CrystFEL

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Documentation

Changes

CrystFEL version 0.11.1, 8 October 2024

Full release notes and accompanying screencast.

Introduction of Julia bindings for libcrystfel
General cleanup of libcrystfel API
Improvements to CI/CD setup (Parthasarathy Tirumalai)
GUI: Improve "jump to frame" feature
GUI: Improve Slurm progress bar for indexing
GUI: Add exclusive option for Slurm jobs
Catch NaNs in GGPM model [Gitlab #109]
GUI: Use SVG icons
indexamajig: Fix memory leak due to missing H5Sclose calls
indexamajig: Fix bug with --peaks=hdf5 --no-revalidate
indexamajig: Fix distorted cell distributions with xgandalf [GitLab #95]
indexamajig: Fix rare left-handed cells
indexamajig: Add ASAP::O acknowledgements
indexamajig: Fix buffer overrun with long temporary folder names (Philipp Middendorf)
indexamajig: Fix "-i -" (stdin) [GitHub #12]
indexamajig: Avoid writing empty Mille records [GitHub #9]
indexamajig: Defer writing Mille data until crystal is accepted [GitLab #99]
indexamajig: Avoid writing Mille records with incomplete local gradients
align_detector: Fix crash when 'pede' is not easily found [GitHub #8]
align_detector: Fix several problems with geometry file output [GitHub #11 & others]
align_detector: Add --out-of-plane-tilts and --camera-length
GUI: Copy geometry file for detector refinement [Gitlab #101]
GUI: Fix unclosed bracket in script file [Gitlab #106]
Allow basic geometry refinement without hierarchy [Gitlab #96]
Allow detector panel groups to appear at top of geometry file
Improve documentation about geometry hierarchy and refinement [GitHub #10]
Fix out-of-date documentation about geometry refinement [Gitlab #97]
Fix minor bug in unmerged sig(I) calculation at low photon counts
process_hkl: Fix ancient bug with --even-only multi-crystal indexing
partialator: Add filename/frame ID to --unmerged-output

CrystFEL version 0.11.0, 17 April 2024

Full release notes for version 0.11.0.

New detector geometry refinement system, using Millepede-II
New Homebrew formula and better build/test support for Mac OS (Parthasarathy Tirumalai)
Removal of CMake build system
Removal of pattern_sim and partial_sim
get_hkl: Read MTZ files
GUI: Add configuration of Slurm reservation and QoS
GUI: Put Slurm parameters into script, for easy re-use
partialator: Add --unmerged-output
compare_hkl: Accept --fom=cchalf as synonym for --fom=cc (and others)
Complain more loudly if mask information in geometry file is incomplete
indexamajig: Add --cpu-pin
indexamajig/list_events: Catch common error "-i input.h5"
indexamajig: Add ASAP::O producer (hits-only stream)

CrystFEL version 0.10.2, 20 February 2023

Full release notes for version 0.10.2.

New tutorial added (doc/articles/tutorial.rst)
New documentation on point group choice (doc/articles/pointgroup.rst)
Add Dockerfile and container CI setup (Silvan Schön)
Added scripts/install-indexers
indexamajig: Add --peakfinder8-fast (Alexandra Tolstikova)
indexamajig: Add --asdf-fast (Alexandra Tolstikova)
indexamajig: fixed --wait-for-file (#65)
indexamajig: Add --cell-parameters-only
indexamajig: Don't require camera length estimate if static value is given
indexamajig: re-implement and improve --profile
indexamajig: Return value 5 if no files could be processed
indexamajig: Fix harvest file JSON syntax (#68)
indexamajig: Put MsgPack peaks through validation procedure
indexamajig: Fix ZMQ request-reply sequence
indexamajig: Refuse to overwrite a stream
indexamajig: Avoid trouble with negative peaks in prediction refinement
indexamajig: Add ASAP::O and Seedee interfaces
indexamajig: Improve shutdown at end of data
partialator: Use default event ID when none given in --custom-split
partial_sim and pattern_sim: Fixed parameter handling (#78)
Dropped support for pre-2015 stream formats
asdf: Fix an integer overflow with the number of triplets
Recognise '.nx5' as HDF5
Set upper limit on number of peaks found by "zaef"
Improve handling of bad CBF files
Fixed peak coordinates when loading a stream (#66)
GUI: Add colour scale widget
GUI: Overhaul figure of merit calculation
GUI: Add menu items for detector-shift and peakogram
GUI: Add custom icons for tasks
GUI: Optionally show resolution rings
GUI: Use sbatch/scancel/scontrol instead of SLURM API
GUI: Honour fixed profile radius for single frame indexing (#61)
GUI: Better handling of error-filled indexamajig logs
GUI: Fix stream re-scan logic (#64)
GUI: Fix scrolling on Wayland
GUI: Add 'desktop' file (fixes window icons on Wayland)
GUI: Correct a mis-labelled field (Jerome Kieffer)
Build system: Allow building without HDF5
Build system: Disable OpenCL by default

