def MakeErrorTable(baseGs, baseDs, altGs, altDs, outfile=None):
if outfile is not None:
fp = open(outfile, 'a')
else:
fp = None
DataOut(latexHead, fp=fp)
dElems = np.array(sorted(baseDs.keys()))
gElems = np.array(sorted(baseGs.keys()))
# 19 element/ion colums will fit on a sideways table page
# Note: Assume the giants and dwarfs _should_ have the same number of ions
halfway = int(round(len(dElems) / 2 + 0.1,
0)) # F*ing Python floating points!
DataOut(r'r' * halfway + '} \n', fp=fp)
for ionSet, sType, baseAbs, abSet in [(dElems[:halfway], 'Dwarf', baseDs, altDs), \
(gElems[:halfway], 'Giant', baseGs, altGs), \
(dElems[halfway:], 'Dwarf', baseDs, altDs), \
(gElems[halfway:], 'Giant', baseGs, altGs)]:
# Do the column headers once for the Dwarfs, only
if sType == 'Dwarf':
columnHead = r'\multicolumn{1}{l}{Parameter} '
for ion in ionSet:
columnHead = columnHead + r'& \multicolumn{{1}}{{c}}{{{0}}} '.format(
el.getIonName(ion))
DataOut(columnHead + r'\\{0}\hline{0}'.format('\n'), fp=fp)
DataOut(r'\multicolumn{{{0:2d}}}{{|c|}}{{{1}s}}\\{2}\hline{2}'.format(
len(ionSet) + 1, sType, '\n'),
fp=fp)
for parmVar in abSet.keys():
rowData = r'\multicolumn{{1}}{{|l|}}{{{0}}}'.format(parmVar)
for ion in ionSet:
rowData = rowData + r' & \multicolumn{{1}}{{r|}}{{{0:1.2f}}}'.format(
abSet[parmVar][ion] - baseAbs[ion])
DataOut(rowData + r'\\{0}'.format('\n'), fp=fp)
DataOut(r'\hline {1}\multicolumn{{1}}{{|l|}}{{{0} Totals}}'.format(
sType, '\n'),
fp=fp)
for ion in ionSet:
subtotal = np.sqrt(sum([max((abSet[RowHeaders[2*i]][ion]-baseAbs[ion])**2, \
(abSet[RowHeaders[2*i+1]][ion]-baseAbs[ion])**2 \
) for i in [0,1,2]]))
DataOut(r' & \multicolumn{{1}}{{r|}}{{{0:1.2f}}}'.format(subtotal),
fp=fp)
DataOut(r'\\{0}\hline{0}'.format('\n'), fp=fp)
DataOut(latexFoot, fp=fp)
if fp: fp.close()
return
def MakeOneLogGPlot(logGPts, abPts, starName='', fileTag=''):
# Draw a logG plot for a single star.
# We want to use a couple of np.array tricks, so...
if len(logGPts) < 2 or len(abPts) < 2: return
Xs = np.array(logGPts)
Ys = np.array(abPts)
ax = pyplot.gca()
pyplot.scatter(Xs, Ys)
pyplot.axhline(0.0, linestyle=':')
interpGs = np.interp([0.1, 0., -0.1], -Ys, Xs)
pyplot.plot(Xs, Ys,
label=r'${0}({1:4.2f}^{{+{2:4.2f}}}_{{-{3:4.2f}}}$)'.\
format(el.getIonName(22.0),interpGs[1],\
interpGs[1]-interpGs[2],\
interpGs[0]-interpGs[1]))
ax.set_xlabel(r'$Log(G)$')
ax.set_ylabel('[TiI/TiII]')
pyplot.legend()
pyplot.savefig(k.ParmPlotDir + 'Logg/' + starName + fileTag + '_logG.png')
pyplot.close()
def MakeLineListTable(ions=[], wls=[], outFile=d.TableDir + 'Table2.dat'):
lines, refs = LL.getLines(elements=ions, wavelengthRange=wls,\
dataFormat=None)
unused1, unused2, weights = RC.GetSolarCorrections()
fp = open(outFile, 'w')
fmt, db = BuildFormatString(table2Format,
DataLabels=table2Labels,
DataUnits=table2Units,
DataExp=table2Desc,
MakeBbBDesc=True)
fp.write(db)
allIons = sorted(set(np.array(lines)[:, 1]))
lineData = []
for i in allIons:
ion = np.round(i, decimals=1)
(elem, state, unused) = el.getIonState(el.getIonName(ion))
ionLines = np.array(
sorted([l for l in lines if np.round(l[1], decimals=1) == ion],
key=lambda l: l[0]))
for line in ionLines:
wl = np.round(line[0], decimals=3)
xp = line[2]
gf = line[3]
if gf < 0:
gfs = '-'
else:
gfs = ''
gf = abs(gf)
try:
qu = int(weights[ion][wl])
except KeyError:
qu = 0
rf = line[5]
lineData.append([elem, state, wl, xp, gfs, gf, qu, rf])
for line in lineData:
fp.write(fmt.format(*line) + '\n')
fp.close()
def QualityPlot(points,
starName,
ion,
fileTag='',
plotTitle='',
pointLabels=None):
# Plot an [X/H]vs.line strength plot, with the points colored by "quality" -
# or how well they correspond to the linear fit (along the linear section of
# the COG) of other measurements with similar excitation potential values.
# The linear portion of the CoG is modeled by an Orthogonal Data Reduction (ODR)
# using a linear function (from sp.odr).
# The quality of a point is measured as an inverse of its distance to the linear
# fit as measured by the ODR.
# The passed data, in the array 'points' is of the form:
# [wl, Ex.Pot., Log(gf), eqw, Log(eqw/wl), [X/H]]
# For now, just bailing if no points were passed
nPoints = len(points)
if nPoints == 0:
return
# assert nPoints>0
# This abSTR measure is basically the log10 of the gravity*abundance*temp
abStrs = np.array(
[line[5] + line[2] + np.log10(line[0]) for line in points])
# We're rounding 'cause...Python.
XPs = np.around(points[:, 1], 4)
minXP = min(XPs)
maxXP = max(XPs)
uniqueXPs = sorted(set(XPs))
XPDelta = maxXP - minXP
normedXPs = [(xp - minXP) / XPDelta for xp in XPs]
# Arrange points to analyze:
# I just want you to be confused by the different indices
pointData = np.array(
zip(abStrs, points[:, 4], XPs, points[:, 5], points[:, 3]))
# Bin our points by nearby XPs
XPBins = [uniqueXPs[0]]
for xp in uniqueXPs:
if xp > XPBins[-1] + k.evBinSize:
XPBins.append(xp)
# We'll weight our linear COG fits by the individual points' [X/H] variance
# Note: we'll change the median once we 'weed out' measurements outside of
# the linear portion of the CoG.
abMed = np.median(points[:, 5])
# abVar = np.std(points[:,5])
linFits = {}
plotPoints = {}
minminErr = 10.
maxmaxErr = 0.
for xp in XPBins:
fitPoints = np.array([
p for p in pointData if p[2] >= xp and p[2] <= xp +
k.evBinSize and p[1] < k.cogPlotLimit - xp * k.cogCorrFactor
])
# fitPoints = np.array([p for p in pointData if p[2]>=xp and p[2]<=xp+k.evBinSize])
if fitPoints.shape[0] < 2:
linFits[xp] = []
plotPoints[xp] = []
continue
# Weight = distance to group median - max = 100 (ie: 1/sigma <=100)
deltas = [abs(ab - abMed) for ab in fitPoints[:, 3]]
pointWeights = u.normalize(
[1. / (500. * d) if d > 0.002 else 1. for d in deltas])
# The linfits dictionary entry will now contain:
# [[Linear fit coefficients], [parameter estimated errors], [covariance matrix],
# [estimated error in x], [estimated error in y]]
linFits[xp], coeffErrs, covariance, xErrs, yErrs = u.odRegress(
fitPoints[:, 0], fitPoints[:, 1], weights=pointWeights)
pointErrs = [np.sqrt(p[0]**2 + p[1]**2) for p in zip(xErrs, yErrs)]
plotPoints[xp] = np.array(
zip(fitPoints[:, 3], fitPoints[:, 1], pointErrs, fitPoints[:, 2],
pointWeights))
minErr = min(pointErrs)
maxErr = max(pointErrs)
if maxErr > maxmaxErr: maxmaxErr = maxErr
if minErr < minminErr: minminErr = minErr
# Calculate the point 'score' based on priors
deltaErr = maxmaxErr - minminErr
for xp in XPBins:
if len(plotPoints[xp]) == 0:
continue
# Normalize the errors for the first prior
normedErrs = np.array([(pe - minminErr) / deltaErr
for pe in plotPoints[xp][:, 2]])
# Normalized XP for second prior, however, we want 0.0eV to be highest
# values, and the highest XP to be valued no lower than 0.5
normedXPs = np.array([
1. - ((px - minXP) / XPDelta) / 2. for px in plotPoints[xp][:, 3]
])
combPriors = u.normalize(
np.array([
(ps[0] * (ps[1]**2) * ps[2])**0.25
for ps in zip(normedErrs, normedXPs, plotPoints[xp][:, 4])
]))
plotPoints[xp] = np.array(
zip(plotPoints[xp][:, 0], plotPoints[xp][:, 1], combPriors))
fig = pyplot.figure()
axes = pyplot.gca()
# Y axis is negative
Ymin = min(pointData[:, 1]) * 1.05
Ymax = max(pointData[:, 1]) * 0.95
Xmin = min(pointData[:, 3]) * 0.95
Xmax = max(pointData[:, 3]) * 1.05
if len(points) < 200:
pointSize = 9
if pointLabels is not None:
# Must have one label for each point (even if it is '')
if len(pointLabels) < len(abStrs):
# Must have labels for all the points
pointLabels = None
else:
pointLabels = None # Seriously, don't label more than 100 points
pointSize = 5
allPlotPts = [] # For median/variance calcs.
