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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
from rsciio.impulse._api import ImpulseCSV, invalid_file_error, invalid_filenaming_error
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
TEST_DATA_PATH = Path(__file__).parent / "data" / "impulse"
# Load a synchronized data log file
def test_read_sync_file():
filename = TEST_DATA_PATH / "StubExperiment_Synchronized data.csv"
s = hs.load(filename, reader="impulse")
assert len(s) == 13
assert s[0].metadata.General.title == "Temperature Measured (degC)"
assert s[0].metadata.Signal.quantity == "degC"
assert s[1].metadata.General.title == "MixValve"
assert s[1].metadata.Signal.quantity == ""
assert s[2].metadata.General.title == "Pin Measured"
assert s[2].metadata.Signal.quantity == ""
assert s[3].metadata.General.title == "Pout Measured"
assert s[3].metadata.Signal.quantity == ""
assert s[4].metadata.General.title == "Pnr Measured"
assert s[4].metadata.Signal.quantity == ""
assert s[5].metadata.General.title == "Fnr"
assert s[5].metadata.Signal.quantity == ""
assert s[6].metadata.General.title == "% Gas1 Measured"
assert s[6].metadata.Signal.quantity == ""
assert s[7].metadata.General.title == "% Gas2 Measured"
assert s[7].metadata.Signal.quantity == ""
assert s[8].metadata.General.title == "% Gas3 Measured"
assert s[8].metadata.Signal.quantity == ""
assert s[9].metadata.General.title == "Channel#1"
assert s[9].metadata.Signal.quantity == ""
assert s[10].metadata.General.title == "Channel#2"
assert s[10].metadata.Signal.quantity == ""
assert s[11].metadata.General.title == "Channel#3"
assert s[11].metadata.Signal.quantity == ""
assert s[12].metadata.General.title == "Channel#4"
assert s[12].metadata.Signal.quantity == ""
class testSyncFile:
def setup_method(self, method):
filename = TEST_DATA_PATH / "StubExperiment_Synchronized data.csv"
self.s_list = hs.load(filename, reader="impulse")
def test_read_metadata(self):
for s in self.s_list:
assert s.metadata.General.date == "06-08-2021"
assert s.metadata.General.time == "13:40:19"
assert s.axes_manager[0].units == "s"
np.testing.assert_allclose(
s.axes_manager[0].scale, 0.5114766839378239, atol=1e-5
)
assert s.axes_manager[0].offset == 0
def test_read_original_metadata(self):
om = self.s_list[0].original_metadata.Impulse_header
assert om.Calibration_value == 0.25
assert om.Description == "Experiment with stub data"
assert om.Experiment_date == "06-08-2021"
assert om.Experiment_duration == "00.00:06:45.416"
assert om.Experiment_time == "13:40:19"
assert om.Gas1 == "H2"
assert om.Gas2 == "CH4"
assert om.Gas3 == "Ar"
assert om.MassSpec_File_Location == ""
assert om.MassSpec_channel_1 == "28 (Nitrogen)"
assert om.MassSpec_channel_2 == "32 (Oxygen)"
assert om.MassSpec_channel_3 == "18 (Water)"
assert om.MassSpec_channel_4 == "44 (Carbon dioxide)"
assert om.Max_temperature == 1100
assert om.Notes == [
"13:46:46: Live note one",
"13:46:52: Live note two",
"13:46:56: Live note three",
]
assert om.Room_temperature == 21
assert om.Sample == "Gold"
assert om.System_version == "G+"
def test_read_data(self):
expected_data = np.load(TEST_DATA_PATH / "StubExperiment_Synchronized data.npy")
np.testing.assert_allclose(self.s_list.T, expected_data)
class testSyncFileCSVreader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "StubExperiment_Synchronized data.csv"
self.isf = ImpulseCSV(self.filename)
def test_read_column_name(self):
assert self.isf.column_name == [
"Temperature Measured",
"MixValve",
"Pin Measured",
"Pout Measured",
"Pnr Measured",
"Fnr",
"% Gas1 Measured",
"% Gas2 Measured",
"% Gas3 Measured",
"Channel#1",
"Channel#2",
"Channel#3",
"Channel#4",
]
def test_read_data(self):
dicts = (
self.isf._data_dictionary[key] for key in self.isf.logged_quantity_name_list
)
data = np.vstack(list(dicts))
expected_data = np.load(TEST_DATA_PATH / "StubExperiment_Synchronized data.npy")
np.testing.assert_allclose(data.T, expected_data)
# Loading a random csv file
def test_loading_random_csv_file():
filename = TEST_DATA_PATH / "random_csv_file.csv"
with pytest.raises(IOError) as cm:
ImpulseCSV(filename)
cm.match(invalid_file_error)
# Loading a csv file with an incorrect filename
def test_loading_invalid_impulse_filename():
filename = TEST_DATA_PATH / "changed_file_name.csv"
with pytest.raises(IOError) as cm:
hs.load(filename, reader="impulse")
cm.match(invalid_filenaming_error)
# Test raw data file
class testRawFile:
def setup_method(self, method):
filename = TEST_DATA_PATH / "StubExperiment_Heat raw.csv"
self.s_list = hs.load(filename, reader="impulse")
def test_read_metadata(self):
for s in self.s_list:
assert s.metadata.General.date == "06-08-2021"
assert s.metadata.General.time == "13:40:19"
assert s.axes_manager[0].units == "s"
np.testing.assert_allclose(
s.axes_manager[0].scale, 0.5114766839378239, atol=1e-5
)
assert s.axes_manager[0].offset == 0
def test_read_original_metadata(self):
om = self.s_list[0].original_metadata.Impulse_header
assert om.Calibration_value == 0.25
assert om.Description == "Experiment with stub data"
assert om.Experiment_date == "06-08-2021"
assert om.Experiment_duration == "00.00:06:45.416"
assert om.Experiment_time == "13:40:19"
assert om.Gas1 == "H2"
assert om.Gas2 == "CH4"
assert om.Gas3 == "Ar"
assert om.MassSpec_File_Location == ""
assert om.MassSpec_channel_1 == "28 (Nitrogen)"
assert om.MassSpec_channel_2 == "32 (Oxygen)"
assert om.MassSpec_channel_3 == "18 (Water)"
assert om.MassSpec_channel_4 == "44 (Carbon dioxide)"
assert om.Max_temperature == 1100
assert om.Notes == [
"13:46:46: Live note one",
"13:46:52: Live note two",
"13:46:56: Live note three",
]
assert om.Room_temperature == 21
assert om.Sample == "Gold"
assert om.System_version == "G+"
class testRawFileCSVreader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "StubExperiment_Heat raw.csv"
self.isf = ImpulseCSV(self.filename)
def test_read_column_name(self):
assert self.isf.column_name == ["Temperature Measured"]
def test_read_start_datetime(self):
assert self.isf.start_datetime == "2021-08-06T13:40:19.000000"
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