def test_works(self) :
fname ='/a_place/in_a_very/deep/directory/with_a_very/long/name.dat'
abbr = utils.abbreviate_file_path(fname)
self.assertEqual(abbr, 'long/name.dat')
abbr = utils.abbreviate_file_path(abbr)
self.assertEqual(abbr, 'long/name.dat')
fname = 'name'
abbr = utils.abbreviate_file_path(fname)
self.assertEqual(abbr, fname)
def __init__(self, fname, memmap=False):
self.verify_ordering = True
self.fname = fname
# The passed file name is assumed to be a GBT spectrometer fits file.
self.hdulist = pyfits.open(self.fname, 'readonly', memmap=memmap)
if len(self.hdulist) < 2:
raise DataError("Fits file missing data extension")
logger.info("Opened GBT fits file: %s" % abbreviate_file_path(fname))
fits_data = self.hdulist[1].data
n_records = len(fits_data)
self._fits_data = fits_data
try:
names = fits_data.names
except AttributeError:
names = fits_data._names
self._field_names = names
# Figure out the scan and sub-band content of the file.
if 'SCAN' in names:
self._scans_all = fits_data.field('SCAN')
scans = np.unique(self._scans_all)
np.sort(scans)
self._scans = scans
else:
self._scans_all = np.zeros(len(n_records))
self._scans = np.array([0])
# Round the frequencies to nearest 10 kHz as we only need to tell the
# difference between one sub-band and the other.
self._bands_all = np.round(fits_data.field('CRVAL1'), -4)
bands = np.unique(self._bands_all)
np.sort(bands)
self._bands = bands
def write(self, file_name):
"""Write stored data to file.
Parameters
----------
file_name : string
File name to write data to.
"""
# Add the data
Col = pyfits.Column(name='DATA', format=self.data_format,
array=self.data)
columns = [Col,]
# Add all the other stored fields.
for field_name in self.field.iterkeys() :
Col = pyfits.Column(name=field_name,
format=self.formats[field_name],
array=np.asarray(self.field[field_name]))
columns.append(Col)
coldefs = pyfits.ColDefs(columns)
# Create fits header data units, one for the table and the mandatory
# primary.
tbhdu = pyfits.new_table(coldefs)
prihdu = pyfits.PrimaryHDU()
# Add the write history.
fname_abbr = abbreviate_file_path(file_name)
self.history.add('Written to file.', ('File name: ' + fname_abbr,))
# Add the history to the header.
write_history_header(prihdu.header, self.history)
# Combine the HDUs and write to file.
hdulist = pyfits.HDUList([prihdu, tbhdu])
hdulist.writeto(file_name, clobber=True)
logger.info('Wrote data to file: %s' % fname_abbr)
def read(self, scans=None, bands=None) :
"""Read in data from the fits file.
This method reads data from the fits file including the files history.
It is done one scan and one band at a time. Each scan and band is
returned as an instance of :class:`SpecBlock` class.
Parameters
----------
scans : tuple of integers
Which scans in the file to be processed. A list of
integers, with 0 corresponding to the lowest numbered scan.
Default is all of them.
bands : tuple of integers
Which intermediate frequencies (also called frequency windows)
to process. A list of integers with 0 corresponding to the
lowest frequency present. Default is all of them.
Returns
-------
blocks : list
List of :class:`SpecBlock` objects read from file.
"""
# We want scans and bands to be a sequence of indicies.
if scans is None :
scans = range(len(self.scans))
elif not hasattr(scans, '__iter__') :
scans = (scans, )
elif len(scans) == 0 :
scans = range(len(self.scans))
if bands is None :
bands = range(len(self.bands))
elif not hasattr(bands, '__iter__') :
bands = (bands, )
elif len(bands) == 0 :
bands = range(len(self.bands))
logger.info("Reading scans %s and bands %s" % (str(scans), str(bands)))
blocks = [] # Sequence of output SpecBlock objects.
for scan_ind in scans :
for band_ind in bands :
# Choose the appropriate records from the file, get that data.
records_sb = self.get_scan_band_records(scan_ind, band_ind)
block_sb = SpecBlock(records_sb["DATA"])
# Masked data is stored in FITS files as float('nan')
block_sb.data[np.logical_not(np.isfinite(
block_sb.data))] = ma.masked
# Now iterate over the fields and add them
# to the data block.
for field, field_axes in SPEC_FIELDS.iteritems() :
if not field in self._field_names :
continue
# First get the 'FITS' format string.
field_format = self.hdulist[1].columns.formats[
self.hdulist[1].columns.names.index(field)]
which_data = [slice(None)] * 2
for ii, single_axis in enumerate(block_sb.axes[:-1]):
# For each axis, slice out all the data except the
# stuff we need.
if single_axis in field_axes :
#field_shape.append(block_sb.shape[ii])
pass
else :
which_data[ii] = 0
field_data = records_sb[tuple(which_data)][field]
block_sb.set_field(field, field_data, field_axes,
field_format)
if not hasattr(self, 'history'):
self.history = get_history_header(self.hdulist[0].header)
#self.set_history(Data_sb)
fname_abbr = abbreviate_file_path(self.fname)
self.history.add('Read from file.', ('File name: ' +
fname_abbr, ))
block_sb._history = History(self.history)
block_sb.verify()
blocks.append(block_sb)
logger.info("Read finished")
return blocks