for xp in XPBins:
if len(plotPoints[xp]) != 0:
pyplot.scatter(plotPoints[xp][:, 0],
plotPoints[xp][:, 1],
figure=fig,
marker='o',
s=pointSize,
c=1. - plotPoints[xp][:, 2],
cmap=pyplot.get_cmap('CMRmap'),
edgecolors='None')
allPlotPts.extend(plotPoints[xp])
# It's possible that we've weeded a bit too heavily, in which case,
# we're done.
if len(allPlotPts) < 2:
pyplot.close()
return
abMed = np.median(np.array(allPlotPts)[:, 0])
abVar = np.std(np.array(allPlotPts)[:, 0])
# Plot the median abundance value
axes.plot([abMed, abMed], [Ymin, Ymax], linestyle='--', color='r')
axes.plot([abMed - abVar, abMed - abVar], [Ymin, Ymax],
linestyle=':',
color='c')
axes.plot([abMed + abVar, abMed + abVar], [Ymin, Ymax],
linestyle=':',
color='c')
pyplot.text(0.65,
0.25,
r'{0}({1:3d}): {2:1.3f}+/-{3:1.3f}'.format(
el.getIonName(ion), nPoints, abMed, abVar),
transform=axes.transAxes,
fontsize='smaller')
cb = pyplot.colorbar()
cb.set_label('Point \"Quality\" (Score)')
cb.set_ticks([0., 0.5, 1.0])
# cb.set_ticklabels(['{0:1.2f}'.format(minminErr), '{0:1.2f}'.format(minminErr+(maxmaxErr-minminErr)/2.), '{0:1.2f}'.format(maxmaxErr)])
cb.set_ticklabels(['1.00', '0.50', '0.00'])
# Write in a (tiny) label next to each point
if pointLabels is not None:
for coord in zip(abStrs.tolist(), wls.tolist(), pointLabels):
# Place the label below and right of the point
pyplot.text(coord[0] + 0.02 * (Xmax - Xmin),
coord[1] - 0.03 * (Ymax - Ymin),
coord[2],
color='k',
fontsize='xx-small')
# Axes labels and ranges
axes.set_ylim([Ymin, Ymax])
axes.set_xlim([Xmin, Xmax])
axes.set_xlabel('[{0}/H]'.format(el.getIonName(ion)))
axes.set_ylabel(r'$Log(EQW/\lambda)$')
if plotTitle is not '':
axes.set_title(plotTitle)
saveDirName = dirs.CoGPlotsDir + el.getIonName(ion) + '/'
try:
os.stat(saveDirName)
except:
os.mkdir(saveDirName[:-1])
pyplot.savefig('{0}{1}_{2}{3}.png'.format(saveDirName, starName,
el.getIonName(ion), fileTag),
figure=fig)
pyplot.close()
def COGPlot(points,
starName,
ion,
fileTag='',
plotTitle='',
pointLabels=None,
fitXPLines=False):
# Plot a curve of growth (COG)
# The linear portion of the CoG is modeled by least squares (numpy polyfid for
# a 1-d polynomial.
# The passed data, in the array 'points' is of the form:
# [wl, Ex.Pot., Log(gf), eqw, Log(eqw/wl), [X/H]]
# For now, just bailing if no points were passed
if len(points) == 0:
return
assert len(points) > 0
# We'll weight our linear COG fits by the individual points' [X/H] variance
abMed = np.median(points[:, 5])
# abVar = np.std(points[:,5])
## Quick experiment - what does the plot look like if we use the median abundance
## instead of the measured?
## We'll color the points with ex.pot. for this one.
# abStrs = np.array([abMed+line[2]+np.log10(line[0]) for line in points])
abStrs = np.array(
[line[5] + line[2] + np.log10(line[0]) for line in points])
# We're rounding 'cause...Python.
XPs = np.around(points[:, 1], 4)
minXP = min(XPs)
maxXP = max(XPs)
uniqueXPs = sorted(set(XPs))
deltaXP = maxXP - minXP
# Arrange points to analyze:
# I just want you to be confused by the different indices
pointData = np.array(
zip(abStrs, points[:, 4], XPs, points[:, 5], points[:, 3], points[:,
0]))
linFits = {}
plotPoints = {}
XPBins = [uniqueXPs[0]]
for xp in uniqueXPs:
if xp > XPBins[-1] + k.evBinSize:
XPBins.append(xp)
minminErr = 10.
maxmaxErr = 0.
for xp in XPBins:
fitPoints = np.array(
[p for p in pointData if p[2] >= xp and p[2] <= xp + k.evBinSize])
if fitPoints.shape[0] < 3:
linFits[xp] = None
plotPoints[xp] = None
continue
# Weight = distance to group median - max = 100 (ie: 1/sigma <=100)
deltas = [(abs(ab - abMed))**2 for ab in fitPoints[:, 3]]
pointWeights = [1. / (500. * d) if d > 0.002 else 1. for d in deltas]
# The linfits dictionary entry will now contain:
# [[Linear fit coefficients], [parameter estimated errors], [covariance matrix],
# [estimated error in x], [estimated error in y]]
linFits[xp], coeffErrs, covariance, xErrs, yErrs = u.odRegress(
fitPoints[:, 0], fitPoints[:, 1], weights=pointWeights)
pointErrs = [np.sqrt(p[0]**2 + p[1]**2) for p in zip(xErrs, yErrs)]
plotPoints[xp] = np.array(
zip(fitPoints[:, 0], fitPoints[:, 1], pointErrs, fitPoints[:, 5]))
minErr = min(pointErrs)
maxErr = max(pointErrs)
if maxErr > maxmaxErr: maxmaxErr = maxErr
if minErr < minminErr: minminErr = minErr
# Normalize the errors for plotting
deltaErr = maxmaxErr - minminErr
for xp in XPBins:
if plotPoints[xp] == None:
continue
pointErrs = plotPoints[xp][:, 2]
normedErrs = np.array([(pe - minminErr) / deltaErr
for pe in pointErrs])
plotPoints[xp] = np.array(
zip(plotPoints[xp][:, 0], plotPoints[xp][:, 1], normedErrs,
plotPoints[xp][:, 3]))
fig = pyplot.figure()
axes = pyplot.gca()
# Y axis is negative
Xmin = min(pointData[:, 0]) * 1.1
Xmax = max(pointData[:, 0]) * 0.9
Xmed = np.median(pointData[:, 0])
Ymin = min(pointData[:, 1]) * 0.9
Ymax = max(pointData[:, 1]) * 1.1
legendCount = 0
# fp =open('/home/mikelum/Dropbox/CodeCloud/MyTools/ClusterAnalysis/Plots/slopes.txt','a')
for xp in XPBins:
if plotPoints[xp] is None:
continue
# fp.write('---------------\n{0} {1:1.2f}eV ({2:2d}): {3:2.3f}\n '.format(el.getIonName(ion), xp, len(plotPoints[xp]), linFits[xp][0]))
# Plot the fit
minX = min(plotPoints[xp][:, 0])
minY = linFits[xp][0] * minX + linFits[xp][1]
maxX = max(plotPoints[xp][:, 0])
maxY = linFits[xp][0] * maxX + linFits[xp][1]
normedXP = ((xp - minXP) / deltaXP)
plt = axes.plot([minX, maxX], [minY, maxY],
color=pyplot.get_cmap('CMRmap')(normedXP))
# Plot the points:
# Color by distance to fit:
# axes.scatter(plotPoints[xp][:,0], plotPoints[xp][:,1], figure=fig, marker='o', s=8, c=plotPoints[xp][:,2], cmap=pyplot.get_cmap('CMRmap'), edgecolors='None')
