DIALS 3.17.1

.azure-pipelines/ci-conda-env.txt

@@ -16,6 +16,7 @@ conda-forge::hdf5>=1.12,<1.13
 conda-forge::jpeg
 conda-forge::matplotlib-base
 conda-forge::mrcfile
+conda-forge::natsort
 conda-forge::numpy
 conda-forge::nxmx
 conda-forge::orderedset

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.17.dev
+current_version = 3.18.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<release>[a-z]+)?(?P<patch>\d+)?

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 <https://github.com/cctbx/dxtbx/issues/659>`_)
+- Better handle spectra calibration for bad data in XTC format using new parameter: ``spectrum_required=``. (`#674 <https://github.com/cctbx/dxtbx/issues/674>`_)
+- Add Bruker and miniCBF format readers for the ELDICO ED-1 electron diffractometer with DECTRIS QUADRO detector. (`#682 <https://github.com/cctbx/dxtbx/issues/682>`_)
+- ``FormatSMVTimePix_SU``: Always mask out the central cross of virtual pixels. (`#683 <https://github.com/cctbx/dxtbx/issues/683>`_)
+- Add format reader for ISIS SXD detector. (`#687 <https://github.com/cctbx/dxtbx/issues/687>`_)
+- Detector distance can now be manually overridden for multi-panel detectors. (`#698 <https://github.com/cctbx/dxtbx/issues/698>`_)
+- Add format reader to read time of flight Laue data from MANDI. (`#703 <https://github.com/cctbx/dxtbx/issues/703>`_)
+- Additional features for `FormatXTCRayonix` (`#723 <https://github.com/cctbx/dxtbx/issues/723>`_)
+
+
+Bugfixes
+--------
+
+- Importing the (deprecated and removed) ``dxtbx.datablock`` module failed to display warning properly. (`#665 <https://github.com/cctbx/dxtbx/issues/665>`_)
+- Fix scan comparison for scan properties changes (`#669 <https://github.com/cctbx/dxtbx/issues/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 <https://github.com/cctbx/dxtbx/issues/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 <https://github.com/cctbx/dxtbx/issues/679>`_)
+- Fixed some properties not being correctly parsed in `Scan.from_dict`. (`#688 <https://github.com/cctbx/dxtbx/issues/688>`_)
+- Negative rotation angles are now allowed, the goniometer axis will be inverted if necessary. (`#690 <https://github.com/cctbx/dxtbx/issues/690>`_)
+- ``dials.import`` now uses natural sorting on input data, instead of strict sorting. (`#697 <https://github.com/cctbx/dxtbx/issues/697>`_)
+- Fix setting detector distance for single panel detectors that have a hierarchy. (`#699 <https://github.com/cctbx/dxtbx/issues/699>`_)
+- Better recognition for SMV images from MLFSOM and other simulators from James Holton. (`#708 <https://github.com/cctbx/dxtbx/issues/708>`_)
+- Fix error introduced in ``FormatSMVJHSim`` causing test failures. (`#710 <https://github.com/cctbx/dxtbx/issues/710>`_)
+- `PolychromaticBeam` can now be copied with `copy.deepcopy`. (`#711 <https://github.com/cctbx/dxtbx/issues/711>`_)
+- Add missing argument to `PolychromaticBeamPickleSuite.getinitargs`. (`#714 <https://github.com/cctbx/dxtbx/issues/714>`_)
+
+
+Misc
+----
+
+- `#620 <https://github.com/cctbx/dxtbx/issues/620>`_, `#667 <https://github.com/cctbx/dxtbx/issues/667>`_, `#670 <https://github.com/cctbx/dxtbx/issues/670>`_, `#689 <https://github.com/cctbx/dxtbx/issues/689>`_, `#691 <https://github.com/cctbx/dxtbx/issues/691>`_, `#694 <https://github.com/cctbx/dxtbx/issues/694>`_, `#696 <https://github.com/cctbx/dxtbx/issues/696>`_, `#701 <https://github.com/cctbx/dxtbx/issues/701>`_, `#704 <https://github.com/cctbx/dxtbx/issues/704>`_, `#707 <https://github.com/cctbx/dxtbx/issues/707>`_, `#713 <https://github.com/cctbx/dxtbx/issues/713>`_
+
+
 dxtbx 3.17.0 (2023-11-03)
 =========================
 

