from ggg import *
import threading
import time
import mmm
class subc(threading.Thread):
def __init__(self):
threading.Thread.__init__(self)
def run(self):
print 'sleep 3s...\n'
time.sleep(3)
print 'sleep 3s end\n'
print '%s set event...' % threading.currentThread().getName()
event.set()
print '%s set event end' % threading.currentThread().getName()
t2 = mmm.mmm()
t2.setDaemon(True)
t2.start()
t1 = subc()
t1.setDaemon(True)
t1.start()
t2.join()
print '---'
def calc_masked_aperture(ap, image, method='mmm', mask=None):
positions = ap.positions
extents = np.zeros((len(positions), 4), dtype=int)
if isinstance(ap, EllipticalAnnulus):
radius = ap.a_out
elif isinstance(ap, CircularAnnulus):
radius = ap.r_out
elif isinstance(ap, CircularAperture):
radius = ap.r
elif isinstance(ap, EllipticalAperture):
radius = ap.a
extents[:, 0] = positions[:, 0] - radius + 0.5
extents[:, 1] = positions[:, 0] + radius + 1.5
extents[:, 2] = positions[:, 1] - radius + 0.5
extents[:, 3] = positions[:, 1] + radius + 1.5
ood_filter, extent, phot_extent = get_phot_extents(image, positions,
extents)
x_min, x_max, y_min, y_max = extent
x_pmin, x_pmax, y_pmin, y_pmax = phot_extent
bkg = np.zeros(len(positions))
area = np.zeros(len(positions))
for i in range(len(bkg)):
if isinstance(ap, EllipticalAnnulus):
fraction = elliptical_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.a_out, ap.b_out, ap.theta, 0,
1)
b_in = ap.a_in * ap.b_out / ap.a_out
fraction -= elliptical_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.a_in, b_in, ap.theta,
0, 1)
elif isinstance(ap, CircularAnnulus):
fraction = circular_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.r_out, 0, 1)
fraction -= circular_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.r_in, 0, 1)
elif isinstance(ap, CircularAperture):
fraction = circular_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.r, 0, 1)
elif isinstance(ap, EllipticalAperture):
fraction = elliptical_overlap_grid(x_pmin[i], x_pmax[i],
y_pmin[i], y_pmax[i],
x_max[i] - x_min[i],
y_max[i] - y_min[i],
ap.a, ap.b, ap.theta, 0,
1)
pixel_data = image[y_min[i]:y_max[i], x_min[i]:x_max[i]] * fraction
if mask is not None:
pixel_data[mask[y_min[i]:y_max[i], x_min[i]:x_max[i]]] = 0.0
good_pixels = pixel_data[pixel_data != 0.0].flatten()
if method == 'mmm':
skymod, skysigma, skew = mmm(good_pixels)
bkg[i] = skymod
elif method == 'sum':
bkg[i] = np.sum(good_pixels)
elif method == 'max':
bkg[i] = np.nanmax(good_pixels)
area[i] = len(good_pixels)
return bkg, area
def aper(image,xc,yc, phpadu=1, apr=5, zeropoint=25,
skyrad=[40,60], badpix=[0,0], setskyval = None, minsky=[],
skyisempty=False, exact = False, readnoise = 0,
verbose=True, debug=False,ignoreneg=False):
""" Compute concentric aperture photometry on one ore more stars
(adapted for IDL from DAOPHOT, then translated from IDL to Python).
APER can compute photometry in several user-specified aperture radii.
A separate sky value is computed for each source using specified inner
and outer sky radii.
By default, APER uses a magnitude system where a magnitude of
25 corresponds to 1 flux unit. APER returns both
fluxes and magnitudes.
REQUIRED INPUTS:
image - input image array
xc - scalar x value or 1D array of x coordinates.
yc - scalar y value or 1D array of y coordinates
OPTIONAL KEYWORD INPUTS:
phpadu - Photons per Analog Digital Units, numeric scalar. Converts
the data numbers in IMAGE to photon units. (APER assumes
Poisson statistics.)
apr - scalar or 1D array of photometry aperture radii in pixel units.
zeropoint - zero point for converting flux (in ADU) to magnitudes
skyrad - Two element list giving the inner and outer radii
to be used for the sky annulus
badpix - Two element list giving the minimum and maximum value
of a good pix. If BADPIX[0] is equal to BADPIX[1] then
it is assumed that there are no bad pixels.
exact - By default, APER counts subpixels, but uses a polygon
approximation for the intersection of a circular aperture with
a square pixel (and normalize the total area of the sum of the
pixels to exactly match the circular area). If the /EXACT
keyword, then the intersection of the circular aperture with a
square pixel is computed exactly. The /EXACT keyword is much
slower and is only needed when small (~2 pixels) apertures are
used with very undersampled data.
print - if set and non-zero then APER will also write its results to
a file aper.prt. One can specify the output file name by
setting PRINT = 'filename'.
verbose - Print warnings, status, and ancillary info to the terminal
setskyval - Use this keyword to force the sky to a specified value
rather than have APER compute a sky value. SETSKYVAL
can either be a scalar specifying the sky value to use for
all sources, or a 3 element vector specifying the sky value,
the sigma of the sky value, and the number of elements used
to compute a sky value. The 3 element form of SETSKYVAL
is needed for accurate error budgeting.
