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# -*- coding: utf-8 -*-
# Copyright 2007-2023 The HyperSpy developers
#
# This file is part of RosettaSciIO.
#
# RosettaSciIO 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.
#
# RosettaSciIO 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 RosettaSciIO. If not, see <https://www.gnu.org/licenses/#GPL>.
import sys
from pathlib import Path
import numpy as np
import pytest
from rsciio.tia._api import file_reader, load_ser_file
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
t = pytest.importorskip("traits.api", reason="traits not installed")
TEST_DATA_PATH = Path(__file__).parent / "data" / "tia"
TEST_DATA_PATH_NEW = TEST_DATA_PATH / "new"
TEST_DATA_PATH_OLD = TEST_DATA_PATH / "old"
@pytest.fixture(scope="function")
def prepare_non_zero_float():
import tarfile
kwargs = {"filter": "data"} if sys.version_info.minor >= 12 else {}
tgz_fname = TEST_DATA_PATH_OLD / "non_float_meta_value_zeroed.tar.gz"
with tarfile.open(tgz_fname, "r:gz") as tar:
tar.extractall(path=TEST_DATA_PATH_OLD, **kwargs)
yield
# teardown code
(TEST_DATA_PATH_OLD / "non_float_meta_value_zeroed.emi").unlink()
(TEST_DATA_PATH_OLD / "non_float_meta_value_zeroed_1.ser").unlink()
def test_load_emi_old_new_format():
# TIA old format
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
hs.load(fname0)
# TIA new format
fname1 = TEST_DATA_PATH_NEW / "128x128_TEM_acquire-sum1.emi"
hs.load(fname1)
def test_load_image_content():
# TEM image of the beam stop
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s0 = hs.load(fname0)
data = np.load(fname0.with_suffix(".npy"))
np.testing.assert_array_equal(s0.data, data)
def test_load_ser_reader_old_new_format():
# test TIA old format
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire_1.ser"
header0, data0 = load_ser_file(fname0)
assert header0["SeriesVersion"] == 528
# test TIA new format
fname1 = TEST_DATA_PATH_NEW / "128x128_TEM_acquire-sum1_1.ser"
header1, data1 = load_ser_file(fname1)
assert header1["SeriesVersion"] == 544
def test_load_no_acquire_date(caplog):
fname = TEST_DATA_PATH_OLD / "no_AcquireDate.emi"
s = hs.load(fname)
assert not hasattr(s.metadata.General, "date")
assert not hasattr(s.metadata.General, "time")
assert "AcquireDate not found in metadata" in caplog.text
def test_load_more_ser_than_metadata(caplog):
fname = TEST_DATA_PATH_OLD / "more_ser_then_emi_metadata.emi"
s0, s1 = hs.load(fname, only_valid_data=True)
assert hasattr(s0.original_metadata, "ObjectInfo")
assert not hasattr(s1.original_metadata, "ObjectInfo")
assert "more_ser_then_emi_metadata.emi did not contain any metadata" in caplog.text
def test_load_non_zero_float(prepare_non_zero_float, caplog):
fname = TEST_DATA_PATH_OLD / "non_float_meta_value_zeroed.emi"
s = hs.load(fname)
assert (
s.original_metadata.ObjectInfo.ExperimentalDescription.as_dictionary()[
"OBJ Aperture_um"
]
== "V"
)
assert "Expected decimal value for OBJ Aperture" in caplog.text
def test_load_diffraction_point():
fname0 = TEST_DATA_PATH_OLD / "64x64_diffraction_acquire.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (64, 64)
assert s0.axes_manager.signal_dimension == 2
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "TEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 0.101571, rtol=1e-5)
assert s0.axes_manager[0].units == "1 / nm"
