def run_ell(file_in, file_tab, file_dat, mag, **ellipse_par):
# prochaine etape : mettre en argument sous une certaine forme les parametres associes epar des taches 1) strict minimum sous forme de dico fixe 2) tout pouvoir changer sous forme de dictionnaire et tester les cles ...
# import iraf packages
iraf.stsdas()
iraf.analysis()
iraf.isophote()
p = Popen("ds9", shell = True)
time.sleep(5)
iraf.display(file_in, 1)
set_iraf_param(ellipse_par)
# iraf.lpar(iraf.geompar)
iraf.ellipse(file_in, file_tab, mag0 = str(mag), verbose = "no")
# iraf.lpar(iraf.isoimap)
iraf.isoimap(file_in, file_tab)
iraf.tproject(file_tab, "temp.fits", "SMA,INTENS,INT_ERR,ELLIP,ELLIP_ERR, PA, PA_ERR, X0, Y0, TFLUX_C, TMAG_E,NPIX_E")
iraf.tprint("temp.fits", pwidth = 200, Stdout = file_dat)
iraf.imdel("temp.fits")
p.kill()
def run(args):
"""Generate the residual image using Ellipse run."""
"""Call the STSDAS.ANALYSIS.ISOPHOTE package"""
if args.isophote is None:
if args.verbose:
print '\n' + SEP
print "## Call STSDAS.ANALYSIS.ISOPHOTE() "
print SEP
iraf.stsdas()
iraf.analysis()
iraf.isophote()
iraf.ttools()
def run(args):
"""Generate the residual image using Ellipse run."""
"""Call the STSDAS.ANALYSIS.ISOPHOTE package"""
if args.isophote is None:
if args.verbose:
print '\n' + SEP
print "## Call STSDAS.ANALYSIS.ISOPHOTE() "
print SEP
iraf.stsdas()
iraf.analysis()
iraf.isophote()
iraf.ttools()
def __init__(self,
shortparlists,
parlists,
FitsDir,
logfile,
verbose=1,
clean_up=1,
skyKey='ALIGNSKY',
hdrGain=0,
crlower=None,
imNsci=1):
self.modName = string.split(string.split(str(self))[0], '.')[0][1:]
self.shortparlists = shortparlists
self.parlists = parlists
self.Fits = FitsDir
self.verbose = verbose
self.crmasks = {} # cosmic ray masks names
self.removeList = []
self.clean_up = clean_up
self.skyKey = skyKey
self.hdrGain = hdrGain
self.crlower = crlower
if imNsci < 1:
raise ValueError, 'Error: pyblot got imNsci = ' + imNsci
self.imNsci = imNsci
self.logfile = logfile
print self.modName, 'version', __version__
self.logfile.write('Instantiating ' + self.modName + ' version ' +
__version__)
# make sure these packages are loaded
iraf.stsdas()
iraf.toolbox()
iraf.imgtool()
iraf.fourier()
iraf.fitting()
iraf.ttools()
iraf.analysis()
iraf.dither()
# flush the cash! twice!
iraf.flpr()
iraf.flpr()
iraf.reset(imtype='fits') # seems to make deriv task a bit happier
iraf.set(tmp='./')
def pyraf_bmodel(binary,
parent,
output=None,
highar=False,
verbose=False,
interp='spline',
backgr=0.0):
"""Wrapper of the `Pyraf` `bmodel` function to build 2-D model.
For details about the `bmodel` task, please see:
http://stsdas.stsci.edu/cgi-bin/gethelp.cgi?bmodel
Parameters
----------
binary: str
Location of the output binary file from `ellipse` task.
parent: str
Location of the input image that `ellipse` run is based on.
output: str, optional
Name of the output FITS image
highar: boolen, optional
Whether to include the higher-order Fourier component. Default: False.
verbose: boolen, optional
Verbose mode. Default: False.
interp: str, optional
The interpolation mode used by the `trebin` task.
Allowed values are: nearest | linear | poly3 | spline. Default: spline.
Returns
-------
model: ndarray
2-D model image of the `ellipse` results.
"""
# Initiate the isophote module in IRAF/STSDAS
try:
from pyraf import iraf
iraf.stsdas()
iraf.analysis()
iraf.isophote()
except ImportError:
raise Exception("# Unfortunately, you need to install pyraf first.")
# Make sure the files are available
if not os.path.isfile(binary):
raise FileNotFoundError(
"# Can not find the binary output file: {}".format(binary))
if not os.path.isfile(parent):
raise FileNotFoundError(
"# Can not find the input image: {}".format(parent))
# Name of the output FITS file
if output is None:
output = os.path.splitext(binary)[0] + '_model.fits'
# Remove the output file if it exists
if os.path.isfile(output):
os.remove(output)
# Check the interpolation method
if interp not in PYRAF_INTERP:
raise Exception("# Wrong interpolation method! Choices are {}".format(
PYRAF_INTERP))
# Higher-order harmonic modes
highar_str = "yes" if highar else "no"
verbose_str = "yes" if verbose else "no"
try:
iraf.bmodel(binary,
output,
parent=parent,
interp=interp,
highar=highar_str,
backgr=backgr,
verbose=verbose_str)
except Exception:
warnings.warn("# Something is wrong with the Bmodel task!")
