def rippleToMaps(rpl, vecSet, step=1):
"""RippleToMaps(rpl, vecSet, step=1)
Applies a vector set to a RPL/RAW file pair producing a dictionary of MapImage objects /
indexed by RegionOfInterest objects."""
width = rpl.getColumns()
height = rpl.getRows()
vecs = vecSet.getVectors()
planes = epq.MapImage(width, height, len(vecs), str(vecSet))
rpl.setSpan(step, step)
for r in xrange(0, height, step):
if dt2.isTerminated():
break
for c in xrange(0, width, step):
if dt2.isTerminated():
break
rpl.setPosition(r, c)
krs = vecSet.getKRatios(rpl)
kra = []
for vec in vecs:
kra.append(krs.getKRatio(vec.getROI()))
planes.inc(c, r, kra)
return planes
def rippleToMaps(rpl, vecSet, step=1):
"""RippleToMaps(rpl, vecSet, step=1)
Applies a vector set to a RPL/RAW file pair producing a dictionary of MapImage objects /
indexed by RegionOfInterest objects."""
width = rpl.getColumns()
height = rpl.getRows()
vecs = vecSet.getVectors()
planes = epq.MapImage(width, height, len(vecs), str(vecSet))
rpl.setSpan(step, step)
for r in xrange(0, height, step):
if dt2.isTerminated():
break
for c in xrange(0, width, step):
if dt2.isTerminated():
break
rpl.setPosition(r, c)
krs = vecSet.getKRatios(rpl)
kra = []
for vec in vecs:
kra.append(krs.getKRatio(vec.getROI()))
planes.inc(c,r,kra)
return planes
def quantify(rpl,
stds,
refs={},
preferred=(),
elmByDiff=None,
elmByStoic=None,
assumedStoic={},
mask=None,
step=1,
visualize=False,
zaf=None,
withUnc=False):
"""quantify(rpl,stds,[refs={}],[preferred=()],[elmByDiff=None],[elmByStoic=None],[assumedStoic={}], [mask=None],[zaf=None], [withUnc=False])
Quantify a ripple/raw spectrum object based on the standards, references and other parameters specified. /
The arguments are the same as dtsa2.multiQuant. An additional 'mask' argument allows uninteresting pixels /
to be ignored (not quantified.) The mask should be an object like a BufferedImage with a getRGB(x,y) method. /
The pixel is ignored if mask.getRGB(x,y)==0. The result is written to a RPL/RAW file in FLOAT format.
> import javax.imageio.ImageIO as io
> mask = io.read(jio.File("c:/image.png"))
> zaf = epq.CorrectionAlgorithm.NullCorrection for k-ratios"""
oldSt = None
try:
if (zaf != None) and isinstance(zaf, epq.CorrectionAlgorithm):
oldSt = epq.AlgorithmUser.getGlobalStrategy()
newSt = epq.AlgorithmUser.getGlobalStrategy()
newSt.addAlgorithm(epq.CorrectionAlgorithm, zaf)
epq.AlgorithmUser.applyGlobalOverride(newSt)
det = rpl.getProperties().getDetector()
e0 = rpl.getProperties().getNumericProperty(
epq.SpectrumProperties.BeamEnergy)
mq = dt2.multiQuant(det, e0, stds, refs, preferred, elmByDiff,
elmByStoic, assumedStoic)
base = rpl.getProperties().getTextProperty(
epq.SpectrumProperties.SourceFile)
compRpl = base.replace(".rpl", "_comp.rpl")
compRaw = base.replace(".rpl", "_comp.raw")
compTxt = base.replace(".rpl", "_comp.txt")
status = file(compTxt, "wt")
status.write("File:\t%s\n" % base)
status.write("Results:\t%s\n" % compRpl)
status.write("Detector:\t%s\n" % det)
status.write("Beam energy\t%g keV\n" % e0)
status.write("Standards\n")
i = 0
elms = [] # Ensures the plane order is correct
if det.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (
det, det.getChannelCount(), rpl.getChannelCount())
return
for elm, std in stds.iteritems():
if std.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (
std, std.getChannelCount(), rpl.getChannelCount())
return
status.write("\t%d\t%s\t%s\n" % (i, elm, std))
elms.append(dt2.element(elm))
i = i + 1
if len(refs) > 0:
status.write("References\n")
for xrt, ref in refs.iteritems():
if ref.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (
ref, ref.getChannelCount(), rpl.getChannelCount())
status.write("\t%s\t%s\n" % (xrt, ref))
if len(preferred) > 0:
status.write("Preferred transitions\n")
for xrt in preferred:
status.write("\t%s for %s\n" % (xrt, xrt.getElement()))
if elmByDiff:
status.write("Element by difference: %s\n" % elmByDiff)
if elmByStoic:
status.write("Element by Stoiciometry: %s\n" % elmByStoic)
status.write("Element\tValence\n")
for elm, stoic in assumedStoic.iteritems():
status.write("\t%s\t%g\n" % (elm, stoic))
comps = ept.RippleFile((rpl.getColumns() + step - 1) / step,
(rpl.getRows() + step - 1) / step,
len(stds) + 1, ept.RippleFile.FLOAT, 8,
ept.RippleFile.DONT_CARE_ENDIAN, compRpl,
compRaw)
uncert = None
if withUnc:
uncRaw = base.replace(".rpl", "_unc.raw")
uncRpl = base.replace(".rpl", "_unc.rpl")
uncert = ept.RippleFile((rpl.getColumns() + step - 1) / step,
(rpl.getRows() + step - 1) / step,
len(stds) + 1, ept.RippleFile.FLOAT, 8,
ept.RippleFile.DONT_CARE_ENDIAN, uncRpl,
uncRaw)
dumpIt = False
if dumpIt:
dumpRpl = base.replace(".rpl", "_dump.rpl")
dumpRaw = base.replace(".rpl", "_dump.raw")
dump = ept.RippleFile((rpl.getColumns() + step - 1) / step,
(rpl.getRows() + step - 1) / step,
rpl.getChannelCount(),
ept.RippleFile.UNSIGNED, 4,
ept.RippleFile.DONT_CARE_ENDIAN, dumpRpl,
dumpRaw)
rpl.setSpan(step, step)
for r in xrange(0, rpl.getRows(), step):
if dt2.isTerminated():
break
dt2.StdOut.append(".")