# Color by Ex. Pot.
axes.scatter(plotPoints[xp][:, 0],
plotPoints[xp][:, 1],
figure=fig,
marker='o',
s=8,
color=pyplot.get_cmap('CMRmap')(normedXP),
edgecolors='None')
# Legend Key
axes.text(0.75,
0.35 - legendCount * 0.05,
r'{0:1.2f}eV: {1:2.3f}'.format(xp, linFits[xp][0]),
transform=axes.transAxes,
color=pyplot.get_cmap('CMRmap')(normedXP),
fontsize='smaller')
legendCount += 1
# slopes = np.array([[(p[3],(p[1]-a[1])/(p[0]-a[0])) if (p[0]-a[0]) != 0. else (p[3],float('nan')) for p in plotPoints[xp]] for a in plotPoints[xp]])
# diagIndex = 0
# for p in slopes:
# var = abs(linFits[xp][0]/np.nanmean(p[:,1]))
# if var > 2. or var< 0.5:
# fp.write(' -**')
# fp.write('{0:4.3f}:{1:2.3f}'.format(p[diagIndex,0], np.nanmean(p[:,1])))
# if var > 2. or var< 0.5:
# fp.write('**- ')
# else:
# fp.write(' ')
# diagIndex += 1
# fp.write('\n')
# fp.close()
# Plot the linear CoG limit
axes.plot([4, 14], [k.cogPlotLimit, k.cogPlotLimit], linestyle=':')
# cb = pyplot.colorbar()
# cb.set_label('Excitation Potential (eV)')
# cb.set_ticks([0., 0.5, 1.0])
# cb.set_ticklabels(['{0:1.2f}'.format(minXP), '{0:1.2f}'.format(minXP+(maxXP-minXP)/2.), '{0:1.2f}'.format(maxXP)])
# Write in a (tiny) label next to each point
if pointLabels is not None:
for coord in zip(abStrs.tolist(), XPs.tolist(), pointLabels):
# Place the label below and right of the point
axes.text(coord[0] + 0.02 * (Xmax - Xmin),
coord[1] - 0.03 * (Ymax - Ymin),
coord[2],
color='k',
fontsize='xx-small')
# Axes labels and ranges
axes.set_ylim([Ymin, Ymax])
axes.set_xlim([Xmin, Xmax])
axes.set_xlabel(r'$Log(A*gf*\lambda)$')
axes.set_ylabel(r'$Log(EQW/\lambda)$')
if plotTitle is not '':
axes.set_title(plotTitle)
saveDirName = dirs.CoGPlotsDir + el.getIonName(ion) + '/'
try:
os.stat(saveDirName)
except:
os.mkdir(saveDirName[:-1])
pyplot.savefig('{0}{1}_{2}{3}.png'.format(saveDirName, starName,
el.getIonName(ion), fileTag),
figure=fig)
pyplot.close()
def AbSTRPlot(starName,
ion,
points,
redSet=np.array([]),
greenSet=np.array([]),
blueSet=np.array([]),
lowLimit=None,
hiLimit=None,
fileTag='',
plotTitle='',
labelPoints=None):
# For now, just bailing if no points were passed
if len(points) == 0:
return
assert len(points) > 0
# Labels?
blackLabels = []
redLabels = []
greenLabels = []
blueLabels = []
# Plot the passed (np.array) point array in an external file
abundances = points[:, 0]
STRs = points[:, 1]
# Xmax = max(abundances)
# Xmin = min(abundances)
Ymin = min(STRs)
Ymax = max(STRs)
# # Use an arbitrary Solar+1.0/-1.5 in [X/H] space for the plot limits
# solarAB = el.atnoLU(int(ion))[3]
# pyplot.axis([np.round(solarAB-0.5,1), np.round(solarAB+1.0,1), np.round(Ymin,1)-0.5, np.round(Ymax,1)+0.5])
axes = pyplot.gca()
if len(points) < 500:
pointSize = 5
if labelPoints is not None:
# Must have one label for each point (even if it is '')
if len(labelPoints) < len(abundances):
# Must have labels for all the "black" (data) points
labelPoints = None
else:
# Note that array slicing will automatically return empty members
# for indices beyond the sliced array length
blackLabels = labelPoints[:len(abundances)]
redLabels = labelPoints[len(abundances):len(abundances) +
len(redSet)]
greenLabels = labelPoints[len(abundances) +
len(redSet):len(abundances) +
len(redSet) + len(greenSet)]
blueLabels = labelPoints[len(abundances) + len(redSet) +
len(greenSet):len(abundances) +
len(redSet) + len(greenSet) +
len(blueSet)]
else:
labelPoints = None # Seriously, don't label more than 30 points
pointSize = 3
pyplot.scatter(abundances, STRs, marker='.', s=pointSize + 2)
# Write in a (tiny) wavelength reference next to each point
if len(blackLabels) > 0:
for coord in zip(abundances.tolist(), STRs.tolist(), blackLabels):
# Place the label below and right of the point
pyplot.text(coord[0] + 0.02,
coord[1] - 0.03,
coord[2],
color='k',
fontsize='xx-small')
if len(redSet) > 0:
if len(redSet) < 30:
pointSize = 5
else:
pointSize = 3
redAbs = redSet[:, 0]
redSTRs = redSet[:, 1]
Ymin = min(Ymin, min(redAbs))
Ymax = max(Ymax, max(redSTRs))
pyplot.scatter(redAbs, redSTRs, marker='x', color='red', s=pointSize)
for i in range(len(redLabels)):
pyplot.text(redSet[i, 0] + 0.02,
redSet[i, 1] - 0.03,
redLabels[i],
color='r',
fontsize='xx-small')
if len(greenSet) > 0:
if len(greenSet) < 30:
pointSize = 5
else:
pointSize = 3
greenAbs = greenSet[:, 0]
greenSTRs = greenSet[:, 1]
Ymin = min(Ymin, min(greenAbs))
Ymax = max(Ymax, max(greenSTRs))
pyplot.scatter(greenAbs,
greenSTRs,
marker='x',
color='green',
s=pointSize)
for i in range(len(greenLabels)):
pyplot.text(greenSet[i, 0] + 0.02,
greenSet[i, 1] - 0.03,
greenLabels[i],
color='g',
fontsize='xx-small')
if len(blueSet) > 0:
if len(blueSet) < 30:
pointSize = 5
else:
pointSize = 3
blueAbs = blueSet[:, 0]
blueSTRs = blueSet[:, 1]
Ymin = min(Ymin, min(blueAbs))
Ymax = max(Ymax, max(blueSTRs))
pyplot.scatter(blueAbs,
blueSTRs,
marker='x',
color='blue',
s=pointSize)
for i in range(len(blueLabels)):
pyplot.text(blueSet[i, 0] + 0.02,
blueSet[i, 1] - 0.03,
blueLabels[i],
color='b',
fontsize='xx-small')
# DEBUGGING
# axes.set_ylim([min(STRs)-0.1, max(STRs)+0.1])
axes.set_xlim([min(abundances) - 0.1, max(abundances) + 0.1])
axes.set_ylim([np.round(Ymin, 1) - 0.2, np.round(Ymax, 1) + 0.2])
axes.set_xlabel('[{0}/H]'.format(el.getIonName(ion)))
axes.set_ylabel('STR. value')
if plotTitle is not '':
axes.set_title(plotTitle)
# Detection Limit?
if lowLimit is not None:
detXs = np.array([min(abundances) - 1.0, max(abundances) + 1.0])
detYs = lowLimit[0] * detXs + lowLimit[1]
pyplot.plot(detXs.tolist(), detYs.tolist(), 'k--')
# CoG Limit?
if hiLimit is not None:
detYs = hiLimit[0] * detXs + hiLimit[1]
pyplot.plot(detXs.tolist(), detYs.tolist(), 'k-.')
# Plot the best-fit abundance line
# Note: We're trying to fit a (hopefully) vertical line, which is ummmm...
# ...bad for typical linear regression methods. So, we swap X and Y, and
# pretend we're fitting a horizontal line (which also give us the ability to
# use p-values to claim "vertical-ness"
allPoints = zip(STRs.tolist(), abundances.tolist())
# abFitPoints = np.array([point for point in allPoints if point[0]>(lowLimit[0]*point[1] + lowLimit[1])])
abFitPoints = np.array(allPoints)
# avgExPot = np.mean(abFitPoints[:,0])
# Red = Low corrections
# weightArray = [10.0*(4.0-abs(avgExPot-x)) for x in abFitPoints[:,0]]
# abSlope, abIntercept = sp.polyfit(abFitPoints[:,0], abFitPoints[:,1], 1, w=weightArray)
# pyplot.text(0.80, 0.9, 'slope={0:5.1f}\n[{1}/H]={2:1.2f}+/-{3:1.2f}'.format(1./abSlope, el.getIonName(ion), np.mean(abundances), np.std(abundances)), transform=axes.transAxes, color='r', fontsize='smaller')
# detYs = np.array([np.round(Ymin,1)-0.5, np.round(Ymax,1)+0.5])
# detXs = abSlope*detYs + abIntercept
# pyplot.plot(detXs.tolist(), detYs.tolist(), 'r:')
# Green = unweighted fit
# abSlope, abIntercept, rv, pv, err = sp.stats.linregress(abFitPoints[:,0], abFitPoints[:,1])
# pyplot.text(0.80, 0.9, 'slope={0:5.1f}\nR^2-value={1:1.4f}\n[{2}/H]={3:1.2f}+/-{4:1.2f}({5:3d})'.format(1./abSlope, rv**2, el.getIonName(ion), np.mean(abundances), np.std(abundances),len(abundances)), transform=axes.transAxes, color='g', fontsize='smaller')
if len(redSet) > 0:
pyplot.text(0.75,
0.95,
'[{0}/H]={1:1.2f}+/-{2:1.2f}({3:3d})'.format(
el.getIonName(ion), np.mean(redAbs), np.std(redAbs),
len(redSet)),
transform=axes.transAxes,
color='r',
fontsize='smaller')
# else:
# pyplot.text(0.75, 0.95, '(No data)', transform=axes.transAxes, color='r', fontsize='smaller')
if len(greenSet) > 0:
pyplot.text(0.75,
0.90,
'[{0}/H]={1:1.2f}+/-{2:1.2f}({3:3d})'.format(
el.getIonName(ion), np.mean(greenAbs),
np.std(greenAbs), len(greenSet)),
transform=axes.transAxes,
color='g',
fontsize='smaller')
# else:
# pyplot.text(0.75, 0.90, '(No data)', transform=axes.transAxes, color='g', fontsize='smaller')
if len(blueSet) > 0:
pyplot.text(0.75,
0.85,
'[{0}/H]={1:1.2f}+/-{2:1.2f}({3:3d})'.format(
el.getIonName(ion), np.mean(blueAbs), np.std(blueAbs),
len(blueSet)),
transform=axes.transAxes,
color='b',
fontsize='smaller')
# else:
# pyplot.text(0.75, 0.85, '(No Data)', transform=axes.transAxes, color='b', fontsize='smaller')
pyplot.text(0.75,
0.80,
'[{0}/H]={1:1.2f}+/-{2:1.2f}({3:3d})'.format(
el.getIonName(ion), np.mean(abundances),
np.std(abundances), len(abundances)),
transform=axes.transAxes,
color='k',
fontsize='smaller')
# detYs = np.array([np.round(Ymin,1)-0.5, np.round(Ymax,1)+0.5])
# detXs = abSlope*detYs + abIntercept
# pyplot.plot(detXs.tolist(), detYs.tolist(), 'g:')
# Do the same for just the points in the linear region of the CoG
# linearPoints = np.array([point for point in allPoints if point[0]<(hiLimit[0]*point[1] + hiLimit[1])])
# abSlope, abIntercept, rv, pv, err = sp.stats.linregress(linearPoints[:,0], linearPoints[:,1])
# pyplot.text(0.50, 0.9, 'slope={0:5.1f}\nR^2-value={1:1.4f}\[email protected]={2:1.2f}'.format(1./abSlope, rv**2, abIntercept), transform=axes.transAxes, color='g', fontsize='smaller')
