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66a8d09
feat(imaging): Hyperspectral Data Loader (Issue #175) (#223)
KedoKudo Feb 13, 2026
ebb146f
feat(imaging): Batch Fitting Orchestrator for Parallel SAMMY Executio…
KedoKudo Feb 16, 2026
8be248b
feat(imaging): add progress tracking and graceful shutdown to batch o…
KedoKudo Feb 16, 2026
d209604
fix(imaging): address Copilot review feedback on orchestrator PR
KedoKudo Feb 16, 2026
42c87a1
chore: update pixi.lock for tqdm dependency
KedoKudo Feb 16, 2026
1b1e63b
fix(imaging): wait for running futures before breaking on shutdown
KedoKudo Feb 16, 2026
e05a80c
ci: remove pinned pixi-version from CI workflows
KedoKudo Feb 16, 2026
7436451
fix(imaging): address remaining Copilot review comments
KedoKudo Feb 16, 2026
3c849c1
fix(imaging): move shutdown drain to after executor exit
KedoKudo Feb 16, 2026
7359d01
Merge pull request #225 from lanl/feature/178-progress-checkpointing
KedoKudo Feb 16, 2026
2c3012f
feat(imaging): add ResultsAggregator and HDF5 round-trip for 2D imagi…
KedoKudo Feb 16, 2026
bd6c5d7
fix(imaging): validate isotope ordering by name before assigning abun…
KedoKudo Feb 16, 2026
7cee298
fix(imaging): address Copilot review comments on aggregator PR
KedoKudo Feb 16, 2026
18688a6
Merge pull request #227 from lanl/feature/176-results-aggregation
KedoKudo Feb 16, 2026
089840a
feat(imaging): add backend abstraction, per-job timeout, and retry lo…
KedoKudo Feb 17, 2026
2cd267e
fix(imaging): use wait(FIRST_COMPLETED) for timeout and fresh executo…
KedoKudo Feb 17, 2026
802139d
fix(imaging): address Copilot review comments on orchestrator PR #228
KedoKudo Feb 17, 2026
cdbbcb8
fix(imaging): remove Docker backend and fix timeout clock start (#228)
KedoKudo Feb 17, 2026
4cd4db4
Merge pull request #228 from lanl/feature/177-parallel-sammy-execution
KedoKudo Feb 17, 2026
56f9e74
feat(imaging): add TempFileManager for batch temp file lifecycle (#174)
KedoKudo Feb 17, 2026
867091c
fix(imaging): address Copilot review on temp file management PR
KedoKudo Feb 17, 2026
040fd82
fix(imaging): enter TempFileManager context in fit_pixels for disk ca…
KedoKudo Feb 17, 2026
54d3c75
fix(imaging): address 8 Copilot review comments on temp file management
KedoKudo Feb 17, 2026
5de8258
Merge pull request #229 from lanl/feature/174-temp-file-management
KedoKudo Feb 17, 2026
a7f336a
feat(imaging): add AbundanceMapGenerator and AbundanceMapVisualizer (…
KedoKudo Feb 17, 2026
2c56f6a
Merge pull request #230 from lanl/feature/179-abundance-map-generator
KedoKudo Feb 17, 2026
498e6f1
test(imaging): add end-to-end validation suite for 2D imaging pipelin…
KedoKudo Feb 17, 2026
adfb58a
fix(tests): address Copilot review on validation test PR
KedoKudo Feb 17, 2026
c4df6fe
Merge pull request #231 from lanl/feature/180-validation
KedoKudo Feb 17, 2026
d5a5dc3
feat(imaging): 2D resonance imaging pipeline with two-pass SAMMY fitt…
KedoKudo Feb 20, 2026
0b111cf
Merge remote-tracking branch 'origin/next' into feature/172-2d-imaging
KedoKudo Feb 20, 2026
4cb5429
fix(imaging): adapt orchestrator to new FitConfig-based InpManager API
KedoKudo Feb 20, 2026
8bad8ba
fix: resolve Copilot review issues on PR #238
KedoKudo Feb 20, 2026
218db62
fix(imaging): bound in-flight futures and fix pass-2 error tracking
KedoKudo Feb 20, 2026
4401b2c
fix(imaging): use bounded submission for retry rounds
KedoKudo Feb 20, 2026
c0ed9d9
fix(imaging): route directory sources through HyperspectralLoader.fro…
KedoKudo Feb 20, 2026
7b4b971
