def init2():
from pyrap.images import image
im = image("/home/tasse/Desktop/FITS/image_049_073.img.restored.fits")
PMaj = (im.imageinfo()["restoringbeam"]["major"]["value"])
PMin = (im.imageinfo()["restoringbeam"]["minor"]["value"])
PPA = (im.imageinfo()["restoringbeam"]["positionangle"]["value"])
print(
ModColor.Str(" - Using psf (maj,min,pa)=(%6.2f, %6.2f, %6.2f)" %
(PMaj, PMin, PPA),
col='green',
Bold=False))
ToSig = (1. / 3600.) * (np.pi / 180.) / (2. * np.sqrt(2. * np.log(2)))
PMaj *= ToSig
PMin *= ToSig
PPA *= np.pi / 180
b = im.getdata()[0, 0, :, :]
b = b[3000:4000, 3000:4000] #[100:250,200:350]
c = im.coordinates()
incr = np.abs(c.dict()["direction0"]["cdelt"][0])
print(
ModColor.Str(" - Psf Size Sigma_(Maj,Min) = (%5.1f,%5.1f) pixels" %
(PMaj / incr, PMin / incr),
col="green",
Bold=False))
Islands = ClassIslands.ClassIslands(b, 10., Boost=1, DoPlot=1)
#Islands.Noise=30e-3
Islands.FindAllIslands()
sourceList = []
ImOut = np.zeros_like(b)
pylab.ion()
for i in range(len(Islands.ListX)):
#comment='Isl %i/%i' % (i+1,len(Islands.ListX))
#pBAR.render(int(100* float(i+1) / len(Islands.ListX)), comment)
xin, yin, zin = np.array(Islands.ListX[i]), np.array(
Islands.ListY[i]), np.array(Islands.ListS[i])
xm = int(np.sum(xin * zin) / np.sum(zin))
ym = int(np.sum(yin * zin) / np.sum(zin))
#Fit=ClassPointFit(xin,yin,zin,psf=(PMaj/incr,PMin/incr,PPA),noise=Islands.Noise)
Fit = ClassPointFit(xin,
yin,
zin,
psf=(PMaj / incr, PMin / incr, PPA),
noise=Islands.Noise[xm, ym])
sourceList += Fit.DoAllFit()
Fit.PutFittedArray(ImOut)
xlist = []
ylist = []
slist = []
for ijs in sourceList:
i, j, s = ijs
xlist.append(i)
ylist.append(j)
slist.append(s)
Islands.FittedComps = (xlist, ylist, slist)
Islands.FitIm = ImOut
Islands.plot()
def fillNoise(self):
return
A=self.A
print ModColor.Str("Fill blanks with noise...")
Avec=A.reshape((A.shape[1]*A.shape[0],))
ind=np.where(np.abs(Avec)>1e-8)[0]
Avec=Avec[ind]
rms=findrms.findrms(Avec)
imnoise=np.random.randn(A.shape[0],A.shape[1])*rms
ind=np.where(np.abs(A)<1e-8)
A[ind]=imnoise[ind]
print ModColor.Str(" rms in the image: %6.2f mJy"%(rms*1000.),col="green",Bold=False)
print ModColor.Str(" done ...")
def Save(self):
infile=self.infile
print ModColor.Str(" SkyModel PROPERTIES: ")
print " - SkyModel File Name: %s"%ModColor.Str(infile,col="green")
if self.REGFile!=None: print " - ds9 region file: %s"%ModColor.Str(self.REGFile,col="green")
npext=""
if not(".npy" in infile): npext=".npy"
self.NpFile="%s%s"%(infile,npext)
np.save(infile,self.SourceCat)
FileClusterCat="%s.ClusterCat.npy"%(self.infile)
print " - ClusterCat File Name: %s"%ModColor.Str(FileClusterCat,col="green")
np.save(FileClusterCat,self.ClusterCat)
self.PrintBasics()
def VorToReg(self,regFile,vor,radius=0.1,Col="red"):
print>>log,"Writing voronoi in: %s"%ModColor.Str(regFile,col="blue")
f=open(regFile,"w")
f.write("# Region file format: DS9 version 4.1\n")
ss0='global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0'
ss1=' fixed=0 edit=1 move=1 delete=1 include=1 source=1\n'
f.write(ss0+ss1)
f.write("fk5\n")
CoordMachine=self.CoordMachine
regions, vertices = vor.regions,vor.vertices
for region in regions:
if len(region)==0: continue
polygon0 = vertices[region]
P=polygon0.tolist()
polygon=np.array(P+[P[0]])
for iline in range(polygon.shape[0]-1):
x0,y0=CoordMachine.lm2radec(np.array([polygon[iline][0]]),np.array([polygon[iline][1]]))
x1,y1=CoordMachine.lm2radec(np.array([polygon[iline+1][0]]),np.array([polygon[iline+1][1]]))
x0*=180./np.pi
y0*=180./np.pi
x1*=180./np.pi
y1*=180./np.pi
f.write("line(%f,%f,%f,%f) # line=0 0 color=%s dash=1\n"%(x0,y0,x1,y1,Col))
#f.write("line(%f,%f,%f,%f) # line=0 0 color=red dash=1\n"%(x1,y0,x0,y1))
f.close()
def ComputeNoiseMap(self):
print ModColor.Str("Compute noise map...")