# detXs = abSlope*detYs + abIntercept
# pyplot.plot(detXs.tolist(), detYs.tolist(), 'g:')
# pyplot.xlabel('[{0}/H]'.format(el.getIonName(ion)))
# pyplot.ylabel('Ex.Pot.')
saveDirName = dirs.XPAbPlotsDir + el.getIonName(ion) + '/'
try:
os.stat(saveDirName)
except:
os.mkdir(saveDirName[:-1])
pyplot.savefig('{0}{1}_{2}{3}.png'.format(saveDirName, starName,
el.getIonName(ion), fileTag))
pyplot.close()
def PlotXPAbs(starData,
clusterName='NGC-0752',
ionList=kAllIonList,
fileTag='',
labelPlot=True,
labelPoints=False,
showTrendLine=False,
modelAtms=None,
pradks=None,
referenceCorrect=False):
# Make XP vs. Ab for the passed star
# One element per plot.
starName = starData[0]
starParmTuple = tuple(starData[1:])
isGiant = RC.isGiantStar(starParmTuple)
if isGiant:
modelPath = k.GiantModelPath
else:
modelPath = k.DwarfModelPath
if modelAtms == None or pradks == None:
modelFiles = mk.findDataFiles(modelPath)
modelAtms, pradks = mk.LoadModels(modelFiles)
abdict, uncorrLines, unusedMin, unusedMax = \
AB.CalcAbsAndLines(clusterName+' '+starName,
tuple(starData[1:6]), ionList=ionList,
modelAtms=modelAtms, pradks=pradks)
# uncorrLines:
# # {elem.ion:[[Wavelength, Ex.Pot., logGf, eqw, logRW, abund],...]}
if referenceCorrect:
if isGiant: # Obligatory comment on bad Giant corrections, and using
# Solar instead.
correctDict, referenceLines, lineWeights = \
RC.GetSolarCorrections(ionList=ionList,
modelAtms=modelAtms,
pradks=pradks)
else:
correctDict, referenceLines, lineWeights = \
RC.GetDwarfCorrections(ionList=ionList,
modelAtms=modelAtms,
pradks=pradks)
correctionsAvailable = False
if len(correctDict) > 0 and len(referenceLines) > 0:
correctionsAvailable = True
for ion in ionList:
if ion not in uncorrLines.keys():
continue
# Does this element have NLTE corrections available? Note: we do
# this BEFORE Solar corrections, which assumes that the same
# NLTE corrections are already applied to any Solar corrections
# we use.
if ion in NLTEIons:
LTELines = AB.CorrectNLTEAbs(ion, uncorrLines[ion],
tuple(starData[1:6]))
else:
if ion in uncorrLines.keys():
LTELines = uncorrLines[ion]
else:
# Either synthesized lines, or none available
LTELines = np.array([])
# Do we want the "reference corrected" abundances?
if referenceCorrect and correctionsAvailable:
tempAdj,tempAll = \
RC.SortAndFilterLines(LTELines,
ion,
tuple(starData[1:6]),
solarCorrect=referenceCorrect,
solarLines=referenceLines[ion],
solarCorrs=correctDict[ion],
lineWeights=lineWeights[ion])
# correctedLines:
# [[ab, line STR score, wl, "quality"], ...]
# allLines:
# [[ab, line STR score, wl],...]
# We want to use np.arrays, so...
allLines = np.array(tempAll)
correctedLines = np.array(tempAdj)
if len(allLines) == 0 or len(correctedLines) == 0:
correctionsAvailable = False
elif len(allLines) == 1 or len(correctedLines) == 1:
print('Single Line determination:{0}'.format(starData[0]))
print(allLines, correctedLines)
# One plot per ion.
if labelPlot:
plotLabel = 'XP vs Ab for [{2}/H] in {0} {1}.'.\
format(clusterName, starName, el.getIonName(ion))
else:
plotLabel = ''
if referenceCorrect and correctionsAvailable:
tempPoints = []
for line in uncorrLines[ion]:
correctedAbs = [l[0] for l in correctedLines if \
u.in_range(l[2],line[0]-0.05, line[0]+0.05)]
if len(correctedAbs) > 0:
tempPoints.append(
[line[1],
np.mean(correctedAbs), line[3], line[0]])
else:
tempPoints.append([line[1], line[5], line[3], line[0]])
XPAbPoints = np.array(tempPoints)
else:
XPAbPoints = np.array([[line[1],line[5],line[3],line[0]]\
for line in uncorrLines[ion]])
if labelPoints:
# Label the points with the wavelength
pointLabels = ['{0:2.3f}'.format(point[3]) \
for point in XPAbPoints]
else:
pointLabels = None
ps.XPAbPlot(XPAbPoints,
starName,
ion,
fileTag=fileTag + 'XPAb',
plotTitle=plotLabel,
pointLabels=pointLabels,
showTrendLine=showTrendLine)
def PlotClusterAbs(clusterName='NGC-0752',
ionList=kAllIonList,
fileTag='',
mass=1.2,
metallicity=0.0,
solarRelative=False,
referenceCorrect=False):
giantParms = GetGiantStarParms(clusterName=clusterName,\
mass=mass, metallicity=metallicity)
modelFiles = mk.findDataFiles(k.GiantModelPath)
gAtms, gPradks = mk.LoadModels(modelFiles)
modelFiles = mk.findDataFiles(k.DwarfModelPath)
dAtms, dPradks = mk.LoadModels(modelFiles)
gAbs = GetAbsForStars(giantParms,\
gModelAtms=gAtms, gPradks=gPradks,\
dModelAtms=dAtms, dPradks=dPradks,\
referenceCorrect=referenceCorrect)
gIons = sorted([ion for ion in gAbs.keys() if ion in ionList])
if solarRelative:
gElems = [gAbs[i][0] for i in gIons]
else:
solarFeH = PA.ptoe[25][PA.abIdx]
starIons = gAbs.keys()
starFeH = GetStarFeH(gAbs)
gElems = [
gAbs[i][0] - PA.ptoe[int(i) - 1][PA.abIdx] - starFeH for i in gIons
]
gVar = [gAbs[i][1] for i in gIons]
dwarfParms = GetDwarfStarParms(clusterName=clusterName,\
mass=mass, metallicity=metallicity)
dAbs = GetAbsForStars(dwarfParms,\
gModelAtms=gAtms, gPradks=gPradks,\
dModelAtms=dAtms, dPradks=dPradks,\
referenceCorrect=referenceCorrect)
dIons = sorted([ion for ion in dAbs.keys() if ion in ionList])
if solarRelative:
dElems = [dAbs[i][0] for i in dIons]
else:
# solarFeH = PA.ptoe[25][PA.abIdx] - calculated in giants, above
starIons = dAbs.keys()
starFeH = GetStarFeH(dAbs)
dElems = [
dAbs[i][0] - PA.ptoe[int(i) - 1][PA.abIdx] - starFeH for i in dIons
]
dVar = [dAbs[i][1] for i in dIons]
ionLUT = {}
for num, ion in enumerate(sorted(set(dIons + gIons))):
ionLUT[ion] = num
ionLabels = [' -', ' ']
for ion in sorted(ionLUT.keys()):
ionLabels.append(el.getIonName(ion))
ionLabels.append(' ')
fig = pyplot.figure()
ax = fig.gca()
ax.errorbar([ionLUT[ion] for ion in gIons], gElems, yerr=gVar, fmt='rs',\
label=clusterName+' giants')
ax.errorbar([ionLUT[ion] for ion in dIons], dElems, yerr=dVar, fmt='bo',\
label=clusterName+' dwarfs')
ax.xaxis.set_major_locator(pyplot.MultipleLocator(1))
ax.set_xticklabels(ionLabels, rotation='vertical')
ax.set_xlabel('Ion')
ax.set_xlim(left=-1, right=len(ionLUT.keys()))
if solarRelative:
ax.set_ylabel('[X/H]')
else:
ax.set_ylabel('[X/Fe]')
# ax.set_ylim(bottom=-0.4, top=0.5)
if not solarRelative:
ax.set_ylim(bottom=np.average(gElems + dElems) - 0.5,
top=np.average(gElems + dElems) + 0.5)
else:
ax.set_ylim(bottom=0, top=9)
ax.legend(numpoints=1)
ax.axhline(y=0.0,
xmin=-1,
xmax=len(ionLUT.keys()),
color='g',
linestyle='--')
# pyplot.show()
pyplot.savefig(dirs.PlotDir + clusterName + 'Abs' + fileTag + '.png')
pyplot.close()
return
def MakeAbTable(clusterName='NGC-0752',
starDataList=None,
ions=kAllIonList,
outFilename=k.TempAbOutFilename,
filterBlends=False,
referenceCorrect=False,
useDAOSpec=False,
headerLeft='',
headerRight=''):
if starDataList == None:
starDataList = GetAllStarParms(clusterName=clusterName)
# Lookup the abundance(s) for the passed star(s), and create a LaTeX chart
tableDict = GetAbTable(clusterName, starDataList, ions, filterBlends,
referenceCorrect, useDAOSpec)
giantNames = np.array([s[0] for s in starDataList \
if RC.isGiantStar(s[1:5])])