CrystFEL version 0.10.1, 14 January 2022

Full release notes for version 0.10.1.

GUI: Proper overlines for reflection indices
GUI: Allow import of multiple streams at once
GUI: Fix for image panning after change of beam centre
GUI: Fix for pixel value display at high zoom with "slanty" pixels
GUI: Addition of checkbox "Rescan streams wihen changing frame"
GUI: Crystal and project names will be added to MTZ
GUI: Copy environment from parent process for SLURM jobs
GUI: Addition of SLURM time limit field
Build system: Auto-compilation of dependencies when using Meson
Build system: Fix detection of OpenCL and SLURM
Overhaul Doxygen API docs
Geometry files: Wavelength (or photon energy etc) must be specified
Geometry files: Experiment-space directions of fs/ss vectors must be specified
Geometry files: Removal of rail direction
Geometry files: Addition of mask_edge_pixels
indexamajig: Switch from pixel distance to fraction of cell axis, when pairing peaks
indexamajig: Add --data-format, implement HDF5s from online data source
indexamajig: Shut down cleanly on SIGUSR1 (useful for online data)
indexamajig: Generate per-frame profiling data
MTZ export: Split into "plain" and "Bijvoet" modes of operation
XDS export: Bug fix (missing 'S'!)
compare_hkl: Bug fix for FoM reflection pair selection
partialator: Handle spaces in custom split file
partialator: Gracefully handle zero crystals in split dataset

CrystFEL version 0.10.0, 12th August 2021

Full release notes for version 0.10.0.

New GUI ('crystfel') added, replacing 'hdfsee' which has been removed
Added ZeroMQ interface for streaming data processing
Added Meson build system
get_hkl can now write XDS and MTZ directly
Removed geoptimiser
Removed wide-bandwidth features
Added 'parameter harvest files' to indexamajig and partialator
Better handling of static masks with multi-event files
Added 'FromFile' indexing
Added scripts/display-hdf5 and scripts/make-csplit
New DataTemplate API
New Stream API, allowing random access and better recreation of processing
Bug fix for asdf indexing, vastly increasing speed and success rate
Big speed improvement for TakeTwo
Speed improvement for detector pixel coordinate transformation
Speed improvement for UnitCell
Speed improvement for creation of bad pixel maps from bad regions
Fixed a large memory leak in cell_tool
Fix large number of "rejected" reflections
Support for units in geometry file distances (eg 'clen = 43 mm')
Support for wavelength and electron accelerating voltage in geometry file
Added detector_shift_x/y to geometry file
Added peak_list_type to geometry file
Added flag_{lessthan,morethan,equal} to geometry file
Added peak_list to geometry file (no more --hdf5-peaks)
Added requirement for fs/ss bad regions to name a panel
indexamajig: Added --no-image-data and --no-mask-data
partialator, process_hkl: Handle multiple input streams
partialator: Reject crystals with large profile radii
indexamajig: Added --wavelength-estimate and --camera-length-estimate
indexamajig: Added --max-indexer-threads
Figure of merit calculations moved to libcrystfel
Removed badrow culling
compare_hkl: Removed --intensity-shells

