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Commit 84e40a5
Image simulations workflow (#766)
* testing/simulate: added Pujol denoising estimator of shear bias
* Running SP v2.0 on image simulations, up to -j 8
* SP v2.0 running on image simulations including ngmix
* Running on im sims incl final cat
* ÃÃÂadded datetime to Mh run
* Âinit v2.0: cd in new subdirÂ
* ÂÂimage sims run updates
* Âsmall changes
* output mean e to ngmix log
* doc
* ÂÂrun script : added --retry
* im_sims docker deployment
* added .py to executables
* fixe pyproject bug
* pyproject moved back to exe scripts without extension
* running create_final_cat.py on image_sims
* Pipeline running on image sims
* config files: change batch size to 1 (default)
* snakemake setup for image simulations
* fixed snakefile
* test for zero size FITS output files
* zero-size output fixes
* more automatisation for image sims snakemake
* ngmix+vignets: handling of empty input PSF cats; scripts: improved snakemake running
* retarget(im_sims): revert incidental stale-base edits to shared modules
Keep only genuine sims-enablement; revert shared-module changes that were
side-effects of the stale ngmix_v2.0 base and collide with in-flight work:
- make_cat: restore HSM_G*_PSF grammar (fix/ngmix-psf-columns) + spread_model
(714847c, split-761); drops the input_file_List NameError
- vignetmaker: drop broad try/except churn (_w_log AttributeError -> test fail)
- mask: restore CDSCLIENT_PATH knob (live in 4 example configs)
- restore pipeline_tutorial.md (toc.rst ref -> Sphinx build) + run_scratch_local.sh
Verification branch only; not for push. Grounds the #766 review.
* retarget(im_sims): slim to ShapePipe module enablement; orchestration -> sp_validation
The image-sims workflow splits by concern along the repo dependency arrow
(shapepipe produces catalogues; sp_validation consumes + validates them):
- ShapePipe (this PR): only the pipeline-module changes needed to run on
background-free sims -- the fake_psf module, ngmix BKG_SUB path, numeric
sim-exposure-ID handling (exp_utils/sextractor/merge_headers), the
cfis_image_sims module configs, create_final_cat's image_sims mode, and
make_data_pujol.
- sp_validation (separate PR): the snakemake orchestration + the
merge/calibrate/m-bias half, rebuilt on sp_validation's native container
workflow. The orchestration files removed here are preserved in git history
(origin/im_sims) and move there.
Incidental stale-base edits to shared modules/standard configs/tests reverted
to ngmix_v2.0 (which already carries the fixes: 662fad4 HSM g-cols,
714847c spread_model). Retargeted onto ngmix_v2.0; uv.lock regenerated.
* fix(im_sims): restore image-sims job dispatch in the ShapePipe runner
The ngmix_v2.0 retarget slimmed run_job_sp_canfar_v2.0.bash and
job_sp_canfar_v2.0.bash of their image-sims code paths, leaving #766 unable
to run the image-sims pipeline at all: run_job had no -t/--type dispatch (so
the sp_validation workflow's `-t image_sims` was silently swallowed and it
ran standard-DATA mode), and its job-1024 completeness check referenced
ngmix_interp_runner, a runner that exists nowhere in the codebase.
job_sp_canfar rejected `-r symlink` ("vos only for v2.0"), named the Gie and
make_cat configs for the data path only, and still invoked shapepipe_run.py
(the console entry point is `shapepipe_run`, no extension, since 797eeff).
run_job: restored the canonical image-sims runner (full -t/--type dispatch —
cfis_image_sims config dir, symlink retrieve, tile_det=sx, faked Uz
weight-uncompress, fake_psf under job 512, job-2048 make_cat, and the correct
ngmix_runner check). Made it relocatable per #766's goal: a self-derived
$SP_ROOT replaces ~/shapepipe for sourcing functions.sh/job_list_help.bash
and resolving config dirs, and job_sp_canfar is invoked by explicit repo path
(it is not on the container PATH). run_tile_job now re-anchors cwd to the tile
work dir on entry: SP_RUN/SP_CONFIG derive from cwd, and run_exp_job leaves
cwd in the last exposure dir, so when run_job is called once for the whole
pipeline (-j 4095, as the workflow does) the post-exposure tile jobs would
otherwise execute in the stale exposure dir.
job_sp_canfar: kept the ngmix_v2.0 base — the #746 NUMBER_LIST mechanism that
matches the new-grammar container (the canonical runner still uses the retired
shapepipe_run -e flag and would crash) — and grafted the image-sims bits:
accept `-r symlink`, config_exp_Gie_$retrieve, config_tile_Mc_$psf (the config
present in cfis_image_sims and matching run_job's job-2048 check), the bare
`shapepipe_run` entry point, and a self-derived $SP_ROOT.
