From fab96da709e63538a0333f6d25cd255a4131dd6c Mon Sep 17 00:00:00 2001
From: Brendan Sullivan <sullivanbt@ornl.gov>
Date: Thu, 26 Jul 2018 12:34:31 -0400
Subject: [PATCH] Re #22811 move parameters from algorithms to param files
---
.../IntegratePeaksProfileFitting.py | 36 +++++++------------
instrument/CORELLI_Parameters.xml | 30 ++++++++++++++++
instrument/MANDI_Parameters.xml | 28 +++++++++++++++
instrument/MANDI_Parameters_2015_08_01.xml | 30 ++++++++++++++++
instrument/MANDI_Parameters_2016_02_01.xml | 30 ++++++++++++++++
instrument/TOPAZ_Parameters.xml | 29 +++++++++++++++
scripts/SCD_Reduction/BVGFitTools.py | 8 +++--
scripts/SCD_Reduction/ICCFitTools.py | 10 +++---
8 files changed, 169 insertions(+), 32 deletions(-)
diff --git a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
index b2363518668..c38a7219d37 100644
--- a/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
+++ b/Framework/PythonInterface/plugins/algorithms/IntegratePeaksProfileFitting.py
@@ -116,30 +116,18 @@ class IntegratePeaksProfileFitting(PythonAlgorithm):
# statement.
# If you change these values or add an instrument, documentation should also be changed.
instrumentName = peaks_ws.getInstrument().getFullName()
- mindtBinWidth = 15
- maxdtBinWidth = 50
- nTheta = 50
- nPhi = 50
- fracHKL = 0.4
- dQPixel = 0.003
- if instrumentName == 'MANDI':
- pass
- elif instrumentName == 'TOPAZ':
- mindtBinWidth = 2
- maxdtBinWidth = 15
- nTheta=50
- nPhi = 50
- fracHKL = 0.4
- dQPixel = 0.01
- elif instrumentName == 'CORELLI':
- mindtBinWidth = 2
- maxdtBinWidth = 60
- nTheta=50
- nPhi = 50
- fracHKL = 0.4
- dQPixel = 0.007
- else:
- logger.warning("Instrument name {} not found! Falling back on default parameters!".format(instrumentName))
+ try:
+ nTheta = peaks_ws.getInstrument().getIntParameter("numBinsTheta")[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]
+
+ except:
+ raise
+ logger.error("Cannot find all parameters in instrument parameters file.")
+ sys.exit(1)
neigh_length_m=3
qMask = ICCFT.getHKLMask(UBMatrix, frac=fracHKL, dQPixel=dQPixel,dQ=dQ)
diff --git a/instrument/CORELLI_Parameters.xml b/instrument/CORELLI_Parameters.xml
index b560efec73c..a8167e41032 100644
--- a/instrument/CORELLI_Parameters.xml
+++ b/instrument/CORELLI_Parameters.xml
@@ -40,6 +40,36 @@
<value val="16" />
</parameter>
+ <!-- Number of polar bins for BVG histogramming when profile fitting -->
+ <parameter name="numBinsTheta" type="int">
+ <value val="50" />
+ </parameter>
+
+ <!-- Number of azimuthal bins for BVG histogramming when profile fitting -->
+ <parameter name="numBinsPhi" type="int">
+ <value val="50" />
+ </parameter>
+
+ <!-- Fraction along (h,k,l) to use for profile fitting. 0.5 is the next peak. -->
+ <parameter name="fracHKL">
+ <value val="0.4" />
+ </parameter>
+
+ <!-- Side length of each voxel for fitting in units of angstrom^-1 -->
+ <parameter name="dQPixel">
+ <value val="0.007" />
+ </parameter>
+
+ <!-- Minimum spacing for profile fitting the TOF profile. Units of microseconds -->
+ <parameter name="mindtBinWidth">
+ <value val="2" />
+ </parameter>
+
+ <!-- Maximum spacing for profile fitting the TOF profile. Units of microseconds -->
+ <parameter name="maxdtBinWidth">
+ <value val="60" />
+ </parameter>
+
</component-link>
</parameter-file>
diff --git a/instrument/MANDI_Parameters.xml b/instrument/MANDI_Parameters.xml
index 8833ec7f5d2..dcaa2ca55f3 100644
--- a/instrument/MANDI_Parameters.xml
