def extract(self, params={}, saveCatalog=False, saveConfig=False):
sex = SExtractor()
# default params
sex.config['PIXEL_SCALE'] = 0.45
sex.config['BACK_TYPE'] = "AUTO"
sex.config['SATUR_LEVEL'] = 60000
sex.config['DETECT_THRESH'] = 3.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['PARAMETERS_LIST'] = [
"NUMBER", "XWIN_IMAGE", "YWIN_IMAGE", "FLUX_BEST", "FWHM_IMAGE",
"FLAGS"
]
# update values from user params
sex.config.update(params)
# ok, here we go!
try:
sex.run(self._filename, clean=False)
result = sex.catalog()
return result
finally:
if saveCatalog:
shutil.move(sex.config['CATALOG_NAME'], saveCatalog)
if saveConfig:
shutil.move(sex.config['CONFIG_FILE'], saveConfig)
sex.clean(config=True, catalog=True, check=True)
def extract(self, params={}, saveCatalog=False, saveConfig=False):
sex = SExtractor()
# default params
sex.config['PIXEL_SCALE'] = 0.45
sex.config['BACK_TYPE'] = "AUTO"
sex.config['SATUR_LEVEL'] = 60000
sex.config['DETECT_THRESH'] = 3.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['PARAMETERS_LIST'] = ["NUMBER",
"XWIN_IMAGE", "YWIN_IMAGE",
"FLUX_BEST", "FWHM_IMAGE",
"FLAGS"]
# update values from user params
sex.config.update(params)
# ok, here we go!
try:
sex.run(self._filename, clean=False)
result = sex.catalog()
return result
finally:
if saveCatalog:
shutil.move(sex.config['CATALOG_NAME'], saveCatalog)
if saveConfig:
shutil.move(sex.config['CONFIG_FILE'], saveConfig)
sex.clean(config=True, catalog=True, check=True)
def solveField(fullfilename, findstarmethod="astrometry.net"):
"""
@param: fullfilename entire path to image
@type: str
@param: findstarmethod (astrometry.net, sex)
@type: str
Does astrometry to image=fullfilename
Uses either astrometry.net or sex(tractor) as its star finder
"""
pathname, filename = os.path.split(fullfilename)
pathname = pathname + "/"
basefilename, file_xtn = os.path.splitext(filename)
# *** enforce .fits extension
if file_xtn != ".fits":
raise ValueError("File extension must be .fits it was = %s\n" % file_xtn)
# *** check whether the file exists or not
if os.path.exists(fullfilename) == False:
raise IOError("You selected image %s It does not exist\n" % fullfilename)
# version 0.23 changed behavior of --overwrite
# I need to specify an output filename with -o
outfilename = basefilename + "-out"
image = Image.fromFile(fullfilename)
try:
ra = image["CRVAL1"] # expects to see this in image
except:
raise AstrometryNetException("Need CRVAL1 and CRVAL2 and CD1_1 on header")
try:
dec = image["CRVAL2"]
except:
raise AstrometryNetException("Need CRVAL1 and CRVAL2 and CD1_1 on header")
width = image["NAXIS1"]
height = image["NAXIS2"]
radius = 10.0 * abs(image["CD1_1"]) * width
wcs_filename = pathname + outfilename + ".wcs"
if findstarmethod == "astrometry.net":
line = "solve-field %s --no-plots --overwrite -o %s --ra %f --dec %f --radius %f" % (
fullfilename, outfilename, ra, dec, radius)
elif findstarmethod == "sex":
sexoutfilename = pathname + outfilename + ".xyls"
line = "solve-field %s --no-plots --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE " \
"--sort-column MAG_ISO --sort-ascending --width %d --height %d --ra %f --dec %f --radius %f" % (
sexoutfilename, outfilename, width, height, ra, dec, radius)
sex = SExtractor()
sex.config['BACK_TYPE'] = "AUTO"
sex.config['DETECT_THRESH'] = 3.0
sex.config['DETECT_MINAREA'] = 18.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['CATALOG_TYPE'] = "FITS_1.0"
sex.config['CATALOG_NAME'] = sexoutfilename
sex.config['PARAMETERS_LIST'] = ["X_IMAGE", "Y_IMAGE", "MAG_ISO"]
sex.run(fullfilename)
else:
log.error("Unknown option used in astrometry.net")
