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(batch_file_path)
try:
parser.parse_batch_file()
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_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(batch_file_path)
try:
parser.parse_batch_file()
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_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(batch_file_path)
# Act
output = parser.parse_batch_file()
# Assert
self.assertTrue(len(output) == 2)
first_line = output[0]
# Should have 5 user specified entries and 3 period entries
self.assertTrue(len(first_line) == 8)
self.assertTrue(first_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(first_line[BatchReductionEntry.SampleScatterPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.SampleTransmission] == "2")
self.assertTrue(first_line[BatchReductionEntry.SampleTransmissionPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.SampleDirect] == "3")
self.assertTrue(first_line[BatchReductionEntry.SampleDirectPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.Output] == "test_file")
self.assertTrue(first_line[BatchReductionEntry.UserFile] == "user_test_file")
second_line = output[1]
# Should have 3 user specified entries and 2 period entries
self.assertTrue(len(second_line) == 5)
self.assertTrue(second_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(second_line[BatchReductionEntry.SampleScatterPeriod] == ALL_PERIODS)
self.assertTrue(second_line[BatchReductionEntry.CanScatter] == "2")
self.assertTrue(second_line[BatchReductionEntry.CanScatterPeriod] == ALL_PERIODS)
self.assertTrue(second_line[BatchReductionEntry.Output] == "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(batch_file_path)
# Act
output = parser.parse_batch_file()
# Assert
self.assertTrue(len(output) == 2)
first_line = output[0]
# Should have 5 user specified entries and 3 period entries
self.assertTrue(len(first_line) == 8)
self.assertTrue(first_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(first_line[BatchReductionEntry.SampleScatterPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.SampleTransmission] == "2")
self.assertTrue(first_line[BatchReductionEntry.SampleTransmissionPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.SampleDirect] == "3")
self.assertTrue(first_line[BatchReductionEntry.SampleDirectPeriod] == ALL_PERIODS)
self.assertTrue(first_line[BatchReductionEntry.Output] == "test_file")
self.assertTrue(first_line[BatchReductionEntry.UserFile] == "user_test_file")
second_line = output[1]
# Should have 3 user specified entries and 2 period entries
self.assertTrue(len(second_line) == 5)
self.assertTrue(second_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(second_line[BatchReductionEntry.SampleScatterPeriod] == ALL_PERIODS)
self.assertTrue(second_line[BatchReductionEntry.CanScatter] == "2")
self.assertTrue(second_line[BatchReductionEntry.CanScatterPeriod] == ALL_PERIODS)
self.assertTrue(second_line[BatchReductionEntry.Output] == "test_file2")
BatchCsvParserTest._remove_csv(batch_file_path)
def on_batch_file_load(self):
"""
Loads a batch file and populates the batch table based on that.
"""
try:
# 1. Get the batch file from the view
batch_file_path = self._view.get_batch_file_path()
if not batch_file_path:
return
if not os.path.exists(batch_file_path):
raise RuntimeError("The batch file path {} does not exist. Make sure a valid batch file path"
" has been specified.".format(batch_file_path))
self._table_model.batch_file = batch_file_path
# 2. Read the batch file
batch_file_parser = BatchCsvParser(batch_file_path)
parsed_rows = batch_file_parser.parse_batch_file()
# 3. Populate the table
self._table_model.clear_table_entries()
for index, row in enumerate(parsed_rows):
self._add_row_to_table_model(row, index)
self._table_model.remove_table_entries([len(parsed_rows)])
self.update_view_from_table_model()
self._beam_centre_presenter.on_update_rows()
self._masking_table_presenter.on_update_rows()
except RuntimeError as e:
self.sans_logger.error("Loading of the batch file failed. {}".format(str(e)))
self.display_warning_box('Warning', 'Loading of the batch file failed', str(e))
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(batch_file_path)
# Act
output = parser.parse_batch_file()
# Assert
self.assertEqual(len(output), 2)
first_line = output[0]
# Should have 5 user specified entries and 3 period entries
self.assertEqual(len(first_line), 8)
self.assertEqual(first_line[BatchReductionEntry.SampleScatter], "1")
self.assertEqual(first_line[BatchReductionEntry.SampleScatterPeriod],
ALL_PERIODS)
self.assertEqual(first_line[BatchReductionEntry.SampleTransmission],
"2")
self.assertEqual(
first_line[BatchReductionEntry.SampleTransmissionPeriod],
ALL_PERIODS)
self.assertEqual(first_line[BatchReductionEntry.SampleDirect], "3")
self.assertEqual(first_line[BatchReductionEntry.SampleDirectPeriod],
ALL_PERIODS)
self.assertEqual(first_line[BatchReductionEntry.Output], "test_file")
self.assertEqual(first_line[BatchReductionEntry.UserFile],
"user_test_file")
second_line = output[1]
# Should have 3 user specified entries and 2 period entries
self.assertEqual(len(second_line), 5)
self.assertEqual(second_line[BatchReductionEntry.SampleScatter], "1")
self.assertEqual(second_line[BatchReductionEntry.SampleScatterPeriod],
ALL_PERIODS)
self.assertEqual(second_line[BatchReductionEntry.CanScatter], "2")
self.assertEqual(second_line[BatchReductionEntry.CanScatterPeriod],
ALL_PERIODS)
self.assertEqual(second_line[BatchReductionEntry.Output], "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(batch_file_path)
# Act
output = parser.parse_batch_file()
# Assert
self.assertTrue(len(output) == 1)
first_line = output[0]
# Should have 5 user specified entries and 3 period entries
self.assertTrue(len(first_line) == 5)
self.assertTrue(first_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(first_line[BatchReductionEntry.SampleScatterPeriod] == 7)
self.assertTrue(first_line[BatchReductionEntry.CanScatter] == "2")
self.assertTrue(first_line[BatchReductionEntry.CanScatterPeriod] == 3)
self.assertTrue(first_line[BatchReductionEntry.Output] == "test_file2")
BatchCsvParserTest._remove_csv(batch_file_path)
def on_batch_file_load(self):
"""
Loads a batch file and populates the batch table based on that.