Verified on candide against the post-#761 container: `-t image_sims` selects
cfis_image_sims + symlink + sx and runs Git -> faked-Uz -> Fe -> Gie(7/7) ->
Sp -> Ma -> Mh_exp, each in its correct work dir with new-grammar shapepipe_run.
The two scripts run from the bind-mounted repo, so the container supplies only
the Python stack.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019Jd85D8xNZZ43FgesabSnk
* fix(im_sims): add SM_DO_CLASSIFICATION to the image-sims make_cat config
The image-sims make_cat config lacked SM_DO_CLASSIFICATION, which the newer
make_cat_runner reads unconditionally (NoOptionError -> job 2048 crashed,
so the per-tile final_cat was never built). The image-sims pipeline has no
spread_model_runner stage (make_cat inputs are sextractor + fake_psf + ngmix
only), so there is nothing to classify: set it False. With this, a single
tile completes end-to-end (Git -> ... -> ngmix -> make_cat), producing a
2345-object final_cat-233-293.fits against the post-#761 container.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019Jd85D8xNZZ43FgesabSnk
* fix(im_sims): new-grammar final_cat.param for the image-sims pipeline
create_final_cat selects this column list from the per-tile make_cat output
into final_cat_{sim}.hdf5; the list was still old-grammar (NGMIX_ELL_*,
NGMIX_Tpsf_*, NGMIX_T_PSFo_*, NGMIX_MOM_FAIL) while the post-#761 make_cat
writes NGMIX_G{1,2}_*, NGMIX_T_PSF_ORIG/RECONV_*, so the merge died on
'NGMIX_Tpsf_2M' is not in list.
Rewrite to the v2 grammar, mirroring example/cfis/final_cat.param minus the
two columns the simulation pipeline does not emit (IMAFLAGS_ISO: no
imaging-flag masking stage; NGMIX_MOM_FAIL: superseded by NGMIX_MCAL_TYPES_FAIL,
which is included). Verified: all 65 columns present in the per-tile cat, merge
-> extract -> calibrate runs clean on 1z2z_grid_1.
Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D9atA9VPrg7VMC7oBArny9
* fix(mask): don't crash stdout handling when star masking is off
With HALO_MAKE and SPIKE_MAKE both False (the image-sims mask config),
find_stars never runs, so _CDS_stdout is never set and the unconditional
read at the end of make_mask raised AttributeError for every CCD. The
flag files were already written, so each mask stage 'failed' with 40
bookkeeping errors and exit 1, relying on the runner's continue-on-error
to keep the pipeline alive. Guard the CDS block with hasattr, matching
the WeightWatcher/rm blocks below it.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01TWURLMoixhuMqVrPVdRmCp
* ngmix: position-seeded per-object RNG for Pujol noise cancellation (#796)
Add an opt-in SEED_FROM_POSITION knob to the ngmix module (default False).
When on, the object loop replaces the tile-level RNG with a per-object
RandomState seeded from the object's sky position, and rebuilds the prior
from that same RNG, so every stochastic step of the fit is a deterministic
function of (ra, dec, ccd).
Why: image-sim m-bias uses the Pujol estimator — the same scene under
different applied shears, with shear response read from the branch difference
of the SAME objects. Metacal's fixnoise adds a counter-noise realisation from
an RNG seeded per tile, so an object gets different added noise in different
branches (detection order differs) and the noise fails to cancel in the
difference, inflating sigma_m. Seeding per object from position makes the same
object draw the same added noise AND the same fit guesses in every branch, so
both cancel and the m-bias error shrinks. Design and box math are Fabian's
issue #796.
The prior must be rebuilt per object, not just the RNG: the ngmix guesser
draws its initial guess via prior.sample(), which consumes the RNG the prior
was CONSTRUCTED with (ngmix 2.4.0 guessers.py / joint_prior.py). A per-object
RNG alone would leave the guess drawing from the shared tile stream and break
cancellation. The fixnoise counter-noise itself rides on the observation's
attached noise image (use_noise_image=True), which prepare_ngmix_weights draws
from the per-object RNG — so no fresh draw from the bootstrapper RNG is needed.
