def test_removing_from_ads_calls_any_change_handle(self):
CreateSampleWorkspace(OutputWorkspace="ws1")
self.project.anyChangeHandle = mock.MagicMock()
ADS.remove("ws1")
self.assertEqual(1, self.project.anyChangeHandle.call_count)
def tearDown(self):
ADS.clear()
if os.path.exists(self.pr.recovery_directory_hostname):
shutil.rmtree(self.pr.recovery_directory_hostname)
if os.path.exists(self.working_directory):
shutil.rmtree(self.working_directory)
def test_saveGSS(self):
""" Test to Save a GSAS file to match V-drive
"""
# Create a test data file and workspace
binfilename = "testbin.dat"
self._createBinFile(binfilename)
datawsname = "TestInputWorkspace"
self._createDataWorkspace(datawsname)
# Execute
alg_test = run_algorithm("SaveVulcanGSS",
InputWorkspace = datawsname,
BinFilename = binfilename,
OutputWorkspace = datawsname+"_rebinned",
GSSFilename = "tempout.gda")
self.assertTrue(alg_test.isExecuted())
# Verify ....
outputws = AnalysisDataService.retrieve(datawsname+"_rebinned")
#self.assertEqual(4, tablews.rowCount())
# Delete the test hkl file
os.remove(binfilename)
AnalysisDataService.remove("InputWorkspace")
AnalysisDataService.remove(datawsname+"_rebinned")
return
def test_LoadHKLFile(self):
""" Test to load a .hkl file
"""
# 1. Create a test file
hklfilename = "test.hkl"
self._createHKLFile(hklfilename)
# 2.
alg_test = run_algorithm("LoadFullprofFile", Filename = hklfilename,
OutputWorkspace = "Foo", PeakParameterWorkspace = "PeakParameterTable")
self.assertTrue(alg_test.isExecuted())
# 3. Verify some values
tablews = AnalysisDataService.retrieve("PeakParameterTable")
self.assertEqual(4, tablews.rowCount())
# alpha of (11 5 1)/Row 0
self.assertEqual(0.34252, tablews.cell(0, 3))
# 4. Delete the test hkl file
os.remove(hklfilename)
AnalysisDataService.remove("PeakParameterTable")
AnalysisDataService.remove("Foo")
return
def get_weighted_peak_centres(self):
""" Get the peak centers found in peak workspace.
Guarantees: the peak centers and its weight (detector counts) are exported
:return: 2-tuple: list of 3-tuple (Qx, Qy, Qz)
list of double (Det_Counts)
"""
# get PeaksWorkspace
if AnalysisDataService.doesExist(self._myPeakWorkspaceName) is False:
raise RuntimeError('PeaksWorkspace %s does ot exit.' % self._myPeakWorkspaceName)
peak_ws = AnalysisDataService.retrieve(self._myPeakWorkspaceName)
# get peak center, peak intensity and etc.
peak_center_list = list()
peak_intensity_list = list()
num_peaks = peak_ws.getNumberPeaks()
for i_peak in xrange(num_peaks):
peak_i = peak_ws.getPeak(i_peak)
center_i = peak_i.getQSampleFrame()
intensity_i = peak_i.getIntensity()
peak_center_list.append((center_i.X(), center_i.Y(), center_i.Z()))
peak_intensity_list.append(intensity_i)
# END-FOR
return peak_center_list, peak_intensity_list
def test_that_can_find_can_reduction_if_it_exists(self):
# Arrange
test_director = TestDirector()
state = test_director.construct()
tagged_workspace_names = {None: "test_ws",
OutputParts.Count: "test_ws_count",
OutputParts.Norm: "test_ws_norm"}
SANSFunctionsTest._prepare_workspaces(number_of_workspaces=4,
tagged_workspace_names=tagged_workspace_names,
state=state,
reduction_mode=ISISReductionMode.LAB)
# Act
workspace, workspace_count, workspace_norm = get_reduced_can_workspace_from_ads(state, output_parts=True,
reduction_mode=ISISReductionMode.LAB) # noqa
# Assert
self.assertTrue(workspace is not None)
self.assertTrue(workspace.name() == AnalysisDataService.retrieve("test_ws").name())
self.assertTrue(workspace_count is not None)
self.assertTrue(workspace_count.name() == AnalysisDataService.retrieve("test_ws_count").name())
self.assertTrue(workspace_norm is not None)
self.assertTrue(workspace_norm.name() == AnalysisDataService.retrieve("test_ws_norm").name())
# Clean up
SANSFunctionsTest._remove_workspaces()
def test_that_can_load_isis_nexus_file_with_event_data_and_multi_period(self):
# Arrange
state = SANSLoadTest._get_simple_state(sample_scatter="LARMOR00013065.nxs",
calibration="80tubeCalibration_18-04-2016_r9330-9335.nxs")
# Act
output_workspace_names = {"SampleScatterWorkspace": "sample_scatter",
"SampleScatterMonitorWorkspace": "sample_monitor_scatter"}
load_alg = self._run_load(state, publish_to_cache=True, use_cached=True, move_workspace=False,
output_workspace_names=output_workspace_names)
# Assert
expected_number_of_workspaces = [4, 0, 0, 0, 0, 0]
expected_number_on_ads = 1
workspace_type = [EventWorkspace, None, None, None, None, None]
self._do_test_output(load_alg, expected_number_of_workspaces, expected_number_on_ads, workspace_type)
# Check that calibration is added
self.assertTrue(SANSLoadTest._has_calibration_been_applied(load_alg))
# Confirm that the ADS workspace contains the calibration file
try:
AnalysisDataService.retrieve("80tubeCalibration_18-04-2016_r9330-9335")
on_ads = True
except RuntimeError:
on_ads = False
self.assertTrue(on_ads)
# Cleanup
remove_all_workspaces_from_ads()
def _run_createws(self, wsname):
"""
Run create workspace storing the output in the named workspace
"""
data = [1.0,2.0,3.0]
alg = run_algorithm('CreateWorkspace',DataX=data,DataY=data,NSpec=1,UnitX='Wavelength', child=True)
AnalysisDataService.addOrReplace(wsname, alg.getProperty("OutputWorkspace").value)
def edit_matrix_workspace(sq_name, scale_factor, shift, edited_sq_name=None):
"""
Edit the matrix workspace of S(Q) by scaling and shift
:param sq_name: name of the SofQ workspace
:param scale_factor:
:param shift:
:param edited_sq_name: workspace for the edited S(Q)
:return:
"""
# get the workspace
if AnalysisDataService.doesExist(sq_name) is False:
raise RuntimeError('S(Q) workspace {0} cannot be found in ADS.'.format(sq_name))
if edited_sq_name is not None:
simpleapi.CloneWorkspace(InputWorkspace=sq_name, OutputWorkspace=edited_sq_name)
sq_ws = AnalysisDataService.retrieve(edited_sq_name)
else:
sq_ws = AnalysisDataService.retrieve(sq_name)
# get the vector of Y
sq_ws = sq_ws * scale_factor
sq_ws = sq_ws + shift
if sq_ws.name() != edited_sq_name:
simpleapi.DeleteWorkspace(Workspace=edited_sq_name)
simpleapi.RenameWorkspace(InputWorkspace=sq_ws, OutputWorkspace=edited_sq_name)
assert sq_ws is not None, 'S(Q) workspace cannot be None.'
