/
kepffi.py
executable file
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kepffi.py
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import math
import numpy as np
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
import kepio, kepmsg, kepkey
import sys, os, urllib, time, re
# global variables
ffifile = False; aperfile = False; maskfile = 'KeplerFFI.txt'
plotfile = 'KeplerFFI.png'; pimg = None; mask = []; zscale = False
xmin = 0.0; xmax = 1000.0; ymin = 0.0; ymax = 1000.0; zmin = False; zmax = False
kepid = ''; ra = ''; dec = ''; kepmag = ''; season = ''; quarter = -1
skygroup = ''; channel = ''; module = ''; output = ''; column = ''; row = ''
colmap='jet'; aid = None; cid = None; did = None; eid = None; fid = None
pkepmag = None; pkepid = None; pra = None; pdec = None; cmdLine = False
# -----------------------------------------------------------
# core code
def kepffi(ffifile,kepid,ra,dec,aperfile,imin,imax,iscale,cmap,npix,
verbose,logfile,status,cmdLine=False):
global pimg, zscale, zmin, zmax, xmin, xmax, ymin, ymax, quarter
global kepmag, skygroup, season, channel
global module, output, row, column, maskfile, plotfile
global pkepid, pkepmag, pra, pdec, colmap, mask
# input arguments
status = 0
np.seterr(all="ignore")
maskfile = 'kepffi-' + str(kepid) + '.txt'
plotfile = 'kepffi-' + str(kepid) + '.png'
zmin = imin; zmax = imax; zscale = iscale; colmap = cmap
# logg the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPFFI -- '
call += 'ffifile='+ffifile+' '
call += 'kepid='+str(kepid)+' '
call += 'ra='+ra+' '
call += 'dec='+dec+' '
call += 'aperfile='+aperfile+' '
call += 'imin='+str(imin)+' '
call += 'imax='+str(imax)+' '
call += 'iscale='+str(iscale)+' '
call += 'cmap'+str(cmap)+' '
call += 'npix='+str(npix)+' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPFFI started at',logfile,verbose)
# reference color map
if cmap == 'browse':
status = cmap_plot(cmdLine)
# open existing mask file
if kepio.fileexists(aperfile):
lines, status = kepio.openascii(aperfile,'r',logfile,verbose)
for line in lines:
line = line.strip().split('|')
y0 = int(line[3])
x0 = int(line[4])
pixels = line[5].split(';')
for pixel in pixels:
m = y0 + int(pixel.split(',')[0])
n = x0 + int(pixel.split(',')[1])
mask.append(str(m)+','+str(n))
status = kepio.closeascii(lines,logfile,verbose)
# RA and Dec conversion
if kepid == 'None' or kepid == 'none' or kepid.strip() == '':
try:
mra = float(ra)
mdec = float(dec)
except:
try:
mra, mdec = sex2dec(ra, dec)
except:
txt = 'ERROR -- no sensible RA and Dec coordinates provided'
sys.exit(txt)
# open FFI FITS file
if status == 0:
ffi, status = openfits(ffifile,'readonly')
try:
quarter = ffi[0].header['QUARTER']
except:
try:
dateobs = ffi[0].header['DATE-OBS']
if dateobs == '2009-04-24': quarter = 0
if dateobs == '2009-04-25': quarter = 0
if dateobs == '2009-04-26': quarter = 0
if dateobs == '2009-06-19': quarter = 2
if dateobs == '2009-08-19': quarter = 2
if dateobs == '2009-09-17': quarter = 2
if dateobs == '2009-10-19': quarter = 3
if dateobs == '2009-11-18': quarter = 3
if dateobs == '2009-12-17': quarter = 3
except:
txt = 'ERROR -- cannot determine quarter when FFI was taken. Either a\n'
txt += 'QUARTER or DATE-OBS keyword is expected in the primary header'
sys.exit(txt)
if quarter == 0: quarter = 1
if quarter < 0:
txt = 'ERROR -- cannot determine quarter from FFI. Try downloading a new\n'
txt += 'version of KeplerFFI.py from http://keplergo.arc.nasa.gov'
sys.exit()
if int(quarter) == 0:
season = 3
else:
season = (int(quarter) - 2) % 4
# locate target in MAST
try:
kepid,ra,dec,kepmag,skygroup,channel,module,output,row,column \
= MASTKepID(kepid,season)
pkepmag = kepmag; pkepid = kepid
except:
kepid,ra,dec,kepmag,skygroup,channel,module,output,row,column \