# when there is a solution astrometry.net creates a file with .solved
# added as extension.
is_solved = pathname + outfilename + ".solved"
# if it is already there, make sure to delete it
if os.path.exists(is_solved):
os.remove(is_solved)
log.debug("SOLVE %s" % line)
# *** it would be nice to add a test here to check
# whether astrometrynet is running OK, if not raise a new exception
# like AstrometryNetInstallProblem
log.debug('Starting solve-field...')
t0 = time.time()
solve = Popen(line.split()) # ,env=os.environ)
solve.wait()
log.debug('Solve field finished. Took %3.2f sec' % (time.time() - t0))
# if solution failed, there will be no file .solved
if (os.path.exists(is_solved) == False):
raise NoSolutionAstrometryNetException(
"Astrometry.net could not find a solution for image: %s %s" % (fullfilename, is_solved))
return wcs_filename
def solveField(fullfilename, findstarmethod="astrometry.net"):
"""
@param: fullfilename entire path to image
@type: str
@param: findstarmethod (astrometry.net, sex)
@type: str
Does astrometry to image=fullfilename
Uses either astrometry.net or sex(tractor) as its star finder
"""
pathname, filename = os.path.split(fullfilename)
pathname = pathname + "/"
basefilename, file_xtn = os.path.splitext(filename)
# *** enforce .fits extension
if (file_xtn != ".fits"):
raise ValueError(
"File extension must be .fits it was = %s\n" % file_xtn)
# *** check whether the file exists or not
if (os.path.exists(fullfilename) == False):
raise IOError(
"You selected image %s It does not exist\n" % fullfilename)
# version 0.23 changed behavior of --overwrite
# I need to specify an output filename with -o
outfilename = basefilename + "-out"
image = Image.fromFile(fullfilename)
try:
ra = image["CRVAL1"] # expects to see this in image
except:
raise AstrometryNetException(
"Need CRVAL1 and CRVAL2 and CD1_1 on header")
try:
dec = image["CRVAL2"]
except:
raise AstrometryNetException(
"Need CRVAL1 and CRVAL2 and CD1_1 on header")
width = image["NAXIS1"]
height = image["NAXIS2"]
radius = 5.0 * abs(image["CD1_1"]) * width
if findstarmethod == "astrometry.net":
line = "solve-field %s -d 10,20,30,40,50,60,70,80,90,100 --overwrite -o %s --ra %f --dec %f --radius %f" % (
fullfilename, outfilename, ra, dec, radius)
elif findstarmethod == "sex":
sexoutfilename = pathname + outfilename + ".xyls"
line = "solve-field %s -d 10,20,30,40,50,60,70,80,90,100 --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE --sort-column MAG_ISO --sort-ascending --width %d --height %d --ra %f --dec %f --radius %f" % (
sexoutfilename, outfilename, width, height, ra, dec, radius)
# line = "solve-field %s --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE --sort-column MAG_ISO --sort-ascending --width %d --height %d" %(sexoutfilename, outfilename,width, height)
# could use --guess-scale for unreliable mounts:
# line = "solve-field %s --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE --sort-column MAG_ISO --sort-ascending --width %d --height %d --guess-scale" %(sexoutfilename, outfilename, width, height)
sex = SExtractor()
sex.config['BACK_TYPE'] = "AUTO"
sex.config['DETECT_THRESH'] = 3.0
sex.config['DETECT_MINAREA'] = 18.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['CATALOG_TYPE'] = "FITS_1.0"
#sex.config['CATALOG_TYPE'] = "ASCII"
sex.config['CATALOG_NAME'] = sexoutfilename
sex.config['PARAMETERS_LIST'] = ["X_IMAGE", "Y_IMAGE", "MAG_ISO"]
sex.run(fullfilename)
else:
log.error("Unknown option used in astrometry.net")