RETURNS:
mags - NAPER by NSTAR array giving the magnitude for each star in
each aperture. (NAPER is the number of apertures, and NSTAR
is the number of stars). A flux of 1 digital unit is assigned
a zero point magnitude of 25.
magerr - NAPER by NSTAR array giving error in magnitude
for each star. If a magnitude could not be deter-
mined then ERRAP = 9.99.
flux - NAPER by NSTAR array giving fluxes
fluxerr - NAPER by NSTAR array giving error in each flux
sky - NSTAR element array giving sky value for each star
skyerr - NSTAR element array giving error in sky values
outstr - string for each star and aperture reporting the mag and err
PROCEDURES USED:
MMM, PIXWT()
NOTES:
Reasons that a valid magnitude cannot be computed include the following:
(1) Star position is too close (within 0.5 pixels) to edge of the frame
(2) Less than 20 valid pixels available for computing sky
(3) Modal value of sky could not be computed by the procedure MMM
(4) *Any* pixel within the aperture radius is a "bad" pixel
APER was modified in June 2000 in two ways: (1) the /EXACT keyword was
added (2) the approximation of the intersection of a circular aperture
with square pixels was improved (i.e. when /EXACT is not used)
REVISON HISTORY:
Adapted to IDL from DAOPHOT June, 1989 B. Pfarr, STX
Adapted for IDL Version 2, J. Isensee, July, 1990
Code, documentation spiffed up W. Landsman August 1991
TEXTOUT may be a string W. Landsman September 1995
FLUX keyword added J. E. Hollis, February, 1996
SETSKYVAL keyword, increase maxsky W. Landsman, May 1997
Work for more than 32767 stars W. Landsman, August 1997
Converted to IDL V5.0 W. Landsman September 1997
Don't abort for insufficient sky pixels W. Landsman May 2000
Added /EXACT keyword W. Landsman June 2000
Allow SETSKYVAL = 0 W. Landsman December 2000
Set BADPIX[0] = BADPIX[1] to ignore bad pixels W. L. January 2001
Fix chk_badpixel problem introduced Jan 01 C. Ishida/W.L. February 2001
Converted from IDL to python D. Jones January 2014
Adapted for hstphot project S. Rodney July 2014
"""
if verbose > 1:
import time
tstart = time.time()
elif verbose: import time
if debug :
import pdb
pdb.set_trace()
# Set parameter limits
if len(minsky) == 0: minsky = 20
#minsky = -1000.
# Number of columns and rows in image array
s = np.shape(image)
ncol = s[1]
nrow = s[0]
if setskyval is not None :
if not np.iterable(setskyval) :
setskyval = [setskyval,0.,1.]
assert len(setskyval)==3, 'Keyword SETSKYVAL must contain 1 or 3 elements'
skyrad = [ 0., max(apr) + 1]
skyrad = asfarray(skyrad)
if not np.iterable( xc ):
xc = np.array([xc])
yc = np.array([yc])
assert len(xc) == len(yc), 'xc and yc arrays must be identical length.'
if not np.iterable( apr ) :
apr = np.array( [ apr ] )
Naper = len( apr ) # Number of apertures
Nstars = len( xc ) # Number of stars to measure
# String array to display mags for all apertures in one line for each star
outstr = [ '' for star in range(Nstars)]
# Declare arrays
mag = zeros( [ Nstars, Naper])
magerr = zeros( [ Nstars, Naper])
flux = zeros( [ Nstars, Naper])
fluxerr = zeros( [ Nstars, Naper])
badflag = zeros( [ Nstars, Naper])
sky = zeros( Nstars )
skyerr = zeros( Nstars )
area = np.pi*apr*apr # Area of each aperture
if exact:
bigrad = apr + 0.5
smallrad = apr/np.sqrt(2) - 0.5
if setskyval is None :
