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import json
from pathlib import Path
import numpy as np
import pytest
from rsciio.bruker import file_reader
from rsciio.utils.tests import assert_deep_almost_equal
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
test_files = [
"30x30_instructively_packed_16bit_compressed.bcf",
"16x16_12bit_packed_8bit.bcf",
"P45_the_default_job.bcf",
"test_TEM.bcf",
"Hitachi_TM3030Plus.bcf",
"over16bit.bcf",
"bcf_v2_50x50px.bcf",
"bcf-edx-ebsd.bcf",
]
np_files = ["30x30_16bit.npy", "30x30_16bit_ds.npy"]
spx_files = ["extracted_from_bcf.spx", "bruker_nano.spx"]
TEST_DATA_DIR = Path(__file__).parent / "data" / "bruker"
def test_load_16bit():
# test bcf from hyperspy hs.load function level
# some of functions can be not covered
# it cant use cython parsing implementation, as it is not compiled
filename = TEST_DATA_DIR / test_files[0]
print("testing bcf instructively packed 16bit...")
s = hs.load(filename)
bse, hype = s
# Bruker saves all images in true 16bit:
assert bse.data.dtype == np.uint16
assert bse.data.shape == (30, 30)
np_filename = TEST_DATA_DIR / np_files[0]
np.testing.assert_array_equal(hype.data[:, :, 222:224], np.load(np_filename))
assert hype.data.shape == (30, 30, 2048)
assert hype.axes_manager.navigation_shape == (30, 30)
assert hype.axes_manager.signal_shape == (2048,)
assert bse.metadata.get_item("Stage.x", full_path=False) == 66940.81
assert hype.metadata.get_item("Stage.x", full_path=False) == 66940.81
def test_load_16bit_reduced():
filename = TEST_DATA_DIR / test_files[0]
print("testing downsampled 16bit bcf...")
s = hs.load(filename, downsample=4, cutoff_at_kV=10)
bse, hype = s
# sem images are never downsampled
assert bse.data.shape == (30, 30)
assert bse.axes_manager.signal_shape == (30, 30)
assert bse.axes_manager.navigation_shape == ()
np_filename = TEST_DATA_DIR / np_files[1]
np.testing.assert_array_equal(hype.data[:, :, 222:224], np.load(np_filename))
assert hype.data.shape == (8, 8, 1047)
assert hype.axes_manager.navigation_shape == (8, 8)
assert hype.axes_manager.signal_shape == (1047,)
# Bruker saves all images in true 16bit:
assert bse.data.dtype == np.uint16
# hypermaps should always return unsigned integers:
assert str(hype.data.dtype)[0] == "u"
def test_load_16bit_cutoff_zealous():
filename = TEST_DATA_DIR / test_files[0]
print("testing downsampled 16bit bcf with cutoff_at_kV=zealous...")
hype = hs.load(filename, cutoff_at_kV="zealous", select_type="spectrum_image")
assert hype.data.shape == (30, 30, 2048)
assert hype.axes_manager.navigation_shape == (30, 30)
assert hype.axes_manager.signal_shape == (2048,)
def test_load_16bit_cutoff_auto():
filename = TEST_DATA_DIR / test_files[0]
print("testing downsampled 16bit bcf with cutoff_at_kV=auto...")
hype = hs.load(filename, cutoff_at_kV="auto", select_type="spectrum_image")
assert hype.data.shape == (30, 30, 2048)
assert hype.axes_manager.navigation_shape == (30, 30)
assert hype.axes_manager.signal_shape == (2048,)
def test_load_8bit():
bse_sig_shapes = [(16, 16), (100, 75)] # identical to hype nav shapes
hype_sig_shapes = [(2048,), (2048,)]
for i, bcffile in enumerate(test_files[1:3]):
filename = TEST_DATA_DIR / bcffile
print("testing simple 8bit bcf...")
