def plotSpec(self, filename=None, plotother=False):
"""
Determine the current state of the widget entries and plot the
spectrum accordingly.
"""
# Should I use the default name?
if plotother:
# No - put filename to None
filename = None
else:
# Yes - read it from the entry
filename = self.lastplotname
# Now, if no filename is defined yet, open a dialog to ask for a file to be
# plotted
if not filename:
filename = tkFileDialog.askopenfilename(parent=self, initialdir=config.options["outpath"].value)
if filename: self.lastplotname = filename
else: return
# Not yet implemented :
# LOOP OVER RANGES - WHEN THERE ARE SEVERAL RANGES DEFINED - DO WE WANT THIS?
# Check that the file to plot (still) exists and then ask the task manager
# to execute the 'plotspec' task.
if os.path.exists(filename):
taskManager.runTask(tasks.plotspec, filename, usebiggles=self.usebiggles.get())
else:
messageLog.put_warning('Could not open file for plotting - Skipped (%s)' % filename)
def plotSpec(self, filename=None, plotother=False):
"""
Determine the current state of the widget entries and plot the
spectrum accordingly.
"""
# Should I use the default name?
if plotother:
# No - put filename to None
filename = None
else:
# Yes - read it from the entry
filename = self.lastplotname
# Now, if no filename is defined yet, open a dialog to ask for a file to be
# plotted
if not filename:
filename = tkFileDialog.askopenfilename(
parent=self, initialdir=config.options["outpath"].value)
if filename: self.lastplotname = filename
else: return
# Not yet implemented :
# LOOP OVER RANGES - WHEN THERE ARE SEVERAL RANGES DEFINED - DO WE WANT THIS?
# Check that the file to plot (still) exists and then ask the task manager
# to execute the 'plotspec' task.
if os.path.exists(filename):
taskManager.runTask(tasks.plotspec,
filename,
usebiggles=self.usebiggles.get())
else:
messageLog.put_warning(
'Could not open file for plotting - Skipped (%s)' % filename)
def getwavedef1D(frame):
"""
Extract and return the wavelength definition vector [ordernumber, zero
wavelength offset, wavelength step] using the FITS header keywords of a
1-dimensional spectrum.
"""
# Read and store the appropriate headers
try:
npixels = frame[0].header['NAXIS1']
zerowave = frame[0].header['CRVAL1']
refpix = frame[0].header['CRPIX1']
wstep = frame[0].header['CDELT1']
except KeyError:
# Error when reading headers!
messageLog.put_warning('Could not find FITS headers defining the wavelength solution')
return None
# Determine starting (reference) wavelength
woffset = zerowave + (refpix - 1.0) * wstep
# And create the wavelength vector
wavearray = numpy.zeros((1, 4), dtype=numpy.float64)
wavearray[0, :] = [0, 0, woffset, wstep]
# Return the vector to the caller
return wavearray
def helcorr(frame):
# NB: This routine assumes that the file containes the 'DATE-AVG' keyword,
# which is currently only added by the MEF post-processing scripts
#
# To be checked : which epoch are RA and DEC given in, and which role
# does EQUINOX play in this?
"""
Determine the heliocentric velocity correction from the frame headers
"""
# Read the appropriate headers
try:
dateavg = frame[0].header['DATE-AVG']
except KeyError:
# Error when reading headers!
messageLog.put_warning('Could not find DATE-AVG header: skipping heliocentric velocity calculation')
return
try:
ra = float(frame[0].header['RA'])
dec = float(frame[0].header['DEC'])
epoch = float(frame[0].header['EQUINOX'])
except KeyError:
