rc179: everything on rc178 after its merge into main (#88), except the CHANGELOG

The rc178 branch continued after #88 was squash-merged; this is its content from b9ada7914 (the tree
#88 squashed) to 094eee31a, as one change on main. The individual commits stay on the rc178 branch:

- still battery: --cold evicts each set's input from the page cache; Alvra pixel masks; manifest fixes
- AGIPD: converter to one rigid panel per module, int16 photons, mask folded in; still battery reads the converted sets
- DetectorModules: panel look-up by id, plane -> panel, plane bounds and a per-pixel walk; mask size checked
- tests: [PanelLayout] equivalence harness, stacked vs assembled panel layout
- Dense per-pixel maps through the panel table (panel layout stage 1)
- Panel id on spots and the panel table in the start message
- Viewer and preview show a panel detector as it lies on the detector plane
- Panel layout stage 3: per-panel spot finding (CPU+GPU, CCL) and raster algorithms on the plane raster
- Panel layout stage 2: prediction and Bragg integration through the panel table
- XTC reader: frames handed up as stored, streams indexed in parallel
- XFEL reader: integer frames stay integer, one gain, placement by panel
- EXTERNAL_TEST_DATA_STILLS.md: images used vs the entry for every set; drop "Not in the battery"
- still battery: EuXFEL sets read the depositors' Cheetah CXI files directly; AGIPD converter removed
- float32_to_int16.py: a non-finite pixel becomes -32768, the int16 error marker, not a zero count
- CrystFEL geometry: read the pixel masks and bad regions instead of ignoring them
- Panel layout stage 5: the XFEL reader hands up the stored frame and its panel table
- Panel table persisted in NXmx; modulation grid and pre-scan memo key on the plane
- still battery: Alvra sets take their pixel mask from the CrystFEL geometry, not --mask-good
- still battery: take the deposited model as mmCIF where the RCSB has no PDB-format file
- still battery: dimple gets PDB-format coordinates converted from an mmCIF-only deposition
- stills fixed cost: geometry refinement and pre-scan do the same work in less wall time
- stills geometry sample and trial spot finding run as many workers as the image pass
- Stills integration: background ring reach measured on empty apertures, radial curvature from the whole frame
- StillsPartialityRefine: the partiality width is the run's, measured on the crystals, not the prediction window's
- MergeOnTheFly: capture term and multiplicative outlier band for the stills merge (both opt-in)
- Stills given a cell: the written cell is the mean over the frames that are merged
- Stills: the radial curvature correction decided per run on the same empty apertures
- StillsPartialityRefine: measure the run width only on shells with signal
- Stills pre-scan: report the paired z of the radial-correction comparison
- module placement: the five concurrent fits each keep every thread
- still battery: score R-free against the deposited data through the same dimple protocol
- still battery: the R-free target is the lower of the deposition's dimple and published values
- Stills: background clip follows the radial curve; signal disk from the lattice spacing
- Stills keep an overloaded observation as a lower bound instead of dropping it
- Stills: drop the lattice-spacing signal disk; the correction decision back on the plain clip
- battery: R-free against the deposition without refinement only, one protocol for rotation and stills
- still battery: EuXFEL sets run on a 2,000-image subset for now
- stills geometry refinement: fit the detector distance and the cell together
- stills geometry refinement: a distance given with --detector-distance is held in the joint fit
- Metal integration engine: back to its panel-s5 kernels; Mac stills keep the old clip, no saturation count
- Metal integration test: the CPU comparison runs on a rotation experiment
- Stills: kept overloads go back to the drop where they are not concentrated at low resolution
- stills distance search: an absolute 30-3000 mm scan, a sample found without d-limits, the fit iterated
- battery results: XFEL still battery 20261022-1358 on rc178 0cf62452c - 12 sets, cold, R_free unrefined
