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kepmask.py
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kepmask.py
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import pylab, numpy, pyfits
from pylab import *
from matplotlib import *
from numpy import *
import kepio, kepmsg, kepkey, kepplot
import sys, time, re, math
# global variables
infile = False; aperfile = False; maskfile = 'mask.txt'
plotfile = 'kepmask.png'; pxdim = 0; pydim = 0; 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; bid = None; cid = None; did = None; eid = None; fid = None
pkepmag = None; pkepid = None; pra = None; pdec = None
cmdLine = False
# -----------------------------------------------------------
# core code
def kepmask(infile,mfile,pfile,tabrow,imin,imax,iscale,cmap,verbose,logfile,status,cLine=False):
global pimg, zscale, zmin, zmax, xmin, xmax, ymin, ymax, quarter
global pxdim, pydim, kepmag, skygroup, season, channel
global module, output, row, column, maskfile, plotfile
global pkepid, pkepmag, pra, pdec, colmap, cmdLine
# input arguments
status = 0
numpy.seterr(all="ignore")
zmin = imin; zmax = imax; zscale = iscale; colmap = cmap
maskfile = mfile; plotfile = pfile
cmdLine = cLine
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPMASK -- '
call += 'infile='+infile+' '
call += 'maskfile='+mfile+' '
call += 'plotfile='+pfile+' '
call += 'tabrow='+str(tabrow)+' '
call += 'imin='+str(imin)+' '
call += 'imax='+str(imax)+' '
call += 'iscale='+str(iscale)+' '
call += 'cmap='+str(cmap)+' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPMASK started at',logfile,verbose)
# reference color map
if cmap == 'browse':
status = cmap_plot()
# open TPF FITS file and check tabrow exists
if status == 0:
tpf, status = kepio.openfits(infile,'readonly',logfile,verbose)
if status == 0:
try:
naxis2 = tpf['TARGETTABLES'].header['NAXIS2']
except:
txt = 'ERROR -- KEPMASK: No NAXIS2 keyword in ' + infile + '[TARGETTABLES]'
status = kepmsg.err(logfile,txt,True)
if status == 0 and tabrow > naxis2:
txt = 'ERROR -- KEPMASK: tabrow is too large. There are ' + str(naxis2) + ' rows in the table.'
status = kepmsg.err(logfile,txt,True)
if status == 0:
status = kepio.closefits(tpf,logfile,verbose)
# read TPF data pixel image
if status == 0:
kepid, channel, skygroup, module, output, quarter, season, \
ra, dec, column, row, kepmag, xdim, ydim, pixels, status = \
kepio.readTPF(infile,'FLUX',logfile,verbose)
img = pixels[tabrow]
pkepid = copy(kepid)
pra = copy(ra)
pdec = copy(dec)
pkepmag = copy(kepmag)
pxdim = copy(xdim)
pydim = copy(ydim)
pimg = copy(img)
# print target data
if status == 0:
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('')
# subimage of channel for plot
if status == 0:
ymin = copy(row)
ymax = ymin + ydim
xmin = copy(column)
xmax = xmin + xdim
# intensity scale
if status == 0:
pimg, imin, imax = kepplot.intScale1D(pimg,zscale)
if zmin and zmax and 'log' in zscale:
zmin = log10(zmin)
zmax = log10(zmax)
elif zmin and zmax and 'sq' in zscale:
zmin = sqrt(zmin)
zmax = sqrt(zmax)
elif zmin and zmax and 'li' in zscale:
zmin *= 1.0
zmax *= 1.0
else:
zmin = copy(imin)
zmax = copy(imax)
# nstat = 2; pixels = []
# work = array(sort(img),dtype=float32)
# for i in range(len(work)):
# if 'nan' not in str(work[i]):
# pixels.append(work[i])
# pixels = array(pixels,dtype=float32)
# if int(float(len(pixels)) / 10 + 0.5) > nstat:
# nstat = int(float(len(pixels)) / 10 + 0.5)
# if not zmin:
# zmin = median(pixels[:nstat])
# if not zmax:
# zmax = median(pixels[-nstat:])
# if 'log' in zscale:
# pimg = log10(pimg)
# if 'sq' in zscale:
# pimg = sqrt(pimg)
# plot limits
ymin = float(ymin) - 0.5
ymax = float(ymax) - 0.5
xmin = float(xmin) - 0.5
xmax = float(xmax) - 0.5
# plot style
try:
params = {'backend': 'png',
'axes.linewidth': 2.5,
'axes.labelsize': 24,
'axes.font': 'sans-serif',