# Error when reading headers!
messageLog.put_warning('Could not read object coordinates: skipping heliocentric velocity calculation')
return
# Example of header card :
# DATE-AVG= '2003-12-13T16:52:12.0' / Midpoint of observation
# Extract useful data from header
year = int(dateavg[0:4])
month = int(dateavg[5:7])
day = int(dateavg[8:10])
ut = dateavg[11:]
# Obtain the heliocentric correction from IRAF
vhelio = irafWrappers.rvcorrect(year, month, day, ut, ra / 15.0, dec, epoch)
# Write result to frame header
frame[0].header.update('VHELIO', vhelio)
frame[0].header.add_history('Added header card for heliocentric velocity')
messageLog.put('Added header card VHELIO with heliocentric velocity', 5)
def fixheaders(frame):
# Make sure header cards GAIN and RDNOISE are defined
# Gain = 1.0 and RDNOISE = 0.0 are the only feasible assumptions one can
# make if nothing else is known.
data = pyfits.open(frame, 'update')
try:
gain = data[0].header['GAIN']
except KeyError:
data[0].header.update('GAIN', 1.0)
messageLog.put_warning('Could not find GAIN header: assumed GAIN = 1.0')
data[0].header.add_history('Inserted missing GAIN header card, assumed GAIN = 1.0')
try:
rdnoise = data[0].header['RDNOISE']
except KeyError:
data[0].header.update('RDNOISE', 0.0)
messageLog.put_warning('Could not find RDNOISE header: assumed RDNOISE = 0.0')
data[0].header.add_history('Inserted missing RDNOISE header card, assumed RDNOISE = 0.0')
data.close()
def removefiles(*patterns):
"""
Remove files with UNIX-like filename pattern matching.
No questions asked, so be careful!
"""
# 'patterns' is an array or tuple of filename patterns. Can, of course,
# also be inidividual file names.
# Loop over patterns
for pattern in patterns:
# Split off the directory path
(dirname, filepattern) = os.path.split(pattern)
# Get a list of all files in the directory
try:
filelist = os.listdir(dirname)
except OSError, errstr:
# Succeed even if the directory was not there (and put warning in log)
messageLog.put_warning(errstr, 9)
return
# Check each file in the directory list
for file in filelist:
# And see if it's name matches the pattern
if fnmatch.fnmatch(file, filepattern):
# If yes, (try to) remove it from the system
messageLog.put('Removing file : "%s"' % file, 7)
try:
os.remove(os.path.join(dirname, file))
except OSError, errstr:
# Succeed even if there were no files (and put warning in log)
messageLog.put_warning(errstr, 9)
def removefiles(*patterns):
"""
Remove files with UNIX-like filename pattern matching.
No questions asked, so be careful!
"""
# 'patterns' is an array or tuple of filename patterns. Can, of course,
# also be inidividual file names.
# Loop over patterns
for pattern in patterns:
# Split off the directory path
(dirname, filepattern) = os.path.split(pattern)
# Get a list of all files in the directory
try:
filelist = os.listdir(dirname)
except OSError, errstr:
# Succeed even if the directory was not there (and put warning in log)
messageLog.put_warning(errstr, 9)
return
# Check each file in the directory list
for file in filelist:
# And see if it's name matches the pattern
if fnmatch.fnmatch(file, filepattern):
# If yes, (try to) remove it from the system
messageLog.put('Removing file : "%s"' % file, 7)
try:
os.remove(os.path.join(dirname, file))
except OSError, errstr:
# Succeed even if there were no files (and put warning in log)
messageLog.put_warning(errstr, 9)
def save(outfile=None, optionlist=[], ignore_options=[]):
"Save the current values of options to disk"
# Only proceed if outfile is defined
if outfile:
# Create an object that will only contain the elements that are
# supposed to be written to disk
outconfig = configobj.ConfigObj(options['default_savefile'].value)
# If optionlist is defined, only select the listed items
if optionlist: keys = optionlist
# Otherwise, select all
else: keys = outconfig['main'].keys()