"""
try:
# 1. Get the batch file from the view
batch_file_path = self._view.get_batch_file_path()
if not batch_file_path:
return
if not os.path.exists(batch_file_path):
raise RuntimeError(
"The batch file path {} does not exist. Make sure a valid batch file path"
" has been specified.".format(batch_file_path))
# 2. Read the batch file
batch_file_parser = BatchCsvParser(batch_file_path)
parsed_rows = batch_file_parser.parse_batch_file()
# 3. Clear the table
self._view.clear_table()
# 4. Populate the table
for row in parsed_rows:
self._populate_row_in_table(row)
# 5. Populate the selected instrument and the correct detector selection
self._setup_instrument_specific_settings()
# 6. Perform calls on child presenters
self._masking_table_presenter.on_update_rows()
self._settings_diagnostic_tab_presenter.on_update_rows()
self._beam_centre_presenter.on_update_rows()
except RuntimeError as e:
self.sans_logger.error(
"Loading of the batch file failed. Ensure that the path to your files has been added"
" to the Mantid search directories! See here for more details: {}"
.format(str(e)))
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(batch_file_path)
# Act
output = parser.parse_batch_file()
# Assert
self.assertTrue(len(output) == 1)
first_line = output[0]
# Should have 5 user specified entries and 3 period entries
self.assertTrue(len(first_line) == 5)
self.assertTrue(first_line[BatchReductionEntry.SampleScatter] == "1")
self.assertTrue(first_line[BatchReductionEntry.SampleScatterPeriod] == 7)
self.assertTrue(first_line[BatchReductionEntry.CanScatter] == "2")
self.assertTrue(first_line[BatchReductionEntry.CanScatterPeriod] == 3)
self.assertTrue(first_line[BatchReductionEntry.Output] == "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 currenlty 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.NistQxy)
elif key == "SaveCanSAS" or key == "SaveCanSAS1D":
save_algs.append(SaveType.CanSAS)
elif key == "SaveCSV":
save_algs.append(SaveType.CSV)
elif key == "SaveNXcanSAS":
save_algs.append(SaveType.NXcanSAS)
else:
raise RuntimeError(
"The save format {0} is not known.".format(key))
output_mode = OutputMode.Both
else:
output_mode = OutputMode.PublishToADS
# Get the information from the csv file
batch_csv_parser = BatchCsvParser(filename)
parsed_batch_entries = batch_csv_parser.parse_batch_file()
# Get a state with all existing settings
for parsed_batch_entry in parsed_batch_entries:
# 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 BatchReductionEntry.UserFile in list(parsed_batch_entry.keys()):
user_file = parsed_batch_entry[BatchReductionEntry.UserFile]
MaskFile(user_file)
# Sample scatter
sample_scatter = parsed_batch_entry[BatchReductionEntry.SampleScatter]
sample_scatter_period = parsed_batch_entry[
BatchReductionEntry.SampleScatterPeriod]
AssignSample(sample_run=sample_scatter, period=sample_scatter_period)
# Sample transmission
if (BatchReductionEntry.SampleTransmission in list(
parsed_batch_entry.keys()) and BatchReductionEntry.SampleDirect
in list(parsed_batch_entry.keys())):
sample_transmission = parsed_batch_entry[
BatchReductionEntry.SampleTransmission]
sample_transmission_period = parsed_batch_entry[
BatchReductionEntry.SampleTransmissionPeriod]
sample_direct = parsed_batch_entry[
BatchReductionEntry.SampleDirect]
sample_direct_period = parsed_batch_entry[
BatchReductionEntry.SampleDirectPeriod]
TransmissionSample(sample=sample_transmission,
direct=sample_direct,
period_t=sample_transmission_period,
period_d=sample_direct_period)
# Can scatter
if BatchReductionEntry.CanScatter in list(parsed_batch_entry.keys()):
can_scatter = parsed_batch_entry[BatchReductionEntry.CanScatter]
can_scatter_period = parsed_batch_entry[
BatchReductionEntry.CanScatterPeriod]
AssignCan(can_run=can_scatter, period=can_scatter_period)
# Can transmission
if (BatchReductionEntry.CanTransmission in list(
parsed_batch_entry.keys()) and BatchReductionEntry.CanDirect
in list(parsed_batch_entry.keys())):
can_transmission = parsed_batch_entry[
BatchReductionEntry.CanTransmission]
can_transmission_period = parsed_batch_entry[
BatchReductionEntry.CanTransmissionPeriod]
can_direct = parsed_batch_entry[BatchReductionEntry.CanDirect]
can_direct_period = parsed_batch_entry[
BatchReductionEntry.CanDirectPeriod]
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[BatchReductionEntry.Output]