print('[DB...BAT] S(Q) workspace that is edit is {0}'.format(sq_ws))
def cleanup(self):
if AnalysisDataService.doesExist(self._input_wksp):
DeleteWorkspace(self._input_wksp)
if AnalysisDataService.doesExist(self._output_wksp):
DeleteWorkspace(self._output_wksp)
if AnalysisDataService.doesExist(self._correction_wksp):
DeleteWorkspace(self._correction_wksp)
def test_setTitle(self):
run_algorithm('CreateWorkspace', OutputWorkspace='ws1',DataX=[1.,2.,3.], DataY=[2.,3.], DataE=[2.,3.],UnitX='TOF')
ws1 = AnalysisDataService['ws1']
title = 'test_title'
ws1.setTitle(title)
self.assertEquals(title, ws1.getTitle())
AnalysisDataService.remove(ws1.getName())
def test_add_raises_error_if_name_exists(self):
data = [1.0,2.0,3.0]
alg = run_algorithm('CreateWorkspace',DataX=data,DataY=data,NSpec=1,UnitX='Wavelength', child=True)
name = "testws"
ws = alg.getProperty("OutputWorkspace").value
AnalysisDataService.addOrReplace(name, ws)
self.assertRaises(RuntimeError, AnalysisDataService.add, name, ws)
def test_batch_reduction_on_multiperiod_file(self):
# Arrange
# Build the data information
data_builder = get_data_builder(SANSFacility.ISIS)
data_builder.set_sample_scatter("SANS2D0005512")
data_info = data_builder.build()
# Get the rest of the state from the user file
user_file_director = StateDirectorISIS(data_info)
user_file_director.set_user_file("MASKSANS2Doptions.091A")
# Set the reduction mode to LAB
user_file_director.set_reduction_builder_reduction_mode(ISISReductionMode.LAB)
state = user_file_director.construct()
# Act
states = [state]
self._run_batch_reduction(states, use_optimizations=False)
# Assert
# We only assert that the expected workspaces exist on the ADS
expected_workspaces = ["5512p1rear_1D_2.0_14.0Phi-45.0_45.0", "5512p2rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p3rear_1D_2.0_14.0Phi-45.0_45.0", "5512p4rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p5rear_1D_2.0_14.0Phi-45.0_45.0", "5512p6rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p7rear_1D_2.0_14.0Phi-45.0_45.0", "5512p8rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p9rear_1D_2.0_14.0Phi-45.0_45.0", "5512p10rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p11rear_1D_2.0_14.0Phi-45.0_45.0", "5512p12rear_1D_2.0_14.0Phi-45.0_45.0",
"5512p13rear_1D_2.0_14.0Phi-45.0_45.0"]
for element in expected_workspaces:
self.assertTrue(AnalysisDataService.doesExist(element))
# Clean up
for element in expected_workspaces:
AnalysisDataService.remove(element)
def setUp(self):
self.working_directory = tempfile.mkdtemp()
self.ws1_name = "ws1"
self.project_ext = ".mtdproj"
ADS.addOrReplace(self.ws1_name, CreateSampleWorkspace(OutputWorkspace=self.ws1_name))
project_saver = projectsaver.ProjectSaver(self.project_ext)
project_saver.save_project(workspace_to_save=[self.ws1_name], directory=self.working_directory)
def recover_selected_checkpoint(self, selected):
"""
Recover the passed checkpoint
:param selected: String; Checkpoint name to be recovered
"""
# If this is a valid file then it should only be the checkpoint here
if os.path.exists(selected):
selected = os.path.basename(selected)
self.is_recovery_running = True
self.presenter.change_start_mantid_to_cancel_label()
ADS.clear()
# Recover given the checkpoint selected
pid_dir = self.project_recovery.get_pid_folder_to_load_a_checkpoint_from()
selected = selected.replace(" ", "T")
checkpoint = os.path.join(pid_dir, selected)
self.selected_checkpoint = selected
try:
self._start_recovery_of_checkpoint(checkpoint)
except Exception as e:
