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_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_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_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_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_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 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)