# dwarfNames = np.array([s[0] for s in starDataList
# if not RC.isGiantStar(s[1],s[2])])
# Iron abundance is listed as [Fe/H], all others will be [X/Fe].
# Compile a cluster/dwarfs/giants average table entry.
# Entries are of the form:
# {Ion:[[star ab, star line quality], ...], ...}
clusterDict = {}
dwarfDict = {}
giantDict = {}
for star in tableDict.keys():
# Place this stars measures into the proper category dictionary
if star in giantNames:
catDict = giantDict
else:
catDict = dwarfDict
starFe = GetStarFeH(tableDict[star])
for ion in tableDict[star].keys():
solarIonH = PA.ptoe[int(ion) - 1][PA.abIdx]
if tableDict[star][ion][0] == 0.:
continue
if ion not in [26.0, 26.1]:
# Adjust values for [X/Fe]
tableDict[star][ion][0] = tableDict[star][ion][0]\
- solarIonH\
- starFe
if ion in clusterDict.keys():
clusterDict[ion].append([tableDict[star][ion][0],\
tableDict[star][ion][3]])
else:
clusterDict[ion] = [[tableDict[star][ion][0],\
tableDict[star][ion][3]]]
if ion in catDict.keys():
catDict[ion].append([tableDict[star][ion][0],\
tableDict[star][ion][3]])
else:
catDict[ion] = [[tableDict[star][ion][0],\
tableDict[star][ion][3]]]
idxName = clusterName + ' (all)'
tableDict[idxName] = {}
for ion in clusterDict.keys():
# If each star's ab measurement for are "independent measures" of the
# cluster abundance, we should divide the stdev by sqrt(num_measures)...
# Calcs broken into separate lines for readability.
cMean = np.mean([l[0] for l in clusterDict[ion]])
cStd = np.std([l[0] for l in clusterDict[ion]])
cScoreMean = np.mean([l[1] for l in clusterDict[ion]])
tableDict[idxName][ion] = \
[cMean, cStd, len(clusterDict[ion]), cScoreMean]
idxName = clusterName + ' (dwarfs)'
tableDict[idxName] = {}
for ion in dwarfDict.keys():
dMean = np.mean([l[0] for l in dwarfDict[ion]])
dStd = np.std([l[0] for l in dwarfDict[ion]])
dScoreMean = np.mean([l[1] for l in dwarfDict[ion]])
tableDict[idxName][ion] = \
[dMean, dStd, len(dwarfDict[ion]), dScoreMean]
idxName = clusterName + ' (giants)'
tableDict[idxName] = {}
for ion in giantDict.keys():
gMean = np.mean([l[0] for l in giantDict[ion]])
gStd = np.std([l[0] for l in giantDict[ion]])
gScoreMean = np.mean([l[1] for l in giantDict[ion]])
tableDict[idxName][ion] = \
[gMean, gStd, len(giantDict[ion]), gScoreMean]
ions = sorted(list(set(ions)))
# The cluster name starts with "N", so it will be first in the list
nameList = sorted(tableDict.keys())
outfile = open(outFilename, 'w')
latexHeader = kLaTexHeader1 + '\\rhead{\\textbf{' + headerRight\
+ '}}\n\\lhead{\\textbf{' + headerLeft\
+ '}}\n\\begin{document}\n'
outfile.write(latexHeader)
# New page/table:
for tableCount in range(int(len(nameList) / 6) + 1):
outfile.write('\\begin{landscape}\n'\
+ '\\hspace*{-5cm}\n'\
+ '\\begin{tabular}{|l|l|l|l|l|l|l|')
outfile.write('}\n\\multicolumn{1}{l}{Ion}')
for name in nameList[tableCount * 6:(tableCount + 1) * 6]:
outfile.write(' & \\multicolumn{{1}}{{l}}{{{0}}}'.format(name))
outfile.write('\\\\\n\\hline\n')
# A little bit of stupidity to put FeI and FeII at the top of the table:
printIons = sorted(ions)
printIons.remove(26.)
printIons.remove(26.1)
printIons = [26.0, 26.1] + printIons
for ion in printIons:
if int(ion) == 26:
outfile.write('[{0}/H]'.format(el.getIonName(ion)))
else:
outfile.write('[{0}/Fe]'.format(el.getIonName(ion)))
for star in nameList[tableCount * 6:(tableCount + 1) * 6]:
if ion in tableDict[star].keys(
) and tableDict[star][ion][2] > 0:
outfile.write(' & {0:3.2f}$\pm${1:3.2f} ({2:d}, {3:1.1f})'.\
format(tableDict[star][ion][0],
tableDict[star][ion][1],
tableDict[star][ion][2],
tableDict[star][ion][3]))
else:
outfile.write(' & \multicolumn{1}{c|}{---}')
outfile.write('\\\\\n\\hline\n')
# Place a double line after the Fe/H measures
if ion == 26.1:
outfile.write('\\hline\n')
outfile.write('\\label{{tab:752Abs-{0}}}\n'.format(tableCount + 1) +
'\\end{tabular}\n\\end{landscape}\n' + '\\clearpage\n')
outfile.write('\\end{document}\n')
outfile.close()
def MakeTAbPlots(clusterName='NGC-0752',
starDataList=None,
ionList=STP.kAllIonList,
fileTag='',
useSubfigures=False,
referenceCorrect=False):
# Create a bunch of .ps plots with the star's effective temperature vs. [X/Fe]
# for all ions in the optional passed list. One ion per plot
if starDataList == None:
starDataList = STP.GetAllStarParms(clusterName=clusterName)
abTable = STP.GetAbTable(clusterName=clusterName,
starDataList=starDataList,
ions=ionList,
referenceCorrect=referenceCorrect)
solarFeH = PA.ptoe[25][PA.abIdx]
clusterFeH = \
0.75*np.mean([abTable[star][26.0][0] for star in abTable.keys()])+\
0.25*np.mean([abTable[star][26.1][0] for star in abTable.keys() \
if 26.1 in abTable[star].keys()])
for ion in ionList:
solarIonH = PA.ptoe[int(ion) - 1][PA.abIdx]
fig = pyplot.figure()
ax = pyplot.gca()
redGPoints = []
magGPoints = []
bluDPoints = []
cyaDPoints = []
for star in starDataList:
starName = star[0]
if starName not in abTable.keys():
continue
starIons = sorted(abTable[starName].keys())
if ion not in starIons:
continue
starParms = star[1:]
# Get the Fe/H for this star. Note: We don't do Fe/Fe comps.
if int(ion) != 26:
# If both ions are measured, weight 75/25 for FeI/FeII
if 26.0 in starIons and 26.1 in starIons:
starFe = 0.75*abTable[starName][26.0][0]\
+ 0.25*abTable[starName][26.1][0]\
- solarFeH
else:
starFe = abTable[starName][26.0][0] - solarFeH
else:
starFe = 0.
