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The upcoming v12.0 release of the stack has been frozen. Please do not add anything here. Add new notes to the F16 release notes. |
These draft notes cover the major updates made by Data Release Production to the LSST stack since release 11.0 (Summer 2015). Please record significant updates here so that they can ultimately be incorporated into the notes accompanying the Winter 2016 release.
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Major Functionality and Interface Changes
Dumping task configuration parameters now includes documentation
Add the option of excluding mask planes before coaddition
The user-configurable paramter 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4866 |
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Dumping task configuration parameters now includes documentation
That is, running ${TASK} ... --show config
displays not only the names and That is, running ${TASK} ... --show config
displays not only the names and values of the configuration but also associated documentation.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4235 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5050 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5427 |
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Add a measurement Add a measurement algorithm which records source flux in an aperture scaled to the PSF
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4847 |
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Add
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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 defaultThis 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-48215284 |
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Add
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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 (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 configurationAdded function lsst.afw.coord.averageCoord
, which will return an average coordinate (accounting for spherical geometry) given a list of input coordinates.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4933 |
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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.)
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-35183384 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-43584780 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5007 |
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Restructure PsfFitter
algorithm
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 coordinatesThe PsfFitter
routine has been refined to better accord with the meas_base
measurement framework. This includes modernized error handling.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4830 |
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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.
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.)
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-48783518 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5084 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4837 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5082 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5130 |
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Aperture correction on coadd measurements
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 visitsAperture corrections are now enabled for measurements performed on coadds.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5086 |
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By default, Footprint
s return by SourceDetectionTask
are now grown by a multiple of the PSF size.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4410 |
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Enable measurement of "sky objects" in coadd processing
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 cycleSky 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
.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-48404837 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5288 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4236 |
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Bright object masks
Aperture correction on coadd measurements
Aperture corrections are now enabled for measurements performed on coaddsGiven 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4831 |
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Overhaul ProcessCcdTask and subtasks, including eliminating camera-specific variants
By default, Footprint
s return by SourceDetectionTask
are now grown by a multiple of the PSF sizeOverhauled ProcessCcdTask and CalibrateTask to simplify the code and eliminate the need for camera-specific variants. See Changes to ProceessCcdTask and Subtasks for details.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4692 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5348 |
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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:
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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
.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4840 |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4768 |
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Bug Fixes
The following fixes resolve problems visible to end users.
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.orgWhen persisting to a FITS file, these header cards were previously, incorrectly, stored as integers.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4133 |
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Fix bug when identifying existing peaks in a merge
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.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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-2978 |
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Fix situation in which the getChildren
method of SourceCatalog
may return the wrong information
Overhaul ProcessCcdTask and subtasks, including eliminating camera-specific variants
Overhauled ProcessCcdTask and CalibrateTask to simplify the code and eliminate the need for camera-specific variants. See Changes to ProceessCcdTask and Subtasks for detailsThe 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.
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serverId | 9da94fb6 | serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-2976 |
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Fix warping when the WCS have different coordinate systems
Warping assumed that the the sky representation of both WCS was identical.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-41625348 |
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CModel
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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.
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-3821 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-3821 |
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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 unneccessary, but also made them more complicated to use, particularly in testing.
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:
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astropy_table = lsst_catalog.asAstropy() |
and (in Astropy >= v1.2):
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-3940 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4125 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-4218 |
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Updates to Skymap packages
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 dataAdd functions to return patches and tracts which contain given coordinates, i.e. conversions between celestial coordinates and tract,patch indicies. 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-3775 |
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Port bugfixes in meas_extensions_shapeHSM from HSC to LSST
Various bug fixes to the shapeHSM measurement algorithm were ported and include:
- Ensuring masks have same xy0 as images
- Fixing scaling coefficient in ellipticity error when using distortion
- Provide appropriate mask for variance image when measuring median variance around object
- Change from standard deviation to variance in the sky value when calling GalSim hsm code, as required by GalSim
- Fixes to unit tests to comply with above changes, and the port from the HSC framework to the LSST framework
Bug Fixes
The following fixes resolve problems visible to end users.
