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StarCluster.py
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StarCluster.py
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'''
@ autor: Xuan
@ mail: [email protected]
Conjunto de funciones para leer imagenes .FIT y obtener cantidades fotometricas
Lee los .FIT, obtiene estrellas, permite obtener calibraciones, etc.
Las imagenes deben estar:
- Alineadas
- Contener el filtro en la cabecera (L, R, G/V, B) (recomendable, aunque se pueden introducir a mano)
- Para obtener todas las cantidades, deben existir al menos medidas para filtos R,G,B
- Debe existir una estrella de referencia y se deben conocer sus datos y posicion en la imagen
========================================================================================================
========= Resumen de contenidos
Conjunto de funciones para derivar cantidades fisicas y realizar parametrizaciones.
Temperatura, luminosidad, magnitud absoluta, radio estelar, etcetera.
Clase Star
Input: magnitud para cada filtro (ya calibrada), posicion en la imagen...
Metodos para calcular todas las cantidades fisicas
ClaseStarCluster
Inputs:
- Path a las imagenes (y filtros en caso de que no esten en las cabezeras)
- Area de interes
- Estrella de referencia (objeto Star), debe contener posicion y magnitudes
- Distancia al cumulo
- Nombre del cumulo
- Otros parametros de analisis (fwhm de ajuste de las estrellas, umbral respecto el fondo, etc)
Metodos:
- Resta el fondo
- Calibra magnitudes
- Identifica estrellas y dibuja area de referencia, 'sources' identificadas, etc
- Crea los objetos Star a partir de los diferentes filtros, calculando todas las magnitudes fisicas posibles
- Produce imagenes y tablas de la identificacion y calibracion y tablas de datos como output del analisis
Clase StarPlotter
Inputs: path a la tabla de datos (output de StarCluster) y parametros de estilo
Dibuja el diagrama HR y otras representaciones graficas
==============================================================================================
REQUISITOS (software)
- python 2.7 (no he probado si funciona en python 3.x)
- numpy
- matplotlib
- astropy y sus requisitos
- photoutils y sus requisitos
==============================================================================================
>> Ejemplo para trabajar con 'sources' (estellas candidatas en un filtro). Puedes hacer esto
>> para identificar el area del cumulo y la posicion (en pixeles) de las estrellas de referencia:
areaCluster = [800, 1200, 800, 1200] # De referencia, iremosmo dificandolo
fr = StarCluster('data/M29/', area = areaCluster)
fr.RemoveBkgImages()
fr.SetBkgSigmaThr(4)
fr.SetSourceFWHM(5)
fr.SetSourceRadius(10)
fr.GetListOfBrightestSources('V', 20, [0,3000,0,3000])
fr.DrawImage('V', '', 'sources', 20, [0,3000,0,3000])
>> Ejemplo de analisis de un cluster:
# Define los inputs, incluyendo al menos una estrella de referencia (con su posicion el la imagen):
clusterName = 'M52'
clusterArea = [1280, 1710, 960, 1380]
path = 'data/M52/'
path = './M52/'
refStar = Star([1398, 1087], name = 'HIP 115542', R = 7.84, V = 8.292, B = 9.345)
# Crea el objeto StarCluster con los inputs y establece los parametros segun tus necesidades:
fr = StarCluster(path, area = clusterArea, refStar = refStars, outdir = outdir, clusterName = name, verbose = 1)
fr.RemoveBkgImages()
fr.SetRGBtoBVR(True)
fr.SetBkgSigmaThr(4)
fr.SetSourceFWHM(5)
fr.SetSourceRadius(10)
fr.SetDistance(153.) # Parsec
# Ejecuta la identificacion de estrellas y lacalibracion
fr.SetStars()
fr.CalibrateStars()
# Guarda todos los resultados
fr.DrawAll()
>> Dibuja bonitos diagramas a partir de las tablas de datos, output del analisis:
plotter = StarPlotter(name, './M52/', addTaxis = True, baseStarArea = 150)
plotter.CreateColorMagDiagram('ColorMagnitude')
plotter.CreateHRdiagram('HRdiagram')
plotter.DrawRmVtoBmV('RmVtoBmV')
'''
import numpy as np
import os, sys
from photutils import datasets
from photutils import DAOStarFinder
import matplotlib.pyplot as plt
