def getSize(self, file): ''' This function can be used to get the size of the image. It actually returns a simple information found from the image header, however, when parsed correctly the image size is available. ''' self.file = file head = I.imheader(self.file, Stdout=1) return head
def getSize(self, file):
'''
This function can be used to get the size of the image. It actually
returns a simple information found from the image header, however,
when parsed correctly the image size is available.
'''
self.file = file
head = I.imheader(self.file, Stdout=1)
return head
def get_image_size(images):
result = iraf.imheader(images=images, longheader=0, Stdout=1)
if result[0] == '':
return None
array = {}
for item in result:
res = re.search(r'(.*)\[([0-9]+),([0-9]+)\]', item)
array[res.group(1)] = [int(res.group(2)), int(res.group(3))]
if len(array.keys()) == 1:
return array[array.keys()[0]]
else:
return array
def find_param_with_comment(filename, comment):
header_long = iraf.imheader(filename, lo=True, Stdout=True)
for header_val in header_long:
trimmed = header_val.replace(' = ',
'!^!^!').replace(' / ',
'!^!^!').split('!^!^!')
if len(trimmed) < 3:
continue
elif trimmed[2] == comment:
return trimmed[0]
else:
pass
return 'NullReturn'
def get_comment(filename, paramname):
header_long = iraf.imheader(filename, lo=True, Stdout=True)
for header_val in header_long:
trimmed = header_val.replace(' = ',
'!^!^!').replace(' / ',
'!^!^!').split('!^!^!')
if len(trimmed) < 3:
continue
elif trimmed[1].strip() == paramname:
return trimmed[2].strip()
else:
pass
return 'NullReturn'
def getCenter(imgs):
'''
getCenter: Uses the Iraf imcntr task to find the centers of a list of objects
Inputs: a list of image filenames <imgs> (see getIter()) to find the centers of.
Outputs: a numpy array with shape (len(imgs), 3), of the form
... ... ...
<img_name> <center_x> <center_y>
... ... ...
where all three fields are strings.
'''
out = np.full((len(imgs),3),"-1",dtype=object)
shape_re = re.compile(r"\[(?P<rows>\d+),(?P<cols>\d+)\]")
center_re = re.compile(r"x:\s+(?P<center_x>\d+\.\d*)\s+y:\s+(?P<center_y>\d+\.\d*)")
for i in range(0,len(imgs)):
header_string = iraf.imheader(imgs[i],Stdout=1)[0]
shape = shape_re.search(header_string)
rows,cols = -1,-1
if shape:
rows = int(shape.group("rows"))
cols = int(shape.group("cols"))
else:
sys.exit(1)
#end if
center_string = iraf.imcntr(imgs[i],rows/2,cols/2,cboxsize=31, Stdout=1)[0]
center = center_re.search(center_string)
center_x,center_y = "-1","-1"
if center:
center_x = str(int(float(center.group("center_x"))))
center_y = str(int(float(center.group("center_y"))))
else:
sys.exit(1)
#end if
out[i,0] = imgs[i]
out[i,1] = center_x
out[i,2] = center_y
#end loop
return out
z22 = float(z22)
_z11, _z22, goon = agnkey.util.display_image(
'original.fits', 1, z11, z22, False)
answ = raw_input(">>>>> Cuts OK [y/n] [y]?")
if not answ:
answ = 'y'
elif answ == 'no':
answ = 'n'
z11 = float(_z11)
z22 = float(_z22)
# else:
# z11=float(_z11)
# z22=float(_z22)
if not _interactive and xx0:
_dimension = string.split((string.split(
iraf.imheader('original', Stdout=1)[0], ']')[0]),
'[')[1]
aa, bb = string.split(_dimension, ',')
aa, bb = float(aa) / 2, float(bb) / 2
_vec = str(aa) + ' ' + str(bb) + ' 1'
vector = [_vec]
ff = open('tmplabel', 'w')
for i in vector:
ff.write(i + ' \n')
ff.close()
if _show:
iraf.tvmark(1, 'tmplabel', autol='no', mark="circle", radii=10, inter='no', label='no',
number='yes', \
pointsize=20, txsize=2, color=204)
os.system('cp tmplabel ' + img + '.sn.coo')
else:
def extract(image,trace,sigma,bk):
if sigma < 1.:
sigma = 1.