= MASTRADec(mra,mdec,8.0,season)
ra,dec = dec2sex(ra,dec)
pra = ra; pdec = dec
print kepid,ra,dec,kepmag,skygroup,channel,module,output,row,column
# read and close FFI FITS file
img, status = readimage(ffi,int(channel))
status = closefits(ffi)
# print target data
print ''
print ' KepID: %s' % kepid
print ' RA (J2000): %s' % ra
print 'Dec (J2000): %s' % dec
print ' KepMag: %s' % kepmag
print ' SkyGroup: %2s' % skygroup
print ' Season: %2s' % str(season)
print ' Channel: %2s' % channel
print ' Module: %2s' % module
print ' Output: %1s' % output
print ' Column: %4s' % column
print ' Row: %4s' % row
print ''
# subimage of channel for plot
ymin = int(max([int(row)-npix/2,0]))
ymax = int(min([int(row)+npix/2+1,img.shape[0]]))
xmin = int(max([int(column)-npix/2,0]))
xmax = int(min([int(column)+npix/2+1,img.shape[1]]))
# intensity scale
nstat = 2; pixels = []
for i in range(ymin,ymax+1):
for j in range(xmin,xmax+1):
pixels.append(img[i,j])
pixels = np.array(np.sort(pixels),dtype=np.float32)
if int(float(len(pixels)) / 10 + 0.5) > nstat:
nstat = int(float(len(pixels)) / 10 + 0.5)
if not zmin:
zmin = np.median(pixels[:nstat])
if not zmax:
zmax = np.median(pixels[-nstat:])
if 'log' in zscale:
img = np.log10(img)
zmin = math.log10(zmin)
zmax = math.log10(zmax)
if ('sq' in zscale):
img = np.sqrt(img)
zmin = math.sqrt(zmin)
zmax = math.sqrt(zmax)
pimg = img[ymin:ymax,xmin:xmax]
# plot limits
ymin = float(ymin) - 0.5
ymax = float(ymax) - 0.5
xmin = float(xmin) - 0.5
xmax = float(xmax) - 0.5
# plot style
if status == 0:
plt.figure(figsize=[10,7])
plotimage(cmdLine)
# render plot
plt.ion()
plt.show()
return
# -----------------------------------------------------------
# plot channel image
def plotimage(cmdLine):
global aid, cid, did, eid, fid
# print FFI and source location data on plot
plt.clf()
plt.axes([0.73,0.09,0.25,0.4])
plt.text(0.1,1.0,' KepID: %s' % pkepid,fontsize=12)
plt.text(0.1,0.9,' RA (J2000): %s' % pra,fontsize=12)
plt.text(0.1,0.8,'Dec (J2000): %s' % pdec,fontsize=12)
plt.text(0.1,0.7,' KepMag: %s' % pkepmag,fontsize=12)
plt.text(0.1,0.6,' SkyGroup: %2s' % skygroup,fontsize=12)
plt.text(0.1,0.5,' Season: %2s' % str(season),fontsize=12)
plt.text(0.1,0.4,' Channel: %2s' % channel,fontsize=12)
plt.text(0.1,0.3,' Module: %2s' % module,fontsize=12)
plt.text(0.1,0.2,' Output: %1s' % output,fontsize=12)
plt.text(0.1,0.1,' Column: %4s' % column,fontsize=12)
plt.text(0.1,0.0,' Row: %4s' % row,fontsize=12)
plt.setp(plt.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
plt.xlim(0.0,1.0)
plt.ylim(-0.05,1.12)
# clear button
plt.axes([0.73,0.87,0.25,0.09])
plt.text(0.5,0.5,'CLEAR',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
plt.setp(plt.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
plt.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
plt.xlim(0.0,1.0)
plt.ylim(0.0,1.0)
aid = plt.connect('button_press_event',clicker1)
# dump custom aperture to file button
plt.axes([0.73,0.77,0.25,0.09])
plt.text(0.5,0.5,'DUMP',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
plt.setp(plt.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
plt.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
plt.xlim(0.0,1.0)
plt.ylim(0.0,1.0)
cid = plt.connect('button_press_event',clicker3)
# print window to png file button
plt.axes([0.73,0.67,0.25,0.09])
plt.text(0.5,0.5,'PRINT',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
plt.setp(plt.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
plt.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
plt.xlim(0.0,1.0)
plt.ylim(0.0,1.0)
did = plt.connect('button_press_event',clicker4)
# print close plot file button
plt.axes([0.73,0.57,0.25,0.09])
plt.text(0.5,0.5,'CLOSE',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
