def plotEmLines(EADir, galaxy, plotType, emLineInd, emLineFancy, nFP, dataInd):
units = '$' + galaxy.myHDU[dataInd].header['BUNIT'] + '$'
# galaxy.printInfo()
hex_at_Cen, gal_at_Cen = fE.getCenters(galaxy.myHDU, galaxy.PLATEIFU,
dataInd)
print("plotEmLines(" + galaxy.PLATEIFU + ")")
# cycle through 11 chosen wavelengths
for j in emLineInd.keys():
# print(plotType + ": " + j)
slice = EmissionLineSlice.EmissionLineSlice(galaxy, emLineInd[j], j,
emLineFancy[j], units)
############ data Correction #############
# dC.printDataInfo(dataMat)
############ action #############
# average = get_average(galaxy, slice)
# print(galaxy.PLATEIFU, slice.myName, average)
actuallyPlot(EADir, galaxy, plotType, nFP, dataInd, slice)
def plotReSpectra(EADir, galaxy, DAPtype, plotType, dataInd, dataCube, waveVec):
nFP = dF.assure_path_exists(os.path.join(
EADir, DAPtype, 'PLOTS', 'DAP', galaxy.PLATEIFU, 'ReSpectra'))
# unitsY = hdu[0].header['BUNIT']
unitsX = 'Wavelength (Angstroms)'
# unitsY = '$' + unitsY + '$'
# unitsX = '$' + unitsX + '$'
unitsY = '$f_{\\lambda}$ ' + \
' (' + '$10^{-17}$' + 'erg/s/cm' + '$^{2}$' + '/Ang)'
hex_at_Cen, gal_at_Cen = fE.getCenters(
galaxy.myHDU, galaxy.PLATEIFU, dataInd)
refPnt = [hex_at_Cen[1], hex_at_Cen[0]]
radii = [0.25, .5, 1.0]
# radii = [1, 2, 3]
# ReSpectra, dictRadiiSpaxNum = createRadialSpectra(waveVec, dataCube, radii, refPnt, Re)
NormalizedReSpectra, dictRadiiSpaxNum = createRadialSpectra(
waveVec, dataCube, radii, refPnt, galaxy.Re, normWavelength=5500)
# ReSpectra, dictWedgeSpaxNum = createWedgeSpectra(dataCube, radii, refPnt, Re, hdu, plate_IFU, dataInd, center)
# plotSideBySideSpectra(plate_IFU, radii, waveVec, ReSpectra, dictRadiiSpaxNum, unitsX, unitsY, EADir, nFP, '123')
# plotStackedSpectra(plate_IFU, radii, waveVec, ReSpectra, dictRadiiSpaxNum, unitsX, unitsY, EADir, nFP)
plotStackedSpectra(galaxy.PLATEIFU, radii, waveVec, NormalizedReSpectra, dictRadiiSpaxNum,
unitsX, unitsY, EADir, nFP, extraLabel='Normed')
def plotLonePlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
plotType='',
vmax=None,
vmin=None):
hex_at_Cen, gal_at_Cen = fE.getCenters(galaxy.myHDU, galaxy.PLATEIFU,
dataInd)
# print("Masking " + str(round(float(sum(sum(maskMat)) * 100) /
# (maskMat.shape[0] * maskMat.shape[1]), 2)) + ' percent of the data matrix; ~40 percent is great data')
aspectRatio = 34.0 / 13
height = 19.0 / 2
fig = plt.figure(figsize=(height * aspectRatio / 2, height))
fig.subplots_adjust(hspace=0.25)
# plt.figure()
plt.suptitle(plotTitle, fontsize=fontsize + 5, fontweight='bold')
is_eps = True
axes1 = plt.subplot(1, 1, 1)
if is_eps:
axes1.set_rasterized(True)
spatiallyResolvedPlot(galaxy, plotType, newFileName, dataInd, slice,
hex_at_Cen, gal_at_Cen, vmax, vmin, axes1)
# fig.tight_layout()
try:
# plt.show()
# print(jello)
# print("saving to " + os.path.join(nFP, newFileName + 'lone.png'))
if is_eps:
plt.savefig(os.path.join(nFP, newFileName + 'lone.eps'),
format='eps')
else:
plt.savefig(os.path.join(nFP, newFileName + 'lone.png'))
except AttributeError:
print("Error generating plots. Plot not saved :: " +
os.path.join(nFP, newFileName + '.png'))
#print(jello)
plt.close()
def plotQuadPlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
vmax=None,
vmin=None):
hex_at_Cen, gal_at_Cen = fE.getCenters(galaxy.myHDU, galaxy.PLATEIFU,
dataInd)
# print("Masking " + str(round(float(sum(sum(maskMat)) * 100) /
# (maskMat.shape[0] * maskMat.shape[1]), 2)) + ' percent of the data matrix; ~40 percent is great data')
aspectRatio = 17.0 / 13
height = 19
fig = plt.figure(figsize=(height * aspectRatio, height))
fig.subplots_adjust(hspace=0.25)
# plt.figure()
plt.suptitle(plotTitle, fontsize=fontsize + 5, fontweight='bold')
axes1 = plt.subplot(2, 2, 1)
opticalImage(EADir, galaxy, dataInd, axes1)
# dOP.plotHexagon(axes1, plate_IFU)
axes2 = plt.subplot(2, 2, 2)
spatiallyResolvedPlot(galaxy, "", newFileName, dataInd, slice, hex_at_Cen,
gal_at_Cen, vmax, vmin, axes2)
plotAxisCrossSections(galaxy, slice, hex_at_Cen, gal_at_Cen, axes2)
# fig.tight_layout()
try:
# plt.show()
# print(jello)
print("saving to " + os.path.join(nFP, newFileName + 'quad.png'))
plt.savefig(os.path.join(nFP, newFileName + 'quad.png'))
except AttributeError:
print("Error generating plots. Plot not saved :: " +
os.path.join(nFP, newFileName + '.png'))
#print(jello)
plt.close()
def plotReSpectra(EADir, galaxy, DAPtype, plotType, dataInd, dataCube,
waveVec):
print("plotReSpectra(" + galaxy.PLATEIFU + ")")
nFP = dF.assure_path_exists(
os.path.join(EADir, DAPtype, 'PLOTS', 'DAP', galaxy.PLATEIFU,
'ReSpectra'))
# unitsY = hdu[0].header['BUNIT']
unitsX = '$\\lambda$ (Ang)'
# unitsY = '$' + unitsY + '$'
# unitsX = '$' + unitsX + '$'
hex_at_Cen, gal_at_Cen = fE.getCenters(galaxy.myHDU, galaxy.PLATEIFU,
dataInd)
refPnt = [hex_at_Cen[1], hex_at_Cen[0]]
radii_buckets = [(0, 1), (1, 2), (2, 3)]
normed = True
eps = True
if normed:
unitsY = '$f_{\\lambda}$ / $f_{5500 nm}$'
else:
unitsY = '$f_{\\lambda}$ ' + \
' (' + '$10^{-17}$' + 'erg/s/cm' + '$^{2}$' + '/Ang)'
ReSpectraValues, dictRadiiSpaxNum = createRadiiRangesBuckets(
waveVec,
dataCube,
radii_buckets,
refPnt,
galaxy.Re,
normWavelength=5500 if normed else None)
# write_csv(nFP, galaxy.PLATEIFU, waveVec, radii_buckets, ReSpectraValues)
# plotSideBySideSpectra(galaxy.PLATEIFU, radii_buckets, waveVec, ReSpectraValues, dictRadiiSpaxNum,
# unitsX, unitsY, EADir, nFP, normed, eps)
plotSharingAxesSpectra(galaxy.PLATEIFU, radii_buckets, waveVec,
ReSpectraValues, dictRadiiSpaxNum, unitsX, unitsY,
EADir, nFP, normed, eps)
def createWedgeSpectra(dataCube, radii, refPnt, Re, hdu, plate_IFU, dataInd,
center):
ReSpectra = [np.zeros(dataCube.shape[0]) for i in range(len(radii) * 4)]
spaxCounts = np.zeros(len(radii) * 4)
dictWedgeSpaxNum = {}
hex_at_Cen, gal_at_Cen = fE.getCenters(hdu, plate_IFU, dataInd)
axisCoordMaj, mMaj, bMaj = pT.getAxisLineProperties(
plate_IFU, 'major', center, gal_at_Cen, hex_at_Cen)
axisCoordMin, mMin, bMin = pT.getAxisLineProperties(
plate_IFU, 'minor', center, gal_at_Cen, hex_at_Cen)
wedgeLabelMat = createWedgeLabelMat(dataCube[0].shape, radii, Re, refPnt,
mMaj, bMaj, mMin, bMin)
# plt.figure()
# plt.imshow(wedgeLabelMat, origin='lower', interpolation='nearest')
# plt.colorbar()
# plt.show()
# print(jello)
for y in range(wedgeLabelMat.shape[0]):
for x in range(wedgeLabelMat.shape[1]):
for mod in range(1, 5):
