def examples():
import glob
#import unicorn.inspect
import pysao
os.chdir(os.getenv('THREEDHST') + '/3DHST_VariableBackgrounds/GS25')
RGB_PATH = os.getenv('RELEASE') + 'v4.0/RGB/All/'
ds9 = pysao.ds9()
#### Objects with fits
x = unicorn.inspect.ImageClassifier(glob.glob('ZFIT/PNG/*zfit.png'),
FITS_PATH='2D/FITS/',
logfile='inspect_zfit',
RGB_PATH=RGB_PATH,
ds9=ds9)
#### Raw 2D files, including objects not fit
x = unicorn.inspect.ImageClassifier(glob.glob('2D/PNG/*png'),
FITS_PATH='2D/FITS/',
logfile='inspect_raw2d',
RGB_PATH=RGB_PATH,
ds9=ds9)
def go_pointing(pointing='goodss-25', RELEASE='/Volumes/Voyager/TEST_SPECTRA_v4.1/GOODS-S/INTERLACE_v4.1/', RGB_PATH='/Volumes/Voyager/TEST_SPECTRA_v4.1/RGB_goodss/',show_ds9=True):
"""
Classify a 3D-HST pointing
"""
import glob
#from unicorn import inspect
field = '-'.join(pointing.split('-')[:-1])
### Example paths for v4.0 and earlier releases
#PNG_PATH = '%s/%s/%s-WFC3_v4.0_SPECTRA/%s/ZFIT/PNG/' %(RELEASE, field, field, pointing)
#FITS_PATH = '%s/%s/%s-WFC3_v4.0_SPECTRA/%s/2D/FITS/' %(RELEASE, field, field, pointing)
#PNG_PATH = '%s/%s/WFC3/%s/ZFIT/PNG/' %(RELEASE, field, pointing)
#FITS_PATH = '%s/%s/WFC3/%s/2D/FITS/' %(RELEASE, field, pointing)
PNG_PATH = FITS_PATH = RELEASE
if show_ds9:
import pysao
ds9=pysao.ds9()
x = ImageClassifier(images=glob.glob(PNG_PATH+pointing+'*new_zfit.png'), RGB_PATH=RGB_PATH, FITS_PATH=FITS_PATH, logfile='%s_inspect.info' %(pointing), ds9=ds9)
else:
x = ImageClassifier(images=glob.glob(PNG_PATH+pointing+'*new_zfit.png'), RGB_PATH=RGB_PATH, FITS_PATH=FITS_PATH, logfile='%s_inspect.info' %(pointing))
return x
def get_drizzled_cutouts():
### Optinally display products to ds9 with, e.g., pysao.ds9
try:
import pysao
ds9 = pysao.ds9()
ds9.set('scale limits -0.08 8')
ds9.set('lock colorbar')
ds9.set('frame lock wcs')
ds9.set('tile')
for f in range(6):
ds9.frame(f+1)
except:
ds9 = None
### Full mosaic, also provides a reference WCS
im_mosaic = pyfits.open('../../MACS1149/Catalog/MACS1149-F160W_drz_sci.fits')
wcs_mosaic = stwcs.wcsutil.HSTWCS(im_mosaic, ext=0)
### Get cutout of NX pixels around the center position from the reference mosaic
NX, pix_scale = 50, 0.065
wcs_mosaic.updatePscale(pix_scale)
line_wavelengths = {'O2':3727, 'Ne3':3869, 'Hb':4861, 'O3':5007, 'Ha':6563., 'S2':6724}
### Object
stats = {'id':404, 'z':1.40707, 'lines':{'G141':['O3','Ha','S2'], 'G102':['O2']}}
stats = {'id':1422, 'z':2.27763, 'lines':{'G141':['O2','Hb','O3']}}
stats = {'id':1917, 'z':1.89105, 'lines':{'G141':['Hb','O3'], 'G102':['O2']}}
stats = {'id':2315, 'z':1.8936, 'lines':{'G141':['Hb','O3'], 'G102':['O2']}}
stats = {'id':2389, 'z':1.8936, 'lines':{'G141':['Hb','O3'], 'G102':['O2']}}
stats = {'id':3746, 'z':1.2477, 'lines':{'G141':['O3','Ha','S2'], 'G102':['O2','Hb','O3']}}
import collections
drizzled = collections.OrderedDict()
for grism in stats['lines'].keys():
files=glob.glob('MACS1149-???-%s_%05d*2D.fits' %(grism, stats['id']))
for line in stats['lines'][grism]:
lam = line_wavelengths[line]*(1+stats['z'])
drizzled['%s_%s' %(grism, line)] = driz_from_twod(files, lam=lam, pixfrac=0.5, wcs_mosaic=wcs_mosaic, ds9=ds9)
### Show all
keys = drizzled.keys()
for i, key in enumerate(keys):
print 'Frame %d: %s' %(i+1, key)
ds9.frame(i+1)
ds9.view(drizzled[key][1], header=drizzled[key][2])
def examples():
import glob
#import unicorn.inspect
import pysao
os.chdir(os.getenv('THREEDHST') + '/3DHST_VariableBackgrounds/GS25')
RGB_PATH = os.getenv('RELEASE') + 'v4.0/RGB/All/'
ds9 = pysao.ds9()
#### Objects with fits
x = unicorn.inspect.ImageClassifier(glob.glob('ZFIT/PNG/*zfit.png'), FITS_PATH='2D/FITS/', logfile='inspect_zfit', RGB_PATH=RGB_PATH, ds9=ds9)
#### Raw 2D files, including objects not fit
x = unicorn.inspect.ImageClassifier(glob.glob('2D/PNG/*png'), FITS_PATH='2D/FITS/', logfile='inspect_raw2d', RGB_PATH=RGB_PATH, ds9=ds9)
def obj_lookup(dir, obj):
import pysao
cat = table.Table.read(dir + '/A2744_cat.dat', format = 'ascii')['id', 'X_IMAGE', 'Y_IMAGE']
obj = cat[cat['id'] == obj]
X_IMAGE = str(np.rint(obj['X_IMAGE'][0]))
Y_IMAGE = str(np.rint(obj['Y_IMAGE'][0]))
#print obj
ds9 = pysao.ds9()
ds9.set('file 160.fits')
ds9.set('regions file zheng2014.reg')
ds9.set('scale log 99.5')
ds9.set('scale limits -.1 10')
ds9.set('cmap value 10.0889 0.358543')
#ds9.xpa_help('pan')
panstring = 'pan to ' + X_IMAGE + ' ' + Y_IMAGE + ' image'
ds9.set(panstring)
a = raw_input('Press ENTER to exit...')