fix(imaging): demote per-pixel log calls from INFO/WARNING to DEBUG
KedoKudo Feb 20, 2026
c186523
fix(imaging): promote retry round and batch summary to WARNING level
KedoKudo Feb 20, 2026
4f6c932
fix(nuclear): correct field indices in _get_atomic_number_from_mass_file
KedoKudo Feb 21, 2026
176869b
Merge pull request #243 from lanl/fix/pu241-atomic-number-lookup
KedoKudo Feb 21, 2026
42f652d
fix(imaging): silence loguru in worker processes to fix log flooding
KedoKudo Feb 21, 2026
7e60f8b
update notebook output cell
KedoKudo Feb 21, 2026
f38c236
Merge pull request #239 from lanl/fix/imaging-logging-verbosity
KedoKudo Feb 21, 2026
2f2d014
feat(imaging): add DataDegrader for controlled hyperspectral degradat…
KedoKudo Feb 20, 2026
4067f87
fix(imaging): export DataDegrader from imaging module __init__.py
KedoKudo Feb 21, 2026
6f3fb65
Merge pull request #240 from lanl/feature/187-data-degrader
KedoKudo Feb 21, 2026
4b0279e
feat(imaging): add SparsityAssessor for SNR-based severity classifica…
KedoKudo Feb 20, 2026
3244f09
fix(imaging): derive resonance depth from spatial-mean spectrum, remo…
KedoKudo Feb 21, 2026
731190d
fix(imaging): clamp resonance_depth to non-negative before SNR scoring
KedoKudo Feb 21, 2026
a0f0fb0
fix(imaging): return SNR=0 when resonance_depth is zero (overshoot case)
KedoKudo Feb 21, 2026
83da31f
Merge pull request #241 from lanl/feature/183-sparsity-assessor
KedoKudo Feb 21, 2026
a08ec8e
feat(imaging): add SpatialBinner + bin_size param in analyze_imaging …
KedoKudo Feb 20, 2026
792ee0e
fix(imaging): binned pixel iteration, edge cropping, and uncertainty …
KedoKudo Feb 21, 2026
e4a40f2
fix(imaging): remap ROI to binned coordinates when bin_size > 1
KedoKudo Feb 21, 2026
124be30
fix(imaging): validate ROI bounds in binned pixel iterator instead of…
KedoKudo Feb 21, 2026
bb580f3
fix(imaging): validate ROI against original image before binning
KedoKudo Feb 21, 2026
04fd765
fix(imaging): success_mask NaN edges, empty ROI, and zero-sized bin v…
KedoKudo Feb 21, 2026
06ed2ea
fix(imaging): make bin_size keyword-only, fix unbin_map for bin_size=1
KedoKudo Feb 21, 2026
ae03b8b
fix(imaging): mask pixels outside original ROI after unbinning
KedoKudo Feb 21, 2026
042e5ae
fix(imaging): promote padded output to float before NaN fill in unbin…
KedoKudo Feb 21, 2026
41e7f54
fix(imaging): address Copilot review - metadata, docstrings
KedoKudo Feb 21, 2026
63d7633
Merge pull request #242 from lanl/feature/186-spatial-binner
KedoKudo Feb 21, 2026
b666bb0
feat(imaging): add PhysicsRecovery for TRINIDI-style NNLS density rec…
KedoKudo Feb 22, 2026
d91592e
fix(imaging): apply ROI/stride in physics recovery, validate energy g…
KedoKudo Feb 22, 2026
0ae98ca
fix(imaging): validate ROI bounds and guard against NaN/Inf spectra
KedoKudo Feb 22, 2026
679c9e3
fix(imaging): accept empty remapped ROI in physics recovery
KedoKudo Feb 22, 2026
f731aab
fix(imaging): correct import path for convert_csv_to_sammy_twenty
KedoKudo Feb 22, 2026
b97013d
fix(imaging): address Copilot review — validation, docs, safety
KedoKudo Feb 22, 2026
48726ea
fix(imaging): address Copilot review — dictionary validation, logging…
KedoKudo Feb 22, 2026
5683186
fix(imaging): reject checkpoint args in physics recovery path
KedoKudo Feb 22, 2026
0da24b4
Merge pull request #244 from lanl/feature/184-physics-recovery
KedoKudo Feb 22, 2026
202011f
feat(notebook): add sparsity, degrader, binning, and recovery demos (…
KedoKudo Feb 22, 2026
77f7c22
fix(notebook): use stronger degradation to reach L2/L3 severity, inde…
KedoKudo Feb 22, 2026
e4cd0c0