# Fail "Silently" by setting failed run to true, setting checkpoint to tried and closing the view.
logger.debug("Project Recovery: " + str(e))
self.has_failed_run = True
self._update_checkpoint_tried(selected)
self.presenter.close_view()
def test_len_increases_when_item_added(self):
wsname = 'ADSTest_test_len_increases_when_item_added'
current_len = len(AnalysisDataService)
self._run_createws(wsname)
self.assertEquals(len(AnalysisDataService), current_len + 1)
# Remove to clean the test up
AnalysisDataService.remove(wsname)
def open_selected_in_editor(self, selected):
"""
Open the passed checkpoint in the editor
:param selected: String; Checkpoint name to be opened
"""
self.is_recovery_running = True
ADS.clear()
# Open editor for this checkpoint
pid_dir = self.project_recovery.get_pid_folder_to_load_a_checkpoint_from()
selected = selected.replace(" ", "T")
checkpoint = os.path.join(pid_dir, selected)
try:
self.project_recovery.open_checkpoint_in_script_editor(checkpoint)
except Exception as e:
if isinstance(e, KeyboardInterrupt):
raise
# Fail "silently"
self.has_failed_run = True
if self.has_failed_run:
self._update_checkpoint_tried(selected)
self.is_recovery_running = False
self.presenter.close_view()
def retrieve_hkl_from_spice_table(self):
""" Get averaged HKL from SPICE table
HKL will be averaged from SPICE table by assuming the value in SPICE might be right
:return:
"""
# get SPICE table
spice_table_name = get_spice_table_name(self._myExpNumber, self._myScanNumber)
assert AnalysisDataService.doesExist(spice_table_name), 'Spice table for exp %d scan %d cannot be found.' \
'' % (self._myExpNumber, self._myScanNumber)
spice_table_ws = AnalysisDataService.retrieve(spice_table_name)
# get HKL column indexes
h_col_index = spice_table_ws.getColumnNames().index('h')
k_col_index = spice_table_ws.getColumnNames().index('k')
l_col_index = spice_table_ws.getColumnNames().index('l')
# scan each Pt.
hkl = numpy.array([0., 0., 0.])
num_rows = spice_table_ws.rowCount()
for row_index in xrange(num_rows):
mi_h = spice_table_ws.cell(row_index, h_col_index)
mi_k = spice_table_ws.cell(row_index, k_col_index)
mi_l = spice_table_ws.cell(row_index, l_col_index)
hkl += numpy.array([mi_h, mi_k, mi_l])
# END-FOR
self._spiceHKL = hkl/num_rows
return
def test_DNSFRSelfCorrection(self):
outputWorkspaceName = "DNSFlippingRatioCorrTest_Test4"
# consider normalization=1.0 as set in self._create_fake_workspace
dataws_sf = self.__sf_nicrws - self.__sf_bkgrws
dataws_nsf = self.__nsf_nicrws - self.__nsf_bkgrws
alg_test = run_algorithm("DNSFlippingRatioCorr", SFDataWorkspace=dataws_sf,
NSFDataWorkspace=dataws_nsf, SFNiCrWorkspace=self.__sf_nicrws.getName(),
NSFNiCrWorkspace=self.__nsf_nicrws.getName(), SFBkgrWorkspace=self.__sf_bkgrws.getName(),
NSFBkgrWorkspace=self.__nsf_bkgrws.getName(), SFOutputWorkspace=outputWorkspaceName+'SF',
NSFOutputWorkspace=outputWorkspaceName+'NSF')
self.assertTrue(alg_test.isExecuted())
# check whether the data are correct
ws_sf = AnalysisDataService.retrieve(outputWorkspaceName + 'SF')
ws_nsf = AnalysisDataService.retrieve(outputWorkspaceName + 'NSF')
# dimensions
self.assertEqual(24, ws_sf.getNumberHistograms())
self.assertEqual(24, ws_nsf.getNumberHistograms())
self.assertEqual(2, ws_sf.getNumDims())
self.assertEqual(2, ws_nsf.getNumDims())
# data array: spin-flip must be zero
for i in range(24):
self.assertAlmostEqual(0.0, ws_sf.readY(i)[0])
# data array: non spin-flip must be nsf - sf^2/nsf
nsf = np.array(dataws_nsf.extractY())
sf = np.array(dataws_sf.extractY())
refdata = nsf + sf
for i in range(24):
self.assertAlmostEqual(refdata[i][0], ws_nsf.readY(i)[0])
run_algorithm("DeleteWorkspace", Workspace=outputWorkspaceName + 'SF')
run_algorithm("DeleteWorkspace", Workspace=outputWorkspaceName + 'NSF')
run_algorithm("DeleteWorkspace", Workspace=dataws_sf)
run_algorithm("DeleteWorkspace", Workspace=dataws_nsf)
return
def test_exportFileNew(self):
""" Test to export logs without header file
"""
# Generate the matrix workspace with some logs
ws = self.createTestWorkspace()
AnalysisDataService.addOrReplace("TestMatrixWS", ws)
# Test algorithm
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord001.txt",
SampleLogNames = ["run_number", "duration", "proton_charge", "proton_charge", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge", "MinPCharge", "MeanPCharge"],
SampleLogOperation = [None, None, "sum", "min", "average"],
FileMode = "new")
# Validate
self.assertTrue(alg_test.isExecuted())
# Locate file
outfilename = alg_test.getProperty("OutputFilename").value
try:
ifile = open(outfilename)
lines = ifile.readlines()
ifile.close()
except IOError as err:
print("Unable to open file {0}.".format(outfilename))
self.assertTrue(False)
return
# Last line cannot be empty, i.e., before EOF '\n' is not allowed
lastline = lines[-1]
self.assertTrue(len(lastline.strip()) > 0)
# Number of lines
self.assertEquals(len(lines), 2)
# Check line
firstdataline = lines[1]
terms = firstdataline.strip().split("\t")
self.assertEquals(len(terms), 5)
# Get property
pchargelog = ws.getRun().getProperty("proton_charge").value
sumpcharge = numpy.sum(pchargelog)
minpcharge = numpy.min(pchargelog)
avgpcharge = numpy.average(pchargelog)
v2 = float(terms[2])
self.assertAlmostEqual(sumpcharge, v2)
v3 = float(terms[3])
self.assertAlmostEqual(minpcharge, v3)
v4 = float(terms[4])
self.assertAlmostEqual(avgpcharge, v4)
# Remove generated files
os.remove(outfilename)
AnalysisDataService.remove("TestMatrixWS")
return
def _createTwoCurves(self, datawsname):
""" Create data workspace
"""
E = np.arange(-50, 50, 1.0)
# curve 1
I = 1000 * np.exp(-E**2/10**2)
err = I ** .5
# curve 2
I2 = 1000 * (1+np.sin(E/5*np.pi))
err2 = I ** .5
# workspace
ws = WorkspaceFactory.create(
"Workspace2D", NVectors=2,
XLength = E.size, YLength = I.size
)
# curve1
ws.dataX(0)[:] = E
ws.dataY(0)[:] = I
ws.dataE(0)[:] = err
# curve2
ws.dataX(1)[:] = E
ws.dataY(1)[:] = I2
ws.dataE(1)[:] = err2
# Add to data service
AnalysisDataService.addOrReplace(datawsname, ws)
return E, I, err, I2, err2
def _createDataWorkspace(self, datawsname):
""" Create data workspace
"""
import math
tof0 = 4900.
