def minimalInput(filename):
"""
Simplest way of calling :func:`tube.calibrate`
The minimal input for the calibration is the integrated workspace
and the known positions.
Even though it is easy to call, the calibration performs well, but there are ways to improve
the results, as it is explored after.
.. image:: /images/outputOfMinimalInput.png
"""
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor)
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def provideTheExpectedValue(filename):
"""
Giving the expected value for the position of the peaks in pixel.
The :func:`~Examples.minimalInput` let to the calibrate to guess the position of the pixels
among the tubes. Although it works nicelly, providing these expected values may improve the results.
This is done through the **fitPar** parameter.
"""
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar)
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def CalibrateWish(RunNumber, PanelNumber):
'''
:param RunNumber: is the run number of the calibration.
:param PanelNumber: is a string of two-digit number of the panel being calibrated
'''
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "WISH"
filename = str(RunNumber)
CalibratedComponent = 'WISH/panel' + PanelNumber
# Get calibration raw file and integrate it
print("Loading", filename)
rawCalibInstWS = mantid.Load(filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
CalibInstWS = mantid.Integration(rawCalibInstWS, RangeLower=1, RangeUpper=20000)
mantid.DeleteWorkspace(rawCalibInstWS)
print("Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate")
# Give y-positions of slit points (gotten for converting first tube's slit point to Y)
# WISH instrument has a particularity. It is composed by a group of upper tubes and lower tubes,
# they are disposed 3 milimiters in difference one among the other
lower_tube = numpy.array([-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
upper_tube = numpy.array(lower_tube + 0.003)
funcForm = 9 * [1] # 9 gaussian peaks
print("Created objects needed for calibration.")
# Get the calibration and put it into the calibration table
# calibrate the lower tubes
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, lower_tube, funcForm,
rangeList=list(range(0, 76)), outputPeak=True)
# calibrate the upper tubes
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, upper_tube, funcForm,
rangeList=list(range(76, 152)),
calibTable=calibrationTable,
# give the calibration table to append data
outputPeak=peakTable # give peak table to append data
)
print("Got calibration (new positions of detectors)")
# Apply the calibration
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
print("Applied calibration")
# == Save workspace ==
# uncomment these lines to save the workspace
# nexusName = "TubeCalibDemoWish" + PanelNumber + "Result.nxs"
# mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoWishResult.nxs', "Result of Running TubeCalibWishMerlin_Simple.py")
# print("saved calibrated workspace (CalibInstWS) into Nexus file", nexusName)
# == Reset dafault instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
def improvingCalibrationOfListOfTubes(filename):
"""
Analysing the result of provideTheExpectedValue it was seen that the calibration
of some tubes was not good.
.. note::
This method list some of them, there are a group belonging to window B2 that shows
only 2 peaks that are not dealt with here.
If first plot the bad ones using the **plotTube** option. It them, find where they fail, and how
to correct their peaks, using the **overridePeaks**.
If finally, applies the calibration again with the points corrected.
"""
from tube_calib_fit_params import TubeCalibFitParams
# not_good = [19,37, 71, 75, 181, 186, 234, 235, 245, 273, 345]
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
# calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
# fitPar=fitPar, outputPeak=True, plotTube=not_good, rangeList=not_good)
# CalibInstWS = loadingStep(filename)
# it is defined as the mean values around the neighbours
define_peaks = {19: [10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
71: [8.62752, 85.074, 124.919, 164.116, 246.82], # the last one was bad - check if we can inprove
75: [14.4285, 90.087, 128.987, 167.047, 242.62], # the last one was bad - check if we can inprove
181: [11.726, 94.0496, 137.816, 180, 255], # the third peak was lost
186: [11.9382, 71.5203, 107, 147.727, 239.041], # lost the second peak
234: [4.84, 82.7824, 123.125, 163.945, 241.877], # the first one was bad
235: [4.84, 80.0077, 121.002, 161.098, 238.502], # the first one was bad
245: [9.88089, 93.0593, 136.911, 179.5, 255], # the third peak was bad
273: [18.3711, 105.5, 145.5, 181.6, 243.252], # lost first and third peaks
345: [4.6084, 87.0351, 128.125, 169.923, 245.3] # the last one was bad
}
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks)
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def changeMarginAndExpectedValue(filename):
"""
To fit correctly, it is important to have a good window around the peak. This windown is defined
by the **margin** parameter.
