From d15ff8c0a987c5007df5cf16d131d2152821a268 Mon Sep 17 00:00:00 2001 From: DiamondLightSource-build-server Date: Wed, 17 Apr 2024 17:16:23 +0100 Subject: [PATCH] dxtbx 3.19.0 Changelog towncrier --name=dxtbx --version='3.19.0' --- CHANGELOG.rst | 39 +++++++++++++++++++++++++++++++++++++++ newsfragments/620.misc | 1 - newsfragments/659.feature | 1 - newsfragments/665.bugfix | 1 - newsfragments/667.misc | 1 - newsfragments/669.bugfix | 1 - newsfragments/670.misc | 1 - newsfragments/674.feature | 1 - newsfragments/676.bugfix | 6 ------ newsfragments/679.bugfix | 1 - newsfragments/682.feature | 1 - newsfragments/683.feature | 1 - newsfragments/687.feature | 1 - newsfragments/688.bugfix | 1 - newsfragments/689.misc | 1 - newsfragments/690.bugfix | 2 -- newsfragments/691.misc | 1 - newsfragments/694.misc | 1 - newsfragments/696.bugfix | 1 - newsfragments/697.bugfix | 1 - newsfragments/698.feature | 1 - newsfragments/699.bugfix | 1 - newsfragments/701.misc | 1 - newsfragments/703.feature | 1 - newsfragments/704.misc | 1 - newsfragments/707.misc | 1 - newsfragments/708.bugfix | 2 -- newsfragments/710.bugfix | 1 - newsfragments/711.bugfix | 1 - newsfragments/713.misc | 1 - newsfragments/714.bugfix | 1 - newsfragments/723.feature | 1 - 32 files changed, 39 insertions(+), 38 deletions(-) delete mode 100644 newsfragments/620.misc delete mode 100644 newsfragments/659.feature delete mode 100644 newsfragments/665.bugfix delete mode 100644 newsfragments/667.misc delete mode 100644 newsfragments/669.bugfix delete mode 100644 newsfragments/670.misc delete mode 100644 newsfragments/674.feature delete mode 100644 newsfragments/676.bugfix delete mode 100644 newsfragments/679.bugfix delete mode 100644 newsfragments/682.feature delete mode 100644 newsfragments/683.feature delete mode 100644 newsfragments/687.feature delete mode 100644 newsfragments/688.bugfix delete mode 100644 newsfragments/689.misc delete mode 100644 newsfragments/690.bugfix delete mode 100644 newsfragments/691.misc delete mode 100644 newsfragments/694.misc delete mode 100644 newsfragments/696.bugfix delete mode 100644 newsfragments/697.bugfix delete mode 100644 newsfragments/698.feature delete mode 100644 newsfragments/699.bugfix delete mode 100644 newsfragments/701.misc delete mode 100644 newsfragments/703.feature delete mode 100644 newsfragments/704.misc delete mode 100644 newsfragments/707.misc delete mode 100644 newsfragments/708.bugfix delete mode 100644 newsfragments/710.bugfix delete mode 100644 newsfragments/711.bugfix delete mode 100644 newsfragments/713.misc delete mode 100644 newsfragments/714.bugfix delete mode 100644 newsfragments/723.feature diff --git a/CHANGELOG.rst b/CHANGELOG.rst index cb89dc0a5..a3b734a5b 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -1,3 +1,42 @@ +dxtbx 3.19.0 (2024-04-17) +========================= + +Features +-------- + +- Add format reader for Jungfrau4M serial images from beamline ID29 at ESRF. (`#659 `_) +- Better handle spectra calibration for bad data in XTC format using new parameter: ``spectrum_required=``. (`#674 `_) +- Add Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector. (`#682 `_) +- ``FormatSMVTimePix_SU``: Always mask out the central cross of virtual pixels. (`#683 `_) +- Add format reader for ISIS SXD detector. (`#687 `_) +- Detector distance can now be manually overridden for multi-panel detectors. (`#698 `_) +- Add format reader to read time of flight Laue data from MANDI. (`#703 `_) +- Additional features for `FormatXTCRayonix` (`#723 `_) + + +Bugfixes +-------- + +- Importing the (deprecated and removed) ``dxtbx.datablock`` module failed to display warning properly. (`#665 `_) +- Fix scan comparison for scan properties changes (`#669 `_) +- Eiger Support: Invert the module dimensions, only for older firmware versions. See https://media.dectris.com/230203-Release_Notes-DECTRIS_EIGER2.pdf for reference. (`#676 `_) +- ``FormatMRC``: Better handling of extended headers. (https://github.com/ccpem/mrcfile/issues/50), and extended headers are ignored if they contain junk values. (`#679 `_) +- Fixed some properties not being correctly parsed in `Scan.from_dict`. (`#688 `_) +- Negative rotation angles are now allowed, the goniometer axis will be inverted if necessary. (`#690 `_) +- ``dials.import`` now uses natural sorting on input data, instead of strict sorting. (`#697 `_) +- Fix setting detector distance for single panel detectors that have a hierarchy. (`#699 `_) +- Better recognition for SMV images from MLFSOM and other simulators from James Holton. (`#708 `_) +- Fix error introduced in ``FormatSMVJHSim`` causing test failures. (`#710 `_) +- `PolychromaticBeam` can now be copied with `copy.deepcopy`. (`#711 `_) +- Add missing argument to `PolychromaticBeamPickleSuite.getinitargs`. (`#714 `_) + + +Misc +---- + +- `#620 `_, `#667 `_, `#670 `_, `#689 `_, `#691 `_, `#694 `_, `#696 `_, `#701 `_, `#704 `_, `#707 `_, `#713 `_ + + dxtbx 3.17.0 (2023-11-03) ========================= diff --git a/newsfragments/620.misc b/newsfragments/620.misc deleted file mode 100644 index ba905f660..000000000 --- a/newsfragments/620.misc +++ /dev/null @@ -1 +0,0 @@ -Add properties table to Scan diff --git a/newsfragments/659.feature b/newsfragments/659.feature deleted file mode 100644 index c374981ed..000000000 --- a/newsfragments/659.feature +++ /dev/null @@ -1 +0,0 @@ -Add format class to read Jungfrau4M serial images from beamline ID29 at ESRF diff --git a/newsfragments/665.bugfix b/newsfragments/665.bugfix deleted file mode 100644 index a0a44e441..000000000 --- a/newsfragments/665.bugfix +++ /dev/null @@ -1 +0,0 @@ -Importing the (deprecated and removed) ``dxtbx.datablock`` module failed to display warning properly. diff --git a/newsfragments/667.misc b/newsfragments/667.misc deleted file mode 100644 index c3baae2da..000000000 --- a/newsfragments/667.misc +++ /dev/null @@ -1 +0,0 @@ -Fix oscillation not being set correctly in ``Scan.set_image_range``. diff --git a/newsfragments/669.bugfix b/newsfragments/669.bugfix deleted file mode 100644 index 1e1d974b1..000000000 --- a/newsfragments/669.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix scan comparison for scan properties changes diff --git a/newsfragments/670.misc b/newsfragments/670.misc deleted file mode 100644 index d01880165..000000000 --- a/newsfragments/670.misc +++ /dev/null @@ -1 +0,0 @@ -Fix regression test after scan changes diff --git a/newsfragments/674.feature b/newsfragments/674.feature deleted file mode 100644 index 8eca3c80b..000000000 --- a/newsfragments/674.feature +++ /dev/null @@ -1 +0,0 @@ -Better handle spectra calibration for bad data in XTC format using new parameter: spectrum_required diff --git a/newsfragments/676.bugfix b/newsfragments/676.bugfix deleted file mode 100644 index 5ba08c119..000000000 --- a/newsfragments/676.bugfix +++ /dev/null @@ -1,6 +0,0 @@ -Eiger support: following bug fix in DECTRIS file writer, invert the module -dimensions only for older firmware versions. See - -https://media.dectris.com/230203-Release_Notes-DECTRIS_EIGER2.pdf - -for reference (Corrected data size orientation) diff --git a/newsfragments/679.bugfix b/newsfragments/679.bugfix deleted file mode 100644 index c5bf1354a..000000000 --- a/newsfragments/679.bugfix +++ /dev/null @@ -1 +0,0 @@ -``FormatMRC``: better handling of extended headers: padding is supported in mrcfile>=1.5.0 (https://github.com/ccpem/mrcfile/issues/50), and extended headers are ignored if they contain junk values. diff --git a/newsfragments/682.feature b/newsfragments/682.feature deleted file mode 100644 index b2f5f2af7..000000000 --- a/newsfragments/682.feature +++ /dev/null @@ -1 +0,0 @@ -Add Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector. diff --git a/newsfragments/683.feature b/newsfragments/683.feature deleted file mode 100644 index 207eb5eff..000000000 --- a/newsfragments/683.feature +++ /dev/null @@ -1 +0,0 @@ -``FormatSMVTimePix_SU``: Always mask out the central cross of virtual pixels that have been reconstructed from wide edge pixels. diff --git a/newsfragments/687.feature b/newsfragments/687.feature deleted file mode 100644 index d84a13b80..000000000 --- a/newsfragments/687.feature +++ /dev/null @@ -1 +0,0 @@ -Add format reader for ISIS SXD detector. diff --git a/newsfragments/688.bugfix b/newsfragments/688.bugfix deleted file mode 100644 index 96cdd168b..000000000 --- a/newsfragments/688.