if wedgeLabelMat[y, x] % 5 == mod:
currDist = mF.calculateDistance(x, y, refPnt[0], refPnt[1])
for r in range(len(radii)):
if currDist <= radii[r] * Re:
index = mod + r * 5 - 1
if index > 4:
index -= 1
if index > 9:
index -= 1
ReSpectra[index] = ReSpectra[index] + \
dataCube[:, y, x]
return ReSpectra, dictWedgeSpaxNum
def createWedgeSpectra(dataCube, radii, refPnt, Re, hdu, plate_IFU, dataInd, center):
ReSpectra = [np.zeros(dataCube.shape[0]) for i in range(len(radii) * 4)]
spaxCounts = np.zeros(len(radii) * 4)
dictWedgeSpaxNum = {}
hex_at_Cen, gal_at_Cen = fE.getCenters(hdu, plate_IFU, dataInd)
axisCoordMaj, mMaj, bMaj = pT.getAxisLineProperties(
plate_IFU, 'major', center, gal_at_Cen, hex_at_Cen)
axisCoordMin, mMin, bMin = pT.getAxisLineProperties(
plate_IFU, 'minor', center, gal_at_Cen, hex_at_Cen)
wedgeLabelMat = createWedgeLabelMat(
dataCube[0].shape, radii, Re, refPnt, mMaj, bMaj, mMin, bMin)
# plt.figure()
# plt.imshow(wedgeLabelMat, origin='lower', interpolation='nearest')
# plt.colorbar()
# plt.show()
# print(jello)
for y in range(wedgeLabelMat.shape[0]):
for x in range(wedgeLabelMat.shape[1]):
for mod in range(1, 5):
if wedgeLabelMat[y, x] % 5 == mod:
currDist = mF.calculateDistance(x, y, refPnt[0], refPnt[1])
for r in range(len(radii)):
if currDist <= radii[r] * Re:
index = mod + r * 5 - 1
if index > 4:
index -= 1
if index > 9:
index -= 1
ReSpectra[index] = ReSpectra[index] + \
dataCube[:, y, x]
return ReSpectra, dictWedgeSpaxNum
def plotQuadPlot(EADir, galaxy, nFP, dataInd, slice, newFileName, plotTitle, vmax=None, vmin=None):
hex_at_Cen, gal_at_Cen = fE.getCenters(
galaxy.myHDU, galaxy.PLATEIFU, dataInd)
# print("Masking " + str(round(float(sum(sum(maskMat)) * 100) /
# (maskMat.shape[0] * maskMat.shape[1]), 2)) + ' percent of the data matrix; ~40 percent is great data')
aspectRatio = 17.0 / 13
height = 19
fig = plt.figure(figsize=(height * aspectRatio, height))
fig.subplots_adjust(hspace=0.25)
# plt.figure()
plt.suptitle(plotTitle, fontsize=fontsize + 5, fontweight='bold')
axes1 = plt.subplot(2, 2, 1)
opticalImage(EADir, galaxy, dataInd, axes1)
# dOP.plotHexagon(axes1, plate_IFU)
axes2 = plt.subplot(2, 2, 2)
spatiallyResolvedPlot(galaxy, "", newFileName, dataInd,
slice, hex_at_Cen, gal_at_Cen, vmax, vmin, axes2)
simple = 'No'
if simple == 'No':
plotAxisCrossSections(galaxy, slice, hex_at_Cen, gal_at_Cen, axes2)
# fig.tight_layout()
try:
#plt.show()
#print(jello)
plt.savefig(os.path.join(nFP, newFileName + '.png'))
except AttributeError:
print("Error generating plots. Plot not saved :: "+ os.path.join(nFP, newFileName + '.png'))
#print(jello)
plt.close()
def plot(self, EADir, galaxy, plotType):
if plotType == 'sfh':
plotSFH(EADir, galaxy)
else:
if plotType == 'flux_elines':
if not galaxy.myFilename.startswith(plotType):
print("No plots of type (" + plotType +
") to make for the file " + galaxy.myFilename)
return
if plotType == 'indices.cs':
if not galaxy.myFilename.startswith(plotType[:7]):
print("No plots of type (" + plotType +
") to make for the file " + galaxy.myFilename)
return
galaxy.setCenterType('HEX')
galaxy.pullRe(EADir, 'MPL-4')
NAXIS3 = fE.getNAXIS3(galaxy.myHDU)
titleHdr = fE.getTitleHeaderPrefix(galaxy.myHDU)
