def test_find_missing_projection_number():
test_input = [
EXPECTED_HEADER_FOR_IMAT_LOG_FILE,
["ignored line"],
[
"timestamp", "Projection: 0 angle: 0.0", "counts before: 12345",
"counts_after: 45678"
],
[
"timestamp", "Projection: 1 angle: 0.1", "counts before: 12345",
"counts_after: 45678"
],
[
"timestamp", "Projection: 2 angle: 0.2", "counts before: 12345",
"counts_after: 45678"
],
]
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.projection_numbers()) == 3
# nothing missing
logfile.raise_if_angle_missing(
["file_000.tif", "file_001.tif", "file_002.tif"])
# image file missing
assert_raises(RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_002.tif"])
# image file missing
assert_raises(RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_001.tif"])
assert_raises(
RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_001.tif", "file_002.tif", "file_003.tif"])
def test_counts_compare():
logfile = IMATLogFile(TXT_LOG_FILE, "/tmp/fake")
logfile_from_csv = IMATLogFile(CSV_LOG_FILE, "/tmp/fake")
assert len(logfile.counts().value) == len(logfile_from_csv.counts().value)
assert logfile.counts().value[0] == logfile_from_csv.counts().value[0]
assert logfile.counts().value[1] == logfile_from_csv.counts().value[1]
assert logfile.counts().value[2] == logfile_from_csv.counts().value[2]
def test_parsing_log_file():
test_input = [["ignored line"], ["ignored line"],
[
"timestamp", "projection index and angle: 0.100",
"counts before", "counts_after"
]]
logfile = IMATLogFile(test_input)
assert len(logfile.projection_angles().value) == 1
assert logfile.projection_angles().value[0] == np.deg2rad(
0.1), f"Got: {logfile.projection_angles().value[0]}"
def test_parsing_log_file():
test_input = [
EXPECTED_HEADER_FOR_IMAT_LOG_FILE, ["ignored line"],
[
"timestamp", "Projection: 0 angle: 0.1", "counts before: 12345",
"counts_after: 45678"
]
]
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.projection_angles().value) == 1
assert logfile.projection_angles().value[0] == np.deg2rad(
0.1), f"Got: {logfile.projection_angles().value[0]}"
assert logfile.counts().value[0] == (45678 - 12345)
def test_find_missing_projection_number(test_input):
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.projection_numbers()) == 3
# nothing missing
logfile.raise_if_angle_missing(
["file_000.tif", "file_001.tif", "file_002.tif"])
# image file missing
assert_raises(RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_002.tif"])
# image file missing
assert_raises(RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_001.tif"])
assert_raises(
RuntimeError, logfile.raise_if_angle_missing,
["file_000.tif", "file_001.tif", "file_002.tif", "file_003.tif"])
def load_log(log_file) -> IMATLogFile:
data = []
with open(log_file, 'r') as f:
for line in f:
data.append(line.strip().split(" "))
return IMATLogFile(data)
def test_counts():
test_input = [
EXPECTED_HEADER_FOR_IMAT_LOG_FILE,
["ignored line"],
[
"timestamp", "Projection: 0 angle: 0.0", "counts before: 12345",
"counts_after: 45678"
],
[
"timestamp", "Projection: 1 angle: 0.1", "counts before: 45678",
"counts_after: 84678"
],
[
"timestamp", "Projection: 2 angle: 0.2", "counts before: 84678",
"counts_after: 124333"
],
]
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.counts().value) == 3
assert logfile.counts().value[0] == 45678 - 12345
assert logfile.counts().value[1] == 84678 - 45678
assert logfile.counts().value[2] == 124333 - 84678
def generate_csv_logfile() -> IMATLogFile:
data = [
CSVLogParser.EXPECTED_HEADER_FOR_IMAT_CSV_LOG_FILE,
"Sun Feb 10 00:22:04 2019,Projection,0,angle: 0.0,Monitor 3 before: 4577907,Monitor 3 after: 4720271",
"Sun Feb 10 00:22:37 2019,Projection,1,angle: 0.3152,Monitor 3 before: 4729337,Monitor 3 after: 4871319",
"Sun Feb 10 00:23:10 2019,Projection,2,angle: 0.6304,Monitor 3 before: 4879923,Monitor 3 after: 5022689",
"Sun Feb 10 00:23:43 2019,Projection,3,angle: 0.9456,Monitor 3 before: 5031423,Monitor 3 after: 5172216",
"Sun Feb 10 00:24:16 2019,Projection,4,angle: 1.2608,Monitor 3 before: 5180904,Monitor 3 after: 5322691",
"Sun Feb 10 00:24:49 2019,Projection,5,angle: 1.576,Monitor 3 before: 5334225,Monitor 3 after: 5475239",
"Sun Feb 10 00:25:22 2019,Projection,6,angle: 1.8912,Monitor 3 before: 5483964,Monitor 3 after: 5626608",
"Sun Feb 10 00:25:55 2019,Projection,7,angle: 2.2064,Monitor 3 before: 5635673,Monitor 3 after: 5777316",
"Sun Feb 10 00:26:29 2019,Projection,8,angle: 2.5216,Monitor 3 before: 5786535,Monitor 3 after: 5929002",
"Sun Feb 10 00:27:02 2019,Projection,9,angle: 2.8368,Monitor 3 before: 5938142,Monitor 3 after: 6078866",
