172 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	54968a245f	viewer: the file manager starts where the data is, and follows a dataset opened elsewhere ... Two things a beamline user did every session by hand. The browser's default root now resolves JUNGFRAUJOCH_DATA_ROOT, then the root last used, then - for an SLS account, which is eNNNNN against a pNNNNN group - /sls/mx/data/pNNNNN/raw, then home. The environment variable stays the general mechanism and keeps precedence; the account rule is there because it needs nothing rolled out to benefit from it. Both go through DefaultRoot(), so a reset resolves them the same way a first run does. A dataset opened from the File menu or over D-Bus now expands and selects itself in the browser when it lies inside the current root. Containment is tested on resolved paths, so a sibling directory sharing a prefix is not inside it. Neither says anything when it does not apply: an account that is not a beamline one, a directory that is not there, a dataset outside the root - each is a bare return, because for everyone who is not at this one facility the condition should be invisible. Following never writes the root, so the location the user chose is still the location they get back. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011GxZqDiFP3KqriBhNdcR56	2026-09-13 12:21:59 +02:00
leonarski_fandClaude Fable 5	7d872fd762	viewer: plot choices persist per dataset kind, and settings reset live ... The dataset-info plot remembers the selected quantity and the Grid/Per-image toggle states across restarts, with grid scans and standard scans each keeping their own favourite (QSettings groups datasetInfoPlot/gridScan and /standard). Choices are stored as the combo item's data code, not its index, so a saved choice survives the plot list changing and a code no longer offered falls back to the first item. Favourites are saved on every explicit user action and applied whenever a dataset of the other kind loads; loads of the same kind keep the in-session state, and the live-source default still wins until the user picks. The unconditional Grid auto-check on grid scans moved into the favourite's default, so unchecking Grid on a grid dataset now sticks. View > "Reset all settings to defaults" clears the whole settings store after confirmation and brings the running session to a first-start state in place: default layout, window size, display settings (Indigo, Auto off, HDR off), plot choices, and the file manager root. Because the live state then equals the defaults, saving on close stays enabled and later changes persist as usual. File > Quit now closes the main window instead of calling QApplication::quit(), so closeEvent runs and the persistent settings are saved on that path too - previously they were saved only when the window was closed by the window manager. The file manager root persistence was audited and left unchanged: saved on every successful change, restored behind JUNGFRAUJOCH_DATA_ROOT, and a vanished directory falls back to the home directory. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WbjnQhutnboy4qbxwmgDAX	2026-09-13 10:16:55 +02:00
leonarski_fandClaude Fable 5	337ea76fda	viewer: the composite plot reads on two coloured axes, and fluorescence goes ... The "Spots + background" dataset plot now scales each quantity on its own axis - background on the left, spot count on the right - with each axis's labels and line coloured like its curve, so which axis reads which quantity is visible at a glance. Each axis is ranged from its own series alone, so live growth of one quantity never rescales the other; on top of that the background's range is inflated upward and the spot count's downward, each by its own span, so the two curves occupy separate halves of the plot instead of crossing. The spot count stays the primary series (current-image marker, hover, click-to-load, overlays). Trade-off accepted: the spots axis shows ticks below zero in its empty lower band. The per-image plot selector no longer offers the X-ray fluorescence spectrum; the reader-side fluorescence plumbing is untouched. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WbjnQhutnboy4qbxwmgDAX	2026-09-13 09:33:38 +02:00
leonarski_f	a5ba1f8e95	docs: what a rugnux run costs in host and device memory ... Measured on rc.169 over rotation sweeps from 2.5 to 18 megapixels: both peaks fall in scaling and merging, and both track the number of integrated observations rather than the detector size - two sweeps on the same detector differ five-fold. Device memory is linear in -N at about 8 bytes per detector pixel per worker over a fixed floor, so the 16 GB card that fits four light runs fits one heavy one. --no-merge and -N lower the peak; --no-export-unmerged was measured and does not - it saves disk, not RAM. Also records what happens when the card is too small: device decode, the beam-stop projection and an indexer thread degrade to the host, everything else fails the run with a non-zero exit rather than returning a short dataset.	2026-09-13 07:37:14 +02:00
leonarski_fandClaude Opus 5	99910e187e	beam stop: a ring is only flat once the polarization is divided out ... The shadow test compares a pixel with the median of its ring, which assumes the background is flat around a ring with nothing in the beam. It is not: a polarized source suppresses the background in its own plane by 1 - sin^2(2 theta), a factor of three at 2 theta = 55 degrees and four at 70. That is several times the dip the test is looking for, so on a short-distance geometry the two horizontal lobes of every outer ring read as shadow. Measured over the corpus it cost one dataset 5.1 % of its detector, and another 11.2 %, with nothing visible under either mask. The mean projection is therefore divided by the Kahn factor before the ring comparison, and the Poisson deficit multiplies it back in so the significance is still the significance of the counts that were recorded. The factor is the geometry's own CalcAzIntPolarizationCorr, evaluated about the centre the caller named rather than the one in the file: the azimuth is the whole point of this correction, and the geometry is what knows where the polarization plane lies once the detector is tilted, the stored image quarter-turned or the detector rotated in its own plane. Six corpus datasets are quarter-turned, and a flat-detector formula on the stored image's own axes gets them 90 degrees out of phase - measured, it takes one of them from 16.5 % masked to 22.8 % where the geometry takes it to 4.4 %. Polarization is also the only correction a ring carries that varies along it; solid angle, detector and air absorption are functions of 2 theta and the ring median absorbs them. Measured, mask fraction of the detector: a clean 110 mm sweep 0.82 -> 0.51 %, a clean 200 mm 18 Mpx sweep 0.94 -> 0.80 %, a 150 mm sweep whose header centre is 351 px out 5.05 -> 0.74 %, and the sweep with a third of the detector behind a pin 32.22 -> 32.83 %. Clean detectors lose mask, a real obstruction gains it. Across 151 corpus datasets nothing gains more than a tenth of a percent from the correction and 26 lose some, 6 of them by more than 3 percentage points. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-13 07:36:57 +02:00