import astropy
from matplotlib.pyplot import figure
import matplotlib.patches as patches
import matplotlib.pyplot as plt
from photutils import aperture_photometry, CircularAperture
from astropy.visualization import *
#=========== Read fits and extract info
#========================================================================
def LoadFitImage(path, area = []):
''' Opens a .fit image and returns the float 2D array and the filter (read from the header) '''
if not os.path.isfile(path):
print 'ERROR: not found file ' + path
return
hdu = astropy.io.fits.open(path)[0] #datasets.load_star_image()
filter = ''
if 'FILTER' in hdu.header: filter = hdu.header['FILTER']
image = hdu.data.astype(float)
if not len(area) > 0:
return image, filter
x0, x1, y0, y1 = area
recImg = hdu.data[x0:x1, y0:y1].astype(float)
return image, filter, recImg
def GetBkgMedianAndSigma(image):
''' Obtains the background as median of the image and the sigma '''
from astropy.stats import mad_std
bkg = np.median(image)
bkg_sigma = mad_std(image)
return [bkg, bkg_sigma]
def GetSources(image, fwhm = 5., thr = 3, dataformat = '%.2g'):
''' Find stars with a given fwhm and threshold '''
bkg,bkgsigma = GetBkgMedianAndSigma(image)
daofind = DAOStarFinder(fwhm = fwhm, threshold = thr*bkgsigma)
sources = daofind(image)
for col in sources.colnames: sources[col].info.format = dataformat
return sources
def GetBrightestSource(a):
''' Find the brightest star in an image or a group of stars '''
if isinstance(a, astropy.table.table.Table): # Table of stars
maxflux = max(a['flux'])
minmag = min(a['mag'])
bs = a[0]
for s in a:
#if s['flux'] == maxflux: bs = s
if s['mag'] == minmag: bs = s
return bs
elif isinstance(a, numpy.ndarray): # Image
return GetBrightestSources(GetSources(a))
else:
print '[GetBrightestSources] ERROR: unknown type ', type(a)
def GetListOfBightestSources(sources, nSources = 10, area = []):
x = sources['xcentroid']; y = sources['ycentroid']; coor = np.transpose([x,y])
magb = sources['mag']
c = [z for _, z in sorted(zip(magb,coor))]
xb,yb = np.transpose(c[:])#[:nSources])
magb = sorted(magb)[:]#[:nSources]
x = []; y = []; mag = []
if len(area) >= 4:
x0, x1, y0, y1 = area
for i in range(len(xb)):
xs = xb[i]; ys = yb[i];
if xs < x1 and xs > x0 and ys < y1 and ys > y0:
x.append(xs); y.append(ys); mag.append(magb[i])
x = x[:nSources]; y = y[:nSources]; mag = mag[:nSources]
else:
x = xb[:nSources]; y = yb[:nSources]; mag = magb[:nSources]
return [x, y, mag]
def GetSourceInPos(sources, px, py, thr = 5):
''' Looks for a source in [px, py] from all stars in the given list '''
for s in sources:
x = s['xcentroid']
y = s['ycentroid']
if abs(x-px) < thr and abs(y-py) < thr: return s
print '[GetSourceInPos] WARNING: not found source in position [x, y] = [%i, %i]'%(px, py)
return 0
def GetStarInPos(stars, px, py, thr = 5):
''' Looks for a star in [px, py] from all stars in the given list '''
mindist = 1000000
for s in stars:
dist = s.GetDistToPoint(px, py)
if dist < mindist:
mindist = dist
closestStar = s
if mindist < thr: return s
else: print '[GetStarInPos] WARNING: not found star in position [x, y] = [%i, %i]'%(px, py)
return 0
def GetMagnitudeCorrectionForStars(sources, xpos, ypos, mag):
''' Returns constant to calibrate mangitudes '''
refStar = GetSourceInPos(sources, xpos, ypos)
starMag = refStar['mag']
k = mag + starMag
return k
def GetMagCorrFromRefStar(sources, star, filter):
''' Returns constant to calibrate mangitudes using a reference star as input '''
x = star.GetX()
y = star.GetY()
mag = star.GetMag(filter)
return GetMagnitudeCorrectionForStars(sources, xpos, ypos, mag)
def CalibrateSources(sources, k):
''' Returns the list of sources with calibrated mangitude '''
for s in sources: s['mag'] += k
return sources
def CalibrateSourcesFromRefStar(sources, star, filter):
''' Returns the list of sources with calibrated magnitude using a reference star as input '''
return CalibrateSources(sources, GetMagCorrFromRefStar(sources, star, filter))
def SetForm(val, n = 4, form = '%1.2f'):