#print ds9.get('cmap value')
ds9.set('exit')
def displayFit( self, **kwargs ):
# get ready to show the IFU overlaid on the image provided by imageFile
self.drawIFU( **kwargs )
self.drawStars( **kwargs )
# load region files with IFU and star coordinates
ds9 = pysao.ds9()
ds9.load_fits( kwargs[ 'imageFile' ] )
ds9.set( 'regions load ifu.reg' )
ds9.set( 'regions load stars.reg' )
# pan the ds9 frame to center on the IFU
xPan = self.bestOffset[ 0 ] / 3600. + self.centerCoords[ 0 ]
yPan = self.bestOffset[ 1 ] / 3600. + self.centerCoords[ 1 ]
coords = ICRS( ra = xPan, dec = yPan, unit = ( u.degree, u.degree ) )
ds9.set( 'pan to %(x)s %(y)s wcs fk5' % { "x": coords.ra.to_string(),
"y": coords.dec.to_string() } )
ds9.set( 'scale zscale' ) # set to zscale
raw_input( "Press ENTER when finished" )
def go_pointing(
pointing='goodss-25',
RELEASE='/Volumes/Voyager/TEST_SPECTRA_v4.1/GOODS-S/INTERLACE_v4.1/',
RGB_PATH='/Volumes/Voyager/TEST_SPECTRA_v4.1/RGB_goodss/',
show_ds9=True):
"""
Classify a 3D-HST pointing
"""
import glob
#from unicorn import inspect
field = '-'.join(pointing.split('-')[:-1])
### Example paths for v4.0 and earlier releases
#PNG_PATH = '%s/%s/%s-WFC3_v4.0_SPECTRA/%s/ZFIT/PNG/' %(RELEASE, field, field, pointing)
#FITS_PATH = '%s/%s/%s-WFC3_v4.0_SPECTRA/%s/2D/FITS/' %(RELEASE, field, field, pointing)
#PNG_PATH = '%s/%s/WFC3/%s/ZFIT/PNG/' %(RELEASE, field, pointing)
#FITS_PATH = '%s/%s/WFC3/%s/2D/FITS/' %(RELEASE, field, pointing)
PNG_PATH = FITS_PATH = RELEASE
if show_ds9:
import pysao
ds9 = pysao.ds9()
x = ImageClassifier(images=glob.glob(PNG_PATH + pointing +
'*new_zfit.png'),
RGB_PATH=RGB_PATH,
FITS_PATH=FITS_PATH,
logfile='%s_inspect.info' % (pointing),
ds9=ds9)
else:
x = ImageClassifier(images=glob.glob(PNG_PATH + pointing +
'*new_zfit.png'),
RGB_PATH=RGB_PATH,
FITS_PATH=FITS_PATH,
logfile='%s_inspect.info' % (pointing))
return x
import scipy.spatial
import matplotlib.pyplot as plt
import numpy as np
class Picker(object):
def __init__(self, xy):
self.kdtree = scipy.spatial.KDTree(xy)
def pick(self):
pos = plt.ginput()
return self.kdtree.query(pos[0])
import pysao
ds9 = pysao.ds9()
ds9.set("tile")
ds9.set('mode crosshair')
ds9.set("frame 1")
ds9.set("file 2mass_J.fits")
ds9.set("scale zscale")
ds9.set("frame 2")
ds9.set("file 2mass_H.fits")
ds9.set("scale zscale")
ds9.set('lock crosshair wcs')
import atpy
tbl = atpy.Table("2mass_table.xml")
x = tbl["Jmag"]
def finding_chart(self, target, ds9, trange=[-6, 6] * u.hr, ticks=1 * u.hr,
fov=1 * u.arcmin, frame=1, dss=True):
"""Plot a DS9 finding chart for a moving target.
Parameters
----------
target : SolarSysObject
The target to observe.
ds9 : pysao.ds9
Plot to this DS9 instance.
trange : Quantity, optional
Plot the target's path over this time span, centered on the
observer's date (`self.date`).
ticks : Quantity, optional
Plot tick marks using this interval. The first tick is a circle.
fov : Quantity, optional
Angular size of a box or rectangle to draw, indicating your
instrument's FOV, or `None`.
frame : int, optional
DS9 frame number to display image.
dss : bool, optional
Set to `True` to retrieve a DSS image.
