Merge pull request #654 from toastisme/beam-probe-types

Add probe to phil params and make probe in .expt human readable

CMakeLists.txt

@@ -3,7 +3,7 @@ cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 project(dxtbx LANGUAGES C CXX)
 
 # Add the included modules
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/")
 
 # General cmake environment configuration
 include(SetDefaultBuildRelWithDebInfo) # Default builds to release with debug info

newsfragments/299.bugfix

@@ -0,0 +1 @@
+Panel geometry definitions in PHIL are merged by panel id before constructing panels

newsfragments/439.bugfix

@@ -0,0 +1 @@
+``flumpy``: Fix case where incorrect ``flex.vec2``, ``flex.vec3`` could be generated.

newsfragments/621.feature

@@ -0,0 +1 @@
+Add new Beam class "PolychromaticBeam" for polychromatic/multi-wavelength/wide bandpass experiments.

newsfragments/626.feature

@@ -0,0 +1 @@
+Update Format handling to reflect move of Eiger detector from PETRA P14 to P13.

newsfragments/633.bugfix

@@ -0,0 +1 @@
+Slicing of imageset objects is now consistently 0-based, including for the sliced data accessor. Previously, the data accessor had to be accessed with the original index offsets.

newsfragments/645.feature

@@ -0,0 +1 @@
+Add partial support for the Rigaku Oxford Diffraction file format.

newsfragments/647.feature

@@ -0,0 +1 @@
+The ``Beam`` model now has a ``probe`` value to keep track of the type of radiation.

newsfragments/650.misc

@@ -0,0 +1 @@
+Format classes are now tested against invalid binary data with dials-data, for when dials-regression is not present.

src/dxtbx/boost_python/flumpy.cc

@@ -520,6 +520,13 @@ py::object vec_from_numpy(py::array np_array) {
 
  static_assert(VecType<int>::fixed_size == 2 || VecType<int>::fixed_size == 3,
  "Only vec2/vec3 supported");
+
+ // Only accept arrays that have a dimension higher than 1 - we want
+ // numpy.array([1,2,3]) to fail but numpy.array([[1,2,3]]) to work
+ if (np_array.ndim() == 1) {
+ throw std::invalid_argument("Array for conversion to vec must be multidimensional");
+ }
+
  // Only accept arrays whose last dimension is the size of this object
  if (np_array.shape(np_array.ndim() - 1) != VecType<int>::fixed_size) {
  throw std::invalid_argument("Input array last dimension is not size "

src/dxtbx/dxtbx_model_ext.pyi

@@ -22,6 +22,8 @@ from scitbx.array_family import shared as flex_shared
 # Attempt to use the stub typing for flex-inheritance
 from scitbx.array_family.flex import FlexPlain
 
+from dxtbx_model_ext import Probe # type: ignore
+
 # TypeVar for the set of Experiment models that can be joint-accepted
 # - profile, imageset and scalingmodel are handled as 'object'
 TExperimentModel = TypeVar(
@@ -113,6 +115,37 @@ class Beam(BeamBase):
  @staticmethod
  def from_dict(data: Dict) -> Beam: ...
  def to_dict(self) -> Dict: ...
+ @staticmethod
+ def get_probe_from_name(name: str) -> Probe: ...
+
+class PolychromaticBeam(Beam):
+ @overload
+ def __init__(self, beam: PolychromaticBeam) -> None: ...
+ @overload
+ def __init__(self, direction: Vec3Float) -> None: ...
+ @overload
+ def __init__(
+ self,
+ direction: Vec3Float,
+ divergence: float,
+ sigma_divergence: float,
+ deg: bool = ...,
+ ) -> None: ...
+ @overload
+ def __init__(
+ self,
+ direction: Vec3Float,
+ divergence: float,
+ sigma_divergence: float,
+ polarization_normal: Vec3Float,
+ polarization_fraction: float,
+ flux: float,
+ transmission: float,
+ deg: bool = ...,
+ ) -> None: ...
+ @staticmethod
+ def from_dict(data: Dict) -> PolychromaticBeam: ...
+ def to_dict(self) -> Dict: ...
 
 class CrystalBase:
  @property

src/dxtbx/format/FormatCBFMini.py

@@ -8,6 +8,7 @@
 from __future__ import annotations
 
 import binascii
+import datetime
 import os
 import pathlib
 import sys
@@ -73,6 +74,20 @@ def __init__(self, image_file, **kwargs):
  self._raw_data = None
  super().__init__(image_file, **kwargs)
 
+ @staticmethod
+ def _get_timestamp_from_raw_header(
+ header: str | list[str],
+ ) -> datetime.datetime | None:
+ """Given a raw header, or lines from, attempt to extract the timestamp field"""
+ if isinstance(header, str):
+ header = header.splitlines()
+ timestamp = None
+ for record in header:
+ if len(record[1:].split()) <= 2 and record.count(":") == 2:
+ timestamp = datetime.datetime.fromisoformat(record[1:].strip())
+ break
+ return timestamp
+
  def _start(self):
  """Open the image file, read the image header, copy it into a
  dictionary for future reference."""

src/dxtbx/format/FormatCBFMiniEigerPetraP14.py

@@ -3,6 +3,7 @@
 
 from __future__ import annotations
 
+import datetime
 import sys
 
 from dxtbx.format.FormatCBFMiniEiger import FormatCBFMiniEiger
@@ -19,11 +20,21 @@ def understand(image_file):
 
  header = FormatCBFMiniEiger.get_cbf_header(image_file)
 
+ # Valid from 22nd May 2021
+ expected_serial = "E-32-0129"
+ if timestamp := FormatCBFMiniEiger._get_timestamp_from_raw_header(header):
+ # We have a timestamp. Let's see what detector we should expect
+
+ # Before 22nd May 2021
+ if timestamp < datetime.datetime(2021, 5, 22):
+ expected_serial = "E-32-0107"
+
+ # Find the line recording detector serial, and check
  for record in header.split("\n"):
  if (
  "# detector" in record.lower()
  and "eiger" in record.lower()
- and "E-32-0107" in record
+ and expected_serial in record
  ):
  return True
 

src/dxtbx/format/FormatGatanDM4.py

@@ -21,6 +21,7 @@
 )
 from dxtbx.format.Format import Format
 from dxtbx.format.FormatMultiImage import FormatMultiImage
+from dxtbx.model.beam import Probe
 
 
 def read_tag(f, byteorder):
@@ -358,6 +359,7 @@ def _beam(self):
  wavelength=wavelength,
  polarization=(0, 1, 0),
  polarization_fraction=0.5,
+ probe=Probe.electron,
  )
 
  def _scan(self):

src/dxtbx/format/FormatMRC.py

@@ -19,6 +19,7 @@
 from dxtbx.format.Format import Format
 from dxtbx.format.FormatMultiImage import FormatMultiImage
 from dxtbx.model import ScanFactory
+from dxtbx.model.beam import Probe
 
 logger = logging.getLogger("dials")
 
@@ -226,6 +227,7 @@ def _beam(self):
  wavelength=wavelength,
  polarization=(0, 1, 0),
  polarization_fraction=0.5,
+ probe=Probe.electron,
  )