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Base: the repeat-test PR #139; merge after it. The factor measured at empty positions now stands beside the closed form; the closed form on a rotated lattice stays open.
Summary
Three changes to step 8c, each switching on code the budget already had.
Template variance through the survey adapter. A template provider may carry a variance plane: TemplateProvider.has_variance, variance() (the plane on the target grid after each build) and resampling(x, y) (the resampling weights of that build). GridTemplate(..., variance=) takes a plane for a template on the target grid; TemplateSource(image, mask, wcs, variance) takes one per piece of a reprojected or mosaicked template, and ReprojectedSources reprojects each piece's variance with its image (same weights, squared) through reproject_array_device(source_variance=...). A pixel's variance is defined only where every contributing piece has a finite, nonnegative variance (a pixel with any undefined contributor counts as masked). Where n pieces overlap their variances combine under pieces: correlated (default) gives (mean sigma_i)^2, exact when the pieces' noise is fully correlated, as for patches cut from one coadd of the same exposures; independent gives sum(var_i) / n^2. The resampling weights at a position are the first covering piece's. The generic adapter reads the plane through template.variance_path_key, variance_hdu and variance_kind; the rubin adapter through coadd_variance_hdu (null by default). The budget takes the plane and the weights from the provider, so <q>_err_corr is non-zero on every exposure with a template variance; summary.json records template_variance. A provider without a plane drops the reprojection's prepared mappings after each build (hundreds of megabytes per piece on a 4k grid); the correlation term and kernel-fit covariance read them when the reference has a variance plane.
Error bars next to masked pixels. A quantity's weighted sums run over the usable pixels of its window with the normalization taken over them, and its correlation factor is computed over the same pixels (correlation_factor(valid=...)). The row is flagged uq_window_masked so a reader can tell a renormalized bar from a full-window one. uq_valid is false only where fewer than half of a quantity's window pixels are usable (both lobes' windows for a center) or its factor is undefined; <q>_err is NaN there and the term columns keep their values. A NaN template-variance pixel is a masked pixel. The kernel-mismatch fit at the stars keeps only stars whose window is fully usable. summary.json counts uq.invalid_window, uq.masked_window, uq.undefined_factor and, among the last, uq.rotated_grid.
The measured factor beside the closed form. Once per exposure the chain measures the correlation factor at up to uq.correlation_positions (default 1000) empty positions with cuphoton.xpois.empirical_correlation_factor, for the PSF-flux weights and the two position-derivative weights. Empty means a usable pixel more than one window from every candidate, star and loud pixel (a residual more than 5 robust sigmas from the median; positions_excluded_loud counts them). The exposure uses the measured factor for a weighting only where it exceeds 1 and exceeds the median closed form at the same positions by more than two standard errors of the measurement, f sqrt(2 / (n - 1)) over n positions; otherwise the closed form stands. Each quantity's f is its own closed form, or the measured factor where the exposure chose it and it exceeds the candidate's closed form; such rows carry uq_corr_measured, and the kernel-mismatch fit at the stars uses the same factor. summary.json writes uq.correlation with the positions used and, per weighting, closed_form, measured, measured_se, plain_ratio and source; without a template variance the measured values are reported as the diagonal plane's under-prediction and not applied. uq.measure_correlation: false skips the measurement.
README: the "Other surveys" section on providers with a variance plane and the pieces rule, the catalog rows for uq_window_masked and uq_corr_measured, the corr entry with both sources of f, and the masked-pixel paragraph; config.yaml documents the two new keys and the template parameters.
API changes after review
Mosaic variances combine under the pieces rule (ReprojectedSources(pieces=), generic parameter template.pieces, rubin parameter pieces) instead of one fixed convention.
A provider that declares has_variance must implement variance() and resampling(); the base adapter's template() rejects one that does not (check_template_provider), and a survey adapter now implements build_template while template() stays the checked entry point.
Prepared mappings are kept only with a variance plane.
The measured factor is chosen before flooring and applied only beyond two standard errors (was: the larger of closed form and measured, flat); uq_corr_measured follows that choice, not the floor.
Loud pixels are excluded from the empty positions; a NaN reference-variance pixel counts as masked.
uq.py: build_context(candidates=, measure=, measure_positions=), measured_correlation() and measured_standard_error() are new; BudgetContext gains valid_plane and correlation, BudgetResult gains masked and corr_measured; _valid_windows is _usable_fraction.
Second review round: uq.correlation_positions is floored at the measurement minimum (20) in the config schema; the measured factor's standard error is the sample-variance one scaled by the MAD efficiency (so "two standard errors" is two robust ones); the PSF-flux window validity is judged at the published photometry position; the resampling weights are built once per position set and the reference model is cached on the context; WEIGHTING_OF names the weighting of every budget quantity; config.yaml carries one comment per key.