rinsq = skyrad[0]**2
routsq = skyrad[1]**2
# Compute the limits of the submatrix. Do all stars in vector notation.
lx = (xc-skyrad[1]).astype(int) # Lower limit X direction
ly = (yc-skyrad[1]).astype(int) # Lower limit Y direction
ux = (xc+skyrad[1]).astype(int) # Upper limit X direction
uy = (yc+skyrad[1]).astype(int) # Upper limit Y direction
lx[where(lx < 0)[0]] = 0
ux[where(ux > ncol-1)[0]] = ncol-1
nx = ux-lx+1 # Number of pixels X direction
ly[where(ly < 0)[0]] = 0
uy[where(uy > nrow-1)[0]] = nrow-1
ny = uy-ly +1 # Number of pixels Y direction
dx = xc-lx # X coordinate of star's centroid in subarray
dy = yc-ly # Y coordinate of star's centroid in subarray
# Find the edge of the subarray that is closest to each star
# and then flag any stars that are too close to the edge or off-image
edge = zeros(len(dx))
for i,dx1,nx1,dy1,ny1 in zip(range(len(dx)),dx,nx,dy,ny):
edge[i] = min([(dx[i]-0.5),(nx[i]+0.5-dx[i]),(dy[i]-0.5),(ny[i]+0.5-dy[i])])
badstar = np.where( (xc<0.5) | (xc>ncol-1.5) |
(yc<0.5) | (yc>nrow-1.5), 1, 0 )
if np.any( badstar ) :
nbad = badstar.sum()
print('WARNING - ' + str(nbad) + ' star positions outside image')
if verbose :
tloop = time.time()
for i in range(Nstars): # Compute magnitudes for each star
#print i,Nstars
while True :
# mimic GOTO statements : break out of this while block whenever
# we decide this star is bad
apflux = asarray([np.nan]*Naper)
apfluxerr = asarray([np.nan]*Naper)
apmag = asarray([np.nan]*Naper)
apmagerr = asarray([np.nan]*Naper)
skymod = 0. # Sky mode
skysig = 0. # Sky sigma
skyskw = 0. # Sky skew
error1 = asarray([np.nan]*Naper)
error2 = asarray([np.nan]*Naper)
error3 = array([np.nan]*Naper)
apbad = np.ones( Naper )
if badstar[i]: # star is bad, return NaNs for all values
break
rotbuf = image[ ly[i]:uy[i]+1,lx[i]:ux[i]+1 ] #Extract subarray from image
shapey,shapex = np.shape(rotbuf)[0],np.shape(rotbuf)[1]
# RSQ will be an array, the same size as ROTBUF containing the square of
# the distance of each pixel to the center pixel.
dxsq = ( arange( nx[i] ) - dx[i] )**2
# if ny[i] < 0:
# if verbose:
# print("WARNING : aperture extends outside the image!")
# continue
# if nx[i] < 0:
# if verbose:
# print("WARNING : aperture extends outside the image!")
# continue
try:
rsq = np.ones( [ny[i], nx[i]] )
except:
print 'negative dimension'
break
for ii in range(ny[i]):
rsq[ii,:] = dxsq + (ii-dy[i])**2
if exact:
nbox = range(nx[i]*ny[i])
xx = (nbox % nx[i]).reshape( ny[i], nx[i])
yy = (nbox/nx[i]).reshape(ny[i],nx[i])
x1 = np.abs(xx-dx[i])
y1 = np.abs(yy-dy[i])
else:
r = np.sqrt(rsq) - 0.5 #2-d array of the radius of each pixel in the subarray
rsq,rotbuf = rsq.reshape(shapey*shapex),rotbuf.reshape(shapey*shapex)
if setskyval is None :
# skypix will be 1-d array of sky pixels
skypix = np.zeros( rsq.shape )
# Select pixels within sky annulus,
skypix[where(( rsq >= rinsq ) &
( rsq <= routsq ))[0]] = 1
if badpix[0]!=badpix[1] :
# Eliminate pixels above or below the badpix threshold vals
skypix[where(((rotbuf < badpix[0]) | (rotbuf > badpix[1])) &
(skypix == 1))[0]] = 0
sindex = where(skypix)[0]
nsky = len(sindex)
if ( nsky < minsky ): # Insufficient sky pixels?
if verbose:
print("ERROR: nsky=%i is fewer than minimum %i valid pixels in the sky annulus."%(nsky,minsky))
break
skybuf = rotbuf[ sindex[0:nsky] ]
if skyisempty :
# The sky annulus is (nearly) empty of stars, (as in a diff image)
# so we can simply compute the sigma-clipped mean of all pixels in
# the annulus
skybufclipped = sigmaclip( skybuf, low=4.0, high=4.0)
try:
skymod = np.mean( skybufclipped )[0]
skysig = np.std( skybufclipped )[0]
except:
print 'sky buff excepted'
skymod, skysig, skyskw = mmm.mmm(skybuf, readnoise=readnoise, minsky=minsky)
skyskw = -999#skew( skybufclipped )
else:
# Compute the sky mode, sigma and skewness using the
# mean/median/mode algorithm in mmm.py, which assumes that
# most of the outlier pixels are positive.
skymod, skysig, skyskw = mmm.mmm(skybuf,readnoise=readnoise,minsky=minsky)
skyvar = skysig**2 #Variance of the sky brightness
sigsq = skyvar/nsky #Square of standard error of mean sky brightness
if ( skysig < 0.0 ):
# If the modal sky value could not be determined, then all
# apertures for this star are bad. So skip to the next.
break
if skysig > 999.99: skysig = 999 #Don't overload output formats
if skyskw < -99: skyskw = -99
if skyskw > 999.9: skyskw = 999.9
else:
skymod = setskyval[0]
skysig = setskyval[1]
nsky = setskyval[2]
skyvar = skysig**2
sigsq = skyvar/nsky
skyskw = 0
for k in range(Naper): # Find pixels within each aperture
thisapd = array([])
if ( edge[i] >= apr[k] ): #Does aperture extend outside the image?