# If ignore_options was defined, modify the keylist
if ignore_options:
for ignore_key in ignore_options:
if ignore_key in keys:
keys.remove(ignore_key)
# Loop over options
for key in keys:
try:
outvalue = options[key].value
except KeyError:
messageLog.put_warning("Could not write value for %s - continuing" % key)
return
# Process arrays of files
if options[key].type in ('filelist', 'fitsfilelist'):
# Cast to array of strings
if type(outvalue) != type([]): outvalue = [outvalue]
# And attach directory name is necessary
filelist = outvalue
outvalue = []
for filename in filelist:
if os.path.dirname(filename) == options[key].indir.value :
filename = os.path.basename(filename)
outvalue.append(filename)
if options[key].type in ('fitsfile', 'outfitsfile'):
if os.path.dirname(outvalue) == options[key].indir.value :
outvalue = os.path.basename(outvalue)
# Copy the options into the output object
try:
outconfig['main'][key] = outvalue
messageLog.put("Wrote value for %s to %s" % (key, outfile), 9)
except KeyError:
messageLog.put_error("Cannot write configuration option '%s'." % key)
try:
# Now, open the output file in write mode
filehandle = open(outfile, mode='w')
# Write the data
outconfig.write(filehandle)
# Close the output file
filehandle.close()
except Exception, errstr:
messageLog.put_error("Could not save config to %s : %s" % (outfile, errstr))
# Inform user
messageLog.put("Wrote configuration to %s" % outfile, 5)
def findNewFiles(self):
"""
Find files that are not yet listed in the queue of unprocessed
files, and match these with the filename filter pattern
"""
# Retrieve the current value of the filename pattern from the widget
pattern = config.options['filename_filter'].value
# Retrieve the current value of the data input directory
inpath = config.options['inpath'].value
# Read the directory contents
contents = [os.path.join(inpath, file) for file in os.listdir(inpath)]
# Check the obtained list of files agains the existing directory list
# Remove files that already existed in the directory list
# ORDER of if-statements is important!
iterlist = copy.copy(self.dirlist)
for file in iterlist:
if file not in contents:
# Hmm... a strange situation. Apparently a file listed in self.dirlist
# DISappeared from the directory. Adjust the lists accordingly
messageLog.put_warning(
'File %s disappeared from directory - updating lists' %
file, 5)
self.dirlist.remove(file)
# Do NOT swap the following two statements!
# Is this file already in the list of processed files?
if file in self.reducedfiles: self.reducedfiles.remove(file)
# Is this file already in the list of unprocessed files?
if file in self.newfiles: self.newfiles.remove(file)
if file in contents:
# Normal situation, all files in self.dirlist are also in the current
# directory listing. Remove these files one-by-one from the list, so that
# the remaining files are those that are the new files in the input
# directory (this time).
contents.remove(file)
# Now loop over the remaining files
for file in contents:
# And append these to 'self.dirlist' for future reference
self.dirlist.append(file)
# Only look at the filename (disregard from directory path)
basename = os.path.basename(file)
# Make sure that (1) the 'file' is not a directory entry, (2) that it
# matches the filename filter pattern, and (3) that it not yet in
# the unprocessed or processed list.
if ((not os.path.isdir(file))
and (fnmatch.fnmatch(basename, pattern))
and (file not in self.reducedfiles)
and (file not in self.newfiles)):
messageLog.put('Appending file to the queue', 9)
# Only then, append the file to the list of files to process.
self.newfiles.append(file)
# Finally, update queue sizes on screen
self.updateQueueSize()
def flipframe(frame, direction=0, extension=0):
# Retrieved the x and y coordinate vectors
(xvec, yvec) = WCSvector(frame, extension)
