def create_masker(state, detector_type):
"""
Provides the appropriate masker.
:param state: a SANSState object
:param detector_type: either HAB or LAB
:return: the corresponding slicer
"""
data_info = state.data
instrument = data_info.instrument
# TODO remove this shim
if instrument is SANSInstrument.LARMOR or instrument is SANSInstrument.LOQ or\
instrument is SANSInstrument.SANS2D or instrument is SANSInstrument.ZOOM: # noqa
run_number = data_info.sample_scatter_run_number
file_name = data_info.sample_scatter
_, ipf_path = get_instrument_paths_for_sans_file(file_name)
spectra_block = SpectraBlock(ipf_path, run_number, instrument,
detector_type)
masker = MaskerISIS(spectra_block)
else:
masker = NullMasker()
NotImplementedError(
"create_masker: Other instruments are not implemented yet.")
return masker
def reset_to_defaults_for_instrument(self, file_information = None):
r_range = {}
instrument = None
if file_information:
instrument_file_path = get_instrument_paths_for_sans_file(file_information=file_information)
r_range = get_named_elements_from_ipf_file(instrument_file_path[1],
["beam_centre_radius_min", "beam_centre_radius_max"], float)
instrument = file_information.get_instrument()
self._max_iterations = 10
self._r_min = r_range["beam_centre_radius_min"] if "beam_centre_radius_min" in r_range else 60
self._r_max = r_range["beam_centre_radius_max"] if "beam_centre_radius_max" in r_range else 280
self._left_right = True
self._up_down = True
self._tolerance = 0.0001251
self._lab_pos_1 = ''
self._lab_pos_2 = ''
self._hab_pos_2 = ''
self._hab_pos_1 = ''
self.scale_1 = 1000
self.scale_2 = 1000
self.COM = False
self.verbose = False
self.q_min = 0.01
self.q_max = 0.1
self._component = DetectorType.LAB
self.update_lab = True
self.update_hab = True
if instrument == SANSInstrument.LARMOR:
self.scale_1 = 1.0
def setup_idf_and_ipf_content(move_info, data_info):
# Get the IDF and IPF path since they contain most of the import information
file_name = data_info.sample_scatter
idf_path, ipf_path = get_instrument_paths_for_sans_file(file_name)
# Set the detector names
set_detector_names(move_info, ipf_path)
# Set the monitor names
set_monitor_names(move_info, idf_path)
def test_that_finds_idf_and_ipf_paths(self):
# Arrange
file_name = "SANS2D00022024"
# Act
idf_path, ipf_path = get_instrument_paths_for_sans_file(file_name)
# Assert
self.assertTrue(idf_path is not None)
self.assertTrue(ipf_path is not None)
self.assertTrue("Definition" in idf_path)
self.assertTrue("Parameters" in ipf_path)
def test_that_finds_idf_and_ipf_paths(self):
# Arrange
file_name = "SANS2D00022024"
# Act
idf_path, ipf_path = get_instrument_paths_for_sans_file(file_name)
# Assert
self.assertTrue(idf_path is not None)
self.assertTrue(ipf_path is not None)
self.assertTrue("Definition" in idf_path)
self.assertTrue("Parameters" in ipf_path)
def set_default_incident_monitor(normalize_monitor_info, data_info):
"""
The default incident monitor is stored on the IPF.