leonarski_fandClaude Opus 5	d412306c77	beam stop: a shadow does not have to touch the direct beam ... The shadow finder kept only the low region connected to the beam centre, flooding outward from seeds within 4 px of it. That is written for the beam stop and its holder arm, an object that touches the direct beam. Hardware that stands in the beam further out - a pin, a loop - casts a shadow that begins some way out in radius, with lit detector between it and the stop, and no bridge crosses that gap. On a sweep where such a shadow covers 38 % of the detector the per-ring test found the whole of it and connectivity then discarded 950 k pixels, leaving the beam-stop disk alone; those pixels went into integration as measured-and-near-zero. What makes the test specific instead is size: keep the connected components that hold at least MIN_SHADOW_PIXELS core pixels. A shadow is cast by something physical and is correspondingly large, while the background wanders a pixel or two at a time. Measured on five clean in-house sweeps spanning 0.05 to 9.5 counts/px/frame of background, every one returns exactly one such component - the beam stop - and the largest spurious candidate anywhere is 74 pixels, a 27x margin. MIN_EXPECTED_COUNTS becomes a Poisson significance. A ratio says nothing when the background behind it is a handful of photons, so the deficit is now required to be significant against its own scatter, sqrt(2 (E - N + N ln(N/E))) over the pooled counts. This is what makes the comparison scale-free rather than tuned to one exposure: rebuilt from six frames of a low-background sweep, the same thresholds without it mask three quarters of the detector and with it mask none of it. The index of dispersion, measured over the frames, does NOT do this job - it is 1.0 inside the shadow and 1.0 outside it, because a shadowed pixel is Poisson at a low rate and a lit one is Poisson at a high rate. Only the rate relative to the ring separates them. The rest follows: the core ratio moves 0.35 -> 0.50 and the half-shadow reach 0.72 within 14 px -> 0.75 within 30 px, since a pin's penumbra is much wider than a beam stop edge's; the ring walk that finds the rings lying wholly inside the stop keeps its own threshold so the central disk does not move; and those rings join the region after the size filter rather than being asked to be large themselves. On the shadowed sweep this takes the mask from 16,587 px (0.66 %) to 818,184 px (32.32 %), against 956,705 px (37.79 %) for the reference implementation, at a precision of 0.92 against it. Clean sweeps move from 0.60 % to 0.82 %, the width of the same arm. One thing this costs: an empty mask used to be a statement about the beam centre, because the seeds were placed at it. It no longer is, and a centre wrong by a couple of hundred pixels now draws the rings across the background's own fall-off and returns a large spurious mask instead of an empty one. The log message says so. The fix is ordering - the centre is measured from this same projection a moment later - and is not attempted here. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-13 07:36:57 +02:00
leonarski_f	1b28dd2072	rugnux: a first pass that finds no lattice tries a leaner, shallower one ... A crystal sitting in a crystalline powder floods the first pass with spots that are not its own. Two in-house crystals gave 2112 spots a frame against the 80 a clean crystal on the same beamline gives, and no scheme indexed a single validation frame; the FFT took a 10-30 A cell out of the shells. A third dataset, with no powder at all, failed for the neighbouring reason: its file beam centre is 170 px out, and the measured centre was tested with the full spot list, indexed nothing there either, and was thrown away. Powder rings are now MEASURED from each run's own pre-scan spots rather than read off the fixed hexagonal-ice list, and reported on every run (POWDER_*) whether or not anything acted on them - hexagonal ice is the only phase that can be named in advance, and 16 of the 24 rings on one of these crystals are ice while the rest are not. A first pass that ends with no usable lattice then retries over how much of each frame it reads: the strongest 30, 80, 200 or all spots an image, each at the file's resolution and at the resolutions a quarter and a half of this sample's own spots lie coarser than, with the measured rings set aside where there are any. Decided late on the validation-frame count, the way the rotation-axis sign already is, and adopted only on a win of a sixth of the frames. The same ladder is asked inside the beam-centre check, where a centre that is wrong and a spot list that is too deep otherwise hide each other. Measured over 146 datasets: unchanged on all of them - the open arm scores 91/99 either way and the 46 SLS datasets are identical on every scientific field - while the three that failed now index. The deposited cell is recovered to 0.1% on the beam-centre case, at 100% of frames and 0.597 A.	2026-09-13 07:36:48 +02:00
leonarski_f	ea37056fe9	rugnux: judge the two-pass on the signal each pass measured, not on a pooled CC1/2 ... The rotation two-pass reverts to the header geometry when the refined pass looks worse. It decided that on the search merge's pooled, uncut, pre-correction P1 CC1/2 - a number that reads 0.13 on a crystal whose data merge at 0.995, and that moves 0.93 to 0.76 between two runs whose merged data agree to 0.7% of R_meas. Two crystals were sent back to a geometry that ships 22% fewer reflections than the one they refused. Compare instead what each pass MEASURED: reflections merged at I/sigma >= 2. Against an external arbiter that objective agrees with which geometry is the more accurate one on 23 of 27 arm-dataset pairs, where self-consistency measures agree on 13 of 27. Count it on both sides over the centring-allowed reflections, so a pass that finds a centring the other did not is not judged on the extinguished half its P1 merge holds as noise (two crystals compared merges holding 2.0x the reflections of the other), and ask the axial-row arm only where the two passes are in the same setting, which is the only case where the two counts are counts of the same reflections. The bar is a decisive loss rather than a bare inequality: the two passes never integrate the same way - the canonical pass integrates at the measured spot width and predicts with the pre-pass's smoothed mosaicity - so a difference that small is not evidence about the geometry either way.	2026-09-13 07:36:19 +02:00