When persisting to a FITS file, these header cards were previously, incorrectly, stored as integers.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-33844133 |
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Fix
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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 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-47982978 |
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Fix
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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 metThe deblender incorrectly scaled the variance plane in deblended sources with the fraction of the total flux assigned to the source. This has been corrected.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-48452976 |
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Fix
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warping when the WCS have different coordinate systems
Warping assumed that the the sky representation of both WCS was identicalThis fixes a but 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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-48364162 |
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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.
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-5109 |
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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.
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.
Jira |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4856 |
---|
|
Upgraded WCSLIB to version 5.13
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 unneccessary, but also made them more complicated to use, particularly in testingVersion 5.13 of WCSLIB resolves memory corruption errors that could crash the stack in some circumstances.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4904 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | RFC-89 |
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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4946 |
---|
|
Jira |
---|
|
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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated, |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-3793 |
---|
|
Fix rotation for instrument signature removal in obs_subaru
Updates to Skymap packages
Add functions to return patches and tracts which contain given coordinates, i.e. conversions between celestial coordinates and tract,patch indicies. 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.
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server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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
.
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---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4836 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-5109 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-6063 |
---|
|
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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4904 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | RFC-89 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4946 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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).
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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 propagages to the end user to notify them that something has gone awry. This warning was being incorrectly suppressed.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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 NaN
s; CONSTANT
would throw. This has now been changed so that CONSTANT
also returns NaN
s.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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: doc = "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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-6151 |
---|
|
Build and code improvements
These improvements should not usually be visible to end users. They may, however, be important for developers.
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
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4063 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4071 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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
.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4428 |
---|
|
Efficiency improvement in converting Mask
s to DefectList
s
The previous version of routine was extremely memory intensive when large numbers of pixels were masked.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-2983 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4835 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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 clusterApproximately 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).
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4998 |
---|
|
Correct coding errors in meas_extensions_shapeHSM
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-3369 |
---|
|
Some minor errors when this code was converted to the meas_base
framework left it unusable. These have been corrected. Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4780 |
---|
|
Build and code improvements
These improvements should not usually be visible to end users. They may, however, be important for developers.
Work-around incompatibilities with NumPy 1.10
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.NumPy 1.10 introduced API changes which were incompatible with existing usage in the stack. The latter has been updated to match
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4063 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4071 |
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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4238 |
---|
|
When building boost warn user if user-config.jam or site-config.jam exists
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 futureBuilding 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4198 |
---|
|
Remove deprecated Task.display()
method
,status,resolution | serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-5590 |
---|
|
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
. Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4428 |
---|
|
Efficiency improvement in converting Mask
s to DefectList
s
Fix incorrect linking against Anaconda-provided libraries when using CMake
Some external packages -- mariadb
, 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; in the end, this results in a build failure. We have adjusted the build process of the affected packages to work around this errorThe previous version of routine was extremely memory intensive when large numbers of pixels were masked.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4800 |
---|
|
Add a new task parallelization framework
5771-303d-a785-1b6c5ab0f2d2 | key | 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.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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-2983609 |
---|
|
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-4835 |
---|
|
Adjust test tolerances to be compatible with MKL-based NumPy
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 underdesireable 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 CLO postAnaconda 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-51084719 |
---|
|
Now possible to directly get a Filter
's canonical name and aliases
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 equivalentsAdded 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.
Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | 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. Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-55904008 |
---|
|
Some external packages -- mariadb
, 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; in the end, this results in a build failure. We have adjusted the build process of the affected packages to work around this error. Jira |
---|
server | JIRA |
---|
columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
---|
serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
---|
key | DM-5609 |
---|
|
Fix incorrect linking against Anaconda-provided libraries when using CMake
Jira |
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server | JIRA |
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columns | key,summary,type,created,updated,due,assignee,reporter,priority,status,resolution |
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serverId | 9da94fb6-5771-303d-a785-1b6c5ab0f2d2 |
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key | DM-55955966 |
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