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>
158 lines
5.3 KiB
C++
158 lines
5.3 KiB
C++
// SPDX-FileCopyrightText: 2024 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
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// SPDX-License-Identifier: GPL-3.0-only
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#include <algorithm>
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#include <cmath>
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#include "AzimuthalIntegrationSettings.h"
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#include "JFJochException.h"
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#define check_max(param, val, max) if ((val) > (max)) throw JFJochException(JFJochExceptionCategory::InputParameterAboveMax, param)
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#define check_min(param, val, min) if ((val) < (min)) throw JFJochException(JFJochExceptionCategory::InputParameterBelowMin, param)
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#define check_finite(param, val) if (!std::isfinite(val)) throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, param)
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AzimuthalIntegrationSettings::AzimuthalIntegrationSettings() {
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UpdateBinCount();
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::SolidAngleCorrection(bool input) {
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solid_angle_correction = input;
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return *this;
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::QRange_recipA(float low, std::optional<float> high) {
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check_finite("Low Q for azimuthal integration", low);
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check_min("Low Q for azimuthal integration", low, minQ_recipA);
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if (high.has_value()) {
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check_finite("High Q for azimuthal integration", *high);
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check_max("High Q for azimuthal integration", *high, maxQ_recipA);
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if (*high <= low)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"High Q must be higher than low Q");
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}
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requested_high_q_recipA = high;
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low_q_recipA = low;
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// Until ResolveHighQ runs, an unset limit keeps the value the bins were last built from.
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high_q_recipA = high.value_or(high_q_recipA);
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UpdateBinCount();
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return *this;
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}
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void AzimuthalIntegrationSettings::ResolveHighQ(float detector_max_q_recipA) {
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if (requested_high_q_recipA.has_value())
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return;
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high_q_recipA = std::clamp(detector_max_q_recipA, low_q_recipA + q_spacing, maxQ_recipA);
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UpdateBinCount();
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::QSpacing_recipA(float input) {
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check_finite("Q spacing for azimuthal integration", input);
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check_min("Q spacing for azimuthal integration", input, minQ_recipA);
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q_spacing = input;
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UpdateBinCount();
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return *this;
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}
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bool AzimuthalIntegrationSettings::IsSolidAngleCorrection() const {
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return solid_angle_correction;
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}
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float AzimuthalIntegrationSettings::GetHighQ_recipA() const {
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return high_q_recipA;
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}
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std::optional<float> AzimuthalIntegrationSettings::GetRequestedHighQ_recipA() const {
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return requested_high_q_recipA;
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}
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float AzimuthalIntegrationSettings::GetLowQ_recipA() const {
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return low_q_recipA;
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}
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float AzimuthalIntegrationSettings::GetQSpacing_recipA() const {
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return q_spacing;
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::BkgEstimateQRange_recipA(float low, float high) {
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check_finite("Low Q for background estimation", low);
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check_finite("High Q for background estimation", high);
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check_max("High Q for background estimation", high, maxQ_recipA);
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check_min("Low Q for background estimation", low, minQ_recipA);
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if (high <= low)
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throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
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"High Q must be higher than low Q");
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bkg_estimate_low_q_recipA = low;
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bkg_estimate_high_q_recipA = high;
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return *this;
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}
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float AzimuthalIntegrationSettings::GetBkgEstimateLowQ_recipA() const {
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return bkg_estimate_low_q_recipA;
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}
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float AzimuthalIntegrationSettings::GetBkgEstimateHighQ_recipA() const {
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return bkg_estimate_high_q_recipA;
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::PolarizationCorrection(bool input) {
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polarization_correction = input;
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return *this;
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}
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bool AzimuthalIntegrationSettings::IsPolarizationCorrection() const {
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return polarization_correction;
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::AzimuthalBinCount(int32_t input) {
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check_min("Azimuthal bin count", input, 1);
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check_max("Azimuthal bin count", input, 512);
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azim_bins = input;
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UpdateBinCount();
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return *this;
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}
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AzimuthalIntegrationSettings &AzimuthalIntegrationSettings::ForceCPUinFPGAWorkflow(bool input) {
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force_cpu_in_fpga_workflow = input;
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return *this;
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}
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bool AzimuthalIntegrationSettings::IsForceCPUinFPGAWorkflow() const {
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return force_cpu_in_fpga_workflow;
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}
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int32_t AzimuthalIntegrationSettings::GetQBinCount() const {
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return q_bins;
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}
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int32_t AzimuthalIntegrationSettings::GetAzimuthalBinCount() const {
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return azim_bins;
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}
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int32_t AzimuthalIntegrationSettings::GetBinCount() const {
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return total_bins;
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}
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uint16_t AzimuthalIntegrationSettings::QToBin(float q) const {
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return std::min<uint16_t>(GetBinCount() - 1, std::floor(std::max(0.0f, (q - GetLowQ_recipA()) / GetQSpacing_recipA())));
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}
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uint16_t AzimuthalIntegrationSettings::GetBin(float q, float phi_deg) const {
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if (q < low_q_recipA || q >= high_q_recipA)
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return UINT16_MAX;
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if (phi_deg < 0.0 || phi_deg >= 360)
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return UINT16_MAX;
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int16_t q_bin = std::floor((q - low_q_recipA) / q_spacing);
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int16_t phi_bin = std::floor(phi_deg / 360.0f * azim_bins);
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return q_bin + phi_bin * GetQBinCount();
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}
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void AzimuthalIntegrationSettings::UpdateBinCount() {
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q_bins = std::ceil((high_q_recipA - low_q_recipA) / q_spacing);
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total_bins = q_bins * azim_bins;
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}
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