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Fix indentation errors in calibration modules #27

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Aug 28, 2014
Merged

Fix indentation errors in calibration modules #27

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82393f7
Re #10159. Fixing whitespace issue.
peterfpeterson Aug 22, 2014
4008508
Re #10159. Fixing python whitespace issues.
peterfpeterson Aug 22, 2014
7e5b8ea
Re #10159. Fixing python whitespace issues.
peterfpeterson Aug 22, 2014
26c54dc
Re #10159. Fixing python whitespace issues.
peterfpeterson Aug 22, 2014
e49ad7d
Re #10159. Fixing python whitespace issues.
peterfpeterson Aug 25, 2014
d6f4ed7
Re #10159. Fixing python whitespace issues.
peterfpeterson Aug 25, 2014
f1fcbd8
Re #10159. Hopefully fixing the sphinx builds.
peterfpeterson Aug 27, 2014
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115 changes: 57 additions & 58 deletions Code/Mantid/scripts/Calibration/Examples/TubeCalibDemoMaps_All.py
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Original file line number Diff line number Diff line change
Expand Up @@ -70,16 +70,16 @@ def loadingStep(filename):

def minimalInput(filename):
"""
Simplest way of calling :func:`tube.calibrate`
Simplest way of calling :func:`tube.calibrate`


The minimal input for the calibration is the integrated workspace
and the knwon positions.

Eventhough it is easy to call, the calibration performs well, but there are ways to improve
the results, as it is explored after.
Eventhough 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
.. image:: /images/outputOfMinimalInput.png

"""
CalibInstWS = loadingStep(filename)
Expand All @@ -89,7 +89,6 @@ def minimalInput(filename):
# 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 ==
Expand All @@ -99,9 +98,9 @@ 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. Altough it works nicelly, providing these expected values may improve the results.
This is done through the **fitPar** parameter.
The :func:`~Examples.minimalInput` let to the calibrate to guess the position of the pixels
among the tubes. Altough 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)
Expand All @@ -118,30 +117,30 @@ def provideTheExpectedValue(filename):

# == Get the calibration and put results into calibration table ==
calibrationTable = tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar)
fitPar=fitPar)
# == Apply the Calibation ==
ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)

def changeMarginAndExpectedValue(filename):
"""
To fit correcly, it is important to have a good window around the peak. This windown is defined
by the **margin** parameter.
To fit correcly, 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**.
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 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.
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:
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:
The result deteriorate, as you can see:

.. image:: /images/calibrateChangeMarginAndExpectedValue.png
.. image:: /images/calibrateChangeMarginAndExpectedValue.png

"""
from tube_calib_fit_params import TubeCalibFitParams
Expand All @@ -159,7 +158,7 @@ def changeMarginAndExpectedValue(filename):

# == 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)
fitPar=fitPar, plotTube=[1,10,100], outputPeak=True, margin=10)
# == Apply the Calibation ==
ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)

Expand All @@ -169,7 +168,7 @@ def changeMarginAndExpectedValue(filename):
def improvingCalibrationSingleTube(filename):
"""
The :func:`~Examples.provideTheExpectedValue` provided a good solution, but there are few
tubes whose calibration was not so good.
tubes whose calibration was not so good.

This method explores how to deal with these tubes.

Expand All @@ -179,16 +178,16 @@ def improvingCalibrationSingleTube(filename):
it is possible to list all the tubes that are not so good.

Unfortunatelly, 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.
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.
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,
(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
Expand All @@ -209,7 +208,7 @@ def improvingCalibrationSingleTube(filename):

# == 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])
fitPar=fitPar, outputPeak=True, plotTube=[18,19,20], rangeList=[18,19,20])

ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)

Expand All @@ -226,7 +225,7 @@ def improvingCalibrationSingleTube(filename):
# == Get the calibration and put results into calibration table ==
# we will not plot anymore, because it will not plot the overrided peaks
calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True, rangeList=[18,19,20], overridePeaks=overridePeaks)
fitPar=fitPar, outputPeak=True, rangeList=[18,19,20], overridePeaks=overridePeaks)

ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)
#check using the InstrumentView and you will see that it is better than before
Expand All @@ -235,14 +234,14 @@ def improvingCalibrationSingleTube(filename):
def improvingCalibrationOfListOfTubes(filename):
"""
Analysing the result of provideTheExpectedValue it was seen that the calibration
of some tubes was not good.
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.
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**.
to correct their peaks, using the **overridePeaks**.
If finally, applies the calibration again with the points corrected.
"""
from tube_calib_fit_params import TubeCalibFitParams
Expand Down Expand Up @@ -281,7 +280,7 @@ def improvingCalibrationOfListOfTubes(filename):
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)
fitPar=fitPar, outputPeak=True, overridePeaks=define_peaks)

ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)

Expand All @@ -291,14 +290,14 @@ def calibrateB2Window(filename):

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.
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.
how it worked.

The picture shows the output, look that only a section of the B2 Window was calibrated.
The picture shows the output, look that only a section of the B2 Window was calibrated.

.. image:: /images/calibrateB2Window.png
.. image:: /images/calibrateB2Window.png

"""
from tube_calib_fit_params import TubeCalibFitParams
Expand All @@ -319,7 +318,7 @@ def calibrateB2Window(filename):

# == 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)
fitPar=fitPar, outputPeak=True, plotTube=[b2_range[0], b2_range[-1]], rangeList=b2_range)

ApplyCalibration( Workspace=CalibInstWS, PositionTable=calibrationTable)

Expand All @@ -328,24 +327,24 @@ def calibrateB2Window(filename):
def findThoseTubesThatNeedSpecialCareForCalibration(filename):
"""
The example :func:`provideTheExpectedValue` has shown its capability to calibrate almost
all tubes, but, as explored in the :func:`improvingCalibrationOfListOfTubes` and
:func:`improvingCalibrationSingleTube` there are
all tubes, but, as explored in the :func:`improvingCalibrationOfListOfTubes` and
:func:`improvingCalibrationSingleTube` there are
some tubes that could not be calibrated using that method.

The goal of this method is to show one way to find the tubes that will require special care.

It will first perform the same calibration seen in :func:`provideTheExpectedValue`,
them, it will process the **peakTable** output of the calibrate method when enabling the
parameter **outputPeak**.
It will first perform the same calibration seen in :func:`provideTheExpectedValue`,
them, it will process the **peakTable** output of the calibrate method when enabling the
parameter **outputPeak**.

It them creates the Peaks workspace, that is the diffence of the peaks position from the
expected values of the peaks positions for all the tubes. This allows to spot what are the
tubes whose fitting are outliers in relation to the others.
It them creates the Peaks workspace, that is the diffence of the peaks position from the
expected values of the peaks positions for all the tubes. This allows to spot what are the
tubes whose fitting are outliers in relation to the others.

.. image:: /images/plotingPeaksDifference.png
.. image:: /images/plotingPeaksDifference.png

The final result for this method is to output using **plotTube** the result of the fitting
to all the 'outliers' tubes.
The final result for this method is to output using **plotTube** the result of the fitting
to all the 'outliers' tubes.
"""
from tube_calib_fit_params import TubeCalibFitParams
CalibInstWS = loadingStep(filename)
Expand All @@ -362,7 +361,7 @@ def findThoseTubesThatNeedSpecialCareForCalibration(filename):

# == Get the calibration and put results into calibration table ==
calibrationTable, peakTable= tube.calibrate(CalibInstWS, CalibratedComponent, knownPos, funcFactor,
fitPar=fitPar, outputPeak=True)
fitPar=fitPar, outputPeak=True)

# == now, lets investigate the peaks

Expand Down Expand Up @@ -414,11 +413,11 @@ def completeCalibration(filename):
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
aquired 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.
"""
It also improves the result of the calibration because it deals with the E door. The
aquired 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
Expand Down Expand Up @@ -467,10 +466,10 @@ def completeCalibration(filename):

complete_range = range(648)