dt2.StdOut.flush()
for c in xrange(0, rpl.getColumns(), step):
if dt2.isTerminated():
break
if visualize:
dt2.clearSpectra()
dt2.display(rpl)
comps.setPosition(c / step, r / step)
if (mask == None) or ((mask.getRGB(c, r) & 0xFFFFFF) > 0):
try:
rpl.setPosition(c, r)
rs = epq.SpectrumUtils.copy(rpl)
if dumpIt:
# print "%d\t%d\t%d\t%d" % (c, r, c / step, r / step)
dump.setPosition(c / step, r / step)
dump.write(epq.SpectrumUtils.toIntArray(rs))
res = mq.compute(rs)
comp = res.getComposition()
if visualize:
rpl.getProperties().setCompositionProperty(
epq.SpectrumProperties.
MicroanalyticalComposition, comp)
dt2.annotComposition()
tmp, unc = [], []
sU = 0.0
for elm in elms:
tmp.append(comp.weightFraction(elm, True))
u = comp.weightFractionU(elm, True).uncertainty()
unc.append(u)
sU = sU + u * u
tmp.append(comp.sumWeightFraction())
unc.append(jl.Math.sqrt(sU))
if dumpIt:
print tmp
comps.write(tmp)
if uncert:
uncert.write(unc)
except (epq.EPQException, Exception, jl.Exception), e:
msg = "row = %d, col = %d failed: %s" % (r, c, e)
print msg
status.write(msg + "\n")
for elm, std in stds.iteritems():
comps.write(0.0)
if uncert:
uncert.write(unc)
if visualize:
dt2.setAnnotation("row = %d, col = %d failed." %
(r, c))
else:
for elm, std in stds.iteritems():
comps.write(0.0)
if uncert:
uncert.write(unc)
comps.write(1.0)
if uncert:
uncert.write(1.0)
comps.close()
if uncert:
uncert.close()
if dumpIt:
dump.close()
status.close()
def quantify(rpl, stds, refs={}, preferred=(), elmByDiff=None, elmByStoic=None, assumedStoic={}, mask=None, step=1, visualize=False, zaf=None, withUnc=False):
"""quantify(rpl,stds,[refs={}],[preferred=()],[elmByDiff=None],[elmByStoic=None],[assumedStoic={}], [mask=None],[zaf=None], [withUnc=False])
Quantify a ripple/raw spectrum object based on the standards, references and other parameters specified. /
The arguments are the same as dtsa2.multiQuant. An additional 'mask' argument allows uninteresting pixels /
to be ignored (not quantified.) The mask should be an object like a BufferedImage with a getRGB(x,y) method. /
The pixel is ignored if mask.getRGB(x,y)==0. The result is written to a RPL/RAW file in FLOAT format.