leonarski_fandClaude Fable 5	7b868fb9f5	viewer: raster window composition and remote-display repaint throttling ... Over "ssh -X" the viewer was near unusable, and the July finding that every repaint uploads the whole window (5.3 MiB at the default size) regardless of how small the damage is turns out to have a single cause: the reciprocal-space window constructed a QOpenGLWidget at startup, and one dormant QOpenGLWidget - unmapped, in a window nobody ever opened - switches Qt's window composition onto the OpenGL swapchain path. That path re-presents the entire window on every flush (and is also the llvmpipe CPU burn seen on headless boxes). The reciprocal-space window was a placeholder feature and is removed; with it gone Qt flushes through the raster backing store, which sends only the damaged region. On top of that, interactions that repainted once per input event are held to the hover cadence (15 Hz) on remote sessions only: panning accumulates its pixel delta, wheel zoom its steps, a recolour burst its final value, live playback keeps only the newest frame (the worker ack stays per-frame), and the toolbar counter/slider readbacks coalesce the same way. Each throttle applies inline with a single-shot tail, the same shape as the existing hover limiter, so the view always lands exactly where the gesture put it. Local sessions are unchanged - every event still applies inline. Remote sessions are detected once at startup (xcb platform and a DISPLAY with a host part, i.e. "localhost:10.0" from SSH forwarding or "host:0"); the JFJOCH_VIEWER_REMOTE environment variable and a View-menu toggle override the detection in either direction. Measured through a byte-counting X relay against Xvfb with MIT-SHM disabled (client-to-server bytes are what the SSH link carries), same scripted interaction sequence, 1200x1100 window, KiB: rc169 removal only removal+throttles hover, 50 motions 82088 2040 2040 pan, 50 motions 290046 12087 4778 wheel zoom x10 71143 12603 7649 ctrl-wheel x6 65672 7194 4797 frame step x10 284572 21454 21454 Removing the reciprocal-space window from the source measured byte-identical to only deferring its GL view to first show, confirming the cost is the live QOpenGLWidget, not the code being compiled in. The image panel renders pixel-identically (AE=0) to rc169 after identical zoom+pan gestures, with the throttles on and off. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WbjnQhutnboy4qbxwmgDAX	2026-09-12 22:38:45 +02:00
leonarski_f	d1d1748fed	docs: typographical fixes in the hardware and deployment pages ... Jungfruajoch, frotend, allways, statisitics, pixed point, "the two has to be purchases separately", "servers are the moment", "how it processed". These pages are published to Read The Docs.	2026-09-12 22:38:32 +02:00
leonarski_fandClaude Opus 5	50a23c2945	docs: six instruction-shaped sentences become plain statements ... A prose pass over docs/ for text that reads as written by, or addressed to, a language model. The documentation is almost entirely in the house voice already; what needed changing was six hollow directives in the older infrastructure pages ('it is important to ensure...', 'extra care has to be taken...', a leftover 'Be explicit about the gaps' addressed to the document's own author). Each is rewritten as a statement of fact with the technical content untouched. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011GxZqDiFP3KqriBhNdcR56	2026-09-12 22:38:32 +02:00
leonarski_f	43decf99a8	report: REPORT_VERSION counts releases, not format changes ... The constant went to 14 on the reasoning that the format history above it listed thirteen entries while the number still read 7. That is backwards. A reader only ever meets the report that was built from main, so a bump inside a release branch numbers a format nobody received, and several of those entries shipped together in one release. Seven is what main ships; this release changes the format once, so it is eight. The convention is now written down beside the constant and in the report documentation, because this is the second time it has been read the other way.	2026-09-12 22:38:32 +02:00
leonarski_fandClaude Opus 5	f8763ca875	rugnux report: parsable comments, honest build provenance, terms of use ... Every line of <prefix>_report.txt is now KEY= value, a # comment, or blank (REPORT_VERSION 14; warnings print as "# WARNING:"), so a consumer keeps the data by dropping the # lines. The header records the exact build: the git commit, stamped at BUILD time by common/GitInfoStamp.cmake so it cannot go stale in a reconfigured tree, with -dirty marking uncommitted changes; the CMAKE_CXX_FLAGS of the build, because two builds of one commit can differ by flags alone; and the release page of exactly this version, whose tag is the version string. The foot states authorship and terms of use: GPLv3, free for academic institutions and commercial companies alike. Every sentence phrased as a directive to the reader ("Read the shell table rather than quoting a single number", "Do not refine against the written reflections", "Treat the reported cell as a supercell candidate", "believe the _BEFORE_SEARCH one") is rewritten as a statement of fact about the measurement: a report describes the data, it does not instruct whoever - or whatever - reads it. Also fixed: REPORT_VERSION had stayed at 7 while its own history comment reached 13; ANISOTROPY_D_MIN_* printed "nan" against the report's own no-placeholder rule; "1 condition(s) need attention"; "rises by" on a signed quantity. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011GxZqDiFP3KqriBhNdcR56	2026-09-12 22:38:32 +02:00
jungfrauandClaude Opus 5	9efe72f9b1	licenses: list libcurl in the notices ... libcurl is fetched and statically linked into the shipped jfjoch_viewer, but it had no row, no licence text and no COLLECT.sh entry. Its collection is the one that only resolves after a viewer-enabled configure, which is noted at the entry. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01B6iekpDa2xiKobEj1R5xnp	2026-09-12 14:00:17 -04:00
jungfrauandClaude Opus 5	4f3d2f85b6	licenses: follow the dependency updates in the notices ... Versions in the fetched-at-build-time table, and the two licence texts that changed with them: HDF5 2.2.0 appends the Apache-2.0 text to its BSD-3-Clause-style licence, and libjpeg-turbo 3.2.0 rewrote its licence sections (the licence set is unchanged: IJG + BSD-3-Clause + zlib). Abseil gets a row and a licence text of its own. It was always linked in, arriving as Ceres' git submodule; now that the build fetches it explicitly it is listed rather than left implicit. docs/THIRD_PARTY_NOTICES.md regenerated by the update_version.sh recipe. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01B6iekpDa2xiKobEj1R5xnp	2026-09-12 13:30:14 -04:00
leonarski_fandClaude Opus 5	0ca6b251e5	jfjoch_viewer: no settings section is wider than the panel it sits in ... Measured every section's content minimum width against the 330 px the settings dock gives it (the powder one, fixed yesterday, sat at 278): geometry 346, unit cell 355, goniometer 322, spot finding 370, indexing 321, bragg 287, scaling 297, azint 243, reference 149 Five over. Three causes, none of them about the section: - addRow("", w) reserves the label column and puts the widget in the field column, so a checkbox's whole width was added to the widest label. addRow(w) spans both columns instead, which is what a label-less row means anyway. Spot finding 370 -> 251. - A spin box is never narrower than its longest possible value, suffix included, and these rows hold two or three abreast. The unit moves to the row label, which is how the panel names units elsewhere ("High resolution [Å]"): "a, b, c [Å]", "Beam origin [px]", "Detector tilt [°]", "Step x, y [μm]", "Radii r1/r2/r3 [px]". A cell length can still be four digits and three decimals, so those six fields also divide the row rather than demand their own width. - A combo is never narrower than its longest entry - the same thing that pinned the powder panel. "Flex (best per-image refinement)" set the indexing section's width; it elides now, as the calibrant does. Every section is now 291 or less, and none of them moves the dock. Two inspector changes in the same panel: - An axis that is present but does not turn covers no angular range, so the image angle is stated as one number rather than "-145° + 0°". - Sample-head angles that stay put during a run - an SLS Smargon writes chi and phi - get a row of their own, "chi 0° / phi 0°". Both its labels stay empty for a file that carries none, so it costs nothing where it means nothing. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011oVDk7aukYqfPZBLHn5nGg	2026-09-12 07:31:54 +02:00
