156 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	7039aa4e45	Stop treating a goniometer axis and a grid scan as alternatives ... They are not alternatives: a grid is usually collected at a particular head position, so an axis and a grid describe different parts of the same setup. The exclusion was enforced independently in four places - the API converter, the CBOR serializer, the writer and the reader - and each silently dropped the grid scan when an axis was present. Nothing warned. The writer now builds one chain from the base outwards, spindle -> chi -> phi -> helical -> grid translations, instead of two branches. NXmx applies the deepest dependency first, so the sample ends up innermost, which is what it physically is: the grid stage rides on the head and the head rides on the spindle. The grid translations consequently move inside the rotation - identical to before at omega = 0, and right rather than wrong when it is not. A grid scan with no axis at all now writes a stationary omega. NXmx has no way to say "there is no rotation", and a sample chain of translations alone is not something readers accept: dxtbx raises outright on it, so every grid-scan master we have written so far cannot be opened by DIALS. Measured on a file matching the new chain: dials.import reads it. At 0 degrees the rotation is the identity whatever the axis points along, so the conventional vector carries no geometric claim - it only has to be well formed. The API change is deliberately not breaking: no field changes type or cardinality, only the prose saying the two were exclusive, and a request that set both used to lose one silently and now does not. JFJochReader_GridScan asserted the absence of a goniometer; it now asserts the axis is present and stationary, which is the contract that matters - a grid scan must not read back as a sweep. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 22:25:08 +02:00
leonarski_fandClaude Opus 5	b35672a0c3	Read any rotation axis by name, and tell a stationary axis from a sweep ... Two things the goniometer handling conflated. The axis name is free-form everywhere that writes it - the API imposes only minLength, the CBOR map uses the name as its key, and tests/CBORTest.cpp round trips one literally called "z" - but the reader looked for exactly "/entry/sample/transformations/omega". A sweep recorded as "phi" therefore came back as stills, in the viewer and in rugnux, with nothing to indicate it. The reader now walks the transformations group and takes whichever axis is a rotation, preferring one that turns; the grid scan is read independently rather than as the else-branch of the same test, since a grid scan can be taken at a given head position. Second: "an axis is defined" and "the axis is turning" were the same question, answered inconsistently - GetImagesPerFile checked the increment, IsRotationIndexing did not, and the CBOR decoder deleted zero-increment axes outright so the ambiguity could never surface. GoniometerAxis::IsScanning now asks it explicitly and the call sites go through it, so a stationary axis can be carried without being mistaken for rotation data. That mistake is not hypothetical: RotationIndexerCounter leaves its stride at zero for a zero increment, and Process() then never fires, so indexing would silently never run. Keeping stationary axes is also what lets the writer state where the head was for a still or a grid scan, which is the next step. JFJochReader_Goniometer_NonOmegaName covers the naming case through the writer and back; nothing did before, because both existing round trips use "omega". Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 22:20:41 +02:00
leonarski_fandClaude Opus 5	1f4f77fe42	Choose images_per_file from the acquisition when it is not given ... The value means three different things at once. It is the unit of writer parallelism - whole files go round-robin to the writers, (image_number / images_per_file) % socket.size() in ZMQStream2Pusher::SendImage and TCPStreamPusher - it multiplies writer memory linearly, since every data-file plugin reserves per file, and it decides whether a legacy master is readable at all, because dxtbx follows only the first data file of one. That last point is what makes a flat default wrong. Measured with DIALS on a 2500-image rotation sweep written as legacy: split into five files it reports 2500 images and then raises IndexError beyond image 499, so it half-works silently; in one file all 2500 read. AutoPROC does not read VDS, so legacy has to stay the default, which leaves the file count as the only lever. So make it optional and resolve it from the acquisition. A rotation sweep of at most 20000 images goes into one data file - rotation datasets are small enough, and one writer keeps up with them. A grid scan splits on whole fast-axis rows, so a file is a meaningful piece of the grid. Stills and serial keep 1000, where the image count far exceeds it and the parallelism and the bounded writer memory are what matter. An explicit value is always taken literally. GetImagesPerFile is the single place this is resolved, and it must always return a fixed non-zero number, because everything downstream - receiver, pusher, puller, writer - requires one. That was already true of the old 0 = "one file" spelling; 0 is now gone from the API and omitting the field says the same thing better. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 21:57:12 +02:00
