linearize methods on the camera mapper to return an instance. See the obs_subaru package for an example.
• For LinearizeLookupTable and other linearizers that store detector-specific data, the obs_ package developer must pickle one linearizer for each detector and make them available as dataset type “linearizer”.
• If the camera does not want linearization then no “linearizer” dataset type is required because IsrTask realizes linearization is not wanted before it tries to unpersist the linearizer. You may leave IsrConfig.doLinearize set to its default value of True without significant performance penalty.

[DM-5462, RFC-164]

Amplifier information catalogs have changed¶

The format of amplifier information catalogs has changed. Your versions of afw and associated obs_ packages must be compatible or else you will get errors when building a camera mapper (thus when running any nearly any command-line task).

Amplifier information catalogs have a new field as of DM-6147: suspect level. If the value is not nan then pixels whose values are above this level are masked as SUSPECT.

The only cameras that specify a suspect level, so far, are HSC and SuprimeCam. However, a value can be set for any camera, if desired. SUSPECT is intended to indicate pixels with doubtful values due to errors that are difficult to correct accurately, e.g. a regime where linearity correction is not very stable.

In addition, saturation level in the amplifier information catalog is now a floating point value (instead of an integer) and a value of nan means ‘do not mask pixels as SAT.’

[DM-6147]

Changes in how background subtraction is done¶

Background estimation in Python is now done using different routines in meas_algorithms.

There is a new task SubtractBackgroundTask, with full documentation and a working example.

The existing function getBackground (which fits a background) is replaced by SubtractBackgroundTask.fitBackground. Changes from getBackground are:

• getBackground could return None if the fit failed; in that situation fitBackround will raise RuntimeError instead of returning None.
• The argument image was renamed to maskedImage, for clarity.
• The config is not passed as an argument.
• The debug display code uses different keys and is updated to use afw.display.

The existing function estimateBackground (which subtract a background from an exposure) is replaced by SubtractBackgroundTask.run. Changes from estimateBackground are:

• You may pass in a background model (an lsst.afw.math.BackgroundList).
• It returns a struct containing the updated background model.
• The config is not passed as an argument.
• The debug display code displays the unsubtracted image and uses different keys and is updated to use afw.display.

The task’s config SubtractBackgroundConfig replaces the old BackgroundConfig. The field algorithm may no longer be None; you must use the string "NONE", instead. See discussion on Community for details.

[DM-5323, RFC-155]

Star selectors have changed¶

Star selectors are now tasks. They were already configurable and many added logs; now they are standard tasks.

The star selector registry starSelectorRegistry was gone for awhile. Now that it is back, using a registry field from that registry is the preferred way to specify a star selector as a subtask of another task.

Added BaseStarSelectorTask (but for awhile it was called StarSelectorTask) an abstract base class for star selectors with the following methods:

• selectStars an abstract method that takes a catalog of sources and returns a catalog of stars.
• makePsfCandidates a concrete method that takes a catalog of stars (as returned by selectStars and produces PSF candidates; it also returns a sub-catalog of those stars that were successfully turned into PSF candidates (which is usually all of them).
• run a concrete method that selects stars, makes them into PSF candidates and optionally flags the stars.

[RFC-154, DM-5532]

Backward-incompatible changes to ProcessCcdTask and subtasks¶

Persist LTVn headers as floating point numbers¶

When persisting to a FITS file, these header cards were previously, incorrectly, stored as integers. [DM-4133]

Fix bug when identifying existing peaks in a merge¶

If two separate footprints from the same catalog are merged due to an existing merged object which overlaps both of them the flags of which peaks are being detected were not being propagated. This issue caused apparent dropouts of sources and has now been fixed. [DM-2978]

Fix situation in which the getChildren method of SourceCatalog may return the wrong information¶

The getChildren method requires that the result must be sorted by parent. This is naturally the case when the catalog is produced by detection or deblending tasks. However, if multiple catalogs are concatenated together this condition may no longer be true. The getChildren method was updated to raise an exception if the precondition of sorting is not met. [DM-2976]

Fix warping when the WCS have different coordinate systems¶

Warping assumed that the sky representation of both WCS was identical. [DM-4162]

Correct bad default minInitialRadius for CModel¶

The minInitialRadius configuration parameter had a default that is too small, causing many galaxies to be fit with point source models, leading to bad star/galaxy classifications. [DM-3821]