#sigma = sigma*2
#print sigma,"sigma"
original_file = pyfits.open(image)
original_header = iraf.imheader(images=image,longheader=1,Stdout=1)
image = pyfits.getdata(image)
image = transpose(image)
line = []
peak = []
step = 200
i = 0
while i < len(image):
crop = image[i]
bk_i = []
signal_i = []
### uncomment this to see where the extraction is taking place
# plt.plot(crop)
# plt.axvline(x=trace[i])
# plt.show()
x = arange(0,len(crop)+0.1-1,0.1)
y = interpolate.interp1d(arange(0,len(crop)),crop)
y = y(x)
weights = []
for j in range(len(x)):
for n in bk:
if x[j] > n[0] and x[j] < n[1]:
bk_i.append(y[j])
if x[j] > trace[i] - sigma and x[j] < trace[i] + sigma:
signal_i.append(y[j])
weights.append(gaussian([1,trace[i],sigma,0],x[j]))
if len(bk_i) > 0:
bk_i = median(bk_i)
else:
bk_i = 0
if len(signal_i) > 0:
pass
else:
signal_i = [0]
weights = [1]
signal_i = array(signal_i)
weights = array(weights)
line.append(i+1)
peak.append(sum(signal_i)-bk_i*len(signal_i))
#peak.append(sum(signal_i*weights)-sum(bk_i*weights))
i = i + 1
### Uncomment to plot spectrum
# plt.clf()
# plt.plot(line,peak)
# plt.show()
data = transpose(array([line,peak]))
f = open("spectrum.flux","w")
functions.write_table(data,f)
f.close()
os.system("rm spectrum.fits")
iraf.rspectext(
input = "spectrum.flux",\
output = "spectrum.fits",\
title = "",\
flux = 0,\
dtype = "interp")
update_fitsheader(original_header,original_file,"spectrum.fits")
original_file.close()
iraf.hedit('master$dark', 'EXPTIME,EXPOSURE', 1, update='yes', ver='no')
###############################################################################
# Make comment
if not noReduce:
iraf.hedit('master$dark',
'OBS_I',
'Combined darks, bias removed',
add='yes',
ver='no')
###############################################################################
# Show what we have done
print
iraf.imstat.unlearn()
iraf.imstat.setParam('fields', 'image,npix,mean,midpt,mode,stddev,min,max')
iraf.imstat('RAW$@list$dark,T$@list$dark,master$dark-uns,master$dark')
###############################################################################
# Dump the relevant information to the log
sys.stdout = open('log/3.log', 'w')
print 'darkcombine parameters'
print
iraf.ccdred.darkcombine.lParam()
print
iraf.imheader('master$dark', longheader='yes')
iraf.ccdred.zerocombine('RAW$@list$bias', output='master$bias')
###############################################################################
# Make comment
iraf.hedit('master$bias',
'OBS_I',
'Combined biases 1, 2 and 3',
add='yes',
ver='no')
###############################################################################
# Show what we have done
print
iraf.imstat.unlearn()
iraf.imstat.setParam('fields', 'image,npix,mean,midpt,mode,stddev,min,max')
iraf.imstat('RAW$@list$bias,master$bias')
###############################################################################
# Dump the relevant information to the log
sys.stdout = open('log/2.log', 'w')
print
print 'zerocombine parameters'
print
iraf.ccdred.zerocombine.lParam()
print
iraf.imheader('master$bias', longheader='yes')
###########################################################################
# Make comment
if not config.noReduce:
iraf.hedit('master$norm-flat-' + filter,
'OBS_I',
'Combined flats, bias removed',
add='yes',
ver='no')
###########################################################################
print
iraf.imstat('RAW$@list$flat-' + filter + ',' + 'T$@list$flat-' + filter +
',' + 'master$flat-' + filter + ',' + 'master$norm-flat-' +
filter,
fields='image,npix,mean,midpt,mode,stddev,min,max')
###########################################################################
# Dump the relevant information to the log
sys.stdout = open('log/4.' + filter + '.log', 'w')
print 'flatcombine parameters'
print
iraf.ccdred.flatcombine.lParam()
print
iraf.imheader('master$norm-flat-' + filter, longheader='yes')
sys.stdout = oldstdout
z22 = _z22
else:
z22 = float(z22)
_z11, _z22, goon = agnkey.util.display_image('original.fits', 1, z11, z22, False)
answ = raw_input(">>>>> Cuts OK [y/n] [y]?")