if exact:
mask = zeros(ny[i]*nx[i])
x1,y1 = x1.reshape(ny[i]*nx[i]),y1.reshape(ny[i]*nx[i])
good = where( ( x1 < smallrad[k] ) & (y1 < smallrad[k] ))[-1]
Ngood = len(good)
if Ngood > 0: mask[good] = 1
bad = where( (x1 > bigrad[k]) | (y1 > bigrad[k] ))[-1]
mask[bad] = -1
gfract = where(mask == 0.0)[0]
Nfract = len(gfract)
if Nfract > 0:
yygfract = yy.reshape(ny[i]*nx[i])[gfract]
xxgfract = xx.reshape(ny[i]*nx[i])[gfract]
mask[gfract] = pixwt.Pixwt(dx[i],dy[i],apr[k],xxgfract,yygfract)
mask[gfract[where(mask[gfract] < 0.0)[0]]] = 0.0
thisap = where(mask > 0.0)[0]
thisapd = rotbuf[thisap]
fractn = mask[thisap]
else:
# approximating the circular aperture shape
rshapey,rshapex = np.shape(r)[0],np.shape(r)[1]
thisap = where( r.reshape(rshapey*rshapex) < apr[k] )[0] # Select pixels within radius
thisapd = rotbuf.reshape(rshapey*rshapex)[thisap]
thisapr = r.reshape(rshapey*rshapex)[thisap]
fractn = apr[k]-thisapr
fractn[where(fractn > 1)[0]] = 1
fractn[where(fractn < 0)[0]] = 0 # Fraction of pixels to count
full = zeros(len(fractn))
full[where(fractn == 1)[0]] = 1.0
gfull = where(full)[0]
Nfull = len(gfull)
gfract = where(1 - full)[0]
factor = (area[k] - Nfull ) / np.sum(fractn[gfract])
fractn[gfract] = fractn[gfract]*factor
else:
if verbose :
print("WARNING : aperture extends outside the image!")
continue
# END "if exact ... else ..."
# Check for any bad pixel values (nan,inf) and those outside
# the user-specified range of valid pixel values. If any
# are found in the aperture, raise the badflux flag.
apbad[k] = 0
if not np.all( np.isfinite(thisapd) ) :
if verbose :
print("WARNING : nan or inf pixels detected in aperture.\n"
"We're setting these to 0, but the photometry"
"may be biased.")
thisapd[np.isfinite()==False] = 0
apbad[k] = 1
fractn = 0
if badpix[0] < badpix[1] :
ibadpix = np.where((thisapd<=badpix[0]) | (thisapd>=badpix[1]))
if len(ibadpix[0]) > 0 :
if verbose :
print("WARNING : pixel values detected in aperture"
" that are outside of the allowed range "
" [%.1f , %.1f] \n"%(badpix[0],badpix[1]) +
"We're treating these as 0, but the "
"photometry may be biased.")
thisapd[ibadpix] = 0
apbad[k] = 1
# Sum the flux over the irregular aperture
apflux[k] = np.sum(thisapd*fractn)
# END for loop over apertures
g = where(np.isfinite(apflux))[0]
Ng = len(g)
if Ng > 0:
# Subtract sky from the integrated brightnesses
apflux[g] = apflux[g] - skymod*area[g]
# Compute flux error
error1[g] = area[g]*skyvar #Scatter in sky values
error2[g] = where( apflux[g]>=0, apflux[g]/phpadu, 0 ) #Random photon noise
error3[g] = sigsq*area[g]**2 #Uncertainty in mean sky brightness
apfluxerr[g] = np.sqrt(error1[g] + error2[g] + error3[g])
good = where (apflux > 0.0)[0] # Are there any valid integrated fluxes?
Ngood = len(good)
if ( Ngood > 0 ) : # convert valid fluxes to mags
apmagerr[good] = 1.0857*apfluxerr[g]/apflux[g] #1.0857 = log(10)/2.5
apmag[good] = zeropoint-2.5*np.log10(apflux[g])
break # Closing the 'while True' loop.
# TODO : make a more informative output string
outstr[i] = '%.3f,%.3f :'%(xc[i],yc[i]) + \
' '.join( [ '%.4f+-%.4f'%(apmag[ii],apmagerr[ii])
for ii in range(Naper) ] )
sky[i] = skymod
skyerr[i] = skysig
mag[i,:] = apmag
magerr[i,:]= apmagerr
flux[i,:] = apflux
fluxerr[i,:]= apfluxerr
badflag[i,:] = apbad
if Nstars == 1 :
sky = sky[0]
skyerr = skyerr[0]
mag = mag[0]
magerr = magerr[0]
flux = flux[0]
fluxerr = fluxerr[0]
badflag = badflag[0]
outstr = outstr[0]
if verbose>1:
print('hstphot.aper took %.3f seconds'%(time.time()-tstart))
print('Each of %i loops took %.3f seconds'%(Nstars,(time.time()-tloop)/Nstars))
return(mag,magerr,flux,fluxerr,sky,skyerr,badflag,outstr)
def tv(self,img,min=None,max=None,cmap=None) :
"""
main display routine: displays image with optional scaling
Args:
img: a numpy array OR a fits HDU
Keyword args:
min=, max= : optional scaling arguments
"""
# load data array depending on input type
if isinstance(img, (np.ndarray)) :
data = img
elif isinstance(img.data, (np.ndarray)) :
data = img.data
else :
print('input must be numpy array or have data attribute that is')
return
# set figure and axes
plt.figure(self.fig.number)
plt.axes(self.ax)
#self.ax.cla()
#self.ax.axis('off')
# make last image not visible so we don't see anything if new image is smaller
if self.axlist[self.current] is not None: self.axlist[self.current].set_visible(False)
# load new image data onto rolling stack
current= (self.current+1) % 4
self.images += 1
if self.images > 4 : self.images = 4
self.current = current
self.imglist.pop(current)
self.imglist.insert(current,data)
self.img = data
# save the header if we have one
if hasattr(img,'header') :
self.hdrlist.pop(current)
self.hdrlist.insert(current,img.header)
self.hdr=img.header
else :
self.hdr=None
# get autodisplay parameters if needed, and save display params
if min is None :
min = 0.