:param normalize_monitor_info: a StateNormalizeMonitor object on which we set the default value
:param data_info: a StateData object
"""
file_name = data_info.sample_scatter
_, ipf_path = get_instrument_paths_for_sans_file(file_name)
named_element = "default-incident-monitor-spectrum"
monitor_spectrum_tag_to_search = [named_element]
found_monitor_spectrum = get_named_elements_from_ipf_file(ipf_path, monitor_spectrum_tag_to_search, int)
if named_element in found_monitor_spectrum:
normalize_monitor_info.incident_monitor = found_monitor_spectrum[named_element]
def get_detector_size_from_sans_file(state, detector):
instrument_file = get_instrument_paths_for_sans_file(state.data.sample_scatter)
if detector == DetectorType.HAB:
x_dim = get_named_elements_from_ipf_file(instrument_file[1], "high-angle-detector-num-columns",
float)['high-angle-detector-num-columns']
y_dim = get_named_elements_from_ipf_file(instrument_file[1], "high-angle-detector-num-rows",
float)['high-angle-detector-num-rows']
else:
x_dim = get_named_elements_from_ipf_file(instrument_file[1], "low-angle-detector-num-columns", float)[
'low-angle-detector-num-columns']
y_dim = get_named_elements_from_ipf_file(instrument_file[1], "low-angle-detector-num-rows", float)[
'low-angle-detector-num-rows']
return x_dim, y_dim
def get_detector_size_from_sans_file(state, detector):
instrument_file = get_instrument_paths_for_sans_file(state.data.sample_scatter)
if detector == DetectorType.HAB:
x_dim = get_named_elements_from_ipf_file(instrument_file[1], "high-angle-detector-num-columns",
float)['high-angle-detector-num-columns']
y_dim = get_named_elements_from_ipf_file(instrument_file[1], "high-angle-detector-num-rows",
float)['high-angle-detector-num-rows']
else:
x_dim = get_named_elements_from_ipf_file(instrument_file[1], "low-angle-detector-num-columns", float)[
'low-angle-detector-num-columns']
y_dim = get_named_elements_from_ipf_file(instrument_file[1], "low-angle-detector-num-rows", float)[
'low-angle-detector-num-rows']
return x_dim, y_dim
def test_that_monitors_can_be_found_v2(self):
# Arrange
test_file = "LOQ74044"
file_information_factory = SANSFileInformationFactory()
file_information = file_information_factory.create_sans_file_information(test_file)
full_file_path = file_information.get_file_name()
idf, _ = get_instrument_paths_for_sans_file(full_file_path)
# Act
results = get_monitor_names_from_idf_file(idf)
# Assert
self.assertTrue(len(results) == 2)
for key, value in list(results.items()):
self.assertTrue(value == ("monitor"+str(key)))
def set_default_monitors(calculate_transmission_info, data_info):
"""
The default incident monitor is stored on the IPF.
:param calculate_transmission_info: a StateCalculateTransmission object on which we set the default value
:param data_info: a StateData object
"""
file_name = data_info.sample_scatter
_, ipf_path = get_instrument_paths_for_sans_file(file_name)
incident_tag = "default-incident-monitor-spectrum"
transmission_tag = "default-transmission-monitor-spectrum"
monitors_to_search = [incident_tag, transmission_tag]
found_monitor_spectrum = get_named_elements_from_ipf_file(ipf_path, monitors_to_search, int)
if incident_tag in found_monitor_spectrum:
calculate_transmission_info.default_incident_monitor = found_monitor_spectrum[incident_tag]
if transmission_tag in found_monitor_spectrum:
calculate_transmission_info.default_transmission_monitor = found_monitor_spectrum[transmission_tag]
def test_that_monitors_can_be_found_v2(self):
# Arrange
test_file = "LOQ74044"
file_information_factory = SANSFileInformationFactory()
file_information = file_information_factory.create_sans_file_information(test_file)
full_file_path = file_information.get_file_name()
idf, _ = get_instrument_paths_for_sans_file(full_file_path)
# Act
results = get_monitor_names_from_idf_file(idf)
# Assert
self.assertTrue(len(results) == 2)
for key, value in results.items():
self.assertTrue(value == ("monitor"+str(key)))
def get_position_steps(self, state):
instrument_file = get_instrument_paths_for_sans_file(state.data.sample_scatter)
position_1_step = get_named_elements_from_ipf_file(
instrument_file[1], ["centre-finder-step-size"], float)['centre-finder-step-size']
try:
position_2_step = get_named_elements_from_ipf_file(
instrument_file[1], ["centre-finder-step-size2"], float)['centre-finder-step-size2']
except:
position_2_step = position_1_step
