From aee6eb74bb640b4c681cf5feacc3ddf6ab0e3598 Mon Sep 17 00:00:00 2001
From: Brendan Sullivan <sullivanbt@ornl.gov>
Date: Fri, 27 Jul 2018 15:27:06 -0400
Subject: [PATCH] Re #22811 move mask size to instrument param file
---
.../IntegratePeaksProfileFitting.py | 12 +++++----
instrument/CORELLI_Parameters.xml | 5 ++++
instrument/MANDI_Parameters.xml | 5 ++++
instrument/MANDI_Parameters_2015_08_01.xml | 4 +++
instrument/MANDI_Parameters_2016_02_01.xml | 5 ++++
instrument/TOPAZ_Parameters.xml | 5 ++++
scripts/SCD_Reduction/BVGFitTools.py | 14 +++++-----
scripts/SCD_Reduction/ICCFitTools.py | 27 ++++++++++---------
8 files changed, 51 insertions(+), 26 deletions(-)
diff --git a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
index c38a7219d37..d37667e0e1c 100644
--- a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
+++ b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
@@ -118,11 +118,12 @@ class IntegratePeaksProfileFitting(PythonAlgorithm):
instrumentName = peaks_ws.getInstrument().getFullName()
try:
nTheta = peaks_ws.getInstrument().getIntParameter("numBinsTheta")[0]
- nPhi = peaks_ws.getInstrument().getIntParameter("numBinsPhi")[0]
+ nPhi = peaks_ws.getInstrument().getIntParameter("numBinsPhi")[0]
mindtBinWidth = peaks_ws.getInstrument().getNumberParameter("mindtBinWidth")[0]
- maxdtBinWidth = peaks_ws.getInstrument().getNumberParameter("maxdtBinWidth")[0]
- fracHKL = peaks_ws.getInstrument().getNumberParameter("fracHKL")[0]
- dQPixel = peaks_ws.getInstrument().getNumberParameter("dQPixel")[0]
+ maxdtBinWidth = peaks_ws.getInstrument().getNumberParameter("maxdtBinWidth")[0]
+ fracHKL = peaks_ws.getInstrument().getNumberParameter("fracHKL")[0]
+ dQPixel = peaks_ws.getInstrument().getNumberParameter("dQPixel")[0]
+ peakMaskSize = peaks_ws.getInstrument().getIntParameter("peakMaskSize")[0]
except:
raise
@@ -170,7 +171,8 @@ class IntegratePeaksProfileFitting(PythonAlgorithm):
maxdtBinWidth=maxdtBinWidth,
pplmin_frac=pplmin_frac, pplmax_frac=pplmax_frac,
forceCutoff=forceCutoff, edgeCutoff=edgeCutoff,
- instrumentName=instrumentName)
+ instrumentName=instrumentName,
+ peakMaskSize=peakMaskSize)
# First we get the peak intensity
peakIDX = Y3D/Y3D.max() > fracStop
diff --git a/instrument/CORELLI_Parameters.xml b/instrument/CORELLI_Parameters.xml
index a8167e41032..d7421bdbedb 100644
--- a/instrument/CORELLI_Parameters.xml
+++ b/instrument/CORELLI_Parameters.xml
@@ -70,6 +70,11 @@
<value val="60" />
</parameter>
+ <!-- Size of peak mask for background calculation in units of dQPixel -->
+ <parameter name="peakMaskSize" type="int">
+ <value val="10" />
+ </parameter>
+
</component-link>
</parameter-file>
diff --git a/instrument/MANDI_Parameters.xml b/instrument/MANDI_Parameters.xml
index dcaa2ca55f3..9ac7e699e5c 100644
--- a/instrument/MANDI_Parameters.xml
+++ b/instrument/MANDI_Parameters.xml
@@ -63,6 +63,11 @@
<value val="50" />
</parameter>
+<!-- Size of peak mask for background calculation in units of dQPixel -->
+<parameter name="peakMaskSize" type="int">
+ <value val="5" />
+</parameter>
+
</component-link>
</parameter-file>
diff --git a/instrument/MANDI_Parameters_2015_08_01.xml b/instrument/MANDI_Parameters_2015_08_01.xml
index fef3a0458b8..2de3d3e5077 100644
--- a/instrument/MANDI_Parameters_2015_08_01.xml
+++ b/instrument/MANDI_Parameters_2015_08_01.xml
@@ -63,6 +63,10 @@
<value val="50" />
</parameter>
+<!-- Size of peak mask for background calculation in units of dQPixel -->