leonarski_fandClaude Opus 5	259b43154e	Writer: refuse a mistyped stream, and mark unreadable VDS frames ... Two ways the written files could misdescribe themselves without anyone noticing. The pixel format is stated twice and the two were never compared: each image carries its own type as a CBOR tag, which is what the data files are written with, while the master is typed from the start message. A stream whose header contradicts its images produced data files of one type under a master declaring another, and with NXmxVDS, HDF5 then converts silently on every read. HDF5DataFile::CreateFile now checks the two agree and refuses the run otherwise - the point where the values first meet, so it covers every path into the writer. Two test fixtures were relying on exactly that inconsistency. The HDF5 writer tests wrote uint16 buffers under a JUNGFRAU experiment, which converts to photon counts by default and so declares int16; they never read the pixels back, so it went unnoticed. The receiver-lite tests feed frames from compression_benchmark.h5, which really are signed int16, through a DECTRIS experiment, which declares unsigned by default - the same class of bug the pixel_signed propagation fixed on the live path. Both now declare what they send. Second: a virtual dataset whose source file is absent reads as the fill value, and HDF5 defaults that to zero, so a data file that was not copied alongside the master is indistinguishable from frames of genuine zero counts. Measured with DIALS on a four-file set with one file removed: 25 frames of pure zeros, no error and no warning. The image VDS is now filled with the error marker instead, which sits outside underload_value..saturation_value, so a reader masks those frames. Same measurement after the change: -32768 throughout, which DIALS excludes. Only the images ask for a fill value; the per-image metadata datasets keep the default. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 21:44:04 +02:00
leonarski_fandClaude Opus 5	28cb185325	rugnux: log the detector geometry in XDS's convention ... XDS is never handed this geometry - the durin plugin gives it image data only (plugin_get_header returns dimensions, bytes per pixel, pixel size and frame count, nothing more) and XDS refines its own from XDS.INP. That is exactly what makes printing ours in the same convention useful: it turns "does our geometry agree with XDS's refinement" into reading two logs side by side. The two laboratory frames already coincide - x along increasing detector column, y along increasing row, z along the beam - so nothing is converted. XDS places a pixel at x_lab(i,j) = (i-ORGX)*QX*X_axis + (j-ORGY)*QY*Y_axis + DISTANCE*(X_axis x Y_axis) which is DiffractionGeometry::LabCoord with X_axis = poni_rot*(1,0,0) and Y_axis = poni_rot*(0,1,0). The axes are taken as differences of LabCoord so they track whatever the geometry currently is, tilt included, and a tilt goes out as the two axis vectors rather than as angles - the form XDS itself reports after refinement. Two traps are handled and documented: ORGX/ORGY are 1-based, XDS counting pixels from 1 where we count from 0; and they are the PONI, the foot of the perpendicular from the crystal, which is what our beam centre is too but is not the direct beam once the detector is tilted. ROTATION_AXIS is printed as stored. The direction is right, the frames being shared, but its sign has not been cross-checked against an XDS refinement, so a flip there should be read as unconfirmed rather than as a real disagreement. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 20:54:26 +02:00
leonarski_fandClaude Opus 5	659ba0d5b9	Cross-check a tilted detector against pyFAI and DIALS ... Nothing constrained the tilted geometry. Every existing test is either self-consistent or moves one angle at a time, and every file CI writes has zero tilt - where a swapped axis, a reversed composition order and a wrong pivot all give exactly the same answer. Two real bugs lived in that gap. Two checks, because there are two things to guard. DiffractionGeometry_Tilted_vs_PyFAI_and_DIALS pins the model itself: all three PONI angles non-zero and of mixed sign, compared per pixel against reference positions from pyFAI (an independent implementation of the convention) and from DIALS, to 2 um. Because the references are quoted in their own frames and the test applies the documented mappings - pyFAI (t1,t2,t3) -> our (x,y,z), and imgCIF = ours turned 180 degrees about x - it pins those relations too, not just the arithmetic. The comment gives the snippets to regenerate both sets. tests/nxmx_geometry_dials_test.py guards the writer, which is where the bugs actually were and which the unit test cannot reach. CI writes a master, patches the geometry in and asks DIALS where the panel is. Only the angle VALUES are patched; the axis vectors, the depends_on chain and the pivot stay as the writer emitted them, so they remain under test. Verified to fail on the pre-fix encoding: 7.3 mm, exit 1, naming the chain as the thing to look at. Recorded in both, because it cost an hour: compare via get_origin() and the fast/slow axes, NOT get_pixel_lab_coord(), which applies a parallax correction from the sensor thickness that Jungfraujoch does not model - about 0.1 mm at the detector edge, easily mistaken for a geometry error. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 20:50:38 +02:00