t = form%val
while len(t) < n: t+=' '
return t
def GetInfoStar(index, stars):
''' Gets all info from one star '''
s = stars[index]
t = ''
t += ' ' + SetForm(index, 4, '%i') + ' |'
t += ' ' + SetForm(s.GetX(), 4, '%i') + ' |'
t += ' ' + SetForm(s.GetY(), 4, '%i') + ' |'
t += ' ' + SetForm(s.GetMag('B'), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetMag('V'), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetMag('R'), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetAbsMag(), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetBolometricMag(), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetLumi(), 8, '%1.2g') + ' |'
t += ' ' + SetForm(s.GetBmV(), 6, '%1.3f') + ' |'
t += ' ' + SetForm(s.GetT(), 5, '%1.0f') + ' |'
t += ' ' + SetForm(s.GetRadius(), 5, '%1.2f') + ' |'
t += '\n'
return t
def PrintStarData(stars):
t = ''
head = '\n'
head += '======================================================================================================\n'
head += ' id | X | Y | B | V | R | VMag | BolMag | Lumi | B-V | T (K) | Rad \n'
head += '------------------------------------------------------------------------------------------------------\n'
#head+= ' 0001 | 9999 | 0000 | 00.000 | 00.000 | 00.000 | 00.000 | 00.000 | 1.00e+11 | 00.000 | 10000 | 10000 \n'
for i in range(len(stars)):
if i%50 == 0: t += head
t += GetInfoStar(i, stars)
return t
#=========== Formulas and parametrizations
#========================================================================
from numpy import log10
def GetBGRfromRGB(filter, R, G, B):
''' Gets the BGR transformation from RGB filters '''
CB_BG = 0.280; CB_GR = 0.600;
CV_BG = 0.542; CV_GR =-0.064;
CR_BG = 0.051; CR_GR = 0.468;
if filter == 'B':
f = B + CB_BG*(B-G) + CB_GR*(G-R)
elif filter == 'V':
f = B + CV_BG*(B-G) + CV_GR*(G-R)
elif filter == 'R':
f = B + CR_BG*(B-G) + CR_GR*(G-R)
return f
def ApplyRGBtoBVRtoStar(star, globalfac = 0):
oG = star.GetMag('V')+globalfac
oR = star.GetMag('R')+globalfac
oB = star.GetMag('B')+globalfac
R = GetBGRfromRGB('R', oR, oG, oB)
B = GetBGRfromRGB('B', oR, oG, oB)
V = GetBGRfromRGB('V', oR, oG, oB)
star.SetMag(R, 'R')
star.SetMag(B, 'B')
star.SetMag(V, 'V')
def Interpolate(T0, T1, k0, k1, T):
''' Interpolate between two values... used to get bolometric corrections '''
if float(T1)-float(T0) == 0.: return 0.
f = (float(T) - float(T0))/(float(T1)-float(T0))
k = k0 + (k1-k0)*f
return k
def GetBolometricCorrection(T):
''' Returns a bolometric correction from filer V, based on the star temperature.
Assumed a luminosity class V (mains sequence), but the correction is not so different for
Red giants or supergiants.
Linear interpolation from tabulated data.
Ref: http://www.as.utexas.edu/~sj/a358-sp06/lec3.pt2.pdf, Table 3.7. '''
k = 0; T0 = 0; T1 = 0; k0 = 0; k1 = 1;
if T < 2640:
warningError = '[WARNING] No bolometric correction for Temperature < 2640 k!! That\'s too cold!!! (T = %1.0f k)';
T1 = 2640; T0 = 0
k1 = -4.10; k0 = -8
elif T < 3240:
T1 = 3240; T0 = 2640
k1 = -2.73; k0 = -4.10
elif T < 3850:
T1 = 3850; T0 = 3240
k1 = -1.28; k0 = -2.73
elif T < 4350:
T1 = 4380; T0 = 3850
k1 = -0.72; k0 = -1.28
elif T < 5250:
T1 = 5250; T0 = 4350
k1 = -0.31; k0 = -0.72
elif T < 5770:
T1 = 5770; T0 = 5250
k1 = -0.21; k0 = -0.31
elif T < 5860:
T1 = 5860; T0 = 5770
k1 = -0.20; k0 = -0.21
elif T < 6030:
T1 = 6030; T0 = 5860
k1 = -0.18; k0 = -0.20
elif T < 6440:
T1 = 6440; T0 = 6030
k1 = -0.14; k0 = -0.18
elif T < 7200:
T1 = 7200; T0 = 6440
k1 = -0.09; k0 = -0.14
elif T < 8200:
T1 = 8200; T0 = 7200
k1 = -0.15; k0 = -0.09
elif T < 9520:
T1 = 9520; T0 = 8200
k1 = -0.30; k0 = -0.15
elif T < 11900:
T1 = 11900; T0 = 9520
k1 = -0.80; k0 = -0.30
elif T < 13000:
T1 = 13000; T0 = 11900
k1 = -1.02; k0 = -0.80
elif T < 15400:
T1 = 15400; T0 = 13000
k1 = -1.46; k0 = -1.02
elif T < 18700:
T1 = 18700; T0 = 15400
k1 = -1.94; k0 = -1.46
elif T < 22000:
T1 = 22000; T0 = 18700
k1 = -2.35; k0 = -1.94
elif T < 30000:
T1 = 30000; T0 = 22000
k1 = -3.16; k0 = -2.35
elif T < 33000:
T1 = 33000; T0 = 30000