delta = 0.001
numpts = 200
vecx = []
vecy = []
vece = []
tof = tof0
for n in range(numpts):
vecx.append(tof)
vecy.append(math.sin(tof0))
vece.append(1.)
tof = tof * (1+delta)
# ENDFOR
vecx.append(tof)
dataws = api.CreateWorkspace(DataX = vecx, DataY = vecy, DataE = vece, NSpec = 1,
UnitX = "TOF")
# Add to data service
AnalysisDataService.addOrReplace(datawsname, dataws)
return dataws
def testConvertUnits(self):
# test whether CorrectTof+ConvertUnits+ConvertToDistribution will give the same result as TOFTOFConvertTOFToDeltaE
OutputWorkspaceName = "outputws1"
alg_test = run_algorithm("CorrectTOF", InputWorkspace=self._input_ws, EPPTable=self._table, OutputWorkspace=OutputWorkspaceName)
self.assertTrue(alg_test.isExecuted())
wscorr = AnalysisDataService.retrieve(OutputWorkspaceName)
# convert units, convert to distribution
alg_cu = run_algorithm("ConvertUnits", InputWorkspace=wscorr, Target='DeltaE', EMode='Direct', EFixed=2.27, OutputWorkspace=OutputWorkspaceName+'_dE')
ws_dE = AnalysisDataService.retrieve(OutputWorkspaceName+'_dE')
alg_cd = run_algorithm("ConvertToDistribution", Workspace=ws_dE)
# create reference data for X axis
tof1 = 2123.33867005
dataX = self._input_ws.readX(0) - tof1
tel = 8189.5 - tof1
factor = m_n*1e+15/eV
newX = 0.5*factor*16.0*(1/tel**2 - 1/dataX**2)
# compare
# self.assertEqual(newX[0], ws_dE.readX(0)[0])
self.assertTrue(np.allclose(newX, ws_dE.readX(0), atol=0.01))
# create reference data for Y axis and compare to the output
tof = dataX[:-1] + 5.25
newY = self._input_ws.readY(0)*tof**3/(factor*10.5*16.0)
# compare
self.assertTrue(np.allclose(newY, ws_dE.readY(0), rtol=0.01))
run_algorithm("DeleteWorkspace", Workspace=ws_dE)
run_algorithm("DeleteWorkspace", Workspace=wscorr)
def test_LoadPRFFile(self):
""" Test to load a .prf file
"""
# 1. Create test .prf file
prffilename = "test.prf"
self._createPrfFile(prffilename)
# 2. Execute the algorithm
alg_test = run_algorithm("LoadFullprofFile",
Filename = prffilename,
OutputWorkspace = "Data",
PeakParameterWorkspace = "Info")
self.assertTrue(alg_test.isExecuted())
# 3. Check data
dataws = AnalysisDataService.retrieve("Data")
self.assertEqual(dataws.getNumberHistograms(), 4)
self.assertEqual(len(dataws.readX(0)), 36)
# value
self.assertEqual(dataws.readX(0)[13], 5026.3223)
self.assertEqual(dataws.readY(1)[30], 0.3819)
# 4. Clean
os.remove(prffilename)
AnalysisDataService.remove("Data")
AnalysisDataService.remove("Info")
return
def test_exportFileAppend(self):
""" Test to export logs without header file
"""
# Generate the matrix workspace with some logs
ws = self.createTestWorkspace()
AnalysisDataService.addOrReplace("TestMatrixWS", ws)
# Test algorithm
# create new file
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord.txt",
SampleLogNames = ["run_number", "duration", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge"],
SampleLogOperation = [None, None, "sum"],
FileMode = "new")
# append
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord.txt",
SampleLogNames = ["run_number", "duration", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge"],
SampleLogOperation = [None, None, "sum"],
FileMode = "fastappend")
# Validate
self.assertTrue(alg_test.isExecuted())
# Locate file
outfilename = alg_test.getProperty("OutputFilename").value
try:
print "Output file is %s. " % (outfilename)
ifile = open(outfilename)
lines = ifile.readlines()
ifile.close()
except IOError as err:
print "Unable to open file %s. " % (outfilename)
self.assertTrue(False)
return
# Last line cannot be empty, i.e., before EOF '\n' is not allowed
lastline = lines[-1]
self.assertTrue(len(lastline.strip()) > 0)
# Number of lines
self.assertEquals(len(lines), 3)
# Check line
firstdataline = lines[1]
terms = firstdataline.strip().split("\t")
self.assertEquals(len(terms), 3)
#
# # Remove generated files
os.remove(outfilename)
AnalysisDataService.remove("TestMatrixWS")
return
def _determine_factors(self, q_high_angle, q_low_angle, mode, scale, shift):
# We need to make suret that the fitting only occurs in the y direction
constant_x_shift_and_scale = ', f0.Shift=0.0, f0.XScaling=1.0'
# Determine the StartQ and EndQ values
q_min, q_max = self._get_start_q_and_end_q_values(rear_data=q_low_angle, front_data=q_high_angle)
# We need to transfer the errors from the front data to the rear data, as we are using the the front data as a model, but