"""
import matplotlib.pyplot as plt
import pysao
from ..ephem import Earth, SolarSysObject
assert isinstance(target, SolarSysObject), "target must be a SolarSysObject"
trange = u.Quantity(trange, u.hr)
ticks = u.Quantity(ticks, u.hr)
ds9 = ds9 if ds9 is not None else pysao.ds9()
# DSS
g = Earth.observe(target, self.date, ltt=True)
ds9.set('frame {}'.format(frame))
ds9.set('dsssao frame current')
ds9.set('dsssao size 60 60')
ds9.set('dsssao coord {} {}'.format(
g['ra'].to_string(u.hr, sep=':'),
g['dec'].to_string(u.deg, sep=':')))
ds9.set('dsssao close')
ds9.set('cmap b')
ds9.set('align')
# FOV
if fov is not None:
if fov.size == 1:
fov = [fov, fov]
fov_deg = u.Quantity(fov, u.deg).value
reg = 'fk5; box {} {} {} {} 0'.format(
g['ra'].to_string(u.hr, sep=':'),
g['dec'].to_string(u.deg, sep=':'),
fov_deg[0], fov_deg[1])
ds9.set('regions', reg)
# path
dt = np.linspace(trange[0], trange[1], 31)
g = Earth.observe(target, self.date + dt, ltt=True)
for i in range(len(g) - 1):
ds9.set('regions', 'fk5; line {} {} {} {}'.format(
g[i]['ra'].to_string(u.hr, sep=':'),
g[i]['dec'].to_string(u.deg, sep=':'),
g[i+1]['ra'].to_string(u.hr, sep=':'),
g[i+1]['dec'].to_string(u.deg, sep=':')))
# ticks
dt1 = np.arange(0, trange[0].value, -ticks.value)
if dt1[-1] != trange[0].value:
dt1 = np.concatenate((dt1, [trange[0].value]))
dt2 = np.arange(ticks.value, trange[1].value, ticks.value)
if dt2[-1] != trange[0].value:
dt2 = np.concatenate((dt2, [trange[1].value]))
dt = np.concatenate((dt1[::-1], dt2)) * u.hr
del dt1, dt2
g = Earth.observe(target, self.date + dt, ltt=True)
for i in range(len(g)):
s = 'fk5; point({},{}) # point=cross'.format(
g[i]['ra'].to_string(u.hr, sep=':'),
g[i]['dec'].to_string(u.deg, sep=':'))
if i == 0:
s = s.replace('cross', 'circle')
ds9.set('regions', s)
g = Earth.observe(target, self.date, ltt=True)
ds9.set('regions', 'fk5; point({},{}) # point=x'.format(
g['ra'].to_string(u.hr, sep=':'),
g['dec'].to_string(u.deg, sep=':')))
return ds9
def ds9_mark(self, mask=None, sizekey='FLUX_RADIUS', ds9=None, doload=True, clearmarks=True, frame=None):
"""
Mark the sextracted outputs on ds9.
Note that this requires `pysao` to be installed.
Parameters
----------
mask : array or None
A mask that will be applied to the x/y/size arrays to get the sample
to mark or None to show everything
sizekey : str or number
The name of the column to use as the size of the circles or a
number for them all to be the same. If key is missing, default=5.
ds9 : None or pysao.ds9 instance
if None, a new DS9 will be started, otherwise the instance to use
doload : bool
If True, loads the file.
clearmarks : bool
If True, clears the marks
"""
import pysao
#try to get in existing ds9 if one wasn't given, otherwise make one
if ds9 is None:
ds9 = getattr(self, 'lastds9', None)
if ds9 is not None:
#check that it's still alive
try:
ds9.get('') # should just give all the XPA options
except RuntimeError:
# exernally killed
self.lastds9 = ds9 = None
if ds9 is None:
if self.verbose:
print("didn't find old ds9 - starting a new one")
ds9 = self.lastds9 = pysao.ds9()
currfn = ds9.get('iis filename').strip()
if currfn != self.lastimgfn:
if self.verbose:
print("Current filename {0} does not match {1}. Reloading.".format(currfn, self.lastimgfn))
ds9.load_fits(self.lastimgfn)
elif clearmarks:
#delete existing marks
ds9.set('regions delete all')
tab = self.get_output()
if isinstance(sizekey, basestring):
try:
sz = tab[sizekey]
except KeyError:
if self.verbose:
print("didn't find key {0} defaulting to 5 px".format(sizekey))
sz = [5] * len(tab)
else:
sz = [sizekey] * len(tab)
try:
x = tab['X_IMAGE']
y = tab['Y_IMAGE']
except KeyError:
try:
x = tab['XWIN_IMAGE']
y = tab['YWIN_IMAGE']
except KeyError:
raise KeyError('Could not find X_IMAGE/Y_IMAGE or XWIN_IMAGE/YWIN_IMAGE')
if mask is not None:
x = x[mask]
y = y[mask]
sz = np.array(sz)[mask]
ds9.mark(x, y, sz)
return ds9
def atd5():
"""
Verify that mosaicAD gives the correct WCS information for the mosaiced data.
Given a GMOS input file, the MosaicAD object method as_astrodata
creates an output AstroData object. This object 'SCI' header have the
CRPIX1 and CPRIX2 for the reference extension header. The value
CRPIX1 should match the value explained in the Success Criteria
section. The value CRPIX2 is unchanged.