# MMM... MAYBE NOT TRUE...
# Comment : flipping the xvec and yvec below is not really
# necessary, because the xnewmin and ynewmin will still be the
# lowest pixel number in the (flipped) xvec and yvec. However,
# exchanging the xvec and yvec is _very_ relevant.
# NB: xaxis is axis nr 1, and yaxis is axis nr 0
flippeddata = frame[extension].data
# Rotate 'n' times 90 degrees
# x -> x, y -> y
if direction == 0:
flippeddata = flippeddata
# x -> -y, y -> x
elif direction == 1:
flippeddata = _flipaxis(flippeddata, axis=1)
flippeddata.transpose()
yvec = _flipaxis(yvec, axis=0)
# x -> -x, y -> -y
elif direction == 2:
flippeddata = _flipaxis(flippeddata, axis=1)
flippeddata = _flipaxis(flippeddata, axis=0)
xvec = _flipaxis(xvec, axis=0)
yvec = _flipaxis(yvec, axis=0)
# x -> y, y -> -x
elif direction == 3:
flippeddata = _flipaxis(flippeddata, axis=0)
flippeddata.transpose()
xvecnew = yvec
yvec = _flipaxis(xvec, axis=0)
xvec = xvecnew
del(xvecnew)
# Rotate 'n' times 90 degrees, and transpose
# x -> y, y -> x
elif direction == 4:
flippeddata.transpose()
xvecnew = yvec
yvec = xvec
xvec = xvecnew
del(xvecnew)
# x -> -x, y -> y
elif direction == 5:
flippeddata = _flipaxis(flippeddata, axis=1)
xvec = _flipaxis(xvec, axis=0)
# x -> -y, y -> -x
elif direction == 6:
flippeddata = _flipaxis(flippeddata, axis=1)
flippeddata = _flipaxis(flippeddata, axis=0)
flippeddata.transpose()
# x -> x, y -> -y
elif direction == 7:
flippeddata = _flipaxis(flippeddata, axis=0)
yvec = _flipaxis(yvec, axis=0)
else:
messageLog.put_warning('Frame orientation parameter out of range - ignored')
# Determine 'new' vector minima and stepsize
xnewbin = abs(xvec[2] - xvec[1])
ynewbin = abs(yvec[2] - yvec[1])
xnewmin = xvec.min()
ynewmin = yvec.min()
# Update header values accordingly
frame[extension].header.update('CRVAL1', xnewmin)
frame[extension].header.update('CRPIX1', 1)
frame[extension].header.update('CDELT1', xnewbin)
frame[extension].header.update('CTYPE1', 'PIXEL')
frame[extension].header.update('CRVAL2', ynewmin)
frame[extension].header.update('CRPIX2', 1)
frame[extension].header.update('CDELT2', ynewbin)
frame[extension].header.update('CTPYE2', 'PIXEL')
# Store the rotated and flipped data in fits object
frame[extension].data = flippeddata
# And adjust the image headers to reflect the data
frame[extension].update_header()
def run():
"""
Main program entry, initializing and starting the main window and managing
its 'mainloop'
"""
# Get and check command-line options
#
# NB: The -c (enable-calib) option is now deprecated
#
try:
opts, args = getopt.getopt(sys.argv[1:], "cs", ["calib", "scrollbar"])
except getopt.GetoptError:
# print help information and exit:
print "Unknown command line parameter. Allowed optional parameters are : "
#print "-c [file] Load calibration file at startup"
print "-s / --scrollbar Add vertical scrollbar is screen does not fit"
sys.exit(2)
#enablecalib = False
hasscrollbar = False
for option, parameter in opts:
if option in ("-c", "--calib"):
print "The -c option is deprecated. You can now always access the calibs submenu."
# enablecalib = True
if option in ("-s", "--scrollbar"):
hasscrollbar = True
# Display a welcome message in the message log
messageLog.put('=' * 65)
messageLog.put("Welcome to FIEStool - the automatic data processing tool")
messageLog.put("for the FIES spectrograph at the Nordic Optical Telescope")
messageLog.put("Copyright (c) 2005 NOTSA; All Rights Reserved")
messageLog.put("This is version %s (%s), written by %s" %
(_version, _date, _author))
messageLog.put('=' * 65)
messageLog.put("Right-click on any item to obtain instantaneous help")
messageLog.put('=' * 65)
# And tell the user what warnings and errors look like
messageLog.put_warning("This is a sample warning")
messageLog.put_error("This is a sample error")
messageLog.put('=' * 65)
# Now, check if a default config file exists; if yes, load it.
try:
config.load(config.options['default_savefile'].value)
except IOError:
messageLog.put_warning('No default configuration file found!')
pass
# Now, try to load the autoLoader config file.
try:
config.load_raw(config.options['default_autoload_savefile'].value)
except IOError:
messageLog.put_warning(
'No default autoloader configuration file found!')