+++ b/instrument/MANDI_Parameters.xml
@@ -33,7 +33,35 @@
<value val="255" />
</parameter>
+<!-- Number of polar bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsTheta" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Number of azimuthal bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsPhi" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Fraction along (h,k,l) to use for profile fitting. 0.5 is the next peak. -->
+<parameter name="fracHKL">
+ <value val="0.4" />
+</parameter>
+<!-- Side length of each voxel for fitting in units of angstrom^-1 -->
+<parameter name="dQPixel">
+ <value val="0.003" />
+</parameter>
+
+<!-- Minimum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="mindtBinWidth">
+ <value val="15" />
+</parameter>
+
+<!-- Maximum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="maxdtBinWidth">
+ <value val="50" />
+</parameter>
</component-link>
diff --git a/instrument/MANDI_Parameters_2015_08_01.xml b/instrument/MANDI_Parameters_2015_08_01.xml
index 656e899ba71..fef3a0458b8 100644
--- a/instrument/MANDI_Parameters_2015_08_01.xml
+++ b/instrument/MANDI_Parameters_2015_08_01.xml
@@ -33,6 +33,36 @@
<value val="255" />
</parameter>
+<!-- Number of polar bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsTheta" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Number of azimuthal bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsPhi" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Fraction along (h,k,l) to use for profile fitting. 0.5 is the next peak. -->
+<parameter name="fracHKL">
+ <value val="0.4" />
+</parameter>
+
+<!-- Side length of each voxel for fitting in units of angstrom^-1 -->
+<parameter name="dQPixel">
+ <value val="0.003" />
+</parameter>
+
+<!-- Minimum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="mindtBinWidth">
+ <value val="15" />
+</parameter>
+
+<!-- Maximum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="maxdtBinWidth">
+ <value val="50" />
+</parameter>
+
</parameter-file>
diff --git a/instrument/MANDI_Parameters_2016_02_01.xml b/instrument/MANDI_Parameters_2016_02_01.xml
index c3471773d9f..9b8c188b408 100644
--- a/instrument/MANDI_Parameters_2016_02_01.xml
+++ b/instrument/MANDI_Parameters_2016_02_01.xml
@@ -33,4 +33,34 @@
<value val="255" />
</parameter>
+<!-- Number of polar bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsTheta" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Number of azimuthal bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsPhi" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Fraction along (h,k,l) to use for profile fitting. 0.5 is the next peak. -->
+<parameter name="fracHKL">
+ <value val="0.4" />
+</parameter>
+
+<!-- Side length of each voxel for fitting in units of angstrom^-1 -->
+<parameter name="dQPixel">
+ <value val="0.003" />
+</parameter>
+
+<!-- Minimum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="mindtBinWidth">
+ <value val="15" />
+</parameter>
+
+<!-- Maximum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="maxdtBinWidth">
+ <value val="50" />
+</parameter>
+
</parameter-file>
diff --git a/instrument/TOPAZ_Parameters.xml b/instrument/TOPAZ_Parameters.xml
index 0151036048a..ff52c5ebdd2 100644
--- a/instrument/TOPAZ_Parameters.xml
+++ b/instrument/TOPAZ_Parameters.xml
@@ -109,6 +109,35 @@ detScale={13:1.046504,14:1.259293,16:1.02449,17:1.18898,18:0.88014,19:0.98665,\
<value val="255" />