Correct algebraic error in CModel uncertainty calculation¶

There was a simple but important algebra error in the uncertainty calculation, making the uncertainty a strong function of magnitude. [DM-3821]

NaiveDipoleCentroid and NaiveDipoleFlux algorithms no longer require a centroid slot¶

Previously, initializing these algorithms was only possible if a centroid was already defined. That was not only unnecessary, but also made them more complicated to use, particularly in testing. [DM-3940]

Update (some) example code to run with recent stack versions¶

Changes in afw::table had broken examples/calibrateTask.py in pipe_tasks. It has now been updated to comply with the latest afw::table API. [DM-4125]

Fix a failure to appropriately log failed task execution¶

When task execution fails, we add a message to the log (with level FATAL). In some cases, the very act of attempting to log this message could throw an exception, and information about the original error was lost. This has now been resolved. [DM-4218]

Updates to Skymap packages¶

Add functions to return patches and tracts which contain given coordinates, i.e. conversions between celestial coordinates and tract,patch indices. Functions include findClosestTractPatchList, findAllTract, and findTractPatchList which finds the closets tract and patch that overlaps coordinates, finds all tracts which include the specified coordinate, and finds tracts and patches that overlap a region respectively. [DM-3775]

Fix variance in coadded images¶

Warping images in order to coadd them loses variance into covariance. This is mitigated by scaling the variance plane of the coadd. The scaling was being applied incorrectly in some cases. This has now been fixed. [DM-4798]

Fix variance in deblended sources¶

The deblender incorrectly scaled the variance plane in deblended sources with the fraction of the total flux assigned to the source. This has been corrected. [DM-4845]

Fix logic for applying aperture corrections¶

This fixes a bug whereby the aperture corrections were being applied only after all the measurement plugins had run through, independent of their execution order. This resulted in plugins whose measurements rely on aperture corrected fluxes (i.e. with execution order > APCORR_ORDER) being applied prior to the aperture correction, leading to erroneous results. The only plugin that was affected by this at this time was base_ClassificationExtendedness. [DM-4836]

More uniform support for assigning to catalog columns¶

Assignment of scalars or NumPy arrays to columns of afw.table.Catalog objects (e.g. catalog["column"] = value) is now more uniformly supported across types (support was inconsistent before, and never allowed scalar or augmented assignment). Flag columns still do not support column assignment, and Flag column access still returns a copy, not a view, because Flag values are stored internally as individual bits within a larger integer. [DM-4856]

Upgraded WCSLIB to version 5.13¶

Version 5.13 of WCSLIB resolves memory corruption errors that could crash the stack in some circumstances. [DM-4904, RFC-89, DM-4946, DM-3793]

Fix rotation for instrument signature removal in obs_subaru¶

Approximately half of the HSC CCDs are rotated 180 deg with respect to the others. Two others have 90 deg rotations and another two have 270 deg rotations (see HSC CCD layout). The raw images for the rotated CCDs thus need to be rotated to match the rotation of their associated calibration frames (in the context of how they have currently been ingested) prior to applying the corrections. This is accomplished by rotating the exposure using the rotated context manager function in obs_subaru‘s isr.py and the nQuarter specification in the policy file for each CCD. Currently, rotated uses afw‘s rotateImageBy90 (which apparently rotates in a counter-clockwise direction) to rotated the exposure by 4 - nQuarter turns. This turns out to be the wrong rotation for the odd nQuarter CCDs. This issue fixes this bug, leading to much improved processing of HSC CCD’s 100, 101, 102, and 103. Note that, in the future, the ingestion of the calibration data will be updated such that no rotations are necessary (so they will then be removed from obs_subaru accordingly). [DM-4998]

Fix a silent failure to apply config overrides¶

When applying a config override, using a variable which hadn’t been defined should throw a NameError, which ultimately propagates to the end user to notify them that something has gone awry. This warning was being incorrectly suppressed. [DM-5729]

Correctly set flags for bad SdssShape measurements.¶

The SdssShape algorithm provides both shape and flux measurements. In some cases, a failed shape measurement could go un-noticed, resulting in an incorrect and unflagged flux measurement being associated with that source. This is now checked for, and bad fluxes are appropriately flagged. [DM-3935]

Fix CONSTANT background interpolation of bad data¶

When performing interpolation over bad data (e.g. every pixel masked), all interpolation types other than CONSTANT would return NaNs; CONSTANT would throw. This has now been changed so that CONSTANT also returns NaNs. [DM-5797]