dataInd = 0
dictPlotTitles_Index, dictPlotTitles_Error, dictPlotTitles_Pair = self.createDictionaries(
galaxy, NAXIS3, titleHdr, dataInd)
PIPE3D_Dir = os.path.join(EADir, "MPL-4", "PLOTS", "PIPE3D")
if plotType == 'requested':
requestedWithin = [['velocity', 'stellar population'], [
'Ha'], ['Hd'], ['Halpha']]
dictPlotTitles_Index, dictPlotTitles_Error, dictPlotTitles_Pair = self.removeNonRequested(
dictPlotTitles_Index, dictPlotTitles_Error, dictPlotTitles_Pair, requestedWithin)
nFP = dF.assure_path_exists(os.path.join(
PIPE3D_Dir, plotType, galaxy.PLATEIFU))
nFPraw = ''
else:
nFP = dF.assure_path_exists(os.path.join(
PIPE3D_Dir, galaxy.PLATEIFU, plotType))
nFPraw = dF.assure_path_exists(os.path.join(
PIPE3D_Dir, galaxy.PLATEIFU, plotType, 'RAW'))
if not bool(dictPlotTitles_Index):
print("No plots of type (" + plotType +
") to make for the file " + galaxy.myFilename)
return
elif nFPraw != '':
hex_at_Cen, gal_at_Cen = fE.getCenters(
galaxy.myHDU, galaxy.PLATEIFU, dataInd)
for key in dictPlotTitles_Index.keys():
if key in dictPlotTitles_Error.values():
continue
dataMat, maskMat, newFileName, plotTitle, units = self.prepData(
dictPlotTitles_Index, key, galaxy, dataInd, NAXIS3)
if dataMat is None:
continue
aspectRatio = 16.0 / 13
height = 10
fig = plt.figure(figsize=(aspectRatio * height, height))
plt.suptitle(galaxy.PLATEIFU + " :: " + newFileName)
axes = plt.gca()
slice = self.createSlice(dataMat, maskMat, units)
pF.spatiallyResolvedPlot(galaxy,
plotType,
newFileName,
dataInd,
slice,
hex_at_Cen,
gal_at_Cen,
None,
None,
axes)
# fig.tight_layout()
# plt.show()
# print(jello)
plt.savefig(os.path.join(nFPraw,newFileName + '.png'))
# print(jello)
plt.close()
if bool(dictPlotTitles_Error):
for key in dictPlotTitles_Error.keys():
dataMat, maskMat, newFileName, plotTitle, units = self.prepData(
dictPlotTitles_Index, key, galaxy, dataInd, NAXIS3)
if dataMat is None:
continue
keyOfError = dictPlotTitles_Error[key]
errMat = galaxy.myHDU[dataInd].data[dictPlotTitles_Index[keyOfError]]
slice = self.createSlice(dataMat, maskMat, units)
slice.setError(errMat)
pF.plotQuadPlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
vmax=None,
vmin=None)
if bool(dictPlotTitles_Pair):
for key in dictPlotTitles_Pair.keys():
dataMat1, maskMat1, newFileName1, plotTitle1, units1 = self.prepData(
dictPlotTitles_Index, key, galaxy, dataInd, NAXIS3)
dataMat2, maskMat2, newFileName2, plotTitle2, units2 = self.prepData(
dictPlotTitles_Index, dictPlotTitles_Pair[key], galaxy, dataInd, NAXIS3)
if dataMat1 is None or dataMat2 is None:
continue
slice1 = self.createSlice(dataMat1, maskMat1, units1)
slice2 = self.createSlice(dataMat2, maskMat2, units2)
pF.plotComparisonPlots(galaxy,
dataInd,
nFP,
EADir,
plotType,
newFileName1,
newFileName2,
slice1,
slice2,
hex_at_Cen,
gal_at_Cen
)
def plot(self, EADir, galaxy, plotType):
if plotType == 'sfh' and self.DAPtype == 'MPL-4':
plotSFH(EADir, galaxy)
else:
if not self.are_there_plots_to_make(galaxy.myFilename, plotType):
return
# print(galaxy.myFilename)
# print(plotType)
PIPE3D_Dir = os.path.join(EADir, self.DAPtype, "PLOTS", "PIPE3D")
# print("PIPE3D_Dir=" + str(PIPE3D_Dir))
galaxy.setCenterType('HEX')