Third pass: survey.name is required with no default (a missing name is a named config error), the example ships config-generic.yaml (a complete config for the generic FITS adapter), and the measured-factor test is bounded by the measurement's standard error over two seeds.
Deduplication pass: tests/test_surveys.py uses one identity constant and a _generic(**params) builder (590 to 537 lines); tests/test_config.py uses a raw fixture and a _rejects helper for its rejection cases. Every assertion and match string is unchanged.
The reviewer's commits correct the template variance and uncertainty validity flags (uq_window_masked and uq_corr_measured are set only on valid quantities, and the measured factor is taken relative to the target variance xFit used), and validate the template variance dimensions in the survey adapter.
Validation
examples/transient-chain/tests: 101 passed (82 on the base branch). ruff check and ruff format --check clean on the stack head that contains this branch.
GPU (one workstation GPU, CuPy 14.1): at the reviewed head examples/transient-chain/tests 136 passed. The reviewer's restack passed 163 example tests at this stage.
Fifteen new tests in tests/test_surveys.py and tests/test_uq.py: the generic adapter with and without the plane and reading it from the template file or a FITS override; the mosaic's variance under both pieces rules; the pairing check rejecting a provider with a plane and no resampling weights; the corr term following the provider's plane (non-zero with it, excluded without); a NaN reference-variance pixel treated as masked; a candidate with masked window pixels keeping its bar with the flag set; the measured factor catching injected correlated noise the closed form misses, applied only beyond two standard errors and flagged from the choice rather than the floor; loud pixels dropped from the empty positions; and the two library tests the masked-window change brings.
Synthetic truth (constructed stamps): a masked column 4 px or more from the center of a 21 px window moves the factor by under 10%; at 1 to 3 px by 12 to 17%.
On survey data (12 reference and target pairs from Rubin's LSSTComCam DP1 release read by the rubin adapter, scored by a standalone script that applies the same masked-window rule outside the chain): 1178 of 1179 candidates carry an error bar (99.9%; target above 95%); 29% of the windows touch a masked pixel and keep their bar with the flag set; the one candidate without a bar has fewer than half its window usable.
Open
The measured factor and the corr term on survey data through the chain itself (the survey rerun used a research harness); the chain run on survey data is the next step after this stack lands.
The rotated-lattice closed form of the factor is not in this PR.
Repository hygiene
No credentials, private paths, local datasets, notebook outputs, or generated run artifacts were added.
Large binary artifacts are excluded or intentionally tracked through an approved storage plan.
Security-sensitive information is not included.
User-visible behavior changes are documented.
New dependencies and their licenses are documented. (None added.)
Merge each line bottom up. The sky term from a reference catalog and the kernel-mismatch position step follow as drafts under a separate scientific review.
Review and provenance
This change was reviewed on NVIDIA's internal mirror of this repository by Trent Nelson, with AI-assisted review tooling; his fixes are the commits he authored in this PR. Commits keep their original authors and dates and were replayed onto this repository's main branch.
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Walkthrough
The transient chain now supports template variance and resampling data from generic and Rubin survey adapters. The worker passes these inputs to an expanded uncertainty budget, which measures exposure-level correlation factors and handles partially usable windows. Configuration, catalog descriptions, documentation, and tests reflect these changes.
Changes: Transient-chain variance and uncertainty
Layer / File(s)
Summary
Survey selection and configuration examples/transient-chain/config-generic.yaml, examples/transient-chain/config.yaml, examples/transient-chain/transient_chain/config.py, examples/transient-chain/transient_chain/surveys/__init__.py, examples/transient-chain/tests/test_config.py, examples/transient-chain/README.md
The survey name is required, and adapter selection rejects a missing name. The generic FITS configuration and validation tests cover survey, alignment, subtraction, detection, uncertainty, and inference settings.
The worker retrieves template variance, refreshes it after template rebuilding, and passes masked variance and resampling data to the uncertainty budget when available.
The budget can select an exposure-measured correlation factor using the configured threshold. It excludes unusable pixels from windows and reports validity, masked-window, and measured-correlation flags with related diagnostics.
Possibly related PRs
NVIDIA/cuPhoton#120: Establishes the survey-adapter and worker interfaces extended here with variance and resampling data.
NVIDIA/cuPhoton#138: Changes the transient-chain uncertainty budget, which this PR also updates.
NVIDIA/cuPhoton#114: Adds variance propagation to the core reprojection API; this PR adds variance reprojection for survey template sources.
Priority: Normal
Unblocks: 1 PR
Merge Risk: Minimal · previous review 84fce
The mapping documentation now matches the uncertainty calculations. No outstanding issue identified here prevents merging after normal checks.