plt.setp(plt.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
plt.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
plt.xlim(0.0,1.0)
plt.ylim(0.0,1.0)
eid = plt.connect('button_press_event',clicker5)
# plot the image window
ax = plt.axes([0.08,0.09,0.63,0.88])
plt.subplots_adjust(0.06,0.1,0.93,0.88)
plt.gca().xaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
labels = ax.get_yticklabels()
plt.setp(labels, 'rotation', 90)
plt.imshow(pimg,aspect='auto',interpolation='nearest',origin='lower',
vmin=zmin,vmax=zmax,extent=(xmin,xmax,ymin,ymax),cmap=colmap)
plt.gca().set_autoscale_on(False)
plt.xlabel('Pixel Column Number', {'color' : 'k'})
plt.ylabel('Pixel Row Number', {'color' : 'k'})
plt.grid()
# plot the mask
if colmap in ['Greys','binary','bone','gist_gray','gist_yarg',
'gray','pink','RdGy']:
sqcol = 'g'
alpha = 0.5
else:
sqcol = '#ffffee'
alpha = 0.8
for pixel in mask:
m = int(pixel.split(',')[0])
n = int(pixel.split(',')[1])
y = [m-0.5,m+0.5,m+0.5,m-0.5,m-0.5]
x = [n-0.5,n-0.5,n+0.5,n+0.5,n-0.5]
plt.fill(x,y,sqcol,alpha=alpha,ec=sqcol)
# print x,y
fid = plt.connect('key_press_event',clicker6)
# render plot
plt.ion()
plt.show()
return
# -----------------------------------------------------------
# target data retrieval from MAST based upon KepID
def MASTKepID(id,season):
global skygroup, column, row
# build mast query
url = 'http://archive.stsci.edu/kepler/kepler_fov/search.php?'
url += 'action=Search'
url += '&kic_kepler_id=' + id
url += '&max_records=100'
url += '&verb=3'
url += '&outputformat=CSV'
# retrieve results from MAST
lines = urllib.urlopen(url)
for line in lines:
line = line.strip()
out = line.split(',')
if len(out) > 0:
kepid = out[3]
ra = out[0]
dec = out[1]
kepmag = out[43]
skygroup = out[74]
channel = out[95 + season * 5]
module = out[96 + season * 5]
output = out[97 + season * 5]
row = out[98 + season * 5]
column = out[99 + season * 5]
else:
txt = 'ERROR -- no target found with KepID %s' % id
sys.exit(txt)
return kepid,ra,dec,kepmag,skygroup,channel,module,output,row,column
# -------------------------------------
# detector location retrieval based upon RA and Dec
def MASTRADec(ra,dec,darcsec,season):
global skygroup, column, row
# WCS data
cd1_1 = 0.000702794927969
cd1_2 = -0.000853190160515
cd2_1 = -0.000853190160515
cd2_2 = -0.000702794927969
cd = np.array([[cd1_1,cd1_2],[cd2_1,cd2_2]])
cd = linalg.inv(cd)
# coordinate limits
x1 = 1.0e30
x2 = x1
darcsec /= 3600.0
ra1 = ra - darcsec / 15.0 / cos(dec * pi / 180)
ra2 = ra + darcsec / 15.0 / cos(dec * pi / 180)
dec1 = dec - darcsec
dec2 = dec + darcsec
# build mast query
url = 'http://archive.stsci.edu/kepler/kepler_fov/search.php?'
url += 'action=Search'
url += '&kic_degree_ra=' + str(ra1) + '..' + str(ra2)
url += '&kic_dec=' + str(dec1) + '..' + str(dec2)
url += '&max_records=100'
url += '&verb=3'
url += '&outputformat=CSV'
# retrieve results from MAST: nearest KIC source to supplied coordinates
z = ''
x = 1.0e30
lines = urllib.urlopen(url)
for line in lines:
line = line.strip()
if (len(line) > 0 and
'Kepler' not in line and
'integer' not in line and
'no rows found' not in line):
out = line.split(',')
r = (float(out[6].split(' ')[0]) +
float(out[6].split(' ')[1]) / 60.0 +
float(out[6].split(' ')[2]) / 3600.0) * 15.0
d = (float(out[7].split(' ')[0]) +
float(out[7].split(' ')[1]) / 60.0 +
float(out[7].split(' ')[2]) / 3600.0)
a = sqrt((abs(r - ra) / 15.0 / cos(d * pi / 180))**2 + abs(d - dec)**2)
if a < x:
x = a
z = line.split(',')
if len(z) > 0:
kepid = None
kepmag = None
skygroup = out[73]
channel = out[94 + season * 5]
module = out[95 + season * 5]
output = out[96 + season * 5]
else:
txt = 'ERROR -- row and column could not be calculated. Is location on silicon?'