SConscript

@@ -176,7 +176,8 @@ if not env_etc.no_boost_python and hasattr(env_etc, "boost_adaptbx_include"):
         LIBS=env_etc.libs_python
         + env_etc.libm
         + env_etc.dxtbx_libs
-        + env_etc.dxtbx_hdf5_libs,
+        + env_etc.dxtbx_hdf5_libs
+        + env["LIBS"],
     )
 
     dxtbx_format_image_ext_sources = [

newsfragments/737.bugfix

@@ -0,0 +1 @@
+Fix case where old I03 Eiger nexus data (pre-2020) would fail to process.

setup.py

@@ -8,7 +8,7 @@
 
 # Static version number which is updated by bump2version
 # Do not change this manually - use 'bump2version <major/minor/patch/release>'
-__version_tag__ = "3.17.dev"
+__version_tag__ = "3.18.0"
 
 setup_kwargs = {
     "name": "dxtbx",

src/dxtbx/CMakeLists.txt

@@ -11,7 +11,7 @@ Python_add_library( dxtbx_format_nexus_ext MODULE format/boost_python/nexus_ext.
 target_link_libraries( dxtbx_format_nexus_ext PRIVATE  Boost::python CCTBX::scitbx hdf5::hdf5 )
 
 Python_add_library( dxtbx_imageset_ext MODULE boost_python/imageset_ext.cc )
-target_link_libraries( dxtbx_imageset_ext PUBLIC Boost::python CCTBX::scitbx )
+target_link_libraries( dxtbx_imageset_ext PUBLIC Boost::python CCTBX::scitbx CCTBX::scitbx::boost_python )
 
 Python_add_library( dxtbx_format_image_ext
     MODULE

src/dxtbx/array_family/flex_table_suite.h

@@ -330,6 +330,80 @@ namespace dxtbx { namespace af { namespace flex_table_suite {
     }
   };
 
+  struct column_range_to_string_visitor : public boost::static_visitor<std::string> {
+    template <typename U>
+    std::string operator()(const U &column) const {
+      std::ostringstream os;
+      os << column[0] << " - " << column[column.size() - 1] << "\n";
+      return os.str();
+    }
+  };
+
+  template <typename T>
+  struct compare_column_visitor : public boost::static_visitor<bool> {
+    T &self;
+    typename T::key_type key;
+    compare_column_visitor(T &self_, typename T::key_type key_)
+        : self(self_), key(key_) {}
+
+    template <typename U>
+    bool operator()(const U &other_column) const {
+      U self_column = self[key];
+      DXTBX_ASSERT(self_column.size() == other_column.size());
+      for (std::size_t i = 0; i < self_column.size(); ++i) {
+        if (self_column[i] != other_column[i]) {
+          return false;
+        }
+      }
+      return true;
+    }
+
+    bool operator()(const scitbx::af::shared<double> &other_column) const {
+      scitbx::af::shared<double> self_column = self[key];
+      double eps = 1e-7;
+      DXTBX_ASSERT(self_column.size() == other_column.size());
+      for (std::size_t i = 0; i < self_column.size(); ++i) {
+        if (std::abs(self_column[i] - other_column[i]) > eps) {
+          return false;
+        }
+      }
+      return true;
+    }
+
+    bool operator()(const scitbx::af::shared<vec2<double> > &other_column) const {
+      scitbx::af::shared<vec2<double> > self_column = self[key];
+      double eps = 1e-7;
+      DXTBX_ASSERT(self_column.size() == other_column.size());
+      for (std::size_t i = 0; i < self_column.size(); ++i) {
+        if (std::abs(self_column[i][0] - other_column[i][0]) > eps) {
+          return false;
+        }
+        if (std::abs(self_column[i][1] - other_column[i][1]) > eps) {
+          return false;
+        }
+      }
+      return true;
+    }
+
+    bool operator()(const scitbx::af::shared<vec3<double> > &other_column) const {
+      scitbx::af::shared<vec3<double> > self_column = self[key];
+      double eps = 1e-7;
+      DXTBX_ASSERT(self_column.size() == other_column.size());
+      for (std::size_t i = 0; i < self_column.size(); ++i) {
+        if (std::abs(self_column[i][0] - other_column[i][0]) > eps) {
+          return false;
+        }
+        if (std::abs(self_column[i][1] - other_column[i][1]) > eps) {
+          return false;
+        }
+        if (std::abs(self_column[i][2] - other_column[i][2]) > eps) {
+          return false;
+        }
+      }
+      return true;
+    }
+  };
+
   /**
    * Initialise the column table from a list of (key, column) pairs
    * @param columns The list of columns
@@ -359,6 +433,22 @@ namespace dxtbx { namespace af { namespace flex_table_suite {
     return column.apply_visitor(visitor);
   }
 