Deviation from #796: Fabian combines the 3-arcsec position boxes as
box_x + box_y, which collides along anti-diagonals — boxes (10,20) and (11,19)
both give seed 30, so two distinct objects share a noise stream. This replaces
the sum with a Cantor pairing (a bijection on the non-negative integers) after
a zig-zag fold that maps signed box indices (Dec can be negative) onto
non-negative ones, reduced mod 2**32 into the valid RandomState seed range.
The box math is kept exactly as his: floor(ra*3600/3)+(ccd+1),
floor(dec*3600/3)+(ccd+2), first-epoch coordinates (coord_list[0] convention),
so all epochs of one object share the stream.
Off by default => production path is byte-identical to develop (verified:
metacal g for all five types matches unmodified develop bit-for-bit; the full
fast suite passes, 326 tests). New property tests cover the seed's range,
sub-box jitter invariance, adjacent-box distinctness, and the resolved
anti-diagonal collision.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01J9qEVRCWEekT5ACNB3rjkq
* sims config: enable SEED_FROM_POSITION for the A/B noise-cancellation run
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UvQvyJTEwYcLCwDEgpWMJ6
* running smoother on im sims
* Fix nfev_fit int64 dtype lock crashing batch-saved ngmix output
compile_results filled nfev_fit with np.nan on failed fits, the only
int-like column with a float fallback. With SAVE_BATCH enabled,
save_results locks column dtypes from batch 1; if that batch has no
failures the column locks to int64, and the first later batch with a
failure feeds NaN into it, raising "cannot convert float NaN to
integer" on append. Use ngmix's own -1 failed/absent-nfev sentinel
instead of NaN, keeping the column int64 across every batch.
Fixes #795
* im sims: coverage scan script for (near-)empty input tiles
Companion to the coverage rule in the Snakefile: scans input weight
maps (subsampled), writes tile_coverage_grid_{num}.yaml with an
exclude list read at DAG-build time. Weight-map location is taken
from the get-images ini of the 1p2z variant. Plus two felt fibers
documenting the blank-tile and thread-exhaustion findings.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* restore apptainer_noslurm.sh dropped in im_sims_candide merge
The image_sims_pipeline Snakefile invokes all container commands through
this wrapper; it strips SLURM/PMI/PMIX/OMPI env vars that crash OpenMPI
inside apptainer on SLURM compute nodes. No replacement exists in
run_scratch_local.sh or run_job_sp_canfar_v2.0.bash.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* Retire in-repo image_sims Snakemake orchestrator
The image-simulation pipeline's orchestration now lives in sp_validation
(companion PR #225), which drives ShapePipe via `run_job -t image_sims
--config_dir`. The in-repo Snakemake driver under
scripts/image_sims_pipeline/ (Snakefile, info.py, monitor_mbias.py,
config.yaml.template) is superseded and removed to keep a single source
of orchestration truth.
Its coverage-scan helper, check_tile_coverage.py, is the one piece of
reusable logic with no equivalent elsewhere; it moves to scripts/python/
alongside the other run-directly helpers (create_final_cat.py, etc.) and
gains the executable bit to match that directory's convention and its own
shebang.
docs/source/image_sims_calibration.md documented only this retired
orchestrator (its Snakemake targets, info.py, monitor_mbias.py) and was
an orphan page not wired into any Sphinx toctree; it is removed with the
code it described. History of the old pipeline is preserved in the
.felt/ notes, which are left untouched as a chronological record.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012Z3fwStiamMsEswbJ66BeF
* run_job: add -c/--config_dir to override computed config dir
The runner self-computes config_dir from --type (example/cfis for data,
example/cfis_image_sims for image_sims) and threads it through the cfis
symlinks, SP_CONFIG, and job_sp_canfar's own -c. That hardcodes the .ini
tree to the in-repo example dirs.
Add an optional -c/--config_dir that, when given, overrides the computed
config_dir uniformly for any --type. The override is applied after the
type branch, so when the flag is absent config_dir is byte-for-byte the
historical value and every existing caller (test_tile_det.py, functions.sh,
the sp_validation im_pipeline rule) is unaffected. This lets the
sp_validation workflow point every stage at an explicit .ini tree, per the
image-sims boundary rule (workflow selects and parameterizes the tree).
