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Changes in this development version
-----------------------------------
- New integration framework in indexamajig - see "--integration" option.
- partialator was extensively worked on.
- The "Lorentz factor" was added to partial_sim (and partialator).
- CCano was added as a figure of merit to compare_hkl.
- 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.
- A compilation failure (when FFTW3 was unavailable) was fixed.
- docs/stream-format.txt was added.
- scripts/create-xscale was fixed.
- 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
---------------------------------------
- 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.
- 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
--------------------------------------
- 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.
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