pass
# Create the absolute top-level root window. Destroying this kills 'everything'!
root = Tk()
# Make the root window variable in width and height
root.rowconfigure(0, weight=1)
root.columnconfigure(0, weight=1)
# Give it a title
root.title('FIEStool - Data reduction for the FIES spectrograph')
# Initialize the main window, with 'root' as its parent
main = mainWindow(root, hasscrollbar)
if hasscrollbar:
# This puts the focus right, and will give the canvas child real sizes
root.deiconify()
root.focus_set()
root.grab_set()
root.wait_visibility()
# Show the canvas
main.canvas.grid(row=0, column=0, sticky=N + S + E + W)
# Determine width and heigth of the contained frame
canvaschild = main.canvas.children.values()[0]
neededwidth = canvaschild.winfo_width()
neededheight = canvaschild.winfo_height()
maxheight = main.canvas.winfo_screenheight()
maxwidth = main.canvas.winfo_screenwidth()
neededheight = min(maxheight, neededheight)
neededwidth = min(maxwidth, neededwidth)
# Set the canvas size and enable scrolling
main.canvas.config(width=neededwidth, height=neededheight)
main.canvas.config(scrollregion=main.canvas.bbox("all"))
else:
# Display the main window
main.grid(sticky=N + E + S + W)
# Catch the 'delete window' signal that may be triggered by the window
# manager if the user clicks on its 'close' button
root.protocol("WM_DELETE_WINDOW", main.really_quit)
# Start the mainloop. The program executing pauses here, only to execute events
# generated by the main window (which in essence is everything)
###############
main.mainloop()
###############
# Apparently an event triggered an exit out of the mainloop (see main.reallyquit)
messageLog.put("Destroying widgets")
# Destroy the root window and all its children
root.destroy()
# This message will never arrive, though...
messageLog.put("Program finished - EXIT FIEStool")
# Return to caller (main)
return
def run():
"""
Main program entry, initializing and starting the main window and managing
its 'mainloop'
"""
# Get and check command-line options
#
# NB: The -c (enable-calib) option is now deprecated
#
try:
opts, args = getopt.getopt(sys.argv[1:], "cs", ["calib", "scrollbar"])
except getopt.GetoptError:
# print help information and exit:
print "Unknown command line parameter. Allowed optional parameters are : "
#print "-c [file] Load calibration file at startup"
print "-s / --scrollbar Add vertical scrollbar is screen does not fit"
sys.exit(2)
#enablecalib = False
hasscrollbar = False
for option, parameter in opts:
if option in ("-c", "--calib"):
print "The -c option is deprecated. You can now always access the calibs submenu."
# enablecalib = True
if option in ("-s", "--scrollbar"):
hasscrollbar = True
# Display a welcome message in the message log
messageLog.put('='*65)
messageLog.put("Welcome to FIEStool - the automatic data processing tool")
messageLog.put("for the FIES spectrograph at the Nordic Optical Telescope")
messageLog.put("Copyright (c) 2005 NOTSA; All Rights Reserved")
messageLog.put("This is version %s (%s), written by %s" % (_version, _date, _author))
messageLog.put('='*65)
messageLog.put("Right-click on any item to obtain instantaneous help")
messageLog.put('='*65)
# And tell the user what warnings and errors look like
messageLog.put_warning("This is a sample warning")
messageLog.put_error("This is a sample error")
messageLog.put('='*65)
# Now, check if a default config file exists; if yes, load it.
try:
config.load(config.options['default_savefile'].value)
except IOError:
messageLog.put_warning('No default configuration file found!')
pass
# Now, try to load the autoLoader config file.
try:
config.load_raw(config.options['default_autoload_savefile'].value)
except IOError:
messageLog.put_warning('No default autoloader configuration file found!')