assert s0.axes_manager[0].name == "x"
np.testing.assert_allclose(s0.axes_manager[1].scale, 0.101571, rtol=1e-5)
assert s0.axes_manager[1].units == "1 / nm"
assert s0.axes_manager[1].name == "y"
def test_load_diffraction_line_scan():
fname0 = TEST_DATA_PATH_NEW / "16x16-line_profile_horizontal_5x128x128_EDS.emi"
s0 = hs.load(fname0)
# s0[0] contains EDS
assert s0[0].data.shape == (5, 4000)
assert s0[0].axes_manager.signal_dimension == 1
assert s0[0].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0[0].axes_manager[0].scale, 3.68864, rtol=1e-5)
assert s0[0].axes_manager[0].units == "nm"
np.testing.assert_allclose(s0[0].axes_manager[1].scale, 5.0, rtol=1e-5)
assert s0[0].axes_manager[1].units == "eV"
assert s0[0].axes_manager[0].name == "x"
assert s0[0].axes_manager[1].name == "Energy"
# s0[1] contains diffraction patterns
assert s0[1].data.shape == (5, 128, 128)
assert s0[1].axes_manager.signal_dimension == 2
assert s0[1].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0[1].axes_manager[0].scale, 3.68864, rtol=1e-5)
assert s0[1].axes_manager[0].units == "nm"
assert s0[1].axes_manager[1].units == "1 / nm"
assert s0[1].axes_manager[0].name == "x"
np.testing.assert_allclose(s0[1].axes_manager[1].scale, 0.174353, rtol=1e-5)
np.testing.assert_allclose(s0[1].axes_manager[2].scale, 0.174353, rtol=1e-5)
assert s0[1].axes_manager[2].units == "1 / nm"
assert s0[1].axes_manager[1].units == "1 / nm"
assert s0[1].axes_manager[1].name == "x"
assert s0[1].axes_manager[2].name == "y"
def test_load_diffraction_area_scan():
fname0 = TEST_DATA_PATH_NEW / "16x16-diffraction_imagel_5x5x256x256_EDS.emi"
s0 = hs.load(fname0)
# s0[0] contains EDS
assert s0[0].data.shape == (5, 5, 4000)
assert s0[0].axes_manager.signal_dimension == 1
assert s0[0].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0[0].axes_manager[0].scale, 1.87390, rtol=1e-5)
assert s0[0].axes_manager[0].units == "nm"
np.testing.assert_allclose(s0[0].axes_manager[1].scale, -1.87390, rtol=1e-5)
assert s0[0].axes_manager[1].units == "nm"
np.testing.assert_allclose(s0[0].axes_manager[2].scale, 5.0, rtol=1e-5)
assert s0[0].axes_manager[2].units == "eV"
# s0[1] contains diffraction patterns
assert s0[1].data.shape == (5, 5, 256, 256)
assert s0[1].axes_manager.signal_dimension == 2
assert s0[1].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0[1].axes_manager[0].scale, 1.87390, rtol=1e-5)
assert s0[1].axes_manager[0].units == "nm"
np.testing.assert_allclose(s0[1].axes_manager[2].scale, 0.174353, rtol=1e-5)
assert s0[1].axes_manager[2].units == "1 / nm"
assert s0[0].axes_manager[0].name == "x"
assert s0[0].axes_manager[1].name == "y"
assert s0[0].axes_manager[2].name == "Energy"
np.testing.assert_allclose(s0[1].axes_manager[0].scale, 1.87390, rtol=1e-5)
assert s0[1].axes_manager[0].name == "x"
np.testing.assert_allclose(s0[1].axes_manager[1].scale, -1.87390, rtol=1e-5)
assert s0[1].axes_manager[1].units == "nm"
assert s0[1].axes_manager[1].name == "y"
assert s0[1].axes_manager[2].name == "x"
np.testing.assert_allclose(s0[1].axes_manager[3].scale, 0.174353, rtol=1e-5)
assert s0[1].axes_manager[3].units == "1 / nm"
assert s0[1].axes_manager[3].name == "y"
def test_load_spectrum_point():
fname0 = TEST_DATA_PATH_OLD / "16x16-point_spectrum-1x1024.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (1, 1024)