This examples shows how the results worsen if we change the margin from its default value **15**
to **10**.
It shows how to see the fitted values using the **plotTube** parameter.
It will also output the peaks position and save them, through the **outputPeak** option and
the :func:`tube.savePeak` method.
An example of the fitted data compared to the acquired data to find the peaks positions:
.. image:: /images/calibratePlotFittedData.png
The result deteriorate, as you can see:
.. image:: /images/calibrateChangeMarginAndExpectedValue.png
"""
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
knownPos,
funcFactor,
fitPar=fitPar,
plotTube=[1, 10, 100],
outputPeak=True,
margin=10)
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS,
CalibrationTable=calibrationTable)
tube.savePeak(peakTable, 'TubeDemoMaps01.txt')
def calibrateB2Window(filename):
"""
There are among the B2 window tubes, some tubes that are showing only 2 strips.
Those tubes must be calibrated separated, as the known positions are not valid.
This example calibrate them, using only 4 known values: 2 edges and 2 peaks.
Run this example, and them see the worksapce in the calibrated instrument and you will see
how it worked.
The picture shows the output, look that only a section of the B2 Window was calibrated.
.. image:: /images/calibrateB2Window.png
"""
from tube_calib_fit_params import TubeCalibFitParams
# b2 with 2 peaks range
b2_range = list(range(196, 212)) + list(range(222, 233))
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, 0.16, 0.50], [2, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable = tube.calibrate(
CalibInstWS,
CalibratedComponent,
knownPos,
funcFactor,
fitPar=fitPar,
outputPeak=True,
plotTube=[b2_range[0], b2_range[-1]],
rangeList=b2_range)
mantid.ApplyCalibration(Workspace=CalibInstWS,
CalibrationTable=calibrationTable)
# Get fitting parameters
fitPar = TubeCalibFitParams(ExpectedPositions, ExpectedHeight, ExpectedWidth)
fitPar.setAutomatic(True)
print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
knownPos,
funcForm,
fitPar=fitPar,
outputPeak=True)
print("Got calibration (new positions of detectors) ")
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
print("Applied calibration")
# == Save workspace ==
mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoMapsResult.nxs',
"Result of Running TCDemoMaps_B1.py")
print(
"saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMapsResult.nxs"
)
# == Save Peak File ==
tube.savePeak(peakTable, 'TubeDemoMaps01.txt')
def calibrateMerlin(filename):
# == Set parameters for calibration ==
rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 20000 #
# Get calibration raw file and integrate it
rawCalibInstWS = mantid.LoadRaw(
filename) # 'raw' in 'rawCalibInstWS' means unintegrated.
print("Integrating Workspace")
CalibInstWS = mantid.Integration(rawCalibInstWS,
RangeLower=rangeLower,
RangeUpper=rangeUpper)
mantid.DeleteWorkspace(rawCalibInstWS)
print(
"Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
)
# the known positions are given in pixels inside the tubes and transformed to provide the positions
# with the center of the tube as the origin
knownPositions = 2.92713867188 * (numpy.array([
27.30074322, 92.5, 294.65178585, 362.37861919, 512.77103043,
663.41425323, 798.3223896, 930.9, 997.08480835
]) / 1024 - 0.5)
funcForm = numpy.array([2, 2, 1, 1, 1, 1, 1, 2, 2], numpy.int8)
