def test_bare_comment_without_hash_ignored(self):
content = " MANTID_BATCH_FILE,foo,bar"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
output = parser.parse_batch_file(batch_file_path)
self.assertEqual(0, len(output))
def test_that_does_not_return_excluded_keywords(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,1,sample_trans,2,sample_direct_beam,3,output_as,test_file,user_file,user_test_file\n" \
"sample_sans,1,can_sans,2,output_as,test_file2,"","", background_sans, background\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
# Act
output = parser.parse_batch_file(batch_file_path)
# Assert
self.assertEqual(len(output), 2)
first_line = output[0]
self.assertEqual(first_line.sample_scatter, "1")
self.assertEqual(first_line.sample_scatter_period, ALL_PERIODS)
self.assertEqual(first_line.sample_transmission, "2")
self.assertEqual(first_line.sample_transmission_period, ALL_PERIODS)
self.assertEqual(first_line.sample_direct, "3")
self.assertEqual(first_line.sample_direct_period, ALL_PERIODS)
self.assertEqual(first_line.output_name, "test_file")
self.assertEqual(first_line.user_file, "user_test_file")
second_line = output[1]
# Should have 3 user specified entries and 2 period entries
self.assertEqual(second_line.sample_scatter, "1")
self.assertEqual(second_line.sample_scatter_period, ALL_PERIODS)
self.assertEqual(second_line.can_scatter, "2")
self.assertEqual(second_line.can_scatter_period, ALL_PERIODS)
self.assertEqual(second_line.output_name, "test_file2")
BatchCsvParserTest._remove_csv(batch_file_path)
def test_that_parses_two_lines_correctly(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,1,sample_trans,2,sample_direct_beam,3,output_as,test_file,user_file,user_test_file\n" \
"sample_sans,1,can_sans,2,output_as,test_file2\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
# Act
output = parser.parse_batch_file(batch_file_path)
# Assert
self.assertEqual(len(output), 2)
first_line = output[0]
self.assertEqual(first_line.sample_scatter, "1")
self.assertEqual(first_line.sample_scatter_period, ALL_PERIODS)
self.assertEqual(first_line.sample_transmission, "2")
self.assertEqual(first_line.sample_transmission_period, ALL_PERIODS)
self.assertEqual(first_line.sample_direct, "3")
self.assertEqual(first_line.sample_direct_period, ALL_PERIODS)
self.assertEqual(first_line.output_name, "test_file")
self.assertEqual(first_line.user_file, "user_test_file")
second_line = output[1]
self.assertEqual(second_line.sample_scatter, "1")
self.assertEqual(second_line.sample_scatter_period, ALL_PERIODS)
self.assertEqual(second_line.can_scatter, "2")
self.assertEqual(second_line.can_scatter_period, ALL_PERIODS)
self.assertEqual(second_line.output_name, "test_file2")
BatchCsvParserTest._remove_csv(batch_file_path)
def test_that_raises_when_can_transmission_is_specified_incompletely(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,test,output_as,test, can_trans,, can_direct_beam, test\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
with self.assertRaises(ValueError):
parser.parse_batch_file(batch_file_path)
BatchCsvParserTest._remove_csv(batch_file_path)
def test_that_raises_when_sample_scatter_is_missing(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,,output_as,test_file\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
with self.assertRaises(ValueError):
parser.parse_batch_file(batch_file_path)
BatchCsvParserTest._remove_csv(batch_file_path)
def test_that_raises_when_unknown_keyword_is_used(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,74044,output_as,test,new_key_word,test\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
with self.assertRaises(KeyError):
parser.parse_batch_file(batch_file_path)
BatchCsvParserTest._remove_csv(batch_file_path)
def test_raises_if_the_batch_file_uses_key_as_val(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,sample_trans,74024,sample_direct_beam,74014,can_sans,74019,can_trans,74020," \
"can_direct_beam,output_as, first_eim\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
with self.assertRaises(KeyError):
parser.parse_batch_file(batch_file_path)
BatchCsvParserTest._remove_csv(batch_file_path)
def test_can_parse_sample_geometries(self):
batch_file_row = [
"sample_sans", "1", "sample_trans", "", "sample_direct_beam", "",
"can_sans", "", "can_trans", "", "can_direct_beam", "",
"output_as", "", "user_file", "", "sample_thickness", "5",
"sample_height", "5", "sample_width", "5"
]
parser = BatchCsvParser()
parser._parse_csv_row(batch_file_row, 0)
def test_opens_correct_file(self):
mocked_handle = mock.mock_open()
expected_file_path = "/foo/bar.csv"
parser = BatchCsvParser()
patchable = "builtins.open"
with mock.patch(patchable, mocked_handle):
parser.save_batch_file(rows=[], file_path=expected_file_path)
mocked_handle.assert_called_with(expected_file_path, "w", newline="")
def test_that_does_not_raise_when_output_is_missing(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,test,output_as,\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
try:
parser.parse_batch_file(batch_file_path)
except RuntimeError as e:
self.fail(
"Batch files are not required to contain output names as these can be autogenerated. "
"Therefore we did not expect a RuntimeError to be raised when parsing batch file without an "
"output name. Error raised was: {}".format(str(e)))
BatchCsvParserTest._remove_csv(batch_file_path)
def test_can_parse_file_with_empty_final_column(self):
"""There was a bug where certain batch files with an empty final column (no user file provided)
would not be treated as a column and therefore the batch file would be read as having only 15
rows.