Resources:
gmos_file='../data/gS20120420S0033.fits'
gsaoi_file='../data/guS20120413S0048.fits'
ds9 running
"""
import pywcs
try:
from stsci.numdisplay import display
except ImportError:
from numdisplay import display
print '\n atd5 REQUIREMENT.......'
print ('***** Given an AstroData object, the system shall update the header keywords '
' CRPIX1 and CRPIX2 in the output mosaiced AD object to match the requested '
'transformations')
gmos_file='../data/gS20120420S0033.fits'
gsaoi_file='../data/guS20120413S0048.fits'
from astrodata import AstroData
from gempy.adlibrary.mosaicAD import MosaicAD
# This is the default Mosaic function
from gempy.mosaic.gemMosaicFunction import gemini_mosaic_function
ad = AstroData(gmos_file)
# Creates a mosaicAD object using the input ad and the
# default mosaic function name gemini_mosaic_function.
# 'SCI' is the default extname.
mo = MosaicAD(ad, gemini_mosaic_function)
#
outad = mo.as_astrodata()
# NOTE: The ref_ext is the left most amplifier in
# reference block. For GMOS the reference block
# (2,1). E.G. for a 6-amp GMOS exposure the left
# most exposure is 3.
refblk = mo.geometry.ref_block
col,row = refblk[0], refblk[1]
amp_per_block = mo._amps_per_block
ref_ext = col*amp_per_block+1
ocrpix1 = ad['SCI',ref_ext].header['CRPIX1']
xgap = mo.geometry.gap_dict['transform_gaps'][col,row][0]
blksz_x,blksz_y = mo.geometry.blocksize
# Success Criteria 1.
# Get the x2 value from coords['amp_mosaic_coord'][refblk]
xoff = mo.coords['amp_mosaic_coord'][max(0,col-1)][1]
print ocrpix1 + xoff + xgap, 'should match: '
print outad['SCI',1].header['CRPIX1']
# Success Criteria 2.
# For a GSAOI file,
ad = AstroData(gsaoi_file)
if ad.instrument() != 'GSAOI':
print '******** file is not GSAOI ************'
mo = MosaicAD(ad, gemini_mosaic_function)
outad = mo.as_astrodata()
outhdr = outad['SCI'].header
inhdr = ad['SCI',2].header
# The values should be the same.
print 'Crpix1 values (in,out):',inhdr["CRPIX1"],outhdr['CRPIX1']
print 'Crpix2 values (in,out):',inhdr["CRPIX2"],outhdr['CRPIX2']
# Success Criteria 3.
# For a GMOS file in extension #2
hdr = ad['SCI',2].header
wcs = pywcs.WCS(hdr)
import pysao
# Bring up a ds9 display by instantiating the pysao object
ds9 = pysao.ds9()
# Display the image
ds9.view(ad['SCI',2].data, frame=1)
# display(ad['SCI',2].data,frame=1)
print 'Click on any object:'
X,Y,f,k = ds9.readcursor()
# Get X,Y values from an object on the ds9 display
# Get ra,dec
ra,dec = wcs.wcs_pix2sky(X,Y,1)
# Generate the mosaic_data for this ad using
# as_astrodata method.
# Display the mosaic mosaic_data for the 'SCI' extension
mosaic_data = mo.mosaic_image_data()
# Display the mosaic
ds9.view(mosaic_data,frame=2)
# display(ad['SCI',2].data,frame=1)
print 'Click on the same object:'
MX,MY,f,k = ds9.readcursor()
#display(mosaic_data,frame=2)
# Measure X,Y of the same object, named this MX,MY
# Get the wcs from the mosaic header
mhdr = outad['SCI'].header
mwcs = pywcs.WCS(mhdr)
mra,mdec = mwcs.wcs_pix2sky(MX,MY,1)
print 'These RA,DEC should be pretty close:',(ra[0],mra[0]),(dec[0],mdec[0])
def atd3():
"""
Verify that MosaicAD can merge associated binary tables
Create a mosaic from the input AD object. It is up to the tester to
see if there is one IMAGE extension name 'SCI' and one BINTABLE
extension with the same number and values of EXTVER -these are
associated. The as_astrodata method creates the mosaic. Please
see the Procedure for the steps performed to verify the correctness
of the merging.
Resources:
1) gmos_file = '../data/N20120121S0175_ccMeasured.fits'
2) Uses pysao
"""
from astrodata import AstroData
from gempy.adlibrary.mosaicAD import MosaicAD
# This is the default Mosaic function
from gempy.mosaic.gemMosaicFunction import gemini_mosaic_function
print '\n atd3 REQUIREMENT.......'
print ('***** Given an AstroData object with associated binary table, the system '
'shall merge the tables')
gmos_file = '../data/N20120121S0175_ccMeasured.fits'
ad = AstroData(gmos_file)
# 1) Make sure that we have an IMAGE and BINTABLE extension
# with the same number and values of extver in one IMAGE and
# BINTABLE extension.
# 2) Creates a mosaicAD object using the input AD and the
# default mosaic function named gemini_mosaic_function.
# 3) The 'column_names' parameter in MosaicAD has as
# default values the X_IMAGE, Y_IMAGE and X_WORLD,
# Y_WORLD column names. The reference catalog have
# RAJ2000 and DEJ2000. For more information please the
# documentation about MosaicAD.
mo = MosaicAD(ad, gemini_mosaic_function)
# Now create the output AstroData object.
outad = mo.as_astrodata()
# Check that the output table has been merged correctly by
# verifying that the duplicates rows are deleted and that the
# new X,Y values for objects have been calculated correctly
# based on the new WCS.
#
# Get input rows and remove duplicates. Output the content
# of the resulting AD object which should show the
# associated IMAGE and BINTABLE extensions.
print outad.info()
# Save to a filename
from os import path
nn = path.basename(ad.filename)
outad.write(path.splitext(nn)[0]+'_AD.fits',clobber=True)
# Verify that (X,Y) values in the merged tables correspond
# the object positions.
# The output catalog table name should be 'OBJCAT' and
# pixel coordinates X_IMAGE and Y_IMAGE with corresponding
# world coordinates Y_WORLD and Y_WORLD.
tab = outad['OBJCAT'].data
# Form a list of tuples (x_pixel,y_pixel)
xy=[(x,y) for x,y in zip(tab.field('X_IMAGE'), tab.field('Y_IMAGE'))]