> import javax.imageio.ImageIO as io
> mask = io.read(jio.File("c:/image.png"))
> zaf = epq.CorrectionAlgorithm.NullCorrection for k-ratios"""
oldSt = None
try:
if (zaf != None) and isinstance(zaf, epq.CorrectionAlgorithm):
oldSt = epq.AlgorithmUser.getGlobalStrategy()
newSt = epq.AlgorithmUser.getGlobalStrategy()
newSt.addAlgorithm(epq.CorrectionAlgorithm, zaf)
epq.AlgorithmUser.applyGlobalOverride(newSt)
det = rpl.getProperties().getDetector()
e0 = rpl.getProperties().getNumericProperty(epq.SpectrumProperties.BeamEnergy)
mq = dt2.multiQuant(det, e0, stds, refs, preferred, elmByDiff, elmByStoic, assumedStoic)
base = rpl.getProperties().getTextProperty(epq.SpectrumProperties.SourceFile)
compRpl = base.replace(".rpl", "_comp.rpl")
compRaw = base.replace(".rpl", "_comp.raw")
compTxt = base.replace(".rpl", "_comp.txt")
status = file(compTxt, "wt")
status.write("File:\t%s\n" % base)
status.write("Results:\t%s\n" % compRpl)
status.write("Detector:\t%s\n" % det)
status.write("Beam energy\t%g keV\n" % e0)
status.write("Standards\n")
i = 0;
elms = [] # Ensures the plane order is correct
if det.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (det, det.getChannelCount(), rpl.getChannelCount())
return
for elm, std in stds.iteritems():
if std.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (std, std.getChannelCount(), rpl.getChannelCount())
return
status.write("\t%d\t%s\t%s\n" % (i, elm, std))
elms.append(dt2.element(elm))
i = i + 1
if len(refs) > 0:
status.write("References\n")
for xrt, ref in refs.iteritems():
if ref.getChannelCount() != rpl.getChannelCount():
print "ERROR: The number of channels in %s (%d) doesn't match the number of channels in the RPL file (%d)." % (ref, ref.getChannelCount(), rpl.getChannelCount())
status.write("\t%s\t%s\n" % (xrt, ref))
if len(preferred) > 0:
status.write("Preferred transitions\n")
for xrt in preferred:
status.write("\t%s for %s\n" % (xrt, xrt.getElement()))
if elmByDiff:
status.write("Element by difference: %s\n" % elmByDiff)
if elmByStoic:
status.write("Element by Stoiciometry: %s\n" % elmByStoic)
status.write("Element\tValence\n")
for elm, stoic in assumedStoic.iteritems():
status.write("\t%s\t%g\n" % (elm, stoic))
comps = ept.RippleFile((rpl.getColumns() + step - 1) / step, (rpl.getRows() + step - 1) / step, len(stds) + 1, ept.RippleFile.FLOAT, 8, ept.RippleFile.DONT_CARE_ENDIAN, compRpl, compRaw)
uncert = None
if withUnc:
uncRaw = base.replace(".rpl", "_unc.raw")
uncRpl = base.replace(".rpl", "_unc.rpl")
uncert = ept.RippleFile((rpl.getColumns() + step - 1) / step, (rpl.getRows() + step - 1) / step, len(stds) + 1, ept.RippleFile.FLOAT, 8, ept.RippleFile.DONT_CARE_ENDIAN, uncRpl, uncRaw)
dumpIt = False
if dumpIt:
dumpRpl = base.replace(".rpl", "_dump.rpl")
dumpRaw = base.replace(".rpl", "_dump.raw")
dump = ept.RippleFile((rpl.getColumns() + step - 1) / step, (rpl.getRows() + step - 1) / step, rpl.getChannelCount(), ept.RippleFile.UNSIGNED, 4, ept.RippleFile.DONT_CARE_ENDIAN, dumpRpl, dumpRaw)
rpl.setSpan(step, step)
for r in xrange(0, rpl.getRows(), step):
if dt2.isTerminated():
break
dt2.StdOut.append(".")
dt2.StdOut.flush()
for c in xrange(0, rpl.getColumns(), step):
if dt2.isTerminated():
break
if visualize:
dt2.clearSpectra()
dt2.display(rpl)
comps.setPosition(c / step, r / step)
if (mask == None) or ((mask.getRGB(c, r) & 0xFFFFFF) > 0):
try:
rpl.setPosition(c, r)
rs = epq.SpectrumUtils.copy(rpl)
if dumpIt:
# print "%d\t%d\t%d\t%d" % (c, r, c / step, r / step)
dump.setPosition(c / step, r / step)
dump.write(epq.SpectrumUtils.toIntArray(rs))
res = mq.compute(rs)
comp = res.getComposition()
if visualize:
rpl.getProperties().setCompositionProperty(epq.SpectrumProperties.MicroanalyticalComposition, comp)
dt2.annotComposition()
tmp, unc = [], []
sU = 0.0
for elm in elms:
tmp.append(comp.weightFraction(elm, True))
u = comp.weightFractionU(elm, True).uncertainty()
unc.append(u)
sU = sU + u*u
tmp.append(comp.sumWeightFraction())
unc.append(jl.Math.sqrt(sU))
if dumpIt:
print tmp
comps.write(tmp)
if uncert:
uncert.write(unc)
except (epq.EPQException, Exception, jl.Exception), e:
msg = "row = %d, col = %d failed: %s" % (r, c, e)
print msg
status.write(msg + "\n")
for elm, std in stds.iteritems():
comps.write(0.0)
if uncert:
uncert.write(unc)
if visualize:
dt2.setAnnotation("row = %d, col = %d failed." % (r, c))
else:
for elm, std in stds.iteritems():
comps.write(0.0)
if uncert:
uncert.write(unc)
comps.write(1.0)
if uncert:
uncert.write(1.0)
comps.close()
if uncert:
uncert.close()
if dumpIt:
dump.close()
status.close()