- battery results: still summary gains the resolution of our merge and of the deposition
- Pre-scan masks a pixel at the saturation limit on most frames, as one holding the error value
- Stills keep an overload as a lower bound only where it has pixels at the limit; run-level gate removed
- XFEL reader: a per-frame mask is read the way the frames are, its chunk inflated outside the HDF5 lock
- stills distance search: every centre scanned with a wider acceptance, a larger sample where nothing indexes
- rugnux usage: --beam-center-check describes the absolute 30-3000 mm stills distance scan, not the old 60-160 % grid
- stills: detector tilt refined in the geometry pre-pass, kept where held-out frames agree
- CLAUDE.md: the changelog is written once, just before the merge into main - condensed one-liners of what users get
- broker: serve the placed model and its maps of the last rugnux live run (/rugnux/model.cif, /rugnux/map.ccp4)
- frontend: Mol* viewer of the placed model and its density on the Rugnux live page
- writer: _model.cif from rugnux live keeps the input model's metadata, as the served model.cif does
- rugnux live maps: one unit cell centred on the model; the viewer opens on all of it
- Anomalous difference map: ANOM/PHANOM in _maps.mtz, /rugnux/map.ccp4?type=anom, a magenta mesh in the viewer
- Mol* viewer: open with the maps drawn within 10 A of the centre of view
- Mol* viewer: aaredb's structure-viewer setup, on a black stage
- rugnux: the gain of a stills file that states none is read off its single-photon peak where the background resolves photons
- Mol* viewer: in line with AareDB's StructureView at its current head (8ece2c2)
- ACKNOWLEDGEMENT: the web frontend's Mol* viewer follows AareDB's setup (G. Gotthard, PSI)
- stills tilt decision: the modules stay where the run placed them
- still battery: no distance pins and no per-set tuning flags; gain from the data except where a file's baseline hides it
- battery results: rc178 6f6f69 - full still battery and full rotation battery with REFMAC
- Bragg integration: a CCD rotation sweep's sigmas at the measured gain, intensities in photons
- BackgroundGain: the gain of a frame that resolves photons is the spacing of its photon peaks, so a baseline left in the frame no longer hides it
- ShadowFinder: measure the background's azimuthal modulation instead of predicting it from the polarization
- BackgroundGain: one gain estimate for rotation and stills; the still battery no longer gives EuXFEL 152 its gain
- ShadowFinder: measure the modulation robustly under a wide one-sided shadow
- ShadowFinderTest: a one-sided shadow is not fitted as part of the background's modulation
- ShadowFinder: back to the predicted polarization factor, in the plane the background shows
- MXAnalysisAfterFPGA: the Bragg engine's edge mask in the image's layout, so raw / untransformed FPGA runs start again
- battery results: still battery on rc178 e54f55 replaces the earlier rc178 still tables
- XFELReader: per-frame mask and photon conversion without a library call or a branch per pixel
- stills geometry trial: the hypotheses a search asks are indexed side by side
- stills tilt decision: the fits start beside the pre-scan and the geometry trial
- XFELReader: a deflated frame is inflated and converted a piece at a time, while it is in the cache
- XFELReader: a byte-shuffled frame is unshuffled a piece at a time, a whole pixel per step
- GeometryRefiner: residuals carry only the blocks a fit moves; beam and distance one block
- GeometryRefiner: a spot's residual differentiates its observed and predicted halves apart
- docs: EXTERNAL_TEST_DATA lists every open-arm battery set, with corrected values and counts
- battery: doc_check.py cross-checks the manifests against the dataset pages
- stills module placement: the placement fit gets half the threads, each held-out fit an eighth
- still battery: the EuXFEL sets run on all their frames, as the published still runs did
- battery results: still battery on rc178 a0ce6c, cold on a quiet machine, replaces the earlier rc178 table
- macOS build: explicit size_t in the XFEL reader's row bounds; parentheses in the CPU preprocessor's select

