-
Notifications
You must be signed in to change notification settings - Fork 35
/
kepclip.py
256 lines (203 loc) · 7.75 KB
/
kepclip.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
import numpy as np
import sys
from astropy.io import fits as pyfits
from matplotlib import pyplot as plt
import kepio, kepmsg, kepkey, kepstat
def kepclip(infile, outfile, ranges, plot, plotcol, clobber, verbose, logfile,
status, cmdLine=False):
# startup parameters
status = 0
labelsize = 32
ticksize = 24
xsize = 18
ysize = 10
lcolor = '#0000ff'
lwidth = 1.0
fcolor = '#ffff00'
falpha = 0.2
# log the call
hashline = '----------------------------------------------------------------------------'
kepmsg.log(logfile,hashline,verbose)
call = 'KEPCLIP -- '
call += 'infile='+infile+' '
call += 'outfile='+outfile+' '
call += 'ranges='+ranges + ' '
plotit = 'n'
if (plot): plotit = 'y'
call += 'plot='+plotit+ ' '
call += 'plotcol='+plotcol+ ' '
overwrite = 'n'
if (clobber): overwrite = 'y'
call += 'clobber='+overwrite+ ' '
chatter = 'n'
if (verbose): chatter = 'y'
call += 'verbose='+chatter+' '
call += 'logfile='+logfile
kepmsg.log(logfile,call+'\n',verbose)
# start time
kepmsg.clock('KEPCLIP started at',logfile,verbose)
# test log file
logfile = kepmsg.test(logfile)
# clobber output file
if clobber: status = kepio.clobber(outfile,logfile,verbose)
if kepio.fileexists(outfile):
message = 'ERROR -- KEPCLIP: ' + outfile + ' exists. Use --clobber'
status = kepmsg.err(logfile,message,verbose)
# time ranges for region
if status == 0:
t1 = []; t2 = []
t1, t2, status = kepio.timeranges(ranges,logfile,verbose)
# open input file
if status == 0:
instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
tstart, tstop, bjdref, cadence, status = kepio.timekeys(instr,infile,logfile,verbose,status)
if status == 0:
try:
work = instr[0].header['FILEVER']
cadenom = 1.0
except:
cadenom = cadence
# fudge non-compliant FITS keywords with no values
if status == 0:
instr = kepkey.emptykeys(instr,file,logfile,verbose)
# input data
if status == 0:
table = instr[1].data
# read time and flux columns
if status == 0:
barytime, status = kepio.readtimecol(infile,table,logfile,verbose)
if status == 0:
flux, status = kepio.readfitscol(infile,table,plotcol,logfile,verbose)
if status == 0:
barytime = barytime + bjdref
if 'flux' in plotcol.lower():
flux = flux / cadenom
# filter input data table
if status == 0:
naxis2 = 0
work1 = np.array([],'float64')
work2 = np.array([],'float32')
for i in range(len(barytime)):
if (np.isfinite(barytime[i]) and np.isfinite(flux[i]) and flux[i] != 0.0):
reject = False
for j in range(len(t1)):
if (barytime[i] >= t1[j] and barytime[i] <= t2[j]):
reject = True
if not reject:
table[naxis2] = table[i]
work1 = np.append(work1,barytime[i])
work2 = np.append(work2,flux[i])
naxis2 += 1
# comment keyword in output file
if status == 0:
status = kepkey.history(call,instr[0],outfile,logfile,verbose)
# write output file
if status == 0:
instr[1].data = table[:naxis2]
comment = 'NaN cadences removed from data'
status = kepkey.new('NANCLEAN',True,comment,instr[1],outfile,logfile,verbose)
instr.writeto(outfile)
# clean up x-axis unit
if status == 0:
barytime0 = float(int(tstart / 100) * 100.0)
barytime = work1 - barytime0
xlab = 'BJD $-$ %d' % barytime0
# clean up y-axis units
if status == 0:
try:
nrm = len(str(int(work2.max())))-1
except:
nrm = 0
flux = work2 / 10**nrm
ylab = '10$^%d$ e$^-$ s$^{-1}$' % nrm
# data limits
xmin = barytime.min()
xmax = barytime.max()
ymin = flux.min()
ymax = flux.max()
xr = xmax - xmin
yr = ymax - ymin
# clear window, plot box
if status == 0 and plot:
plt.figure(figsize=[xsize,ysize])
plt.clf()
ax = plt.axes([0.05,0.1,0.94,0.88])
# force tick labels to be absolute rather than relative
plt.gca().xaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
plt.gca().yaxis.set_major_formatter(plt.ScalarFormatter(useOffset=False))
# rotate y labels by 90 deg
labels = ax.get_yticklabels()
plt.setp(labels, 'rotation', 90, fontsize=12)
# plot line data
ltime = [barytime[0]]; ldata = [flux[0]]
for i in range(1,len(flux)):
if (barytime[i-1] > barytime[i] - 0.025):
ltime.append(barytime[i])
ldata.append(flux[i])
else:
ltime = np.array(ltime, dtype=np.float)
ldata = np.array(ldata, dtype=np.float)
plt.plot(ltime,ldata,color=lcolor,linestyle='-',linewidth=lwidth)
ltime = []; ldata = []
ltime = np.array(ltime, dtype=np.float)
ldata = np.array(ldata, dtype=np.float)
plt.plot(ltime,ldata,color=lcolor,linestyle='-',linewidth=lwidth)
# plot fill data
barytime = np.insert(barytime,[0],[barytime[0]])
barytime = np.append(barytime,[barytime[-1]])
flux = np.insert(flux,[0],[0.0])
flux = np.append(flux,[0.0])
plt.fill(barytime,flux,fc=fcolor,linewidth=0.0,alpha=falpha)
plt.xlim(xmin-xr*0.01,xmax+xr*0.01)
if ymin-yr*0.01 <= 0.0:
plt.ylim(1.0e-10,ymax+yr*0.01)
else:
plt.ylim(ymin-yr*0.01,ymax+yr*0.01)
plt.xlabel(xlab, {'color' : 'k'})
plt.ylabel(ylab, {'color' : 'k'})
plt.grid()
# render plot
if status == 0 and plot:
plt.ion()
plt.show()
# close input file
if status == 0:
status = kepio.closefits(instr,logfile,verbose)
# end time
if (status == 0):
message = 'KEPCLIP completed at'
else:
message = '\nKEPCLIP aborted at'
kepmsg.clock(message,logfile,verbose)
# main
if '--shell' in sys.argv:
import argparse
parser = argparse.ArgumentParser(description='Remove unwanted time '
'ranges from Kepler time series data')
parser.add_argument('--shell', action='store_true',
help='Are we running from the shell?')
parser.add_argument('infile', help='Name of input file', type=str)
parser.add_argument('outfile', help='Name of FITS file to output',
type=str)
parser.add_argument('ranges',
help='List of time domain ranges to be excluded',
type=str)
parser.add_argument('--plot', action='store_true', help='Plot result?')
parser.add_argument('--plotcol', '-p',help='Data column to plot',
default='SAP_FLUX', dest='plotcol', type=str)
parser.add_argument('--clobber', action='store_true',
help='Overwrite output file?')
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='kepclip.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
kepclip(args.infile, args.outfile, args.ranges, args.plot, args.plotcol,
args.clobber, args.verbose, args.logfile, args.status,cmdLine)
else:
from pyraf import iraf
parfile = iraf.osfn("kepler$kepclip.par")
t = iraf.IrafTaskFactory(taskname="kepclip", value=parfile, function=kepclip)