Accommodate pixel padding when unpersisting reference catalog matches¶

The reference object loader in meas_algorithm‘s loadReferenceObjects.py grows the bbox by the config parameter pixelMargin (padding to add to 4 all edges of the bounding box [pixels]) when setting the radius of the sky circle to be searched in the reference catalog. This is set to 50 by default but was not reflected by the radius parameter set in the metadata, which left open the possibility that some matches could reside outside the circle searched within the unpersisted radius. Additionally, the match metadata was being set after the exposure’s WCS had been updated, also leading to an inconsistency with the sky circle that was actually searched. We now ensure that the actual sky circle that was searched for reference objects is the one set and persisted in the match metadata. [DM-5686]

Correct misleading filter fallback error message¶

When failing to load a calib, if fallbackFilterName was not set, a confusing and apparently unrelated error message would be generated (Unknown value type for filter: <type 'NoneType'>). This has been corrected to properly inform the user about the issue. [DM-6151]

Work-around incompatibilities with NumPy 1.10¶

NumPy 1.10 introduced API changes which were incompatible with existing usage in the stack. The latter has been updated to match. [DM-4063, DM-4071, DM-4238].

When building boost warn user if user-config.jam or site-config.jam exists¶

Building boost can fail if a user-config.jam or site-config.jam exist and have options which conflict with the LSST build configuration process. Introduce a warning message if either of these files are found to notify the user. [DM-4198]

Remove deprecated Task.display() method¶

This method has been deprecated since release 9.2 (S14). It has been removed from the codebase, and all stack code updated to directly interface with afw.display or to use helper functions defined in meas_astrom. [DM-4428]

Efficiency improvement in converting Masks to DefectLists¶

The previous version of routine was extremely memory intensive when large numbers of pixels were masked. [DM-4800]

Add a new task parallelization framework¶

The ctrl_pool package has been added to the LSST stack. This is a high-level parallelization framework used for distributing Task execution across a cluster, based on an MPI process pool. It is based on work carried out on Hyper Suprime-Cam. It is not intended to be the long-term solution to parallelized processing in the LSST stack, but meets our data processing needs until the fully-fledged parallelization middleware is available. [DM-2983, DM-4835, DM-5409]

Add parallel-processing top level tasks¶

The new pipe_drivers package builds upon ctrl_pool, above, to provide command-line scripts which coordinate distributed execution of the single-frame, coaddition and multiband processing steps using either the Python multiprocessing module or with a SLURM batch scheduler on a cluster. [DM-3368, DM-3369, DM-3370]

Adjust test tolerances to be compatible with MKL-based NumPy¶

Anaconda 2.5 ships, by default, with a version of NumPy built against Intel MKL rather than OpenBLAS. This can change some numerical results slightly, necessitating a change to test tolerances. [DM-5108]

Now possible to directly get a Filter’s canonical name and aliases¶

Added the convenience methods getCanonicalName and getAliases to lsst.afw.image.Filter, accessible from both C++ and Python. These return the canonical name and the aliases, respectively, of the filter. This information was previously only available through an awkward sequence of method calls. [DM-4816]

Fix build issues with recent clang¶

Recent releases of the clang C/C++ compiler, as shipped with Apple XCode, caused build failures in the stack. Although we believe this may be a problem with clang, we have worked around it within the stack code. We hope to track down the source of the error and, if appropriate, report it to the clang developers in future. [DM-5590, DM-5609]

Fix incorrect linking against Anaconda-provided libraries when using CMake¶

Some external packages—mariadb and mariadbclient—use a CMake based build system. This can incorrectly link against some libraries bundled with the Anaconda Python distribution, rather than the system-provided equivalents, resulting in a build failure. We have adjusted the build process of the affected packages to work around this error. [DM-5595]

Execute afw test suite when afwdata is not available¶

Some tests in the afw package rely on data from the afwdata package. The test suite would search for afwdata, and skip all of the afw tests if afwdata is not available. This check has been made smarter, so that only tests which actually require afwdata are now skipped. [DM-609]

Disable implicit threading¶

Low-level threading packages (such as OpenBLAS or MKL) can implicitly use many threads. Since the LSST stack also parallelizes at a higher level (e.g. using Python’s multiprocessing module), this can cause undesirable contention. We now disable implicit threading when explicitly parallelizing at a higher level to protect the user from this. Implicit threading can be re-enabled by setting the LSST_ALLOW_IMPLICIT_THREADS environment variable. For more details, see this Community post. [DM-4719]