k1 = -3.33; k0 = -3.16
elif T < 38000:
T1 = 38000; T0 = 33000
k1 = -3.68; k0 = -3.33
elif T < 44500:
T1 = 45000; T0 = 38000
k1 = -4.40; k0 = -3.68
else:
T1 = 52500; T0 = 45000
k1 = -4.75; k0 = -4.40
k = Interpolate(T0, T1, k0, k1, T)
return k
def GetTforBmV(d):
''' Parametric formula to get the effective temperature from B-V color index '''
C1 = 3.979145;
C2 = -0.654499;
C3 = 1.74069;
C4 = -4.608815;
C5 = 6.7926;
C6 = -5.39691;
C7 = 2.19297;
C8 = -0.359496;
logt = C1 + C2*d + C3*d*d + C4 * d*d*d + C5 * d*d*d*d + C6 * d*d*d*d*d + C7 * d*d*d*d*d*d + C8 * d*d*d*d*d*d*d
if(logt > 20): logt = 0
return pow(10,logt);
def plotRelationBmVvsT():
''' Plot the correction factor B-V to temperature '''
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(-0.3, 1.9, 1000)
y = [GetTforBmV(ix) for ix in x]
plt.plot(x,y,'r')
plt.ylabel('Temperature (K)')
plt.xlabel('B-V')
plt.show()
def GetAbsMagnitudeFromMagAndDistance(m, d):
''' Returns the absolute magnitud from the relative magnitude and the distance '''
# d in parsecs
M = m - 5*(np.log10(d/10)-1)
return M
def lyToParsec(d):
''' Lihgt years to parsecs '''
return float(d)/3.2616
def GetBolometricMagnitude(M, T):
''' Returns the bolometric magnitud from the magnitude and the temperature '''
Mbol = GetBolometricCorrection(T) + M
return Mbol
def GetLumiFromMbol(mbol):
''' Gets the luminosity of a star in units of sun luminosity from the bolometric magnitude '''
mbolSun = 4.74;
l = pow(10, 0.4*(mbolSun - mbol))
return l
def LumiSolToWatt(lum):
''' From solar luminisities to watts '''
Lsun = 3.828e26 # 3.0128e28
return lum*Lsun
def GetStarRadius(lumi, temp):
''' Gets the radius of the star using the total luminosity and Stefan-Botlzmann's law.
The input lumi must be in watt and temperature in kelvin.
If lumi < 10^10, will assume it's on solar lumis '''
if lumi < 1e10: lumi = LumiSolToWatt(lumi)
sigma = 5.67e-8 # watt m-2 K-4
T4 = temp*temp*temp*temp
pi = 3.141592
r2 = lumi/(4*pi*sigma*T4)
solarRadius = 6.96e8
return np.sqrt(r2)/solarRadius
#===============================================================
#========== Drawing
def GetColor(t):
''' Get the color from a temperature '''
if(t > 1000): t = float(t)/1000
# < 2k: Brown
if t < 2: return '#630202'
# 2k to 5.5k Red-orange-yellow
elif t < 2.2: return '#d60000'
elif t < 2.4: return '#f70c0c'
elif t < 2.6: return '#fc351b'
elif t < 2.8: return '#fc531a'
elif t < 3.0: return '#ff6021'
elif t < 3.2: return '#ff7220'
elif t < 3.4: return '#ff8020'
elif t < 3.7: return '#ff9620'
elif t < 4.0: return '#ffb420'
elif t < 4.3: return '#ffe120'
elif t < 4.6: return '#ffed66'
elif t < 5.0: return '#fff296'
elif t < 5.5: return '#fff9d1'
# 5.5k to 8k White
elif t < 6.0: return '#fffced'
elif t < 6.5: return '#f3ffed'
elif t < 7.0: return '#ffffff'
elif t < 7.5: return '#f4fffb'
elif t < 8.0: return '#f4fffc'
# 8k to 30k Light blue to dark blue
elif t < 9.0: return '#e5fffc'
elif t < 10: return '#c2fcf5'
elif t < 11: return '#a0fff3'
elif t < 12: return '#a0ebff'
elif t < 13: return '#a0d7ff'
elif t < 14: return '#7fc9ff'
elif t < 15: return '#6bbdf9'
elif t < 16: return '#49b2ff'
elif t < 17: return '#38aaff'
elif t < 18: return '#28a1fc'
elif t < 19: return '#1498fc'
elif t < 20: return '#1484fc'
elif t < 22: return '#1465fc'
elif t < 24: return '#144afc'
elif t < 26: return '#142ffc'
elif t < 28: return '#1418ff'
elif t < 30: return '#1430ff'
# > 30k Purple
elif t < 32: return '#233dff'
elif t < 35: return '#1632ff'
elif t < 40: return '#161dff'
elif t < 45: return '#200cff'
elif t < 50: return '#4122f4'
elif t < 55: return '#552ffc'
elif t < 60: return '#6b3aff'
else : return '#a782ff'
#========== Class Star
#===============================================================
class Star:
''' Stores the magnitudes for each filter for a given star. The calibration must be done before! '''
def SetDistance(self, d):
''' Sets the distance to the star, in parsec '''
self.distance = d
def SetMag(self, mag, filter = 'L'):
''' Sets the magnitude (has to be already calibrated!) for a filter '''
