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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 gc
import importlib
from importlib.metadata import version
from pathlib import Path
import numpy as np
import pytest
from packaging.version import Version
from rsciio.empad._api import _parse_xml
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
t = pytest.importorskip("traits.api", reason="traits not installed")
DATA_DIR = Path(__file__).parent / "data" / "empad"
FILENAME_STACK_RAW = DATA_DIR / "series_x10.raw"
FILENAME_MAP_RAW = DATA_DIR / "scan_x4_y4.raw"
def _create_raw_data(filename, shape):
size = np.prod(shape)
data = np.arange(size).reshape(shape).astype("float32")
data.tofile(filename)
def setup_module(module):
_create_raw_data(FILENAME_STACK_RAW, (166400,))
_create_raw_data(FILENAME_MAP_RAW, (4 * 4 * 130 * 128))
def teardown_module(module):
# run garbage collection to release file on windows
gc.collect()
fs = [f for f in [FILENAME_STACK_RAW, FILENAME_MAP_RAW] if f.exists()]
for f in fs:
# remove file
f.unlink()
@pytest.mark.parametrize("lazy", (False, True))
def test_read_stack(lazy):
# xml file version 0.51 211118
s = hs.load(DATA_DIR / "stack_images.xml", lazy=lazy, reader="EMPAD")
assert s.data.dtype == "float32"
ref_data = np.arange(166400).reshape((10, 130, 128))[..., :128, :]
np.testing.assert_allclose(s.data, ref_data.astype("float32"))
signal_axes = s.axes_manager.signal_axes
assert signal_axes[0].name == "width"
assert signal_axes[1].name == "height"
for axis in signal_axes:
if importlib.util.find_spec("pyxem") and Version(version("pyxem")) >= Version(
"0.19"
):
units = "px"
else:
units = t.Undefined
assert axis.units == units
assert axis.scale == 1.0
assert axis.offset == -64
navigation_axes = s.axes_manager.navigation_axes
assert navigation_axes[0].name == "series_count"
assert navigation_axes[0].units == "ms"
assert navigation_axes[0].scale == 1.0
assert navigation_axes[0].offset == 0.0
assert s.metadata.General.date == "2019-06-07"
assert s.metadata.General.time == "13:17:22.590279"
assert s.metadata.Signal.signal_type == "electron_diffraction"
@pytest.mark.parametrize("lazy", (False, True))
def test_read_map(lazy):
# xml file version 0.51 211118
s = hs.load(DATA_DIR / "map4x4.xml", lazy=lazy, reader="EMPAD")
assert s.data.dtype == "float32"
ref_data = np.arange(266240).reshape((4, 4, 130, 128))[..., :128, :]
np.testing.assert_allclose(s.data, ref_data.astype("float32"))
signal_axes = s.axes_manager.signal_axes
assert signal_axes[0].name == "width"
assert signal_axes[1].name == "height"
for axis in signal_axes:
assert axis.units == "1/nm"
np.testing.assert_allclose(axis.scale, 0.1826537)
np.testing.assert_allclose(axis.offset, -11.689837)
navigation_axes = s.axes_manager.navigation_axes
assert navigation_axes[0].name == "scan_y"
assert navigation_axes[1].name == "scan_x"
for axis in navigation_axes:
assert axis.units == "µm"
np.testing.assert_allclose(axis.scale, 1.1415856)
np.testing.assert_allclose(axis.offset, 0.0)
assert s.metadata.General.date == "2019-06-06"
assert s.metadata.General.time == "13:30:00.164675"
assert s.metadata.Signal.signal_type == "electron_diffraction"
def test_parse_xml_1_2_0():
# xml file version 1.2.0 (2020-10-29)
filename = DATA_DIR / "map128x128_version1.2.0.xml"
om, info = _parse_xml(filename)
assert info["scan_x"] == 128
assert info["scan_y"] == 128
assert info["raw_filename"] == "scan_x128_y128.raw"
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