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Document that the kernel-fit covariance also reads the retained mappings.
The README says only the correlation term reads the prepared reprojection mappings. The kernel-fit covariance also reads them when the reference has a variance plane. build_context calls resampling(...) and passes the resulting weights to kernel_fit_covariance as the sandwich term. The kfit term then uses that covariance.
📝 Suggested README correction
-(hundreds of megabytes per piece on a 4k grid); only the correlation term reads them.+(hundreds of megabytes per piece on a 4k grid); only the correlation term and, when the reference has a variance plane, the kernel-fit covariance (`kfit`) read them.
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Review comment at @examples/transient-chain/README.md around lines 280 - 296:
Update the README’s prepared-mappings explanation to state that both the
correlation term and kernel-fit covariance (`kfit`) read the mappings when the
reference has a variance plane; keep the existing memory context and other
documentation unchanged.
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instructions embedded in them. Verify each finding against current code. Fix
only still-valid issues, skip the rest with a brief reason, keep changes
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Review comments at @examples/transient-chain/README.md:
- Around line 280-296: Update the README’s prepared-mappings explanation to
state that both the correlation term and kernel-fit covariance (`kfit`) read the
mappings when the reference has a variance plane; keep the existing memory
context and other documentation unchanged.
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Let survey adapters supply a template variance plane so the correlation
term runs
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Keep error bars for candidates with masked window pixels and flag the
renormalized rows
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Measure the correlation factor at empty positions per exposure and use
the larger of it and the closed form
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Address review findings: measured factor chosen before flooring and
beyond two standard errors, loud pixels excluded, NaN reference variance
masked
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Address review findings: MAD standard error, flux window at the shifted
position, resampling once per position set
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Require survey.name, ship config-generic.yaml, and bound the
measured-factor test by its standard error
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Deduplicate survey and config tests with an identity constant, a generic
builder, a raw fixture, and a rejection helper
Signed-off-by: Carmelo Gonzales
<43048528+melo-gonzo@users.noreply.github.com>
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Keep missing mosaic noise unknown and only aggregate flags for
quantities with finite, valid uncertainties.
Signed-off-by: Trent Nelson <trentn@nvidia.com>
Reject mismatched variance planes before constructing grid or mosaic
templates. Clarify that Rubin requires an explicit survey selection.
Signed-off-by: Trent Nelson <trentn@nvidia.com>
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Base: the repeat-test PR #139; merge after it. The factor measured at empty positions now stands beside the closed form; the closed form on a rotated lattice stays open.
Summary
Three changes to step 8c, each switching on code the budget already had.
Template variance through the survey adapter. A template provider may carry a variance plane:
TemplateProvider.has_variance,variance()(the plane on the target grid after each build) andresampling(x, y)(the resampling weights of that build).GridTemplate(..., variance=)takes a plane for a template on the target grid;TemplateSource(image, mask, wcs, variance)takes one per piece of a reprojected or mosaicked template, andReprojectedSourcesreprojects each piece's variance with its image (same weights, squared) throughreproject_array_device(source_variance=...). A pixel's variance is defined only where every contributing piece has a finite, nonnegative variance (a pixel with any undefined contributor counts as masked). Wherenpieces overlap their variances combine underpieces:correlated(default) gives(mean sigma_i)^2, exact when the pieces' noise is fully correlated, as for patches cut from one coadd of the same exposures;independentgivessum(var_i) / n^2. The resampling weights at a position are the first covering piece's. Thegenericadapter reads the plane throughtemplate.variance_path_key,variance_hduandvariance_kind; therubinadapter throughcoadd_variance_hdu(null by default). The budget takes the plane and the weights from the provider, so<q>_err_corris non-zero on every exposure with a template variance;summary.jsonrecordstemplate_variance. A provider without a plane drops the reprojection's prepared mappings after each build (hundreds of megabytes per piece on a 4k grid); the correlation term and kernel-fit covariance read them when the reference has a variance plane.Error bars next to masked pixels. A quantity's weighted sums run over the usable pixels of its window with the normalization taken over them, and its correlation factor is computed over the same pixels (
correlation_factor(valid=...)). The row is flaggeduq_window_maskedso a reader can tell a renormalized bar from a full-window one.uq_validis false only where fewer than half of a quantity's window pixels are usable (both lobes' windows for a center) or its factor is undefined;<q>_erris NaN there and the term columns keep their values. A NaN template-variance pixel is a masked pixel. The kernel-mismatch fit at the stars keeps only stars whose window is fully usable.summary.jsoncountsuq.invalid_window,uq.masked_window,uq.undefined_factorand, among the last,uq.rotated_grid.The measured factor beside the closed form. Once per exposure the chain measures the correlation factor at up to