# when there is a solution astrometry.net creates a file with .solved
# added as extension.
is_solved = pathname + outfilename + ".solved"
# if it is already there, make sure to delete it
if (os.path.exists(is_solved)):
os.remove(is_solved)
print "SOLVE", line
# *** it would be nice to add a test here to check
# whether astrometrynet is running OK, if not raise a new exception
# like AstrometryNetInstallProblem
solve = Popen(line.split()) # ,env=os.environ)
solve.wait()
# if solution failed, there will be no file .solved
if (os.path.exists(is_solved) == False):
raise NoSolutionAstrometryNetException(
"Astrometry.net could not find a solution for image: %s %s" % (fullfilename, is_solved))
# wcs_imgname will be the old fits file with the new header
# wcs_solution is the solve-field solution file
wcs_imgname = pathname + outfilename + "-wcs" + ".fits"
wcs_solution = pathname + outfilename + ".wcs"
shutil.copyfile(wcs_solution, wcs_solution + ".fits")
if (os.path.exists(wcs_imgname) == True):
iraf.imdelete(wcs_imgname)
# create a separate image with new header
iraf.artdata()
iraf.imcopy(fullfilename, wcs_imgname)
iraf.hedit(wcs_imgname, "CD1_1,CD1_2,CD2_1,CD2_2,CRPIX1,CRPIX2,CRVAL1,CRVAL2,RA,DEC,ALT,AZ",
add="no", addonly="no", delete="yes",
verify="no", show="no", update="yes")
iraf.mkheader(images=wcs_imgname, headers=wcs_solution + ".fits",
append="yes", verbose="no", mode="al")
return(wcs_imgname)
def main(argv):
from optparse import OptionParser
parser = OptionParser()
parser.add_option('-i',
'--image',
help='Fit image file with donuts to measure.',
type='string')
parser.add_option(
'-p',
'--parameters',
help='Base donut json parameters. Position will be overwritten.',
type='string')
parser.add_option('--mpithreads',
help='Number of threads to start mpi with (default 4)',
type='int',
default=4)
parser.add_option('--display',
help='Display image and load catalog on ds9?',
action='store_true',
default=False)
parser.add_option('--overwrite',
help='Run in overwrite mode?',
action='store_true',
default=False)
opt, args = parser.parse_args(argv)
# Run sextractor on image to get catalog list
sex = SExtractor()
# default params
sex.config['PIXEL_SCALE'] = 0.55
sex.config['BACK_TYPE'] = "AUTO"
sex.config['SATUR_LEVEL'] = 60000
sex.config['DETECT_MINAREA'] = 200
sex.config['DETECT_THRESH'] = 10.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['PARAMETERS_LIST'] = [
"NUMBER", 'X_IMAGE', 'Y_IMAGE', "XWIN_IMAGE", "YWIN_IMAGE",
"FLUX_BEST", "FWHM_IMAGE", "FLAGS"
]