# we want to take into account the errors of both workspaces.
error_correction = ErrorTransferFromModelToData()
front_data_corrected, rear_data_corrected = error_correction.get_error_corrected(rear_data=q_low_angle,
front_data=q_high_angle,
q_min=q_min, q_max=q_max)
fit = self.createChildAlgorithm('Fit')
# We currently have to put the front_data into the ADS so that the TabulatedFunction has access to it
front_data_corrected = AnalysisDataService.addOrReplace('front_data_corrected', front_data_corrected)
front_in_ads = AnalysisDataService.retrieve('front_data_corrected')
function = 'name=TabulatedFunction, Workspace="' + str(
front_in_ads.name()) + '"' + ";name=FlatBackground"
fit.setProperty('Function', function)
fit.setProperty('InputWorkspace', rear_data_corrected)
constant_x_shift_and_scale = 'f0.Shift=0.0, f0.XScaling=1.0'
if mode == Mode.BothFit:
fit.setProperty('Ties', constant_x_shift_and_scale)
elif mode == Mode.ShiftOnly:
fit.setProperty('Ties', 'f0.Scaling=' + str(scale) + ',' + constant_x_shift_and_scale)
elif mode == Mode.ScaleOnly:
fit.setProperty('Ties', 'f1.A0=' + str(shift) + '*f0.Scaling,' + constant_x_shift_and_scale)
else:
raise RuntimeError('Unknown fitting mode requested.')
fit.setProperty('StartX', q_min)
fit.setProperty('EndX', q_max)
fit.setProperty('CreateOutput', True)
fit.execute()
param = fit.getProperty('OutputParameters').value
AnalysisDataService.remove(front_in_ads.name())
# The outparameters are:
# 1. Scaling in y direction
# 2. Shift in x direction
# 3. Scaling in x direction
# 4. Shift in y direction
scale = param.row(0)['Value']
if scale == 0.0:
raise RuntimeError('Fit scaling as part of stitching evaluated to zero')
# In order to determine the shift, we need to remove the scale factor
shift = param.row(3)['Value'] / scale
return (shift, scale)
def test_observeClear_calls_clearHandle_when_set_on_ads_its_cleared(self):
CreateSampleWorkspace(OutputWorkspace="ws")
self.fake_class.observeClear(True)
self.fake_class.clearHandle = mock.MagicMock()
ADS.clear()
self.assertEqual(self.fake_class.clearHandle.call_count, 1)
def tearDown(self):
self.cleanup_names.append(self.wsname)
for name in self.cleanup_names:
try:
AnalysisDataService.remove(name)
except KeyError:
pass
self.cleanup_names = []
def get_ads_workspace_references():
"""
Gets a list of handles of available workspaces on the ADS
@return: the workspaces on the ADS.
"""
for workspace_name in AnalysisDataService.getObjectNames():
yield AnalysisDataService.retrieve(workspace_name)
def populate_combobox(self, combo):
ws_list = AnalysisDataService.getObjectNames()
for ws in ws_list:
ws_object = AnalysisDataService.retrieve(ws)
if not ws.startswith("__") and combo.findText(ws)<0\
and hasattr(ws_object, "getNumberHistograms")\
and ws_object.getNumberHistograms()==1:
combo.addItem(ws)
def _assert_list_in_ADS(self, workspace_name_list):
ads_list = AnalysisDataService.getObjectNames()
for item in workspace_name_list:
self.assertTrue(item in ads_list)
def tearDownClass(cls):
AnalysisDataService.clear()
def _get_project_size(workspace_names):
project_size = 0
for name in workspace_names:
project_size += AnalysisDataService.retrieve(name).getMemorySize()
return project_size
def fit_tof_iteration(sample_data, container_data, runs, flags):
"""
Performs a single iterations of the time of flight corrections and fitting
workflow.
:param sample_data: Loaded sample data workspaces
:param container_data: Loaded container data workspaces
:param runs: A string specifying the runs to process
:param flags: A dictionary of flags to control the processing
:return: Tuple of (workspace group name, pre correction fit parameters,
final fit parameters, chi^2 values)
"""
# Transform inputs into something the algorithm can understand
if isinstance(flags['masses'][0], list):
mass_values = _create_profile_strs_and_mass_list(
copy.deepcopy(flags['masses'][0]))[0]
profiles_strs = []
for mass_spec in flags['masses']:
profiles_strs.append(
_create_profile_strs_and_mass_list(mass_spec)[1])
else:
mass_values, profiles_strs = _create_profile_strs_and_mass_list(
flags['masses'])
background_str = _create_background_str(flags.get('background', None))
intensity_constraints = _create_intensity_constraint_str(
flags['intensity_constraints'])
ties = _create_user_defined_ties_str(flags['masses'])
num_spec = sample_data.getNumberHistograms()
pre_correct_pars_workspace = None
pars_workspace = None
max_fit_iterations = flags.get('max_fit_iterations', 5000)
output_groups = []
chi2_values = []
for index in range(num_spec):
if isinstance(profiles_strs, list):
profiles = profiles_strs[index]
else:
profiles = profiles_strs
suffix = _create_fit_workspace_suffix(index, sample_data,
flags['fit_mode'],
flags['spectra'],
flags.get('iteration', None))
# Corrections
corrections_args = dict()
# Need to do a fit first to obtain the parameter table
pre_correction_pars_name = runs + "_params_pre_correction" + suffix
corrections_fit_name = "__vesuvio_corrections_fit"
ms.VesuvioTOFFit(InputWorkspace=sample_data,
WorkspaceIndex=index,
Masses=mass_values,
MassProfiles=profiles,
Background=background_str,
IntensityConstraints=intensity_constraints,
Ties=ties,
OutputWorkspace=corrections_fit_name,
FitParameters=pre_correction_pars_name,
MaxIterations=max_fit_iterations,
Minimizer=flags['fit_minimizer'])
ms.DeleteWorkspace(corrections_fit_name)
corrections_args['FitParameters'] = pre_correction_pars_name
# Add the mutiple scattering arguments
corrections_args.update(flags['ms_flags'])
corrected_data_name = runs + "_tof_corrected" + suffix
linear_correction_fit_params_name = runs + "_correction_fit_scale" + suffix
if flags.get('output_verbose_corrections', False):
corrections_args[
"CorrectionWorkspaces"] = runs + "_correction" + suffix
corrections_args[
"CorrectedWorkspaces"] = runs + "_corrected" + suffix
if container_data is not None:
corrections_args["ContainerWorkspace"] = container_data
ms.VesuvioCorrections(