+  template <typename T>
+  bool compare_columns(T &self, T &other) {
+    typedef typename T::const_iterator iterator;
+    // Implicitly assumed that self and other are the same size
+    DXTBX_ASSERT(self.nrows() == other.nrows());
+    bool same_column;
+    for (iterator it = other.begin(); it != other.end(); ++it) {
+      compare_column_visitor<T> visitor(self, it->first);
+      same_column = it->second.apply_visitor(visitor);
+      if (!same_column) {
+        return false;
+      }
+    }
+    return true;
+  }
+
   /**
    * Delete a column of data
    * @param self The column table

src/dxtbx/datablock.py

@@ -2,7 +2,7 @@
 
 import warnings
 
-from dxtbx.experiment_list import (
+from dxtbx.model.experiment_list import (
     BeamComparison,
     DetectorComparison,
     FormatChecker,

src/dxtbx/dxtbx_model_ext.pyi

@@ -36,6 +36,14 @@ Vec6Float = Tuple[float, float, float, float, float, float]
 Vec9Float = Tuple[float, float, float, float, float, float, float, float, float]
 Vec2Int = Tuple[int, int]
 Vec4Int = Tuple[int, int, int, int]
+ScanPropertyTypes = Union[
+    flex.int,
+    flex.double,
+    flex.bool,
+    flex.std_string,
+    flex.vec2_double,
+    flex.vec3_double,
+]
 
 class BeamBase:
     @property
@@ -165,6 +173,8 @@ class PolychromaticBeam(Beam):
         sample_to_source_distance: float = ...,
         deg: bool = ...,
     ) -> None: ...
+    def set_wavelength_range(self, wavelength_range: Vec2Float) -> None: ...
+    def get_wavelength_range(self) -> Vec2Float: ...
     @staticmethod
     def from_dict(data: Dict) -> PolychromaticBeam: ...
     def to_dict(self) -> Dict: ...
@@ -745,6 +755,14 @@ class Scan(ScanBase):
         batch_offset: int,
         deg: bool = ...,
     ) -> None: ...
+    @overload
+    def __init__(
+        self,
+        image_range: Vec2Int,
+        properties_table: Dict,
+        batch_offset: int,
+        deg: bool = ...,
+    ) -> None: ...
     def append(self, other: Scan, scan_tolerance: float) -> None: ...
     @staticmethod
     def from_dict(data: Dict) -> Scan: ...
@@ -788,6 +806,22 @@ class Scan(ScanBase):
     def get_oscillation_range(self, deg: bool = ...) -> Vec2Float: ...
     def get_valid_image_ranges(self, i: str) -> List[Vec2Int]: ...
     def set_valid_image_ranges(self, i: str, ranges: List[Vec2Int]) -> None: ...
+    def get_properties(self) -> dict: ...
+    def set_properties(self, properties: dict) -> None: ...
+    def has_property(self, key: str) -> bool: ...
+    def get_property(self, key: str) -> ScanPropertyTypes: ...
+    @overload
+    def set_property(self, key: str, value: flex.double) -> None: ...
+    @overload
+    def set_property(self, key: str, value: flex.bool) -> None: ...
+    @overload
+    def set_property(self, key: str, value: flex.int) -> None: ...
+    @overload
+    def set_property(self, key: str, value: flex.std_string) -> None: ...
+    @overload
+    def set_property(self, key: str, value: flex.vec2_double) -> None: ...
+    @overload
+    def set_property(self, key: str, value: flex.vec3_double) -> None: ...
     @overload
     def is_angle_valid(self, angle: float, deg: bool = ...) -> bool: ...
     @overload