def _findxycenter(hdr, im,ext,log):
def xy_tran(out):
"""
Function to transform blue coordinates to red frame coordinates
"""
xref = out[1] - 990.5897
yref = out[0] - 37.82109
x = -0.9985259*xref - 0.0178984*yref
y = -0.0181331*xref + 0.9991414*yref
return y,x
#hdr = pf.getheader(file)
#im = pf.getdata(file)
xcen = hdr.get('xcen')
ycen = hdr.get('ycen')
if (xcen == None):
#ratio,xc,yc = peak2halo('',image=im)
#xcen = xc
#ycen = yc
#if (xcen < 0 or ycen < 0):
if True:
if ext == 2:
# register blue frame to red's frame coordinate system
im = nd.geometric_transform (im,xy_tran)
try:
ndis.display(im,zscale=False)
except IOError,err:
sys.stderr.write('\n ***** ERROR: %s Start DS9.\n' % str(err))
sys.exit(1)
print " Mark center with left button, then use 'q' to continue, 's' to skip."
cursor = ndis.readcursor(sample=0)
cursor = cursor.split()
if cursor[3] == 's':
hdr.update("XCEN",-1, "Start mask x-center")
hdr.update("YCEN",-1, "Start mask y-center")
updated = True
print '\nFrame skipped... ****Make sure not to use it in your science script. ***\n'
#return updated,xcen,ycen,im
return xcen,ycen,im
x1 = float(cursor[0])
y1 = float(cursor[1])
xcen,ycen = gcentroid(im, x1,y1,9)
xcen = xcen[0]
ycen = ycen[0]
hdr.update("XCEN",xcen, "Start mask x-center")
hdr.update("YCEN",ycen, "Start mask y-center")
log.info(' (%.2f,%.2f) :: ' % (xcen,ycen)+('red','blue')[ext-1])
def getCpoints(self):
"""
Get control points from a pair of Red and Blue pinholes
frames from the NICI camera.
You already have frames 1 and 2 (red and blue)
from a pinhole image up in DS9.
Please select at least 6 corresponding points.
Once you click 'r' in the Red frame, a red circle is drawn
around the pinhole and a Blue circle is drawn 'near' the
blue pinhole; click 'b' there to record the position.
Press 'q' to finish.
"""
i=0; j=0
xkey = ''
print "*** Please get at least 6 corresponding pinholes."
while xkey != 'q':
cursor = ndis.readcursor(sample=0)
ss = cursor.split()
print ss
xkey = ss.pop()
if xkey not in ('r','b','q'):
print "Please choose a control point on the 'r' or 'b' frame,"
print " then hit 'r' for red frame or 'b' for 'blue' frame"
continue
im = {'r':self.imr, 'b':self.imb, 'q':0}[xkey]
if xkey == 'q': break
x,y = np.asfarray(ss[:2])
xc,yc = gcentroid(im[y-10:y+10,x-10:x+10],10,10)
xc,yc = x+xc[0]-10,y+yc[0]-10
if xkey == 'r':
#print "xc,yc: ",xc,yc,x+xc-10,y+yc-10
self.xyr[i] = xc,yc; i+=1
ov.circle(x=xc,y=yc,radius=10,color=ov.C_RED,frame=1)
xn = 990.5897 - 0.9985259*x - 0.0178984*y
yn = 37.82109 - 0.0181331*x + 0.9991414*y
#xc,yc = gcentroid(self.imb[yn-13:y+13,xn-13:x+13],13,13)
#xc,yc = xn+xc[0]-10,yn+yc[0]-10
ov.circle(x=xn,y=yn,radius=10,color=ov.C_BLUE, frame=2)
print self.xyr[i-1]
if xkey == 'b':
self.xyb[j] = xc,yc; j+=1
print self.xyb[j-1]
self.npin = j
self.xyr = np.resize(self.xyr,[j,2])
self.xyb = np.resize(self.xyb,[j,2])
def nici_cntrd(im,hdr,center_im=True):
"""
Read xcen,ycen and update header if necessary
If the automatic finding of the center mask fails, then
the interactive session will start. The SAOIMAGE/ds9
display must be up. If the default port is busy, then it will
use port 5199, so make sure you start "ds9 -port 5199".