sys.exit(txt)
# convert coordinates to decimal for the two targets, determine distance from input
zra,zdec = sex2dec(z[6],z[7])
dra = zra - ra
ddec = zdec - dec
drow = cd[0,0] * dra + cd[0,1] * ddec
dcol = cd[1,0] * dra + cd[1,1] * ddec
# pixel coordinates of the nearest KIC target
row = z[97 + season * 5]
column = z[98 + season * 5]
# pixel coordinate of target
row = str(int(float(row) + drow + 0.5))
column = str(int(float(column) + dcol + 0.5))
return kepid,ra,dec,kepmag,skygroup,channel,module,output,row,column
# -----------------------------------
# convert sexadecimal hours to decimal degrees
def sex2dec(ra,dec):
ra = re.sub('\s+','|',ra.strip())
ra = re.sub(':','|',ra.strip())
ra = re.sub(';','|',ra.strip())
ra = re.sub(',','|',ra.strip())
ra = re.sub('-','|',ra.strip())
ra = ra.split('|')
outra = (float(ra[0]) + float(ra[1]) / 60 + float(ra[2]) / 3600) * 15.0
dec = re.sub('\s+','|',dec.strip())
dec = re.sub(':','|',dec.strip())
dec = re.sub(';','|',dec.strip())
dec = re.sub(',','|',dec.strip())
dec = re.sub('-','|',dec.strip())
dec = dec.split('|')
if float(dec[0]) > 0.0:
outdec = float(dec[0]) + float(dec[1]) / 60 + float(dec[2]) / 3600
else:
outdec = float(dec[0]) - float(dec[1]) / 60 - float(dec[2]) / 3600
return outra, outdec
# -----------------------------------
# convert decimal RA and Dec to sexagesimal
def dec2sex(ra,dec):
if ra < 0.0 or ra > 360.0 or dec < -90.0 or dec > 90.0:
txt = 'ERROR -- badly defined RA and Dec provided'
sys.exit()
tmp = ra / 15
ra_h = str(int(tmp))
tmp = (tmp - float(ra_h)) * 60.0
ra_m = str(int(tmp))
tmp = (tmp - float(ra_m)) * 6000.0
print tmp, float(int(tmp + 0.5))
ra_s = '%.2f' % (float(int(tmp + 0.5)) / 100)
if dec < 0.0:
tmp = -dec
else:
tmp = dec
dec_h = str(int(tmp))
tmp = (tmp - float(dec_h)) * 60.0
dec_m = str(int(tmp))
tmp = (tmp - float(dec_m)) * 600.0
dec_s = '%.1f' % (int(tmp + 0.5) / 10)
if dec < 0.0:
dec_h = '-' + dec_h
outra = ra_h + ':' + ra_m + ':' + ra_s
outdec = dec_h + ':' + dec_m + ':' + dec_s
return outra, outdec
# -----------------------------------------------------------
# open HDU structure
def openfits(file,mode):
status = 0
try:
struct = pyfits.open(file,mode=mode)
except:
txt = 'ERROR -- cannot open ' + file + ' as a FITS file'
sys.exit(txt)
return struct, status
# -----------------------------------------------------------
# close HDU structure
def closefits(struct):
status = 0
try:
struct.close()
except:
txt = 'ERROR -- cannot close HDU structure'
sys.exit(txt)
return status
# -----------------------------------------------------------
# read image from HDU structure
def readimage(struct,hdu):
status = 0
try:
imagedata = struct[hdu].data
except:
txt = 'ERROR -- cannot read image data from HDU ' + str(hdu)
sys.exit(txt)
return imagedata, status
# -----------------------------------------------------------
# clear all pixels from pixel mask
def clicker1(event):
global mask, aid, cid, did, eid, fid
if event.inaxes:
if event.button == 1:
if (event.x > 585 and event.x < 783 and
event.y > 488 and event.y < 537):
plt.disconnect(aid)
plt.disconnect(cid)
plt.disconnect(did)
plt.disconnect(eid)
plt.disconnect(fid)
mask = []
plt.clf()
plotimage(cmdLine)
return
# -----------------------------------------------------------
# dump custom aperture definition file
def clicker3(event):
global aid, cid, did, eid, fid
if event.inaxes:
if event.button == 1:
if (event.x > 585 and event.x < 783 and
event.y > 432 and event.y < 480):
masktxt = 'NEW|'
masktxt += skygroup + '|'
masktxt += '{' + re.sub('\s+',':',str(ra))
masktxt += ',' + re.sub('\s+',':',str(dec))
masktxt += '},TAD_NO_HALO,TAD_NO_UNDERSHOOT_COLUMN|'
masktxt += row + '|'
masktxt += column + '|'
for coord in sorted(set(mask)):
masktxt += str(int(coord.split(',')[0]) - int(row)) + ','
masktxt += str(int(coord.split(',')[1]) - int(column)) + ';'
if os.path.isfile(maskfile):
os.remove(maskfile)
out = open(maskfile,'a')
out.write(masktxt[:-1]+'\n')
out.close()