# The calibration will follow different steps for sets of tubes
# For the door9, the best points to define the known positions are the 1st edge, 5 peaks, last edge.
points7 = knownPositions[[0, 2, 3, 4, 5, 6, 8]]
points7func = funcForm[[0, 2, 3, 4, 5, 6, 8]]
door9pos = points7
door9func = points7func
CalibratedComponent = 'MERLIN/door9' # door9
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(
CalibInstWS,
CalibratedComponent,
door9pos,
door9func,
outputPeak=True,
margin=30,
rangeList=list(range(20))
# because 20, 21, 22, 23 are defective detectors
)
print(
"Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt"
)
analisePeakTable(peakTable, 'door9_tube1_peaks')
# For the door8, the best points to define the known positions are the 1st edge, 5 peaks, last_edge
door8pos = points7
door8func = points7func
CalibratedComponent = 'MERLIN/door8'
calibrationTable, peakTable = tube.calibrate(
CalibInstWS,
CalibratedComponent,
door8pos,
door8func,
outputPeak=True, # change to peakTable to append to peakTable
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door8_peaks')
# For the doors 7,6,5,4, 2, 1 we may use the 9 points
doorpos = knownPositions
doorfunc = funcForm
CalibratedComponent = ['MERLIN/door%d' % (i) for i in [7, 6, 5, 4, 2, 1]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door1to7_peaks')
# The door 3 is a special case, because it is composed by diffent kind of tubes.
# door 3 tubes: 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
# obeys the same rules as the doors 7, 6, 5, 4, 2, 1
# For the tubes 3_3, 3_2, 3_1 -> it is better to skip the central peak
# For the tubes 1_x (smaller tube below), it is better to take the final part of known positions: peak4,peak5,edge6,edge7
# For the tubes 2_x (smaller tube above, it is better to take the first part of known positions: edge1, edge2, peak1,peak2
# NOTE: the smaller tubes they have length = 1.22879882813, but 1024 detectors
# so we have to correct the known positiosn by multiplying by its lenght and dividing by the longer dimension
from tube_calib_fit_params import TubeCalibFitParams
# calibrating tubes 1_x
CalibratedComponent = ['MERLIN/door3/tube_1_%d' % (i) for i in range(1, 9)]
half_diff_center = (
2.92713867188 -
1.22879882813) / 2 # difference among the expected center position for
# both tubes here a little bit of attempts is necessary.
# The effective center position and lengh is different for the calibrated tube, that is the reason,
# the calibrated values of the smaller tube does not seems aligned with the others. By, finding the
# 'best' half_diff_center value, the alignment occurs nicely.
half_diff_center = 0.835 #
# the knownpositions were given with the center of the bigger tube as origin, to convert
# to the center of the upper tube as origin is necessary to subtract them with the half_diff_center
doorpos = knownPositions[[5, 6, 7, 8]] - half_diff_center
doorfunc = [1, 1, 2, 2]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
# so we will give the aproximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([216, 527, 826, 989])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
doorpos,
doorfunc,
outputPeak=True,
fitPar=fitPar,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_tube1_peaks')
# calibrating tubes 2_x
CalibratedComponent = ['MERLIN/door3/tube_2_%d' % (i) for i in range(1, 9)]
# the knownpositions were given with the center of the bigger tube as origin, to convert
# to the center of the lower tube as origin is necessary to sum them with (len_big - len_small)/2
doorpos = knownPositions[[0, 1, 2, 3]] + half_diff_center
# print doorpos
doorfunc = [2, 2, 1, 1]
# for the smal tubes, automatically searching for the peak position in pixel was not working quite well,
# so we will give the aproximate position for these tubes through fitPar argument
fitPar = TubeCalibFitParams([50, 202, 664, 815])
fitPar.setAutomatic(True)
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
fitPar=fitPar,
margin=30)
analisePeakTable(peakTable, 'door3_tube2_peaks')
# calibrating tubes 3_3,3_2,3_1
CalibratedComponent = ['MERLIN/door3/tube_3_%d' % (i) for i in [1, 2, 3]]
doorpos = knownPositions[[0, 1, 2, 3, 5, 6, 7, 8]]
doorfunc = funcForm[[0, 1, 2, 3, 5, 6, 7, 8]]