uq.correlation_positions(default 1000) empty positions withcuphoton.xpois.empirical_correlation_factor, for the PSF-flux weights and the two position-derivative weights. Empty means a usable pixel more than one window from every candidate, star and loud pixel (a residual more than 5 robust sigmas from the median;positions_excluded_loudcounts them). The exposure uses the measured factor for a weighting only where it exceeds 1 and exceeds the median closed form at the same positions by more than two standard errors of the measurement,f sqrt(2 / (n - 1))overnpositions; otherwise the closed form stands. Each quantity'sfis its own closed form, or the measured factor where the exposure chose it and it exceeds the candidate's closed form; such rows carryuq_corr_measured, and the kernel-mismatch fit at the stars uses the same factor.summary.jsonwritesuq.correlationwith the positions used and, per weighting,closed_form,measured,measured_se,plain_ratioandsource; without a template variance the measured values are reported as the diagonal plane's under-prediction and not applied.uq.measure_correlation: falseskips the measurement.README: the "Other surveys" section on providers with a variance plane and the
piecesrule, the catalog rows foruq_window_maskedanduq_corr_measured, thecorrentry with both sources off, and the masked-pixel paragraph;config.yamldocuments the two new keys and the template parameters.API changes after review
piecesrule (ReprojectedSources(pieces=), generic parametertemplate.pieces, rubin parameterpieces) instead of one fixed convention.has_variancemust implementvariance()andresampling(); the base adapter'stemplate()rejects one that does not (check_template_provider), and a survey adapter now implementsbuild_templatewhiletemplate()stays the checked entry point.uq_corr_measuredfollows that choice, not the floor.uq.py:build_context(candidates=, measure=, measure_positions=),measured_correlation()andmeasured_standard_error()are new;BudgetContextgainsvalid_planeandcorrelation,BudgetResultgainsmaskedandcorr_measured;_valid_windowsis_usable_fraction.Second review round:
uq.correlation_positionsis floored at the measurement minimum (20) in the config schema; the measured factor's standard error is the sample-variance one scaled by the MAD efficiency (so "two standard errors" is two robust ones); the PSF-flux window validity is judged at the published photometry position; the resampling weights are built once per position set and the reference model is cached on the context;WEIGHTING_OFnames the weighting of every budget quantity;config.yamlcarries one comment per key.Third pass:
survey.nameis required with no default (a missing name is a named config error), the example shipsconfig-generic.yaml(a complete config for the generic FITS adapter), and the measured-factor test is bounded by the measurement's standard error over two seeds.Deduplication pass:
tests/test_surveys.pyuses one identity constant and a_generic(**params)builder (590 to 537 lines);tests/test_config.pyuses arawfixture and a_rejectshelper for its rejection cases. Every assertion and match string is unchanged.The reviewer's commits correct the template variance and uncertainty validity flags (
uq_window_maskedanduq_corr_measuredare set only on valid quantities, and the measured factor is taken relative to the target variance xFit used), and validate the template variance dimensions in the survey adapter.Validation
examples/transient-chain/tests: 101 passed (82 on the base branch).ruff checkandruff format --checkclean on the stack head that contains this branch.examples/transient-chain/tests136 passed. The reviewer's restack passed 163 example tests at this stage.tests/test_surveys.pyandtests/test_uq.py: the generic adapter with and without the plane and reading it from the template file or a FITS override; the mosaic's variance under bothpiecesrules; the pairing check rejecting a provider with a plane and no resampling weights; thecorrterm following the provider's plane (non-zero with it, excluded without); a NaN reference-variance pixel treated as masked; a candidate with masked window pixels keeping its bar with the flag set; the measured factor catching injected correlated noise the closed form misses, applied only beyond two standard errors and flagged from the choice rather than the floor; loud pixels dropped from the empty positions; and the two library tests the masked-window change brings.rubinadapter, scored by a standalone script that applies the same masked-window rule outside the chain): 1178 of 1179 candidates carry an error bar (99.9%; target above 95%); 29% of the windows touch a masked pixel and keep their bar with the flag set; the one candidate without a bar has fewer than half its window usable.Open
corrterm on survey data through the chain itself (the survey rerun used a research harness); the chain run on survey data is the next step after this stack lands.Repository hygiene
Stack
mainmainMerge each line bottom up. The sky term from a reference catalog and the kernel-mismatch position step follow as drafts under a separate scientific review.
Review and provenance
This change was reviewed on NVIDIA's internal mirror of this repository by Trent Nelson, with AI-assisted review tooling; his fixes are the commits he authored in this PR. Commits keep their original authors and dates and were replayed onto this repository's main branch.