fix(notebook): address Copilot review — proper init, stride var, full…
KedoKudo Feb 22, 2026
6e1c03d
Merge pull request #245 from lanl/feature/189-imaging-notebook
KedoKudo Feb 22, 2026
0cb77ce
fix(imaging): read zeroth-order transmission in forward-model mode
KedoKudo Feb 22, 2026
a53a1c4
feat(imaging): add NMF spectral decomposition for noise-robust recove…
KedoKudo Feb 22, 2026
860815a
fix(imaging): handle NaN in NMF, decouple labeling from instance stat…
KedoKudo Feb 22, 2026
16f4d99
fix(imaging): guard NaN in correlation matrix, persist spectral_basis…
KedoKudo Feb 22, 2026
dbc480c
Merge pull request #246 from lanl/feature/185-nmf-recovery
KedoKudo Feb 22, 2026
da09297
feat(imaging): add hybrid NMF+NNLS recovery via denoise_nmf parameter
KedoKudo Feb 22, 2026
ce9f679
fix(imaging): prevent spurious cancellation of queued futures and ref…
KedoKudo Feb 22, 2026
4cea251
fix(imaging): advance stall detection when zombie timed-out workers b…
KedoKudo Feb 22, 2026
62596c5
research: add noise recovery notebooks (NB0 baseline + NB1 T-domain+TV)
KedoKudo Feb 23, 2026
20883cc
feat(imaging): add vary-flag overrides for SAMMY fitting params and P…
KedoKudo Feb 24, 2026
634ea08
research(NB1): update T-domain notebook to ppm metrics and verified c…
KedoKudo Feb 25, 2026
6ad6a2d
research(NB2): add spatial denoising notebook with verified conclusions
KedoKudo Feb 25, 2026
2477d3e
research: rebuild noise recovery notebooks with physical ground truth
KedoKudo Feb 25, 2026
554c96b
Implement feature X to enhance user experience and fix bug Y in module Z
KedoKudo Feb 25, 2026
c9c8d99
Refactor code structure for improved readability and maintainability
KedoKudo Feb 25, 2026
4f59564
research: update NB0/NB1 conclusions with verified numbers from re-run
KedoKudo Feb 26, 2026
c0cde15
fix(notebooks): clarify count-domain Poisson noise model per PR review
KedoKudo Feb 26, 2026
417f9ab
Merge pull request #249 from lanl/feature/172-noise-recovery-research
KedoKudo Feb 26, 2026
33e4148
Merge remote-tracking branch 'origin/next' into feature/172-2d-imaging
KedoKudo Feb 26, 2026
f9646ae
Refactor code structure for improved readability and maintainability
KedoKudo Feb 28, 2026
ae03af7
Merge remote-tracking branch 'origin/next' into feature/172-2d-imaging
KedoKudo Mar 30, 2026
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1 change: 0 additions & 1 deletion .github/workflows/package.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@ jobs:
- uses: actions/checkout@v6
- uses: prefix-dev/setup-pixi@v0.9.4
with:
pixi-version: v0.41.4
manifest-path: pyproject.toml
- name: build pypi package
run: |
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1 change: 0 additions & 1 deletion .github/workflows/unittest.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,6 @@ jobs:
- uses: actions/checkout@v6
- uses: prefix-dev/setup-pixi@v0.9.4
with:
pixi-version: v0.41.4
manifest-path: pyproject.toml
- name: run unit tests
run: |
Expand Down
6 changes: 6 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -214,3 +214,9 @@ _version.py

# ignore any scratch spaces or temporary files
.scratch/

# Ignore local Claude Code instructions (user-specific)
CLAUDE.md

# Ignore debug images
_debug_images/
1,025 changes: 1,025 additions & 0 deletions examples/Notebooks/pleiades_2d_imaging.ipynb

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1,284 changes: 1,284 additions & 0 deletions examples/Notebooks/pleiades_noise_recovery_nb0_ground_truth.ipynb

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