def compareCompositions(specs, comp, withSigma=False, normalize=False, prop=epq.SpectrumProperties.MicroanalyticalComposition):
"""Syntax: compareCompositions(specs, comp=createMaterial(), [withSigma=False], [normalize=False], [prop=epq.SpectrumProperties.MicroanalyticalComposition]
Tabulate the comparison between the compositions of the specified spectra with the specified composition."""
res = {}
elms = ju.TreeSet()
for spec in specs:
c = spec.getProperties().getObjectWithDefault(prop, None)
if c != None:
res[spec] = c
elms.addAll(c.getElementSet())
str = "Name"
for elm in elms:
str = "%s\t%s-diff\t%s-frac" % (str, elm.toAbbrev(), elm.toAbbrev())
if withSigma:
str = "%s\t%s-sig" % (str, elm.toAbbrev())
print str
str="Nominal"
for elm in elms:
str = "%s\t%g\t" % (str, comp.weightFraction(elm,normalize)*100)
if withSigma:
str="%s\t" % str
print str
for spec in res:
c = res[spec]
str = "%s" % spec
for elm in elms:
u = c.weightFractionU(elm, normalize)
err = 100 *(u.doubleValue()-comp.weightFraction(elm,normalize))
str = "%s\t%g\t%g" % (str, err, err/comp.weightFraction(elm,normalize))
if withSigma:
if u.uncertainty()>0:
str = "%s\t%g" % (str, err / (100.0 * u.uncertainty()))
else:
str = "%s\t-" % str
print str
def tabulateCompositions2(specs, withErrs=False, normalize=False, prop=epq.SpectrumProperties.MicroanalyticalComposition):
"""Syntax: tabulateCompositions2(specs,[withErrs=False],[normalize=False],[prop=epq.SpectrumProperties.MicroanalyticalComposition])
Tabulate the compositions associated with the specified collection of spectra. Rows
represent spectra and columns represent elements."""
res = {}
elms = ju.TreeSet()
for spec in specs:
c = spec.getProperties().getObjectWithDefault(prop, None)
if c != None:
res[spec] = c
elms.addAll(c.getElementSet())
str = "Name"
for elm in elms:
str = "%s\t%s" % (str, elm.toAbbrev())
if withErrs:
str = "%s\td%s" % (str, elm.toAbbrev())
print str
for spec in res:
c = res[spec]
str = "%s" % spec
for elm in elms:
u = c.weightFractionU(elm, normalize)
str = "%s\t%g" % (str, 100 * u.doubleValue())
if withErrs:
str = "%s\t%g" % (str, 100.0 * u.uncertainty())
print str
def compStats(comps, norm=0):
"""compStats(comps, norm=0)
Compute compositional statistics for the list of Composition objects.
Parameters
----------
comps A list of Composition objects.
Example: [comp1, comp2, comp3]
norm An integer. Default: 0.
If norm=1, the Composition objects are normalized to 100%; otherwise not.
Returns
-------
None. Prints results to the command line
"""
elms = ju.TreeSet()
for comp in comps:
elms.addAll(comp.getElementSet())
dss = dict()
for elm in elms:
dss[elm] = epu.DescriptiveStatistics()
for comp in comps:
for elm in elms:
dss[elm].add(comp.weightPercent(elm, norm))
return dss
def compStats(comps, norm=False):
"""Syntax: compStats([comp1,comp2,...,compN],norm=False)
Compute compositional statistics for the list of Composition objects. If norm=1,
then the Composition objects are normalized to 100%; otherwise not."""
