DIALS 3.19.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.18.0
+current_version = 3.19.1
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<release>[a-z]+)?(?P<patch>\d+)?

CHANGELOG.rst

@@ -1,3 +1,12 @@
+DIALS 3.19.1 (2024-05-23)
+=========================
+
+Bugfixes
+--------
+
+- Fix case where old I03 Eiger nexus data (pre-2020) would fail to process. (`#737 <https://github.com/cctbx/dxtbx/issues/737>`_)
+
+
 dxtbx 3.19.0 (2024-04-17)
 =========================
 

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__ = "3.18.0"
+__version_tag__ = "3.19.1"
 
 setup_kwargs = {
  "name": "dxtbx",

src/dxtbx/format/FormatNXmxDLS.py

@@ -1,48 +1,77 @@
 from __future__ import annotations
 
+import contextlib
 import datetime
-import os
+import logging
 from functools import cached_property
 from pathlib import Path
-from typing import Union
 
 import h5py
 import numpy as np
 import nxmx
 
 from dxtbx.format.FormatNXmx import FormatNXmx
 
+logger = logging.getLogger(__name__)
 
-def get_bit_depth_from_meta(meta_file_name):
+
+def get_bit_depth_from_meta(meta_file_name: Path) -> int:
  with h5py.File(meta_file_name) as f:
- return int(f["/_dectris/bit_depth_image"][()])
+ with contextlib.suppress(KeyError):
+ return int(f["/_dectris/bit_depth_image"][()])
+
+ # This might be a very old meta file, that only had 'datatype'?
+ if "datatype" in f:
+ unique_vals = np.unique(f["datatype"])
+ if not len(unique_vals) == 1:
+ raise RuntimeError(
+ f"Error: Could not determine bit depth from metafile {meta_file_name} (multiple bit depths)"
+ )
+ return np.dtype(unique_vals[0]).itemsize * 8
+
+ raise RuntimeError("Cannot determine metafile bit depth")
 
 
-def find_meta_filename(master_like: Union[str, Path]) -> Union[str, Path]:
+def find_meta_filename(master_like: Path) -> Path:
  """
  Find the path to the '..._meta.h5' file in the same directory as the master file.
  Args:
  master_like: File path of the master HDF5 file.
+
  Returns:
  File path of the HDF5 metadata '..._meta.h5' file.
+
+ Raises:
+ RuntimeError: If no meta-file was found.
  """
 
- def _local_visit(name):
+ def _local_visit(name) -> Path | None:
  obj = f[name]
  if not hasattr(obj, "keys"):
  return None
  for k in obj.keys():
  kclass = obj.get(k, getlink=True, getclass=True)
  if kclass is h5py._hl.group.ExternalLink:
- kfile = obj.get(k, getlink=True).filename
- if kfile.split(".")[0].endswith("meta"):
+ kfile = master_like.parent / obj.get(k, getlink=True).filename
+ if kfile.stem.endswith("meta"):
  return kfile
+ return None
 
- master_dir = os.path.split(master_like)[0]
+ master_like = Path(master_like)
  with h5py.File(master_like) as f:
  meta_filename = f.visit(_local_visit)
 
- return os.path.join(master_dir, meta_filename)
+ if meta_filename is None:
+ # Try a fallback of looking for a file named the same but "meta.h5"
+ look_for = master_like.with_name(
+ master_like.stem.removesuffix("_master") + "_meta.h5"
+ )
+ if look_for.is_file():
+ meta_filename = look_for
+ else:
+ raise RuntimeError(f"Could not find h5 meta file for {master_like}")
+
+ return meta_filename
 
 
 class FormatNXmxDLS(FormatNXmx):
@@ -76,11 +105,14 @@ def _start(self):
  # See https://jira.diamond.ac.uk/browse/MXGDA-3674
  try:
  self._bit_depth_readout = get_bit_depth_from_meta(self._meta)
- except Exception:
+ except RuntimeError:
+ logger.warning(
+ "Could not determine bit depth of legacy image data: Falling back to default of 16"
+ )
  self._bit_depth_readout = 16
 
  @cached_property
- def _meta(self):
+ def _meta(self) -> Path:
  return find_meta_filename(self._image_file)
 
  def _get_nxmx(self, fh: h5py.File):