assert s0.axes_manager.signal_dimension == 1
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
# single spectrum should be imported as 1D data, not 2D
# TODO: the following calibration is wrong because it parse the
# 'Dim-1_CalibrationDelta' from the ser header, which is not correct in
# case of point spectra. However, the position seems to be saved in
# 'PositionX' and 'PositionY' arrays of the ser header, so it should
# be possible to workaround using the position arrays.
# np.testing.assert_almost_equal(
# s0.axes_manager[0].scale, 1.0, places=5)
# np.testing.assert_equal(s0.axes_manager[0].units, '')
# np.testing.assert_is(s0.axes_manager[0].name, 'Position index')
np.testing.assert_allclose(s0.axes_manager[1].scale, 0.2, rtol=1e-5)
assert s0.axes_manager[1].units == "eV"
assert s0.axes_manager[1].name == "Energy"
fname1 = TEST_DATA_PATH_OLD / "16x16-2_point-spectra-2x1024.emi"
s1 = hs.load(fname1)
assert s1.data.shape == (2, 1024)
assert s1.axes_manager.signal_dimension == 1
assert s1.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0.axes_manager[1].scale, 0.2, rtol=1e-5)
assert s0.axes_manager[1].units == "eV"
assert s0.axes_manager[1].name == "Energy"
def test_load_spectrum_line_scan():
fname0 = TEST_DATA_PATH_OLD / "16x16-line_profile_horizontal_10x1024.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (10, 1024)
assert s0.axes_manager.signal_dimension == 1
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 0.123034, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(s0.axes_manager[1].scale, 0.2, rtol=1e-5)
assert s0.axes_manager[1].units == "eV"
assert s0.axes_manager[0].name == "x"
assert s0.axes_manager[1].name == "Energy"
fname1 = TEST_DATA_PATH_OLD / "16x16-line_profile_diagonal_10x1024.emi"
s1 = hs.load(fname1)
assert s1.data.shape == (10, 1024)
assert s1.axes_manager.signal_dimension == 1
assert s1.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s1.axes_manager[0].scale, 0.166318, rtol=1e-5)
assert s1.axes_manager[0].units == "nm"
np.testing.assert_allclose(s1.axes_manager[1].scale, 0.2, rtol=1e-5)
assert s1.axes_manager[1].units == "eV"
assert s0.axes_manager[0].name == "x"
def test_load_spectrum_area_scan():
fname0 = TEST_DATA_PATH_OLD / "16x16-spectrum_image-5x5x1024.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (5, 5, 1024)
assert s0.axes_manager.signal_dimension == 1
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 0.120539, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(s0.axes_manager[1].scale, -0.120539, rtol=1e-5)
assert s0.axes_manager[1].units == "nm"
np.testing.assert_allclose(s0.axes_manager[2].scale, 0.2, rtol=1e-5)
assert s0.axes_manager[2].units == "eV"
assert s0.axes_manager[2].name == "Energy"
assert s0.axes_manager[1].name == "y"
assert s0.axes_manager[2].name == "Energy"
def test_load_spectrum_area_scan_not_square():
fname0 = TEST_DATA_PATH_NEW / "16x16-spectrum_image_5x5x4000-not_square.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (5, 5, 4000)
assert s0.axes_manager.signal_dimension == 1
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 1.98591, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(s0.axes_manager[1].scale, -4.25819, rtol=1e-5)
assert s0.axes_manager[1].units == "nm"
np.testing.assert_allclose(s0.axes_manager[2].scale, 5.0, rtol=1e-5)
assert s0.axes_manager[2].units == "eV"
def test_load_search():
fname0 = TEST_DATA_PATH_NEW / "128x128-TEM_search.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (128, 128)
np.testing.assert_allclose(s0.axes_manager[0].scale, 5.26121, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(s0.axes_manager[1].scale, 5.26121, rtol=1e-5)
assert s0.axes_manager[1].units == "nm"
fname1 = TEST_DATA_PATH_OLD / "16x16_STEM_BF_DF_search.emi"
s1 = hs.load(fname1)
assert len(s1) == 2
for s in s1:
assert s.data.shape == (16, 16)
assert s.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s.axes_manager[0].scale, 22.026285, rtol=1e-5)
assert s.axes_manager[0].units == "nm"
np.testing.assert_allclose(s.axes_manager[1].scale, 22.026285, rtol=1e-5)
assert s.axes_manager[1].units == "nm"
def test_load_stack_image_preview():
fname0 = TEST_DATA_PATH_OLD / "64x64x5_TEM_preview.emi"
s0 = hs.load(fname0)
assert s0.data.shape == (5, 64, 64)
assert s0.axes_manager.signal_dimension == 2
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "TEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 1.0, rtol=1e-5)
assert s0.axes_manager[0].units is t.Undefined
np.testing.assert_allclose(s0.axes_manager[1].scale, 6.281833, rtol=1e-5)
assert s0.axes_manager[1].units == "nm"
np.testing.assert_allclose(s0.axes_manager[2].scale, 6.281833, rtol=1e-5)
assert s0.axes_manager[2].units == "nm"
assert s0.axes_manager[0].units is t.Undefined
assert s0.axes_manager[0].scale == 1.0
assert s0.axes_manager[0].name is t.Undefined
assert s0.axes_manager[1].name == "x"
assert s0.axes_manager[2].name == "y"
fname2 = TEST_DATA_PATH_NEW / "128x128x5-diffraction_preview.emi"