'axes.fontweight' : 'bold',
'text.fontsize': 12,
'legend.fontsize': 12,
'xtick.labelsize': 14,
'ytick.labelsize': 14}
pylab.rcParams.update(params)
except:
pass
if status == 0:
pylab.figure(figsize=[10,7])
plotimage(cmdLine)
return
# -----------------------------------------------------------
# plot channel image
def plotimage(cmdLine=False):
global aid, bid, cid, did, eid, fid
# print image and source location data on plot
ion()
pylab.clf()
pylab.axes([0.73,0.09,0.25,0.4])
pylab.text(0.1,1.0,' KepID: %s' % pkepid,fontsize=12)
pylab.text(0.1,0.9,' RA (J2000): %s' % pra,fontsize=12)
pylab.text(0.1,0.8,'Dec (J2000): %s' % pdec,fontsize=12)
pylab.text(0.1,0.7,' KepMag: %s' % pkepmag,fontsize=12)
pylab.text(0.1,0.6,' SkyGroup: %2s' % skygroup,fontsize=12)
pylab.text(0.1,0.5,' Season: %2s' % str(season),fontsize=12)
pylab.text(0.1,0.4,' Channel: %2s' % channel,fontsize=12)
pylab.text(0.1,0.3,' Module: %2s' % module,fontsize=12)
pylab.text(0.1,0.2,' Output: %1s' % output,fontsize=12)
pylab.text(0.1,0.1,' Column: %4s' % column,fontsize=12)
pylab.text(0.1,0.0,' Row: %4s' % row,fontsize=12)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
xlim(0.0,1.0)
ylim(-0.05,1.12)
# clear button
pylab.axes([0.73,0.86,0.25,0.11])
pylab.text(0.5,0.5,'CLEAR',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
pylab.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
xlim(0.0,1.0)
ylim(0.0,1.0)
aid = connect('button_press_event',clicker1)
# load mask button
pylab.axes([0.73,0.74,0.25,0.11])
pylab.text(0.5,0.5,'LOAD',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
pylab.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
xlim(0.0,1.0)
ylim(0.0,1.0)
bid = connect('button_press_event',clicker2)
# dump custom aperture to file button
pylab.axes([0.73,0.62,0.25,0.11])
pylab.text(0.5,0.5,'DUMP',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
pylab.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
xlim(0.0,1.0)
ylim(0.0,1.0)
cid = connect('button_press_event',clicker3)
# print window to png file button
pylab.axes([0.73,0.50,0.25,0.11])
pylab.text(0.5,0.5,'PRINT',fontsize=24,weight='heavy',
horizontalalignment='center',verticalalignment='center')
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
pylab.fill([0.0,1.0,1.0,0.0,0.0],[0.0,0.0,1.0,1.0,0.0],'#ffffee')
xlim(0.0,1.0)
ylim(0.0,1.0)
did = connect('button_press_event',clicker4)
# set the image window location and size
ax = pylab.axes([0.07,0.09,0.63,0.88])
# force tick labels to be absolute rather than relative
pylab.gca().xaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.gca().yaxis.set_major_formatter(pylab.ScalarFormatter(useOffset=False))
pylab.subplots_adjust(0.06,0.1,0.93,0.88)
labels = ax.get_yticklabels()
setp(labels, 'rotation', 90)
# plot the image window
imgsum = empty((pydim,pxdim))
n = 0
for i in range(pydim):
for j in range(pxdim):
imgsum[i,j] = pimg[n]
n += 1
imshow(imgsum,aspect='auto',interpolation='nearest',origin='lower',
extent=(xmin,xmax,ymin,ymax),cmap=colmap,vmin=zmin,vmax=zmax)
pylab.gca().set_autoscale_on(False)
xlabel('Pixel Column Number', {'color' : 'k'})
ylabel('Pixel Row Number', {'color' : 'k'})
# 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])
x = [m-0.5,m+0.5,m+0.5,m-0.5,m-0.5]
y = [n-0.5,n-0.5,n+0.5,n+0.5,n-0.5]
pylab.fill(x,y,sqcol,alpha=alpha,ec=sqcol)
fid = connect('key_press_event',clicker6)
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
return
# -----------------------------------------------------------
# clear all pixels from pixel mask
def clicker1(event):
global mask, aid, bid, cid, did, eid, fid
if event.inaxes:
if event.button == 1:
if (event.x > 601 and event.x < 801 and
event.y > 492 and event.y < 522):
disconnect(aid)
disconnect(bid)
disconnect(cid)
disconnect(did)
disconnect(eid)
disconnect(fid)
mask = []
pylab.clf()
plotimage(cmdLine)
return
