def read_data(self, f_start=None, f_stop=None, t_start=None, t_stop=None):
""" Read data
"""
self._setup_selection_range(f_start=f_start,
f_stop=f_stop,
t_start=t_start,
t_stop=t_stop)
#check if selection is small enough.
if self.isheavy():
logger.warning(
"Selection size of %.2f GB, exceeding our size limit %.2f GB. Instance created, header loaded, but data not loaded, please try another (t,v) selection."
% (self._calc_selection_size() /
(1024.**3), self.MAX_DATA_ARRAY_SIZE / (1024.**3)))
self.data = np.array([0], dtype=self._d_type)
return None
#Convert input frequencies into what their corresponding channel number would be.
self._setup_chans()
#Update frequencies ranges from channel number.
self._setup_freqs()
self.data = self.h5["data"][self.t_start:self.t_stop, :,
self.chan_start_idx:self.chan_stop_idx]
def read_data(self, f_start=None, f_stop=None, t_start=None, t_stop=None):
""" Read data.
"""
self._setup_selection_range(f_start=f_start,
f_stop=f_stop,
t_start=t_start,
t_stop=t_stop)
#check if selection is small enough.
if self.isheavy():
logger.warning(
"Selection size of %.2f GB, exceeding our size limit %.2f GB. Instance created, "
"header loaded, but data not loaded, please try another (t,v) selection."
% (self._calc_selection_size() /
(1024.**3), self.MAX_DATA_ARRAY_SIZE / (1024.**3)))
self.data = np.array([0], dtype=self._d_type)
return None
#Convert input frequencies into what their corresponding channel number would be.
self._setup_chans()
#Update frequencies ranges from channel number.
self._setup_freqs()
n_chans = self.header['nchans']
n_chans_selected = self.selection_shape[self.freq_axis]
n_ifs = self.header['nifs']
# Load binary data
f = open(self.filename, 'rb')
f.seek(int(self.idx_data))
# now check to see how many integrations requested
n_ints = self.t_stop - self.t_start
# Seek to first integration
f.seek(int(self.t_start * self._n_bytes * n_ifs * n_chans), 1)
#Loading data
self.data = np.zeros((n_ints, n_ifs, n_chans_selected),
dtype=self._d_type)
for ii in range(n_ints):
for jj in range(n_ifs):
f.seek(int(self._n_bytes * self.chan_start_idx),
1) # 1 = from current location
dd = np.fromfile(f, count=n_chans_selected, dtype=self._d_type)
# Reverse array if frequency axis is flipped
# if self.header['foff'] < 0:
# dd = dd[::-1]
self.data[ii, jj] = dd
f.seek(int(self._n_bytes * (n_chans - self.chan_stop_idx)),
1) # Seek to start of next block
# Give the FD back to the O/S.
f.close()
def __init__(self,
filename,
f_start=None,
f_stop=None,
t_start=None,
t_stop=None,
load_data=True,
max_load=1.):
""" Constructor.
Args:
filename (str): filename of blimpy file.
f_start (float): start frequency, in MHz
f_stop (float): stop frequency, in MHz
t_start (int): start time bin
t_stop (int): stop time bin
"""
super(FilReader, self).__init__()
self.header_keywords_types = sigproc.header_keyword_types
if filename and os.path.isfile(filename):
self.filename = filename
self.load_data = load_data
self.header = self.read_header()
self.file_size_bytes = os.path.getsize(self.filename)
self.idx_data = sigproc.len_header(self.filename)
self.n_channels_in_file = self.header['nchans']
self.n_beams_in_file = self.header[
'nifs'] #Placeholder for future development.
self.n_pols_in_file = 1 #Placeholder for future development.
self._n_bytes = int(self.header['nbits'] /
8) #number of bytes per digit.
self._d_type = self._setup_dtype()
self._setup_n_ints_in_file()
self.file_shape = (self.n_ints_in_file, self.n_beams_in_file,
self.n_channels_in_file)
if self.header['foff'] < 0:
self.f_end = self.header['fch1']
self.f_begin = self.f_end + self.n_channels_in_file * self.header[
'foff']
else:
self.f_begin = self.header['fch1']
self.f_end = self.f_begin + self.n_channels_in_file * self.header[
'foff']
self.t_begin = 0
self.t_end = self.n_ints_in_file
#Taking care all the frequencies are assigned correctly.
self._setup_selection_range(f_start=f_start,
f_stop=f_stop,
t_start=t_start,
t_stop=t_stop,
init=True)
#Convert input frequencies into what their corresponding channel number would be.
self._setup_chans()
#Update frequencies ranges from channel number.
self._setup_freqs()
self.freq_axis = 2
self.time_axis = 0
self.beam_axis = 1 # Place holder
#EE ie.
