Release 11.0 (2015-09-24)¶
These release notes document notable changes since 10.1, which was the Winter 2015 release.
Source | Identifier |
---|---|
Git tag | 11.0 |
EUPS distrib | v11_0 |
See also:
- Qserv release notes
- Webserv release notes
- Science User Interface release notes
- Characterization Metric Report (DMTR-11)
Major Functionality and Interface Changes¶
Improved semantics for loading Exposure
s and MaskedImage
s 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 Exposure
s and MaskedImage
s 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 FunctorKey
s 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 FunctorKey
s 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.
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 Footprint
s 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 Footprint
s 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 Footprint
s 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 Peak
s per
Footprint
, and the size and area of Footprint
s.
[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.
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 SourceRecord
s. 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]
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]
Bug Fixes¶
The following fixes resolve problems visible to end users.
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
Footprint
s. Unfortunately, in some circumstances (notably when
dealing with particularly large Footprint
s) 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]
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]
Build and code improvements¶
These improvements should not usually be visible to end users. They may be important for developers, however.
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.
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
Footprint
s are clipped.
[DM-2914]