We now add an empty final row in the parser if there are 15 rows and the last row provided is
a batch file key"""
batch_file_row = [
"sample_sans", "1", "sample_trans", "", "sample_direct_beam", "",
"can_sans", "", "can_trans", "", "can_direct_beam", "",
"output_as", "", "user_file"
]
parser = BatchCsvParser()
parser._parse_csv_row(batch_file_row, 0)
def test_that_parses_period_selection(self):
content = "# MANTID_BATCH_FILE add more text here\n" \
"sample_sans,1p7,can_sans,2P3,output_as,test_file2\n"
batch_file_path = BatchCsvParserTest._save_to_csv(content)
parser = BatchCsvParser()
# Act
output = parser.parse_batch_file(batch_file_path)
# Assert
self.assertEqual(len(output), 1)
first_line = output[0]
self.assertEqual(first_line.sample_scatter, "1")
self.assertEqual(first_line.sample_scatter_period, 7)
self.assertEqual(first_line.can_scatter, "2")
self.assertEqual(first_line.can_scatter_period, 3)
self.assertEqual(first_line.output_name, "test_file2")
BatchCsvParserTest._remove_csv(batch_file_path)
def test_parses_row_to_csv_correctly(self):
test_row = RowEntries()
test_row.sample_scatter = "SANS2D00022025"
test_row.sample_transmission = "SANS2D00022052"
test_row.sample_direct = "SANS2D00022022"
test_row.output_name = "another_file"
test_row.user_file = "a_user_file.txt"
test_row.sample_thickness = "1.0"
test_row.sample_height = 5.0
test_row.sample_width = 5.4
expected = "sample_sans,SANS2D00022025," \
"sample_trans,SANS2D00022052,"\
"sample_direct_beam,SANS2D00022022," \
"can_sans,," \
"can_trans,," \
"can_direct_beam,,"\
"output_as,another_file," \
"user_file,a_user_file.txt," \
"sample_thickness,1.0,"\
"sample_height,5.0," \
"sample_width,5.4"
mocked_handle = mock.mock_open()
parser = BatchCsvParser()
patchable = "builtins.open"
with mock.patch(patchable, mocked_handle):
parser.save_batch_file(rows=[test_row], file_path='')
result = mocked_handle()
args, kwargs = result.write.call_args
# Strip new lines etc
self.assertTrue(isinstance(args[0], str))
written = args[0].replace('\n', '').replace('\r', '')
self.assertEqual(expected, written)
def BatchReduce(filename, format, plotresults=False, saveAlgs=None, verbose=False, # noqa
centreit=False, reducer=None, combineDet=None, save_as_zero_error_free=False): # noqa
"""
@param filename: the CSV file with the list of runs to analyse
@param format: type of file to load, nxs for Nexus, etc.
@param plotresults: if true and this function is run from Mantidplot a graph will be created for the results of each reduction
@param saveAlgs: this named algorithm will be passed the name of the results workspace and filename (default = 'SaveRKH').
Pass a tuple of strings to save to multiple file formats
@param verbose: set to true to write more information to the log (default=False)
@param centreit: do centre finding (default=False)
@param reducer: if to use the command line (default) or GUI reducer object
@param combineDet: that will be forward to WavRangeReduction (rear, front, both, merged, None)
@param save_as_zero_error_free: Should the reduced workspaces contain zero errors or not
@return final_setings: A dictionary with some values of the Reduction - Right Now:(scale, shift)
"""
if saveAlgs is None:
saveAlgs = {'SaveRKH': 'txt'}
# From the old interface
_ = format
_ = reducer
_ = verbose
if centreit:
raise RuntimeError("The beam centre finder is currently not supported.")
if plotresults:
raise RuntimeError("Plotting the results is currently not supported.")