print 'Wrote custom aperture definition file ' + maskfile
return
# -----------------------------------------------------------
# print plot to png with left-mouse click
def clicker4(event):
if event.inaxes:
if event.button == 1:
if (event.x > 585 and event.x < 783 and
event.y > 377 and event.y < 425):
plt.savefig(plotfile)
print 'Wrote plot hardcopy file ' + plotfile
return
# -----------------------------------------------------------
# close plot and exit program
def clicker5(event):
global mask, aid, cid, did, eid, fid, done
if event.inaxes:
if event.button == 1:
if (event.x > 585 and event.x < 783 and
event.y > 320 and event.y < 368):
plt.disconnect(aid)
plt.disconnect(cid)
plt.disconnect(did)
plt.disconnect(eid)
plt.disconnect(fid)
return
# -----------------------------------------------------------
# this function will be called with every click of the mouse
def clicker6(event):
global mask, aid, cid, did, eid, fid
if event.inaxes:
if event.key == 'x':
if colmap in ['Greys','binary','bone','gist_gray','gist_yarg',
'gray','pink','RdGy']:
sqcol = 'g'
alpha = 0.5
else:
sqcol = '#ffffee'
alpha = 0.8
m = float(int(event.xdata + 0.5))
n = float(int(event.ydata + 0.5))
txt = str(int(n))+','+str(int(m))
if txt in mask:
tmpmask = []
for pixel in mask:
if pixel != txt:
tmpmask.append(pixel)
mask = tmpmask
else:
mask.append(txt)
plotimage(cmdLine)
# -----------------------------------------------------------
# these are the choices for the image colormap
def cmap_plot(cmdLine):
plt.figure(1, figsize=[5, 10])
plt.ion()
a = outer(ones(10), arange(0, 1, 0.01))
plt.subplots_adjust(top=0.99, bottom=0.00, left=0.01, right=0.8)
maps = [m for m in cm.datad if not m.endswith("_r")]
maps.sort()
l = len(maps) + 1
for i, m in enumerate(maps):
plt.subplot(l,1,i+1)
plt.setp(plt.gca(), xticklabels=[], xticks=[], yticklabels=[],
yticks=[])
plt.imshow(a, aspect='auto', cmap=get_cmap(m), origin="lower")
plt.text(100.85, 0.5, m, fontsize=10)
# render plot
plt.ion()
plt.show()
return 1
# -----------------------------------------------------------
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Plot sub-areas of Kepler '
'Full Frame Images and define custom '
'target apertures')
parser.add_argument('--shell', action='store_true',
help='Are we running from the shell?')
parser.add_argument('ffifile', help='name of input FFI FITS file',
type=str)
parser.add_argument('--kepid', default='',
help='Kepler ID of target from Kepler Input Catalog',
type=str)
parser.add_argument('--ra', default='',
help='Right Ascension of target J2000 [hours or deg]',
type=str)
parser.add_argument('--dec', default='', help='Declination of target J2000 [deg]',
type=str)
parser.add_argument('--aperfile', default='',
help='name of ASCII custom aperture definition file',
type=str)
parser.add_argument('--imin', default=1.5E5,
help='minimum of image intensity scale [e-]',
type=float)
parser.add_argument('--imax', default=5.0E6,
help='minimum of image intensity scale [e-]',
type=float)
parser.add_argument('--iscale', default='logarithmic',
help='type of image intensity scale', type=str,
choices=['linear','logarithmic','squareroot'])
parser.add_argument('--cmap', default='PuBu', help='image colormap',
type=str)
parser.add_argument('--npix', default=30,
help='pixel dimension of subimage', type=float)
parser.add_argument('--verbose', action='store_true',
help='Write to a log file?')
parser.add_argument('--logfile', '-l', help='Name of ascii log file',
default='kepffi.log', dest='logfile', type=str)
parser.add_argument('--status', '-e', help='Exit status (0=good)',
default=0, dest='status', type=int)
args = parser.parse_args()
cmdLine=True
kepffi(args.ffifile, args.kepid, args.ra, args.dec, args.aperfile,
args.imin, args.imax, args.iscale, args.cmap, args.npix,
args.verbose, args.logfile, args.status, cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepffi.par")
t = iraf.IrafTaskFactory(taskname="kepffi", value=parfile, function=kepffi)