leonarski_fandClaude Opus 5	1eefd035c2	rugnux: stop negating Rot3 in the .poni file ... The PONI export mapped the internal angles to pyFAI as (+rot1, -rot2, -rot3). Checked against pyFAI 2026.5.0 directly - building a Geometry from the exported values and comparing calc_pos_zyx against the lab position DiffractionGeometry computes, per pixel over the whole detector and with each angle exercised on its own - the correct mapping is (+rot1, -rot2, +rot3): it agrees to 1.4e-17 m, while negating rot3 puts a pixel 25 mm out on a rot3-only geometry. rot1 and rot2 were already right, which is consistent with how this was originally validated: a LaB6 powder image, where rings sharpened once the rot2 flip was applied. That check could not have caught rot3, because a rotation about the beam leaves q and 2theta invariant and moves only the azimuth - so the error only ever showed up in cake/sector integration, and only for a detector actually rotated about the beam. rot3 is never refined and has no CLI flag, so in practice it is almost always zero. The old comment derived the signs from "a reflection in y between the MX and pyFAI frames". That gives the right answer for rot1 and rot2 and the wrong one for rot3, and pyFAI's own documentation contradicts itself on the direction of its axis 2, so the comment now records the empirical pin instead of a derivation. Calibration_PoniFileAxisConvention previously set rot3 to zero and asserted Rot3 == 0.0 - the one cell that could not fail. It now uses a non-zero rot3. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 20:14:23 +02:00
leonarski_fandClaude Opus 5	03e481ff2a	Export the detector tilt correctly in the NXmx transformation chain ... Three independent errors, all invisible while the tilt is zero - which it is in every test and every CI file, and which is why this survived. 1. rot1 and rot2 carried each other's axis. Jungfraujoch holds the tilt in the PyFAI PONI convention, poni_rot = Rz(-rot3)*Rx(-rot2)*Ry(+rot1), written in the internal frame (x along increasing column, y along increasing row, z along the beam). NXmx uses McStas, which is that frame turned 180 degrees about x - a proper rotation, NOT a mirror - so rotations about y and z reverse sense and those about x do not. Correct vectors are rot1 (0,-1,0), rot2 (1,0,0), rot3 (0,0,-1); only rot3 was already right. 2. The depends_on chain composed the rotations in the reverse order. A chain applies the deepest dependency first, so rot3 has to sit at the root for the product to be R_rot3*R_rot2*R_rot1. Second-order: it only shows up when two angles are non-zero at once. 3. The tilt pivoted about the wrong point. With translation at the root, a reader takes the panel origin as the unrotated vector and merely reorients the panel, while Jungfraujoch rotates the whole sample->pixel vector including the distance. Moving translation inside the rotations fixes the pivot; this was the largest of the three and is invisible to any test that only checks axes. Verified against DIALS 3.27 by comparing the lab position of nine pixels spread over the detector against poni_rot applied to the sample->pixel vector, over nine tilt settings including combined and mixed-sign angles: max error 1.6e-6 mm, which is float32 rounding of the stored metadata. The shipped encoding gives 40.7 mm - 542 pixels - at a (0.2, 0.3, 0.15) rad tilt. Note when comparing by hand that dxtbx applies a parallax correction in its pixel->mm conversion, which Jungfraujoch does not model; get_pixel_lab_coord is therefore not the right comparison point and shows a ~0.1 mm radius-dependent offset that is not a geometry error. Jungfraujoch's own reader is unaffected: it reads rot1/rot2/rot3 by dataset path and never consults the vectors or the chain, which is why the round trip stayed self-consistent throughout. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 19:04:43 +02:00
leonarski_fandClaude Opus 5	fccf2d911a	VERSION: 1.0.0-rc.162 ... Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 18:35:47 +02:00
leonarski_fandClaude Opus 5	2c202dafee	Docs: tighten rc.162 changelog entries and note what _process.h5 links to ... Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 18:34:19 +02:00