# ok, here we go!
log.info('Running sextractor')
sex.run(opt.image, clean=False)
if opt.display:
log.info('Displaying image in ds9')
# Now calculate zernike coef
outname = os.path.basename(opt.image).split('-')[1].replace(
'.fits', '_zern.npy')
cmd = 'mpirun -np %i python ~/Develop/donut/script/donut -i %s -p %s -c %s -o %s' % (
opt.mpithreads, opt.image, opt.parameters, sex.config['CATALOG_NAME'],
outname)
if not os.path.exists(outname) and not opt.overwrite:
log.info('Running donut with %i cores' % opt.mpithreads)
log.debug(cmd)
p = subprocess.Popen(cmd,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
p.wait()
else:
log.warning(
'File %s exists. Run with --overwrite to force reprocess.' %
outname)
log.info('Mapping hexapod position')
zerpar = [
os.path.basename(__file__), '-f', outname, '--max', '100', '--niter',
'3', '-i', opt.image
]
zernmap.main(zerpar)
return 0
def solveField(fullfilename, findstarmethod="astrometry.net"):
"""
@param: fullfilename entire path to image
@type: str
@param: findstarmethod (astrometry.net, sex)
@type: str
Does astrometry to image=fullfilename
Uses either astrometry.net or sex(tractor) as its star finder
"""
pathname, filename = os.path.split(fullfilename)
pathname = pathname + "/"
basefilename,file_xtn = os.path.splitext(filename)
# *** enforce .fits extension
if (file_xtn != ".fits"):
raise ValueError("File extension must be .fits it was = %s\n" %file_xtn)
# *** check whether the file exists or not
if ( os.path.exists(fullfilename) == False ):
raise IOError("You selected image %s It does not exist\n" %fullfilename)
# version 0.23 changed behavior of --overwrite
# I need to specify an output filename with -o
outfilename = basefilename + "-out"
image = Image.fromFile(fullfilename)
try:
ra = image["CRVAL1"] # expects to see this in image
except:
raise AstrometryNetException("Need CRVAL1 and CRVAL2 and CD1_1 on header")
try:
dec = image["CRVAL2"]
except:
raise AstrometryNetException("Need CRVAL1 and CRVAL2 and CD1_1 on header")
width = image["NAXIS1"]
height = image["NAXIS2"]
radius = 5.0 * abs(image["CD1_1"]) * width
if findstarmethod == "astrometry.net":
#line = "solve-field --guess-scale %s --overwrite -o %s" %(fullfilename, outfilename)
line = "solve-field %s --overwrite -o %s --ra %f --dec %f --radius %f" %(fullfilename, outfilename, ra, dec, radius)
print line
elif findstarmethod == "sex":
sexoutfilename = pathname + outfilename + ".xyls"
line = "solve-field %s --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE --sort-column MAG_ISO --sort-ascending --width %d --height %d --ra %f --dec %f --radius %f" %(sexoutfilename, outfilename, width, height, ra, dec, radius)
print "Sextractor command line %s" %line
# using --guess-scale
# line = "solve-field %s --overwrite -o %s --x-column X_IMAGE --y-column Y_IMAGE --sort-column MAG_ISO --sort-ascending --width %d --height %d --guess-scale" %(sexoutfilename, outfilename, width, height)
sex = SExtractor()
sex.config['BACK_TYPE'] = "AUTO"
sex.config['DETECT_THRESH'] = 3.0
sex.config['DETECT_MINAREA'] = 18.0
sex.config['VERBOSE_TYPE'] = "QUIET"
sex.config['CATALOG_TYPE'] = "FITS_1.0"
#sex.config['CATALOG_TYPE'] = "ASCII"
sex.config['CATALOG_NAME'] = sexoutfilename
sex.config['PARAMETERS_LIST'] = ["X_IMAGE","Y_IMAGE","MAG_ISO"]
sex.run(fullfilename)
else:
log.error("Unknown option used in astrometry.net")
# when there is a solution astrometry.net creates a file with .solved
# added as extension.
is_solved = pathname + outfilename + ".solved"
# if it is already there, make sure to delete it
if ( os.path.exists(is_solved)):
os.remove(is_solved)
solve = Popen(line.split()) # ,env=os.environ)
solve.wait()
# if solution failed, there will be no file .solved
if ( os.path.exists(is_solved) == False ):
raise NoSolutionAstrometryNetException("Astrometry.net could not find a solution for image: %s %s" %(fullfilename, is_solved))
# wcs_imgname will be the old fits file with the new header
# wcs_solution is the solve-field solution file
wcs_imgname = pathname + outfilename + "-wcs" + ".fits"
wcs_solution = pathname + outfilename + ".wcs"
shutil.copyfile(wcs_solution,wcs_solution+".fits")
if ( os.path.exists(wcs_imgname) == True ):
iraf.imdelete(wcs_imgname)
# create a separate image with new header
iraf.artdata()
iraf.imcopy(fullfilename,wcs_imgname)
iraf.mkheader(images=wcs_imgname,headers=wcs_solution+".fits",
append="no",verbose="no",mode="al")
return(wcs_imgname)