leonarski_fandClaude Opus 5
16bf3408f0
One changeset, developed together in response to a review of this branch, so the files carry several of the changes at once. Full test suite passes (733 cases). Spot finding - Split ImageSpotFinder into Detect() (flag strong pixels - the expensive per-pixel pass) and ExtractSpots() (CCL + min/max-pix + resolution mask), with Run() = both. The per-image min-pix escalation now detects ONCE and repeats only the cheap extraction, instead of re-running the whole finder four times per frame as it did on the default path. It also keeps the winning attempt's spot list rather than re-extracting it, so the frame that is integrated is exactly the frame that was scored - which a GPU re-extract could not guarantee (float atomic ordering). - spot_finding_time_s no longer swallows indexing time, and indexing_time_s now sums every escalation call instead of reporting only the last. Detection limits follow the detector - The azimuthal-integration upper q and the spot-finding high-resolution limit are now std::optional, in the C++ structs AND in the OpenAPI schema, and resolve to the detector's own maximum (DiffractionExperiment::GetDetectorMaxQ_ recipA). Adaptive detection reads a pixel's ring from the azimuthal bins, so a pixel outside that q range could never be strong - the integration range silently bounded what detection could see, regardless of the requested resolution limit. Regenerated the C++ and TypeScript clients; the viewer and the web frontend each gained a "to detector edge" switch. Detection defaults are now per workflow (measured, not assumed) - Stills: adaptive detection, min-pix chosen per image, no resolution clipping. - Rotation: fixed-threshold finder, min-pix 2, 1.5 A limit. On a 33-crystal rotation battery, adaptive detection helped four hard crystals but deterministically broke three (a lost space group, a halved indexing rate, a collapsed merge), and the detector-edge limit cost indexing on a strong rotation set (100.0 -> 96.8%). Each is still overridable by its flag, and --no-adaptive-spots is new. Indexer seed escalation - Stop escalating once a seed's lattice explains >= 90% of the seed spots. Previously any frame with >= 80 spots always paid three indexer calls, online broker included. Merge-consistency filter - --min-image-cc gated on a per-image CC computed BEFORE the stills partiality post-refinement and never refreshed; the refiner now recomputes it, so the reported CC describes the data that are actually merged. - Replaced the per-call cc_mask argument with one MergeOnTheFly flag, so the merge, the error model and MergeStats can no longer disagree about which images are in (the --scale path merged unfiltered while its statistics were filtered). Per-image B-factor refinement (-B) removed - Measured on four serial-stills datasets: it is a no-op where the per-image fit is well conditioned and actively harmful where it is not (CC1/2 -8.1, R_meas +23.2 on the weakest large-cell set, whose fits hit their [-50, 200] bounds on 14-25% of images). It had also been silently DISCARDED since the partiality post-refinement landed - reported but not applied. Rather than fix and keep a knob with no demonstrated benefit, the flag and the whole image_scale_b_factor chain are gone: setting, scaling fit, message field, CBOR, HDF5 write and read-back, per-image plot, OpenAPI enum, viewer column and checkbox, docs. ScaleOnTheFly no longer needs Ceres at all - the fit is a linear IRLS. (The Wilson per-image b_factor is a different quantity and stays.) Stills partiality width now fits both of its components - sigma^2 = gamma0^2 + (gamma_e*d*)^2 instead of a purely angular gamma_e*d* with gamma0 pinned to 0. Fitted per crystal by least squares of dist_ewald^2 on d*^2. The angular-only width is fitted over a d*^2-dense population, so it was pinned by the high-resolution edge and collapsed at low d*: median partiality 0.008 beyond 13 A for reflections that were plainly recorded, 55% of them under the merge's partiality floor, and the survivors divided by those values - which inflated the merged low-resolution intensity scale 3.6x (~ +9 A^2 of apparent B). Measured on 5000 stills: the ramp flattens to 0.89x, no observation is dropped any more (701750 -> 716811), shell-mean CC1/2 and R-free improve slightly. Note CC1/2, R_meas, completeness and a B-refining R-free are all blind to that ramp, which is why it survived earlier validation; the cost is high-resolution R_meas (98.5 -> 101.9 shell-averaged). Removed dead code from add-then-remove churn - Prediction-time "still partiality" (unreachable: no setter), the phantom IndexingSettings::min_indexed_spot_fraction knob (getter, no setter - now the constant it always was), StillsPartialityRefine's caller-less Settings constructor and its reference to a long-gone env var, ProcessImage's unread bool return, an unused include, and a dead viewer overlay hook. Also - Viewer: the magnifier compared a QImage with itself, so its scene rect was set once ever and it could not pan into a larger dataset; the hover tail timer could fire after leaveEvent and resurrect the resolution readout outside the image. - update_version.sh regenerated the frontend lock file BEFORE bumping the version (every release shipped an off-by-one lock), and did git rm/git add on a path that has not existed since the client moved to src/client - with no set -e, both failed silently. - fpga/pcie_driver/postinstall.sh tested "[ ! occurrences > 0 ]", which is a redirect, not a test, so dkms add never ran. - Unit tests for the adaptive-threshold host functions, which had none. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
118 lines
4.1 KiB
Bash
118 lines
4.1 KiB
Bash
#!/bin/bash
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#
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# Copyright (2019-2024) Paul Scherrer Institute
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#
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# Stop at the first failing command (this script rewrites generated code and version
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# strings in place, so a silently skipped step leaves the tree half-updated).