if max is None :
try :
sky = mmm.mmm(data)
min = sky[0]-5*sky[1]
max = sky[0]+20*sky[1]
except :
min = np.median(data)-5*data.std()
max = np.median(data)+20*data.std()
self.scale = [min,max]
self.scalelist.pop(current)
self.scalelist.insert(current,self.scale)
if cmap != None :
self.cmap = cmap
# display image and new colorbar
dim=np.shape(self.img)
size=np.max([dim[0],dim[1]])
self.ax.set_xlim(dim[1]/2.-size/2.,dim[1]/2.+size/2.)
self.ax.set_ylim(dim[0]/2.-size/2.,dim[0]/2.+size/2.)
#self.ax.set_xlim(-0.5,dim[1]-0.5)
#self.ax.set_ylim(-0.5,dim[0]-0.5)
#print('aspect: ', self.aspect,' xlim: ', self.ax.get_xlim(),' ylim: ',self.ax.get_ylim(), data.shape)
self.aximage = self.ax.imshow(data,vmin=min,vmax=max,cmap=self.cmap,interpolation='nearest',aspect=self.aspect)
old=self.axlist.pop(current)
# if we had a previous image, reload the data with a single value
# so we don't continually accumulate memory (matplotlib doesn't
# describe how memory can be released
z=np.zeros([1,1])
if old is not None : old.set_data(z)
self.axlist.insert(current,self.aximage)
if self.cb is None :
#self.cb = self.fig.colorbar(self.aximage,orientation='horizontal',shrink=0.7,pad=0)
self.cb = self.fig.colorbar(self.aximage,cax=self.cb_ax,orientation='horizontal')
#plt.subplots_adjust(left=-0.15,right=1.15,bottom=-0.10,top=1.00)
else :
self.cb.ax.clear()
self.cb = self.fig.colorbar(self.aximage,cax=self.cb.ax,orientation='horizontal')
self.cblist.pop(current)
self.cblist.insert(current,self.cb)
plt.draw()
def aper(image,xc,yc, phpadu=1, apr=5, zeropoint=25,
skyrad=[40,50], badpix=[0,0], setskyval = None, minsky=[],
skyalgorithm='mmm', exact = False, readnoise = 0,
verbose=True, debug=False):
""" Compute concentric aperture photometry on one ore more stars
(adapted for IDL from DAOPHOT, then translated from IDL to Python).
APER can compute photometry in several user-specified aperture radii.
A separate sky value is computed for each source using specified inner
and outer sky radii.
By default, APER uses a magnitude system where a magnitude of
25 corresponds to 1 flux unit. APER returns both
fluxes and magnitudes.
REQUIRED INPUTS:
image - input image array
xc - scalar x value or 1D array of x coordinates.
yc - scalar y value or 1D array of y coordinates
OPTIONAL KEYWORD INPUTS:
phpadu - Photons per Analog Digital Units, numeric scalar. Converts
the data numbers in IMAGE to photon units. (APER assumes
Poisson statistics.)
apr - scalar or 1D array of photometry aperture radii in pixel units.
zeropoint - zero point for converting flux (in ADU) to magnitudes
skyrad - Two element list giving the inner and outer radii
to be used for the sky annulus
badpix - Two element list giving the minimum and maximum value
of a good pix. If BADPIX[0] is equal to BADPIX[1] then
it is assumed that there are no bad pixels.
exact - By default, APER counts subpixels, but uses a polygon
approximation for the intersection of a circular aperture with
a square pixel (and normalize the total area of the sum of the
pixels to exactly match the circular area). If the /EXACT
keyword, then the intersection of the circular aperture with a
square pixel is computed exactly. The /EXACT keyword is much
slower and is only needed when small (~2 pixels) apertures are
used with very undersampled data.
print - if set and non-zero then APER will also write its results to
a file aper.prt. One can specify the output file name by
setting PRINT = 'filename'.
verbose - Print warnings, status, and ancillary info to the terminal
setskyval - Use this keyword to force the sky to a specified value
rather than have APER compute a sky value. SETSKYVAL
can either be a scalar specifying the sky value to use for
all sources, or a 3 element vector specifying the sky value,
the sigma of the sky value, and the number of elements used
to compute a sky value. The 3 element form of SETSKYVAL
is needed for accurate error budgeting.
skyalgorithm - set the algorithm by which the sky value is determined
Valid options are 'sigmaclipping' or 'mmm'.