Migrate to standard smart pointers¶

C++11 introduced new smart pointer types (std::unique_ptr, std::shared_ptr and std::weak_ptr). We have migrated from the previously used Boost smart pointers to their standard equivalents. [DM-5879, DM-4008, RFC-100, DM-5966]

Improved semantics for loading Exposures and MaskedImages from arbitrary FITS files¶

The Exposure and MaskedImage represent image data with associated mask and variance information. When serialized to FITS, these are stored as three consecutive extensions in the FITS files. It is possible to load Exposures and MaskedImages from multi-extension FITS files which were not generated by LSST, but, due to the limitations of the FITS data model, it is not possible to ensure that the creator of the file adhered to the LSST convention: while an image object may be successfully instantiated, its contents may not be logically consistent.

We now go to greater lengths to check that the information in the file is consistent with the LSST standard, warning the user—and in some cases refusing to proceed—if it does not. [DM-2599]

Improved support for non-standard FITS headers¶

The LSST stack is now capable of loading FITS files which contain non-standard headers of the form PVi_nn (i=1..x, nn=5..16), as written by SCAMP, and EQUINOX headers with a “J” prefix, as written by SkyMapper. [DM-2883, DM-2924, DM-3196]

It is now possible to perform instrument signal removal on an Exposure which has no Detector¶

FakeAmp, a Detector-like object object which supports returning gain and saturation level, was added to make it possible to run updateVariance and saturationDetection if required. (DM-2890)

PVi_j header cards are correctly saved to FITS files¶

This makes it possible to round-trip TPV headers, for example. [DM-2926]

Changes to compound fields and delimiters in catalog schemas¶

In the older (“version 0”) approach to table schemas, we had several compound field types (Point, Moments, Covariance, Coord) which behaved differently from other field types - the square bracket [] operators could not be used to access them, and they could not be accessed as columns (though their scalar subfields – e.g. “x” and “y” for Point – could be). In version 0, we used periods to separate both words and namespace elements in field names, but converted periods to underscores and back when writing to FITS. These schemas were mostly produced by the old measurement framework in meas_algorithms‘ SourceMeasurementTask, which was removed in the 10.1 release.

In the new (“version 1”) approach, compound objects are simply stored in catalogs as their constituent scalars, with helper classes called FunctorKeys provided to pack and unpack them from Records (the FunctorKeys that replace the old compound fields are all in afw/table/aggregates.h). Unlike the original compound fields, there’s no limit to how many types of FunctorKey we can have, or what package they can live in, making the system much more extensible. By making the constituent scalar objects what the Schema object knows about, it will be much easier to map a Schema to other table representations that don’t know about LSST classes (e.g. SQL or Pandas). Most FunctorKeys can be used anywhere a regular Key can be used. Also, in version 1, we use underscores as namespace separators, and CamelCase to separate words, eliminating some ambiguity between word and namespace boundaries. The new measurement framework in meas_base‘s SingleFrameMeasurementTask and ForcedMeasurementTask uses version 1 tables exclusively.

In previous releases of the pipeline, version 0 schemas were deprecated but still supported. They have now been removed, but old catalogs saved as version 0 will still be readable - they will be converted to version 1 on read, with period delimiters converted to underscores, and all compound fields unpacked into scalar fields that can be used with a corresponding FunctorKey. This procedure obviously does not preserve field names, but all slot definitions will be preserved, so code that only relies on slot or minimal schema accessors (getCoord(), getCentroid(), getPsfFlux(), etc.) should not need to be modified. [DM-1766]

Allow for use of Approximate (Chebyshev) model in background estimation¶

In previous releases, the only method for background estimation was to use an interpolation scheme (constant, linear, or various splines). These schemes tend to lead to over-subtraction of the background near bright objects. The Approximate (Chebyshev) approach to background estimation greatly improves the background subtraction around bright objects. The relevant code to use this latter approach (including persistence and backwards compatibility issues) is now in place.