# -----------------------------------------------------------
# load mask from file
def clicker2(event):
global mask, aid, bid, cid, did, eid, fid, done
if event.inaxes:
if event.button == 1:
if (event.x > 601 and event.x < 801 and
event.y > 422 and event.y < 482):
disconnect(aid)
disconnect(bid)
disconnect(cid)
disconnect(did)
disconnect(eid)
disconnect(fid)
try:
lines, status = kepio.openascii(maskfile,'r',None,False)
for line in lines:
mask = []
work = line.strip().split('|')
y0 = int(work[3])
x0 = int(work[4])
work = work[5].split(';')
for i in range(len(work)):
y = int(work[i].split(',')[0]) + y0
x = int(work[i].split(',')[1]) + x0
mask.append(str(x) + ',' + str(y))
pylab.clf()
plotimage(cmdLine)
except:
txt = 'ERROR -- KEPMASK: Cannot open or read mask file ' + maskfile
kepmsg.err(logfile,txt,True)
return
# -----------------------------------------------------------
# dump custom aperture definition file
def clicker3(event):
global aid, bid, cid, did, eid, fid
if event.inaxes:
if event.button == 1:
if (event.x > 601 and event.x < 801 and
event.y > 354 and event.y < 415):
masktxt = 'NEW|'
masktxt += skygroup + '|'
masktxt += str(pkepid)
masktxt += ',TAD_NO_HALO,TAD_NO_UNDERSHOOT_COLUMN|'
masktxt += str(int(row)) + '|'
masktxt += str(int(column)) + '|'
for coord in sorted(set(mask)):
masktxt += str(int(coord.split(',')[1]) - int(row)) + ','
masktxt += str(int(coord.split(',')[0]) - 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 > 601 and event.x < 801 and
event.y > 285 and event.y < 347):
pylab.savefig(plotfile)
print('Wrote plot hardcopy file ' + plotfile)
return
# -----------------------------------------------------------
# this function will be called with every click of the mouse
def clicker6(event):
global mask, aid, bid, cid, did, eid, fid
if event.inaxes:
if event.key == 'x':
if (event.x > 75 and event.x < 580 and
event.y > 53 and event.y < 550):
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(m))+','+str(int(n))
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():
pylab.figure(figsize=[5,10])
ion()
a=outer(ones(10),arange(0,1,0.01))
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):
subplot(l,1,i+1)
pylab.setp(pylab.gca(),xticklabels=[],xticks=[],yticklabels=[],yticks=[])
imshow(a,aspect='auto',cmap=get_cmap(m),origin="lower")
pylab.text(100.85,0.5,m,fontsize=10)
# render plot
if cmdLine:
pylab.show()
else:
pylab.ion()
pylab.plot([])
pylab.ioff()
status = 1
return status
# -----------------------------------------------------------
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Plot, create or edit custom light curve extraction masks for target pixel files')
parser.add_argument('--shell', action='store_true', help='Are we running from the shell?')
parser.add_argument('infile', help='name of input target pixel FITS file', type=str)
parser.add_argument('maskfile', help='name of ASCII custom aperture definition file', type=str)
parser.add_argument('--plotfile', default='', help='name of output PNG plot file', type=str)
parser.add_argument('--tabrow', default=2177, help='The table row containing the image to plot', type=int)
parser.add_argument('--imin', default=1.5e5, help='minimum of image intensity scale [e-]', type=float)
parser.add_argument('--imax', default=5.0e5, help='maximum 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('--verbose', action='store_true', help='Write to a log file?')
parser.add_argument('--logfile', '-l', help='Name of ascii log file', default='kepcotrend.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
kepmask(args.infile, args.maskfile, args.plotfile, args.tabrow, args.imin, args.imax, args.iscale,
args.cmap, args.verbose, args.logfile, args.status, cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepmask.par")
t = iraf.IrafTaskFactory(taskname="kepmask", value=parfile, function=kepmask)