CrystFEL version 0.9.1, 25th June 2020

Full release notes for version 0.9.1.

indexamajig: Fixed default unit cell tolerance (was 1.5 rad, now 1.5 deg)
Improved the sigma estimate for very weak reflections
Fixed bug in unit cell reduction/comparison
Fixed bug when indexing with rhombohedral R cells
indexamajig: Added --pinkIndexer-max-refinement-disbalance
Fixed two problems when reading metadata values from HDF5
partialator: Gracefully handle negative and NaN sigma values
scripts/transfer-geom: Now only writes coffset for panels which had coffset values before
Fixed/improved pinkIndexer documentation and error messages
Fixed build with zlib < 1.2.3.5 (missing gzbuffer routine)
Fixed build with HDF5 >= 1.12
scripts/mtz2hkl, cif2hkl, hkl2hkl: Added missing header

CrystFEL version 0.9.0, 6th February 2020

Full release notes for version 0.9.0.

Introduction of cell_tool
Addition of PinkIndexer interface
Handle CBF files natively, not via CBFlib
Add Spectrum API
New symmetry operation/cell transformation parser
New unit cell comparison algorithm based on Niggli reduction
New prediction calculation which works for electrons and wide bandwidth
indexamajig: Removed --no-cell-combinations
indexamajig: Improvements to indexing result check ("--check-peaks"),
improving results with multi-lattice indexing
indexamajig: Add --zmq-msgpack
indexamajig: Allow individual tolerances for all six parameters
indexamajig: Return non-zero exit status if no patterns were processed
indexamajig: Rename --min-gradient to --min-squared-gradient
indexamajig: Status message updates
indexamajig: Bandwidth now specified in geometry file (not --fix-bandwidth)
indexamajig: Individual tolerances for each cell parameter
indexamajig: Remove 'rescut' integration flag
cell_explorer: Allow enforcement of Bravais lattice type
ambigator: Use pre-defined resolution bins if limits not given
geoptimiser: Use geometry from stream
partialator: Many stability improvements to post-refinement
partialator: Parallelise deltaCChalf calculation
partialator: Add --model=offset for monochromatic synchrotron data
partialator/process_hkl: Allow arbitrary polarisation direction and degree

CrystFEL version 0.8.0, 19th December 2018

Full release notes for version 0.8.0.

Add support for peakfinder9 (Yaroslav Gevorkov)
Add support for XGANDALF indexer (Yaroslav Gevorkov)
Switch to CMake build system (Nicholas Riebesel)
partialator: Stabilisation of B factors by logarithmic merging (Ken Beyerlein)
Handle 16bpp and gzipped CBF files
Introduce make_pixelmap as a core CrystFEL program
indexamajig: Add --wait-for-file
indexamajig: Clean up temporary folders on clean exit
indexamajig: Name and shame slow processing stages
indexamajig: Warn if a frame takes more than 10 minutes to process
Multiple fixes for XDS indexer interface
Fix for indexing centered cells with Mosflm without prior cell parameters
partialator: Fixes and improvements to post-refinement
partialator: Add deltaCChalf rejection test
Add scripts: euxfel-train-analysis, find-multiples and transfer-geom
detector-shift: Click to choose different center
check_{peak_detection,near_bragg}: Warn if stream is older than image
Some fixes for peakfinder8
turbo-index-lsf: Match turbo-index-slurm as closely as possible
sum-peaks: Accept "-" for stdin
geoptimiser: Fix calculation of displacement error
check_hkl: Avoid NaN result for L-test with --zero-negs
compare_hkl: Fix an edge case in calculation of anomalous figures of merit
Handle numbers (e.g. "k-2h") in symmetry operator specifications (e.g. ambigator)
Use GTK3 if available

CrystFEL version 0.7.0, 17th May 2018

Full release notes for version 0.7.0.