InputWorkspace=sample_data,
OutputWorkspace=corrected_data_name,
LinearFitResult=linear_correction_fit_params_name,
WorkspaceIndex=index,
GammaBackground=flags.get('gamma_correct', False),
Masses=mass_values,
MassProfiles=profiles,
IntensityConstraints=intensity_constraints,
MultipleScattering=True,
GammaBackgroundScale=flags.get('fixed_gamma_scaling', 0.0),
ContainerScale=flags.get('fixed_container_scaling', 0.0),
**corrections_args)
# Final fit
fit_ws_name = runs + "_data" + suffix
pars_name = runs + "_params" + suffix
fit_result = ms.VesuvioTOFFit(
InputWorkspace=corrected_data_name,
WorkspaceIndex=0,
Masses=mass_values,
MassProfiles=profiles,
Background=background_str,
IntensityConstraints=intensity_constraints,
Ties=ties,
OutputWorkspace=fit_ws_name,
FitParameters=pars_name,
MaxIterations=max_fit_iterations,
Minimizer=flags['fit_minimizer'])
chi2_values.append(fit_result[-1])
ms.DeleteWorkspace(corrected_data_name)
# Process parameter tables
if pre_correct_pars_workspace is None:
pre_correct_pars_workspace = _create_param_workspace(
num_spec, mtd[pre_correction_pars_name])
if pars_workspace is None:
pars_workspace = _create_param_workspace(num_spec, mtd[pars_name])
spec_num_str = str(sample_data.getSpectrum(index).getSpectrumNo())
current_spec = 'spectrum_' + spec_num_str
_update_fit_params(pre_correct_pars_workspace, index,
mtd[pre_correction_pars_name], current_spec)
_update_fit_params(pars_workspace, index, mtd[pars_name], current_spec)
ms.DeleteWorkspace(pre_correction_pars_name)
ms.DeleteWorkspace(pars_name)
# Process spectrum group
# Note the ordering of operations here gives the order in the WorkspaceGroup
group_name = runs + suffix
output_workspaces = [fit_ws_name, linear_correction_fit_params_name]
if flags.get('output_verbose_corrections', False):
output_workspaces += mtd[
corrections_args["CorrectionWorkspaces"]].getNames()
output_workspaces += mtd[
corrections_args["CorrectedWorkspaces"]].getNames()
ms.UnGroupWorkspace(corrections_args["CorrectionWorkspaces"])
ms.UnGroupWorkspace(corrections_args["CorrectedWorkspaces"])
output_groups.append(
ms.GroupWorkspaces(InputWorkspaces=output_workspaces,
OutputWorkspace=group_name))
# Output the parameter workspaces
params_pre_corr = runs + "_params_pre_correction_iteration_" + str(
flags['iteration'])
params_name = runs + "_params_iteration_" + str(flags['iteration'])
AnalysisDataService.Instance().addOrReplace(
params_pre_corr, pre_correct_pars_workspace)
AnalysisDataService.Instance().addOrReplace(params_name,
pars_workspace)
if len(output_groups) > 1:
result_ws = output_groups
else:
result_ws = output_groups[0]
return (result_ws, pre_correct_pars_workspace, pars_workspace, chi2_values)
def test_project_loading(self):
project_loader = projectloader.ProjectLoader(project_file_ext)
self.assertTrue(project_loader.load_project(working_project_file))
self.assertEqual(ADS.getObjectNames(), ["ws1"])
def tearDown(self):
AnalysisDataService.Instance().clear()
def test_pcolormesh_from_names(self):
ws_name = 'test_pcolormesh_from_names-1'
AnalysisDataService.Instance().addOrReplace(ws_name, self._test_ws)
fig = pcolormesh_from_names([ws_name])
self.assertEqual(1, len(fig.gca().images))
def test_pcolormesh_from_names_calls_pcolormesh(self, pcolormesh_mock):
ws_name = 'test_pcolormesh_from_names_calls_pcolormesh-1'
AnalysisDataService.Instance().addOrReplace(ws_name, self._test_ws)
pcolormesh_from_names([ws_name])
self.assertEqual(1, pcolormesh_mock.call_count)
def PyExec(self):
fn = self.getPropertyValue("Filename")
wsn = self.getPropertyValue("OutputWorkspace")
monitor_workspace_name = self.getPropertyValue(
"OutputMonitorWorkspace")
if monitor_workspace_name == "":
self.setPropertyValue("OutputMonitorWorkspace", wsn + '_Monitors')
# print (fn, wsn)
self.override_angle = self.getPropertyValue("AngleOverride")
self.fxml = self.getPropertyValue("InstrumentXML")
# load data
parms_dict, det_udet, det_count, det_tbc, data = self.read_file(fn)
nrows = int(parms_dict['NDET'])
# nbins=int(parms_dict['NTC'])
xdata = np.array(det_tbc)
xdata_mon = np.linspace(xdata[0], xdata[-1], len(xdata))
ydata = data.astype(np.float)
ydata = ydata.reshape(nrows, -1)
edata = np.sqrt(ydata)
# CreateWorkspace(OutputWorkspace=wsn,DataX=xdata,DataY=ydata,DataE=edata,
# NSpec=nrows,UnitX='TOF',WorkspaceTitle='Data',YUnitLabel='Counts')
nr, nc = ydata.shape
ws = WorkspaceFactory.create("Workspace2D",
NVectors=nr,
XLength=nc + 1,
YLength=nc)
for i in range(nrows):
ws.setX(i, xdata)
ws.setY(i, ydata[i])
ws.setE(i, edata[i])
ws.getAxis(0).setUnit('tof')
AnalysisDataService.addOrReplace(wsn, ws)
# self.setProperty("OutputWorkspace", wsn)
# print ("ws:", wsn)
# ws=mtd[wsn]
# fix the x values for the monitor
for i in range(nrows - 2, nrows):
ws.setX(i, xdata_mon)
self.log().information("set detector IDs")
# set detetector IDs
for i in range(nrows):
ws.getSpectrum(i).setDetectorID(det_udet[i])
# Sample_logs the header values are written into the sample logs
log_names = [
str(sl.encode('ascii', 'ignore').decode())
for sl in parms_dict.keys()
]
log_values = [
str(sl.encode('ascii', 'ignore').decode()) if isinstance(
sl, UnicodeType) else str(sl) for sl in parms_dict.values()
]
for i in range(len(log_values)):
if ('nan' in log_values[i]) or ('NaN' in log_values[i]):
log_values[i] = '-1.0'
AddSampleLogMultiple(Workspace=wsn,
LogNames=log_names,
LogValues=log_values)
SetGoniometer(Workspace=wsn, Goniometers='Universal')
if (self.fxml == ""):
LoadInstrument(Workspace=wsn,
InstrumentName="Exed",
RewriteSpectraMap=True)
else:
LoadInstrument(Workspace=wsn,
Filename=self.fxml,
RewriteSpectraMap=True)
try:
RotateInstrumentComponent(
Workspace=wsn,
ComponentName='Tank',
Y=1,
Angle=-float(parms_dict['phi'].encode('ascii', 'ignore')),
RelativeRotation=False)
except:
self.log().warning(
"The instrument does not contain a 'Tank' component. "
"This means that you are using a custom XML instrument definition. "
"OMEGA_MAG will be ignored.")