find_direction = self.getProperty("Direction").value
if find_direction == FindDirectionEnum.LEFT_RIGHT.value:
position_2_step = 0.0
elif find_direction == FindDirectionEnum.UP_DOWN.value:
position_1_step = 0.0
return position_1_step, position_2_step
def test_that_named_entries_in_instrument_parameter_file_can_be_retrieved(self):
# Arrange
test_file = "LARMOR00003368"
file_information_factory = SANSFileInformationFactory()
file_information = file_information_factory.create_sans_file_information(test_file)
full_file_path = file_information.get_file_name()
_, ipf = get_instrument_paths_for_sans_file(full_file_path)
to_search = ["low-angle-detector-name", "high-angle-detector-short-name"]
# Act
results = get_named_elements_from_ipf_file(ipf, to_search, str)
# Assert
self.assertTrue(len(results) == 2)
self.assertTrue(results["low-angle-detector-name"] == "DetectorBench")
self.assertTrue(results["high-angle-detector-short-name"] == "front")
def test_that_named_entries_in_instrument_parameter_file_can_be_retrieved(self):
# Arrange
test_file = "LARMOR00003368"
file_information_factory = SANSFileInformationFactory()
file_information = file_information_factory.create_sans_file_information(test_file)
full_file_path = file_information.get_file_name()
_, ipf = get_instrument_paths_for_sans_file(full_file_path)
to_search = ["low-angle-detector-name", "high-angle-detector-short-name"]
# Act
results = get_named_elements_from_ipf_file(ipf, to_search, str)
# Assert
self.assertTrue(len(results) == 2)
self.assertTrue(results["low-angle-detector-name"] == "DetectorBench")
self.assertTrue(results["high-angle-detector-short-name"] == "front")
def setup_detectors_from_ipf(reduction_info, data_info):
file_name = data_info.sample_scatter
_, ipf_path = get_instrument_paths_for_sans_file(file_name)
detector_names = {DetectorType.to_string(DetectorType.LAB): "low-angle-detector-name",
DetectorType.to_string(DetectorType.HAB): "high-angle-detector-name"}
names_to_search = []
names_to_search.extend(detector_names.values())
found_detector_names = get_named_elements_from_ipf_file(ipf_path, names_to_search, str)
for detector_type in reduction_info.detector_names.keys():
try:
detector_name_tag = detector_names[detector_type]
detector_name = found_detector_names[detector_name_tag]
except KeyError:
continue
reduction_info.detector_names[detector_type] = detector_name
def create_masker(state, detector_type):
"""
Provides the appropriate masker.
:param state: a SANSState object
:param detector_type: either HAB or LAB
:return: the corresponding slicer
"""
data_info = state.data
instrument = data_info.instrument
if instrument is SANSInstrument.LARMOR or instrument is SANSInstrument.LOQ or\
instrument is SANSInstrument.SANS2D or instrument is SANSInstrument.ZOOM: # noqa
run_number = data_info.sample_scatter_run_number
file_name = data_info.sample_scatter
_, ipf_path = get_instrument_paths_for_sans_file(file_name)
spectra_block = SpectraBlock(ipf_path, run_number, instrument, detector_type)
masker = MaskerISIS(spectra_block, instrument)
else:
masker = NullMasker()
NotImplementedError("MaskFactory: Other instruments are not implemented yet.")
return masker
def reset_to_defaults_for_instrument(self, file_information=None):
r_range = {}
instrument = None
if file_information:
instrument_file_path = get_instrument_paths_for_sans_file(
file_information=file_information)
r_range = get_named_elements_from_ipf_file(
instrument_file_path[1],
["beam_centre_radius_min", "beam_centre_radius_max"], float)
instrument = file_information.get_instrument()
self._max_iterations = 10
self._r_min = r_range[
"beam_centre_radius_min"] if "beam_centre_radius_min" in r_range else 60
self._r_max = r_range[
"beam_centre_radius_max"] if "beam_centre_radius_max" in r_range else 280
self._left_right = True
self._up_down = True
self._tolerance = 0.0001251
self._lab_pos_1 = ''
self._lab_pos_2 = ''
self._hab_pos_2 = ''
self._hab_pos_1 = ''
self.scale_1 = 1000
self.scale_2 = 1000
self.COM = False
self.verbose = False
self.q_min = 0.01
self.q_max = 0.1
self._component = DetectorType.LAB
self.update_lab = True
self.update_hab = True
if instrument == SANSInstrument.LARMOR:
self.scale_1 = 1.0
def PyExec(self):
state = self._get_state()
state_serialized = state.property_manager
logger = Logger("CentreFinder")
logger.notice("Starting centre finder routine...")