+<parameter name="peakMaskSize" type="int">
+ <value val="5" />
+</parameter>
</parameter-file>
diff --git a/instrument/MANDI_Parameters_2016_02_01.xml b/instrument/MANDI_Parameters_2016_02_01.xml
index 9b8c188b408..7af08e9e0ac 100644
--- a/instrument/MANDI_Parameters_2016_02_01.xml
+++ b/instrument/MANDI_Parameters_2016_02_01.xml
@@ -63,4 +63,9 @@
<value val="50" />
</parameter>
+<!-- Size of peak mask for background calculation in units of dQPixel -->
+<parameter name="peakMaskSize" type="int">
+ <value val="5" />
+</parameter>
+
</parameter-file>
diff --git a/instrument/TOPAZ_Parameters.xml b/instrument/TOPAZ_Parameters.xml
index ff52c5ebdd2..b4fddb7ddc5 100644
--- a/instrument/TOPAZ_Parameters.xml
+++ b/instrument/TOPAZ_Parameters.xml
@@ -139,6 +139,11 @@ detScale={13:1.046504,14:1.259293,16:1.02449,17:1.18898,18:0.88014,19:0.98665,\
<value val="15" />
</parameter>
+<!-- Size of peak mask for background calculation in units of dQPixel -->
+<parameter name="peakMaskSize" type="int">
+ <value val="15" />
+</parameter>
+
</component-link>
</parameter-file>
diff --git a/scripts/SCD_Reduction/BVGFitTools.py b/scripts/SCD_Reduction/BVGFitTools.py
index 72d9972b0cf..1897c816320 100644
--- a/scripts/SCD_Reduction/BVGFitTools.py
+++ b/scripts/SCD_Reduction/BVGFitTools.py
@@ -15,7 +15,7 @@ def get3DPeak(peak, peaks_ws, box, padeCoefficients, qMask, nTheta=150, nPhi=150
plotResults=False, zBG=1.96, bgPolyOrder=1, fICCParams=None, oldICCFit=None,
strongPeakParams=None, forceCutoff=250, edgeCutoff=15,
neigh_length_m=3, q_frame='sample', dtSpread=0.03, pplmin_frac=0.8, pplmax_frac=1.5, mindtBinWidth=1,
- maxdtBinWidth=50, figureNumber=2, instrumentName=None):
+ maxdtBinWidth=50, figureNumber=2, instrumentName=None, peakMaskSize=5):
n_events = box.getNumEventsArray()
if q_frame == 'lab':
@@ -31,14 +31,13 @@ def get3DPeak(peak, peaks_ws, box, padeCoefficients, qMask, nTheta=150, nPhi=150
n_events, peak=peak, box=box, qMask=qMask, calc_pp_lambda=True, padeCoefficients=padeCoefficients,
neigh_length_m=neigh_length_m, pp_lambda=None, pplmin_frac=pplmin_frac,
pplmax_frac=pplmax_frac, mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- instrumentName=instrumentName)
+ instrumentName=instrumentName, peakMaskSize=peakMaskSize)
YTOF, fICC, x_lims = fitTOFCoordinate(
box, peak, padeCoefficients, dtSpread=dtSpread, qMask=qMask, bgPolyOrder=bgPolyOrder, zBG=zBG,
plotResults=plotResults, pp_lambda=pp_lambda, neigh_length_m=neigh_length_m, pplmin_frac=pplmin_frac,
pplmax_frac=pplmax_frac, mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- instrumentName=instrumentName)
+ instrumentName=instrumentName, peakMaskSize=peakMaskSize)
chiSqTOF = mtd['fit_Parameters'].column(1)[-1]
-
else: # we already did I-C profile, so we'll just read the parameters
pp_lambda = fICCParams[-1]
fICC = ICC.IkedaCarpenterConvoluted()
@@ -51,7 +50,7 @@ def get3DPeak(peak, peaks_ws, box, padeCoefficients, qMask, nTheta=150, nPhi=150
fICC['HatWidth'] = fICCParams[10]
fICC['KConv'] = fICCParams[11]
goodIDX, _ = ICCFT.getBGRemovedIndices(
- n_events, pp_lambda=pp_lambda, qMask=qMask, instrumentName=instrumentName)
+ n_events, pp_lambda=pp_lambda, qMask=qMask, instrumentName=instrumentName, peakMaskSize=peakMaskSize)
chiSqTOF = fICCParams[4] #Last entry
# Get the 3D TOF component, YTOF
@@ -88,7 +87,6 @@ def get3DPeak(peak, peaks_ws, box, padeCoefficients, qMask, nTheta=150, nPhi=150
