feat(cdi): scaffold NSLS-II CDI (9-ID) coherent diffractive imaging deployment, reverse-engineered#396
Merged
Merged
Conversation
…ve imaging: forward CDI, ptychography, Bragg CDI on a KB nanofocus), reverse-engineered CDI is the NSLS-II coherent-imaging beamline at sector 9-ID: it focuses a coherent beam with a Kirkpatrick-Baez mirror pair, records the far-field diffraction pattern on photon-counting area detectors (Eiger2, Merlin), and recovers the real-space image offline by phase retrieval. Reverse-engineered from public open source updated today (NSLS2/cdi-profile-collection startup scripts + the NSLS2/cditools device classes). Descriptor + docs scaffold; EPICS PVs real and read from source, every value carried confirm; scenarios deferred. Same mode as CHX / HXN. NAME GUARD. This is NSLS-II 9-ID. CORA already models APS 9-ID (the CSSI surface- scattering instrument, deployments/9-id), a different beamline at a different facility with a different PV namespace. CDI lives at XF:09ID* / SR:C09-ID*. The descriptor and the site.yaml comment carry this guard so the two 9-IDs are never conflated, and the APS-9-ID coherent_surface_scattering / grazing_incidence_scattering pending Methods are left untouched. WHY no catalog change, and where the value is. The instrument is NOT the novelty: CDI is a reuse-and-reinforce deployment with zero new families and nothing graduating. The coherent area detectors reuse Camera (the Eiger-to-Camera precedent, also CHX / HXN); the KB nanofocus pair and the vertical / horizontal pre-mirrors reuse Mirror (the FMX / SRX KB precedent); the silicon DCM and the double-multilayer DMM both reuse Monochromator (the CHX Si-DCM-plus-multilayer-DMM precedent); the sample stack reuses Goniometer; the foil intensity monitor FluxMonitor; the white-beam / branch / beam- conditioning slits Slit; the attenuator foils Filter; the undulator InsertionDevice; the master energy a PseudoAxis; the endstation towers LinearStage. The quadrant and diamond beam-position monitors bind the loose BeamPositionMonitor (held; DIAG-1) and the machine reads a loose StorageRing supply (MACHINE-1). The value to CORA is reinforcement: the coherent-detector shape CHX brought and the deferred ptychography HXN brought port to a beamline dedicated to phase-retrieval imaging with no new vocabulary. MODELLING: zero new families, nothing graduates, the catalog is unchanged. The coherent- imaging Methods (forward CDI, ptychography, Bragg CDI) are NOT coined: following 8-ID / CHX (coherent) and HXN (ptychography deliberately not coined; the reconstruction is ComputePort work, not a Method), they are the deferred owner-scope cohort (TECH-1), so no CDI Practice is recorded. CDI's distinctive honest gap is that the profile collection exposes no hardware trigger box (no Zebra / PandA startup file, no shutter PVs); the Eiger2 / Merlin carry internal and external trigger modes, but the floor gating chain is the headline open question (TIMING-1), modelled by what is real, not invented. Wiring: CDI added to the NSLS-II Site beamline list (no Practice, comment explains why); deployments index row; mkdocs nav block; the BeamPositionMonitor promotion-review note broadened to + cdi. Gate: 389 deployment unit tests pass, mkdocs --strict builds clean, adversarial per-file verify (11 independent verifiers vs the cloned source) caught four over-specifications (a non-existent KB bend axis, the DMM mlm1/mlm2 mislabeled as stripe selectors, a stale "deferred xpcs" since graduated, an invented "piezo" actuator), all corrected and re-gated. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…rences The CDI governance page cites (GOV-1) and the descriptor references MACHINE-1 (the loose StorageRing supply readback) three times, but questions.md carried neither row, so both citations pointed nowhere. Every other NSLS-II deployment that binds a StorageRing or cites GOV-1 surfaces these rows; add them to match, keeping the delete-on-answer queue resolvable. Surfaced by the adversarial per-file verification on the PDF twin. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Resolve the append-only conflicts (NSLS-II beamline list, mkdocs nav, deployments index row, the FlowController/BeamPositionMonitor promotion-review notes) against the current main, which has advanced to ISR (#399). Reconcile CDI against i13-1 (#398, merged after CDI was opened): i13-1 is the fleet's first coherent diffractive imaging and coined the pending ptychography Method. CDI no longer claims "first"; it is the second coherent-imaging deployment and the first at NSLS-II / first full source-to-detector one, reinforcing i13-1's pending ptychography Method (ptychography reuses it; forward / Bragg CDI are its single-shot variants, not separately coined). No Practice recorded (CHX discipline). Gate: 424 deployment tests pass, mkdocs --strict clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Coverage report
This PR does not seem to contain any modification to coverable code. |
xmap
added a commit
that referenced
this pull request
Jun 26, 2026
Resolve the NSLS-II beamline list, mkdocs nav, deployments index, and practices-comment conflicts against current main (now at ISR #399 + CDI #396); PDF appends after CDI. No content reconciliation needed: PDF is high-energy total scattering, unrelated to the coherent-imaging cohort. Gate: 431 deployment tests pass, mkdocs --strict clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
What
Scaffolds the NSLS-II CDI deployment (beamline 9-ID), CORA's first dedicated coherent diffractive imaging beamline: forward CDI, ptychography, and Bragg CDI on a KB-nanofocused coherent beam recorded by Eiger2 + Merlin photon-counting detectors, with offline phase retrieval. Reverse-engineered from public open source updated today:
NSLS2/cdi-profile-collectionstartup scripts and theNSLS2/cditoolsdevice classes. Descriptor + docs scaffold; scenarios deferred; every value carriedconfirm.Follows the established CHX / HXN reverse-engineered-scaffold pattern.
Name guard
This is NSLS-II 9-ID, distinct from the existing APS
9-id(CSSI surface-scattering) deployment: different facility, different PV namespace (XF:09ID*/SR:C09-ID*). The descriptor andsite.yamlcomment carry the guard; APS 9-ID'scoherent_surface_scattering/grazing_incidence_scatteringpending Methods are left untouched.Modelling
Camera; KB pair + pre-mirrors toMirror; Si DCM + multilayer DMM toMonochromator; sample stack toGoniometer; foil monitor toFluxMonitor; slits toSlit; foils toFilter; undulator toInsertionDevice; energy toPseudoAxis; towers toLinearStage. LooseBeamPositionMonitor(held) andStorageRing(supply), both already allowed.ComputePortleg, not a Method.TIMING-1question, modelled by what is real (the detector trigger modes), not invented.Files
deployments/cdi/beamline.yaml(23 devices, verified PVs).docs/deployments/cdi/(10 authored pages + generatedbeamline.md).site.yamlbeamline list + no-Practice comment,mkdocs.ymlnav,docs/deployments/index.mdrow, BeamPositionMonitor promotion-review note.Verification
mkdocs build --strictbuilds clean; no em dashes / non-ASCII.bendaxis, DMMmlm1/mlm2mislabeled as stripe selectors, a stale "deferred xpcs" that has graduated, an invented "piezo" actuator) corrected and re-gated.🤖 Generated with Claude Code