]
return IMATLogFile(data, "/tmp/fake")
def generate_logfile() -> IMATLogFile:
data = [
["column headers"], # skipped when parsing
[""], # skipped when parsing
# for each row a list with 4 entries is currently expected
[
"Sun Feb 10 00:22:04 2019", "Projection: 0 angle: 0.0",
"Monitor 3 before: 4577907", "Monitor 3 after: 4720271"
],
[
"Sun Feb 10 00:22:37 2019", "Projection: 1 angle: 0.3152",
"Monitor 3 before: 4729337", "Monitor 3 after: 4871319"
],
[
"Sun Feb 10 00:23:10 2019", "Projection: 2 angle: 0.6304",
"Monitor 3 before: 4879923", "Monitor 3 after: 5022689"
],
[
"Sun Feb 10 00:23:43 2019", "Projection: 3 angle: 0.9456",
"Monitor 3 before: 5031423", "Monitor 3 after: 5172216"
],
[
"Sun Feb 10 00:24:16 2019", "Projection: 4 angle: 1.2608",
"Monitor 3 before: 5180904", "Monitor 3 after: 5322691"
],
[
"Sun Feb 10 00:24:49 2019", "Projection: 5 angle: 1.576",
"Monitor 3 before: 5334225", "Monitor 3 after: 5475239"
],
[
"Sun Feb 10 00:25:22 2019", "Projection: 6 angle: 1.8912",
"Monitor 3 before: 5483964", "Monitor 3 after: 5626608"
],
[
"Sun Feb 10 00:25:55 2019", "Projection: 7 angle: 2.2064",
"Monitor 3 before: 5635673", "Monitor 3 after: 5777316"
],
[
"Sun Feb 10 00:26:29 2019", "Projection: 8 angle: 2.5216",
"Monitor 3 before: 5786535", "Monitor 3 after: 5929002"
],
[
"Sun Feb 10 00:27:02 2019", "Projection: 9 angle: 2.8368",
"Monitor 3 before: 5938142", "Monitor 3 after: 6078866"
]
]
return IMATLogFile(data)
def generate_txt_logfile() -> IMATLogFile:
data = [
TextLogParser.
EXPECTED_HEADER_FOR_IMAT_TEXT_LOG_FILE, # checked if exists, but skipped
"", # skipped when parsing
# for each row a list with 4 entries is currently expected
"Sun Feb 10 00:22:04 2019 Projection: 0 angle: 0.0 Monitor 3 before: 4577907 Monitor 3 after: 4720271", # noqa: E501
"Sun Feb 10 00:22:37 2019 Projection: 1 angle: 0.3152 Monitor 3 before: 4729337 Monitor 3 after: 4871319", # noqa: E501
"Sun Feb 10 00:23:10 2019 Projection: 2 angle: 0.6304 Monitor 3 before: 4879923 Monitor 3 after: 5022689", # noqa: E501
"Sun Feb 10 00:23:43 2019 Projection: 3 angle: 0.9456 Monitor 3 before: 5031423 Monitor 3 after: 5172216", # noqa: E501
"Sun Feb 10 00:24:16 2019 Projection: 4 angle: 1.2608 Monitor 3 before: 5180904 Monitor 3 after: 5322691", # noqa: E501
"Sun Feb 10 00:24:49 2019 Projection: 5 angle: 1.576 Monitor 3 before: 5334225 Monitor 3 after: 5475239", # noqa: E501
"Sun Feb 10 00:25:22 2019 Projection: 6 angle: 1.8912 Monitor 3 before: 5483964 Monitor 3 after: 5626608", # noqa: E501
"Sun Feb 10 00:25:55 2019 Projection: 7 angle: 2.2064 Monitor 3 before: 5635673 Monitor 3 after: 5777316", # noqa: E501
"Sun Feb 10 00:26:29 2019 Projection: 8 angle: 2.5216 Monitor 3 before: 5786535 Monitor 3 after: 5929002", # noqa: E501
"Sun Feb 10 00:27:02 2019 Projection: 9 angle: 2.8368 Monitor 3 before: 5938142 Monitor 3 after: 6078866", # noqa: E501
]
return IMATLogFile(data, "/tmp/fake")
def test_source_file():
test_input = [
EXPECTED_HEADER_FOR_IMAT_LOG_FILE,
["ignored line"],
[
"timestamp", "Projection: 0 angle: 0.0", "counts before: 12345",
"counts_after: 45678"
],
[
"timestamp", "Projection: 1 angle: 0.1", "counts before: 12345",
"counts_after: 45678"
],
[
"timestamp", "Projection: 2 angle: 0.2", "counts before: 12345",
"counts_after: 45678"
],
]
logfile = IMATLogFile(test_input, "/tmp/fake")
assert logfile.source_file == "/tmp/fake"
def test_parsing_log_file(test_input):
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.projection_angles().value) == 1
assert logfile.projection_angles().value[0] == np.deg2rad(
0.1), f"Got: {logfile.projection_angles().value[0]}"
assert logfile.counts().value[0] == (45678 - 12345)
def test_source_file(test_input):
logfile = IMATLogFile(test_input, "/tmp/fake")
assert logfile.source_file == "/tmp/fake"
def test_raise_if_angles_missing_returns_none_if_no_filename_list():
logfile = IMATLogFile(TXT_LOG_FILE, "/tmp/fake")
assert logfile.raise_if_angle_missing(None) is None
def test_counts(test_input):
logfile = IMATLogFile(test_input, "/tmp/fake")
assert len(logfile.counts().value) == 3
assert logfile.counts().value[0] == 45678 - 12345
assert logfile.counts().value[1] == 84678 - 45678
assert logfile.counts().value[2] == 124333 - 84678
def test_ignore_spaces_at_end_of_log_file_header():
test_log_file = TXT_LOG_FILE[:]
test_log_file[0].replace("\n", " \n")
logfile = IMATLogFile(test_log_file, "/tmp/fake")
assert len(logfile.projection_numbers()) == 3
def load_log(log_file: str) -> IMATLogFile:
with open(log_file, 'r') as f:
return IMATLogFile(f.readlines(), log_file)