While the intention is to eventually set the Approximate background subtraction scheme as the default, there is some clean-up and restructuring that needs to be done before resetting the defaults (which may also require adjusting some defaults in the calibrate stage to be more appropriate for the approximation, as opposed to interpolation, scheme). Therefore, the default setting has not been changed (i.e. the default is still to use an interpolation scheme for background estimation). The Chebychev approximation can be selected for background estimation through configuration parameters in the obs_CAMERA packages, i.e. useApprox=True and, optionally, approxOrderX (approximation order in X for background Chebyshev), approxOrderX (approximation order in Y for background Chebyshev: currently approxOrderY must be equal to approxOrderX), weighting (if True, use inverse variance weighting in calculation). [DM-2778]

Multi-band processing for coadds¶

See the description of the multi-band coadd processing work performed in S15 for details. In short, four new command-line Tasks have been added for consistent multi-band coadd processing:

DetectCoaddSourcesTask

Detect sources (generate Footprints for parent sources) and model background for a single band.

MergeDetectionsTask

Merge Footprints and Peaks from all detection images into a single, consistent set of Footprints and Peaks.

MeasureMergedCoaddSourcesTask

Deblend and measure on per-band coadds, starting from consistent Footprints and Peaks for parent objects.

MergeMeasurementsTask

Combine separate measurements from different bands into a catalog suitable for driving forced photometry. Essentially, it must have a centroid, shape, and CModel fit for all objects, even for objects that were not detected on the canonical band. Will assume that all input catalogs already have consistent object lists.

[DM-1945, DM-3139]

Enable use of deblended HeavyFootprints in coadd forced photometry¶

Given the new multi-band processing for coadds (above), we now have a reference catalog that is consistent across all bands. This catalog allows the use of the source’s HeavyFootprints to replace neighbors with noise in forced photometry, thus providing deblended forced photometry and consistent deblending across all bands. This provides much better colors for blended objects as well as measurements for drop-out objects that do not get detected in the canonical band. This functionality has been enabled for forced coadd photometry.

See the description of the multi-band coadd processing work performed in S15 for further motivation of this change. [DM-1954]

Limited the fractional number of masked pixels per source¶

CModel has difficulties modelling backgrounds in vignetted regions of the focal plane, leading to a performance bottleneck. To mitigate the issue, if the fractional number of masked pixels in a particular source exceeds a given threshold, that source will be skipped. [DM-2914]

Peak culling around large objects¶

An excess of “junk” peaks may be observed around large objects. Given the new multi-band processing architecture (above), these must be consistently removed across bands. We therefore provide a method to consistently “cull” this peaks at an earlier stage, immediately after merging and sorting in MergeDetectionsTask. [DM-2914]

Parent Footprints are the union of their children¶

Parent Footprints are now trimmed so that they are strictly the union of their children: any pixels which are not assigned to a child are removed. This mitigates an issue whereby stray flux from the parent was not correctly assigned to the children. Note that this has the consequence that parent Footprints are not necessarily contiguous. [DM-2914]

Large Footprints may be skipped on initial processing¶

For practical processing purposes (specifically total processing time and memory limits due to current hardware limitations), we have the option to skip over objects with large Footprints during large-scale processing, with the intention to return to these objects to “reprocess” them using different hardware in future. The ability to properly record which objects have been skipped and require further processing has been implemented along with optimizations to the deblender configuration for the maximum number of Peaks per Footprint, and the size and area of Footprints. [DM-2914]

Command line tasks for measurement transformation¶

The measurement transformation framework provides a generic mechanism for transforming the outputs of measurement plugins in raw units, such as pixel positions or flux, to calibrated, physical units, such as celestial coordinates or magnitudes. Appropriate transformations are defined on a per-measurement-plugin basis, and may make use of the calibration information and WCS stored with the data.

This system is designed such that the transformation of a given catalog is performed by a command line task. Different catalog types (such as src, forced_src, etc) make use of separate command line tasks. In this release, we provide a variety of tasks to handle different source types.

• Documentation for generic transforms.
• Documentation for SrcTransformTask.
• Documentation for ForcedSrcTransformTask.
• Documentation for CoaddSrcTransformTask.