# spec = np.squeeze(fil_file.data)
# set start of data, at real length of header (future development.)
# self.datastart=self.hdrraw.find('HEADER_END')+len('HEADER_END')+self.startsample*self.channels
#Applying data size limit to load.
if max_load is not None:
if max_load > 1.0:
logger.warning(
'Setting data limit != 1GB, please handle with care!')
self.MAX_DATA_ARRAY_SIZE = max_load * MAX_DATA_ARRAY_SIZE_UNIT
else:
self.MAX_DATA_ARRAY_SIZE = MAX_DATA_ARRAY_SIZE_UNIT
if self.file_size_bytes > self.MAX_DATA_ARRAY_SIZE:
self.large_file = True
else:
self.large_file = False
if self.load_data:
if self.large_file:
if self.f_start or self.f_stop or self.t_start or self.t_stop:
if self.isheavy():
logger.warning(
"Selection size of %.2f GB, exceeding our size limit %.2f GB. Instance created, header loaded, but data not loaded, please try another (t,v) selection."
% (self._calc_selection_size() /
(1024.**3), self.MAX_DATA_ARRAY_SIZE /
(1024.**3)))
self._init_empty_selection()
else:
self.read_data()
else:
logger.warning(
"The file is of size %.2f GB, exceeding our size limit %.2f GB. Instance created, header loaded, but data not loaded. You could try another (t,v) selection."
% (self.file_size_bytes /
(1024.**3), self.MAX_DATA_ARRAY_SIZE /
(1024.**3)))
self._init_empty_selection()
else:
self.read_data()
else:
logger.debug("Skipping loading data ...")
self._init_empty_selection()
else:
raise IOError("Need a file to open, please give me one!")
def __init__(self,
filename,
f_start=None,
f_stop=None,
t_start=None,
t_stop=None,
load_data=True,
max_load=1.):
""" Constructor.
Args:
filename (str): filename of blimpy file.
f_start (float): start frequency, in MHz
f_stop (float): stop frequency, in MHz
t_start (int): start time bin
t_stop (int): stop time bin
"""
super(H5Reader, self).__init__()
if filename and os.path.isfile(filename) and h5py.is_hdf5(filename):
#These values may be modified once code for multi_beam and multi_stokes observations are possible.
self.freq_axis = 2
self.time_axis = 0
self.beam_axis = 1 # Place holder
self.stokes_axis = 4 # Place holder
self.filename = filename
self.filestat = os.stat(filename)
self.filesize = self.filestat.st_size / (1024.0**2)
self.load_data = load_data
self.h5 = h5py.File(self.filename, mode='r')
self.read_header()
self.file_size_bytes = os.path.getsize(self.filename) # In bytes
self.n_ints_in_file = self.h5["data"].shape[self.time_axis] #
self.n_channels_in_file = self.h5["data"].shape[self.freq_axis] #
self.n_beams_in_file = self.header[
'nifs'] #Placeholder for future development.
self.n_pols_in_file = 1 #Placeholder for future development.
self._n_bytes = int(self.header['nbits'] /
8) #number of bytes per digit.
self._d_type = self._setup_dtype()
self.file_shape = (self.n_ints_in_file, self.n_beams_in_file,
self.n_channels_in_file)
if self.header['foff'] < 0:
self.f_end = self.header['fch1']
self.f_begin = self.f_end + self.n_channels_in_file * self.header[
'foff']
else:
self.f_begin = self.header['fch1']
self.f_end = self.f_begin + self.n_channels_in_file * self.header[
'foff']
self.t_begin = 0
self.t_end = self.n_ints_in_file
#Taking care all the frequencies are assigned correctly.
self._setup_selection_range(f_start=f_start,
f_stop=f_stop,
t_start=t_start,
t_stop=t_stop,
init=True)
#Convert input frequencies into what their corresponding channel number would be.
self._setup_chans()
#Update frequencies ranges from channel number.
self._setup_freqs()
#Applying data size limit to load.
if max_load is not None:
if max_load > 1.0:
logger.warning(
'Setting data limit > 1GB, please handle with care!')
self.MAX_DATA_ARRAY_SIZE = max_load * MAX_DATA_ARRAY_SIZE_UNIT
else:
self.MAX_DATA_ARRAY_SIZE = MAX_DATA_ARRAY_SIZE_UNIT
if self.file_size_bytes > self.MAX_DATA_ARRAY_SIZE:
self.large_file = True
else:
self.large_file = False
if self.load_data:
if self.large_file:
#Only checking the selection, if the file is too large.
if self.f_start or self.f_stop or self.t_start or self.t_stop:
if self.isheavy():
logger.warning(
"Selection size of %.2f GB, exceeding our size limit %.2f GB. Instance created, header loaded, but data not loaded, please try another (t,v) selection."
% (self._calc_selection_size() /
(1024.**3), self.MAX_DATA_ARRAY_SIZE /
(1024.**3)))
self._init_empty_selection()
else:
self.read_data()
else:
logger.warning(
"The file is of size %.2f GB, exceeding our size limit %.2f GB. Instance created, header loaded, but data not loaded. You could try another (t,v) selection."
% (self.file_size_bytes /
(1024.**3), self.MAX_DATA_ARRAY_SIZE /
(1024.**3)))
self._init_empty_selection()
else:
self.read_data()
else:
logger.info("Skipping loading data ...")
self._init_empty_selection()
else:
raise IOError("Need a file to open, please give me one!")