# Set up the save algorithms
save_algs = []
if saveAlgs:
for key, _ in list(saveAlgs.items()):
if key == "SaveRKH":
save_algs.append(SaveType.RKH)
elif key == "SaveNexus":
save_algs.append(SaveType.NEXUS)
elif key == "SaveNistQxy":
save_algs.append(SaveType.NIST_QXY)
elif key == "SaveCanSAS" or key == "SaveCanSAS1D":
save_algs.append(SaveType.CAN_SAS)
elif key == "SaveCSV":
save_algs.append(SaveType.CSV)
elif key == "SaveNXcanSAS":
save_algs.append(SaveType.NX_CAN_SAS)
else:
raise RuntimeError("The save format {0} is not known.".format(key))
output_mode = OutputMode.BOTH
else:
output_mode = OutputMode.PUBLISH_TO_ADS
# Get the information from the csv file
batch_csv_parser = BatchCsvParser()
parsed_batch_entries = batch_csv_parser.parse_batch_file(filename)
# Get a state with all existing settings
for parsed_batch_entry in parsed_batch_entries:
assert isinstance(parsed_batch_entry, RowEntries)
# A new user file. If a new user file is provided then this will overwrite all other settings from,
# otherwise we might have cross-talk between user files.
if parsed_batch_entry.user_file:
MaskFile(parsed_batch_entry.user_file)
# Sample scatter
sample_scatter = parsed_batch_entry.sample_scatter
sample_scatter_period = parsed_batch_entry.sample_scatter_period
AssignSample(sample_run=sample_scatter, period=sample_scatter_period)
# Sample transmission
if parsed_batch_entry.sample_transmission and parsed_batch_entry.sample_direct:
sample_direct = parsed_batch_entry.sample_direct
sample_direct_period = parsed_batch_entry.sample_direct_period
sample_transmission = parsed_batch_entry.sample_transmission
sample_transmission_period = parsed_batch_entry.sample_transmission_period
TransmissionSample(sample=sample_transmission, direct=sample_direct,
period_t=sample_transmission_period, period_d=sample_direct_period)
# Can scatter
if parsed_batch_entry.can_scatter:
can_scatter = parsed_batch_entry.can_scatter
can_scatter_period = parsed_batch_entry.can_scatter_period
AssignCan(can_run=can_scatter, period=can_scatter_period)
# Can transmission
if parsed_batch_entry.can_transmission and parsed_batch_entry.can_direct:
can_transmission = parsed_batch_entry.can_transmission
can_transmission_period = parsed_batch_entry.can_transmission_period
can_direct = parsed_batch_entry.can_direct
can_direct_period = parsed_batch_entry.can_direct_period
TransmissionCan(can=can_transmission, direct=can_direct,
period_t=can_transmission_period, period_d=can_direct_period)
# Name of the output. We need to modify the name according to the setup of the old reduction mechanism
output_name = parsed_batch_entry.output_name
# In addition to the output name the user can specify with combineDet an additional suffix (in addition to the
# suffix that the user can set already -- was there previously, so we have to provide that)
use_reduction_mode_as_suffix = combineDet is not None
# Apply save options
if save_algs:
set_save(save_algorithms=save_algs, save_as_zero_error_free=save_as_zero_error_free)
# Run the reduction for a single
reduced_workspace_name = WavRangeReduction(combineDet=combineDet, output_name=output_name,
output_mode=output_mode,
use_reduction_mode_as_suffix=use_reduction_mode_as_suffix)
# Remove the settings which were very specific for this single reduction which are:
# 1. The last user file (if any was set)
# 2. The last scatter entry
# 3. The last scatter transmission and direct entry (if any were set)
# 4. The last can scatter ( if any was set)
# 5. The last can transmission and direct entry (if any were set)
if parsed_batch_entry.user_file:
director.remove_last_user_file()
director.remove_last_scatter_sample()
if parsed_batch_entry.sample_transmission and parsed_batch_entry.sample_direct:
director.remove_last_sample_transmission_and_direct()
if parsed_batch_entry.can_scatter:
director.remove_last_scatter_can()
if parsed_batch_entry.can_transmission and parsed_batch_entry.can_direct:
director.remove_last_can_transmission_and_direct()
# Plot the results if that was requested, the flag 1 is from the old version.
if plotresults == 1:
if AnalysisDataService.doesExist(reduced_workspace_name):
workspace = AnalysisDataService.retrieve(reduced_workspace_name)
if isinstance(workspace, WorkspaceGroup):
for ws in workspace:
PlotResult(ws.name())
else:
PlotResult(workspace.name())
def test_handles_unknown_data(self):
parser = BatchCsvParser()
with self.assertRaises(SyntaxError):
parser.parse_batch_file('LOQ74044.nxs')
def test_empty_batch_file_name_throws(self):
batch_file_path = "not_there.csv"
parser = BatchCsvParser()
with self.assertRaises(RuntimeError):
parser.parse_batch_file(batch_file_path)