1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
|
# -*- 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.protochips._api import ProtochipsCSV, invalid_file_error
hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
TEST_DATA_PATH = Path(__file__).parent / "data" / "protochips"
# To generate a new reference numpy file
generate_numpy_file = False
def create_numpy_file(filename, obj):
gen = (obj._data_dictionary[key] for key in obj.logged_quantity_name_list)
data = np.vstack(list(gen))
np.save(filename, data.T)
#######################
# Protochips gas cell #
#######################
def test_read_protochips_gas_cell():
filename = TEST_DATA_PATH / "protochips_gas_cell.csv"
s = hs.load(filename, reader="protochips")
assert len(s) == 5
assert s[0].metadata.General.title == "Holder Temperature (Degrees C)"
assert s[0].metadata.Signal.signal_type == ""
assert s[0].metadata.Signal.quantity == "Temperature (Degrees C)"
assert s[1].metadata.General.title == "Holder Pressure (Torr)"
assert s[1].metadata.Signal.signal_type == ""
assert s[1].metadata.Signal.quantity == "Pressure (Torr)"
assert s[2].metadata.General.title == "Tank1 Pressure (Torr)"
assert s[2].metadata.Signal.signal_type == ""
assert s[2].metadata.Signal.quantity == "Pressure (Torr)"
assert s[3].metadata.General.title == "Tank2 Pressure (Torr)"
assert s[3].metadata.Signal.signal_type == ""
assert s[3].metadata.Signal.quantity == "Pressure (Torr)"
assert s[4].metadata.General.title == "Vacuum Tank Pressure (Torr)"
assert s[4].metadata.Signal.signal_type == ""
assert s[4].metadata.Signal.quantity == "Pressure (Torr)"
def get_datetime(dt):
dt_np = np.datetime64(dt)
dt_str = np.datetime_as_string(dt_np)
date, time = dt_str.split("T")
return date, time, dt_np
datetime_gas_cell = get_datetime("2014-12-15T19:07:04.165000")
datetime_gas_cell_no_user = get_datetime("2016-10-17T16:59:20.391000")
def test_loading_random_csv_file():
filename = TEST_DATA_PATH / "random_csv_file.csv"
with pytest.raises(IOError) as cm:
ProtochipsCSV(filename)
cm.match(invalid_file_error)
def test_loading_invalid_protochips_file():
filename = TEST_DATA_PATH / "invalid_protochips_file.csv"
with pytest.raises(IOError) as cm:
hs.load(filename, reader="protochips")
cm.match(invalid_file_error)
class TestProtochipsGasCellCSV:
def setup_method(self, method):
filename = TEST_DATA_PATH / "protochips_gas_cell.csv"
self.s_list = hs.load(filename, reader="protochips")
def test_read_metadata(self):
date, time, dt_np = datetime_gas_cell
for s in self.s_list:
assert s.metadata.General.date == date
assert s.metadata.General.time == time
assert s.axes_manager[0].units == "s"
np.testing.assert_allclose(s.axes_manager[0].scale, 0.25995, atol=1e-5)
assert s.axes_manager[0].offset == 0
def test_read_original_metadata(self):
om = self.s_list[0].original_metadata.Protochips_header
assert (
om.Calibration_file_path == "The calibration files names"
" are saved in the 'Original notes' array of the "
"original metadata."
)
assert om.Holder_Pressure_units == "Torr"
assert om.Holder_Temperature_units == "Degrees C"
assert om.Start_time == datetime_gas_cell[2]
assert om.Holder_Pressure_units == "Torr"
assert om.Tank1_Pressure_units == "Torr"
assert om.Tank2_Pressure_units == "Torr"
assert om.Vacuum_Tank_Pressure_units == "Torr"
assert om.Time_units == "Milliseconds"
assert om.User == "eric"
class TestProtochipsGasCellCSVNoUser:
def setup_method(self, method):
filename = TEST_DATA_PATH / "protochips_gas_cell_no_user.csv"
self.s_list = hs.load(filename, reader="protochips")
def test_read_metadata(self):
date, time, dt_np = datetime_gas_cell_no_user
for s in self.s_list:
assert s.metadata.General.date == date
assert s.metadata.General.time == time
assert s.axes_manager[0].units == "s"
np.testing.assert_allclose(s.axes_manager[0].scale, 0.26029, atol=1e-5)
assert s.axes_manager[0].offset == 0
def test_read_original_metadata(self):
om = self.s_list[0].original_metadata.Protochips_header
assert (
om.Calibration_file_path == "The calibration files names"
" are saved in the 'Original notes' array of the "
"original metadata."
