[BUG]: fix major bugs in PyKE

.gitignore

@@ -58,3 +58,6 @@ target/
 
 # Custom additions
 pyraf
+
+# Mac OSX
+.DS_Store

keparith.py

@@ -12,29 +12,29 @@
 
 
 import sys
-import pyfits
+from astropy.io import fits as pyfits
 import matplotlib.pyplot as plt
 import kepio, kepmsg, kepkey, kepfit, kepstat
-from numpy import median,subtract,maximum,ones,multiply,float32,shape,absolute,mean,std,isfinite,where,nan
+from numpy import median, subtract, maximum, ones, multiply, float32, shape
+from numpy import absolute, mean, std, isfinite, where, nan
 
 __svnid__ = "$Id: keparith.py 4326 2012-07-02 21:49:01Z tsbarcl2 $"
 __url__ = "$URL: svn+ssh://mstill@murzim.amn.nasa.gov/data-repo/trunk/data/flight/go/PyKE/kepler/keparith.py $"
 
 
-def MAD(xx,minSd=1E-16): 
-      """Median Absolute Deviation 
-      """ 
-      med=median(xx,0) 
-      absdev=absolute(subtract(xx,med)) 
-      mad=median(absdev,0) 
-      mad=maximum(mad,multiply(ones(mad.shape,float32), 
-                                           (minSd/1.48))) 
-      return mad 
+def MAD(xx,minSd=1E-16):
+      """Median Absolute Deviation
+      """
+      med = median(xx,0)
+      absdev = absolute(subtract(xx, med))
+      mad=median(absdev, 0)
+      mad=maximum(mad, multiply(ones(mad.shape, float32),(minSd / 1.48)))
+      return mad
 
 
 def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 	,clobber,verbose,logfile,status):
-	# log the call 
+	# log the call
 
 	hashline = '----------------------------------------------------------------------------'
 	kepmsg.log(logfile,hashline,verbose)
@@ -65,33 +65,23 @@ def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 	# clobber output file
 
 	if clobber: status = kepio.clobber(outfile,logfile,verbose)
-	if kepio.fileexists(outfile): 
+	if kepio.fileexists(outfile):
 		message = 'ERROR -- KEPARITH: ' + outfile + ' exists. Use clobber=yes'
 		status = kepmsg.err(logfile,message,verbose)
 
 	## open input file
 
 	instr, status = kepio.openfits(infile,'readonly',logfile,verbose)
-	
+
 	if status == 0:
 		try:
 			test = str(instr[0].header['FILEVER'])
 			version = 2
 		except KeyError:
 			version = 1
-
-
-		# if version == 1:
-		# 	#lc_flux = instr[1].data.field(datacol) + constant
-		# 	lc_flux = instr[1].data.field(datacol)
-		# 	instr[1].data.field(datacol)[:] = (lc_flux - median(lc_flux)) / MAD(lc_flux)
-		# elif version == 2:
-		# 	#lc_flux = instr[1].data.field(datacol) + constant
-		# 	lc_flux = instr[1].data.field(datacol)
-		# 	instr[1].data.field(datacol)[:] = (lc_flux - median(lc_flux)) / MAD(lc_flux)
-
+
 		lc_flux = instr[1].data.field(datacol)
-		
+
 		if datacol == 'SAP_FLUX':
 			errcol = 'SAP_FLUX_ERR'
 			try:
@@ -118,7 +108,6 @@ def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 					haveerr = True
 				except:
 					haveerr = False
-
 		#subtractor he just refers to the number that will be added/subtracted
 		#divided or multiplied
 		if isinstance(constantval,(long,int,float)) and constant == 'None':
@@ -142,14 +131,12 @@ def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 		else:
 			message = 'Your constant term is not in the list of possible functions'
 			status = kepmsg.err(logfile,message,verbose)
-	
+
 	if subtractor == 0. and sign == 'divide' and status == 0:
 		message = 'You are trying to divide by zero: not a good idea.'
 		status = kepmsg.err(logfile,message,verbose)
-
 
-
-	if status == 0:	
+	if status == 0:
 		if sign.lower() == 'add':
 			instr[1].data.field(datacol)[:] = where(isfinite(instr[1].data.field(datacol)[:]),(lc_flux + subtractor),nan)
 		elif sign.lower() == 'subtract':
@@ -165,14 +152,11 @@ def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 		else:
 			message = 'Your operation need to be one of: add, subtract, divide or multiply'
 			status = kepmsg.err(logfile,message,verbose)
-	
+
 	if status == 0:
 		instr.writeto(outfile)
-
-
 	if status == 0:
-		status = kepio.closefits(instr,logfile,verbose)	   
-
+		status = kepio.closefits(instr,logfile,verbose)
 	## end time
 
 	if (status == 0):
@@ -185,34 +169,32 @@ def kepaddconstant(infile,outfile,datacol,constant,constantval,sign
 
 if '--shell' in sys.argv:
 	import argparse
-
-	parser = argparse.ArgumentParser(description='Time invariant algebra on light curve data')
-	parser.add_argument('--shell', action='store_true', help='Are we running from the shell?')
+
+	parser = argparse.ArgumentParser(description='Time invariant algebra '
+                                                      'on light curve 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('--datacol', '-d', default='SAP_FLUX', dest='datacol', help='Name of the column containing the flux time series', type=str)
+	parser.add_argument('--datacol', '-d', default='SAP_FLUX',
+                            dest='datacol',
+                            help='Name of the column containing the flux time series', type=str)
 	parser.add_argument('--constantfunc', '-f', default='None', dest='constantfunc', help='A value calculated from a function to be used in operation', type=str,
 		choices=['None','median','mean','MAD','std','max','range'])
 	parser.add_argument('--constantval', '-v', default='None', dest='constantval', help='Use a given number in operation', type=str)
 	parser.add_argument('--operation', '-o', default='add', dest='operation', help='Add, subtract, multiply, divide flux by a constant', type=str,
 		choices=['add','','subtract','multiply','divide'])
-
 	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='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()
-
 	kepaddconstant(args.infile,args.outfile,args.datacol,args.constantfunc,args.constantval,args.operation,args.clobber,args.verbose,args.logfile,args.status)
-
 
 else:
 	from pyraf import iraf
 	parfile = iraf.osfn("kepler$keparith.par")
 	t = iraf.IrafTaskFactory(taskname="keparith", value=parfile, function=kepaddconstant)
-
-