Boost=self.Boost
Acopy=self.A[0::Boost,0::Boost].copy()
SBox=(self.box[0]/Boost,self.box[1]/Boost)
Noise=np.sqrt(scipy.ndimage.filters.median_filter(np.abs(Acopy)**2,SBox))
self.Noise=np.zeros_like(self.A)
for i in range(Boost):
for j in range(Boost):
s00,s01=Noise.shape
s10,s11=self.Noise[i::Boost,j::Boost].shape
s0,s1=min(s00,s10),min(s10,s11)
self.Noise[i::Boost,j::Boost][0:s0,0:s1]=Noise[:,:][0:s0,0:s1]
print ModColor.Str(" ... done")
ind=np.where(self.Noise==0.)
self.Noise[ind]=1e-10
def PolygonToReg(self,regFile,LPolygon,radius=0.1,Col="red",labels=None):
print("Writing voronoi in: %s"%ModColor.Str(regFile,col="blue"), file=log)
f=open(regFile,"w")
f.write("# Region file format: DS9 version 4.1\n")
ss0='global color=green dashlist=8 3 width=1 font="helvetica 10 normal roman" select=1 highlite=1 dash=0'
ss1=' fixed=0 edit=1 move=1 delete=1 include=1 source=1\n'
f.write(ss0+ss1)
f.write("fk5\n")
CoordMachine=self.CoordMachine
for iFacet,polygon0 in zip(list(range(len(LPolygon))),LPolygon):
#polygon0 = vertices[region]
P=polygon0.tolist()
if len(polygon0)==0: continue
polygon=np.array(P+[P[0]])
ThisText=""
if labels!=None:
lmean0=np.mean(polygon[:,0])
mmean0=np.mean(polygon[:,1])
lmean,mmean,ThisText=labels[iFacet]
# print "!!!!======"
# print lmean0,mmean0
# print lmean,mmean
xm,ym=CoordMachine.lm2radec(np.array([lmean]),np.array([mmean]))
xm*=180./np.pi
ym*=180./np.pi
f.write("point(%f,%f) # text={%s} point=circle 5 color=red width=2\n"%(xm,ym,ThisText))
for iline in range(polygon.shape[0]-1):
L0,M0=np.array([polygon[iline][0]]),np.array([polygon[iline][1]])
x0,y0=CoordMachine.lm2radec(L0,M0)
L1,M1=np.array([polygon[iline+1][0]]),np.array([polygon[iline+1][1]])
x1,y1=CoordMachine.lm2radec(L1,M1)
x0*=180./np.pi
y0*=180./np.pi
x1*=180./np.pi
y1*=180./np.pi
# print "===================="
# print "[%3.3i] %f %f %f %f"%(iline,x0,y0,x1,y1)
# print " %s"%str(L0)
# print " %s"%str(L1)
# print " %s"%str(M0)
# print " %s"%str(M1)
f.write("line(%f,%f,%f,%f) # line=0 0 color=%s dash=1 \n"%(x0,y0,x1,y1,Col))
#f.write("line(%f,%f,%f,%f) # line=0 0 color=red dash=1\n"%(x1,y0,x0,y1))
f.close()
def printStatus(self,DictNode):
print()
print("State:")
for ind in list(DictNode.keys()):
print(ModColor.Str("Cluster %i: "%ind,col="green"))
print(" - ListCluster : %s"%str(DictNode[ind]["ListCluster"]))
print(" - SourceNum : %s"%str(DictNode[ind]["SourceNum"]))
print(" - Flux : %s"%str(DictNode[ind]["TotalFlux"]))
def PrintBasics(self):
infile=self.infile
npext=""
if not(".npy" in infile): npext=".npy"
print " - Numpy catalog file: %s"%ModColor.Str("%s%s"%(infile,npext),col="green")
#print "Oufile: %s"%self.infile_cluster
#if infile_cluster!="":
#print " - Cluster File Name: %s"%self.infile_cluster
print " - Number of Sources = ",self.SourceCat.shape[0]
print " - Number of Directions = ",self.NDir
print
def FindIsland(self,A,Lpix,x,y,dirfrom=-1,threshold=1):
T=threshold
digo=set(range(4))-set([dirfrom])
#print Lpix
#time.sleep(1.)
#if (x,y) in Lpix: return Lpix
pos=(x,y)
S=ModColor.Str("@(%i,%i) "%(x,y),col="blue")
try:
aa=A[x,y]
except:
return
if A[x,y]==False:
#print ModColor.Str("(%i,%i)"%(x,y))
return
if A[x,y]==True:
#print S,ModColor.Str("(%i,%i)"%(x,y),col="green")
Lpix.append((x,y))
if 0 in digo:
this=(x+1,y)
if not(this in Lpix):
#print S,"-> from %i and going to %i"%(dirfrom,0)
self.FindIsland(A,Lpix,x+1,y,dirfrom=2)
if 2 in digo:
this=(x-1,y)
if not(this in Lpix):
#print S,"-> from %i and going to %i"%(dirfrom,2)
self.FindIsland(A,Lpix,x-1,y,dirfrom=0)
if 1 in digo:
this=(x,y+1)
if not(this in Lpix):
#print S,"-> from %i and going to %i"%(dirfrom,1)
self.FindIsland(A,Lpix,x,y+1,dirfrom=3)
if 3 in digo:
this=(x,y-1)
if not(this in Lpix):
#print "-> from %i and going to %i"%(dirfrom,3)
self.FindIsland(A,Lpix,x,y-1,dirfrom=1)
def SaveNP(self):
infile=self.NpFile
np.save(self.NpFile,self.SourceCat)
print " - Numpy catalog file: %s"%ModColor.Str(self.NpFile,col="green")