def read_blob(self,blob_dim,n_blob=0):
"""Read blob from a selection.
"""
n_blobs = self.calc_n_blobs(blob_dim)
if n_blob > n_blobs or n_blob < 0:
raise ValueError('Please provide correct n_blob value. Given %i, but max values is %i'%(n_blob,n_blobs))
# This prevents issues when the last blob is smaller than the others in time.
if blob_dim[self.time_axis]*(n_blob+1) > self.selection_shape[self.time_axis]:
updated_blob_dim = (int(self.selection_shape[self.time_axis] - blob_dim[self.time_axis]*n_blob), 1, int(blob_dim[self.freq_axis]))
else:
updated_blob_dim = [int(i) for i in blob_dim]
blob_start = self._find_blob_start()
blob = np.zeros(updated_blob_dim, dtype=self._d_type)
# EE: For now; also assuming one polarization and one beam.
# Assuming the blob will loop over the whole frequency range.
if self.f_start == self.f_begin and self.f_stop == self.f_end:
blob_flat_size = np.prod(blob_dim)
updated_blob_flat_size = np.prod(updated_blob_dim)
# Load binary data
with open(self.filename, 'rb') as f:
f.seek(int(self.idx_data + self._n_bytes * (blob_start + n_blob*blob_flat_size)))
dd = np.fromfile(f, count=updated_blob_flat_size, dtype=self._d_type)
if dd.shape[0] == updated_blob_flat_size:
blob = dd.reshape(updated_blob_dim)
else:
logger.info('DD shape != blob shape.')
blob = dd.reshape((int(dd.shape[0]/blob_dim[self.freq_axis]),blob_dim[self.beam_axis],blob_dim[self.freq_axis]))
else:
for blobt in range(updated_blob_dim[self.time_axis]):
#Load binary data
with open(self.filename, 'rb') as f:
f.seek(int(self.idx_data + self._n_bytes * (blob_start + n_blob*blob_dim[self.time_axis]*self.n_channels_in_file + blobt*self.n_channels_in_file)))
dd = np.fromfile(f, count=blob_dim[self.freq_axis], dtype=self._d_type)
blob[blobt] = dd
# if self.header['foff'] < 0:
# blob = blob[:,:,::-1]
blob = WaterfallBlob(blob, self.header)
return blob
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.info("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!")