leonarski_fandClaude Opus 5	d01e69e407	rugnux: describe the linked images in _process.h5, not the processing container ... _process.h5 is an NXmxIntegrated master that links to the ORIGINAL image files rather than writing images of its own (write_images = false). Its pixel metadata therefore has to describe those files - but it was filled from experiment_, which Rugnux pins to signed 32-bit because that is the container HDF5MetadataSource hands images out in. The virtual dataset was consequently typed int32 over unsigned 16- or 32-bit sources, so HDF5 converted every value on read: the 0xFFFFFFFF error marker of a uint32 source does not survive, and error_value and underload_value described a container the file does not contain. Our own reader never saw it, because it resolves the mapping and opens the source file itself. Only consumers that go through the virtual view - DIALS, XDS via Durin, plain h5py - read the converted values. Take the format from the reader instead. GetStoredPixelFormat() reports the bit depth and signedness of /entry/data/data as stored, which is deliberately not the same thing as the experiment's image format, and rugnux fills the start message from it. The writer is left alone on purpose: it must be able to produce a master before the mapped files exist, or when they are not readable, and the mapping strips the source directory, so it cannot open them to ask. Measured on a 20-image set with int16 sources: the _process.h5 virtual dataset goes from H5T_STD_I32LE to H5T_STD_I16LE, matching the source, and DIALS reports trusted_range (-32767, 32765) instead of (-2147483647, 32765). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 18:24:31 +02:00
leonarski_fandClaude Opus 5	77c6d0f4ec	Report the stored image depth in bit_depth_readout, and write underload_value ... NXmx has no field for the depth of the stored image - only bit_depth_readout, "how many bits the electronics record per pixel". The two diverge exactly when summation is used: the readout keeps the detector's native width while the summed image must be wider to hold the sum. Every NXmx reader nonetheless takes bit_depth_readout as the width of the stored pixel. dxtbx ignores the non-standard bit_depth_image entirely for a generic NXmx file, derives its masking markers from bit_depth_readout, and raises "Unsupported integer dtype uint32" for a 32-bit image when the field is absent. Reporting the electronic value there would mislead precisely where it differs. So report the image depth in both fields, and drop the machinery that existed to carry the electronic one for a DECTRIS detector: the SIMPLON read, the DetectorSetup setter, and the receiver-side propagation of a key that the DECTRIS stream2 protocol does not even define. JUNGFRAU and PSI EIGER keep their readout depth, which the FPGA acquisition genuinely needs. Also write NXmx underload_value, the lowest valid value. Without it a reader takes the trusted minimum to be -0x7FFFFFFF, so the error-pixel marker sits inside the trusted range and is consumed as an intensity. Measured with DIALS 3.27 on a written file: trusted_range goes from (-2147483647, 32766) to (-32767, 32766), so the INT16_MIN gap pixels are now masked. Third fix in the same area: JFJochReceiverLite::Configure took the image width from the incoming stream but not the sign, while the image itself is forwarded byte-for-byte. A detector sending int32 was re-declared uint32, and the VDS master was typed unsigned over signed data files. Take pixel_signed from the stream too - it and the width are both carried by the one image_dtype key. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 18:15:44 +02:00
leonarski_fandClaude Opus 5	4e6600a96c	Build device code for Volta, and document the driver floor ... CMAKE_CUDA_ARCHITECTURES had no sm_70 entry, and PTX only ever JIT-compiles forwards, so a V100 had no runnable code in the fatbin at all - every kernel launch failed with "no kernel image is available for execution on the device". Append 70 only for a CUDA 12 toolkit: CUDA 13 removed offline compilation for Volta, so an unconditional entry would break the RHEL 9, Ubuntu and Windows builds. 12.8/12.9 still emit it but warn on every .cu, hence -Wno-deprecated-gpu-targets. The append goes after ENABLE_LANGUAGE(CUDA), where the nvcc version is known, matching the existing sm_121 handling. Verified: all 15 CUDA sources compile for sm_70 (including ffbidx, which already guards on __CUDA_ARCH__ >= 700/800), and cuobjdump shows an sm_70 cubin in the built rugnux binary. Consequence worth documenting: a V100 can only run the artefacts built with CUDA 12 - the RHEL 8 packages and the portable Linux .tgz. Document that alongside the minimum NVIDIA driver of every released artefact (525.60.13 for CUDA 12, 580.65.06 for CUDA 13), which applies because the CUDA runtime is linked statically and cuFFT is bundled, so the driver is the only NVIDIA component the target host must supply. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-08-22 18:06:43 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00
leonarski_f	67dca388bd	v1.0.0-rc.160 (#70) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #70 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-19 09:39:28 +02:00
leonarski_f	dd0bffb283	v1.0.0-rc.159 (#69) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-13 13:54:03 +02:00