indexamajig: Auto-detection of indexing methods
indexamajig: New options system - removes confusing "comb","bad","retry" etc.
Most programs now use the symmetry in the reflection files, allowing "-y" options to be omitted.
Ginn partiality model was added.
partialator: Switch to gradient-free minimiser.
geoptimiser: Fixes for rotation and new features for AGIPD.
Speed and accuracy improvements for TakeTwo indexing (Helen Ginn).
process_hkl, partialator and ambigator now include the audit information from the stream in their output files.
pattern_sim: Write orientation and lattice basis vectors into HDF5 file.
hdfsee: Add event ID and peaks/preds/rings to exported image filenames.
indexamajig --serial-start was added (useful when using turbo-index).
indexamajig --overpredict was added (needed for post-refinement)
pattern_sim --flat was added (new reflection profile option)
cell_explorer: Now shows the number of matching cells on terminal.
Felix options were simplified.
scripts/sum-hdf5-files and eiger-badmap were added

CrystFEL version 0.6.3, 24th July 2017

Full release notes for version 0.6.3.

indexamajig --peaks=peakfinder8 was added (Valerio Mariani, Oleksandr Yefanov).
CBF files are now supported as input.
TakeTwo indexing was incorporated (Helen Ginn)
indexamajig: Hung worker processes will now be detected and killed.
Peak locations from HDF5 or CXI files are now offset by 0.5,0.5 (needed for peaks from Cheetah and previously neglected).
Detector panels no longer need to be perpendicular to the X-ray beam.
Detector "rail" direction ("camera length" axis) no longer needs to be along the X-ray beam direction.
Lattice parameters are now checked after prediction refinement as well as before.
Multi-event HDF5 files can now contain peak lists.
The peak list location can now be given in geometry file (instead of --hdf5-peaks)
The number of detector units per photon (rather than per eV) can now be specified in the geometry file.
indexamajig: Small changes to how peaks from HDF5 files are checked.
compare_hkl --fom=d1sig and d2sig were fixed (Wolfgang Brehm).
compare_hkl --min-measurements was added.
New polarisation correction.
Reflection data files now contain audit information (CrystFEL version number and command line parameters).
Improvements to enumeration of events in multi-event files
scripts/detector-shift: Show a heat map, handle different panel resolutions correctly
Add scripts/move-entire-detector, scripts/split-by-mask, scripts/peakogram-stream and scripts/sum-peaks.
scripts/turbo-index was renamed to turbo-index-lsf, and turbo-index-slurm was added (Steve Aplin).
An example geometry file for Eiger was added.
Multiple bug fixes for asdf indexing
cell_explorer: Fixed invisible Greek letters on some systems
Mask paths with fewer placeholders than data paths (e.g. some SACLA files) are now handled properly.
cell_explorer: Added "Save cell" function.
pattern_sim: Multiple bug fixes.
geoptimiser: Multiple bug fixes.
partialator: Fixes for some edge case bugs.
indexamajig: Fix files left open when using XDS indexing.
{check,compare}_hkl: Add warnings for potentially silly option choices.
Remove "data slab" from detector data handling (simplifies internal data structures a lot).
Python scripts were made compatible with Python 3.

CrystFEL version 0.6.2, 21st March 2016

Full release notes for version 0.6.2.

partialator: Stability improvements to scaling algorithm, default --push-res value changed from zero to infinity (no resolution cutoff by default).
partialator: Added --custom-split, --max-rel-B and --output-every-cycle
Added "retry" indexing method to improve indexing rate.
Per-pixel saturation values can now be used (needed for CSPAD dual-gain mode).
Fixed a regression with indexing using MOSFLM introduced near 0.6.1.
indexamajig: Fixed a bug which occasionally caused corrupted stream output ("Failed while reading reflections").
indexamajig: gradient fitting of background now optional and OFF by default.
indexamajig: Added --profile for speed monitoring.
indexamajig: Added "felix" indexing method.
scripts/ave-resolution: Show resolution histogram.
scripts/turbo-index: Added a missing line
hdfsee: Improve quality of display by rounding pixel coordinates.
hdfsee: Can now safely save new geometry file over old one.
Target unit cell is now written to the stream.
pattern_sim: Fixed bugs in --gpu and --powder.
compare_hkl: Avoid double counting of reflections when calculating anomalous figures of merit.
geoptimiser: Major refactoring
ambigator: fixes for a few problem when using very large numbers of correlation coefficients or patterns.
Some crashes and hangs in asdf were fixed.
The "random" partiality model was improved.

