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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>.
from pathlib import Path
import numpy as np
import pytest
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
TEST_DATA_PATH = Path(__file__).parent / "data" / "semper"
# Reference data:
data_signal = np.arange(27, dtype=np.float32).reshape((3, 3, 3)) / 2.0
data_image = np.arange(16, dtype=np.float32).reshape((4, 4)) / 2.0
data_spectrum = np.arange(10, dtype=np.float32) / 2.0
data_image_byte = np.arange(25, dtype=np.byte).reshape(
(5, 5)
) # Odd dim. tests strange read/write
data_image_int16 = np.arange(16, dtype=np.int16).reshape((4, 4))
data_image_int32 = np.arange(16, dtype=np.int32).reshape((4, 4))
data_image_complex = (data_image_int32 + 1j * data_image).astype(np.complex64)
test_title = "This is a test!"
def test_writing_unsupported_data_type(tmp_path):
data = np.arange(5 * 10).reshape((5, 10))
s = hs.signals.BaseSignal(data.astype("int64"))
with pytest.raises(IOError) as cm:
s.save(filename=tmp_path / "test_writing_unsupported_data_type.unf")
cm.match("The SEMPER file format does not support int64 data type")
def test_writing_loading_metadata(tmp_path):
data = np.arange(5 * 10).reshape((5, 10)).astype(np.int8)
s = hs.signals.BaseSignal(data)
s.metadata.set_item("General.date", "2016-08-06")
s.metadata.set_item("General.time", "11:55:00")
fname = tmp_path / "test_write_with_metadata.unf"
s.save(fname)
s2 = hs.load(fname)
np.testing.assert_allclose(s.data, s2.data)
assert s.metadata.General.date == s2.metadata.General.date
assert s.metadata.General.time == s2.metadata.General.time
def test_signal_3d_loading():
signal = hs.load(TEST_DATA_PATH / "example_signal_3d.unf")
np.testing.assert_equal(signal.data, data_signal)
np.testing.assert_equal(signal.original_metadata.IFORM, 2) # float
assert isinstance(signal, hs.signals.BaseSignal)
def test_image_2d_loading():
signal = hs.load(TEST_DATA_PATH / "example_image_2d.unf")
np.testing.assert_equal(signal.data, data_image)
np.testing.assert_equal(signal.original_metadata.IFORM, 2) # float
assert isinstance(signal, hs.signals.Signal2D)
def test_spectrum_1d_loading():
signal = hs.load(TEST_DATA_PATH / "example_spectrum_1d.unf")
np.testing.assert_equal(signal.data, data_spectrum)
np.testing.assert_equal(signal.original_metadata.IFORM, 2) # float
assert isinstance(signal, hs.signals.Signal1D)
def test_image_byte_loading():
signal = hs.load(TEST_DATA_PATH / "example_image_byte.unf")
np.testing.assert_equal(signal.data, data_image_byte)
np.testing.assert_equal(signal.original_metadata.IFORM, 0) # byte
assert isinstance(signal, hs.signals.Signal2D)
def test_image_int16_loading():
signal = hs.load(TEST_DATA_PATH / "example_image_int16.unf")
np.testing.assert_equal(signal.data, data_image_int16)
np.testing.assert_equal(signal.original_metadata.IFORM, 1) # int16
assert isinstance(signal, hs.signals.Signal2D)
def test_image_int32_loading():
signal = hs.load(TEST_DATA_PATH / "example_image_int32.unf")
np.testing.assert_equal(signal.data, data_image_int32)
np.testing.assert_equal(signal.original_metadata.IFORM, 4) # int32
assert isinstance(signal, hs.signals.Signal2D)
def test_image_complex_loading():
signal = hs.load(TEST_DATA_PATH / "example_image_complex.unf")
np.testing.assert_equal(signal.data, data_image_complex)
np.testing.assert_equal(signal.original_metadata.IFORM, 3) # complex
assert isinstance(signal, hs.signals.ComplexSignal)
def test_with_title_loading():
signal = hs.load(TEST_DATA_PATH / "example_with_title.unf")
np.testing.assert_equal(signal.data, data_image)
np.testing.assert_equal(signal.original_metadata.IFORM, 2) # float
np.testing.assert_equal(signal.metadata.General.title, test_title)
assert isinstance(signal, hs.signals.Signal2D)
def test_no_label_loading():
signal = hs.load(TEST_DATA_PATH / "example_no_label.unf")
np.testing.assert_equal(signal.data, data_image)
np.testing.assert_equal(signal.original_metadata.ILABEL, 0)
assert isinstance(signal, hs.signals.Signal2D)
def test_save_and_read_image(tmp_path):
signal_ref = hs.signals.Signal2D(data_image)
signal_ref.metadata.General.title = test_title
signal_ref.save(tmp_path / "example_temp.unf", overwrite=True)
signal = hs.load(tmp_path / "example_temp.unf")
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.metadata.General.title, test_title)
assert isinstance(signal, hs.signals.Signal2D)
def test_save_and_read_byte(tmp_path):
signal_ref = hs.signals.Signal2D(data_image_byte)
signal_ref.metadata.General.title = test_title
signal_ref.save(
tmp_path / "example_temp.unf",
)
signal = hs.load(tmp_path / "example_temp.unf")
np.testing.assert_equal(signal.data, signal_ref.data)
np.testing.assert_equal(signal.metadata.General.title, test_title)
assert isinstance(signal, hs.signals.Signal2D)
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