self.log().warning(
"Please make sure that the detector positions in the instrument definition are correct."
)
# Separate monitors into seperate workspace
__temp_monitors = ExtractSpectra(
InputWorkspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]),
OutputWorkspace=self.getPropertyValue("OutputMonitorWorkspace"))
# ExtractSpectra(InputWorkspace = wsn, WorkspaceIndexList = ','.join([str(s) for s in range(nrows-2, nrows)]),
# OutputWorkspace = wsn + '_Monitors')
MaskDetectors(Workspace=wsn,
WorkspaceIndexList=','.join(
[str(s) for s in range(nrows - 2, nrows)]))
RemoveMaskedSpectra(InputWorkspace=wsn, OutputWorkspace=wsn)
self.setProperty("OutputWorkspace", wsn)
self.setProperty("OutputMonitorWorkspace", __temp_monitors)
def tearDown(self):
ADS.clear()
def get_all_workspace_names(group_names):
workspace_names = []
for group_name in group_names:
workspace_names = add_workspace_names(
workspace_names, AnalysisDataService.retrieve(group_name))
return workspace_names
def tearDown(self):
AnalysisDataService.clear()
def test_exportFileUTC(self):
""" Test to export logs without header file
"""
# Generate the matrix workspace with some logs
ws = self.createTestWorkspace()
AnalysisDataService.addOrReplace("TestMatrixWS", ws)
# Test algorithm
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord001utc.txt",
SampleLogNames = ["run_number", "duration", "run_start", "proton_charge", "proton_charge", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "StartTime", "ProtonCharge", "MinPCharge", "MeanPCharge"],
SampleLogOperation = [None, None, "time", "sum", "min", "average"],
TimeZone = 'UTC',
FileMode = "new")
# Validate
self.assertTrue(alg_test.isExecuted())
# Locate file
outfilename = alg_test.getProperty("OutputFilename").value
try:
ifile = open(outfilename)
lines = ifile.readlines()
ifile.close()
except IOError as err:
print("Unable to open file {0}.".format(outfilename))
self.fail()
return
# Last line cannot be empty, i.e., before EOF '\n' is not allowed
lastline = lines[-1]
self.assertGreater(len(lastline.strip()), 0)
# Number of lines
self.assertEqual(len(lines), 2)
# Check line
firstdataline = lines[1]
terms = firstdataline.strip().split("\t")
self.assertEqual(len(terms), 6)
# Get property
runstarttime = ws.run().getProperty("run_start").value
pchargelog = ws.getRun().getProperty("proton_charge").value
sumpcharge = numpy.sum(pchargelog)
minpcharge = numpy.min(pchargelog)
avgpcharge = numpy.average(pchargelog)
# run start time
v2 = str(terms[2])
self.assertEqual(runstarttime, v2.split("UTC")[0].strip())
v3 = float(terms[3])
self.assertAlmostEqual(sumpcharge, v3)
v4 = float(terms[4])
self.assertAlmostEqual(minpcharge, v4)
v5 = float(terms[5])
self.assertAlmostEqual(avgpcharge, v5)
# Remove generated files
os.remove(outfilename)
AnalysisDataService.remove("TestMatrixWS")
return
def test_plot_from_names_with_non_plottable_workspaces_returns_None(self):
table = WorkspaceFactory.Instance().createTable()
table_name = 'test_plot_from_names_with_non_plottable_workspaces_returns_None'
AnalysisDataService.Instance().addOrReplace(table_name, table)
result = plot_from_names([table_name], errors=False, overplot=False)
self.assertEqual(result, None)
def tearDown(self):
ADS.clear()
if isdir(working_directory):
rmtree(working_directory)
def test_that_manage_workspace_names_raises_on_mix_of_workspaces_and_names(
self):
ws = ["some_workspace", self._test_ws]
AnalysisDataService.Instance().addOrReplace("some_workspace",
self._test_ws)
self.assertRaises(TypeError, workspace_names_dummy_func(ws))
def test_exportFileAppend2(self):
""" Test to export file in appending mode
In this case, the original file will be renamed and a new file will
be creatd
"""
import datetime
import time
# Generate the matrix workspace with some logs
ws = self.createTestWorkspace()
AnalysisDataService.addOrReplace("TestMatrixWS", ws)
# Test algorithm
# create new file
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord.txt",
SampleLogNames = ["run_number", "duration", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge"],
SampleLogOperation = [None, None, "sum"],
FileMode = "new")
# append
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS",
OutputFilename = "TestRecord.txt",
SampleLogNames = ["run_number", "duration", "proton_charge", "SensorA"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge", "SensorA"],
SampleLogOperation = [None, None, "sum", "0"],
FileMode = "append")
# Validate
self.assertTrue(alg_test.isExecuted())
# Locate file
outfilename = alg_test.getProperty("OutputFilename").value
try:
ifile = open(outfilename)
lines = ifile.readlines()
ifile.close()
except IOError as err:
print("Unable to open file {0}.".format(outfilename))
self.fail()
return
# Last line cannot be empty, i.e., before EOF '\n' is not allowed
lastline = lines[-1]