RETURNS:
mags - NAPER by NSTAR array giving the magnitude for each star in
each aperture. (NAPER is the number of apertures, and NSTAR
is the number of stars). A flux of 1 digital unit is assigned
a zero point magnitude of 25.
magerr - NAPER by NSTAR array giving error in magnitude
for each star. If a magnitude could not be deter-
mined then ERRAP = 9.99.
flux - NAPER by NSTAR array giving fluxes
fluxerr - NAPER by NSTAR array giving error in each flux
sky - NSTAR element array giving sky value for each star
skyerr - NSTAR element array giving error in sky values
outstr - string for each star and aperture reporting the mag and err
PROCEDURES USED:
MMM, PIXWT()
NOTES:
Reasons that a valid magnitude cannot be computed include the following:
(1) Star position is too close (within 0.5 pixels) to edge of the frame
(2) Less than 20 valid pixels available for computing sky
(3) Modal value of sky could not be computed by the procedure MMM
(4) *Any* pixel within the aperture radius is a "bad" pixel
APER was modified in June 2000 in two ways: (1) the /EXACT keyword was
added (2) the approximation of the intersection of a circular aperture
with square pixels was improved (i.e. when /EXACT is not used)
REVISON HISTORY:
Adapted to IDL from DAOPHOT June, 1989 B. Pfarr, STX
Adapted for IDL Version 2, J. Isensee, July, 1990
Code, documentation spiffed up W. Landsman August 1991
TEXTOUT may be a string W. Landsman September 1995
FLUX keyword added J. E. Hollis, February, 1996
SETSKYVAL keyword, increase maxsky W. Landsman, May 1997
Work for more than 32767 stars W. Landsman, August 1997
Converted to IDL V5.0 W. Landsman September 1997
Don't abort for insufficient sky pixels W. Landsman May 2000
Added /EXACT keyword W. Landsman June 2000
Allow SETSKYVAL = 0 W. Landsman December 2000
Set BADPIX[0] = BADPIX[1] to ignore bad pixels W. L. January 2001
Fix chk_badpixel problem introduced Jan 01 C. Ishida/W.L. February 2001
Converted from IDL to python D. Jones January 2014
Adapted for hstphot project S. Rodney July 2014
"""
if verbose > 1:
import time
tstart = time.time()
elif verbose: import time
if debug :
import pdb
pdb.set_trace()
# Force np arrays
if not np.iterable( xc ):
xc = np.array([xc])
yc = np.array([yc])
assert len(xc) == len(yc), 'xc and yc arrays must be identical length.'
if not np.iterable( apr ) :
apr = np.array( [ apr ] )
Naper = len( apr ) # Number of apertures
Nstars = len( xc ) # Number of stars to measure
# Set parameter limits
if len(minsky) == 0: minsky = 20
# Number of columns and rows in image array
s = np.shape(image)
ncol = s[1]
nrow = s[0]
if setskyval is not None :
if not np.iterable(setskyval) :
setskyval = [setskyval,0.,1.]
assert len(setskyval)==3, 'Keyword SETSKYVAL must contain 1 or 3 elements'
skyrad = [ 0., np.max(apr) + 1] #use np.max (max function does not work on scalars)
skyrad = asfarray(skyrad)
# String array to display mags for all apertures in one line for each star
outstr = [ '' for star in range(Nstars)]
# Declare arrays
mag = zeros( [ Nstars, Naper])
magerr = zeros( [ Nstars, Naper])
flux = zeros( [ Nstars, Naper])
fluxerr = zeros( [ Nstars, Naper])
badflag = zeros( [ Nstars, Naper])
sky = zeros( Nstars )
skyerr = zeros( Nstars )
area = np.pi*apr*apr # Area of each aperture
if exact:
bigrad = apr + 0.5
smallrad = apr/np.sqrt(2) - 0.5
if setskyval is None :
rinsq = skyrad[0]**2
routsq = skyrad[1]**2
# Compute the limits of the submatrix. Do all stars in vector notation.
lx = (xc-skyrad[1]).astype(int) # Lower limit X direction
ly = (yc-skyrad[1]).astype(int) # Lower limit Y direction
ux = (xc+skyrad[1]).astype(int) # Upper limit X direction
uy = (yc+skyrad[1]).astype(int) # Upper limit Y direction
lx[where(lx < 0)[0]] = 0
ux[where(ux > ncol-1)[0]] = ncol-1
nx = ux-lx+1 # Number of pixels X direction
ly[where(ly < 0)[0]] = 0
uy[where(uy > nrow-1)[0]] = nrow-1
ny = uy-ly +1 # Number of pixels Y direction
dx = xc-lx # X coordinate of star's centroid in subarray
dy = yc-ly # Y coordinate of star's centroid in subarray
# Find the edge of the subarray that is closest to each star
# and then flag any stars that are too close to the edge or off-image
edge = zeros(len(dx))
for i,dx1,nx1,dy1,ny1 in zip(range(len(dx)),dx,nx,dy,ny):
edge[i] = min([(dx[i]-0.5),(nx[i]+0.5-dx[i]),(dy[i]-0.5),(ny[i]+0.5-dy[i])])
badstar = np.where( (xc<0.5) | (xc>ncol-1.5) |
(yc<0.5) | (yc>nrow-1.5), 1, 0 )
if np.any( badstar ) :
nbad = badstar.sum()
print('WARNING [aper.py] - ' + str(nbad) + ' star positions outside image')
if verbose :
tloop = time.time()
for i in range(Nstars): # Compute magnitudes for each star
while True :
# mimic GOTO statements : break out of this while block whenever
# we decide this star is bad
apflux = asarray([np.nan]*Naper)
apfluxerr = asarray([np.nan]*Naper)
apmag = asarray([np.nan]*Naper)
apmagerr = asarray([np.nan]*Naper)
skymod = 0. # Sky mode
skysig = 0. # Sky sigma
skyskw = 0. # Sky skew
error1 = asarray([np.nan]*Naper)
error2 = asarray([np.nan]*Naper)
error3 = array([np.nan]*Naper)
apbad = np.ones( Naper )
if badstar[i]: # star is bad, return NaNs for all values
break
rotbuf = image[ ly[i]:uy[i]+1,lx[i]:ux[i]+1 ] #Extract subarray from image
shapey,shapex = np.shape(rotbuf)[0],np.shape(rotbuf)[1]