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_123_peaks')
# calibrating others inside door3
# 5_8, 5_7, 5_6, 5_5, 5_4, 5_3, 5_2, 5_1, 4_8, 4_7, 4_6, 4_5, 4_4, 4_3, 4_2, 4_1, 3_8, 3_7, 3_6, 3_5, 3_4
part_3 = ['MERLIN/door3/tube_3_%d' % (i) for i in [4, 5, 6, 7, 8]]
part_4 = ['MERLIN/door3/tube_4_%d' % (i) for i in range(1, 9)]
part_5 = ['MERLIN/door3/tube_5_%d' % (i) for i in range(1, 9)]
CalibratedComponent = part_3 + part_4 + part_5
doorpos = knownPositions
doorfunc = funcForm
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
doorpos,
doorfunc,
outputPeak=True,
calibTable=calibrationTable,
margin=30)
analisePeakTable(peakTable, 'door3_peaks')
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS,
PositionTable=calibrationTable)
print("Applied calibration")
def CalibrateWish(run_per_panel_list):
'''
:param run_per_panel_list: is a list of tuples with the run number and the associated panel
run_per_panel_list = [ (17706, 'panel01'), (17705, 'panel02'), (17701, 'panel03'), (17702, 'panel04'), (17695, 'panel05')]
'''
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "WISH"
# definition of the parameters static for the calibration
lower_tube = numpy.array(
[-0.41, -0.31, -0.21, -0.11, -0.02, 0.09, 0.18, 0.28, 0.39])
upper_tube = numpy.array(lower_tube + 0.003)
funcForm = 9 * [1] # 9 gaussian peaks
margin = 15
low_range = list(range(0, 76))
high_range = list(range(76, 152))
kwargs = {'margin': margin}
# it will copy all the data from the runs to have a single instrument with the calibrated data.
whole_instrument = mantid.LoadRaw(str(run_per_panel_list[0][0]))
whole_instrument = mantid.Integration(whole_instrument)
for (run_number, panel_name) in run_per_panel_list:
panel_name = str(panel_name)
run_number = str(run_number)
# load your data and integrate it
ws = mantid.LoadRaw(run_number, OutputWorkspace=panel_name)
ws = mantid.Integration(ws, 1, 20000, OutputWorkspace=panel_name)
# use the TubeSpec object to be able to copy the data to the whole_instrument
tube_set = TubeSpec(ws)
tube_set.setTubeSpecByString(panel_name)
# update kwargs argument before calling calibrate
kwargs['rangeList'] = low_range # calibrate only the lower tubes
calibrationTable = tube.calibrate(ws, tube_set, lower_tube, funcForm,
**kwargs)
# update kwargs
kwargs[
'calibTable'] = calibrationTable # append calib to calibrationtable
kwargs['rangeList'] = high_range # calibrate only the upper tubes
calibrationTable = tube.calibrate(ws, tube_set, upper_tube, funcForm,
**kwargs)
kwargs['calibTable'] = calibrationTable
mantid.ApplyCalibration(ws, calibrationTable)
# copy data from the current panel to the whole_instrument
for i in range(tube_set.getNumTubes()):
for spec_num in tube_set.getTube(i):
whole_instrument.setY(spec_num, ws.dataY(spec_num))
# calibrate the whole_instrument with the last calibrated panel which has the calibration accumulation
# of all the others
mantid.CopyInstrumentParameters(run_per_panel_list[-1][1],
whole_instrument)
mantid.config['default.instrument'] = previousDefaultInstrument
def CalibrateMerlin(RunNumber):
# == Set parameters for calibration ==
previousDefaultInstrument = mantid.config['default.instrument']
mantid.config['default.instrument'] = "MERLIN"
filename = str(RunNumber) # Name of calibration run.
rangeLower = 3000 # Integrate counts in each spectra from rangeLower to rangeUpper
rangeUpper = 20000 #
# Set parameters for ideal tube.
Left = 2.0 # Where the left end of tube should be in pixels (target for AP)
Centre = 512.5 # Where the centre of the tube should be in pixels (target for CP)
Right = 1023.0 # Where the right of the tube should be in pixels (target for BP)
ActiveLength = 2.9 # Active length of tube in Metres
# Set initial parameters for peak finding
ExpectedHeight = 1000.0 # Expected Height of Gaussian Peaks (initial value of fit parameter)
ExpectedWidth = 32.0 # Expected width of centre peak in Pixels (initial value of fit parameter)
ExpectedPositions = [
35.0, 512.0, 989.0
] # Expected positions of the edges and peak in pixels (initial values of fit parameters)
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MERLIN' # Calibrate door 2
# Get calibration raw file and integrate it
print(filename)
rawCalibInstWS = mantid.LoadRaw(filename)