leonarski_fandClaude Opus 5	a7a4c28925	jfjoch_viewer: the inspector states the numbers it used to hide ... Six changes to the desktop viewer, all in what it shows and what it is called: - The left-hand reprocessing panel is titled "Processing" (it sits next to "File manager"); the jobs panel that held that name is "Jobs". - The file manager lists *.cbf beside the HDF5 datasets. A CBF is one frame per file and opening any of them opens its sweep, which is what the File > Open dialog already did. - Image statistics: collection time, detector distance, beam centre and wavelength were in the dataset row's tooltip, where a number nobody hovers over is a number nobody reads. They are rows of their own, in the order a person asks for them - what the dataset is, how it was collected, then what this image contains. Source/instrument and sample are bold like every other value. The B-factor row is gone. - A "Spots + background" plot: spot count on the left axis, background per pixel on the right, since a common scale would flatten one of them. The axis labels take the colour of their line - a legend costs exactly the vertical room those labels need at this dock height. It is what a live (HTTP) connection selects by default, until the user picks something else. - Expanding the powder-calibration section no longer widens the settings panel past the space it has. Two buttons side by side cannot be narrower than both their labels, and a combo is never narrower than its longest entry - a 40-character cell in the calibrant list set the minimum width of the whole dock. One button per row, the cell in a tooltip, and both combos allowed to elide. - The grid/per-image toggles both rebuild the metric selector now. The grid button did not, so leaving per-image mode through it left the per-image plot types listed - X-ray fluorescence offered as a metric of a grid scan - and their values were then read as per-dataset metrics. Each mode also remembers its own selection instead of carrying an index across two unrelated lists. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011oVDk7aukYqfPZBLHn5nGg	2026-09-11 22:07:54 +02:00
leonarski_fandClaude Opus 5	a59be89192	receiver: bound the wait for a start message that never arrives ... JFJochReceiverLite::MeasurementThread polls for the start message with no way out other than the cancelled flag, and JFJochServices::Stop cancels the receiver silently once the detector reads back idle - a silent cancel deliberately does not set cancelled, since it reports that the detector has finished rather than asking for an abort. A run whose start message never came therefore left Stop() waiting on this thread indefinitely, and only an operator pressing cancel got the broker back. Cancel(bool) is overridden to record that the detector has finished, and the pre-start poll gives up five seconds later. The grace is there because the detector can also read back as idle for a moment just after it was armed, so a run is not abandoned the instant the silent cancel arrives; the flag is consulted nowhere else, so images already being processed are untouched. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012bew392LTGP2fkhfRJsMcB	2026-09-11 19:19:45 +02:00
leonarski_fandClaude Opus 5	1da94bdfe2	broker: a cancelled dark-mask collection is not a finished calibration ... DarkMaskAnalysis::GetMask always returns a full-size array - a pixel that saw no frame reads as good - so the dark_mask_result.size() check in TakeDarkMaskInternal accepted a mask measured on nothing. The mask was adopted through LoadDarkBadPixelMask, the state went to Idle and the sequence logged "Calibration sequence done" on a calibration the operator had just cancelled. The dark mask is a single step, so unlike a pedestal sequence there is no later cancel_sequence check to catch it. Refuse it after Stop() the way the check at the top of the same function does: Inactive with the "Mask sequence cancelled" error, matching what the pedestal steps report. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012bew392LTGP2fkhfRJsMcB	2026-09-11 18:53:53 +02:00
leonarski_fandClaude Opus 5	c40e0eb11d	broker: fix deadlock when re-initialising after a DECTRIS run that never started ... A re-initialisation left the previous run's ZMQImagePuller connected: JFJochServices::On replaces its own shared_ptr, but JFJochReceiverService keeps a second reference to the puller of the last run. Two PULL sockets on one PUSH peer share messages round-robin, so the orphaned puller silently took half of the DECTRIS stream - the start message included - and the receiver then waited for a start message that had already been discarded. Once such a run was cancelled, nothing drained the orphaned puller's outside_fifo any more. Its CBOR thread parked in PutBlocking on the full queue (suspend is only tested before the put), the puller thread backed up behind it in cbor_fifo, and neither could reach the disconnect flag again. The next JFJochReceiverService::Start dropped the last reference to that puller, so ~ZMQImagePuller joined two threads that could never exit - while holding state_mutex, inside a calibration sequence that itself holds the state machine's mutex. The whole control plane froze with no way to cancel; only a restart got out of it. * ThreadSafeFIFO gains Stop(), which releases every waiter and makes further blocking operations return at once. Clear() now notifies c_full as well: clearing a full queue used to leave the blocked producer asleep, since the next Get on an empty queue notifies no one. * ZMQImagePuller::Disconnect and TCPImagePuller::Disconnect stop their queues before joining, so a puller whose consumer is gone can always shut down. * JFJochServices::On and ::Off disconnect the previous puller explicitly rather than relying on the shared_ptr going away, so two readers never share the detector stream. ZMQImagePuller_DisconnectWithFullQueue covers the shutdown; it hangs on the previous code. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_012bew392LTGP2fkhfRJsMcB	2026-09-11 18:53:39 +02:00