self.assertGreater(len(lastline.strip()), 0)
# Number of lines
self.assertEqual(len(lines), 2)
# Check line
firstdataline = lines[1]
terms = firstdataline.strip().split("\t")
self.assertEqual(len(terms), 4)
# Locate the previos file
# Rename old file and reset the file mode
# Rename the old one: split path from file, new name, and rename
fileName, fileExtension = os.path.splitext(outfilename)
now = datetime.datetime.now()
nowstr = time.strftime("%Y_%B_%d_%H_%M")
oldfilename = fileName + "_" + nowstr + fileExtension
print("Saved old file is {0}. ".format(oldfilename))
self.assertTrue(os.path.exists(oldfilename))
# Remove generated files
os.remove(outfilename)
os.remove(oldfilename)
AnalysisDataService.remove("TestMatrixWS")
return
def remove_all_workspaces_from_ads():
workspaces_on_the_ads = AnalysisDataService.getObjectNames()
for name in workspaces_on_the_ads:
AnalysisDataService.remove(name)
def tearDown(self):
AnalysisDataService.Instance().clear()
plt.close('all')
def tearDown(self):
if AnalysisDataService.doesExist('ws1'):
DeleteWorkspace('ws1')
if AnalysisDataService.doesExist('ws2'):
DeleteWorkspace('ws2')
def cleanup(self):
ADS.clear()
_try_delete_cal_and_focus_dirs(CWDIR)
def _remove_workspaces():
for element in AnalysisDataService.getObjectNames():
AnalysisDataService.remove(element)
def add_to_ads(workspace_name, workspace):
return AnalysisDataService.addOrReplace(workspace_name, workspace)
def cleanup(self):
ADS.clear()
try:
os.remove(self._peaks_file)
except:
pass
def get_ads_workspace(workspace_name):
return AnalysisDataService.retrieve(workspace_name)
def cleanup(self):
ADS.clear()
try:
os.remove(self._filepath)
except:
pass
def test_that_instantiated_WorkspaceGroup_can_be_added_to_the_ADS(self):
ws_group = WorkspaceGroup()
mtd.add("group1", ws_group)
self.assertEqual(AnalysisDataService.getObjectNames(), ["group1"])
self.assertIsInstance(mtd["group1"], WorkspaceGroup)
def cleanup(self):
ADS.clear()
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 test_sortRecordFileOverride(self):
""" Test to append logs and sort the log record file
"""
# Record 0
ws1 = self.createTestWorkspace(run=10000)
AnalysisDataService.addOrReplace("TestMatrixWS1", ws1)
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS1",
OutputFilename = "TestRecord10.txt",
SampleLogNames = ["run_number", "duration", "proton_charge", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge", "ProtonCharge-Avg"],
SampleLogOperation = [None, None, "min", "average"],
FileMode = "new",
FileFormat = "tab",
OverrideLogValue = ["Duration", "12345", "ProtonCharge-Avg", "32.921"],
OrderByTitle = 'RUN')
# Record 1
ws2 = self.createTestWorkspace(run=11000)
AnalysisDataService.addOrReplace("TestMatrixWS2", ws2)
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS2",
OutputFilename = "TestRecord10.txt",
SampleLogNames = ["run_number", "duration", "proton_charge", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge", "ProtonCharge-Avg"],
SampleLogOperation = [None, None, "min", "average"],
FileMode = "fastappend",
FileFormat = "tab",
OverrideLogValue = ["Duration", "23456", "ProtonCharge-Avg", "22.921"],
OrderByTitle = 'RUN')
# Record 2
ws3 = self.createTestWorkspace(run=10023)
AnalysisDataService.addOrReplace("TestMatrixWS3", ws3)
alg_test = run_algorithm("ExportExperimentLog",
InputWorkspace = "TestMatrixWS3",
OutputFilename = "TestRecord10.txt",
SampleLogNames = ["run_number", "duration", "proton_charge", "proton_charge"],
SampleLogTitles = ["RUN", "Duration", "ProtonCharge", "ProtonCharge-Avg"],
SampleLogOperation = [None, None, "min", "average"],
FileMode = "fastappend",
FileFormat = "tab",
OverrideLogValue = ["Duration", "34567", "ProtonCharge-Avg", "12.921"],
OrderByTitle = 'RUN')
# Verify
# Locate file
outfilename = alg_test.getProperty("OutputFilename").value
try:
ifile = open(outfilename)
lines = ifile.readlines()
ifile.close()
except IOError as err:
print("Unable to open file {0}.".format(outfilename))
self.fail()
return
# Last line cannot be empty, i.e., before EOF '\n' is not allowed
lastline = lines[-1]
self.assertGreater(len(lastline.strip()), 0)
# Number of lines
self.assertEqual(len(lines), 4)
# Check value
for i in range(1, 3):
currline = lines[i]
curr_run = int(currline.split("\t")[0])
curr_min = float(currline.split("\t")[2])
nextline = lines[i+1]
next_run = int(nextline.split('\t')[0])
next_min = float(nextline.split('\t')[2])
self.assertLess(curr_run, next_run)
self.assertLess(curr_min, next_min)
line2 = lines[2]
terms = line2.split("\t")
duration = int(terms[1])
self.assertEqual(duration, 34567)
pchargeavg = float(terms[3])
self.assertAlmostEqual(pchargeavg, 12.921)
# Remove generated files
os.remove(outfilename)
AnalysisDataService.remove("TestMatrixWS1")
AnalysisDataService.remove("TestMatrixWS2")
AnalysisDataService.remove("TestMatrixWS3")
return