# 'raw' in 'rawCalibInstWS' means unintegrated.
print("Integrating Workspace")
CalibInstWS = mantid.Integration(rawCalibInstWS,
RangeLower=rangeLower,
RangeUpper=rangeUpper)
mantid.DeleteWorkspace(rawCalibInstWS)
print(
"Created workspace (CalibInstWS) with integrated data from run and instrument to calibrate"
)
# == Create Objects needed for calibration ==
## In the merlin case, the positions are usually given in pixels, instead of being given in
## meters, to convert to meter and put the origin in the center, we have to apply the following
## transformation:
##
## pos = pixel * length/npixels - length/2 = length (pixel/npixels - 1/2)
##
## for merlin: npixels = 1024
knownPos = ActiveLength * (numpy.array([Left, Centre, Right]) / 1024.0 -
0.5)
funcForm = 3 * [1]
# Get fitting parameters
fitPar = TubeCalibFitParams(ExpectedPositions,
ExpectedHeight,
ExpectedWidth,
margin=40)
print("Created objects needed for calibration.")
# == Get the calibration and put results into calibration table ==
# also put peaks into PeakFile
calibrationTable, peakTable = tube.calibrate(CalibInstWS,
CalibratedComponent,
knownPos,
funcForm,
outputPeak=True,
fitPar=fitPar,
plotTube=list(
range(0, 280, 20)))
print(
"Got calibration (new positions of detectors) and put slit peaks into file TubeDemoMerlin01.txt"
)
# == Apply the Calibation ==
mantid.ApplyCalibration(Workspace=CalibInstWS,
CalibrationTable=calibrationTable)
print("Applied calibration")
# == Save workspace ==
# mantid.SaveNexusProcessed(CalibInstWS, 'TubeCalibDemoMerlinResult.nxs', "Result of Running TubeCalibDemoMerlin_Simple.py")
# print("saved calibrated workspace (CalibInstWS) into Nexus file TubeCalibDemoMerlinResult.nxs")
# == Reset default instrument ==
mantid.config['default.instrument'] = previousDefaultInstrument
def completeCalibration(filename):
"""
This example shows how to use some properties of calibrate method to
join together the calibration done in :func:`provideTheExpectedValue`,
and improved in :func:`calibrateB2Window`, and :func:`improvingCalibrationOfListOfTubes`.
It also improves the result of the calibration because it deals with the E door. The
acquired data cannot be used to calibrate the E door, and trying to do so, produces a bad
result. In this example, the tubes inside the E door are excluded to the calibration.
Using the '''rangeList''' option.
"""
# first step, load the workspace
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# execute the improvingCalibrationOfListOfTubes excluding the range of b2 window
# correct the definition of the peaks for the following indexes
# define_peaks = {19:[10, 80.9771, 123.221, 164.993, 245.717], # the first one was bad
# 37: [6.36, 80.9347, 122.941, 165.104, 248.32], # the first one was bad
# 71: [8.62752, 85.074, 124.919, 164.116, 246.82 ], # the last one was bad - check if we can inprove
# 75: [14.4285, 90.087, 128.987, 167.047, 242.62], # the last one was bad - check if we can inprove
# 181: [11.726, 94.0496, 137.816, 180, 255], # the third peak was lost
# 186:[11.9382, 71.5203, 107, 147.727, 239.041], #lost the second peak
# 234: [4.84, 82.7824, 123.125, 163.945, 241.877], # the first one was bad
# 235: [4.84, 80.0077, 121.002, 161.098, 238.502], # the first one was bad
# 245: [9.88089, 93.0593, 136.911, 179.5, 255], # the third peak was bad
# 273: [18.3711, 105.5, 145.5, 181.6, 243.252],# lost first and third peaks
# 345: [4.6084, 87.0351, 128.125, 169.923, 245.3]} # the last one was bad
define_peaks = {19: [10, 80.9771, 123.221, 164.993, 245.717],
37: [6.36, 80.9347, 122.941, 165.104, 248.32],
71: [8.62752, 85.074, 124.919, 164.116, 246.82],
75: [14.4285, 90.087, 128.987, 167.047, 242.62],
181: [11.726, 94.0496, 137.816, 180, 255],
186: [11.9382, 71.5203, 107, 147.727, 239.041],
234: [4.84, 82.7824, 123.125, 163.945, 241.877],
235: [4.84, 80.0077, 121.002, 161.098, 238.502],
245: [9.88089, 93.0593, 136.911, 179.5, 255],
273: [18.3711, 105.5, 145.5, 181.6, 243.252],
345: [4.6084, 87.0351, 128.125, 169.923, 245.3]}
b2_window = list(range(196, 212)) + list(range(222, 233))
complete_range = list(range(648))