# RSQ will be an array, the same size as ROTBUF containing the square of
# the distance of each pixel to the center pixel.
dxsq = ( arange( nx[i] ) - dx[i] )**2
rsq = np.ones( [ny[i], nx[i]] )
for ii in range(ny[i]):
rsq[ii,:] = dxsq + (ii-dy[i])**2
if exact:
nbox = range(nx[i]*ny[i])
xx = (nbox % nx[i]).reshape( ny[i], nx[i])
yy = (nbox/nx[i]).reshape(ny[i],nx[i])
x1 = np.abs(xx-dx[i])
y1 = np.abs(yy-dy[i])
else:
r = np.sqrt(rsq) - 0.5 #2-d array of the radius of each pixel in the subarray
rsq,rotbuf = rsq.reshape(shapey*shapex),rotbuf.reshape(shapey*shapex)
if setskyval is None :
# skypix will be 1-d array of sky pixels
skypix = np.zeros( rsq.shape )
# Select pixels within sky annulus,
skypix[where(( rsq >= rinsq ) &
( rsq <= routsq ))[0]] = 1
if badpix[0]!=badpix[1] :
# Eliminate pixels above or below the badpix threshold vals
skypix[where(((rotbuf < badpix[0]) | (rotbuf > badpix[1])) &
(skypix == 1))[0]] = 0
sindex = where(skypix)[0]
nsky = len(sindex)
if ( nsky < minsky ): # Insufficient sky pixels?
if verbose:
print("ERROR: nsky=%i is fewer than minimum %i valid pixels in the sky annulus."%(nsky,minsky))
break
skybuf = rotbuf[ sindex[0:nsky] ]
if skyalgorithm.startswith('sigmaclip'):
# The sky annulus is (nearly) empty of stars, (as in a diff image)
# so we can simply compute the sigma-clipped mean of all pixels in
# the annulus
skybufclipped,lothresh,hithresh = sigmaclip( skybuf, low=4.0, high=4.0)
skymod = np.mean( skybufclipped )
skysig = np.std( skybufclipped )
skyskw = skew( skybufclipped )
else:
# Compute the sky mode, sigma and skewness using the
# mean/median/mode algorithm in mmm.py, which assumes that
# most of the outlier pixels are positive.
skymod, skysig, skyskw = mmm.mmm(skybuf,readnoise=readnoise,minsky=minsky)
skyvar = skysig**2 #Variance of the sky brightness
sigsq = skyvar/nsky #Square of standard error of mean sky brightness
if ( skysig < 0.0 ):
# If the modal sky value could not be determined, then all
# apertures for this star are bad. So skip to the next.
break
if skysig > 999.99: skysig = 999 #Don't overload output formats
if skyskw < -99: skyskw = -99
if skyskw > 999.9: skyskw = 999.9
else:
skymod = setskyval[0]
skysig = setskyval[1]
nsky = setskyval[2]
skyvar = skysig**2
sigsq = skyvar/nsky
skyskw = 0
for k in range(Naper): # Find pixels within each aperture
if ( edge[i] >= apr[k] ): #Does aperture extend outside the image?