elms = ju.TreeSet()
for comp in comps:
elms.addAll(comp.getElementSet())
dss = {}
for elm in elms:
dss[elm] = epu.DescriptiveStatistics()
for comp in comps:
for elm in elms:
dss[elm].add(comp.weightPercent(elm, norm))
return dss
def to10dash1(action_code,
sample_id,
specs,
instrument_analysis_date,
analysis_lab_id="N",
srm_id="IIIE",
pkg_lab_id="N",
instrument="E",
instrument_number="2",
spot_size="5",
operator="NWMR",
spectrometer="EDS15",
comment={}):
"""to10dash1(
action_code,
sample_id,
specs,
instrument_analysis_date,
analysis_lab_id="N",
srm_id="IIIE",
pkg_lab_id="N",
instrument="I",
instrument_number="1",
spot_size="5",
operator="NWMR",
spectrometer="EDS15",
comment={}
)
* action_code = "N", "R" or "D"
* sample_id unique id
* specs = selected() or a list of spectra
* instrument_analysis_date = "10-DEC-2020" or equivalent for date of acquisition
* srm_id = "IIIX" where "X" is the letter of your block
* pkg_lab and analysis_lab_id = your lab ID letter
* instrument - Instrument id
* spot_size a number in unspecified units as a string
* operator = "Your initials"
* spectrometer = the spectrometer ID
* comment = { element("Fe"):"Eat more iron", element("Si"):"Sillycone" } or similar
The function prints a line per element for each element in the "MicroanalyticalComposition" property of the selected spectra. The selected spectra are
assumed to come from the same material. The "_error" columns reflect the standard deviation between the spectra not the single spectrum uncertainty."""
def savg(vals):
s = 0.0
for val in vals:
s = s + val
return s / len(vals)
def sstd(vals):
s, s2 = savg(vals), 0.0
for val in vals:
s2 += (val - s) * (val - s)
return jl.Math.sqrt(s2 / len(vals))
elms = ju.TreeSet()
props = specs[0].getProperties()
e0 = props.getNumericProperty(epq.SpectrumProperties.BeamEnergy)
beam_current = "%0.3f" % (props.getNumericProperty(
epq.SpectrumProperties.FaradayBegin), )
for spec in specs:
mat = spec.getProperties().getObjectProperty(
epq.SpectrumProperties.MicroanalyticalComposition)
elms.addAll(mat.getElementSet())
for elm in elms:
comment.setifabsent(elm, "")
wfa, afa, ks, cr = {}, {}, {}, []
for spec in specs:
props = spec.getProperties()
mat = props.getObjectProperty(
epq.SpectrumProperties.MicroanalyticalComposition)
krs = props.getObjectProperty(epq.SpectrumProperties.OptimalKRatios)
cr.append(
epq.SpectrumUtils.integrate(spec, 100.0, 1000.0 * e0) /
props.getNumericProperty(epq.SpectrumProperties.LiveTime))
for elm in elms:
wfa.setifabsent(elm,
[]), afa.setifabsent(elm,
[]), ks.setifabsent(elm, []),
wfa[elm].append(mat.weightFraction(elm, False))
afa[elm].append(mat.atomicPercent(elm))
xrts = krs.optimalDatum(elm)
ks[elm].append(krs.getKRatio(xrts) if xrts != None else 0.0)
full = ""
for elm in elms:
weight_percent = "%0.2f" % (100.0 * savg(wfa[elm]), )
weight_percent_error = "%0.2f" % (100.0 * sstd(wfa[elm]), )
atom_percent = "%0.2f" % (100.0 * savg(afa[elm]), )
atom_percent_error = "%0.2f" % (100.0 * sstd(afa[elm]), )
amount = ("MAJOR" if weight_percent > 10.0 else
("MINOR" if weight_percent > 1.0 else "TRACE"))
k_value = "%0.4f" % (savg(ks[elm]), )
normalization_factor = ""
normalization_model = ""
count_rate = "%0.0f" % (savg(cr))
diffracting_crystal = "NA"
incident_beam_energy = "%0.1f" % (e0, )
star_elemental_comments = comment[elm]
element = str(jl.String(elm.toAbbrev()).toUpperCase())
item = (action_code, sample_id, srm_id, pkg_lab_id, analysis_lab_id,
element, instrument, instrument_number,
instrument_analysis_date, operator, weight_percent,
weight_percent_error, atom_percent, atom_percent_error, amount,
k_value, normalization_factor, normalization_model, count_rate,
diffracting_crystal, spectrometer, e0, beam_current, spot_size,
star_elemental_comments)
res = "%1s%07i %-6s %1s %1s %-3s %-2s %-3s %-11s %12s %12s %12s %12s %12s %5s %12s %12s %3s %12s %-6s %5s %4s %5s %5s %s" % item
full = "%s%s\n" % (full, res)
print(res)
return full[0:-1]