progress = self._get_progress()
self.scale_1 = 1000
self.scale_2 = 1000
verbose = self.getProperty('Verbose').value
x_start = self.getProperty("Position1Start").value
y_start = self.getProperty("Position2Start").value
sample_scatter = self._get_cloned_workspace("SampleScatterWorkspace")
sample_scatter_monitor = self._get_cloned_workspace(
"SampleScatterMonitorWorkspace")
sample_transmission = self._get_cloned_workspace(
"SampleTransmissionWorkspace")
sample_direct = self._get_cloned_workspace("SampleDirectWorkspace")
instrument = sample_scatter.getInstrument()
if instrument.getName() == 'LARMOR':
self.scale_1 = 1.0
can_scatter = self._get_cloned_workspace("CanScatterWorkspace")
can_scatter_monitor = self._get_cloned_workspace(
"CanScatterMonitorWorkspace")
can_transmission = self._get_cloned_workspace(
"CanTransmissionWorkspace")
can_direct = self._get_cloned_workspace("CanDirectWorkspace")
component = self.getProperty("Component").value
tolerance = self.getProperty("Tolerance").value
max_iterations = self.getProperty("Iterations").value
r_min = self.getProperty("RMin").value
r_max = self.getProperty("RMax").value
instrument_file = get_instrument_paths_for_sans_file(
state.data.sample_scatter)
position_1_step = get_named_elements_from_ipf_file(
instrument_file[1], "centre-finder-step-size",
float)['centre-finder-step-size']
try:
position_2_step = get_named_elements_from_ipf_file(
instrument_file[1], "centre-finder-step-size2",
float)['centre-finder-step-size2']
except:
position_2_step = position_1_step
find_direction = self.getProperty("Direction").value
if find_direction == FindDirectionEnum.to_string(
FindDirectionEnum.Left_Right):
position_2_step = 0.0
elif find_direction == FindDirectionEnum.to_string(
FindDirectionEnum.Up_Down):
position_1_step = 0.0
centre1 = x_start
centre2 = y_start
residueLR = []
residueTB = []
centre_1_hold = x_start
centre_2_hold = y_start
for j in range(0, max_iterations + 1):
if (j != 0):
centre1 += position_1_step
centre2 += position_2_step
progress.report("Reducing ... Pos1 " + str(centre1) + " Pos2 " +
str(centre2))
sample_quartiles = self._run_quartile_reduction(
sample_scatter, sample_transmission, sample_direct, "Sample",
sample_scatter_monitor, component, state_serialized, centre1,
centre2, r_min, r_max)
if can_scatter:
can_quartiles = self._run_quartile_reduction(
can_scatter, can_transmission, can_direct, "Can",
can_scatter_monitor, component, state_serialized, centre1,
centre2, r_min, r_max)
for key in sample_quartiles:
sample_quartiles[key] = perform_can_subtraction(
sample_quartiles[key], can_quartiles[key], self)
if mantidplot:
output_workspaces = self._publish_to_ADS(sample_quartiles)
if verbose:
self._rename_and_group_workspaces(j, output_workspaces)
residueLR.append(
self._calculate_residuals(
sample_quartiles[MaskingQuadrant.Left],
sample_quartiles[MaskingQuadrant.Right]))
residueTB.append(
self._calculate_residuals(
sample_quartiles[MaskingQuadrant.Top],
sample_quartiles[MaskingQuadrant.Bottom]))
if (j == 0):
logger.notice("Itr " + str(j) + ": (" +
str(self.scale_1 * centre1) + ", " +
str(self.scale_2 * centre2) + ") SX=" +
str(residueLR[j]) + " SY=" + str(residueTB[j]))
if mantidplot:
self._plot_quartiles(output_workspaces,
state.data.sample_scatter)
else:
# have we stepped across the y-axis that goes through the beam center?
if residueLR[j] > residueLR[j - 1]:
# yes with stepped across the middle, reverse direction and half the step size
position_1_step = -position_1_step / 2
if residueTB[j] > residueTB[j - 1]:
position_2_step = -position_2_step / 2
logger.notice("Itr " + str(j) + ": (" +
str(self.scale_1 * centre1) + ", " +
str(self.scale_2 * centre2) + ") SX=" +
str(residueLR[j]) + " SY=" + str(residueTB[j]))
if (residueLR[j] + residueTB[j]) < (
residueLR[j - 1] + residueTB[j - 1]
) or state.compatibility.use_compatibility_mode:
centre_1_hold = centre1
centre_2_hold = centre2
if abs(position_1_step) < tolerance and abs(
position_2_step) < tolerance:
# this is the success criteria, we've close enough to the center
logger.notice(
"Converged - check if stuck in local minimum! ")
break
if j == max_iterations:
logger.notice(
"Out of iterations, new coordinates may not be the best")
self.setProperty("Centre1", centre_1_hold)
self.setProperty("Centre2", centre_2_hold)
logger.notice("Centre coordinates updated: [{}, {}]".format(
centre_1_hold * self.scale_1, centre_2_hold * self.scale_2))
def PyExec(self):
state = self._get_state()
state_serialized = state.property_manager
logger = Logger("CentreFinder")
logger.notice("Starting centre finder routine...")