CrystFEL version 0.6.1, 3rd August 2015

Full release notes for version 0.6.1.

partialator: big improvements, now works well on most data sets.
indexamajig: prediction refinement added.
"mosflm" indexing method now uses prior cell information when used with mosflm version 7.2.0 or later.
"asdf" indexing method added, which needs no external program.
process_hkl --even-only and --odd-only were added.
External bad pixel masks can now be used (see "mask_file" in geometry file).
indexamajig: Can now use --int-diag with -j n where n>1
Image data filters (e.g. --noise-filter) were fixed.
indexamajig sandbox was redesigned and made more robust.
compare_hkl now uses a B-factor for scaling the datasets.
pattern_sim: spectrum normalisation added.
scripts/ave-resolution and scripts/create-frame-number added.
scripts/plot-predict-refine and scripts/plot-radius-resolution added.
scripts/detector-shift added.
scripts/turbo-index added.
"reax" and "grainspotter" indexing methods removed.
Many other small but important bug fixes and improvements to data quality.

CrystFEL version 0.6.0, 23rd February 2015

Full release notes for version 0.6.0.

The geometry specification was extended to allow multiple events per HDF5 file as well as different panels in different HDF5 locations.
geoptimiser, list_events and whirligig were added.
CrystFEL unit cell files were introduced.
Beam parameter files are no longer used.
indexamajig auto-determination of prediction parameters was added.
indexamajig --fix-profile-radius, --fix-bandwidth and --fix-divergence were added.
pattern_sim --beam-bandwidth, --photon-energy and --nphotons were added.
partial_sim --beam-bandwidth, --photon-energy, --beam-divergence and --profile-radius were added.
Event serial numbers are now written in streams.
indexamajig -e/--image was removed.
process_hkl --stat and --min-cc were added.
render_hkl --highres and --no-axes were added.
partialator --max-adu was added.
2D profile fitting (--integration=prof2d) was fixed.
CSPAD geometry file examples were improved.
compare_hkl --fom=d1sig and d2sig were added.
pattern_sim now simulates detector saturation.
Compression was switched off when saving HDF5 files.
The units conversion for the resolution limit written into the stream was fixed.
The pre-merging Poission error calculation was improved.
A bug in pattern_sim's handling of symmetry was fixed.
{check,compare}_hkl now report the min/max bin ranges.

CrystFEL version 0.5.4a, 11th September 2014

A bug in pattern_sim's handling of symmetry was fixed.
The documentation for indexamajig --tolerance was updated.

CrystFEL version 0.5.4, 5th September 2014

hdfsee calibration mode, ADSC export and scrollbars were added.
Bad regions can now be specified as fs/ss as well as x/y.
"--version" options were added to everything.
partial_sim --background was added.
partialator --reference, --geometry and --beam were removed.
ambigator --corr-matrix was added.
indexamajig --peak-radius and --highres were added.
Handling of bad pixels and overlapping reflections was improved.
ambigator now updates the lattice basis vectors as well as the indices.
pattern_sim can now simulate all point groups on the GPU.
Unit cell output on the command line now uses Angstroms instead of nm.
Beam/crystal properties and mean camera length were added to the stream.
scripts/gen-sfs-expand was added.
Stream reading/writing API was changed and improved.
libcrystfel was made compatible with C++.
get_symop(), get_matrix_name() mark_resolution_range_as_bad() were added.
Prototypes changed for find_panel_number(), *_prepare() (all indexing methods), find_intersections(), image_feature_closest(),
{get,set}_{refineable,scalable}() were removed.
integrate_peak() was removed from the exposed API.