if RC.isGiantStar(starParms):
# if starParms[5] < 50:
# magGPoints.append([starParms[0],
# abTable[starName][ion][0]-solarIonH-starFe,
# abTable[starName][ion][1]])
# else:
redGPoints.append([
starParms[0],
abTable[starName][ion][0] - solarIonH - starFe,
abTable[starName][ion][1]
])
else:
# if starParms[5] < 25:
# cyaDPoints.append([starParms[0],
# abTable[starName][ion][0]-solarIonH-starFe,
# abTable[starName][ion][1]])
# else:
bluDPoints.append([
starParms[0],
abTable[starName][ion][0] - solarIonH - starFe,
abTable[starName][ion][1]
])
dMean = np.mean([l[1] for l in cyaDPoints + bluDPoints])
dStd = np.std([l[1] for l in cyaDPoints + bluDPoints])
ax.axhline(y=dMean, ls='dashed', color='b',
label=r'Dwarf Avg. (${0:4.2f}\pm{1:4.2f}$)'.\
format(dMean,dStd))
ax.axhline(y=dMean - dStd, ls='dotted', color='b')
ax.axhline(y=dMean + dStd, ls='dotted', color='b')
gMean = np.mean([l[1] for l in redGPoints + magGPoints])
gStd = np.std([l[1] for l in redGPoints + magGPoints])
ax.axhline(y=gMean, ls='dashed', color='r',
label=r'Giant Avg. (${0:4.2f}\pm{1:4.2f}$)'.\
format(gMean,gStd))
ax.axhline(y=gMean - gStd, ls='dotted', color='r')
ax.axhline(y=gMean + gStd, ls='dotted', color='r')
ax.axhline(y=0., ls='dashed', color='g', linewidth=1.0,\
label='Solar (${0:4.2f}$)'.\
format(PA.ptoe[int(ion)-1][PA.abIdx]))
pyplot.rcParams.update({'legend.fontsize': 10})
ax.legend()
if dMean > 0. and gMean > 0.:
ax.set_ylim([
min([dMean - 0.5, gMean - 0.5]),
max([dMean + 0.5, gMean + 0.5])
])
elif dMean > 0.:
ax.set_ylim([dMean - 0.5, dMean + 0.5])
elif gMean > 0:
ax.set_ylim([gMean - 0.5, gMean + 0.5])
Xs = [l[0] for l in bluDPoints]
Ys = [l[1] for l in bluDPoints]
Es = [l[2] for l in bluDPoints]
eb = ax.errorbar(Xs, Ys, yerr=Es, fmt='o', color='b')
if len(eb) > 0 and len(eb[-1]) > 0: eb[-1][0].set_linestyle('--')
# Xs = [l[0] for l in cyaDPoints]
# Ys = [l[1] for l in cyaDPoints]
# Es = [l[2] for l in cyaDPoints]
# eb=ax.errorbar(Xs, Ys, yerr=Es, fmt='s', color='c')
# if len(eb)>0 and len(eb[-1])>0: eb[-1][0].set_linestyle('--')
Xs = [l[0] for l in redGPoints]
Ys = [l[1] for l in redGPoints]
Es = [l[2] for l in redGPoints]
eb = ax.errorbar(Xs, Ys, yerr=Es, fmt='o', color='r')
if len(eb) > 0 and len(eb[-1]) > 0: eb[-1][0].set_linestyle('--')
# Xs = [l[0] for l in magGPoints]
# Ys = [l[1] for l in magGPoints]
# Es = [l[2] for l in magGPoints]
# eb=ax.errorbar(Xs, Ys, yerr=Es, fmt='s', color='m')
# if len(eb)>0 and len(eb[-1])>0: eb[-1][0].set_linestyle('--')
ionStr = el.getIonName(ion)
if int(ion) != 26:
ax.set_ylim((-0.5, 0.5))
else:
ax.set_ylim((-0.3, 0.3))
ax.set_xlabel(r'$T_{eff}$ (K)')
if int(ion) != 26:
ax.set_ylabel(r'$[{0}/Fe]$'.format(ionStr))
else:
ax.set_ylabel(r'$[{0}]$'.format(ionStr))
pyplot.savefig('{0}{1}{2}.png'.format(k.PlotDir + 'Elems/', ionStr,
fileTag),
figure=fig)
# pyplot.show()
pyplot.close(fig)
def PlotFeXx(clusterName='NGC-0752', starDataList=None, fileTag='', groupErrors=False,\
ionList=STP.kAllIonList, filterBlends=False, referenceCorrect=False):
# abTable = {starID:element/ion:[X/H, sigma, #, quality score]}
abTable=STP.GetAbTable(clusterName=clusterName, starDataList=starDataList,\
ions=ionList, filterBlends=filterBlends, referenceCorrect=referenceCorrect)
SolarFe = PA.ptoe[25][PA.abIdx]
for ion in ionList:
Xs = []
Ys = []
XErrs = []
YErrs = []
colors = []
allPts = []
SolarY = float(PA.ptoe[int(ion)-1][PA.abIdx])
for star in abTable.keys():
starAbs = abTable[star]
starFe = float(STP.GetStarFeH(starAbs))
if ion in starAbs.keys():
if not(u.is_number(starAbs[ion][0]) and \
u.is_number(starAbs[26.0][1]) and \
u.is_number(starAbs[ion][1])):
continue
adj = SolarY
if ion != 26.0:
adj+=starFe
allPts.append([float(starFe), float(starAbs[ion][0])-adj, float(starAbs[26.0][1]), float(starAbs[ion][1]), ColorLookup(star)])
yElem = EL.getIonName(ion)
fig = pyplot.figure()
axes = fig.gca()
allPts = np.array(allPts)
# allPts = np.array(zip(Xs, Ys, XErrs, YErrs, colors))
gAbs = np.array([p[1] for p in allPts if p[4]=='r']).astype(np.float)
gAvg = np.mean(gAbs)
gStd = np.std(gAbs)
gFeAbs = np.array([p[0] for p in allPts if p[4]=='r']).astype(np.float)
gFeAvg = np.mean(gFeAbs)
gFeStd = np.std(gFeAbs)
dAbs = np.array([p[1] for p in allPts if p[4]=='b']).astype(np.float)
dAvg = np.mean(dAbs)
dStd = np.std(dAbs)
dFeAbs = np.array([p[0] for p in allPts if p[4]=='b']).astype(np.float)
dFeAvg = np.mean(dFeAbs)
dFeStd = np.std(dFeAbs)
axes.axhline(y=gAvg, ls='dashed', color='r',
label=r'Giant Avg. (${0:4.2f}\pm{1:4.2f}$)'.\
format(gAvg,gStd))
axes.axhline(y=gAvg+gStd, ls='dotted', color='r')
axes.axhline(y=gAvg-gStd, ls='dotted', color='r')
axes.axhline(y=dAvg, ls='dashed', color='b',
label=r'Dwarf Avg. (${0:4.2f}\pm{1:4.2f}$)'.\
format(dAvg,dStd))
axes.axhline(y=dAvg+dStd, ls='dotted', color='b')
axes.axhline(y=dAvg-dStd, ls='dotted', color='b')
# axes.axhline(y=SolarY, ls='dashed', color='g',
# label=r'Solar ({0:4.2f})'.format(SolarY))
axes.axhline(y=0., ls='dashed', color='g',
label=r'Solar ({0:4.2f})'.format(SolarY))
Xs = np.array(allPts[:,0]).astype(np.float)
XErrs = np.array(allPts[:,2]).astype(np.float)
xMin = max(np.median(Xs)-0.3, min(Xs)-0.1)
xMax = min(np.median(Xs)+0.3, max(Xs)+0.1)
axes.set_xlim(xMin, xMax)
Ys = np.array(allPts[:,1]).astype(np.float)
YErrs = np.array(allPts[:,3]).astype(np.float)
yMin = min(np.median(Ys)-0.3, min(Ys))
yMax = max(np.median(Ys)+0.3, max(Ys))
axes.set_ylim(yMin, yMax)
axes.set_xlabel('[Fe/H]', fontsize=18)
if ion != 26.0:
axes.set_ylabel('['+yElem+'/Fe]', fontsize=18)
else:
axes.set_ylabel('['+yElem+'/H]', fontsize=18)
if groupErrors:
axes.scatter(gFeAbs, gAbs, marker='o', color='r')
eb = axes.errorbar(gFeAvg, gAvg, xerr=gFeStd,\
linestyle='None', markersize=12., marker='H', color='r', ecolor='r', \
label='Giant Mean', capsize=10., elinewidth=2, markerfacecolor='None')
eb[-1][0].set_linestyle('--')
# eb[-1][1].set_linestyle('--')
eb[-1][0].set_linewidth(2.)
# eb[-1][1].set_linewidth(2.)
axes.scatter(dFeAbs, dAbs, marker='o', color='b')
eb = axes.errorbar(dFeAvg, dAvg, xerr=dFeStd,\
linestyle='None', markersize=12., marker='H', color='b', ecolor='b', \
label='Dwarf Mean', capsize=10., elinewidth=2, markerfacecolor='None')
eb[-1][0].set_linestyle('--')
# eb[-1][1].set_linestyle('--')
eb[-1][0].set_linewidth(2.)
