Bruker XRF fix

rsciio/bruker/__init__.py

@@ -1,7 +1,9 @@
 from ._api import file_reader
+from ._utils import export_metadata
 
 __all__ = [
     "file_reader",
+    "export_metadata",
 ]
 
 

rsciio/bruker/_api.py

@@ -62,11 +62,11 @@
 x2d = XmlToDict(dub_attr_pre_str="XmlClass", tags_to_flatten="ClassInstance")
 
 
-class Container(object):
+class Container:
     pass
 
 
-class SFSTreeItem(object):
+class SFSTreeItem:
     """Class to manage one internal sfs file.
 
     Reading, reading in chunks, reading and extracting, reading without
@@ -285,7 +285,7 @@
         return data
 
 
-class SFS_reader(object):
+class SFS_reader:
     """Class to read sfs file.
     SFS is AidAim software's(tm) single file system.
     The class provides basic reading capabilities of such container.
@@ -450,7 +450,7 @@
         return item
 
 
-class EDXSpectrum(object):
+class EDXSpectrum:
     def __init__(self, spectrum):
         """
         Wrap the objectified bruker EDS spectrum xml part
@@ -499,7 +499,9 @@
                 "ElevationAngle": xrf_header_dict["ExcitationAngle"],
             }
         # USED:
-        self.hv = self.esma_metadata["PrimaryEnergy"]
+        self.hv = self.esma_metadata.get("PrimaryEnergy", None)
+        if self.hv is None:
+            _logger.warning("The beam energy couldn't be found.")
         self.elev_angle = self.esma_metadata["ElevationAngle"]
         date_time = gen_iso_date_time(spectrum_header)
         if date_time is not None:
@@ -527,7 +529,7 @@
         return int(round((en_temp - self.offset) / self.scale))
 
 
-class HyperHeader(object):
+class HyperHeader:
     """Wrap Bruker HyperMaping xml header into python object.
 
     Arguments:
@@ -585,7 +587,7 @@
         semData = root.find("./ClassInstance[@Type='TRTSEMData']")
         self.sem_metadata = x2d.dictionarize(semData)
         # parse values for use in hspy metadata:
-        self.hv = self.sem_metadata.get("HV", 0.0)  # in kV
+        self.hv = self.sem_metadata.get("HV", None)  # in kV
         # image/hypermap resolution in um/pixel:
         if "DX" in self.sem_metadata:
             self.units = "µm"
@@ -610,7 +612,9 @@
         """return python dictionary with aquisition instrument
         mandatory data
         """
-        acq_inst = {"beam_energy": self.hv}
+        acq_inst = {}
+        if self.hv is not None:
+            acq_inst["beam_energy"] = self.hv
         if "Mag" in self.sem_metadata:
             acq_inst["magnification"] = self.sem_metadata["Mag"]
         if detector:
@@ -620,7 +624,8 @@
             acq_inst["Detector"] = det
             # In case of XRF, the primary energy is only defined in
             # the spectrum metadata
-            acq_inst["beam_energy"] = eds_metadata.hv
+            if eds_metadata.hv is not None:
+                acq_inst["beam_energy"] = eds_metadata.hv
 
         return acq_inst
 
@@ -744,9 +749,9 @@
         optimal channel number
         """
         eds_max_energy = self.spectra_data[index].amplification / 1000  # in kV
-        if hasattr(self, "hv") and (self.hv > 0) and (self.hv < eds_max_energy):
+        if self.hv and self.hv > 0 and self.hv < eds_max_energy:
             return self.spectra_data[index].energy_to_channel(self.hv)
-        if (not hasattr(self, "hv")) or (self.hv == 0):
+        if self.hv is None:
             logging.warn(
                 "bcf header contains no node for electron beam "
                 "voltage or such node is absent.\n"
@@ -1542,16 +1547,18 @@
     was used from metadata: TEM or SEM.
     However simple guess can be made using the acceleration
     voltage, assuming that SEM is <= 30kV or TEM is >30kV"""
-    if hv > 30.0:
+    if hv is not None and hv > 30.0:
         mode = "TEM"
     else:
         mode = "SEM"
-    _logger.info(
-        "Guessing that the acquisition instrument is %s " % mode
-        + "because the beam energy is %i keV. If this is wrong, " % hv
-        + "please provide the right instrument using the 'instrument' "
-        + "keyword."
-    )
+
+    if hv is not None:
+        _logger.info(
+            "Guessing that the acquisition instrument is %s " % mode
+            + "because the beam energy is %i keV. If this is wrong, " % hv
+            + "please provide the right instrument using the 'instrument' "
+            + "keyword."
+        )
     return mode
 