# In addition to the output name the user can specify with combineDet an additional suffix (in addtion 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 BatchReductionEntry.UserFile in list(parsed_batch_entry.keys()):
director.remove_last_user_file()
director.remove_last_scatter_sample()
if (BatchReductionEntry.SampleTransmission in list(
parsed_batch_entry.keys()) and BatchReductionEntry.SampleDirect
in list(parsed_batch_entry.keys())): # noqa
director.remove_last_sample_transmission_and_direct()
if BatchReductionEntry.CanScatter in list(parsed_batch_entry.keys()):
director.remove_last_scatter_can()
if (BatchReductionEntry.CanTransmission in list(
parsed_batch_entry.keys()) and BatchReductionEntry.CanDirect
in list(parsed_batch_entry.keys())):
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.getName())
else:
PlotResult(workspace.getName())
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 currenlty 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.NistQxy)
elif key == "SaveCanSAS" or key == "SaveCanSAS1D":
save_algs.append(SaveType.CanSAS)
elif key == "SaveCSV":
save_algs.append(SaveType.CSV)
elif key == "SaveNXcanSAS":
save_algs.append(SaveType.NXcanSAS)
else:
raise RuntimeError("The save format {0} is not known.".format(key))
output_mode = OutputMode.Both
else:
output_mode = OutputMode.PublishToADS
# Get the information from the csv file
batch_csv_parser = BatchCsvParser(filename)
parsed_batch_entries = batch_csv_parser.parse_batch_file()
# Get a state with all existing settings
for parsed_batch_entry in parsed_batch_entries:
# 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 BatchReductionEntry.UserFile in list(parsed_batch_entry.keys()):
user_file = parsed_batch_entry[BatchReductionEntry.UserFile]
MaskFile(user_file)
# Sample scatter
sample_scatter = parsed_batch_entry[BatchReductionEntry.SampleScatter]
sample_scatter_period = parsed_batch_entry[BatchReductionEntry.SampleScatterPeriod]
AssignSample(sample_run=sample_scatter, period=sample_scatter_period)
# Sample transmission
if (BatchReductionEntry.SampleTransmission in list(parsed_batch_entry.keys()) and
BatchReductionEntry.SampleDirect in list(parsed_batch_entry.keys())):
sample_transmission = parsed_batch_entry[BatchReductionEntry.SampleTransmission]
sample_transmission_period = parsed_batch_entry[BatchReductionEntry.SampleTransmissionPeriod]
sample_direct = parsed_batch_entry[BatchReductionEntry.SampleDirect]
sample_direct_period = parsed_batch_entry[BatchReductionEntry.SampleDirectPeriod]
TransmissionSample(sample=sample_transmission, direct=sample_direct,
period_t=sample_transmission_period, period_d=sample_direct_period)
# Can scatter
if BatchReductionEntry.CanScatter in list(parsed_batch_entry.keys()):
can_scatter = parsed_batch_entry[BatchReductionEntry.CanScatter]
can_scatter_period = parsed_batch_entry[BatchReductionEntry.CanScatterPeriod]
AssignCan(can_run=can_scatter, period=can_scatter_period)
# Can transmission
if (BatchReductionEntry.CanTransmission in list(parsed_batch_entry.keys()) and
BatchReductionEntry.CanDirect in list(parsed_batch_entry.keys())):
can_transmission = parsed_batch_entry[BatchReductionEntry.CanTransmission]
can_transmission_period = parsed_batch_entry[BatchReductionEntry.CanTransmissionPeriod]
can_direct = parsed_batch_entry[BatchReductionEntry.CanDirect]
can_direct_period = parsed_batch_entry[BatchReductionEntry.CanDirectPeriod]
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[BatchReductionEntry.Output]
# In addition to the output name the user can specify with combineDet an additional suffix (in addtion 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 BatchReductionEntry.UserFile in list(parsed_batch_entry.keys()):
director.remove_last_user_file()
director.remove_last_scatter_sample()
if (BatchReductionEntry.SampleTransmission in list(parsed_batch_entry.keys()) and
BatchReductionEntry.SampleDirect in list(parsed_batch_entry.keys())): # noqa
director.remove_last_sample_transmission_and_direct()
if BatchReductionEntry.CanScatter in list(parsed_batch_entry.keys()):
director.remove_last_scatter_can()
if (BatchReductionEntry.CanTransmission in list(parsed_batch_entry.keys()) and
BatchReductionEntry.CanDirect in list(parsed_batch_entry.keys())):
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.getName())
else:
PlotResult(workspace.getName())