# this data can not be used to calibrate the E1 window, so, let's remove it.
e1_window = list(range(560, 577))
aux = numpy.setdiff1d(complete_range, b2_window)
# the group that have 3 stripts are all the tubes except the b2 window and e window.
range_3_strips = numpy.setdiff1d(aux, e1_window)
calibrationTable, peak3Table = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks,
rangeList=range_3_strips)
# now calibrate the b2_window REMOVE SECOND PEAK
# define the known positions and function factor (edge, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, 0.16, 0.50], [2, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# apply the calibration for the b2_window 2 strips values
calibrationTable, peak2Table = tube.calibrate(CalibInstWS, CalibratedComponent,
knownPos, # these parameters now have only 4 points
funcFactor,
fitPar=fitPar,
outputPeak=True,
calibTable=calibrationTable, # it will append to the calibTable
rangeList=b2_window)
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
def improvingCalibrationSingleTube(filename):
"""
The :func:`~Examples.provideTheExpectedValue` provided a good solution, but there are few
tubes whose calibration was not so good.
This method explores how to deal with these tubes.
First of all, it is important to identify the tubes that did not work well.
From the outputs of provideTheExpectedValue, looking inside the instrument tree,
it is possible to list all the tubes that are not so good.
Unfortunately, they do not have a single name identifier.
So, locating them it is a little bit trickier.
The :func:`~Examples.findThoseTubesThatNeedSpecialCareForCalibration` shows one way of finding those
tubes. The index is the position inside the PeakTable.
For this example, we have used inspection from the Instrument View.
One of them is inside the A1_Window, 3rd PSD_TUBE_STRIP 8 pack up, 4th PSD_TUBE_STRIP: Index = 8+8+4 - 1 = 19.
In this example, we will ask the calibration to run the calibration only for 3 tubes
(indexes 18,19,20). Them, we will check why the 19 is not working well. Finally, we will try to
provide another peaks position for this tube,
and run the calibration again for these tubes, to improve the results.
This example shows how to use **overridePeaks** option
"""
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
# == Set parameters for calibration ==
# Set what we want to calibrate (e.g whole instrument or one door )
CalibratedComponent = 'MAPS' # Calibrate all
# define the known positions and function factor (edge, peak, peak, peak, edge)
knownPos, funcFactor = [-0.50, -0.16, -0.00, 0.16, 0.50], [2, 1, 1, 1, 2]
# the expected positions in pixels for the special points
expectedPositions = [4.0, 85.0, 128.0, 161.0, 252.0]
fitPar = TubeCalibFitParams(expectedPositions)
fitPar.setAutomatic(True)
# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, plotTube=[18, 19, 20],
rangeList=[18, 19, 20])
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
# reload to reset the calibration applied
CalibInstWS = loadingStep(filename)
# looking into the second line of calibrationTable, you will see that it defines the peaks for the first position
# as 14.9788, -0.303511, 9.74828
# let's change the peak from -0.303511 to 8.14
# to override the peaks definition, we use the overridePeaks
overridePeaks = {19: [8.14, 80.9771, 123.221, 164.993, 245.717]}
# == Get the calibration and put results into calibration table ==
# we will not plot anymore, because it will not plot the overridden peaks
calibrationTable, peakTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, rangeList=[18, 19, 20],
overridePeaks=overridePeaks)
mantid.ApplyCalibration(Workspace=CalibInstWS, PositionTable=calibrationTable)