leonarski_f	451310f43d	v1.0.0-rc.158 (#68) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * Analysis: The azimuthal-integration solid-angle correction now follows the incidence angle to the detector normal (`cos^3` of that angle) instead of `cos^3(2*theta)`, so it is correct for a tilted detector and matches PyFAI `solidAngleArray` and MAX IV azint (unchanged for an untilted detector). Crystal geometry refinement (`XtalOptimizer`) no longer silently ignores an imported PONI `rot3` (rotation about the beam): it is applied as a fixed rotation in the residual so refinement stays consistent with the rest of the pipeline. Polarization and azimuthal binning already honoured `rot3` through the full PONI rotation. * jfjoch_viewer: Open datasets on the WSL2/UNC filesystem (paths starting `\\`); write processing outputs next to the input file, with a Browse button and independent `_process.h5` / merged `.mtz`/`.cif` toggles; and show the determined space group in the merge-statistics window. * rugnux: Accept an absolute `-o` output prefix in offline processing. * Packaging: The self-contained Linux viewer `.tgz` now bundles cuFFT, so it runs without a system CUDA toolkit (`.deb`/`.rpm` are unchanged, distro-managed). * Docs: Bring the analysis references up to date with the code. `docs/CPU_DATA_ANALYSIS.md` now reflects the unified profile-fit Bragg integration engine, multi-lattice indexing, azimuthal phi binning, the radial parallax/bandwidth profile with sub-pixel centring, the rot3d capture-fraction handling and the automatic CC1/2 resolution cutoff, and drops the descriptions of features that were never implemented (French-Wilson amplitudes, the still excitation-error partiality model); `docs/RUGNUX.md` documents the new `--resolution-cutoff`/`--resolution-cc-target`/`--resolution-shells`, `--min-captured-fraction`, `--mosaicity`, `--reference-column`, the azimuthal correction toggles and the geometry-override options, and corrects the `-N` default. The outdated in-source design notes (ICE_RING_DETECTION, BRAGG_INTEGRATION_ENGINE, NEXTGEN_INTEGRATOR) are removed.Reviewed-on: #68 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-12 19:42:29 +02:00
leonarski_f	54c0100e8e	v1.0.0-rc.157 (#67) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Rebrand the offline data-processing subsystem as `rugnux` and consolidate all offline analysis into the single `rugnux` binary - `jfjoch_process` is now `rugnux`, the former `jfjoch_azint` is now `rugnux --azint-only`, and `jfjoch_scale` is now `rugnux --scale` (see the new docs/NAMING.md and docs/RUGNUX.md). Scaling and merging are on by default for rotation and stills (`--no-merge` disables them), replacing the previous opt-in `-M, --scale-merge`. * rugnux: CLI fixes - default `-N` to all hardware threads, parse numeric option arguments strictly (reject non-numeric or trailing input instead of silently yielding 0), require `--wavelength > 0`, and correct the reproduced command line and `--scale` reference-cell handling. * rugnux: De-novo space-group improvements - recover genuine high symmetry and centred Bravais lattices from intensities, add an automatic CC1/2 high-resolution cutoff, and report L-test twinning statistics. * rugnux: Index weakly-diffracting low-resolution rotation data that previously failed (e.g. F-cubic crystals that diffract only to ~4 A on a detector reaching ~1.5 A). The per-frame indexing gate now measures the indexed fraction only within the resolution range the lattice actually diffracts to, so the many sub-diffraction ice/noise spots no longer make the fraction floor unreachable; the two-pass first pass tries several image-sampling schemes (spread across the whole rotation vs a consecutive wedge whose native stride keeps a reflection's rocking curve continuous, letting the FFT resolve a long axis) and keeps the one that indexes the most frames; and the de-novo space-group search no longer discards all reflections (and crashes) when every resolution shell falls below <I/sigma> = 1. * rugnux: Lower the low-resolution R-meas for strongly-diffracting rotation data - drop edge-of-sweep truncated fulls whose rocking curve was captured below `--min-captured-fraction` (default 0.7 for rotation), and report R-meas only over the observations kept by outlier rejection (matching XDS). The 0.7 default also strips the partiality-extrapolated fulls that dominate the intensity second moment on weakly-diffracting crystals, so the de-novo space-group search is no longer starved by the error-model I/sigma floor and recovers the correct symmetry (e.g. the F-cubic Benas crystals: Benas_3 -> F432, Benas_7 -> P6122, instead of P4/P1); on the reference battery every other crystal keeps its space group. * rugnux: Write the refined geometry (beam, tilt, axis) to _process.h5 and place non-standard mmCIF items under a reserved `jfjoch` prefix. * jfjoch_broker: Ordinary acquisition failures (receiver/writer/analysis problems, missed packets, writer disconnect) now return to the Idle state with an Error-severity message, so a run can be retried without an expensive re-initialisation; only failures that leave the detector in an undefined state (new JFJochCriticalException, e.g. PCIe/FPGA faults) go to the Error state and force re-initialisation. * jfjoch_broker: A synchronous /start now reports its failure to the HTTP caller instead of returning HTTP 200, and an incomplete or truncated dataset (missing packets, writer disconnect) is reported as an error rather than a "reduce frame