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu

reader/JFJochXTCReader.cpp

@@ -4,9 +4,12 @@
 #include "JFJochXTCReader.h"
 
 #include <algorithm>
+#include <atomic>
 #include <cmath>
+#include <future>
 #include <map>
 #include <numeric>
+#include <thread>
 
 #include "../common/JFJochException.h"
 #include "../common/Logger.h"
@@ -42,8 +45,24 @@ void JFJochXTCReader::ReadFiles(const std::vector<std::string> &streams) {
     std::string model;
     uint32_t binning = 0;
     size_t damaged = 0;
-    for (const auto &stream: streams) {
-        auto index = xtc::IndexFile(stream);
+    // The streams are indexed in parallel: each is a walk of small reads from one place in the file to the
+    // next, which on a run not in the page cache waits on the disk one read at a time.
+    std::vector<xtc::Index> indices(streams.size());
+    {
+        std::atomic<size_t> next = 0;
+        const size_t nthreads = std::min<size_t>(streams.size(), std::max(1u, std::thread::hardware_concurrency()));
+        std::vector<std::future<void>> workers;
+        for (size_t t = 0; t < nthreads; t++)
+            workers.push_back(std::async(std::launch::async, [&] {
+                for (size_t i = next.fetch_add(1); i < streams.size(); i = next.fetch_add(1))
+                    indices[i] = xtc::IndexFile(streams[i]);
+            }));
+        for (auto &w: workers)
+            w.get();
+    }
+    for (size_t s = 0; s < streams.size(); s++) {
+        const auto &stream = streams[s];
+        const auto &index = indices[s];
         all.insert(all.end(), index.frames.begin(), index.frames.end());
         energies.insert(energies.end(), index.photon_energy_eV.begin(), index.photon_energy_eV.end());
         if (!index.rayonix_model.empty()) {
@@ -142,11 +161,17 @@ CompressedImage JFJochXTCReader::DecodeInto(int64_t image_number, Buffer &buffer
     if (image_number < 0 || static_cast<size_t>(image_number) >= frames_.size())
         throw JFJochException(JFJochExceptionCategory::InputParameterInvalid, "Image number out of range");
     const auto &f = frames_[image_number];
-    buffer.resize(static_cast<size_t>(f.width) * f.height * sizeof(int32_t));
+    const size_t npixel = static_cast<size_t>(f.width) * f.height;
+    buffer.resize(npixel * sizeof(int32_t));
+    scratch.resize(npixel * sizeof(uint16_t));
+    xtc::ReadPixels(f, reinterpret_cast<uint16_t *>(scratch.data()));
+    const auto in = reinterpret_cast<const uint16_t *>(scratch.data());
     auto out = reinterpret_cast<int32_t *>(buffer.data());
-    xtc::ReadFrame(f, out, scratch);
+    const auto offset = static_cast<int32_t>(f.pixel_offset);
+    for (size_t i = 0; i < npixel; i++)
+        out[i] = static_cast<int32_t>(in[i]) - offset;
     if (adu_per_photon_ != 1.0f)
-        for (size_t i = 0; i < static_cast<size_t>(f.width) * f.height; i++)
+        for (size_t i = 0; i < npixel; i++)
             out[i] = static_cast<int32_t>(std::lround(static_cast<float>(out[i]) / adu_per_photon_));
     return CompressedImage(buffer.data(), buffer.size(), f.width, f.height,
                            CompressedImageMode::Int32, CompressionAlgorithm::NO_COMPRESSION);
@@ -169,6 +194,16 @@ bool JFJochXTCReader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset,
 bool JFJochXTCReader::ReadRawImage(int64_t image_number, JFJochReaderRawImage &image) {
     if (image_number < 0 || static_cast<size_t>(image_number) >= frames_.size())
         return false;
+    const auto &f = frames_[image_number];
+    if (f.pixel_offset == 0 && adu_per_photon_ == 1.0f) {
+        // The pixels as the file stores them, two bytes each, where there is nothing to take off or divide
+        // by: the consumer widens them, on the device where there is one.
+        image.image_buffer.resize(static_cast<size_t>(f.width) * f.height * sizeof(uint16_t));
+        xtc::ReadPixels(f, reinterpret_cast<uint16_t *>(image.image_buffer.data()));
+        image.image = CompressedImage(image.image_buffer.data(), image.image_buffer.size(), f.width, f.height,
+                                      CompressedImageMode::Int32, CompressionAlgorithm::UINT16_WIDENED);
+        return true;
+    }
     image.image = DecodeInto(image_number, image.image_buffer, image.read_buffer);
     return true;
 }