s2 = hs.load(fname2)
assert s2.data.shape == (5, 128, 128)
np.testing.assert_allclose(s2.axes_manager[1].scale, 0.042464, rtol=1e-5)
assert s0.axes_manager[0].units is t.Undefined
assert s2.axes_manager[1].units == "1 / nm"
np.testing.assert_allclose(s2.axes_manager[2].scale, 0.042464, rtol=1e-5)
assert s2.axes_manager[2].units == "1 / nm"
fname1 = TEST_DATA_PATH_OLD / "16x16x5_STEM_BF_DF_preview.emi"
s1 = hs.load(fname1)
assert len(s1) == 2
for s in s1:
assert s.data.shape == (5, 16, 16)
assert s.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s.axes_manager[0].scale, 1.0, rtol=1e-5)
assert s.axes_manager[1].units == "nm"
np.testing.assert_allclose(s.axes_manager[1].scale, 21.510044, rtol=1e-5)
def test_load_acquire():
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s0 = hs.load(fname0)
assert s0.axes_manager.signal_dimension == 2
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "TEM"
np.testing.assert_allclose(s0.axes_manager[0].scale, 6.281833, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(s0.axes_manager[1].scale, 6.281833, rtol=1e-5)
assert s0.axes_manager[1].units == "nm"
assert s0.axes_manager[0].name == "x"
assert s0.axes_manager[1].name == "y"
fname1 = TEST_DATA_PATH_OLD / "16x16_STEM_BF_DF_acquire.emi"
s1 = hs.load(fname1)
assert len(s1) == 2
for s in s1:
assert s.data.shape == (16, 16)
assert s.metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
np.testing.assert_allclose(s.axes_manager[0].scale, 21.510044, rtol=1e-5)
assert s.axes_manager[0].units == "nm"
np.testing.assert_allclose(s.axes_manager[1].scale, 21.510044, rtol=1e-5)
assert s.axes_manager[1].units == "nm"
assert s.axes_manager[0].name == "x"
assert s.axes_manager[1].name == "y"
@pytest.mark.parametrize("only_valid_data", (True, False))
def test_load_TotalNumberElements_ne_ValidNumberElements(only_valid_data):
fname0 = TEST_DATA_PATH_OLD / "X - Au NP EELS_2.ser"
s0 = hs.load(fname0, only_valid_data=only_valid_data)
nav_shape = () if only_valid_data else (2,)
assert s0.data.shape == nav_shape + (2048,)
assert len(s0.axes_manager.navigation_axes) == len(nav_shape)
np.testing.assert_allclose(s0.axes_manager[-1].offset, 2160, rtol=1e-5)
np.testing.assert_allclose(s0.axes_manager[-1].scale, 0.2, rtol=1e-5)
fname1 = TEST_DATA_PATH_OLD / "03_Scanning Preview.emi"
s1 = hs.load(fname1, only_valid_data=only_valid_data)
nav_shape = (5,) if only_valid_data else (200,)
assert s1.data.shape == nav_shape + (128, 128)
nav_axes = s1.axes_manager.navigation_axes
sig_axes = s1.axes_manager.signal_axes
assert len(nav_axes) == len(nav_shape)
assert sig_axes[-1].size == sig_axes[1].size == 128
np.testing.assert_allclose(sig_axes[0].scale, 0.38435, rtol=1e-5)
np.testing.assert_allclose(sig_axes[1].scale, 0.38435, rtol=1e-5)
def test_read_STEM_TEM_mode():
# TEM image
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s0 = hs.load(fname0)
assert s0.metadata.Acquisition_instrument.TEM.acquisition_mode == "TEM"
# TEM diffraction
fname1 = TEST_DATA_PATH_OLD / "64x64_diffraction_acquire.emi"
s1 = hs.load(fname1)
assert s1.metadata.Acquisition_instrument.TEM.acquisition_mode == "TEM"
fname2 = TEST_DATA_PATH_OLD / "16x16_STEM_BF_DF_acquire.emi"
# STEM diffraction
s2 = hs.load(fname2)
assert s2[0].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
assert s2[1].metadata.Acquisition_instrument.TEM.acquisition_mode == "STEM"
def test_load_units_scale():
# TEM image
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s0 = hs.load(fname0)
np.testing.assert_allclose(s0.axes_manager[0].scale, 6.28183, rtol=1e-5)
assert s0.axes_manager[0].units == "nm"
np.testing.assert_allclose(
s0.metadata.Acquisition_instrument.TEM.magnification, 19500.0, rtol=1e-5
)
# TEM diffraction
fname1 = TEST_DATA_PATH_OLD / "64x64_diffraction_acquire.emi"
s1 = hs.load(fname1)
np.testing.assert_allclose(s1.axes_manager[0].scale, 0.101571, rtol=1e-5)
assert s1.axes_manager[0].units == "1 / nm"
np.testing.assert_allclose(
s1.metadata.Acquisition_instrument.TEM.camera_length, 490.0, rtol=1e-5
)
# STEM diffraction
fname2 = TEST_DATA_PATH_OLD / "16x16_STEM_BF_DF_acquire.emi"
s2 = hs.load(fname2)
assert s2[0].axes_manager[0].units == "nm"
np.testing.assert_allclose(s2[0].axes_manager[0].scale, 21.5100, rtol=1e-5)
np.testing.assert_allclose(
s2[0].metadata.Acquisition_instrument.TEM.magnification, 10000.0, rtol=1e-5
)
def test_guess_units_from_mode():
from rsciio.tia._api import (
_guess_units_from_mode,
convert_xml_to_dict,
get_xml_info_from_emi,
)
fname0_emi = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
fname0_ser = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire_1.ser"
objects = get_xml_info_from_emi(fname0_emi)
header0, data0 = load_ser_file(fname0_ser)
objects_dict = convert_xml_to_dict(objects[0])
unit = _guess_units_from_mode(objects_dict, header0)
assert unit == "meters"
# objects is empty dictionary
with pytest.warns(
UserWarning, match="The navigation axes units could not be determined."