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set -e
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set -o pipefail
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VERSION=$(<VERSION)
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# Regular expression for semantic versioning with optional pre-release and build metadata
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regex="^([0-9]+)\.([0-9]+)\.([0-9]+)(-[A-Za-z0-9.\-]+)?(\+[A-Za-z0-9.\-]+)?$"
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if [[ $VERSION =~ $regex ]]; then
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major="${BASH_REMATCH[1]}"
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minor="${BASH_REMATCH[2]}"
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patch="${BASH_REMATCH[3]}"
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prerelease="${BASH_REMATCH[4]}"
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build="${BASH_REMATCH[5]}"
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echo "Major version: $major"
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echo "Minor version: $minor"
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echo "Patch version: $patch"
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[ -n "$prerelease" ] && echo "Pre-release version: ${prerelease:1}" # Remove the leading '-'
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[ -n "$build" ] && echo "Build metadata: ${build:1}" # Remove the leading '+'
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else
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echo "Invalid semantic version: $VERSION"
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exit 1
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fi
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OPENAPI_VERSION=7.20.0
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wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/${OPENAPI_VERSION}/openapi-generator-cli-${OPENAPI_VERSION}.jar -O openapi-generator-cli.jar
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SRC=' version:.*'
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DST=" version: $VERSION"
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sed -i -e "s/$SRC/$DST/" broker/jfjoch_api.yaml
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git rm -r broker/gen/model docs/python_client frontend/src/client
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java -jar openapi-generator-cli.jar generate -i broker/jfjoch_api.yaml -o python-client/ -g python --git-host=git.psi.ch --git-repo-id jungfraujoch --git-user-id jungfraujoch --additional-properties=packageName=jfjoch_client,packageVersion=$VERSION
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java -jar openapi-generator-cli.jar generate -i broker/jfjoch_api.yaml -o broker/gen -g cpp-pistache-server
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# Bump package.json BEFORE npm install, so the regenerated package-lock.json records the
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# new version instead of the previous one.
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sed -i "s,\"version\":.*,\"version\": \"$VERSION\"\,," frontend/package.json
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cd frontend
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sed -i s/\".*\"/\"$VERSION\"/g src/version.ts
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npm install
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npm run openapi
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npm run redocly4broker
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cd ..
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mkdir -p docs/python_client/docs
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cp python-client/README.md docs/python_client
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cp python-client/docs/*.md docs/python_client/docs
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# Mirror the root third-party notices into the docs tree so they are published with
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# the documentation. The verbatim license texts (licenses/*.txt) are not part of the
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# docs source tree, so point those links at the repository; the project-license links
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# point at the in-docs LICENSE / FPGA_LICENSE pages.
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REPOBASE=https://gitea.psi.ch/mx/jungfraujoch/src/branch/main
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{
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echo "<!--"
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echo " Auto-generated from THIRD_PARTY_NOTICES.md by update_version.sh — do not hand-edit."
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echo " Edit the canonical THIRD_PARTY_NOTICES.md at the repository root instead."
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echo "-->"
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echo
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sed -e "s,](licenses/,]($REPOBASE/licenses/,g" \
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-e "s,](LICENSE)),](LICENSE.md)),g" \
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-e "s,](fpga/LICENSE),](FPGA_LICENSE.md),g" \
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THIRD_PARTY_NOTICES.md
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} > docs/THIRD_PARTY_NOTICES.md
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git add broker/gen/model/*.cpp broker/gen/model/*.h frontend/src/client docs/python_client/*.md docs/python_client/docs/*.md docs/THIRD_PARTY_NOTICES.md
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sed -i "s,release =.*,release = \'$VERSION\'," docs/conf.py
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cd fpga
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SRC="define JFJOCH_FPGA_MAJOR_VERSION 8'd.*"
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DST="define JFJOCH_FPGA_MAJOR_VERSION 8'd${major}"
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sed -i "s/$SRC/$DST/" hdl/action_config.v
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SRC="define JFJOCH_FPGA_MINOR_VERSION 8'd.*"
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DST="define JFJOCH_FPGA_MINOR_VERSION 8'd${minor}"
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sed -i "s/$SRC/$DST/" hdl/action_config.v
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SRC="define JFJOCH_FPGA_PATCH_VERSION 8'd.*"
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DST="define JFJOCH_FPGA_PATCH_VERSION 8'd${patch}"
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sed -i "s/$SRC/$DST/" hdl/action_config.v
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SRC="define JFJOCH_FPGA_PRERELEASE 64'h.*"
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if [ -n "$prerelease" ]; then
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result=$(printf '%.7s' "${prerelease:1}" | rev | xxd -p -u)
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DST="define JFJOCH_FPGA_PRERELEASE 64'h$result"
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else
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DST="define JFJOCH_FPGA_PRERELEASE 64'h0"
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fi
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sed -i "s/$SRC/$DST/" hdl/action_config.v
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cd pcie_driver
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sed -i s,MODULE_VERSION\(\".*,MODULE_VERSION\(\"$VERSION\"\)\;, jfjoch_drv.c
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sed -i s,VERSION=.*,VERSION=$VERSION, postinstall.sh
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sed -i s,VERSION=.*,VERSION=$VERSION, preuninstall.sh
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sed -i s,PACKAGE_VERSION=.*,PACKAGE_VERSION=$VERSION, dkms.conf
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sed -i s,VERSION=.*,VERSION=$VERSION, install_dkms.sh
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