leonarski_fandClaude Sonnet 5	d24cdfcff4	jfjoch_viewer: navigation keys, one-shot auto-contrast, file manager panel, cleanup ... * Dataset-info plot hover shows a horizontal crosshair alongside the existing vertical one, so a run of hovers reads as a level or a drift at a glance. * `A` applies auto-contrast once instead of switching on persistent Auto mode (a new `oneShotAutoForeground()`, distinct from the toolbar's Auto toggle); pressing it a second time on the same image switches Auto on for good, and pressing it while Auto is already on leaves it on. The value itself comes from one `AutoForegroundValue()` shared with the continuous Auto path. * `Home`/`End`/`Page Up`/`Page Down` navigate the dataset (first/last image, one image forward/back); claimed in the diffraction view's keyPressEvent before QGraphicsView's default handling, which otherwise eats them to scroll the viewport. * Alt+wheel dataset navigation is removed - some window managers already took it before the app ever saw it, per the caveat that used to sit next to its entry in the shortcuts list. * The image strip dock and its dedicated thumbnail-rendering machinery in the reading worker (SetThumbnail*, RenderThumbnail_i) are removed; it cost a lot and nothing else used any of it. * Toolbar text: "Colour" -> "Color". * Color map, Auto and HDR mode now persist across sessions, the same way the window layout already does. * The Inspector's "Dataset:" path wraps at '/' (a zero-width space after each one) instead of being cut off when it doesn't fit one line. * LoadFile no longer reopens an already-open file - it forwards straight to LoadImage instead - which was the likely cause of a D-Bus client's per-image navigation lagging behind the same navigation done via the grid-scan hover. * New file-manager dock (left, tabbed with Settings via tabifyDockWidget): a directory tree filtered to *_master.h5/*_process.h5, rooted at JUNGFRAUJOCH_DATA_ROOT if set, else the last-browsed root, else the home directory. Most beamline users care about opening images, not reprocessing settings, so it's the tab raised by default. Its filter box narrows files only - a directory always passes - because filtering the directories too hid the matching files under any directory whose own name did not match, and hid the root's ancestors, which left the tree with no valid root index until the root was set again by hand. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01PogHY7bWXV4bpctDPdyuDN Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>	2026-09-11 18:45:20 +02:00
leonarski_f	40dd6f25fd	release: version 1.0.0-rc.169	2026-09-10 17:26:55 +02:00
leonarski_f	77bc0cfe52	v1.0.0-rc.168 (#78) ... * rugnux is substantially faster - a corpus of 145 rotation datasets processes in about two thirds of the time - with identical results. * A crystal whose lattice looks more symmetric than it is because the beam centre is off is no longer processed on the wrong cell. * rugnux prints at startup, and writes at the foot of every results report, a short acknowledgement of the X-ray research community whose methods it implements and of the open-source projects it builds on; `ACKNOWLEDGEMENT.md` now ships in every package beside `LICENSE` and `THIRD_PARTY_NOTICES.md`. Reviewed-on: #78 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-10 13:51:16 +02:00
leonarski_f	a39fd29f77	v1.0.0-rc.167 (#77) ... * `rugnux --model` reports CC(model, data) - the correlation of the merged intensities with the placed, scaled model - by resolution shell, on the same shells as CC1/2, with the reflection count and a significance for each. * `rugnux --model` fits the model's scale, anisotropic B and bulk-solvent parameters on the working reflections only, so the R-free it reports is measured against a model no free reflection helped scale. * The bulk-solvent parameters of `rugnux --model` are searched over their physically meaningful range instead of being fitted without bounds, so a model is never scaled with a solvent term that has silently switched itself off. * The rigid-body placement of `rugnux --model` uses the same bounded bulk solvent as the reported fit, so a model is no longer placed against a target carrying a solvent term with no physical meaning. * `rugnux --model` puts the model into the data's own description of the lattice before placing it, so a model whose cell is written on other axes - I-centred where the run indexed C-centred, a different unique axis, a permuted orthorhombic cell - is placed rather than scored where it was read; `MODEL_CHANGE_OF_BASIS=` and `MODEL_SETTING_AS_READ=` report it when it happens. * The rugnux results report opens with a summary - `VERDICT=` (`OK`, `WARNINGS`, `UNUSABLE`, `FAILED`), `VERDICT_TEXT=`, `PATHOLOGY_FLAGS=` with one closed-vocabulary code per condition that warned, and the `WARNING:` lines, which used to close the file - and the sections after it are renumbered 1-5 with no gaps. * `rugnux --developer` writes the full results report - the pipeline-internal keys and the long explanations the default report now leaves out - and `--finalist-ledger` adds the evidence for every space group the search considered, not only the one it adopted. * The results report warns when the merged data carry no usable signal and when too little of reciprocal space was measured inside the fitted resolution, and omits `FITTED_RESOLUTION` where the CC1/2 curve it is fitted on never falls off. * rugnux detects translational pseudo-symmetry and reports it under the `PSEUDO_TRANSLATION` flag as `TNCS_DETECTED=` and the `TNCS_*` keys - a translation the merged data are exactly invariant under is reported as `UNDECLARED_LATTICE_TRANSLATION=` under `LATTICE_TRANSLATION` instead - and a detected pseudo-translation can no longer buy a false screw axis in the space-group search or hide a twin from the L-test (`L_TEST_VS_TNCS=`). * The space-group search determines glide planes from zonal systematic absences, so a non-Sohncke space group such as P 2_1/c or Pbca is named where the run previously stopped at its Sohncke subgroup; `SOHNCKE_SPACE_GROUP=` carries the best Sohncke group beside it on every run that searched, and a centre of symmetry is never claimed. * Where the cell metric carries more rotational symmetry than the Bravais class the indexer named, the extra rotations are put to the intensities and the space-group search is asked again on the metric's own cell - adopted only where the intensities confirm the higher symmetry - so a lattice that is nearly but not exactly hexagonal, or whose reduction landed in a sub-cell, still reaches its true point group. * Systematic-absence calls rest on the evidence rather than on counts: a screw axis whose absent class the data show extinct is no longer refused because a handful of reflections in it read as present, and `SPACE_GROUP_ALTERNATIVES=` no longer drops a candidate that differs only on a zone the sweep never measured. * A reference correlation measured on too few reflections is refused instead of scored zero, so a run given a reference MTZ is no longer reindexed on an operator that mapped almost everything outside the reference's coverage. * A frame counts as indexed from 6 spots on its lattice rather than 9, so a weakly diffracting crystal whose frames cannot carry 9 is no longer refused the lattice it fits; `--min-indexed-spots` overrides it. * `-C` accepts a known cell in any equivalent description - conventional or primitive, centred or not - instead of only the reduced primitive form, so a centred cell given the way it is published no longer makes the run report that it found no lattice. * Each reflection is corrected for the sensor's quantum efficiency at the angle it meets the detector (attenuation lengths from the NIST tables, which also fixes the spot-width parallax term on CdTe) and for the attenuation of the flight path between the sample and its pixel; `--flight-path air|helium|vacuum` declares the medium - default air, since no file states it - and the report says what was assumed and what it was worth. The unmerged MTZ records the factors in new `QE` and `FLIGHT` columns beside `LP`, so raw counts are `I / LP * QE * FLIGHT`, and `_process.h5` in new optional `qe` and `flight` datasets. * Rotation geometry post-refinement fits the crystal and the detector at once, against the observed spot positions and the observed rocking angles together, so the refined distance depends far less on how wrong the file's distance was. * A coarsely sliced sweep integrates correctly: partials are joined into one rocking event by angle rather than by frame count, so two crossings of the Ewald sphere are no longer summed into one full, and at 0.5 degrees per image or coarser the per-frame geometry refinement accepts a spot whose miss the exposure's own rotation accounts for. * `rugnux --mode scale` reports the detector tilt and direct beam of the geometry it re-scaled at, instead of zeros that read as a flat detector, and no longer warns that no image was indexed on a run whose lattice came from its input file. * Every rotation run that determined a space group and merged reports what the mounting cost: `SPINDLE_LOST_UNIQUE_FRACTION=` is the fraction (0-1) of unique reflections the mounting made unmeasurable under the measured point group, also written to the master as `/entry/MX/spindleLostUniqueFraction` and what the mounting warning fires on; `SPINDLE_SYMMETRY_AXIS_ANGLE_DEG=` / `SPINDLE_SYMMETRY_AXIS_ORDER=` describe the mounting in the `--developer` report. * Stills and grid scans carry a per-image `spindle_blind_fraction` - how much of a rotation sweep's blind cone this orientation would make unrecoverable, 0.5 and above calling for a second orientation - through the CBOR stream, HDF5 (`/entry/MX/spindleBlindFraction`), the plot and scan-result APIs, and the viewer and frontend plots; an absent value means the frame could not be assessed and is not a 0. * The results report's `REPORT_VERSION` is 7. Reviewed-on: #77 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-09 07:25:13 +02:00
leonarski_f	680c36c20d	v1.0.0-rc.166 (#76) ... * `rugnux --mode calibration` writes `<prefix>.json` beside the `.poni`, whose `dataset_settings` member is a `jfjoch_broker` `dataset_settings` body as it stands. * `rugnux` and `jfjoch_viewer` read PILATUS miniCBF sweeps natively, without conversion. * Masters written by other facilities open, including Eiger 1.x and third-party NXmx variants. * `rugnux` measures the beam centre on every run, and indexes with it when the file's value indexes nothing. * A detector swung out on a 2theta arm is placed where the file says it stands, and the calibration can hold the tilt fixed. * `rugnux` writes the unmerged MTZ by default, and a P1 merge beside it, so a wrong space group can be re-merged without reprocessing. * Significant improvements to symmetry handling in `rugnux`: the lattice, the point group, the setting and the systematic absences. * The `rugnux` report gives the resolution the CC1/2 fit reached, beside the range the reflections were written to. * The `rugnux` report gives the twinning statistics measured before the space group was decided, beside the ones measured after. * The `rugnux` report gives the strong-direction diffraction limit, and warns when CC1/2 is not monotone with resolution. * `rugnux` ranks screw axes on the evidence their absences carry, rather than on how many control reflections a candidate happens to have. * Twinning is no longer reported when the L-test contradicts it. * The `rugnux` report gives the detector tilt, the measured tilt and the direct beam beside the beam centre, and a post-refined beam centre is judged against the run's own measurement rather than the file's. * `--no-refine-tilt` holds the detector tilt at the value in the file, instead of zeroing it, when the calibration starts from the spots. * The `jfjoch_viewer` grid scan view draws the cells in the proportion of the scan steps, so the map has the shape of the scanned area. Reviewed-on: #76 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-09-02 21:17:31 +02:00
leonarski_f	511be0c366	v1.0.0-rc.165 (#75) ... * `rugnux --model` adopts the model's space group as a label where the data were merged in its enantiomorph, instead of reindexing the reflections - which swapped I(+) with I(-). * `rugnux --model` warns, naming the atom, when the anomalous density at the model's atoms comes out inverted, which means the data and the model are in opposite hands. * `rugnux --model` writes an anomalous difference map (`<prefix>_anom.ccp4`) when the merge kept the Bijvoet split, and names the ten model atoms it peaks highest on as `ANOMALOUS_SITE_01`..`_10`. * `MEAN_ATOM_DENSITY_SIGMA` is read from the map by cubic rather than linear interpolation and comes out around a tenth higher; it is no longer comparable with the figure earlier versions printed. * `rugnux --model` reads an mmCIF coordinate file as well as a PDB one, gzipped or not, taking the format from the file's content rather than its name. * A model `rugnux --model` cannot use is reported as a `WARNING:` line in the results report instead of only in the log. * The rugnux results report has a `10. MODEL VALIDATION` section when `--model` was given; `REPORT_VERSION` is 4, `WARNINGS` moves to section 11 and no existing key changed. * The rugnux results report records how the run was invoked, what it cost and what it ran on: `COMMAND_LINE=`, `WALL_TIME=` and `GPU_COUNT=` / `GPU=`. * rugnux says which GPUs it can see before it starts processing. * `rugnux --export-unmerged` also writes `<prefix>_unmerged.mtz` on a `--no-merge` run, and is ignored on a run with no output prefix instead of writing a file called `_unmerged.mtz`. * `/start` asks the writer whether the run can be written before the detector is armed, so a run whose master file already exists, or whose output directory cannot be created, is refused up front with the writer's own message. This needs the TCP image stream or the built-in HDF5 writer; the ZeroMQ stream is unchanged. * A calibration that fails goes to `Error` carrying the reason instead of `Inactive`, so `/wait_till_done` and `/wait_until_running` report it; a cancelled calibration still goes to `Inactive`. * `/wait_till_done` answers 500 with the message when a collection ended in an error. A cancelled collection and a collection that only triggered a warning still answer 200. * A pending start failure is discarded by `/cancel` and `/deactivate`, as it already was by `/start` and `/initialize`. * `/scan_result` no longer reports the previous run's images after a collection that failed to start, or after `/deactivate`. * The TCP image stream protocol version is 4. `jfjoch_writer` and `jfjoch_broker` have to be of the same release, as before. Reviewed-on: #75	2026-08-27 22:16:54 +02:00