# Now you can use any program to draw points and check for
# location of the xy points on the objects.
# Using DS9 PYSAO module
# Assuming you have the module in your PYTHONPATH
import pysao
# Bring up a ds9 display by instantiating the pysao object
ds9 = pysao.ds9()
# Display the image
ds9.view(outad['SCI'].data)
# ***NOTE***
# Use file tab to display the 'SCI' extension of file
# you save previously. Check for some of these pixel
# coordinates with DS9.
# Now draw the point
tmp=[ds9.set_region('arrow point '+str(x)+' '+str(y)) for x,y in xy]
# Verify for correctly removing duplicates when merging.
# Use python sets()
# Get the first all extensions from the input
# AstroData object. Form a list of tuples (ra,dec)
# from the reference tables in all extensions.
# test for 'REFCAT' existance
if ad['REFCAT'] == None:
raise ValueError('"REFCAT" extension is not in the AstroData object')
rd = []
for tab in ad['REFCAT']:
rd += [(x,y) for x,y in zip(tab.data.field('RAJ2000'),\
tab.data.field('DEJ2000'))]
# Turning rd list to a set will eliminate duplicates.
print 'Number of unique elements from the list:',len(set(rd))
# Now from the outad object
tab = outad['REFCAT'].data
radec=[(x,y) for x,y in zip(tab.field('RAJ2000'), tab.field('DEJ2000'))]
# The number of elements in the output table
print 'The number of elements in the output table:',len(radec)
jj = raw_input("Press Enter to exit the test")
def finding_chart(self,
target,
ds9,
trange=[-6, 6] * u.hr,
ticks=1 * u.hr,
fov=1 * u.arcmin,
frame=1,
dss=True):
"""Plot a DS9 finding chart for a moving target.
Parameters
----------
target : SolarSysObject
The target to observe.
ds9 : pysao.ds9
Plot to this DS9 instance.
trange : Quantity, optional
Plot the target's path over this time span, centered on the
observer's date (`self.date`).
ticks : Quantity, optional
Plot tick marks using this interval. The first tick is a circle.
fov : Quantity, optional
Angular size of a box or rectangle to draw, indicating your
instrument's FOV, or `None`.
frame : int, optional
DS9 frame number to display image.
dss : bool, optional
Set to `True` to retrieve a DSS image.
"""
import matplotlib.pyplot as plt
import pysao
from ..ephem import Earth, SolarSysObject
assert isinstance(target,
SolarSysObject), "target must be a SolarSysObject"
trange = u.Quantity(trange, u.hr)
ticks = u.Quantity(ticks, u.hr)
ds9 = ds9 if ds9 is not None else pysao.ds9()
# DSS
g = Earth.observe(target, self.date, ltt=True)
ds9.set('frame {}'.format(frame))
ds9.set('dsssao frame current')
ds9.set('dsssao size 60 60')
ds9.set('dsssao coord {} {}'.format(g['ra'].to_string(u.hr, sep=':'),
g['dec'].to_string(u.deg,
sep=':')))
ds9.set('dsssao close')
ds9.set('cmap b')
ds9.set('align')
# FOV
if fov is not None:
if fov.size == 1:
fov = [fov, fov]
fov_deg = u.Quantity(fov, u.deg).value
reg = 'fk5; box {} {} {} {} 0'.format(
g['ra'].to_string(u.hr, sep=':'), g['dec'].to_string(u.deg,
sep=':'),
fov_deg[0], fov_deg[1])
ds9.set('regions', reg)
# path
dt = np.linspace(trange[0], trange[1], 31)
g = Earth.observe(target, self.date + dt, ltt=True)
for i in range(len(g) - 1):
ds9.set(
'regions', 'fk5; line {} {} {} {}'.format(
g[i]['ra'].to_string(u.hr, sep=':'),
g[i]['dec'].to_string(u.deg, sep=':'),
g[i + 1]['ra'].to_string(u.hr, sep=':'),
g[i + 1]['dec'].to_string(u.deg, sep=':')))
# ticks
dt1 = np.arange(0, trange[0].value, -ticks.value)
if dt1[-1] != trange[0].value:
dt1 = np.concatenate((dt1, [trange[0].value]))
dt2 = np.arange(ticks.value, trange[1].value, ticks.value)
if dt2[-1] != trange[0].value:
dt2 = np.concatenate((dt2, [trange[1].value]))
dt = np.concatenate((dt1[::-1], dt2)) * u.hr
del dt1, dt2
g = Earth.observe(target, self.date + dt, ltt=True)
for i in range(len(g)):
s = 'fk5; point({},{}) # point=cross'.format(
g[i]['ra'].to_string(u.hr, sep=':'),
g[i]['dec'].to_string(u.deg, sep=':'))
if i == 0:
s = s.replace('cross', 'circle')
ds9.set('regions', s)
g = Earth.observe(target, self.date, ltt=True)
ds9.set(
'regions', 'fk5; point({},{}) # point=x'.format(
g['ra'].to_string(u.hr, sep=':'), g['dec'].to_string(u.deg,
sep=':')))
return ds9
def __init__(self, images = ['UDS_54826.zfit.png', 'UDS_55031.zfit.png'], logfile='inspect_3dhst.info', RGB_PATH='./', RGB_EXTENSION='_vJH_6.png', FITS_PATH='./', load_log=True, ds9=None, rgb_lower=True):
"""
GUI tool for inspecting grism redshift fits
x = unicorn.inspect.ImageClassifier(images=glob.glob('Specz/GOODS-S-25*zfit.png'), RGB_PATH=RGB_PATH, FITS_PATH='Specz/')