useForceParams = peak.getIntensity() < forceCutoff or peak.getRow() <= dEdge or peak.getRow(
) >= nPixels[0] - dEdge or peak.getCol() <= dEdge or peak.getCol() >= nPixels[1] - dEdge
-
#Here we retrieve some instrument specific parameters
try:
doPeakConvolution = peaks_ws.getInstrument().getBoolParameter("fitConvolvedPeak")[0]
@@ -253,7 +251,7 @@ def getXTOF(box, peak):
def fitTOFCoordinate(box, peak, padeCoefficients, dtSpread=0.03, minFracPixels=0.01,
neigh_length_m=3, zBG=1.96, bgPolyOrder=1, qMask=None, plotResults=False,
fracStop=0.01, pp_lambda=None, pplmin_frac=0.8, pplmax_frac=1.5, mindtBinWidth=1,
- maxdtBinWidth=50, instrumentName=None):
+ maxdtBinWidth=50, instrumentName=None, peakMaskSize=5):
# Get info from the peak
tof = peak.getTOF() # in us
@@ -272,7 +270,7 @@ def fitTOFCoordinate(box, peak, padeCoefficients, dtSpread=0.03, minFracPixels=0
neigh_length_m=neigh_length_m, zBG=zBG, pp_lambda=pp_lambda,
pplmin_frac=pplmin_frac, pplmax_frac=pplmax_frac,
mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- instrumentName=instrumentName)
+ instrumentName=instrumentName, peakMaskSize=peakMaskSize)
fitResults, fICC = ICCFT.doICCFit(tofWS, energy, flightPath,
padeCoefficients, fitOrder=bgPolyOrder, constraintScheme=1,
diff --git a/scripts/SCD_Reduction/ICCFitTools.py b/scripts/SCD_Reduction/ICCFitTools.py
index 9c378f849d4..9f0076de238 100644
--- a/scripts/SCD_Reduction/ICCFitTools.py
+++ b/scripts/SCD_Reduction/ICCFitTools.py
@@ -93,7 +93,7 @@ def getQXQYQZ(box):
def getQuickTOFWS(box, peak, padeCoefficients, goodIDX=None, dtSpread=0.03, qMask=None,
pp_lambda=None, minppl_frac=0.8, maxppl_frac=1.5, mindtBinWidth=1, maxdtBinWidth=50,
- constraintScheme=1, instrumentName=None):
+ constraintScheme=1, instrumentName=None, peakMaskSize=5):
"""
getQuickTOFWS - generates a quick-and-dirty TOFWS. Useful for determining the background.
Input:
@@ -130,7 +130,8 @@ def getQuickTOFWS(box, peak, padeCoefficients, goodIDX=None, dtSpread=0.03, qMas
tofWS, ppl = getTOFWS(box, flightPath, scatteringHalfAngle, tof, peak, qMask, dtSpread=dtSpread,
minFracPixels=0.01, neigh_length_m=3, zBG=1.96, pp_lambda=pp_lambda,
calc_pp_lambda=calc_pp_lambda, pplmin_frac=minppl_frac, pplmax_frac=minppl_frac,
- mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth, instrumentName=instrumentName)
+ mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth, instrumentName=instrumentName,
+ peakMaskSize=peakMaskSize)
fitResults, fICC = doICCFit(
tofWS, energy, flightPath, padeCoefficients, fitOrder=1, constraintScheme=constraintScheme,
instrumentName=instrumentName)
@@ -246,10 +247,6 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
cY = nY//2
cZ = nZ//2
dP = peakMaskSize
- if instrumentName == 'TOPAZ':
- dP = 15
- elif instrumentName == 'CORELLI':
- dP = 10
peakMask = qMask.copy()
peakMask[cX-dP:cX+dP, cY-dP:cY+dP, cZ-dP:cZ+dP] = 0
@@ -286,7 +283,7 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
chiSq, h, intens, sigma = getQuickTOFWS(box, peak, padeCoefficients, goodIDX=goodIDX, qMask=qMask, pp_lambda=pp_lambda,
minppl_frac=minppl_frac, maxppl_frac=maxppl_frac, mindtBinWidth=mindtBinWidth,
maxdtBinWidth=maxdtBinWidth, constraintScheme=constraintScheme,
- instrumentName=instrumentName)
+ instrumentName=instrumentName, peakMaskSize=peakMaskSize)
except:
# raise
break
@@ -300,6 +297,7 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
except RuntimeError:
# This is caused by there being fewer datapoints remaining than parameters. For now, we just hope
# we found a satisfactory answer.
+ raise
break
except KeyboardInterrupt:
sys.exit()
@@ -309,7 +307,7 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
chiSq, h, intens, sigma = getQuickTOFWS(box, peak, padeCoefficients, goodIDX=goodIDX, qMask=qMask,
pp_lambda=pp_lambda, minppl_frac=minppl_frac, maxppl_frac=maxppl_frac,
mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- instrumentName=instrumentName)
+ instrumentName=instrumentName, peakMaskSize=peakMaskSize)
if qMask is not None:
return goodIDX*qMask, pp_lambda
return goodIDX, pp_lambda
@@ -375,7 +373,8 @@ def getBGRemovedIndices(n_events, zBG=1.96, calc_pp_lambda=False, neigh_length_m
minppl_frac=pplmin_frac, maxppl_frac=pplmax_frac, qMask=qMask, peak=peak,
box=box, pp_lambda=pp_lambda, peakNumber=peakNumber,
mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- constraintScheme=constraintScheme, instrumentName=instrumentName)
+ constraintScheme=constraintScheme, instrumentName=instrumentName,
+ peakMaskSize=peakMaskSize)
except KeyboardInterrupt:
sys.exit()
except:
@@ -535,7 +534,7 @@ def get_pp_lambda(n_events, hasEventsIDX):
def getTOFWS(box, flightPath, scatteringHalfAngle, tofPeak, peak, qMask, zBG=-1.0, dtSpread=0.02,
minFracPixels=0.005, workspaceNumber=None, neigh_length_m=0, pp_lambda=None, calc_pp_lambda=False,
- padeCoefficients=None, pplmin_frac=0.8, pplmax_frac=1.5,
+ padeCoefficients=None, pplmin_frac=0.8, pplmax_frac=1.5, peakMaskSize=5,
mindtBinWidth=1, maxdtBinWidth=50, constraintScheme=1, instrumentName=None):
"""
Builds a TOF profile from the data in box which is nominally centered around a peak.
@@ -580,7 +579,8 @@ def getTOFWS(box, flightPath, scatteringHalfAngle, tofPeak, peak, qMask, zBG=-1.
calc_pp_lambda=calc_pp_lambda, padeCoefficients=padeCoefficients,
pplmin_frac=pplmin_frac, pplmax_frac=pplmax_frac,
mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
- constraintScheme=constraintScheme, instrumentName=instrumentName)
+ constraintScheme=constraintScheme, instrumentName=instrumentName,
+ peakMaskSize=peakMaskSize)
hasEventsIDX = np.logical_and(goodIDX, qMask)
boxMeanIDX = np.where(hasEventsIDX)
else: # don't do background removal - just consider one pixel at a time
@@ -908,7 +908,7 @@ def integrateSample(run, MDdata, peaks_ws, paramList, UBMatrix, dQ, qMask, padeC
dQPixel=0.005, p=None, neigh_length_m=0, zBG=-1.0, bgPolyOrder=1,
doIterativeBackgroundFitting=False, q_frame='sample',
progressFile=None, minpplfrac=0.8, maxpplfrac=1.5, mindtBinWidth=1, maxdtBinWidth=50,
- keepFitDict=False, constraintScheme=1):
+ keepFitDict=False, constraintScheme=1, peakMaskSize=5):
"""
integrateSample contains the loop that integrates over all of the peaks in a run and saves the results. Importantly, it also handles
errors (mostly by passing and recording special values for failed fits.)
@@ -984,7 +984,8 @@ def integrateSample(run, MDdata, peaks_ws, paramList, UBMatrix, dQ, qMask, padeC
mindtBinWidth=mindtBinWidth,
maxdtBinWidth=maxdtBinWidth,
pplmin_frac=minpplfrac, pplmax_frac=maxpplfrac,
- constraintScheme=constraintScheme, instrumentName=instrumentName)
+ constraintScheme=constraintScheme, instrumentName=instrumentName,
+ peakMaskSize=peakMaskSize)
# --IN PRINCIPLE!!! WE CALCULATE THIS BEFORE GETTING HERE
tofWS = mtd['tofWS']
--
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