s = hs.load(filename)
bse, hype = s[0], s[-1]
# Bruker saves all images in true 16bit:
assert bse.data.dtype == np.uint16
assert bse.axes_manager.navigation_shape == ()
assert bse.axes_manager.signal_shape == bse_sig_shapes[i]
# hypermaps should always return unsigned integers:
assert str(hype.data.dtype)[0] == "u"
assert hype.axes_manager.navigation_shape == bse.axes_manager.signal_shape
assert hype.axes_manager.signal_shape == hype_sig_shapes[i]
def test_hyperspy_wrap():
pytest.importorskip("exspy", reason="exspy not installed.")
filename = TEST_DATA_DIR / test_files[0]
print("testing bcf wrap to hyperspy signal...")
hype = hs.load(filename, select_type="spectrum_image")
np.testing.assert_allclose(hype.axes_manager[0].scale, 1.66740910949362, atol=1e-12)
np.testing.assert_allclose(hype.axes_manager[1].scale, 1.66740910949362, atol=1e-12)
assert hype.axes_manager[1].units == "µm"
np.testing.assert_allclose(hype.axes_manager[2].scale, 0.009999)
np.testing.assert_allclose(hype.axes_manager[2].offset, -0.47225277)
assert hype.axes_manager[2].units == "keV"
assert hype.axes_manager[2].is_binned is True
md_ref = {
"Acquisition_instrument": {
"SEM": {
"beam_energy": 20,
"magnification": 1819.22595,
"Detector": {
"EDS": {
"elevation_angle": 35.0,
"detector_type": "XFlash 6|10",
"azimuth_angle": 90.0,
"real_time": 70.07298,
"energy_resolution_MnKa": 130.0,
}
},
"Stage": {
"tilt_alpha": 0.0,
"rotation": 326.10089,
"x": 66940.81,
"y": 54233.16,
"z": 39194.77,
},
}
},
"General": {
"original_filename": "30x30_instructively_packed_16bit_compressed.bcf",
"title": "EDX",
"date": "2018-10-04",
"time": "13:02:07",
"FileIO": {
"0": {
"operation": "load",
"hyperspy_version": hs.__version__,
"io_plugin": "rsciio.bruker",
}
},
},
"Sample": {
"name": "chevkinite",
"elements": [
"Al",
"C",
"Ca",
"Ce",
"Fe",
"Gd",
"K",
"Mg",
"Na",
"Nd",
"O",
"P",
"Si",
"Sm",
"Th",
"Ti",
],
"xray_lines": [
"Al_Ka",
"C_Ka",
"Ca_Ka",
"Ce_La",
"Fe_Ka",
"Gd_La",
"K_Ka",
"Mg_Ka",
"Na_Ka",
"Nd_La",
"O_Ka",
"P_Ka",
"Si_Ka",
"Sm_La",
"Th_Ma",
"Ti_Ka",
],
},
"Signal": {"quantity": "X-rays (Counts)", "signal_type": "EDS_SEM"},
"_HyperSpy": {
"Folding": {
"original_axes_manager": None,
"original_shape": None,
"signal_unfolded": False,
"unfolded": False,
}
},
}
filename_omd = TEST_DATA_DIR / "30x30_original_metadata.json"
with open(filename_omd) as fn:
# original_metadata:
omd_ref = json.load(fn)
# delete FileIO timestamp since it's runtime dependent
del hype.metadata.General.FileIO.Number_0.timestamp
assert_deep_almost_equal(hype.metadata.as_dictionary(), md_ref)
assert_deep_almost_equal(hype.original_metadata.as_dictionary(), omd_ref)
assert hype.metadata.General.date == "2018-10-04"
assert hype.metadata.General.time == "13:02:07"
assert hype.metadata.Signal.quantity == "X-rays (Counts)"
def test_hyperspy_wrap_downsampled():
filename = TEST_DATA_DIR / test_files[0]
print("testing bcf wrap to hyperspy signal...")