return None
if not os.path.isfile(output):
raise FileNotFoundError(
"# Cannot find the output file: {}".format(output))
else:
model = fits.open(output)[0].data
return model
from matplotlib import pyplot as plt
import numpy as np
from scipy.optimize import minimize
import pandas as pd
# input images
input_filename = "small.fits"
output_table = input_filename.replace(".fits", ".tab")
output_bin = input_filename.replace(".fits", ".bin")
output_cdf = input_filename.replace(".fits", ".cdf")
model_image = input_filename.replace(".fits", "_model.fits")
residual_image = input_filename.replace(".fits", "_res.fits")
# import pacakges
iraf.stsdas()
iraf.analysis()
iraf.isophote()
for f in [
output_bin, output_cdf, output_table, model_image,
model_image.replace("model", "model_new_"),
model_image.replace("model", "res")
]:
if os.path.exists(f):
os.remove(f)
# define parameters for ellipse run
iraf.ellipse.unlearn()
# geompar guess ...
iraf.ellipse.geompar.x0 = 112
#!/usr/bin/env python
print('This version of galTables works for *cutout-24-rot.tab files and *cutout-sdss.tab files. If you are not using rotated 24m files then use galTablesv2.py')
from pylab import *
import glob
from pyraf import iraf
import os
iraf.stsdas()
iraf.analysis()
iraf.toolbox()
iraf.ttools()
flag = str(raw_input('Which files? a=24 b=sdss '))
flag = str(flag)
if flag.find('a') > -1:
tabfiles = glob.glob('*cutout-24-rot.tab')
if flag.find('b') > -1:
tabfiles = glob.glob('*cutout-sdss.tab')
#tabfiles=glob.glob('*.tab')
#print tabfiles
for i in range(len(tabfiles)):
tfile = tabfiles[i]
nfile = tfile.split('.')
dfile = nfile[0]+'.dat'
print tfile,' -> ',dfile
iraf.tprint(table=tfile,pwidth='INDEF',showhdr='no',showunits='no',Stdout=dfile)
#########################################################################################
'''
import os
from pyraf import iraf
from astropy.io import fits
from shutil import copy2
import rsstools as rt
import numpy as np
iraf.noao(_doprint=0)
iraf.twodspec(_doprint=0)
iraf.longslit(_doprint=0)
iraf.apextract(dispaxis='1')
iraf.stsdas(_doprint=0)
iraf.analysis(_doprint=0)
iraf.fitting(_doprint=0)
class arc(object):
def __init__(self, name):
self.name = name
self.noext = os.path.splitext(self.name)[0]
self.idname = rt.makesetups(self.name,"arc")
self.idfits = self.idname+'.fits'
self.linelist = self.idname.split('_')[0].lower()+'.dat'
self.header = self.read_header()
def read_header(self):
return fits.getheader(self.name)
def __str__(self):
return self.name+' : idname --> '+self.idname
def ellipse(image, outname, verbose=False, **kwargs):
"""run ellipse task
image : input image name
outname : output filename
Keywords:
*geompar*
x0, y0 -- required
ellip0 : initial ellipticity (default=0.2)
pa0 : initial PA in degrees ccw from +y (default=20)
sma0 : initial semi-major axis (default=10)
minsma : minimum sma (default=1)
maxsma : maximum sma (default='INDEF')
step : sma step size (default=0.1)
linear : linear sampling of sma? (default='no')
*controlpar*
conver :
"""
# verify input
if 'x0' not in kwargs.keys() or 'y0' not in kwargs.keys():
raise KeyError('x0 or y0 is not found')
# load packages
iraf.stsdas(_doprint=0, motd=False)
iraf.analysis(_doprint=0)
iraf.isophote(_doprint=0)
# reset all parameters
iraf.unlearn('ellipse', 'geompar', 'controlpar', 'samplepar')
iraf.ellipse.interactive = False
iraf.ellipse.xylearn = False # if True, it prompts input upon faling to find center
# geompar
iraf.ellipse.x0 = kwargs.pop('x0')
iraf.ellipse.y0 = kwargs.pop('y0')
iraf.ellipse.ellip0 = kwargs.pop('ellip0', 0.2)
iraf.ellipse.pa0 = kwargs.pop('pa0', 20.0)
iraf.ellipse.sma0 = kwargs.pop('sma0', 10.0)
iraf.ellipse.minsma = kwargs.pop('minsma', 1.)
iraf.ellipse.maxsma = kwargs.pop('maxsma', 'INDEF')
iraf.ellipse.step = kwargs.pop('step', 0.1)
iraf.ellipse.linear = kwargs.pop('linear', 0)
iraf.ellipse.verbose = verbose
# controlpar
iraf.ellipse.conver = kwargs.pop('conver', 0.05)
iraf.ellipse.minit = kwargs.pop('minit', 10)
iraf.ellipse.maxit = kwargs.pop('maxit', 50)
iraf.ellipse.hcenter = kwargs.pop('hcenter', 'no')
# samplepar
iraf.ellipse.tsample = kwargs.pop('tsample', 'none')
iraf.ellipse.harmonics = kwargs.pop('harmonics', 'none')
if verbose:
iraf.lparam('ellipse')
iraf.lparam('geompar')
iraf.lparam('controlpar')
iraf.lparam('samplepar')
# run ellipse
tempname = shorten_iauname(image) + str(uuid.uuid4()) + '.tab'
try:
iraf.ellipse(image, tempname)
# print ascii table
iraf.tprint(tempname, pwidth='INDEF', Stdout=outname)
os.remove(tempname)
except:
print 'ellipse failed'