progress = self._get_progress()
self.scale_1 = 1000
self.scale_2 = 1000
verbose = self.getProperty('Verbose').value
x_start = self.getProperty("Position1Start").value
y_start = self.getProperty("Position2Start").value
sample_scatter = self._get_cloned_workspace("SampleScatterWorkspace")
sample_scatter_monitor = self._get_cloned_workspace("SampleScatterMonitorWorkspace")
sample_transmission = self._get_cloned_workspace("SampleTransmissionWorkspace")
sample_direct = self._get_cloned_workspace("SampleDirectWorkspace")
instrument = sample_scatter.getInstrument()
if instrument.getName() == 'LARMOR':
self.scale_1 = 1.0
can_scatter = self._get_cloned_workspace("CanScatterWorkspace")
can_scatter_monitor = self._get_cloned_workspace("CanScatterMonitorWorkspace")
can_transmission = self._get_cloned_workspace("CanTransmissionWorkspace")
can_direct = self._get_cloned_workspace("CanDirectWorkspace")
component = self.getProperty("Component").value
tolerance = self.getProperty("Tolerance").value
max_iterations = self.getProperty("Iterations").value
r_min = self.getProperty("RMin").value
r_max = self.getProperty("RMax").value
instrument_file = get_instrument_paths_for_sans_file(state.data.sample_scatter)
position_1_step = get_named_elements_from_ipf_file(
instrument_file[1], ["centre-finder-step-size"], float)['centre-finder-step-size']
try:
position_2_step = get_named_elements_from_ipf_file(
instrument_file[1], ["centre-finder-step-size2"], float)['centre-finder-step-size2']
except:
position_2_step = position_1_step
find_direction = self.getProperty("Direction").value
if find_direction == FindDirectionEnum.to_string(FindDirectionEnum.Left_Right):
position_2_step = 0.0
elif find_direction == FindDirectionEnum.to_string(FindDirectionEnum.Up_Down):
position_1_step = 0.0
centre1 = x_start
centre2 = y_start
residueLR = []
residueTB = []
centre_1_hold = x_start
centre_2_hold = y_start
for j in range(0, max_iterations + 1):
if(j != 0):
centre1 += position_1_step
centre2 += position_2_step
progress.report("Reducing ... Pos1 " + str(centre1) + " Pos2 " + str(centre2))
sample_quartiles = self._run_quartile_reduction(sample_scatter, sample_transmission, sample_direct,
"Sample", sample_scatter_monitor, component,
state_serialized, centre1, centre2, r_min, r_max)
if can_scatter:
can_quartiles = self._run_quartile_reduction(can_scatter, can_transmission, can_direct, "Can",
can_scatter_monitor, component, state_serialized, centre1,
centre2, r_min, r_max)
for key in sample_quartiles:
sample_quartiles[key] = perform_can_subtraction(sample_quartiles[key], can_quartiles[key], self)
if mantidplot:
output_workspaces = self._publish_to_ADS(sample_quartiles)
if verbose:
self._rename_and_group_workspaces(j, output_workspaces)
residueLR.append(self._calculate_residuals(sample_quartiles[MaskingQuadrant.Left],
sample_quartiles[MaskingQuadrant.Right]))
residueTB.append(self._calculate_residuals(sample_quartiles[MaskingQuadrant.Top],
sample_quartiles[MaskingQuadrant.Bottom]))
if(j == 0):
logger.notice("Itr {0}: ( {1}, {2} ) SX={3:.5g} SY={4:.5g}".
format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
if mantidplot:
self._plot_quartiles(output_workspaces, state.data.sample_scatter)
else:
# have we stepped across the y-axis that goes through the beam center?
if residueLR[j] > residueLR[j-1]:
# yes with stepped across the middle, reverse direction and half the step size
position_1_step = - position_1_step / 2
if residueTB[j] > residueTB[j-1]:
position_2_step = - position_2_step / 2
logger.notice("Itr {0}: ( {1}, {2} ) SX={3:.5g} SY={4:.5g}".
format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
if (residueLR[j]+residueTB[j]) < (residueLR[j-1]+residueTB[j-1]) or state.compatibility.use_compatibility_mode:
centre_1_hold = centre1
centre_2_hold = centre2
if abs(position_1_step) < tolerance and abs(position_2_step) < tolerance:
# this is the success criteria, we've close enough to the center
logger.notice("Converged - check if stuck in local minimum! ")
break
if j == max_iterations:
logger.notice("Out of iterations, new coordinates may not be the best")
self.setProperty("Centre1", centre_1_hold)
self.setProperty("Centre2", centre_2_hold)
logger.notice("Centre coordinates updated: [{}, {}]".format(centre_1_hold*self.scale_1, centre_2_hold*self.scale_2))