)
assert om.Holder_Pressure_units == "Torr"
assert om.Holder_Temperature_units == "Degrees C"
assert om.Start_time == datetime_gas_cell_no_user[2]
assert om.Holder_Pressure_units == "Torr"
assert om.Tank1_Pressure_units == "Torr"
assert om.Tank2_Pressure_units == "Torr"
assert om.Vacuum_Tank_Pressure_units == "Torr"
assert om.Time_units == "Milliseconds"
class TestProtochipsGasCellCSVReader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "protochips_gas_cell.csv"
self.pgc = ProtochipsCSV(self.filename)
if generate_numpy_file:
create_numpy_file(self.filename.with_suffix(".npy"), self.pgc)
def test_read_column_name(self):
assert self.pgc.column_name == [
"Time",
"Notes",
"Holder Temperature",
"Holder Pressure",
"Tank1 Pressure",
"Tank2 Pressure",
"Vacuum Tank Pressure",
]
def test_read_start_datetime(self):
assert self.pgc.start_datetime == datetime_gas_cell[2]
def test_read_data(self):
gen = (
self.pgc._data_dictionary[key] for key in self.pgc.logged_quantity_name_list
)
data = np.vstack(list(gen))
expected_data = np.load(TEST_DATA_PATH / "protochips_gas_cell.npy")
np.testing.assert_allclose(data.T, expected_data)
def test_read_metadata_header(self):
assert self.pgc.time_units == "Milliseconds"
assert self.pgc.time_units == "Milliseconds"
assert self.pgc.temperature_units == "Degrees C"
assert self.pgc.pressure_units == "Torr"
assert self.pgc.current_units == "Amps"
assert self.pgc.voltage_units == "Volts"
assert self.pgc.resistance_units == "Ohms"
assert self.pgc.user == "eric"
#########################
# Protochips electrical #
#########################
def test_read_protochips_electrical():
filename = TEST_DATA_PATH / "protochips_electrical.csv"
s = hs.load(filename, reader="protochips")
assert len(s) == 6
assert s[0].metadata.General.title == "Channel A Current (Amps)"
assert s[0].metadata.Signal.signal_type == ""
assert s[0].metadata.Signal.quantity == "Current (Amps)"
assert s[1].metadata.General.title == "Channel A Voltage (Volts)"
assert s[1].metadata.Signal.signal_type == ""
assert s[1].metadata.Signal.quantity == "Voltage (Volts)"
assert s[2].metadata.General.title == "Channel A Resistance (Ohms)"
assert s[2].metadata.Signal.signal_type == ""
assert s[2].metadata.Signal.quantity == "Resistance (Ohms)"
assert s[3].metadata.General.title == "Channel B Current (Amps)"
assert s[3].metadata.Signal.signal_type == ""
assert s[3].metadata.Signal.quantity == "Current (Amps)"
assert s[4].metadata.General.title == "Channel B Voltage (Volts)"
assert s[4].metadata.Signal.signal_type == ""
assert s[4].metadata.Signal.quantity == "Voltage (Volts)"
assert s[5].metadata.General.title == "Channel B Resistance (Ohms)"
assert s[5].metadata.Signal.signal_type == ""
assert s[5].metadata.Signal.quantity == "Resistance (Ohms)"
class TestProtochipsElectricalCSVReader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "protochips_electrical.csv"
self.pa = ProtochipsCSV(self.filename)
if generate_numpy_file:
create_numpy_file(self.filename.with_suffix(".npy"), self.pa)
def test_read_column_name(self):
assert self.pa.column_name == [
"Time",
"Notes",
"Channel A Current",
"Channel A Voltage",
"Channel A Resistance",
"Channel B Current",
"Channel B Voltage",
"Channel B Resistance",
]
def test_read_start_datetime(self):
dt = np.datetime64("2014-10-08T16:26:51.738000")
assert self.pa.start_datetime == dt