CrystFEL version 0.5.3a, 14th April 2014

A small but critical bug in ambigator, which prevented it from working, was fixed.
The definition of Rano in the manual was corrected.

CrystFEL version 0.5.3, 9th April 2014

ambigator and cell_explorer were added.
get_hkl -w was fixed, and the option --no-need-all-parts added.
pattern_sim was overhauled: the ability to simulate a finite bandwidth was restored, and a SASE or two-colour spectrum can now be simulated.
All programs which use a random number generator now use a proper random number generator instead of random().
partial_sim --really-random and --images were added.
pattern_sim --template and --no-fringes were added.
check_hkl --ltest and --wilson were added.
process_hkl --max-adu and --min-res were added.
compare/check_hkl --lowres and- -highres were added.
The "rescut" integration flag was added.
The stream format was changed to include peak heights and mean backgrounds.
scripts/fg-graph and truncate-stream were added.
record_image(), random_quaternion(), random_flat(), flat_noise(), gaussian_noise() and poisson_noise() now take an additional gsl_rng argument.
validate_peaks() now takes an additional check_snr argument.

CrystFEL version 0.5.2, 6th December 2013

Reflection sigmas were improved for negative intensities, and the behaviour of "process_hkl --min-snr" was rationalised.
Peak centering ("--integration=rings-cen") was fixed.
XDS default behaviour was fixed to prevent an unexpected axis permutation.
Incorrect handling of monoclinic C cells was fixed.
The counting of saturated peaks was fixed.
hdfsee now needs the beam file (use option -m).
A more than 2 year old bug was fixed in RefList.
indexamajig --int-diag was added.
render_hkl --res-ring was added.
compare_hkl --fom=Rano and Rano/Rsplit was added.
check_hkl --shell-file was added.
get_hkl --cutoff-angstroms was added.
partialator was extensively worked on.
scripts/split-indexed was added.
scripts/Rsplit_surface and clean-stream.py were added (Fedor Chervinskii).
A locale-related problem with hdfsee was fixed.
Histogram, update_partialities_2(), hdfile_is_scalar() and show_matrix() were added to the libcrystfel API.
integrate_all() was changed to incorporate IntDiag.
show_matrix_eqn() was simplified, removing a parameter.

CrystFEL version 0.5.1, 4th July 2013

New integration framework in indexamajig - see "--integration" option.
The "Lorentz factor" was added to partial_sim (and partialator).
CCano was added as a figure of merit to compare_hkl.
Anomalous correlation ratio (CRDano) was added as a figure of merit to compare_hkl (Lorenzo Galli).
XDS indexing was improved.
The calculation of sigma(I) in process_hkl was made more numerically stable.
The polarisation correction in process_hkl was fixed.
The display of feature names (i.e. Miller indices) in hdfsee was fixed.
partialator was extensively worked on.
A compilation failure (when FFTW3 was unavailable) was fixed.
docs/stream-format.txt was added.
scripts/create-xscale was fixed (sigma(I) values were wrong).
Warnings were added to scripts which MUST be modified before use.
polarisation_correction() was added to the API.

CrystFEL version 0.5.0, 19th April 2013

Full release notes for version 0.5.0.

The internal architecture has been changed to accommodate multiple crystals per diffraction pattern.
The stream format has changed as a result of the above.
The indexing logic has reworked to make it easier to control what information is used for indexing and to allow the user to try more indexing options in turn.
Saturated peaks and integrated reflections are now counted and the number included in the stream.
GrainSpotter indexing has been added.
XDS indexing has been added (Cornelius Gati).
The "--nshells" argument was added to check_hkl.
The "--median-filter" argument was added to indexamajig and hdfsee.
The "--filter-cm" argument was removed from indexamajig and hdfsee.
check-near-bragg and check-peak-detection can now be given extra command-line options which will be passed through to hdfsee.
An error in the solid angle calculation was fixed, affecting simulation with pattern_sim (Chun Hong Yoon).
Lattice type, centering and unique axis information is now included in the stream.