if filter == 'L': self.L = mag
elif filter == 'R': self.R = mag
elif filter == 'G': self.V = mag
elif filter == 'V': self.V = mag
elif filter == 'B': self.B = mag
else: print '[Star.SetMag] WARNING: wrong filter (%s)'%filter
def SetName(self, name):
''' Sets the name of the star... only for named stars or reference stars '''
self.name = name
def GetDistance(self):
''' Returns the distance of the star in parsec '''
return self.distance
def GetDistToPoint(self, x, y):
''' Returns the distance, in pixels, of the star to a given point in the image '''
d2 = (x - self.GetX())*(x - self.GetX()) + (y - self.GetY())*(y - self.GetY())
return np.sqrt(d2)
def GetMag(self, filter = ''):
''' Returns the magnitude for a given filter '''
if filter == 'L': return self.L
elif filter == 'R': return self.R
elif filter == 'G': return self.V
elif filter == 'V': return self.V
elif filter == 'B': return self.B
else: return self.V
#mag = self.L if self.L != 0 else sefl.V
# return mag
def GetCoor(self):
''' Returns the coordenates (in pixels) in the image '''
return self.coor
def GetName(self):
''' Returns the name of the star '''
return self.name
def GetT(self):
''' Returns the temperature from the B-V color index '''
return GetTforBmV(self.GetBmV())
def GetAbsMag(self, distance = -1):
''' Returns the absolute magnitude from the rel mag and the distance '''
if distance != -1: self.SetDistance(distance)
return GetAbsMagnitudeFromMagAndDistance(self.GetMag(), self.GetDistance())
def GetBolometricMag(self):
''' Returns the bolometric magnitude from the abs magnitude and the temperature '''
return GetBolometricMagnitude(self.GetAbsMag(), self.GetT())
def GetLumi(self, distance = -1):
''' Returns the luminosity of the star from the bolometric magnitude and the distance '''
if distance != -1: self.SetDistance(distance)
return GetLumiFromMbol(self.GetBolometricMag())
def GetRadius(self):
''' Returns the radius of the star using Stefan-Boltzmann law'''
Lum = self.GetLumi()
T = self.GetT()
return GetStarRadius(Lum, T)
def GetX(self):
''' Returns the X coordinate in the image (in pixels) '''
return self.GetCoor()[0]
def GetY(self):
''' Returns the Y coordinate in the image (in pixels) '''
return self.GetCoor()[1]
def GetBmV(self):
''' Returns the B - V color index '''
return self.GetMag('B') - self.GetMag('V')
def __init__(self, coor, R = -99, V = -99, B = -99, L = -99, distance = -1, name = ''):
self.R = R
self.V = V
self.B = B
self.L = L
self.coor = coor
self.distance = distance
self.name = name
#===============================================================
class StarCluster:
''' Reads .FIT images, substracts bkg, gets stars in a given area, computes star objets...
fr = StarCluster(path) # if filter can be read from the header
fr = StarCluster(); fr.AddImage(pathToImage, 'FILTER') otherwise
area = [x0, x1, y0, y1]
'''
def AddImage(self, pathToImage, filter = ''):
''' Add an image to the list of images of the cluster '''
# If filter == '', takes the filter from the header
img, f, recImg = LoadFitImage(pathToImage)
if not filter == '': f = filter
self.images.append(img)
self.recImages.append(recImg)
self.filters.append(f)
self.removedBkg.append(False)
def LoadImages(self):
path = self.path
files = os.listdir(path)
for image in files:
if not image.endswith('.fit') and not image.endswith('.fits') and not image.endswith('.FIT') and not image.endswith('FITS'): continue
else:
img, filter, recImg = LoadFitImage(path + '/' + image, self.area)
if filter == '':
self.info('Filter not found in file ' + image, mode = 'warn', func = 'StarCluster.LoadImages')
elif filter == 'G': filter = 'V'
self.images.append(img)
self.recImages.append(recImg)
self.filters.append(filter)
self.removedBkg.append(False)
self.PrintLoadedImages()
self.info(' >> Loaded %i images!' % len(self.images), verbose = 0)
def PrintLoadedImages(self):
''' Prints the filters for each loaded image '''
for i in range(len(self.images)):
self.info(' >> Loaded image with filter: ' + self.filters[i], verbose = 1)