hype = hs.load(filename, select_type="spectrum_image", downsample=5)
np.testing.assert_allclose(
hype.axes_manager[0].scale, 8.337045547468101, atol=1e-12
)
np.testing.assert_allclose(
hype.axes_manager[1].scale, 8.337045547468101, atol=1e-12
)
assert hype.axes_manager[1].units == "µm"
def test_get_mode():
filename = TEST_DATA_DIR / test_files[0]
s = hs.load(filename, select_type="spectrum_image", instrument="SEM")
assert s.metadata.Signal.signal_type == "EDS_SEM"
assert isinstance(s, hs.signals.Signal1D)
filename = TEST_DATA_DIR / test_files[0]
s = hs.load(filename, select_type="spectrum_image", instrument="TEM")
assert s.metadata.Signal.signal_type == "EDS_TEM"
assert isinstance(s, hs.signals.Signal1D)
filename = TEST_DATA_DIR / test_files[0]
s = hs.load(filename, select_type="spectrum_image")
assert s.metadata.Signal.signal_type == "EDS_SEM"
assert isinstance(s, hs.signals.Signal1D)
filename = TEST_DATA_DIR / test_files[3]
s = hs.load(filename, select_type="spectrum_image")
assert s.metadata.Signal.signal_type == "EDS_TEM"
assert isinstance(s, hs.signals.Signal1D)
def test_wrong_file():
filename = TEST_DATA_DIR / "Nope.bcf"
with pytest.raises(TypeError):
hs.load(filename)
def test_fast_bcf():
thingy = pytest.importorskip("rsciio.bruker.unbcf_fast")
from rsciio.bruker import _api
for bcffile in test_files:
filename = TEST_DATA_DIR / bcffile
thingy = _api.BCF_reader(filename)
for j in range(2, 5, 1):
print("downsampling:", j)
_api.fast_unbcf = True # manually enabling fast parsing
hmap1 = thingy.parse_hypermap(downsample=j) # using cython
_api.fast_unbcf = False # manually disabling fast parsing
hmap2 = thingy.parse_hypermap(downsample=j) # py implementation
np.testing.assert_array_equal(hmap1, hmap2)
def test_decimal_regex():
from rsciio.utils.tools import sanitize_msxml_float
dummy_xml_positive = [
b"<dummy_tag>85,658</dummy_tag>",
b"<dummy_tag>85,658E-8</dummy_tag>",
b"<dummy_tag>-85,658E-8</dummy_tag>",
b"<dum_tag>-85.658</dum_tag>", # negative check
b"<dum_tag>85.658E-8</dum_tag>",
] # negative check
dummy_xml_negative = [
b"<dum_tag>12,25,23,45,56,12,45</dum_tag>",
b"<dum_tag>12e1,23,-24E-5</dum_tag>",
]
for i in dummy_xml_positive:
assert b"85.658" in sanitize_msxml_float(i)
for j in dummy_xml_negative:
assert b"." not in sanitize_msxml_float(j)
def test_all_spx_loads():
signal_shape = [(1548,), (4096,)]
for i, spxfile in enumerate(spx_files):
filename = TEST_DATA_DIR / spxfile
s = hs.load(filename)
assert s.data.dtype == np.uint64
assert s.metadata.Signal.signal_type == "EDS_SEM"
assert s.axes_manager.navigation_shape == ()
assert s.axes_manager.signal_shape == signal_shape[i]
def test_stand_alone_spx():
filename = TEST_DATA_DIR / "bruker_nano.spx"
s = hs.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 = TEST_DATA_DIR / "bruker_m6_jetstream_file_example.spx"
s = hs.load(filename)
assert s.metadata.Acquisition_instrument.TEM.Detector.EDS.live_time == 28.046
assert s.metadata.Acquisition_instrument.TEM.beam_energy == 50
assert s.axes_manager.signal_shape == (4096,)
assert s.axes_manager.navigation_shape == ()
def test_unsupported_extension():
with pytest.raises(ValueError):
file_reader("fname.unsupported_extension")
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