def test_read_data(self):
gen = (
self.pa._data_dictionary[key] for key in self.pa.logged_quantity_name_list
)
data = np.vstack(list(gen))
expected_data = np.load(TEST_DATA_PATH / "protochips_electrical.npy")
np.testing.assert_allclose(data.T, expected_data)
######################
# Protochips thermal #
######################
def test_read_protochips_thermal():
filename = TEST_DATA_PATH / "protochips_thermal.csv"
s = hs.load(filename, reader="protochips")
assert s.metadata.General.title == "Channel A Temperature (Degrees C)"
assert s.metadata.Signal.signal_type == ""
assert s.metadata.Signal.quantity == "Temperature (Degrees C)"
assert s.metadata.General.notes == "Calibration file name: AD21013_8.cal"
class TestProtochipsThermallCSVReader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "protochips_thermal.csv"
self.pt = ProtochipsCSV(self.filename)
if generate_numpy_file:
create_numpy_file(self.filename.with_suffix(".npy"), self.pt)
def test_read_column_name(self):
assert self.pt.column_name == ["Time", "Notes", "Channel A Temperature"]
def test_read_start_datetime(self):
dt = np.datetime64("2014-12-03T17:15:37.192000")
np.testing.assert_equal(self.pt.start_datetime, dt)
def test_read_data(self):
gen = (
self.pt._data_dictionary[key] for key in self.pt.logged_quantity_name_list
)
data = np.vstack(list(gen))
expected_data = np.load(TEST_DATA_PATH / "protochips_thermal.npy")
np.testing.assert_allclose(data.T, expected_data)
#############################
# Protochips electrothermal #
#############################
def test_read_protochips_electrothermal():
filename = TEST_DATA_PATH / "protochips_electrothermal.csv"
s = hs.load(filename, reader="protochips")
assert len(s) == 4
assert s[0].metadata.General.title == "Channel A Temperature (Degrees C)"
assert s[0].metadata.Signal.signal_type == ""
assert s[0].metadata.Signal.quantity == "Temperature (Degrees C)"
assert s[1].metadata.General.title == "Channel B Current (Amps)"
assert s[1].metadata.Signal.signal_type == ""
assert s[0].metadata.General.notes == "Calibration file name: AD21018_4.cal"
assert s[1].metadata.Signal.quantity == "Current (Amps)"
assert s[2].metadata.General.title == "Channel B Voltage (Volts)"
assert s[2].metadata.Signal.signal_type == ""
assert s[2].metadata.Signal.quantity == "Voltage (Volts)"
assert s[3].metadata.General.title == "Channel B Resistance (Ohms)"
assert s[3].metadata.Signal.signal_type == ""
assert s[3].metadata.Signal.quantity == "Resistance (Ohms)"
class TestProtochipsElectrothermalCSVReader:
def setup_method(self, method):
self.filename = TEST_DATA_PATH / "protochips_electrothermal.csv"
self.pet = ProtochipsCSV(self.filename)
if generate_numpy_file:
create_numpy_file(self.filename.with_suffix(".npy"), self.pet)
def test_read_column_name(self):
assert self.pet.column_name == [
"Time",
"Notes",
"Channel A Temperature",
"Channel B Current",
"Channel B Voltage",
"Channel B Resistance",
]
def test_read_start_datetime(self):
dt = np.datetime64("2014-11-05T14:42:51.369000")
np.testing.assert_equal(self.pet.start_datetime, dt)
def test_read_data(self):
gen = (
self.pet._data_dictionary[key] for key in self.pet.logged_quantity_name_list
)
data = np.vstack(list(gen))
expected_data = np.load(TEST_DATA_PATH / self.filename.with_suffix(".npy"))
np.testing.assert_allclose(data.T, expected_data)
|