"""
xcen = hdr.get('xcen')
ycen = hdr.get('ycen')
updated = False
if (xcen == None):
ratio,xc,yc = peak2halo('',image=im)
#xcen = xc[0]
#ycen = yc[0]
xcen = xc
ycen = yc
if (xcen < 0 or ycen < 0):
try:
ndis.display(im)
except IOError,err:
sys.stderr.write('\n ***** ERROR: %s Start DS9.\n' % str(err))
sys.exit(1)
print " Mark center with left button, then use 'q' to continue, 's' to skip."
cursor = ndis.readcursor(sample=0)
cursor = cursor.split()
if cursor[3] == 's':
hdr.update("XCEN",-1, "Start mask x-center")
hdr.update("YCEN",-1, "Start mask y-center")
updated = True
print '\nFrame skipped... ****Make sure not to use it in your science script. ***\n'
#return updated,xcen,ycen,im
return xcen,ycen,im
x1 = float(cursor[0])
y1 = float(cursor[1])
box = im[y1-64:y1+64,x1-64:x1+64].copy()
box -= scipy.signal.signaltools.medfilt2d(np.float32(box),11)
box = box[32:32+64,32:32+64]
bbx = box * ((box>(-robust_sigma(box)*5)) & \
(box <(15*robust_sigma(box))))
imbb = congrid(bbx,(1024,1024))
ndis.display(imbb, name='bbx')
del imbb
cursor = ndis.readcursor(sample=0)
cursor = cursor.split()
x2 = float(cursor[0])
y2 = float(cursor[1])
xcen,ycen = gcentroid(box, x2/16., y2/16., 4)
xcen = (xcen+x1)[0] - 32
ycen = (ycen+y1)[0] - 32
hdr.update("XCEN",xcen, "Start mask x-center")
hdr.update("YCEN",ycen, "Start mask y-center")
updated = True
def pyexam(scidata, function='both', pixelscale=1, frame=1, \
outFile='testout.txt', verbose=True, pymark=True, \
residuals=False, clip=True, sigma=3, boxSize=9., \
debug=False, niters=4.):
import pylab
from iqtool.gemplotlib import overlay
# Get box size around each object
apertureSize = fit.getApSize(pixelscale, boxSize)
outstring = '%10s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s%12s\n'%('function', 'Cx', 'Cy', 'Bg', 'Peak', 'Wx', 'Wy', 'CooX', 'CooY', 'Ellipticity', 'FWHM_pix','FWHM_arcsec', 'Theta', 'PA_deg', ' FWHMx', 'FWHMy', 'Beta')
outFile.write(outstring)
print 'PYEXAM - Please select objects using spacebar, and press \'q\' when finished'
print ' pressing k, j, r, or e will make plots along with fits'
keystroke = ''
numdisplay.display(scidata, z1=scidata.mean()-scidata.std(),
z2=scidata.mean()+scidata.std(), frame=frame)
if verbose:
print '%10s%12s%12s%12s%12s%12s%12s'%('function', 'Coox', 'CooY', 'FWHMpix',
'FWHMarcsec', 'Ellipticity', 'PAdeg')
gAllstars = []
mAllstars = []
done = 'no'
while done == 'no':
# Get x,y
cursorInput = numdisplay.readcursor(sample=0)
components = cursorInput.split()
xPos = float(components[0])
yPos = float(components[1])
keystroke = components[3]
option = ''
if keystroke == '\\040' or keystroke == 'a' or keystroke == 'k' or keystroke == 'j' or keystroke == 'e' or keystroke == 'r':
print 'PYEXAM - X:',xPos,'Y:',yPos
gfitArray=None
mfitArray=None
gfxn=None
mfxn=None
positionCoords = (xPos,yPos)
stampArray, stampPars = fit.makeStamp(scidata, positionCoords,
apertureSize, outFile, debug=debug)
if stampArray == None: return None, None
gfitPars, gReturnModel, mfitPars, mReturnModel = \
fit.fitprofile(stampArray, function, positionCoords, \
outFile, pixelscale, stampPars, debug=debug, frame=frame)
imageDim = list(scidata.shape) # Gives [y,x] dimensions
#imageDim.reverse() #give [x,y] dimensions
if gfitPars != None:
clipobsPars = ('gauss', gfitPars['CooX'], gfitPars['CooY'],
gfitPars['FWHMpix'],
gfitPars['FWHMarcsec'], gfitPars['Ellip'],
gfitPars['PAdeg'])
iqUtil.printPars(clipobsPars, verbose)
gAllstars.append(gfitPars)
if pymark:
overlay.circle(x=gfitPars['CooX']-1,y=gfitPars['CooY']-1, \
radius=gfitPars['FWHMpix'],frame=frame,\
color=204)