</parameter>
+<!-- Number of polar bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsTheta" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Number of azimuthal bins for BVG histogramming when profile fitting -->
+<parameter name="numBinsPhi" type="int">
+ <value val="50" />
+</parameter>
+
+<!-- Fraction along (h,k,l) to use for profile fitting. 0.5 is the next peak. -->
+<parameter name="fracHKL">
+ <value val="0.4" />
+</parameter>
+
+<!-- Side length of each voxel for fitting in units of angstrom^-1 -->
+<parameter name="dQPixel">
+ <value val="0.01" />
+</parameter>
+
+<!-- Minimum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="mindtBinWidth">
+ <value val="2" />
+</parameter>
+
+<!-- Maximum spacing for profile fitting the TOF profile. Units of microseconds -->
+<parameter name="maxdtBinWidth">
+ <value val="15" />
+</parameter>
</component-link>
diff --git a/scripts/SCD_Reduction/BVGFitTools.py b/scripts/SCD_Reduction/BVGFitTools.py
index e09de245865..72d9972b0cf 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):
+ maxdtBinWidth=50, figureNumber=2, instrumentName=None):
n_events = box.getNumEventsArray()
if q_frame == 'lab':
@@ -30,11 +30,13 @@ def get3DPeak(peak, peaks_ws, box, padeCoefficients, qMask, nTheta=150, nPhi=150
goodIDX, pp_lambda = ICCFT.getBGRemovedIndices(
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)
+ pplmax_frac=pplmax_frac, mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
+ instrumentName=instrumentName)
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)
+ pplmax_frac=pplmax_frac, mindtBinWidth=mindtBinWidth, maxdtBinWidth=maxdtBinWidth,
+ instrumentName=instrumentName)
chiSqTOF = mtd['fit_Parameters'].column(1)[-1]
else: # we already did I-C profile, so we'll just read the parameters
diff --git a/scripts/SCD_Reduction/ICCFitTools.py b/scripts/SCD_Reduction/ICCFitTools.py
index d4a4f045639..9c378f849d4 100644
--- a/scripts/SCD_Reduction/ICCFitTools.py
+++ b/scripts/SCD_Reduction/ICCFitTools.py
@@ -197,7 +197,7 @@ def getPoissionGoodIDX(n_events, zBG=1.96, neigh_length_m=3):
def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3, qMask=None,
peak=None, box=None, pp_lambda=None, peakNumber=-1, minppl_frac=0.8,
maxppl_frac=1.5, mindtBinWidth=1, maxdtBinWidth=50,
- constraintScheme=1, instrumentName=None):
+ constraintScheme=1, instrumentName=None, peakMaskSize=5):
"""
getOptimizedGoodIDX - returns a numpy arrays which is true if the voxel contains events at
the zBG z level (1.96=95%CI). Rather than using Poission statistics, this function
@@ -245,12 +245,12 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
cX = nX//2
cY = nY//2
cZ = nZ//2
- dP = 5
-
+ dP = peakMaskSize
if instrumentName == 'TOPAZ':
dP = 15
- if instrumentName == 'CORELLI':
+ elif instrumentName == 'CORELLI':
dP = 10
+
peakMask = qMask.copy()
peakMask[cX-dP:cX+dP, cY-dP:cY+dP, cZ-dP:cZ+dP] = 0
neigh_length_m=3
@@ -318,7 +318,7 @@ def getOptimizedGoodIDX(n_events, padeCoefficients, zBG=1.96, neigh_length_m=3,
def getBGRemovedIndices(n_events, zBG=1.96, calc_pp_lambda=False, neigh_length_m=3, qMask=None,
peak=None, box=None, pp_lambda=None, peakNumber=-1, padeCoefficients=None,
pplmin_frac=0.8, pplmax_frac=1.5, mindtBinWidth=1, maxdtBinWidth=50,
- constraintScheme=1, instrumentName=None):
+ constraintScheme=1, instrumentName=None, peakMaskSize=5):
"""
getBGRemovedIndices - A wrapper for getOptimizedGoodIDX
Input:
--
GitLab