rate" warning. * jfjoch_broker: Drop uncollected placeholder rows (number = -1) from the scan_result REST endpoint. * jfjoch_broker: Fix the inverted per-image compression ratio reported by the Lite receiver (was compressed/uncompressed instead of uncompressed/compressed). * jfjoch_broker: Bragg integration adds a quantization-noise variance floor with a box-sum fallback, and treats the type-maximum marker as an invalid pixel for unsigned image types. * jfjoch_writer: Detect file-overwrite conflicts at start for back-channel transports, and reset the writer when end-of-collection finalisation fails. * jfjoch_viewer: Preview overlays follow the geometry (resolution/ROI arcs, true beam centre, predictions, coral secondary-lattice spots, legend), add save-as-JPEG, and fix an HTTP live-follow memory leak. * Frontend: Improved aesthetics and usability, and added in-browser pixel-mask and JUNGFRAU-pedestal visualisation. * CI: Name the Windows installer jfjoch-viewer-* instead of jfjoch-*.Reviewed-on: #67 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-11 07:19:11 +02:00
leonarski_f	d6389e12da	v1.0.0-rc.156 (#66) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Major rotation (rot3d) data processing overhaul - robust profile-fit integration, Cauchy-loss scaling with optional absorption surface, de-novo indexing and space-group/centering determination fixes, and merging statistics + ISa in the mmCIF output. * jfjoch_process: Add EXPERIMENTAL ice-ring detection (--detect-ice-rings) that excludes ice reflections from scaling. * Compression: Add BSHUF_ZSTD_RLE_HUFF, make compression size-aware (drop frames that don't fit rather than aborting), and add the jfjoch_recompress tool. * jfjoch_viewer: Report "Multiple lattices detected" and grey out "Analyze dataset" on a live connection. * jfjoch_broker: Write smargon chi/phi goniometer positions to NXmx; read sensor thickness/material from HDF5 metadata. * CI: Build Windows (CUDA and non-CUDA) installers.Reviewed-on: #66 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-07-03 19:18:56 +02:00
leonarski_f	54c667190f	v1.0.0-rc.155 (#65) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_process: Remove pixelrefine option (replaced with ProfileIntegrate2D) * jfjoch_viewer: Some graphical improvements. * jfjoch_viewer: Simplify und unify data analysis settings. * jfjoch_writer: Add TCP keepalive to increase robustness if jfjoch_broker "dies" in the middle of data acquisition. Reviewed-on: #65	2026-06-25 22:01:48 +02:00
leonarski_f	6136f858af	v1.0.0-rc.154 (#64) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Fix to TCP file pusher (remove kernel zero copy to improve reliability) Reviewed-on: #64 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-25 18:12:00 +02:00
leonarski_f	75e401f0e5	v1.0.0-rc.153 (#63) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * jfjoch_broker: Add EXPERIMENTAL pixelrefine mode for image processing * jfjoch_broker: Allow to load user mask from 8-bit and 16-bit TIFF files * jfjoch_broker: Add ROI calculation in non-FPGA workflow * jfjoch_broker: Fixes to TCP image pusher * jfjoch_broker: Remove NUMA bindings * jfjoch_broker: Improvements to indexing * jfjoch_broker: For PSI EIGER, trimming energies are taken from the detector configuration (now compulsory) instead of hardcoded values * jfjoch_writer: Save ROI definitions and the per-pixel ROI bitmap in the master file; azimuthal ROIs support phi (angular) sectors * jfjoch_viewer: Major redesign with dockable panels and saved layouts, plus on-canvas creation/move/resize of box, circle and azimuthal ROIs * jfjoch_viewer: Run jfjoch_process reprocessing jobs from inside the GUI and overlay per-run results Reviewed-on: #63	2026-06-23 20:29:49 +02:00
leonarski_f	c49bd2ac3b	v1.0.0-rc.152 (#62) ... * jfjoch_broker: Fix bounds for azimuthal integration for Q spacing (allow Q of 1e-5) * jfjoch_viewer: Adjust Q bounds for azimuthal integration * jfjoch_azint: Add tool to do quick azimuthal integration Reviewed-on: #62	2026-06-17 20:36:24 +02:00
leonarski_f	ef52dac2ee	v1.0.0-rc.151 (#61) ... * jfjoch_broker: For PSI EIGER detector allow to disable individual half-modules by putting empty hostname Reviewed-on: #61 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-16 14:13:29 +02:00
leonarski_f	90e804acd7	v1.0.0-rc.150 (#60) ... * jfjoch_broker: When in FPGA workflow (with PSI detectors) azimuthal integration might be forced to CPU - this will require more computational power, but it enables more integration bins and reports standard deviation of each bin. * jfjoch_broker: Raise error if one is in FPGA flow and there are too many azimuthal integration bins. Reviewed-on: #60	2026-06-15 20:24:15 +02:00
leonarski_f	ea575f790a	v1.0.0-rc.149 (#59) ... * XDS plugin: Fix HDF5 mutex to run on multiple processors Reviewed-on: #59	2026-06-13 21:27:41 +02:00
leonarski_f	cc3eb8352c	v1.0.0-rc.148 (#58) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_broker: Improve azimuthal integration (add <I^2> calculation) * jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated) * jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin Reviewed-on: #58	2026-06-08 08:30:35 +02:00