):
unit = _guess_units_from_mode({}, header0)
assert unit == "meters"
@pytest.mark.parametrize("stack_metadata", [True, False, 0])
def test_load_multisignal_stack(stack_metadata):
fname0 = TEST_DATA_PATH_NEW / "16x16-line_profile_horizontal_5x128x128_EDS.emi"
s = hs.load([fname0, fname0], stack=True, stack_metadata=stack_metadata)
assert s[0].axes_manager.navigation_shape == (5, 2)
assert s[0].axes_manager.signal_shape == (4000,)
assert s[1].axes_manager.navigation_shape == (5, 2)
assert s[1].axes_manager.signal_shape == (128, 128)
om = s[0].original_metadata
assert om.has_item("stack_elements") is (stack_metadata is True)
def test_load_multisignal_stack_mismatch():
fname0 = TEST_DATA_PATH_NEW / "16x16-diffraction_imagel_5x5x256x256_EDS.emi"
fname1 = TEST_DATA_PATH_NEW / "16x16-diffraction_imagel_5x5x256x256_EDS_copy.emi"
with pytest.raises(ValueError) as cm:
hs.load([fname0, fname1], stack=True)
cm.match("The number of sub-signals per file does not match*")
hs.load([fname0, fname1])
def test_date_time():
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s = hs.load(fname0)
assert s.metadata.General.date == "2016-02-21"
assert s.metadata.General.time == "17:50:18"
fname1 = TEST_DATA_PATH_OLD / "16x16-line_profile_horizontal_10x1024.emi"
s = hs.load(fname1)
assert s.metadata.General.date == "2016-02-22"
assert s.metadata.General.time == "11:50:36"
def test_metadata_TEM():
fname0 = TEST_DATA_PATH_OLD / "64x64_TEM_images_acquire.emi"
s = hs.load(fname0)
assert s.metadata.Acquisition_instrument.TEM.beam_energy == 200.0
assert s.metadata.Acquisition_instrument.TEM.magnification == 19500.0
assert (
s.metadata.Acquisition_instrument.TEM.microscope
== "Tecnai 200 kV D2267 SuperTwin"
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.tilt_alpha, 0.0, rtol=1e-5
)
def test_metadata_STEM():
fname0 = TEST_DATA_PATH_OLD / "16x16_STEM_BF_DF_acquire.emi"
s = hs.load(fname0)[0]
assert s.metadata.Acquisition_instrument.TEM.beam_energy == 200.0
assert s.metadata.Acquisition_instrument.TEM.camera_length == 40.0
assert s.metadata.Acquisition_instrument.TEM.magnification == 10000.0
assert (
s.metadata.Acquisition_instrument.TEM.microscope
== "Tecnai 200 kV D2267 SuperTwin"
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.tilt_alpha, 0.0, rtol=1e-6
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.tilt_beta, 0.0, rtol=1e-6
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.x, -0.000158, rtol=1e-6
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.y, 1.9e-05, rtol=1e-6
)
np.testing.assert_allclose(
s.metadata.Acquisition_instrument.TEM.Stage.z, 0.0, rtol=1e-6
)
def test_metadata_diffraction():
fname0 = TEST_DATA_PATH_OLD / "64x64_diffraction_acquire.emi"
s = hs.load(fname0)
assert s.metadata.Acquisition_instrument.TEM.beam_energy == 200.0
assert s.metadata.Acquisition_instrument.TEM.camera_length == 490.0
assert (
s.metadata.Acquisition_instrument.TEM.microscope
== "Tecnai 200 kV D2267 SuperTwin"
)
def test_unsupported_extension():
with pytest.raises(ValueError):
file_reader("fname.unsupported_extension")
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