def SetArea(self, area):
self.area = area
def SetOutDir(self, outdir):
self.outdir = outdir
if not self.outdir[-1] == '/': self.outdir += '/'
if not os.path.isdir(self.outdir): os.mkdir(self.outdir)
def SetRefStar(self, refStar):
self.refStar = refStar
def AddRefStar(self, refStar):
self.refStar.append(refStar)
def SetClusterName(self, name):
self.name = name
def SetVerbose(self, v):
self.verbose = v
def SetDistance(self, d):
self.distance = d
def SetRGBtoBVR(self, val = True):
self.doRGBtoBVR = val
def RemoveBkgImages(self):
i = 0
for img in self.images:
if not self.removedBkg[i]:
bkg, bkg_sigma = GetBkgMedianAndSigma(img)
self.images[i] -= bkg
self.removedBkg[i] = True
i += 1
def SetBkgSigmaThr(self, b):
self.bkgSigmaThr = b
def SetSourceFWHM(self, f):
self.fwhm = f
def SetSourceRadius(self, s):
self.sourceRadius = s
def GetListOfBrightestSources(self, filter = 'V', nBrightSources = 20, area = [], options = ''):
''' Returns a table with the position of brigtest sources and magnitude '''
img = self.GetImage(filter, 'rec' in options)
sources = GetSources(img, self.fwhm, self.bkgSigmaThr)
X, Y, mag = GetListOfBightestSources(sources, nBrightSources, area)
t = '\n Brightest sources: \n'
t += '========================== \n'
t += ' Mag | X | Y | \n'
t += '-------------------------- \n'
# ' xxx.xxx | xxxxx | xxxxx | \n'
for i in range(len(X)):
t += ' %s | %s | %s |\n'%(SetForm(mag[i],7, '%1.2f'), SetForm(X[i], 5, '%i'), SetForm(Y[i], 5, '%i'))
t += '========================== \n'
self.info(t, verbose = 0)
return t
def DrawImage(self, filter = '', outname = '', options = '', nBrightSources = 20, area = []):
''' Draw the FIT with sources if 'sources' in options and the cropped image if 'rec' in options '''
x0, x1, y0, y1 = self.GetArea()
img = self.GetImage(filter, 'rec' in options)
apc = 0
if len(self.refStar) > 0:
xc = []; yc = []
for s in self.refStar:
xc.append(s.GetX())
yc.append(s.GetY())
posc = (xc, yc)
apc = CircularAperture(posc, 1.8*self.sourceRadius)
if outname != '': fig = plt.figure(num=None, figsize=(30, 20), dpi=100, facecolor='w', edgecolor='k')
else: fig = plt.figure()
ax = fig.add_subplot(111)
tr = PowerStretch(3) + PercentileInterval(98)
img2 = tr(img)
ax.imshow(img2, cmap='gray_r', origin='lower', interpolation='nearest', aspect='auto')
if apc != 0: apc.plot(color='#ff0000', lw = 2)
if 'sources' in options:
sources = GetSources(img, self.fwhm, self.bkgSigmaThr)
x = sources['xcentroid']; y = sources['ycentroid']; pos = (x, y)
bsx, bsy, mag = GetListOfBightestSources(sources, nBrightSources, area)
bsp = (bsx, bsy)
aper = CircularAperture(pos, self.sourceRadius)
aperbs = CircularAperture(bsp, 1.5*self.sourceRadius)
if filter == 'V':
col = '#acef92'; col2 = '#436336'
elif filter == 'B':
col = '#7ed2e5'; col2 = '#1353c1'
elif filter == 'R':
col = '#ffa789'; col2 = '#c63909'
else:
col = '#cccc9d'; col2 = '#70705a'
aper.plot(color = col)
aperbs.plot(color = col2, lw = 2)
if not 'rec' in options:
rect = patches.Rectangle((x0,y0),x1-x0,y1-y0,linewidth=2,edgecolor='#ffc700',facecolor='none')
ax.add_patch(rect)
ax.set_xlabel("X [pixels]", fontsize=10,horizontalalignment='right', position=(1,25))
ax.set_ylabel("Y [pixels]", fontsize=10)
if outname != '':
fig.savefig(self.outdir + outname+'.png')
plt.close()
else: plt.show()
def DrawStars(self, outname = '', options = ''):
''' Draw the stars in positions with a color for each temperature '''
x0, x1, y0, y1 = self.GetArea()
x = []; y = []; T = []
stars = self.CleanStars(self.GetSelectedStars()) if not 'rec' in options else self.CleanStars(self.GetStarsInArea(self.GetSelectedStars()))
for s in stars:
x.append(s.GetX())
y.append(s.GetY())
T.append(s.GetT())
positions = (x, y)
fig = plt.figure(num=None, figsize=(30, 20), dpi=100, facecolor='w', edgecolor='k')
ax = fig.add_subplot(111)
ax.set_xlabel("X [pixels]", fontsize=10,horizontalalignment='right', position=(1,25))
ax.set_ylabel("Y [pixels]", fontsize=10)
#plt.plot(x,y,'ob')
if 'col' in options:
ax.set_facecolor((0, 0, 0))