gfxn = gReturnModel((gfitPars['Bg'], gfitPars['Peak'], \
gfitPars['Cy'], \
gfitPars['Cx'], gfitPars['Wy'], \
gfitPars['Wx'], gfitPars['Theta']+90))
gfitArray = np.zeros(imageDim)
gfitArray[0:stampPars[3],0:stampPars[1]] = gfxn(*np.indices((stampPars[3], stampPars[1])))
if mfitPars != None:
clipobsPars = ('moffat', mfitPars['CooX'],mfitPars['CooY'],
mfitPars['FWHMpix'],
mfitPars['FWHMarcsec'], mfitPars['Ellip'],
mfitPars['PAdeg'])
iqUtil.printPars(clipobsPars, verbose)
print mfitPars['CooX']
print mfitPars['CooY']
print mfitPars['Cx']
print mfitPars['Cy']
mAllstars.append(mfitPars)
if pymark:
overlay.circle(x=mfitPars['CooX'],
y=mfitPars['CooY'], frame=frame,
radius=mfitPars['FWHMpix'], color=212)
mfxn = mReturnModel((mfitPars['Bg'], mfitPars['Peak'], \
mfitPars['Cy'],\
mfitPars['Cx'], mfitPars['Wy'], \
mfitPars['Wx'], mfitPars['Theta']+90, \
mfitPars['Beta']))
mfitArray = np.zeros(imageDim)
mfitArray[0:stampPars[3],0:stampPars[1]] = mfxn(*np.indices((stampPars[3], stampPars[1])))
if keystroke == 'k':
print "PYEXAM - Yslice Plotting"
pylab.clf()
pylab.plot(stampArray.max(0), 'ro')
if mfitArray != None:
pylab.plot(mfitArray.max(0), 'b', label='moffat fit FWHM='+str(mfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],mfitPars['Bg'],1.3*(mfitPars['Bg']+mfitPars['Peak'])])
if gfitArray != None:
pylab.plot(gfitArray.max(0), 'g',label='gauss fit FWHM='+str(gfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],gfitPars['Bg'],1.3*(gfitPars['Bg']+gfitPars['Peak'])])
pylab.legend()
if keystroke == 'j':
print "PYEXAM - Xslice Plotting"
pylab.clf()
pylab.plot(stampArray.max(1), 'ro')
if mfitArray != None:
pylab.plot(mfitArray.max(1), 'b', label='moffat fit FWHM='+str(mfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],mfitPars['Bg'],1.3*(mfitPars['Bg']+mfitPars['Peak'])])
if gfitArray != None:
pylab.plot(gfitArray.max(1), 'g',label='gauss fit FWHM='+str(gfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],gfitPars['Bg'],1.3*(gfitPars['Bg']+gfitPars['Peak'])])
pylab.legend()
if keystroke == 'r':
print "PYEXAM - radial Plotting doesnt work yet!"
print "new version"
#rad1 = np.sqrt(stampArray.max(1)**2 + stampArray.max(0)**2)
pylab.clf()
pylab.plot(stampArray.max(1), 'ro')
if mfitArray != None:
pylab.plot(mfitArray.max(1), 'b', label='moffat fit FWHM='+str(mfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],mfitPars['Bg'],1.3*(mfitPars['Bg']+mfitPars['Peak'])])
if gfitArray != None:
pylab.plot(gfitArray.max(1), 'g',label='gauss fit FWHM='+str(gfitPars['FWHMarcsec']))
pylab.axis([0,stampPars[1]-stampPars[0],gfitPars['Bg'],1.3*(gfitPars['Bg']+gfitPars['Peak'])])
pylab.legend()
if keystroke == 'e':
print 'PYEXAM - Plotting contours'
pylab.clf()
pylab.contour(stampArray)
elif keystroke == 'q':
done = 'yes'
if verbose: print "Done looping through stars"
if clip:
if gAllstars:
if verbose: print "# PYEXAM - performing Gaussian clipping"
gAllstars, gEllMean, gEllSigma, gFWHMMean, gFWHMSigma = \
iqUtil.sigmaClip(gAllstars, outFile, sigma, verbose, niters, garbageStat=garbageStat)
if verbose:
print "PYEXAM - Mean Gaussian Ellipticity:", gEllMean
print "PYEXAM - Mean Gaussian FWHM (""):", gFWHMMean
if mAllstars:
if verbose: print "# PYEXAM - performing Moffat clipping"
mAllstars, mEllMean, mEllSigma, mFWHMMean, mFWHMSigma = \
iqUtil.sigmaClip(mAllstars, outFile, sigma, verbose, niters, garbageStat=garbageStat)
if verbose:
print "PYEXAM - Mean Moffat Ellipticity:", mEllMean
print "PYEXAM - Mean Moffat FWHM (""):", mFWHMMean
for star in gAllstars:
iqUtil.writePars(star, outFile, 'gaussian')
for star in mAllstars:
iqUtil.writePars(star, outFile, 'moffat')
