def test_invalid_files():
from blimpy.io.file_wrapper import open_file
# script should error-out if file does not exist
with pytest.raises(IOError):
open_file(here + 'file_does_not_exist.h5')
# script should error-out if file is not a
# valid blimpy data file
with pytest.raises(NotImplementedError):
open_file(here + '/run_tests.sh')
def test_file_wrapper_open_h5_file():
from blimpy.io.file_wrapper import open_file
h5r = open_file(voyager_h5)
# check all if branches
h5r.populate_timestamps(update_header=False)
h5r.populate_timestamps(update_header=True)
with pytest.raises(ValueError):
h5r.read_blob((300, 300, 300, 300), -1)
# testing to make sure all internal functions are already used
h5r._setup_selection_range(f_start=3, f_stop=4, t_stop=3, t_start=4)
h5r._setup_selection_range()
h5r._init_empty_selection()
# perform reading again and we make sure that
# the user-facing functions survive
h5r.populate_freqs()
# just arbitrary values
h5r.calc_n_blobs(300)
h5r.read_blob((300, 300, 300, 300))
h5r.calc_n_coarse_chan()
h5r.calc_n_coarse_chan(1)
def test_file_wrapper_open_fil_file():
from blimpy.io.file_wrapper import open_file
filr = open_file(voyager_fil)
#print('voyager_fil header:')
#filr.read_header()
filr.calc_n_blobs(300)
filr.read_blob((300, 300, 300, 300))
def h5_to_xarray(self,
path,
out='arr',
f_start=None,
f_stop=None,
max_load=1.,
out_dir=None,
in_blimpy=False,
waterfall_obj=None):
"""Converts h5 file to an xarray DataArray"""
if in_blimpy and waterfall_obj is not None:
container = waterfall_obj.container
#container = path.container
else:
container = fw.open_file(path,
f_start=f_start,
f_stop=f_stop,
max_load=max_load)
snr_data = np.asarray(
[array for array in [data[0] for data in container.data]])
#snr_data = np.asarray([data[0] for data in container.data])
timestamps = container.populate_timestamps()
frequencies = container.populate_freqs()
header = container.header
if not in_blimpy:
del header['DIMENSION_LABELS']
header['n_ints_in_file'] = container.selection_shape[0]
dataset = xr.Dataset(data_vars=dict(snr=(['time',
'freq'], snr_data), ),
coords=dict(
frequency=(['freq'], frequencies),
time=timestamps,
),
attrs=header)
if out_dir is not None:
dataset.to_netcdf(out_dir, format='NETCDF4')
data_array = xr.DataArray(
#data=dict(
# snr=(['time','freq'], snr_data),
# ),
snr_data,
coords=[timestamps, frequencies],
dims=['time', 'freq'],
attrs=header)
#coords=dict(
# frequency=(['freq'], frequencies),
# time=timestamps,
# ),
#attrs=header
#)
if out == 'dataset':
return dataset
else:
return data_array
def test_file_wrapper_open_file():
from blimpy.io.file_wrapper import open_file
open_file(voyager_h5)
open_file(voyager_fil)
with pytest.raises(NotImplementedError):
open_file(here + '/run_tests.sh')
def test_file_wrapper_open_h5_file():
from blimpy.io.file_wrapper import open_file
h5r = open_file(voyager_h5)
'check all if branches'
h5r.populate_timestamps(update_header=False)
h5r.populate_timestamps(update_header=True)
# we are missing at least one if-body
with pytest.raises(ValueError):
h5r.read_blob((300, 300, 300, 300), -1)
'testing to make sure all internal functions'
'are already used'
# h5r._setup_selection_range(init=False)
# h5r._setup_selection_range(init=True)
'h5r.t_begin = 0'
'h5r.t_end = 4'
h5r._setup_selection_range(f_start=3, f_stop=4, t_stop=3, t_start=4)
h5r._setup_selection_range()
#h5r._setup_selection_range()
h5r._init_empty_selection()
# h5r._setup_dtype()
# we will definitely want data files with different dtypes
# h5r._calc_selection_size()
# h5r._calc_selection_shape()
# h5r._setup_chans()
# many unused if branches
#h5r._setup_freqs()
'Now that I have fiddled with all of these internal'
'functions, the true test will be to perform reading again'
'and we make sure that the user-facing functions survive'
h5r.populate_freqs()
# we want to test both if cases,
# but I am working with an outdated version
# that mandates bytestrings
#h5r.isheavy()
'These values do not express any understanding'
'of real-world use cases for the code.'
h5r.calc_n_blobs(300)
h5r.read_blob((300, 300, 300, 300))
#h5r.read_data()
h5r.calc_n_coarse_chan()
h5r.calc_n_coarse_chan(1)
def __init__(self,
filename=None,
f_start=None,
f_stop=None,
t_start=None,
t_stop=None,
load_data=True,
max_load=1.,
header_dict=None,
data_array=None):
""" Class for loading and plotting blimpy data.
This class parses the blimpy file and stores the header and data
as objects:
fb = Waterfall('filename_here.fil')
fb.header # blimpy header, as a dictionary
fb.data # blimpy data, as a numpy array
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 integration ID
t_stop (int): stop integration ID
load_data (bool): load data. If set to False, only header will be read.
max_load (float): maximum data to load in GB. Default: 1GB.
e.g. 0.1 is 100 MB
header_dict (dict): Create blimpy from header dictionary + data array
data_array (np.array): Create blimpy from header dict + data array
"""
##EE super(Waterfall, self).__init__()
if filename:
self.filename = filename
self.ext = os.path.splitext(filename)[-1].lower()
self.container = fw.open_file(filename,
f_start=f_start,
f_stop=f_stop,
t_start=t_start,
t_stop=t_stop,
load_data=load_data,
max_load=max_load)
self.file_header = self.container.header
self.header = self.file_header
self.n_ints_in_file = self.container.n_ints_in_file
self.file_shape = self.container.file_shape
self.file_size_bytes = self.container.file_size_bytes
self.selection_shape = self.container.selection_shape
self.n_channels_in_file = self.container.n_channels_in_file
# These values will 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.logger = logger
self.__load_data()
elif header_dict is not None and data_array is not None:
self.filename = ''
self.header = header_dict
self.data = data_array
self.n_ints_in_file = 0
self._setup_freqs()
else:
self.filename = ''
# Attach methods
self.plot_spectrum = six.create_bound_method(plot_spectrum, self)
self.plot_waterfall = six.create_bound_method(plot_waterfall, self)
self.plot_kurtosis = six.create_bound_method(plot_kurtosis, self)
self.plot_time_series = six.create_bound_method(plot_time_series, self)
self.plot_all = six.create_bound_method(plot_all, self)
self.plot_spectrum_min_max = six.create_bound_method(
plot_spectrum_min_max, self)
def test_file_wrapper_open_fil_file():
from blimpy.io.file_wrapper import open_file
filr = open_file(voyager_fil)
filr.calc_n_blobs(300)
filr.read_blob((300, 300, 300, 300))