# eb[-1][1].set_linewidth(2.)
else:
eb = axes.errorbar(Xs, Ys, yerr=YErrs, xerr=XErrs,\
linestyle='None', marker='o', ecolor=allPts[:,4])
eb[-1][0].set_linestyle(':')
eb[-1][1].set_linestyle(':')
eb[-1][0].set_linewidth(0.5)
eb[-1][1].set_linewidth(0.5)
axes.legend()
pyplot.savefig(dirs.RelAbsDir+'Fe_'+yElem+fileTag+'.png')
pyplot.close()
def PlotAllCombos():
abTable=STP.GetAbTable()
ionsToCombine=[6.0,7.0,8.0,11.0,12.0,13.0,14.0,20.0,22.0,26.0,63.1]
allCombos = u.Cartesian(ionsToCombine,ionsToCombine)
# allCombos = u.Cartesian(STP.kAllIonList, STP.kAllIonList)
elemCombos = np.array([i for i in allCombos if i[0]<i[1]])
SolarFe = PA.ptoe[25][PA.abIdx]
for combo in elemCombos:
Xs = []
Ys = []
XErrs = []
YErrs = []
colors = []
for star in abTable.keys():
starAbs = abTable[star]
if combo[0] in starAbs.keys() and combo[1] in starAbs.keys():
starFe = 0.75*starAbs[26.0][0] + 0.25*starAbs[26.1][0] - SolarFe
SolarX = PA.ptoe[int(combo[0])-1][PA.abIdx]
Xs.append(starAbs[combo[0]][0] - starFe - SolarX)
XErrs.append(starAbs[combo[0]][1])
SolarY = PA.ptoe[int(combo[1])-1][PA.abIdx]
Ys.append(starAbs[combo[1]][0] - starFe - SolarY)
YErrs.append(starAbs[combo[1]][1])
colors.append(ColorLookup(star))
slope, intercept, rVal, pVal, stderr = linregress(Xs, Ys)
xElem = EL.getIonName(combo[0])
yElem = EL.getIonName(combo[1])
fig = pyplot.figure()
ax = fig.gca()
for pt in zip(Xs, Ys, XErrs, YErrs, colors):
if pt[4] == 'm' or pt[4]=='c':
shape='s'
else:
shape='o'
eb = pyplot.errorbar(pt[0], pt[1], yerr=pt[3], xerr=pt[2],\
linestyle='None', marker=shape, color=pt[4])
eb[-1][0].set_linestyle('--')
eb[-1][1].set_linestyle('--')
minX = min(Xs)
maxX = max(Xs)
pyplot.plot([minX,maxX],[intercept+slope*minX, intercept+slope*maxX], 'k:')
xMin = min(np.median(Xs)-0.5, minX)
xMax = max(np.median(Xs)+0.5, maxX)
ax.set_xlim(xMin, xMax)
yMin = min(np.median(Ys)-0.5, min(Ys))
yMax = max(np.median(Ys)+0.5, max(Ys))
ax.set_ylim(yMin, yMax)
pyplot.xlabel('['+xElem+'/Fe]')
pyplot.ylabel('['+yElem+'/Fe]')
ax.text(0.95, 0.01, 'Slope:{0:4.2f}, R-squared:{1:4.2f}, P-val:{2:4.2f}'.format(slope,rVal**2,pVal), fontsize=10, verticalalignment='bottom', horizontalalignment='right', transform=ax.transAxes,)
pyplot.savefig(dirs.RelAbsDir+xElem+'_'+yElem+'.png')
pyplot.close()
def MakeVPlots(clusterName='NGC-0752',
starDataList=None,
fileTag='',
filterBlends=False,
referenceCorrect=False,
useDAOSpec=False,
ions=[20.0]):
# Function plots V_turb vs. sigma [Ca/H] (sigma is the line-to-line
# standard deviation of the measured Ca lines), for a range of V_turb values.
# Intended to provide a spectroscopic confirmation/adjustment
# for photometrically-determined parameters.
if starDataList is None:
starDataList = STP.GetAllStarParms(clusterName=clusterName)
dModelFiles = mk.findDataFiles(k.DwarfModelPath)
dModelAtms, dPradks = mk.LoadModels(dModelFiles)
dCorrectDict, dReferenceLines, dLineWeights = \
RC.GetDwarfCorrections(ionList=ions,
modelAtms=dModelAtms,
pradks=dPradks)
gModelFiles = mk.findDataFiles(k.GiantModelPath)
gModelAtms, gPradks = mk.LoadModels(gModelFiles)
# Note: We're using dwarf corrections for giant stars...
# because they're better than giant corrections for the
# giant stars. This needs to be fixed. :(
gCorrectDict, gReferenceLines, gLineWeights = \
RC.GetSolarCorrections(ionList=ions,
modelAtms=dModelAtms,
pradks=dPradks)
# For now, CaI appears to work best for all stars.
# VI, Ti I/II, Fe I/II, Cr I/II also work, but not as well - (See Reddy, et al. 2012).
# ions = [20.0]
abDict = {}
colorArray=['r','orange','gold','darkgreen','navy',\
'm','saddlebrown','skyblue','hotpink']
for starParms in starDataList:
if RC.isGiantStar(starParms[1:]):
modelAtms = gModelAtms
pradks = gPradks
refLines = gReferenceLines
refDict = gCorrectDict
lineWeights = gLineWeights
else:
modelAtms = dModelAtms
pradks = dPradks
refLines = dReferenceLines
refDict = dCorrectDict
lineWeights = dLineWeights
starPoints = {}
for v in np.linspace(0.5, 3.0, 26):
parmTuple = (starParms[0], starParms[1], starParms[2], v, \
starParms[4], starParms[5], starParms[6])
abDict[v] = STP.GetAbsForStar(parmTuple, ions=ions,\
filterBlends=filterBlends, refCorrect=referenceCorrect,\
refDict=refDict, refLines=refLines, lineWeights=lineWeights,\
useDAOSpec=useDAOSpec, modelAtms=modelAtms, pradks=pradks)
for ion in abDict[v].keys():
if ion not in starPoints.keys():
starPoints[ion] = {}
if abDict[v][ion][0] == 0.:
continue
starPoints[ion][v] = abDict[v][ion][1]
colorIdx = 0
ymaxes = []
for ion in starPoints.keys():
Xs = sorted(np.array(list(starPoints[ion].keys())))
if len(Xs) == 0 or ion in STP.SynthAbsDict.keys():
continue
Ys = np.array([starPoints[ion][x] for x in Xs])
if len(Xs) < 2 or len(Ys) < 2:
continue
Ys = Ys / min(Ys)
ymaxes.append(max(Ys))
try:
minV = Xs[np.where(Ys == min(Ys))[0][0]]
except IndexError:
continue
pyplot.plot(Xs,
Ys,
label=r'$({1}) V_{{turb}}={0:3.1f}km/sec$'.format(
minV, el.getIonName(ion)),
color=colorArray[colorIdx])
pyplot.scatter(Xs, Ys, color=colorArray[colorIdx])
pyplot.axvline(minV, linestyle=':', color=colorArray[colorIdx])
colorIdx += 1
if colorIdx == len(colorArray): colorIdx = 0
ax = pyplot.gca()
ax.set_xlabel(r'$V_{{turb}} km/s$')
ax.set_ylabel('Normalized [X/H] variance')
ax.set_ylim((0., min(5.0, max(ymaxes))))
pyplot.legend(fontsize=8)
pyplot.savefig(k.ParmPlotDir + 'Vturb/' + starParms[0] + fileTag +
'.png')
pyplot.close()
def MakeTeffIonPlots(clusterName='NGC-0752',
starDataList=None,
fileTag='',
filterBlends=False,
referenceCorrect=False,
useDAOSpec=False):
# Function plots Teff vs. [TiI/TiII] for a range of temperatures.
# Intended to provide a spectroscopic confirmation/adjustment
# for photometrically-determined parameters.
if starDataList is None:
starDataList = STP.GetAllStarParms(clusterName=clusterName)
dModelFiles = mk.findDataFiles(k.DwarfModelPath)
dModelAtms, dPradks = mk.LoadModels(dModelFiles)
gModelFiles = mk.findDataFiles(k.GiantModelPath)
gModelAtms, gPradks = mk.LoadModels(gModelFiles)
# Want to watch TiI/TiII
ions = [22.0, 22.1]
abDict = {}
dTeffRange = np.linspace(4500, 7000, 101)
gTeffRange = np.linspace(3500, 6000, 101)
for TeffIdx in range(len(dTeffRange)):
tempParmList = []
for s in starDataList:
if s[1] < k.giantTeffLimit and s[2] < k.giantLogGLimit:
Teff = gTeffRange[TeffIdx]
else:
Teff = dTeffRange[TeffIdx]
tempParmList.append((s[0], Teff, s[2], s[3], s[4], s[5], s[6]))
abDict[Teff] = STP.GetAbTable(clusterName=clusterName,
starDataList=tempParmList,
ions=ions,
filterBlends=filterBlends,
referenceCorrect=referenceCorrect,
useDAOSpec=useDAOSpec,
gModelAtms=gModelAtms,
gPradks=gPradks,
dPradks=dPradks,
dModelAtms=dModelAtms)
starPoints = {}
for Teff in abDict.keys():
for star in abDict[Teff].keys():
if star not in starPoints.keys():
starPoints[star] = {}
# TiI/TiII points:
if 22.0 in abDict[Teff][star].keys() and \
22.1 in abDict[Teff][star].keys():
if 22.0 not in starPoints[star].keys():
starPoints[star][22.0] = {}
starPoints[star][22.0][Teff] =\
abDict[Teff][star][22.0][0] - abDict[Teff][star][22.1][0]
for star in starPoints.keys():
fig = pyplot.figure()
starData = [s for s in starDataList if s[0] == star]
isGiant = False
if len(starData) > 0: isGiant = STP.isGiantStar(starData[0][1:])
for ion in starPoints[star].keys():
Xs = np.array(sorted(starPoints[star][ion].keys()))
Ys = np.array([starPoints[star][ion][x] for x in Xs])
if isGiant:
Xs = Xs - 1000.