CrystFEL version 0.4.3, 10th January 2013

compare_hkl was reworked to simplify the available figures of merit, add CC*, and to be consistent between the overall and resolution shell values. A new option, --intensity-shells, was also added.
Unit cells can now be handled in any setting.
Indexamajig will now examine the unit cell given on the command line, even if the final cell will not be checked (i.e. if --cell-reduction=none). The lattice type will then be given to MOSFLM, which can help a lot in finding the right solution.
Indexamajig now records the number of saturated reflections in the stream.
Indexamajig now processes the peaks obtained using "--peaks=hdf5" to check for bad detector regions, peaks too close to panel edges, etc.
New options "--integrate-saturated", "--use-saturated" and "--integrate found" were added to indexamajig.
A bug was fixed which caused systematically absent (due to centering) reflections to be predicted and integrated.
The colour scaling in hdfsee was improved.
powder_plot was moved to the extra programs repository.
The configure script now checks for HDF5.
Forbidden (due to centering) reflections are now taken into account by check_hkl when calculating the completeness.
The speed of pattern processing was increased significantly (in many cases) by avoiding an unnecessary iteration.
A crystfel.pc file was added, allowing use of "pkg-config --cflags crystfel" and so on.
The new option "--min-measurements" was added to process_hkl.
The wavelength can now be specified in the beam file as an HDF5 path or as an explicit number, just like the camera length. There is no longer any "fallback" to a nominal value (Chun Hong Yoon).

CrystFEL version 0.4.2, 2nd October 2012

A data quality regression, introduced between versions 0.3.0 and 0.4.0, was fixed.
A speed regression, introduced at the same time as the data quality regression, was also fixed (approximately a factor of 2 speed increase with indexamajig).
Centered unit cells are now handled correctly during unit cell reduction.
The same colour scale is now used for every panel by hdfsee.
"get_hkl -w" was fixed.
A spurious "-p" option was removed from scripts/gen-sfs-ano.
Option handling across all programs was fixed to prevent confusion.

CrystFEL version 0.4.1, 29th August 2012

Some compiler warnings with newer versions of GCC were fixed.
Bad pixels are now shown in brown by hdfsee.
Bad pixels are now ignored when calculating the range of the image for the colour scale in hdfsee.
A crash when there were too many unit cell candidates was fixed.
Small typos were fixed in a warning message and pattern_sim(1).
"indexamajig --image" was fixed.

CrystFEL version 0.4.0, 31st July 2012

Full release notes for version 0.4.0.

Performance increase when using indexamajig on multi-core hardware (Chun Hong Yoon).
"max_adu" field was added to geometry file format.
Added masking of inner ("peak") regions of all peaks during the background calculation (Kenneth Beyerlein).
Bandwidth and subsampling was restored to the GPU version of pattern_sim.
Spot prediction and associated partiality calculations were improved.
"profile_radius" field was added to beam file format.
"compare_hkl --shells" now uses separate denominators in each resolution bin for the R-factor calculation.
Removed fields "peak_sep" and "integr_radius" in geometry files.
Bug fix for process_hkl --histogram (Lorenzo Galli).
A bug was fixed in find_panel().
Improvements were made to the build system.
"indexamajig --min-integration-snr" was fixed.
Fixed "process_hkl --start-after" and "--stop-after".
"compare_hkl --sigma-cutoff" added.
Shell resolutions in Angstroms added to the shells files of check_hkl and compare_hkl.
Fixed small compilation problem with Cairo < 1.6.
The tolerances for the cell reduction procedure, "ltl" in match_cell(), is now "const float *ltl" instead of just "float *ltl".
The "peak_sep" field of "struct panel" was removed, and "max_adu" added.
"struct beam_parameters" now contains a new field: "profile_radius".
"write_detector_geometry()" was added to detector.h.
"hdf5_write_image()" was added to hdf5-file.h.

CrystFEL version 0.3.0, 14th March 2012

Initial release of CrystFEL.