pass
# Create the absolute top-level root window. Destroying this kills 'everything'!
root = Tk()
# Make the root window variable in width and height
root.rowconfigure(0, weight=1)
root.columnconfigure(0, weight=1)
# Give it a title
root.title('FIEStool - Data reduction for the FIES spectrograph')
# Initialize the main window, with 'root' as its parent
main = mainWindow(root, hasscrollbar)
if hasscrollbar:
# This puts the focus right, and will give the canvas child real sizes
root.deiconify()
root.focus_set()
root.grab_set()
root.wait_visibility()
# Show the canvas
main.canvas.grid(row=0, column=0, sticky=N+S+E+W)
# Determine width and heigth of the contained frame
canvaschild = main.canvas.children.values()[0]
neededwidth = canvaschild.winfo_width()
neededheight = canvaschild.winfo_height()
maxheight = main.canvas.winfo_screenheight()
maxwidth = main.canvas.winfo_screenwidth()
neededheight = min(maxheight, neededheight)
neededwidth = min(maxwidth, neededwidth)
# Set the canvas size and enable scrolling
main.canvas.config(width=neededwidth, height=neededheight)
main.canvas.config(scrollregion=main.canvas.bbox("all"))
else:
# Display the main window
main.grid(sticky=N+E+S+W)
# Catch the 'delete window' signal that may be triggered by the window
# manager if the user clicks on its 'close' button
root.protocol("WM_DELETE_WINDOW", main.really_quit)
# Start the mainloop. The program executing pauses here, only to execute events
# generated by the main window (which in essence is everything)
###############
main.mainloop()
###############
# Apparently an event triggered an exit out of the mainloop (see main.reallyquit)
messageLog.put("Destroying widgets")
# Destroy the root window and all its children
root.destroy()
# This message will never arrive, though...
messageLog.put("Program finished - EXIT FIEStool")
# Return to caller (main)
return
def getwavedef2D(frame):
"""
Extract and return the wavelength definition vector [ordernumber, zero
wavelength offset, wavelength step] using the FITS header keywords of a
2-dimensional frame, following the IRAF definition. It is a rather dirty
routine.
"""
# Make sure I can find the appropriate headers
if not (frame[0].header.get('WAT0_001', None)):
messageLog.put_warning('Could not find FITS headers defining the wavelength solution')
return None
# Get the number of pixels per order and the number of orders from the headers
npixels = frame[0].header['NAXIS1']
norders = frame[0].header['NAXIS2']
# Create an (empty) output array
wavearray = numpy.zeros((norders, 4), dtype=numpy.float64)
# Get all the FITS header keywords in an array
fullhlist = frame[0].header.items()
wavedef = ""
# And loop over the headers to extract any header that contains (part of)
# the wavelength definition, and store these in one long string object
for name, value in fullhlist:
# Only 68 characters can be part of FITS header value
if name[0:4] == 'WAT2': wavedef = wavedef + value.ljust(68)
# Now it gets very IRAF-specific! Bin the first 16 characters (garbage)
wavedef = wavedef[16:]
# and split the string object into smaller pieces, one for each order
wavedef = wavedef.split('spec')
# Bin the first entry (also garbage)
del(wavedef[0])
# Check that we got the correct number of order definitions from the headers
if len(wavedef) != norders:
messageLog.put_warning('No wavelength solution found', 5)
return None
# Initialize order number counter
linecounter = 0
# Get rid of " and = characters in the string and isolate the parameter values
for line in wavedef:
line = line.replace('"', '')
line = line.replace('=', '')
line = line.split()
# According to IRAF's definition the following parameters can be extracted
# from the line
number = int(line[1])
orderno = int(line[2])
woffset = float(line[4])
wstep = float(line[5])
# Store the order number, zero pixel wavelength and wavelength step in the
# output array
wavearray[linecounter, :] = [number, orderno, woffset, wstep]
linecounter = linecounter + 1
# If an incompatible format was used to define the order locations, complain!
if int(line[3]) != 0:
messageLog.put_error('Error in interpreting spectrum definition')
messageLog.put_warning('Dispersion solution format seems to be non-linear. Trying to make ')
messageLog.put_warning('the best of it. Wavelength scale may be terribly wrong.')
# Finally, return the result to the caller
return wavearray