interpTs = np.interp([-0.1, 0., 0.1], Ys, Xs)
pyplot.scatter(Xs, Ys,
label=r'${0}({1:4.0f}^{{+{2:3.0f}}}_{{-{3:3.0f}}}$)'.\
format(el.getIonName(ion),interpTs[1],\
interpTs[1]-interpTs[0],\
interpTs[2]-interpTs[1]), marker='.')
pyplot.axhline(0.0, linestyle=':')
ax = pyplot.gca()
ax.set_xlabel(r'$T_{{eff}}$')
ax.set_ylabel('[TiI/TiII]')
pyplot.legend()
pyplot.savefig(k.ParmPlotDir + 'Teff/' + star + fileTag + '_TiRel.png')
pyplot.close()
def XPAbPlot(points,
starName,
ion,
fileTag='',
plotTitle='',
pointLabels=None,
showTrendLine=False):
# Plot the Excitation potential vs abundance for the passed points.
# The passed data, in the array 'points' is of the form:
# [[Ex. Pot, [X/H], EQW (mA), wl](A), ...]
# For now, just bailing if no points were passed
if len(points) == 0:
return
assert len(points) > 0
# We're rounding 'cause...Python.
XPs = np.around(points[:, 0], 4)
Abs = points[:, 1]
fig = pyplot.figure()
axes = pyplot.gca()
Xmin = min(XPs) * 0.9
if Xmin == 0.:
Xmin = -0.25
Xmax = max(XPs) + 0.25
Ymin = min(Abs) - 0.2
Ymax = max(Abs) + 0.2
pyplot.scatter(XPs, Abs, figure=fig, marker='o', s=9)
# Write in a (tiny) label next to each point
if pointLabels is not None:
for coord in zip(XPs.tolist(), Abs.tolist(), pointLabels):
# Place the label below and right of the point
pyplot.text(coord[0] + np.random.random() * 0.04 * (Xmax - Xmin),
coord[1] - np.random.random() * 0.06 * (Ymax - Ymin),
coord[2],
color='k',
fontsize='xx-small')
# Fit a line, if desired
if showTrendLine:
slope, intercept, rVal, pVal, err = sp.stats.linregress(XPs, Abs)
pyplot.plot([Xmin, Xmax],
[intercept + slope * Xmin, intercept + slope * Xmax], 'g:')
axes.text(0.95, 0.01, 'Slope:{0:4.2f}, R-squared:{1:4.2f}'.format\
(slope,rVal**2), fontsize=9, verticalalignment='bottom',\
horizontalalignment='right', transform=axes.transAxes,)
# Show mean and standard deviation range:
mean = np.mean(Abs)
std = np.std(Abs)
axes.axhline(y=mean,
ls='dashed',
color='r',
label=r'$[{0}/H]:{1:4.2f}\pm{2:4.2f}$'.format(
el.getIonName(ion), mean, std))
axes.axhline(y=mean - std, ls='dotted', color='r')
axes.axhline(y=mean + std, ls='dotted', color='r')
pyplot.plot([Xmin, Xmax],
[intercept + slope * Xmin, intercept + slope * Xmax], 'g:')
pyplot.plot([Xmin, Xmax],
[intercept + slope * Xmin, intercept + slope * Xmax], 'g:')
# Axes labels and ranges
axes.set_ylim([Ymin, Ymax])
axes.set_xlim([Xmin, Xmax])
axes.set_xlabel('Excitation Potential (eV)')
axes.set_ylabel('Abundance [X/H]')
axes.legend()
if plotTitle is not '':
axes.set_title(plotTitle)
saveDirName = dirs.XPAbPlotsDir + el.getIonName(ion) + '/'
try:
os.stat(saveDirName)
except:
os.mkdir(saveDirName[:-1])
pyplot.savefig('{0}{1}_{2}{3}.png'.format(saveDirName, starName,
el.getIonName(ion), fileTag),
figure=fig)
pyplot.close()
def MakeSolarCompTable(outFilename=k.TempAbOutFilename,
headerLeft='',
headerRight=''):
# Function creates a LaTeX table with elemental abundances as calculated from
# our Solar reference spectrum, based on a "quality" measurement of each line.
# Each column of the table represents a measurement using lines of a particular
# quality or better. The final column is represents all of the measured lines.
corrections, lines, weights = RC.GetSolarCorrections()
# We're going to create one column for each "quality" setting from the
# returned weights list. Basically, each weight is a quality level.
# The columnDict contains:
# {weight:{ion:[ab,std,#lines],...},...}
columnDict = {}
for wt in k.AbWeights:
columnDict[wt] = {}
allIonList = sorted(lines.keys())
for ion in allIonList:
ionLines = lines[ion]
# A single line will not show up as a list of one item. Rather, the
# entire list will be that one line's parameters...grrr.
if not u.is_list(ionLines[0]):
ionLines = [ionLines]
for wt in k.AbWeights:
wtLines = np.array([line for line in ionLines \
if line[0] in weights[ion] and weights[ion][line[0]] >= wt])
if len(wtLines) > 0:
asplundCorr = PA.ptoe[int(ion) - 1][PA.abIdx]
columnDict[wt][ion] = [
np.mean(wtLines[:, 5]) + asplundCorr,
np.std(wtLines[:, 5]),
len(wtLines)
]
# Create a nice column title for each quality type:
nameList = [
r'$\Delta\leq{0:1.2f}$'.format(r[1]) for r in k.AbWeightRanges[:-1]
]
nameList.append('All lines')
outfile = open(outFilename, 'w')
latexHeader = STP.kLaTexHeader1 + '\\rhead{\\textbf{' + headerRight\
+ '}}\n\\lhead{\\textbf{' + headerLeft\
+ '}}\n\\begin{document}\n'
outfile.write(latexHeader)
outfile.write('\\begin{landscape}\n'\
+ '\\hspace*{-5cm}\n'\
+ '\\begin{tabular}{|l|l|l|l|l|l|l|l|l|l|')
outfile.write(
'}\n\\multicolumn{1}{l}{Ion} & \\multicolumn{1}{l}{Asplund (2009)}')
for name in nameList:
outfile.write(' & \\multicolumn{{1}}{{l}}{{{0}}}'.format(name))
outfile.write('\\\\\n\\hline\n')
for ion in allIonList:
outfile.write('{0} & {1:1.2f}$\pm${2:1.2f}'.format(el.getIonName(ion),\
PA.ptoe[int(ion)-1][PA.abIdx],\
PA.ptoe[int(ion)-1][PA.solarErrIdx]))
for wt in k.AbWeights:
if ion in columnDict[wt].keys() and columnDict[wt][ion][2] > 0:
outfile.write(' & {0:1.2f}$\pm${1:1.2f} ({2:d})'.\
format(columnDict[wt][ion][0]-PA.ptoe[int(ion)-1][PA.abIdx],
columnDict[wt][ion][1],
columnDict[wt][ion][2]))
else:
outfile.write(' & \\multicolumn{1}{c|}{---} ')
outfile.write('\\\\\n\\hline\n')
outfile.write('\\label{{tab:SolarAbs}}\n' +
'\\end{tabular}\n\\end{landscape}\n' + '\\clearpage\n')
outfile.write('\\end{document}\n')
outfile.close()
def COGPlot(clusterName,
starData,
ions,
fileTag='',
labelPlot=True,
labelPoints=False,
modelAtms=None,
pradks=None,
makeQualityPlot=False):
# Make Curve of Growth (COG) plots for the passed star
# One element per plot.
# If the makeQualityPlot flag is set, a second plot will be made, with the
# points shaded relative to how well they correspond to the linear fit of
# measurements with similar excitation potentials.
starName = starData[0]
starParmTuple = tuple(starData[1:])
isGiant = RC.isGiantStar(starParmTuple)
if isGiant:
modelPath = k.GiantModelPath
else:
modelPath = k.DwarfModelPath
if modelAtms == None or pradks == None:
modelFiles = mk.findDataFiles(modelPath)
modelAtms, pradks = mk.LoadModels(modelFiles)
abdict, uncorrLines, unusedMin, unusedMax = \
AB.CalcAbsAndLines(clusterName+' '+starName,
tuple(starData[1:6]), ionList=ions,
modelAtms=modelAtms, pradks=pradks)
for ion in ions:
# One plot per ion.
if ion not in uncorrLines.keys():
print('No {0:2.1f} lines for {1}.'.format(ion, starName))
continue
if labelPlot:
plotLabel = 'Curve of Growth for [{2}/H] in {0} {1}.'.\
format(clusterName, starName, el.getIonName(ion))
else:
plotLabel = ''
if labelPoints:
# Label the points with the excitation potential
pointLabels = ['{0:2.3f}'.format(point[1]) \
for point in np.array(uncorrLines[ion])]
else:
pointLabels = None
ps.COGPlot(np.array(uncorrLines[ion]),
starName,
ion,
fileTag=fileTag,
plotTitle=plotLabel,
pointLabels=pointLabels)
if makeQualityPlot:
if labelPlot:
plotLabel = 'Measurement quality for [{2}/H] in {0} {1}.'.\
format(clusterName, starName, el.getIonName(ion))
else:
plotLabel = ''
ps.QualityPlot(np.array(uncorrLines[ion]),
starName,
ion,
fileTag=fileTag + 'QP',
plotTitle=plotLabel,
pointLabels=pointLabels)