leonarski_f	749db470ca	v1.0.0-rc.164 (#74) ... * rugnux now tells you whether a crystal diffracts anisotropically and how far it reaches in each direction, without a second program: a new `9. DIFFRACTION ANISOTROPY` section in `<prefix>_report.txt` and matching `_reflns.pdbx_aniso_B_tensor_*` / `_reflns.jfjoch_aniso_*` items in the merged mmCIF report the anisotropic deltaB, the diffraction limit along each principal direction, and a `NOT DETECTED` / `DETECTED` / `CANNOT DETERMINE` verdict measured against the data set's own systematic error. It is a description only - no intensity is corrected, no reflection is removed, and the merged data do not depend on direction. * rugnux can hand its integrated observations to another scaling program: `--export-unmerged` writes `<prefix>_unmerged.mtz`, an unmerged MTZ readable by aimless, pointless, careless and `iotbx.merging_statistics`, in `--mode mx` and `--mode scale` alike. Each rotation reflection's partials are summed into one full; `--export-unmerged-partials` writes one row per image instead. Intensities carry the Lorentz-polarization factor and nothing else, since those programs scale the data themselves. Lattice-centring absences are not written; screw and glide absences are. * rugnux integrates crystals with broad spots better - where it changes anything, per-shell mean I/sigma improves by up to 31% and R_meas by up to 24% - because on rotation data the integration signal radius is now taken from the crystal's own measured spot width instead of a fixed 4 px. `--adaptive-integration-radius=off` restores the fixed radius and an explicit `--integration-radius` still overrides both. The widened radius applies to the final integration pass only, and a pattern too dense for it is re-integrated at 4 px with a note in the log. * rugnux discards fewer stills reflections for want of a background ring, improving per-shell R_meas over most of the signal-bearing range: the stills background ring now runs to 14 px instead of 12. The gain reverses in shells below a mean I/sigma of about 4. * rugnux determines the space group with thresholds that mean the same thing on a weak crystal as on a strong one: symmetry operators are scored on resolution-normalised intensities (E squared) instead of raw merged intensities, and a reflection counts as genuinely present on its counting significance instead of on the merged I/sigma, which saturates at the merge's own ISa. The search resolution cut is no longer able to move the answer, and the twin-law H bound moves from 1.70 to 1.85, which stops one class of correct high-symmetry assignment being refused as twinning. * rugnux says what the space-group search tested and what it could not: the twin-law disagreement H is printed for every operator together with the adopted point group's H ratio and its bound; alternatives that are not on the reported lattice are named with how their cell differs; and a lattice centring the data could not test - the crystal having been integrated on the primitive sub-cell, so the reflections it extinguishes were never measured - is marked `UNTESTED` and warned about where it is adopted, as coming from the lattice metric rather than from the intensities. * rugnux `--mode scale` re-merges a `_process.h5` in the right symmetry without being told it: the file now records the space group on every run - a two-pass rotation run wrote none before, so re-merging defaulted to P1 - together with the change of basis under `/entry/MX/reindexMatrix` where the lattice was re-seated, and `--mode scale` also reports the Wilson B-factor estimate instead of `WILSON_B= nan`. A file written before this stops with a message naming the two cells and the override to use, instead of failing inside the merge. A third-party reader of a `_process.h5` must apply `reindexMatrix` where it is present. * rugnux installs on its own, as a package called `rugnux` - `dnf install rugnux` or `apt install rugnux` - instead of arriving inside `jfjoch-viewer`. It pulls in none of the acquisition stack, so a machine that only processes data no longer has to carry the broker, the detector libraries or Qt to get it. Installing it over a `jfjoch-viewer` from rc.163 or earlier, which still owns `/usr/bin/rugnux`, upgrades cleanly rather than failing on the duplicate file. * rugnux is also a standalone download, built for arm64 as well as x86_64: `rugnux-<version>-linux-{x86_64|aarch64}-cuda<major>.tgz` and `rugnux-<version>-win64-cuda<major>.zip` on the release page, for machines that are not managed by a package manager. The aarch64 build targets GH200 and DGX Spark, and is untested on hardware. * Every portable Linux binary is now a single self-contained file: cuFFT is linked statically instead of being shipped beside the executable and found through an rpath, so `rugnux` and `jfjoch_viewer` need nothing but an NVIDIA driver, and only to use the GPU. The `.rpm`/`.deb` continue to take cuFFT from the distribution. The developer utilities `jfjoch_extract_hkl` and `jfjoch_recompress` are no longer packaged anywhere. * Jungfraujoch needs six fewer shared libraries on the machine - libopenblas and libmetis, and libgfortran, libquadmath, libgomp and libz behind them - because the Ceres LAPACK, METIS and SuiteSparse back-ends are no longer built. Nothing in the code ever selected them, and results are unchanged. * The PCIe driver DKMS package builds for the kernel it is being installed for instead of the running one, so a module built while a kernel update is being applied loads after the reboot. * The PCIe driver builds on RHEL 9.5 and later, and on their CentOS Stream, Rocky and AlmaLinux equivalents, where the `vm_flags` kernel interface was backported into the 5.14 kernel. * A data collection started with `async_start` that fails to start - a writer refusing to overwrite an existing file, for instance - is reported as an error by `/wait_until_running` and `/wait_till_done` instead of as a timeout and a successful collection respectively. The error message is the one the writer gave. * A calibration that is cancelled or that fails to collect its pedestals is no longer reported as a successful one. The broker goes to `Inactive` with an error message and has to be initialized again, instead of sitting in `Idle` looking ready to measure while holding partial pedestals - data collected in that state was silently mis-converted. * A failed `/initialize` is reported to `/wait_until_running` and `/wait_till_done` as soon as it happens, instead of when their timeout expires. * `space_group_number` accepts space groups up to 230 in the API schema, so cubic space groups can be recorded. The broker always accepted them; the generated clients rejected them before the request was sent. * The results report's `REPORT_VERSION` is 3, two sections having been added. Existing key names and table columns are unchanged. * The merged statistics table has **9** resolution shells instead of 10, which is what XDS reports. The bins were already XDS's - equal steps in 1/d^2 between the lowest- and the highest-resolution reflection the merge kept - so at the same resolution limits the two tables now have the same shell boundaries and can be read row for row. `--resolution-shells` sets a different count. * `rugnux --model` now settles the frame the merged reflections are written in, not only the frame the R-factors and the maps are computed in: the `.mtz`/`.cif`/`.hkl` come out in the model's indexing, and where the data were merged in the model's enantiomorph they take the model's hand and space group - which on anomalous data puts I(+) and I(-) the right way round. The indexing choice is logged with the winning R-free and the runner-up, so a decision made within noise is visible. * `rugnux --model` can resolve the indexing ambiguity of a **serial stills** run, which a model could not do before: structure factors computed from the model become the per-image reference, the same role a reference MTZ plays. It needs the cell and space group up front (`-C` / `-S`). Without one or the other, a merohedral serial run still merges both hands together and says so. * The rugnux documentation opens with a quick start - the default run, and runs with a reference MTZ, with a model, or with the space group and cell pinned - and explains the indexing ambiguity: what it costs on rotation and on serial data, and which of `-z` / `--model` resolves it in each case. The long reference pages now carry a table of contents. Reviewed-on: #74 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-26 22:47:00 +02:00
