Bruker XRF

CHANGES.rst

@@ -47,7 +47,8 @@ RELEASE_next_patch (Unreleased)
 * Fix broken events when changing signal type `#2683 <https://github.com/hyperspy/hyperspy/pull/2683>`_
 * Make DictionaryTreeBrowser lazy by default - see `#368 <https://github.com/hyperspy/hyperspy/issues/368>`_ (`#2623 <https://github.com/hyperspy/hyperspy/pull/2623>`_)
 * Fix setting offset in rebin: the offset was changed in the wrong axis (`#2690 <https://github.com/hyperspy/hyperspy/pull/2690>`_)
-
+* Fix reading XRF bruker file, close `#2689 <https://github.com/hyperspy/hyperspy/issues/2689>`_ (`#2694 <https://github.com/hyperspy/hyperspy/pull/2694>`_)
+* Speed up setting CI on azure pipeline (`#2694 <https://github.com/hyperspy/hyperspy/pull/2694>`_)
 
 Changelog
 *********

conda_environment.yml

@@ -18,15 +18,14 @@ dependencies:
 - prettytable
 - python
 - python-dateutil
-- pyusid
 - pyyaml
 - requests
 - scikit-image
 - scikit-learn
 - scipy
 - sparse
 - sympy
-- tifffile >=2019.07.26
+- tifffile >=2019.07.26,!=2021.3.31
 - toolz
 - tqdm
 - traits

conda_environment_dev.yml

@@ -5,7 +5,7 @@ channels:
 dependencies:
 # We pin freetype and matplotlib for the image comparison
 - freetype=2.9
-- matplotlib=3.1
+- matplotlib-base=3.1
 - cython
 - pytest
 - pytest-mpl

hyperspy/io_plugins/bruker.py

@@ -512,6 +512,7 @@ def __init__(self, spectrum):
         # ESMA could stand for Electron Scanning Microscope Analysis
         spectrum_header = spectrum.find(
             "./ClassInstance[@Type='TRTSpectrumHeader']")
+        xrf_header = TRTHeader.find("./ClassInstance[@Type='TRTXrfHeader']")
 
         # map stuff from harware xml branch:
         self.hardware_metadata = dictionarize(hardware_header)
@@ -530,15 +531,21 @@ def __init__(self, spectrum):
             self.detector_metadata['DetLayers'][i.tag] = dict(i.attrib)
 
         # map stuff from esma xml branch:
-        self.esma_metadata = dictionarize(esma_header)
+        if esma_header:
+            self.esma_metadata = dictionarize(esma_header)
+        if xrf_header:
+            xrf_header_dict = dictionarize(xrf_header)
+            self.esma_metadata = {
+                'PrimaryEnergy':xrf_header_dict['Voltage'],
+                'ElevationAngle':xrf_header_dict['ExcitationAngle']
+                }
         # USED:
         self.hv = self.esma_metadata['PrimaryEnergy']
         self.elev_angle = self.esma_metadata['ElevationAngle']
         date_time = gen_iso_date_time(spectrum_header)
         if date_time is not None:
             self.date, self.time = date_time
 
-        # map stuff from spectra xml branch:
         self.spectrum_metadata = dictionarize(spectrum_header)
         self.offset = self.spectrum_metadata['CalibAbs']
         self.scale = self.spectrum_metadata['CalibLin']

hyperspy/tests/io/test_bruker.py

@@ -216,15 +216,27 @@ def test_decimal_regex():
     for j in dummy_xml_negative:
         assert b'.' not in fix_dec_patterns.sub(b'\\1.\\2', j)
 
+
 def test_all_spx_loads():
     for spxfile in spx_files:
         filename = os.path.join(my_path, 'bruker_data', spxfile)
         s = load(filename)
         assert s.data.dtype == np.uint64
         assert s.metadata.Signal.signal_type == 'EDS_SEM'
 
+
 def test_stand_alone_spx():
     filename = os.path.join(my_path, 'bruker_data', 'bruker_nano.spx')
     s = load(filename)
     assert s.metadata.Sample.elements == ['Fe', 'S', 'Cu']
     assert s.metadata.Acquisition_instrument.SEM.Detector.EDS.live_time == 7.385
+
+
+def test_bruker_XRF():
+    # See https://github.com/hyperspy/hyperspy/issues/2689
+    # Bruker M6 Jetstream SPX
+    filename = os.path.join(my_path, 'bruker_data',
+                            'bruker_m6_jetstream_file_example.spx')
+    s = load(filename)
+    assert s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time == 28.046
+    assert s.metadata.Acquisition_instrument.TEM.beam_energy == 50