ax.patch.set_facecolor((0,0,0))
ax.spines['bottom'].set_color((1,1,1))
ax.spines['top'].set_color((1,1,1))
ax.spines['right'].set_color((1,1,1))
ax.spines['left'].set_color((1,1,1))
ax.yaxis.label.set_color((1,1,1))
ax.xaxis.label.set_color((1,1,1))
ax.tick_params(axis='x', colors=(1,1,1))
ax.tick_params(axis='y', colors=(1,1,1))
for i in range(len(x)):ax.scatter(x[i], y[i], s = 100, color = GetColor(T[i]))
ax.scatter(x[i], y[i], s = 60, color = GetColor(T[i]))
else:
ax.scatter(x, y, s = 60, color = 'k')
if not 'rec' in options:
rect = patches.Rectangle((x0,y0),x1-x0,y1-y0,linewidth=2,edgecolor='#ffc700',facecolor='none')
ax.add_patch(rect)
if outname != '':
fig.savefig(self.outdir + outname+'.png')
plt.close()
else: plt.show()
def DrawAll(self):
filters = ['V', 'B', 'R', 'L']
for i in range(len(filters)):
if not self.isThereFilter(filters[i]): filters.pop(i)
for f in filters:
self.DrawImage(f, outname = 'Img'+f, options = '')
self.DrawImage(f, outname = 'Sources'+f, options = 'sources', nBrightSources = 20)
self.DrawImage(f, outname = 'RecImg'+f, options = 'rec,sources')
self.DrawImage(f, outname = 'RecSources'+f, options = 'rec,sources', nBrightSources = 10)
if len(self.stars) > 0:
self.DrawStars('IdentifiedStars')
self.DrawStars('SelectedStars', 'rec')
self.DrawStars('IdentifiedStarsCol', 'col')
self.DrawStars('SelectedStarsCol', 'rec,col')
starsData = self.PrintStarData()
starsDataAll = self.PrintStarData(1)
infoId = self.GetInfoIdentifiedStars()
t = open(self.outdir + "stars_info.txt", 'w')
t.write(infoId + '\n' + starsData)
t.close()
t = open(self.outdir + "stars_all_info.txt", 'w')
t.write(infoId + '\n' + starsDataAll)
t.close()
self.GetCalibrationData()
t = open(self.outdir + "calibrationData.txt", 'w')
t.write(self.calibData)
t.close()
t = open(self.outdir + 'log.txt', 'w')
t.write(self.log)
t.close()
def GetArea(self):
''' Sets the area and corrects in case of null area '''
x0, x1, y0, y1 = self.area
if not len(self.images) > 0: return self.area
image = self.images[0]
xmax = len(image[0])
ymax = len(image )
if y1 == 0: y1 = ymax
if x1 == 0: x1 = xmax
return [x0, x1, y0, y1]
def GetImage(self, filt = 'V', recImage = False):
''' Returns the image for the given filter '''
for i in range(len(self.images)):
img = self.images[i] if not recImage else self.recImages[i]
fil = self.filters[i]
if filt == fil: return img
self.info('image not found for filter ' + filt, mode = 'warn', func = 'StarCluster.GetImage')
def GetSources(self, filter = '', recImage = False):
''' Gets the sources from images '''
img = self.GetImage(filter) if not recImage else self.GetImage(filter, 1)
sources = GetSources(img, self.fwhm, self.bkgSigmaThr)
return sources
def SetStarsFilter(self, filter = 'V'):
''' Obtain the Star objets from one filter (V by default) '''
self.stars = []
if not self.isThereFilter(filter):
self.info('filter ' + filter + ' not found!!!', mode = 'error', func = 'StarCluster.SetStarsFilters')
sources = self.GetSources(filter)
self.info(' >> Getting stars for filter ' + filter + '... %i stars found!!'%(len(sources)))
for s in sources:
x = s['xcentroid']
y = s['ycentroid']
mag = s['mag']
a = Star(coor = [x,y])
a.SetMag(mag, filter)
self.stars.append(a)
def MatchStars(self, filter):
''' Marches sources if a given filter with stars in a list of stars '''
if not self.isThereFilter(filter): return
if len(self.stars) == 0: return
sources = self.GetSources(filter)
self.info(' >> Getting stars for filter ' + filter + '... %i stars found!!' %len(sources))
for s in sources:
x = s['xcentroid']
y = s['ycentroid']
mag = s['mag']
index = 0; indexMinD = 0; minDist = 10000
for a in self.stars:
dist = a.GetDistToPoint(x,y)
if dist < minDist:
minDist = dist
indexMinD = index
index += 1
if minDist <= 1*self.fwhm:
self.stars[indexMinD].SetMag(mag, filter)
def SetStars(self):
''' Get the stars from the images '''
if len(self.stars) > 0: return
self.SetStarsFilter('B') # Use as reference
if self.isThereFilter('V'): self.MatchStars('V')
if self.isThereFilter('R'): self.MatchStars('R')