# this data can not be used to calibrate the E1 window, so, let's remove it.
# this data can not be used to calibrate the E1 window, so, let's remove it.
e1_window = 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.
# 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,
Expand Down
6 changes: 3 additions & 3 deletions Code/Mantid/scripts/Calibration/Examples/TubeCalibDemoWish_5panels.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def CalibrateWish( run_per_panel_list):

for (run_number, panel_name) in run_per_panel_list:
panel_name = str(panel_name)
run_number = str(run_number)
run_number = str(run_number)
# load your data and integrate it
ws = LoadRaw(run_number, OutputWorkspace=panel_name)
ws = Integration(ws, 1, 20000, OutputWorkspace=panel_name)
Expand All @@ -58,7 +58,7 @@ def CalibrateWish( run_per_panel_list):

# update kwargs
kwargs['calibTable'] = calibrationTable # append calib to calibrationtable
kwargs['rangeList'] = high_range # calibrate only the upper tubes
kwargs['rangeList'] = high_range # calibrate only the upper tubes

calibrationTable = tube.calibrate(ws, tube_set, upper_tube, funcForm, **kwargs)
kwargs['calibTable'] = calibrationTable
Expand All @@ -67,7 +67,7 @@ def CalibrateWish( run_per_panel_list):

# 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):
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
Expand Down
18 changes: 9 additions & 9 deletions Code/Mantid/scripts/Calibration/tube_calib.py
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Expand Up @@ -169,7 +169,7 @@ def fitGaussian(fitPar, index, ws, outputWs):
StartX=str(start), EndX=str(end), Output='Z1')
Fit(InputWorkspace='Z1_Workspace',Function='name=Gaussian,Height=%f,PeakCentre=%f,Sigma=%f' %(height, centre, width),
WorkspaceIndex=2, StartX=str(start), EndX=str(end), Output=outputWs)
CloneWorkspace(outputWs+'_Workspace',OutputWorkspace='gauss_'+str(index))
CloneWorkspace(outputWs+'_Workspace',OutputWorkspace='gauss_'+str(index))
peakIndex = 1

return peakIndex
Expand Down Expand Up @@ -221,9 +221,9 @@ def getPoints ( IntegratedWorkspace, funcForms, fitParams, whichTube, showPlot=F
results.append(peakCentre)

if showPlot:
ws = mtd[calibPointWs + '_Workspace']
fitt_y_values.append(copy.copy(ws.dataY(1)))
fitt_x_values.append(copy.copy(ws.dataX(1)))
ws = mtd[calibPointWs + '_Workspace']
fitt_y_values.append(copy.copy(ws.dataY(1)))
fitt_x_values.append(copy.copy(ws.dataX(1)))

if showPlot:
FittedData = CreateWorkspace(numpy.hstack(fitt_x_values),
Expand Down Expand Up @@ -409,13 +409,13 @@ def getCalibratedPixelPositions( ws, tubePts, idealTubePts, whichTube, peakTestM
for i in range(nDets):
deti = ws.getDetector( whichTube[i])
det_pos = deti.getPos()
pNew = pixels[i]
pNew = pixels[i]
# again, the opeartion float * v3d is not defined, but v3d * float is,
# so, I wrote the new pos as center + unit_vector * (float)
newPos = center + unit_vector * pNew

detIDs.append( deti.getID() )
detPositions.append( newPos )
detIDs.append( deti.getID() )
detPositions.append( newPos )
# print i, detIDs[i], detPositions[i]

return detIDs, detPositions
Expand Down Expand Up @@ -595,8 +595,8 @@ def getCalibrationFromPeakFile ( ws, calibTable, iTube, PeakFile ):
#print len(wht)
if( len(detIDList) == len(wht)): # We have corrected positions
for j in range(len(wht)):
nextRow = {'Detector ID': detIDList[j], 'Detector Position': detPosList[j] }
calibTable.addRow ( nextRow )
nextRow = {'Detector ID': detIDList[j], 'Detector Position': detPosList[j] }
calibTable.addRow ( nextRow )

if(nTubes == 0):
return
Expand Down