leonarski_f	75de40f52b	v1.0.0-rc.147 (#57) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. * jfjoch_viewer: Add reciprocal space viewer * jfjoch_process: Two pass algorithm that does spot finding/indexing + integration of full dataset * jfjoch_process: Improve logic for rotation indexer, to make execution more deterministic (still work in progress) Reviewed-on: #57 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-06-02 11:49:24 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00
leonarski_f	caef26873e	v1.0.0-rc.145 (#55) ... This is an UNSTABLE release. The release has significant modifications for HDF5 writing logic - in case of troubles go back to 1.0.0-rc.144. * **Default HDF5 writing mode is with VDS, not soft-links** - this improves DIALS compatibility and makes format more future-proof, NXmx legacy format might be phased-out in the future. * XDS plugin: Improve performance of VDS reading. * jfjoch_writer: Significant improvement on how file systems I/O are handled through a dedicated pass-through VFD. * jfjoch_writer: Clean-up of HDF5 routines to better handle issues. Reviewed-on: #55	2026-05-06 21:50:02 +02:00
leonarski_f	7d34e8a049	v1.0.0-rc.144 (#54) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve performance of preview JPEG image generator at receiver startup (saving about 150 ms on measurement start for 16M) Reviewed-on: #54 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-05-01 17:06:36 +02:00
leonarski_f	6e0bb971ac	v1.0.0-rc.143 (#53) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Avoid copying gain calibration together with DiffractionExperiment Reviewed-on: #53	2026-04-30 22:16:50 +02:00
leonarski_f	87fde1b32e	v1.0.0-rc.142 (#52) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Support for newer CUDA architectures (notably Blackwell); minimum CUDA version 12.8 * Minor changes to jfjoch_process, jfjoch_fpga_test and jfjoch_lite_perf_test to make them more consistent Reviewed-on: #52 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 16:47:53 +02:00
leonarski_f	d760b12a18	v1.0.0-rc.141 (#51) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Azimuthal integration mapping is generated with parallel computations, significantly reducing setup times * frontend: Fix selection of FFTW in indexing settings Reviewed-on: #51 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-30 13:04:54 +02:00
leonarski_f	239a441ee6	v1.0.0-rc.140 (#50) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: For DECTRIS detectors, ZeroMQ link is persistent, to save time for establishing new connection * jfjoch_broker: Minor bug fixes for rare conditions Reviewed-on: #50	2026-04-29 21:40:22 +02:00
leonarski_f	4878318c27	v1.0.0-rc.139 (#49) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Further reduce startup time for DECTRIS detectors by selectively modifying SIMPLON parameters on `/start` * jfjoch_broker: Further reduce startup time for DECTRIS detectors by not setting beam center and detector distance via SIMPLON API on '/start' * jfjoch_broker: Add an extra message to ZeroMQ puller ready to monitor Lite worklow preparation time * jfjoch_broker: Image buffer configuration is postponed for Lite receiver flow till start message is received * jfjoch_broker: Use nanoseconds internally for frame/image/readout time * jfjoch_broker: Extra messages added for receiver operation (to be removed after debugging finished) * jfojch_broker: Improve profiling of different data analysis steps * jfjoch_broker: Record integration reflection count * jfjoch_broker: Fix bug where ZeroMQ preview frequency was confusing time units (micro vs. milliseconds) * jfjoch_broker: Fix bug where '/wait_till_done' got deadlocked * jfjoch_writer: Fix confusion between NaN and zero in floating-point datasets **Breaking changes**: detector definition is now using nanoseconds to define minimum frame time, minimum count time and readout time. Reviewed-on: #49	2026-04-29 09:50:50 +02:00
leonarski_fandtakaba_k	230480e390	v1.0.0-rc.138 (#48) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. jfjoch_broker: Cleanup DECTRIS start-up code to enable a shorter start time jfjoch_broker: Allow for asynchronous start to allow overlapping detector configuration with other beamline preparations jfjoch_broker: Goniometer axis name is converted to lowercase jfjoch_broker: Fix bug, where wrong HTTP error codes were returned jfjoch_broker: Improve sigma estimation during merging (K. Takaba) --------- Co-authored-by: takaba_k <kiyofumi.takaba@psi.ch> Reviewed-on: #48 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-27 19:56:14 +02:00
leonarski_f	c981e1b91c	v1.0.0-rc.137 (#46) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Better track time for each operation in the processing stack * jfjoch_broker: Rewrite preprocessing of diffraction images in the non-FPGA workflow to better use GPUs (work in progress) * jfjoch_broker: Remove ROI calculation in the non-FPGA workflow (work in progress) * jfjoch_viewer: Toolbar displays image number starting from 1 (instead of 0) Reviewed-on: #46	2026-04-25 19:59:21 +02:00
leonarski_f	c1c170112c	v1.0.0-rc.136 (#45) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Improve logic regarding indexing architecture and thread pools (work in progress). Reviewed-on: #45	2026-04-20 11:54:33 +02:00