galaxy.pullRe(EADir, self.DAPtype)
# print("Re=" + str(galaxy.Re))
NAXIS3 = fE.getNAXIS3(galaxy.myHDU)
# print("NAXIS3=" + str(NAXIS3))
titleHdr = fE.getTitleHeaderPrefix(galaxy.myHDU)
# print("titleHdr=" + str(titleHdr))
dataInd = 0
# print("dataInd=" + str(dataInd))
plotsToMake = self.createDictionaries(galaxy,
NAXIS3,
titleHdr,
dataInd)
numberOfNormalPlotsToMake = sum([1 for p in plotsToMake.keys() if 'index' in plotsToMake[p]])
numberOfErrorPlotsToMake = sum([1 for p in plotsToMake.keys() if 'error' in plotsToMake[p]])
numberOfPairPlotsToMake = sum([1 for p in plotsToMake.keys() if 'pair' in plotsToMake[p]])
print(
"normalPlots=" + str(numberOfNormalPlotsToMake),
"errorPlots=" + str(numberOfErrorPlotsToMake),
"pairPlots=" + str(numberOfPairPlotsToMake)
)
if plotType == 'requested' or plotType == 'requested2':
# if requested plots then remove unecessary plot titles and change directory
requestedWithin = [
['velocity', 'stellar population'],
['Ha'],
['Hd'],
['Halpha']
]
plotsToMake = self.removeNonRequested( plotsToMake, requestedWithin )
numberOfNormalPlotsToMake = sum([1 for p in plotsToMake.keys() if 'index' in plotsToMake[p]])
numberOfErrorPlotsToMake = sum([1 for p in plotsToMake.keys() if 'error' in plotsToMake[p]])
numberOfPairPlotsToMake = sum([1 for p in plotsToMake.keys() if 'pair' in plotsToMake[p]])
print(
"normalPlots=" + str(numberOfNormalPlotsToMake),
"errorPlots=" + str(numberOfErrorPlotsToMake),
"pairPlots=" + str(numberOfPairPlotsToMake)
)
if numberOfNormalPlotsToMake == 0:
print("No plots of type (" + plotType +
") to make for the file " + galaxy.myFilename)
return
nFP, nFPraw = self.create_directories(plotType, PIPE3D_Dir, galaxy.PLATEIFU)
hex_at_Cen, gal_at_Cen = fE.getCenters(
galaxy.myHDU, galaxy.PLATEIFU, dataInd)
for rawPlotTitle, plotInfo in plotsToMake.items():
dataMat, maskMat, newFileName, plotTitle, units = self.prepData(
plotInfo['index'],
rawPlotTitle,
galaxy,
dataInd,
NAXIS3
)
if dataMat is None:
return
slice = self.createSlice(dataMat, maskMat, units)
if nFPraw != '':
try:
self.plotRaw(galaxy,
newFileName,
dataInd,
plotType,
slice,
hex_at_Cen,
gal_at_Cen,
nFPraw)
except Exception as e:
print(e)
plt.close()
continue
if numberOfNormalPlotsToMake < 20:
pF.plotDuoPlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
plotType,
vmax=None,
vmin=None)
if 'error' in plotInfo.keys():
errorPlotTitle = plotInfo['error']
errMat = galaxy.myHDU[dataInd].data[plotsToMake[errorPlotTitle]['index']]
slice.setError(errMat)
try:
pF.plotQuadPlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
vmax=None,
vmin=None)
except Exception as e:
plt.close()
print(e)
if numberOfNormalPlotsToMake >= 20:
pF.plotDuoPlot(EADir,
galaxy,
nFP,
dataInd,
slice,
newFileName,
plotTitle,
vmax=None,
vmin=None)
if 'pair' in plotInfo.keys():
dataMat2, maskMat2, newFileName2, plotTitle2, units2 = self.prepData(
plotInfo['index'], plotsToMake[plotInfo['pair']]['index'], galaxy, dataInd, NAXIS3)
if dataMat2 is None:
return
slice2 = self.createSlice(dataMat2, maskMat2, units2)
pF.plotComparisonPlots(galaxy,
dataInd,
nFP,
EADir,
plotType,
newFileName,
newFileName2,
slice,
slice2,
hex_at_Cen,
gal_at_Cen)
return