if not answ:
answ = 'y'
elif answ == 'no':
answ = 'n'
z11 = float(_z11)
z22 = float(_z22)
# else:
# z11=float(_z11)
# z22=float(_z22)
if not _interactive and xx0:
_dimension = string.split((string.split(iraf.imheader('original', Stdout=1)[0], ']')[0]), '[')[1]
aa, bb = string.split(_dimension, ',')
aa, bb = float(aa) / 2, float(bb) / 2
_vec = str(aa) + ' ' + str(bb) + ' 1'
vector = [_vec]
ff = open('tmplabel', 'w')
for i in vector:
ff.write(i + ' \n')
ff.close()
if _show:
iraf.tvmark(1, 'tmplabel', autol='no', mark="circle", radii=10, inter='no', label='no',
number='yes', \
pointsize=20, txsize=2, color=204)
os.system('cp tmplabel ' + img + '.sn.coo')
else:
answ0 = 'n'
""" This file is meant to be run by itself, demonstrating the Python-to-IRAF
API for use in testing, starting with the very simplest of function calls.
This test is useful in special installations, such as one without IRAF. """
import sys
print("Simple #1 - about to: from pyraf import iraf ...")
from pyraf import iraf
print("Simple #2 - about to import pyraf ...") # should be essentially a no-op
import pyraf
print("Simple #3 - ver is ...")
print(pyraf.__version__)
print("Simple #4 - pwd is ...")
iraf.pwd() # will print
print("Simple #5 - has IRAF is ...")
from pyraf import irafinst
print(str(irafinst.EXISTS))
if not irafinst.EXISTS:
sys.exit(0)
print("Simple #6 - files output is ... (the rest require IRAF)")
iraf.files('file_a.txt,file-b.txt,file.c.txt,,filed.txt')
print("Simple #7 - loading imutil")
iraf.images(_doprint=0) # load images
iraf.imutil(_doprint=0) # load imutil
print("Simple #8 - imaccess to dev$pix is ...")
print(iraf.imaccess("dev$pix"))
print("Simple #9 - imheader of dev$pix is ...")
iraf.imheader("dev$pix")
sys.exit(0)
ref = open(config.root + 'list/' + fn).readline().rstrip()
print
print "Aligning science frames for " + fn + " relto " + ref + "..."
iraf.imdelete("OUT$@list$" + fn)
iraf.imalign(input='INP$@list$' + fn,
reference='INP$' + ref,
coords='align$' + fn + '.coords',
output='OUT$@list$' + fn,
shifts='align$' + fn + '.shift',
niterate=config.align_niter,
trimimages=config.align_trim,
boxsize=config.align_boxsize,
bigbox=config.align_bigbox,
interp_type=config.align_interp)
###############################################################################
# Show what we have done
sys.stdout = open('log/5.log', 'w')
print 'imalign parameters'
print
iraf.imalign.lParam()
print
iraf.imheader('OUT$*', longheader='yes')
sys.stdout = oldstdout
""" This file is meant to be run by itself, demonstrating the Python-to-IRAF
API for use in testing, starting with the very simplest of function calls.
This test is useful in special installations, such as one without IRAF. """
import sys
print("Simple #1 - about to: from pyraf import iraf ...")
from pyraf import iraf
print("Simple #2 - about to import pyraf ...") # should be essentially a no-op
import pyraf
print("Simple #3 - ver is ...")
print(pyraf.__version__)
print("Simple #4 - pwd is ...")
iraf.pwd() # will print
print("Simple #5 - has IRAF is ...")
from pyraf import irafinst
print(str(irafinst.EXISTS))
if not irafinst.EXISTS:
sys.exit(0)
print("Simple #6 - files output is ... (the rest require IRAF)")
iraf.files('file_a.txt,file-b.txt,file.c.txt,,filed.txt')
print("Simple #7 - loading imutil")
iraf.images(_doprint=0) # load images
iraf.imutil(_doprint=0) # load imutil
print("Simple #8 - imaccess to dev$pix is ...")
print(iraf.imaccess("dev$pix"))
print("Simple #9 - imheader of dev$pix is ...")
iraf.imheader("dev$pix")
sys.exit(0)