if exact:
mask = zeros(ny[i]*nx[i])
x1,y1 = x1.reshape(ny[i]*nx[i]),y1.reshape(ny[i]*nx[i])
igoodmag = where( ( x1 < smallrad[k] ) & (y1 < smallrad[k] ))[-1]
Ngoodmag = len(igoodmag)
if Ngoodmag > 0: mask[igoodmag] = 1
bad = where( (x1 > bigrad[k]) | (y1 > bigrad[k] ))[-1]
mask[bad] = -1
gfract = where(mask == 0.0)[0]
Nfract = len(gfract)
if Nfract > 0:
yygfract = yy.reshape(ny[i]*nx[i])[gfract]
xxgfract = xx.reshape(ny[i]*nx[i])[gfract]
mask[gfract] = pixwt.Pixwt(dx[i],dy[i],apr[k],xxgfract,yygfract)
mask[gfract[where(mask[gfract] < 0.0)[0]]] = 0.0
thisap = where(mask > 0.0)[0]
thisapd = rotbuf[thisap]
fractn = mask[thisap]
else:
# approximating the circular aperture shape
rshapey,rshapex = np.shape(r)[0],np.shape(r)[1]
thisap = where( r.reshape(rshapey*rshapex) < apr[k] )[0] # Select pixels within radius
thisapd = rotbuf.reshape(rshapey*rshapex)[thisap]
thisapr = r.reshape(rshapey*rshapex)[thisap]
fractn = apr[k]-thisapr
fractn[where(fractn > 1)[0]] = 1
fractn[where(fractn < 0)[0]] = 0 # Fraction of pixels to count
full = zeros(len(fractn))
full[where(fractn == 1)[0]] = 1.0
gfull = where(full)[0]
Nfull = len(gfull)
gfract = where(1 - full)[0]
factor = (area[k] - Nfull ) / np.sum(fractn[gfract])
fractn[gfract] = fractn[gfract]*factor
else:
if verbose :
print("WARNING [aper.py]: aperture extends outside the image!")
continue
# END "if exact ... else ..."
# Check for any bad pixel values (nan,inf) and those outside
# the user-specified range of valid pixel values. If any
# are found in the aperture, raise the badflux flag.
apbad[k] = 0
if not np.all( np.isfinite(thisapd) ) :
if verbose :
print("WARNING : nan or inf pixels detected in aperture.\n"
"We're setting these to 0, but the photometry"
"may be biased.")
thisapd[np.isfinite(thisapd)==False] = 0
apbad[k] = 1
fractn = 0
if badpix[0] < badpix[1] :
ibadpix = np.where((thisapd<=badpix[0]) | (thisapd>=badpix[1]))
if len(ibadpix[0]) > 0 :
if verbose :
print("WARNING : pixel values detected in aperture"
" that are outside of the allowed range "
" [%.1f , %.1f] \n"%(badpix[0],badpix[1]) +
"We're treating these as 0, but the "
"photometry may be biased.")
thisapd[ibadpix] = 0
apbad[k] = 1
# Sum the flux over the irregular aperture
apflux[k] = np.sum(thisapd*fractn)
# END for loop over apertures
igoodflux = where(np.isfinite(apflux))[0]
Ngoodflux = len(igoodflux)
if Ngoodflux > 0:
if verbose > 2 :
print(" SRCFLUX APFLUX SKYMOD AREA")
for igf in igoodflux :
print("%.4f %.4f %.4f %.4f "%(apflux[igf]-skymod*area[igf],apflux[igf],skymod,area[igf]))
# Subtract sky from the integrated brightnesses
apflux[igoodflux] = apflux[igoodflux] - skymod*area[igoodflux]
# Compute flux error
error1[igoodflux] = area[igoodflux]*skyvar #Scatter in sky values
error2[igoodflux] = np.abs(apflux[igoodflux])/phpadu #Random photon noise
error3[igoodflux] = sigsq*area[igoodflux]**2 #Uncertainty in mean sky brightness
apfluxerr[igoodflux] = np.sqrt(error1[igoodflux] + error2[igoodflux] + error3[igoodflux])
igoodmag = where (apflux > 0.0)[0] # Are there any valid integrated fluxes?
Ngoodmag = len(igoodmag)
if ( Ngoodmag > 0 ) : # convert valid fluxes to mags
apmagerr[igoodmag] = 1.0857*apfluxerr[igoodmag]/apflux[igoodmag] #1.0857 = log(10)/2.5
apmag[igoodmag] = zeropoint-2.5*np.log10(apflux[igoodmag])
break # Closing the 'while True' loop.
# TODO : make a more informative output string
outstr[i] = '%.3f,%.3f :'%(xc[i],yc[i]) + \
' '.join( [ '%.4f+-%.4f'%(apmag[ii],apmagerr[ii])
for ii in range(Naper) ] )
sky[i] = skymod
skyerr[i] = skysig
mag[i,:] = apmag
magerr[i,:]= apmagerr
flux[i,:] = apflux
fluxerr[i,:]= apfluxerr
badflag[i,:] = apbad
if Nstars == 1 :
sky = sky[0]
skyerr = skyerr[0]
mag = mag[0]
magerr = magerr[0]
flux = flux[0]
fluxerr = fluxerr[0]
badflag = badflag[0]
outstr = outstr[0]
if verbose>1:
print('hstphot.aper took %.3f seconds'%(time.time()-tstart))
print('Each of %i loops took %.3f seconds'%(Nstars,(time.time()-tloop)/Nstars))
return(mag,magerr,flux,fluxerr,sky,skyerr,badflag,outstr)
import time
import mmm
class subc(threading.Thread):
def __init__(self):
threading.Thread.__init__(self)
def run(self):
print 'sleep 3s...\n'
time.sleep(3)
print 'sleep 3s end\n'
#global ggg.isflag
print 'subc isflag id: ', id(ggg.isflag)
ggg.isflag = True
print 'subc isflag: ', ggg.isflag
t2 = mmm.mmm()
t2.setDaemon(True)
t2.start()
t1 = subc()
t1.setDaemon(True)
t1.start()
t2.join()
print '---'