 

rsciio/bruker/_utils.py

@@ -0,0 +1,51 @@
+# -*- coding: utf-8 -*-
+#
+# Copyright 2007-2024 The HyperSpy developers
+#
+# This library is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with any project and source this library is coupled.
+# If not, see <https://www.gnu.org/licenses/#GPL>.
+
+import xml.etree.ElementTree as ET
+
+from rsciio._docstrings import FILENAME_DOC
+from rsciio.utils.tools import sanitize_msxml_float
+
+from ._api import SFS_reader
+
+
+def export_metadata(filename, output_filename=None):
+    """
+    Export the metadata from a bcf file to a xml file.
+
+    Parameters
+    ----------
+    %s
+    output_filename : str, pathlib.Path or None
+        The filename of the exported xml file.
+        If ``None``, use "header.xml" as default.
+
+    """
+    sfs = SFS_reader(filename)
+    # all file items in this singlefilesystem class instance is held inside
+    # dictionary hierarchy, we fetch the header:
+    header = sfs.vfs["EDSDatabase"]["HeaderData"]
+    xml_str = sanitize_msxml_float(header.get_as_BytesIO_string().getvalue())
+    xml = ET.ElementTree(ET.fromstring(xml_str))
+
+    if output_filename is None:  # pragma: no cover
+        output_filename = "header.xml"
+    xml.write(output_filename)
+
+
+export_metadata.__doc__ %= FILENAME_DOC

rsciio/tests/test_bruker.py

@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 
-from rsciio.bruker import file_reader
+from rsciio.bruker import export_metadata, file_reader
 from rsciio.utils.tests import assert_deep_almost_equal
 
 hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
@@ -324,3 +324,9 @@ def test_bruker_XRF():
 def test_unsupported_extension():
     with pytest.raises(ValueError):
         file_reader("fname.unsupported_extension")
+
+
+def test_export_xml(tmp_path):
+    export_metadata(
+        TEST_DATA_DIR / test_files[0], output_filename=tmp_path / "header.xml"
+    )

rsciio/tests/test_import.py

@@ -127,7 +127,9 @@ def test_dir_plugins(plugin):
         pytest.importorskip("h5py")
     plugin_module = importlib.import_module(plugin_string)
 
-    if plugin["name"] == "MSA":
+    if plugin["name"] == "Bruker":
+        assert dir(plugin_module) == ["export_metadata", "file_reader"]
+    elif plugin["name"] == "MSA":
         assert dir(plugin_module) == [
             "file_reader",
             "file_writer",
@@ -142,6 +144,7 @@ def test_dir_plugins(plugin):
         ]
     elif plugin["name"] == "DigitalSurf":
         assert dir(plugin_module) == ["file_reader", "file_writer", "parse_metadata"]
+
     elif plugin["writes"] is False:
         assert dir(plugin_module) == ["file_reader"]
     else:

upcoming_changes/326.bugfix.rst

@@ -0,0 +1 @@
+Raise a warning instead of an error when the beam energy can't be found in :ref:`bruker-format` xrf files.

upcoming_changes/326.enhancements.rst

@@ -0,0 +1 @@
+Add :func:`~.bruker.export_metadata` utility function for exporting metadata from :ref:`bruker-format` file.