(DM-2191, DM-3473, DM-3483)

Add NO_DATA mask plane¶

Previously, we have used the EDGE mask plane to indicate both pixels which are off-the-edge of the detector, and hence have no data available, and pixels near the edge which cannot therefore be properly searched for sources. Here, we introduce the NO_DATA plane to refer to the former case and now use EDGE strictly for the latter. [DM-3136]

Add slot for flux used in photometric calibration¶

We define a new slot, CalibFlux, on SourceRecords. This slot is used to record the flux used for photometric calibration, rather than hard-coding the name of a particular algorithm in the PhotoCal task. This slot defaults to a 12 pixel circular aperture flux, the previous default in PhotoCal. [DM-3106, DM-3108]

Table field prefix for aperture flux measurements changed¶

Our aperture flux measurement algorithms take a list of radii, in pixels, which define the radii over which measurements should be made. Previously, the names of the table fields produced by the algorithm were defined purely based on the position of the radius in that list (thus, the first radius listed would produce a flux field named PluginName_0_flux). This has been changed so that the fields are now named after the radius, regardless of its position in the list. Thus, a 12.5 pixel aperture will result in a field named PluginName_12_5_flux, regardless of its position in the list. [DM-3108]

Faster astrometry reference catalog loading¶

The reference catalog loading was optimised by caching HEALpix identifiers for the catalog files. This has been observed to speed up loading times from 144 sec to 12 sec.

The cache is saved as andCache.fits in the astrometry catalog directory. The use of the cache can be disabled through the andConfig.py file (or the AstrometryNetDataConfig) by setting allowCache to False. To prepare a cache, setup astrometry_net_data and use the generateANetCache.py script that now comes in meas_astrom. [DM-3142]

Bad pixels tracked when coadding images¶

When co-adding images, we now keep track of what fraction of the input data for a given pixel was masked. If the total masked data exceeds some user-configurable threshold, the mask is propagated to the coadd. [DM-3137]

Polygon masking in coadded PSFs¶

Polygonal masks are used to define the usable area of the focal plane; they can be used to, for example, exclude vignetted areas from coaddition. We now take account of these masks to determine which PSF images to included when building co-added PSFs. [DM-3243, DM-3528]

Scale counts to reflect CCD-specific zero-points when warping to create coadd inputs¶

[DM-2980]

Solving astrometry with distortions¶

The default astrometry matcher (matchOptimisticB) can now match stars against a reference catalog when the stars are distorted (e.g., at the outskirts of a wide field imager) if there is an estimate of the distortion available. [DM-3492]

Rejection iterations in astrometry fitting¶

Astrometric fitting (FitTanSipWcsTask) now includes support for iterative fitting with rejection. [DM-3492]

Inclusion of external package PSFEx as option for PSF determination¶

PSFEx is currently the state of the art external package for PSF determination, used in projects such as DES. LSST wrappers were created such that PSFEx could be used as a plugin in place of the built in PSF determiner. Tests with Hyper Supreme Camera data have shown that PSFEx out performs the built-in PSF determiner. [DM-2961]

Improvements to CModel magnitude measurement¶

This release includes many miscellaneous improvements and fixes resulting from testing on HSC data, including:

• parameter tuning for computational performance improvement
• correction to uncertainty estimation to account for extrapolation beyond the fit region
• much more robust flagging of failure modes

Interface changes to forced measurement¶

The order of arguments to the forced measurement task was reversed, so that it takes a source catalog followed by an Exposure. This brings it into line with the single frame measurement interface. [DM-3459]

N-way spatial matching¶

A simple utility class for performing spatial matches between multiple catalogs with identical has been added as lsst.afw.table.multiMatch.MultiMatch. This is intended as a stop-gap measure until more flexible and efficient functionality becomes available, but is already usable. [DM-3490]

Display CCD data as laid out in the focal plane¶

It is now possible to use lsst.afw.cameraGeom.utils to display CCD data laid out in the focal plane. An example of how this functionality works in practice is available as an IPython notebook. [DM-2347]

Doxygen documentation now correctly includes LaTeX formatting¶

Correctly referring to MathJax means that LaTeX markup in documentation is nicely formatted. [DM-2545]

Performance regression in Footprint dilation resolved¶

The previous release included improved algorithms for dilating Footprints. Unfortunately, in some circumstances (notably when dealing with particularly large Footprints) this code could actually perform more slowly than the previous implementation. This could have significant performance implications for many image processing operations. This regression has now been rectified, and the new dilation operations are significantly faster than the old ones in all circumstances tested. [DM-2787]

Footprint fixes¶

The following updates/fixes to Footprint handling have been made:

• The default 32-bit heap space used to store FITS variable-length arrays isn’t large enough to store some of our extremely large HeavyFootprints. This persistence issue has been fixed the by switching to 64-bit heap descriptors, which is now supported by FITS.
• Footprint::transform is now properly copying peaks over to the new footprint.
• Footprint::clipTo is now properly removing those peaks lying outside the desired region.
• Several parts of the pipeline assume peaks are sorted from most positive to most negative. We now ensure the cross-band merge code maintains this ordering as much as possible (even though the sorting may not be consistent across different bands).
• The merging of a parent and its children’s Footprints was failing in cases where one or more child Footprints were themselves noncontiguous. This has been fixed by adapting the mergeFootprints code in afw such that it combines all the Footprints in the FootprintSet it uses in its implementation (instead of requiring that the FootprintSet have only one Footprint).