"""
if len(images) == 0:
print 'No images specified'
return False
if not os.path.exists(images[0]):
print 'First image not found (%s), is path correct?' %(images[0])
return False
self.RGB_PATH = RGB_PATH
self.FITS_PATH = FITS_PATH
self.RGB_EXTENSION = RGB_EXTENSION
self.rgb_lower=rgb_lower
#### Check ds9
self.ds9 = ds9
if ds9 is True:
try:
import pysao
self.ds9 = pysao.ds9()
except:
print 'Couldn\'t import pysao to run DS9'
self.ds9 = None
##### Add .fits to filename and make backup if necessary
self.logfile = logfile
if not self.logfile.lower().endswith('.fits'):
self.logfile += '.fits'
if os.path.exists(self.logfile):
bk = glob.glob(self.logfile+'.backup*')
if len(bk) > 0:
bkup_file = self.logfile + '.backup.%03d' %(len(bk))
else:
bkup_file = self.logfile + '.backup'
shutil.copy(self.logfile, bkup_file)
print 'Made copy of %s -> %s' %(self.logfile, bkup_file)
####### Initialize parameters
self.params = {}
self.images = images
self.marked_lines = None
if os.path.exists(self.logfile) & load_log:
self.read_fits()
self.N = len(self.images)
for key in ['line', 'extended', 'absorption', 'unamb', 'misid', 'contam', 'zp', 'tilt', 'investigate', 'star', 'seen', 'bad2d', 'deblend', 'sed']:
if key not in self.params.keys():
self.params[key] = np.zeros(self.N, dtype=np.int)
if self.marked_lines is None:
self.marked_lines = np.zeros((self.N, 5))
if 'comment' not in self.params.keys():
self.params['comment'] = ['---' for i in range(self.N)]
self.i = 0
####### Initialize GUI
master = tk.Toplevel()
simple_twod = False
if 'zfit.png' in self.images[0]:
master.geometry('1050x630')
elif '2D.png' in self.images[0]:
master.geometry('850x750')
simple_twod = True
else:
master.geometry('1050x630')
self.master = master
self.frame = tk.Frame(master)
self.frame.pack()
#### Image Panels
imageFile = Image.open(self.images[0])
im = ImageTk.PhotoImage(imageFile)
self.panel = tk.Label(self.frame , image=im, cursor='target')
# imageFile2 = Image.open(self.images[0].replace('zfit','zfit.2D')).resize((500,202))
# im2 = ImageTk.PhotoImage(imageFile2)
im2 = ImageTk.PhotoImage(self.get_twod_file(self.images[0]))
self.panel2 = tk.Label(self.frame , image=im2)
# self.panel2.configure(image = im2)
# self.panel2.image = im2
#### RGB Panel
im_rgb = ImageTk.PhotoImage(self.get_rgb_file(self.images[0]))
self.panel_rgb = tk.Label(self.frame , image=im_rgb)
#### Keypress binding
self.master.bind("<Key>", self.keypress_event)
#### Mouse binding - right click
self.master.bind("<Button-2>", self.right_click_event)
### For logging slider movements
#self.sliders = {}
self.sliders = {}
######
### Navigation buttons
###
self.button_quit = tk.Button(self.frame, text = '(q)uit', command = self.finish)
self.button_log = tk.Button(self.frame, text = 'Log to (F)ile', command = self.write_fits)
self.button_prev = tk.Button(self.frame, text = '(p)rev', command = self.img_prev)
self.button_next = tk.Button(self.frame, text = '(n)ext', command = self.img_next)
self.buttons = {}
#### Emission lne?
self.sliders['line'] = mySlider(self, text='Emission (l)ine', param=self.params['line'], hotkey='l')
#### Absorption
self.sliders['absorption'] = mySlider(self, text='(a)bs./break', param=self.params['absorption'], hotkey='a')
#### Extended line
self.sliders['extended'] = mySlider(self, text='(e)xtended', param=self.params['extended'], hotkey='e')
#### Unambiguous redshift
self.buttons['unamb'] = myCheckbutton(self, text='(u)nambiguous', param=self.params['unamb'], hotkey='u')
#### Flag contamination
self.sliders['contam'] = mySlider(self, text='(b)ad contam', param=self.params['contam'], hotkey='b')
#### Line misidentification
self.buttons['misid'] = myCheckbutton(self, text='Line (m)isID', param=self.params['misid'], hotkey='m')
#### Tilt?
self.buttons['tilt'] = myCheckbutton(self, text='(t)ilt', param=self.params['tilt'], hotkey='t')
#### Bad z_phot / z_spec or both
self.buttons['zp'] = myCheckbutton(self, text='Bad (z)spec', param=self.params['zp'], hotkey='z')
#### SED problems
self.sliders['sed'] = mySlider(self, text='Bad SED (k)', param=self.params['sed'], hotkey='k', to=2)
#### Flag for manual investigation
self.sliders['investigate'] = mySlider(self, text='(i)nvestigate', param=self.params['investigate'], hotkey='i', to=4)
### Object seen already?
self.buttons['seen'] = myCheckbutton(self, text='SEEN?', param=self.params['seen'], hotkey='xxx')
#### Star?
self.buttons['star'] = myCheckbutton(self, text='(s)tar', param=self.params['star'], hotkey='s')
#### Spectrum problem
self.buttons['bad2d'] = myCheckbutton(self, text='Bad 1D/2D (x)', param=self.params['bad2d'], hotkey='x')
#### Deblend issue
self.buttons['deblend'] = myCheckbutton(self, text='(d)eblend', param=self.params['deblend'], hotkey='d')
### Comment holder
self.tvar = tk.StringVar()
self.e_comment = tk.Label(self.frame, textvariable=self.tvar)
self.e_comment.configure(relief=tk.RIDGE)
self.tvar.set(self.params['comment'][0])
#####################
##### Set up the grid for the GUI elements
self.button_next.grid(row=1, column=4, columnspan=1)
self.button_prev.grid(row=1, column=5, columnspan=1)
self.button_log.grid(row=2, column=4, columnspan=1)
self.button_quit.grid(row=2, column=5, columnspan=1)
self.buttons['seen'].thebutton.grid(row=3, column=5)
self.buttons['star'].thebutton.grid(row=3, column=4)
self.sliders['line'].theslider.grid(row=4, column=0)
self.sliders['absorption'].theslider.grid(row=5, column=0)
self.sliders['extended'].theslider.grid(row=4, column=1)
self.buttons['unamb'].thebutton.grid(row=5, column=1)
self.sliders['contam'].theslider.grid(row=4, column=2)
self.buttons['misid'].thebutton.grid(row=5, column=2)
self.buttons['tilt'].thebutton.grid(row=4, column=3)
self.buttons['zp'].thebutton.grid(row=5, column=3)
self.sliders['sed'].theslider.grid(row=5, column=4)
self.sliders['investigate'].theslider.grid(row=4, column=5)
self.buttons['bad2d'].thebutton.grid(row=4, column=4)
self.buttons['deblend'].thebutton.grid(row=5, column=5)
self.e_comment.grid(row=6, column=0, columnspan=5)
self.canvas = tk.Canvas(self.frame, background="white", height=5)
self.line_tags = []
self.draw_lines()
if simple_twod:
#self.panel.place(x=0, y=0, relwidth=1, relheight=1)
self.panel.grid(row=0, column=1, rowspan=4, columnspan=3)
#self.canvas.grid(row=0, column=1, rowspan=1, columnspan=3)
self.canvas.place(relx=0, rely=0, relwidth=1)
else:
self.panel.grid(row=0, column=0, columnspan=6)
#self.canvas.grid(row=0, column=0, columnspan=6)
self.canvas.place(relx=0, rely=0, relwidth=1)
self.panel.grid()
#self.canvas.grid(row=0, column=0, columnspan=6)
self.panel2.grid(row=1, column=1, columnspan=3, rowspan=3)
self.panel_rgb.grid(row=1, column=0, columnspan=1, rowspan=3)
self.master.mainloop()
def ds9(*args, **kwargs):
return pysao.ds9(path=os.path.expandvars('$DS9'))
def __init__(self,
images=['UDS_54826.zfit.png', 'UDS_55031.zfit.png'],
logfile='inspect_3dhst.info',
RGB_PATH='./',
RGB_EXTENSION='_vJH_6.png',
FITS_PATH='./',
load_log=True,
ds9=None,
rgb_lower=True):
"""
GUI tool for inspecting grism redshift fits
x = unicorn.inspect.ImageClassifier(images=glob.glob('Specz/GOODS-S-25*zfit.png'), RGB_PATH=RGB_PATH, FITS_PATH='Specz/')
"""
if len(images) == 0:
print 'No images specified'
return False
if not os.path.exists(images[0]):
print 'First image not found (%s), is path correct?' % (images[0])
return False
self.RGB_PATH = RGB_PATH
self.FITS_PATH = FITS_PATH
self.RGB_EXTENSION = RGB_EXTENSION
self.rgb_lower = rgb_lower
#### Check ds9
self.ds9 = ds9
if ds9 is True:
try:
import pysao
self.ds9 = pysao.ds9()
except:
print 'Couldn\'t import pysao to run DS9'
self.ds9 = None
##### Add .fits to filename and make backup if necessary
self.logfile = logfile
if not self.logfile.lower().endswith('.fits'):
self.logfile += '.fits'
if os.path.exists(self.logfile):
bk = glob.glob(self.logfile + '.backup*')
if len(bk) > 0:
bkup_file = self.logfile + '.backup.%03d' % (len(bk))
else:
bkup_file = self.logfile + '.backup'
shutil.copy(self.logfile, bkup_file)
print 'Made copy of %s -> %s' % (self.logfile, bkup_file)
####### Initialize parameters
self.params = {}
self.images = images
self.marked_lines = None
if os.path.exists(self.logfile) & load_log:
self.read_fits()
self.N = len(self.images)
for key in [
'line', 'extended', 'absorption', 'unamb', 'misid', 'contam',
'zp', 'tilt', 'investigate', 'star', 'seen', 'bad2d',
'deblend', 'sed'
]:
if key not in self.params.keys():
self.params[key] = np.zeros(self.N, dtype=np.int)
if self.marked_lines is None:
self.marked_lines = np.zeros((self.N, 5))
if 'comment' not in self.params.keys():
self.params['comment'] = ['---' for i in range(self.N)]
self.i = 0
####### Initialize GUI
master = tk.Toplevel()
simple_twod = False
if 'zfit.png' in self.images[0]:
master.geometry('1050x630')
elif '2D.png' in self.images[0]:
master.geometry('850x750')
simple_twod = True
else:
master.geometry('1050x630')
self.master = master
self.frame = tk.Frame(master)
self.frame.pack()
#### Image Panels
imageFile = Image.open(self.images[0])
im = ImageTk.PhotoImage(imageFile)
self.panel = tk.Label(self.frame, image=im, cursor='target')
# imageFile2 = Image.open(self.images[0].replace('zfit','zfit.2D')).resize((500,202))
# im2 = ImageTk.PhotoImage(imageFile2)
im2 = ImageTk.PhotoImage(self.get_twod_file(self.images[0]))
self.panel2 = tk.Label(self.frame, image=im2)
# self.panel2.configure(image = im2)
# self.panel2.image = im2
#### RGB Panel
im_rgb = ImageTk.PhotoImage(self.get_rgb_file(self.images[0]))
self.panel_rgb = tk.Label(self.frame, image=im_rgb)
#### Keypress binding
self.master.bind("<Key>", self.keypress_event)
#### Mouse binding - right click
self.master.bind("<Button-2>", self.right_click_event)
### For logging slider movements
#self.sliders = {}
self.sliders = {}
######
### Navigation buttons
###
self.button_quit = tk.Button(self.frame,
text='(q)uit',
command=self.finish)
self.button_log = tk.Button(self.frame,
text='Log to (F)ile',
command=self.write_fits)
self.button_prev = tk.Button(self.frame,
text='(p)rev',
command=self.img_prev)
self.button_next = tk.Button(self.frame,
text='(n)ext',
command=self.img_next)