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fixed `Scan.from_dict` bug where some properties were not correctly parsed. diff --git a/newsfragments/689.misc b/newsfragments/689.misc deleted file mode 100644 index 0424133d9..000000000 --- a/newsfragments/689.misc +++ /dev/null @@ -1 +0,0 @@ -Add check to `Scan.is_still()` to treat Scans with time_of_flight as not stills. diff --git a/newsfragments/690.bugfix b/newsfragments/690.bugfix deleted file mode 100644 index cb3349977..000000000 --- a/newsfragments/690.bugfix +++ /dev/null @@ -1,2 +0,0 @@ -In DXTBX do not assert the rotation angles for images are positive, and invert -in import with an axis inversion if needed. diff --git a/newsfragments/691.misc b/newsfragments/691.misc deleted file mode 100644 index f7ea22bba..000000000 --- a/newsfragments/691.misc +++ /dev/null @@ -1 +0,0 @@ -Add `tof_helpers.py` for common time of flight functions. diff --git a/newsfragments/694.misc b/newsfragments/694.misc deleted file mode 100644 index fe969bda4..000000000 --- a/newsfragments/694.misc +++ /dev/null @@ -1 +0,0 @@ -NXmx: if reversed, reverse rotation axis. This is part 2 of previous commit. diff --git a/newsfragments/696.bugfix b/newsfragments/696.bugfix deleted file mode 100644 index 1d5fb5f30..000000000 --- a/newsfragments/696.bugfix +++ /dev/null @@ -1 +0,0 @@ -Increase tolerance for a test comparison to avoid spurious failures. diff --git a/newsfragments/697.bugfix b/newsfragments/697.bugfix deleted file mode 100644 index fe0c539f0..000000000 --- a/newsfragments/697.bugfix +++ /dev/null @@ -1 +0,0 @@ -For ``dials.import``: use natural sorting on input data in preference to strict sorting \ No newline at end of file diff --git a/newsfragments/698.feature b/newsfragments/698.feature deleted file mode 100644 index 34add9eac..000000000 --- a/newsfragments/698.feature +++ /dev/null @@ -1 +0,0 @@ -Manual override of the detector distance is now available for multi-panel detectors. diff --git a/newsfragments/699.bugfix b/newsfragments/699.bugfix deleted file mode 100644 index 66e598963..000000000 --- a/newsfragments/699.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix bug when setting the distance for single panel detectors that have a hierarchy. diff --git a/newsfragments/701.misc b/newsfragments/701.misc deleted file mode 100644 index 253df9d66..000000000 --- a/newsfragments/701.misc +++ /dev/null @@ -1 +0,0 @@ -Relax conditions when creating time of flight interpolators to allow time of flight frames to start from zero. diff --git a/newsfragments/703.feature b/newsfragments/703.feature deleted file mode 100644 index 30996d5d8..000000000 --- a/newsfragments/703.feature +++ /dev/null @@ -1 +0,0 @@ -Add `FormatMANDI` to read time of flight Laue data from MANDI. diff --git a/newsfragments/704.misc b/newsfragments/704.misc deleted file mode 100644 index 95b50c6d0..000000000 --- a/newsfragments/704.misc +++ /dev/null @@ -1 +0,0 @@ -Add wavelength range to polychromatic beams. diff --git a/newsfragments/707.misc b/newsfragments/707.misc deleted file mode 100644 index 93e94b50b..000000000 --- a/newsfragments/707.misc +++ /dev/null @@ -1 +0,0 @@ -Fix recently added ESRF Jungfrau4M format class diff --git a/newsfragments/708.bugfix b/newsfragments/708.bugfix deleted file mode 100644 index 4edb80f49..000000000 --- a/newsfragments/708.bugfix +++ /dev/null @@ -1,2 +0,0 @@ -Better recognition for SMV images from MLFSOM and other simulators from -James Holton. diff --git a/newsfragments/710.bugfix b/newsfragments/710.bugfix deleted file mode 100644 index 97e7b0206..000000000 --- a/newsfragments/710.bugfix +++ /dev/null @@ -1 +0,0 @@ -Fix error introduced in FormatSMVJHSim that caused test failures. diff --git a/newsfragments/711.bugfix b/newsfragments/711.bugfix deleted file mode 100644 index 88f42f4b9..000000000 --- a/newsfragments/711.bugfix +++ /dev/null @@ -1 +0,0 @@ -Override `setstate` and `getstate` methods for `PolychromaticBeam` to fix error when using `copy.deepcopy`. diff --git a/newsfragments/713.misc b/newsfragments/713.misc deleted file mode 100644 index 8d7dee373..000000000 --- a/newsfragments/713.misc +++ /dev/null @@ -1 +0,0 @@ -Add `tof_helpers.tof_from_wavelength`. diff --git a/newsfragments/714.bugfix b/newsfragments/714.bugfix deleted file mode 100644 index 47de4a3be..000000000 --- a/newsfragments/714.bugfix +++ /dev/null @@ -1 +0,0 @@ -Add missing argument to `getinitargs` in `PolychromaticBeamPickleSuite`. diff --git a/newsfragments/723.feature b/newsfragments/723.feature deleted file mode 100644 index 6c62e6348..000000000 --- a/newsfragments/723.feature +++ /dev/null @@ -1 +0,0 @@ -Additional features for `FormatXTCRayonix`