[DM-2606]

Fixed error in memory access in interpolation¶

An off-by-one error resulted in an attempt to read beyond the allocated memory. [DM-3112]

Fixed truncated write of certain WCS information to FITS¶

[DM-2931]

Use the correct weighting in photometric calibration¶

Previously, we were incorrectly weighting by errors, rather than inverse errors. [DM-2423]

Remove non-positive variance pixels in coadd creation¶

When interpolating variance maps we can produce negative values. These then cause failures when we try to take the square root. Ultimately, the means of creating variance maps needs to be fixed (which is DM-3201); as a temporary workaround, we replace negative variance values with infinity. [DM-2980]

Task defaults are set correctly for difference imaging¶

The DipoleMeasurementConfig.setDefaults method incorrectly contained a return that was executed before the defaults were actually applied. This has been corrected, and a number of tests updated to rely on those defaults. [DM-3159]

Backend-agnostic interface to displays¶

The image display code no longer makes the assumption that display is carried out using ds9. Rather, an API is available which is independent of the the particular image viewer is in use. A backwards compatibility layer ensures that display through ds9 is still supported, while other backends will be added in future.

[RFC-42, DM-2709, DM-2849, DM-2940, DM-3203, DM-3468]

Measurement framework compiler warnings resolved¶

The measurement framework was refactored to avoid a series of warnings produced by the clang compiler. [DM-2131]

Unsanctioned access to the display by tests suppressed¶

Some unit tests were attempting to write to a display, even when no display was available. On some systems, this directly caused test failures; on others, it could obscure the true cause of failures when a test did fail. [DM-2492, DM-2494]

Unused & obsolete code has been removed from the datarel package¶

This package is effectively obsolete, but is still used in documentation generation which makes removing it entirely complex. For now, therefore, it has simply been trimmed of all unused functionality; it may be removed entirely following DM-2948. [DM-2949]

Reduced verbosity of astrometry.net solver¶

A correction to the way that astrometry.net logging was propagated to the LSST logging system, together with reducing the priority of some messages, leads to a substantial reduction in chatter from astrometry. DM-3141

Ensure that slots are present before initializing algorithms that depend upon them¶

When initializing an algorithm that refers to a particular slot, we resolve the target of the slot and refer to that instead. That means that if the slot definition is changed after measurement has been performed, we are still pointing to the correct information. However, if the algorithm is initialized before the slot it depends on, this resolution could not take place and “circular” aliases could result. We now explicitly check for and throw an error in this case. [DM-3400]

Visualizations for astrometry.net solver¶

It is now possible to display the source positions, distorted source positions and reference positions to assist with debugging. [DM-3209]

Subaru support reinstated¶

The obs_subaru package, which provides packages and tasks specific to the Subaru telescope, has been brought up to date with recent changes to the LSST stack and improvements made during Hyper Suprime Cam development. [DM-1794, DM-3403]

Refactor & document coadd construction¶

A number of minor changes and documentation improvements were made to the CoaddBase, AssembleCoadd, CoaddInputRecorder and MakeCoaddTempExp tasks. These brought the structure of the code better into line with the state-of-the-art development on Hyper Suprime Cam. [DM-2980]

Properly handle masking NaN or saturated values in overscans¶

Resolved an issue where, in certain circumstances, flags in the mask plane for saturated and nan values in overscans were being improperly propagated to all amplifiers in an image. These flags are now applied to the amplifier where the bad values are seen. [DM-2923]

Deblender optimization¶

Several performance optimizations to the (C++) algorithms used in the deblender have been implemented, in particular those which identify objects with significant amounts of their flux attributed to edge pixels. In addition, memory usage was reduced by removing unused mask planes left over from debugging, not storing masks for deblending templates, and by clipping template images when their associated Footprints are clipped. [DM-2914]