#if self.isThereFilter('L'): self.MatchStars('L')
def GetStars(self):
return self.stars
def CleanStars(self, stars = ''):
''' Removes fake stars based on temperature and large difference of filter magnitudes '''
cleanStars = []
if stars == '': stars = self.stars
lumi = []
for s in stars:
T = s.GetT()
V = s.GetMag('V')
R = s.GetMag('R')
B = s.GetMag('B')
if np.std([V,B,R]) > 5: continue
if T < 2000 or T > 50000: continue
cleanStars.append(s)
self.info("Clean stars: %i, orig stars: %i"%(len(cleanStars),len(stars)), verbose = 0)
return cleanStars
def GetStarsInArea(self, stars = ''):
''' Returns the stars in the fixed area of the cluster '''
if stars == '': stars = self.stars
starsInArea = []
x0, x1, y0, y1 = self.area
for s in stars:
x = s.GetX(); y = s.GetY()
if x > x0 and x < x1 and y > y0 and y < y1:
starsInArea.append(s)
self.info('Number of stars in area: %i'%len(starsInArea), mode = 'info', func = 'StarCluster.GetStarsInArea')
return starsInArea
def GetSelectedStars(self, stars = ''):
if stars == '': stars = self.stars
selStars = []
for s in stars:
if s.GetMag('V') != -99 and s.GetMag('B') != -99 and s.GetMag('R') != -99:
s.SetDistance(self.distance)
#if self.doRGBtoBVR: ApplyRGBtoBVRtoStar(s)
selStars.append(s)
self.info('Number of selected stars: %i'%len(selStars), mode = 'info', func = 'StarCluster.GetSelectedStars')
if self.doRGBtoBVR: selStars = self.CalibrateStars(selStars)
return selStars
def GetInfoIdentifiedStars(self):
''' Returns numbers of identified sources of each filter, selected stars, etc... '''
if len(self.stars) == 0:
self.info('There are no stars!', func = 'StarCluster.PrintInfoStars')
return
nB = 0; nV = 0; nR = 0; nL = 0;
for s in self.stars:
if s.GetMag('V') != -99: nV += 1
if s.GetMag('B') != -99: nB += 1
if s.GetMag('R') != -99: nR += 1
if s.GetMag('L') != -99: nL += 1
t = ''
t += '# Sources in filter V: %4i \n' %nV
t += '# Sources in filter B: %4i \n' %nB
t += '# Sources in filter R: %4i \n' %nR
if nL != 0: t+= 'Sources in filter L: %4i\n' %nL
nTotalStars = len(self.stars)
starsInArea = self.GetStarsInArea(self.stars)
nStarsInArea = len(starsInArea)
nSelStars = len(self.CleanStars(starsInArea))
t += '\n'
t += '# Total identified stars: %i\n' %nTotalStars
t += '# Stars in cluster area : %i\n' %nStarsInArea
t += '# Cleaned selected stars: %i\n' %nSelStars
return t
def GetClosestStar(self, star):
''' Looks for the closest star of a given star '''
px = star.GetX()
py = star.GetY()
mindist = 1000000
for s in self.stars:
dist = s.GetDistToPoint(px, py)
if dist < mindist:
mindist = dist
closestStar = s
if mindist < self.fwhm: return s
self.info('not found star in position [x, y] = [%i, %i]'%(px, py), func = 'StarCluster.GetStarInPos', mode = 'warn')
return 0
def GetCalibratingStars(self):
''' Returnss a list with calibrating stars '''
cs = []
for s in self.refStar:
cs.append(self.GetClosestStar(s))
return cs
def GetMagCorrStar(self, filter, refStar = [], calibratingStar = [], kglobal = 0):
''' Returns constant to calibrate mangitudes from ref star for a given filter'''
if isinstance(refStar, Star):
mag = refStar.GetMag(filter)
starMag = calibratingStar.GetMag(filter)
k = mag - starMag
else: # It's a list of stars
if len(refStar) == 0: refStar = self.refStar
if len(calibratingStar) == 0: calibratingStar = self.GetCalibratingStars()
k = []
for i in range(len(refStar)):
mag = refStar[i].GetMag(filter)
starMag = calibratingStar[i].GetMag(filter)
if mag == -99 or starMag == -99: continue
k.append(mag-starMag-kglobal)
return np.average(k), np.std(k)
def GetGlobalMagCorr(self):
''' Returns a global constant '''
filters = ['R', 'L', 'V', 'B']
k = []
for f in filters:
if not self.isThereFilter(f): continue
m,s = self.GetMagCorrStar(f)
k.append(m)
return np.average(k), np.std(k)
def CalibrateStars(self, stars = 0):
''' Gets and applies the magnitude corrections in each filter for all the stars '''
if stars == 0: stars = self.stars
if self.calibData == '': self.GetCalibrationData()
filters = ['V', 'B', 'R', 'L'];