leonarski_f	61c603b274	v1.0.0-rc.163 (#73) ... * Packaging: each package installs its license notices under a directory of its own - `share/doc/jfjoch_broker`, `share/doc/jfjoch_writer`, `share/doc/jfjoch_viewer`, `share/doc/jfjoch_driver_dkms` - instead of all of them into the shared `share/doc/jfjoch`, so `jfjoch` and `jfjoch-writer` can be upgraded one at a time instead of only together. Reviewed-on: #73 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 13:38:29 +02:00
leonarski_fandjungfrau	4dc2534dbf	v1.0.0.rc-162 (#72) ... **Files written by Jungfraujoch now import correctly in DIALS, XDS and pyFAI.** A tilted detector, a grid scan, a still recorded at a goniometer position, and saturated or unreadable pixels were each described in a way that a third-party program acted on wrongly. If you process Jungfraujoch data outside Jungfraujoch, prefer this release to any earlier one. * HDF5: the detector tilt (`rot1`/`rot2`/`rot3`) is exported correctly in the NXmx transformation chain; untilted geometries are unaffected. * HDF5: a still recorded at a goniometer position is no longer read back as a single image, and a grid scan records a stationary spindle so a program that requires a rotation axis can open it. * HDF5: the sample transformation chain is written in mounting order, with a Smargon head position told apart from the spindle, one entry per image, `module_offset` as a float unit vector, and `offset_units` on every offset. * HDF5: saturated, underloaded and unreadable pixels are described so a downstream program masks them - `saturation_value`, `underload_value`, `error_value` and `bit_depth_readout` are written correctly, and a data file missing next to a VDS master reads as the error marker rather than as zero counts. * HDF5: the rotation axis is read back under whatever name it carries, and `mirror_y` records whether the assembled image is mirrored in Y relative to the detector's raw readout. * A grid scan and a goniometer axis can both be set; they are no longer alternatives. * `images_per_file` is chosen from the acquisition when it is not given: a rotation sweep of at most 20000 images goes into a single data file, a grid scan splits on whole fast-axis rows, and stills and serial keep 1000. * The writer refuses a stream whose start message declares a different pixel format than its images carry, and a DECTRIS detector sending signed images is no longer declared unsigned. * The image stream can carry the sample transformation chain (`transformations`, in the END message); a producer that does not send it gets the same chain built by the writer. * rugnux: fixing the space group with `-S` no longer prevents the lattice from being found - a lattice indexed in a different setting is reindexed into that group's own setting, and a run whose crystal does not have that group's lattice stops and names the cell it indexed as, rather than reporting statistics that cannot describe it. * rugnux: the per-image resolution estimate now predicts the resolution the merged data reach rather than the highest-resolution spot found, and is reported as `SPOT_RESOLUTION_ESTIMATE`. * rugnux: two runs of the same command on the same images produce the same merged intensities; the azimuthal profile written alongside them is not yet reproducible in the same way. * rugnux: the offline lattice refinement is bounded by iterations rather than by a wall clock, so a loaded machine can no longer refine to a different lattice; a live acquisition keeps its real-time bound. * rugnux: the detector-frame modulation correction is fitted on a grid spanning the detector, so whether it is applied no longer depends on how far integration reached. * rugnux: the geometry pre-pass no longer writes `<prefix>_01.mtz`, `_01.cif`, `_01.hkl` and `_01_image.dat`; the refined second pass writes those files under `<prefix>`, and that is the result to use. * rugnux: `_process.h5` describes the pixel format of the images it links to, and is written on a thread of its own. * rugnux: the detector geometry is also logged in XDS's convention (`ORGX`/`ORGY`, detector axis vectors, rotation axis), so it can be compared with an XDS refinement. * rugnux: an image integrated in pyFAI through the `.poni` file written by `--mode calibration` comes out with the correct azimuth, and the file declares pyFAI's `orientation`, which needs pyFAI 2024.01 or newer. Radial integration is unchanged. * rugnux: a rotation run is substantially faster throughout - beam-stop detection, first-pass indexing, geometry refinement, integration, scaling and merging - and observations outside the scaling resolution range are dropped as they are ingested. The refined geometry, the space group chosen and the merged statistics are unchanged. * Faster spot finding and indexing, on the broker as well as in rugnux; the spots found and the lattices indexed are unchanged. * A run reserves substantially less GPU memory: nothing is allocated for buffers that are never read, and a worker builds only the engines it uses. * rugnux: with `-N` left at its default the per-image loop of `--mode mx` uses at most 16 workers per GPU, rather than one per hardware thread; an explicit `-N` is obeyed as given. * CUDA 12 builds now contain device code for Volta, so the RHEL 8 packages and the portable Linux `.tgz` run on a V100; the CUDA 13 artefacts (RHEL 9, Ubuntu, Windows) remain Turing and newer. * The build resolves a single Eigen for the whole project, and refuses to configure if Ceres picks up a different one; a build that mixed two Eigen versions was undefined behaviour and crashed at -O2. * Documentation: a security page, and the supported GPU generations and minimum NVIDIA driver version of every released artefact. **Breaking change to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.162, `frontend/src/client`): * `dataset_settings.images_per_file` is no longer `default: 1000` and no longer accepts `0`; it is optional, and its minimum is 1. A client sending `0` (previously "one file for the whole run") is now rejected - omit the field instead, which for a rotation sweep gives the same single file. * `file_writer_format` now defaults to `NXmxVDS`, matching the server's own default and the layout recommended for DIALS, XDS and CrystFEL. A generated client that fills in schema defaults and does not set the format explicitly will write VDS masters where it previously wrote legacy ones; set `NXmxLegacy` explicitly to keep them. --------- Co-authored-by: jungfrau <jungfrau@mx-aare-test.psi.ch> Reviewed-on: #72 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-25 08:21:39 +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