The flag name matches job_sp_canfar_v2.0.bash's own -c/--config_dir.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012Z3fwStiamMsEswbJ66BeF
* fake_psf: source PSF dictionary path from the environment
The cfis_image_sims fake_psf config hardcoded a collaborator-specific
absolute path to the SKiLLS PSF dictionary, coupling the in-repo config
tree to one machine's layout. Replace it with PSF_DICT_PATH = $PSF_DICT,
which the config layer's getexpanded (os.path.expandvars) resolves from
the environment. The orchestrating workflow now exports PSF_DICT from its
psf_dict config key, so the campaign fact lives upstream in the manifest,
not in this repo -- matching the module-config/workflow boundary rule.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012Z3fwStiamMsEswbJ66BeF
* docs(cfis_image_sims): document image-sims job-bit dispatch
Add a README to example/cfis_image_sims/ giving the accurate, per-bit
mapping of the image-sims chain: for each job bit (1..2048), the ShapePipe
module, the .ini file job_sp_canfar_v2.0.bash selects under sim settings,
and the special-casing run_job_sp_canfar_v2.0.bash applies. Every row is
derived by reading the two bash scripts, so the table stays a truthful
reference for the sims path rather than a guess.
Captures the parts that surprise: the faked weight-uncompress at bit 2,
the placeholder bit 64 with fake_psf actually running inside bit 512, the
dashed tile-id convention, forced tile_det=sx, and symlink retrieval. Adds
the parallelism model (per-tile fan-out, in-job SMP, no MPI) and the
$PSF_DICT env requirement for fake_psf.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_012Z3fwStiamMsEswbJ66BeF
* im sims Snakefile small change
* improved reading of merged hdf5 cat for info
* added comment
* fix(packaging): drop stale init_run_v2.0.sh from script-files
The [tool.setuptools] script-files list referenced
scripts/sh/init_run_v2.0.sh, which was removed in b0804ce when the
im_sims retarget moved orchestration to sp_validation. setuptools'
build_editable errors on the missing file, breaking every Docker build
in CI (`uv pip install --no-deps -e .` → "file '...init_run_v2.0.sh'
does not exist").
The other three listed scripts (update_runs_log_file.py,
run_job_sp_canfar_v2.0.bash, job_sp_canfar_v2.0.bash) still exist, so
this removes only the stale entry. Verified with an editable-install
dry-run in the im_sims runtime container: resolves to shapepipe-1.1.0
with no build_editable error.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* chore(im_sims): strip MKDEBUG markers; refresh check_tile_coverage docstring
Polish over the image-sims files this PR touches:
- check_tile_coverage.py: correct the module docstring's stale "the
Snakefile reads the exclude list" wording — orchestration moved to
sp_validation (f01344a), so the caller is now the sp_validation
workflow, not an in-repo Snakefile.
- bin/shapepipe_run.py: drop the "MKDEBUG start/end" print statements
that wrapped main().
- ngmix.py: drop two "# MKDEBUG TODO this needs to be checked!" tags
appended to the zero-sigma / zero-noise weight guards; the preceding
comments already explain why the guards exist.
Only strips MKDEBUG introduced by the im_sims merges; the pre-existing
marker in create_final_cat.py (also on develop) is left untouched.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
* chore: untrack .felt fiber notes that leaked in via im_sims
Two private fiber notes (blank-input-tiles-grid-4, snakemake-crash-
runtimeerror) were committed on origin/im_sims in 9783a2e, before the
develop-side .felt untrack (3d56ec6) landed there, so they survived the
merge into this branch. The repo gitignores /.felt/ and treats it as a
machine-local symlink into the private loom store (see CLAUDE.md); these
tracked files bypass that ignore. Untrack them (kept on disk) so no
fiber content rides into the shared CosmoStat repo. Their operational
lore is preserved in sp_validation's workflow docs.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
---------
Co-authored-by: martinkilbinger <martinkilbinger@cea.fr>
Co-authored-by: Cail Daley <cail.daley@cea.fr>
Co-authored-by: Claude Opus 4.8 <noreply@anthropic.com>1 parent da7a533 commit 84e40a5
45 files changed
Lines changed: 3138 additions & 286 deletions
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- auxdir/CFIS/im_sims_202606
- example/cfis_image_sims
- scripts
- python
- sh
- src/shapepipe
- modules
- fake_psf_package
- mask_package
- ngmix_package
- sextractor_package
- vignetmaker_package
- pipeline
- testing
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