self.buttons = {}
#### Emission lne?
self.sliders['line'] = mySlider(self,
text='Emission (l)ine',
param=self.params['line'],
hotkey='l')
#### Absorption
self.sliders['absorption'] = mySlider(self,
text='(a)bs./break',
param=self.params['absorption'],
hotkey='a')
#### Extended line
self.sliders['extended'] = mySlider(self,
text='(e)xtended',
param=self.params['extended'],
hotkey='e')
#### Unambiguous redshift
self.buttons['unamb'] = myCheckbutton(self,
text='(u)nambiguous',
param=self.params['unamb'],
hotkey='u')
#### Flag contamination
self.sliders['contam'] = mySlider(self,
text='(b)ad contam',
param=self.params['contam'],
hotkey='b')
#### Line misidentification
self.buttons['misid'] = myCheckbutton(self,
text='Line (m)isID',
param=self.params['misid'],
hotkey='m')
#### Tilt?
self.buttons['tilt'] = myCheckbutton(self,
text='(t)ilt',
param=self.params['tilt'],
hotkey='t')
#### Bad z_phot / z_spec or both
self.buttons['zp'] = myCheckbutton(self,
text='Bad (z)spec',
param=self.params['zp'],
hotkey='z')
#### SED problems
self.sliders['sed'] = mySlider(self,
text='Bad SED (k)',
param=self.params['sed'],
hotkey='k',
to=2)
#### Flag for manual investigation
self.sliders['investigate'] = mySlider(
self,
text='(i)nvestigate',
param=self.params['investigate'],
hotkey='i',
to=4)
### Object seen already?
self.buttons['seen'] = myCheckbutton(self,
text='SEEN?',
param=self.params['seen'],
hotkey='xxx')
#### Star?
self.buttons['star'] = myCheckbutton(self,
text='(s)tar',
param=self.params['star'],
hotkey='s')
#### Spectrum problem
self.buttons['bad2d'] = myCheckbutton(self,
text='Bad 1D/2D (x)',
param=self.params['bad2d'],
hotkey='x')
#### Deblend issue
self.buttons['deblend'] = myCheckbutton(self,
text='(d)eblend',
param=self.params['deblend'],
hotkey='d')
### Comment holder
self.tvar = tk.StringVar()
self.e_comment = tk.Label(self.frame, textvariable=self.tvar)
self.e_comment.configure(relief=tk.RIDGE)
self.tvar.set(self.params['comment'][0])
#####################
##### Set up the grid for the GUI elements
self.button_next.grid(row=1, column=4, columnspan=1)
self.button_prev.grid(row=1, column=5, columnspan=1)
self.button_log.grid(row=2, column=4, columnspan=1)
self.button_quit.grid(row=2, column=5, columnspan=1)
self.buttons['seen'].thebutton.grid(row=3, column=5)
self.buttons['star'].thebutton.grid(row=3, column=4)
self.sliders['line'].theslider.grid(row=4, column=0)
self.sliders['absorption'].theslider.grid(row=5, column=0)
self.sliders['extended'].theslider.grid(row=4, column=1)
self.buttons['unamb'].thebutton.grid(row=5, column=1)
self.sliders['contam'].theslider.grid(row=4, column=2)
self.buttons['misid'].thebutton.grid(row=5, column=2)
self.buttons['tilt'].thebutton.grid(row=4, column=3)
self.buttons['zp'].thebutton.grid(row=5, column=3)
self.sliders['sed'].theslider.grid(row=5, column=4)
self.sliders['investigate'].theslider.grid(row=4, column=5)
self.buttons['bad2d'].thebutton.grid(row=4, column=4)
self.buttons['deblend'].thebutton.grid(row=5, column=5)
self.e_comment.grid(row=6, column=0, columnspan=5)
self.canvas = tk.Canvas(self.frame, background="white", height=5)
self.line_tags = []
self.draw_lines()
if simple_twod:
#self.panel.place(x=0, y=0, relwidth=1, relheight=1)
self.panel.grid(row=0, column=1, rowspan=4, columnspan=3)
#self.canvas.grid(row=0, column=1, rowspan=1, columnspan=3)
self.canvas.place(relx=0, rely=0, relwidth=1)
else:
self.panel.grid(row=0, column=0, columnspan=6)
#self.canvas.grid(row=0, column=0, columnspan=6)
self.canvas.place(relx=0, rely=0, relwidth=1)
self.panel.grid()
#self.canvas.grid(row=0, column=0, columnspan=6)
self.panel2.grid(row=1, column=1, columnspan=3, rowspan=3)
self.panel_rgb.grid(row=1, column=0, columnspan=1, rowspan=3)
self.master.mainloop()