leonarski_f	bb9f5c715f	v1.0.0-rc.135 (#44) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * Multiple small bug fixes scattered across the whole code base. (detected with GPT-5.4) * jfjoch_viewer: Improve image render performance Reviewed-on: #44 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-04-16 11:59:59 +02:00
leonarski_f	4a852b4d6b	v1.0.0-rc.134 (#43) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Add better locking for detector object - should help, when detector initialization takes too long * jfjoch_writer: Enable writing single, integrated HDF5 file with both data and metadata * XDS plugin: Add generation of Jungfraujoch plugin for XDS * CI: Add tests with XDS and DIALS (`xia2.ssx`) Reviewed-on: #43	2026-04-09 13:30:47 +02:00
leonarski_f	6133da1377	v1.0.0-rc.133 ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.132. * jfjoch_broker: Use httplib for HTTP server instead of Pistache * jfjoch_broker: Drop OpenSSL support * jfjoch_broker: Base work for multi-lattice support in the future * Update dependencies to more recent versions (spdlog, HDF5, Catch2, httplib) Reviewed-on: #41	2026-03-26 20:50:33 +01:00
leonarski_f	2ab9deb20b	v1.0.0-rc.123 (#40) ... Documentation update Reviewed-on: #40	2026-03-12 12:17:11 +01:00
leonarski_f	166fcdb68f	v1.0.0-rc.131 (#39) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug in saving JUNGFRAU calibration (pedestal/pedestalRMS) * jfjoch_viewer: Fix calibration (pedestal) images being open flipped * jfjoch_process: Add space group detection (EXPERIMENTAL) Reviewed-on: #39	2026-03-07 11:34:04 +01:00
leonarski_f	928789a67c	v1.0.0-rc.130 (#37) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Rotation indexer has two retries if failes * jfjoch_broker: Rotation indexer handles small number of rotation images (like test shot) * jfjoch_broker: Integration calculates background mask based on R2 radius * jfjoch_process: HDF5 files are not saved by default Reviewed-on: #37	2026-03-06 14:38:56 +01:00
leonarski_f	64002f1e29	v1.0.0-rc.129 (#36) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Significant improvements in TCP image socket, as a viable alternative for ZeroMQ sockets (only a single port on broker side, dynamically change number of writers, acknowledgments for written files) * jfjoch_broker: Delta phi is calculated also for still data in Bragg prediction * jfjoch_broker: Image pusher statistics are accessible via the REST interface * jfjoch_writer: Supports TCP image socket and for these auto-forking option Reviewed-on: #36 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-05 22:13:12 +01:00
leonarski_f	3036b1d37f	v1.0.0-rc.128 (#35) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Handle properly reuse of image buffer locations * jfjoch_broker: Fix bug in counting idle slots * jfjoch_broker: Force obtuse angle for monoclinic cells * jfjoch_process: Change scaling refinement tolerance Reviewed-on: #35 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-03-03 22:24:44 +01:00
leonarski_f	f3e0a15d26	v1.0.0-rc.127 (#34) ... This is an UNSTABLE release. The release has significant modifications and bug fixes, if things go wrong, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Default EIGER readout time is 20 microseconds * jfjoch_broker: Multiple improvements regarding performance * jfjoch_broker: Image buffer allows to track frames in preparation and sending * jfjoch_broker: Dedicated thread for ZeroMQ transmission to better utilize the image buffer * jfjoch_broker: Experimental implementation of transmission with raw TCP/IP sockets * jfjoch_writer: Fixes regarding properly closing files in long data collections * jfjoch_process: Scale & merge has been significantly improved, but it is not yet integrated into mainstream code Reviewed-on: #34	2026-03-02 15:57:12 +01:00
leonarski_f	32b681e591	v1.0.0-rc.126 (#33) ... This is an UNSTABLE release. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Fix bug for monoclinic space groups being wrongly refined when beta is much different from 90 deg. Reviewed-on: #33 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-19 07:01:38 +01:00
leonarski_f	1ab257af6c	v1.0.0-rc.125 (#32) ... This is an UNSTABLE release. This version adds scalign and merging. These are experimental at the moment, and should not be used for production analysis. If things go wrong with analysis, it is better to revert to 1.0.0-rc.124. * jfjoch_broker: Improve logic on switching on/off spot finding * jfjoch_broker: Increase maximum spot count for FFBIDX to 65536 * jfjoch_broker: Increase default maximum unit cell for FFT to 500 A (could have performance impact, TBD) * jfjoch_process: Add scalign and merging functionality - program is experimental at the moment and should not be used for production analysis * jfjoch_viewer: Display partiality and reciprocal Lorentz-polarization correction for each reflection * jfjoch_writer: Save more information about each reflection Reviewed-on: #32 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch> Co-committed-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-02-18 16:17:21 +01:00