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Streamline file reading for single segment records, record headers an…
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…d annotation files. These methods all now stack between the public functions, handling mainly i/o, and the parsing functions.
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@Ivorforce
Ivorforce committed Jul 4, 2024
1 parent 39cd94b commit e0f7da4
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Showing 4 changed files with 122 additions and 313 deletions.
194 changes: 36 additions & 158 deletions wfdb/io/_signal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@

import numpy as np

from wfdb.io import download, _coreio, util
from wfdb.io import download
from wfdb.io import util


MAX_I32 = 2147483647
Expand Down Expand Up @@ -1050,9 +1051,7 @@ def smooth_frames(self, sigtype="physical"):


def _rd_segment(
file_name,
dir_name,
pn_dir,
buf,
fmt,
n_sig,
sig_len,
Expand All @@ -1066,7 +1065,6 @@ def _rd_segment(
ignore_skew,
no_file=False,
sig_data=None,
sig_stream=None,
return_res=64,
):
"""
Expand All @@ -1075,14 +1073,6 @@ def _rd_segment(
Parameters
----------
file_name : list
The names of the dat files to be read.
dir_name : str
The full directory where the dat file(s) are located, if the dat
file(s) are local.
pn_dir : str
The PhysioNet directory where the dat file(s) are located, if
the dat file(s) are remote.
fmt : list
The formats of the dat files.
n_sig : int
Expand Down Expand Up @@ -1198,9 +1188,7 @@ def _rd_segment(
for fn in w_file_name:
# Get the list of all signals contained in the dat file
datsignals = _rd_dat_signals(
file_name=fn,
dir_name=dir_name,
pn_dir=pn_dir,
buf,
fmt=w_fmt[fn],
n_sig=len(datchannel[fn]),
sig_len=sig_len,
Expand All @@ -1212,7 +1200,6 @@ def _rd_segment(
sampto=sampto,
no_file=no_file,
sig_data=sig_data,
sig_stream=sig_stream,
)

# Copy over the wanted signals
Expand All @@ -1223,9 +1210,7 @@ def _rd_segment(


def _rd_dat_signals(
file_name,
dir_name,
pn_dir,
buf,
fmt,
n_sig,
sig_len,
Expand All @@ -1237,21 +1222,12 @@ def _rd_dat_signals(
sampto,
no_file=False,
sig_data=None,
sig_stream=None,
):
"""
Read all signals from a WFDB dat file.
Parameters
----------
file_name : str
The name of the dat file.
dir_name : str
The full directory where the dat file(s) are located, if the dat
file(s) are local.
pn_dir : str
The PhysioNet directory where the dat file(s) are located, if
the dat file(s) are remote.
fmt : str
The format of the dat file.
n_sig : int
Expand Down Expand Up @@ -1327,32 +1303,17 @@ def _rd_dat_signals(
if no_file:
data_to_read = sig_data
elif fmt in COMPRESSED_FMTS:
if sig_stream is not None:
data_to_read = _rd_compressed_stream(
fp=sig_stream,
fmt=fmt,
sample_offset=byte_offset,
n_sig=n_sig,
samps_per_frame=samps_per_frame,
start_frame=sampfrom,
end_frame=sampto,
)
else:
data_to_read = _rd_compressed_file(
file_name=file_name,
dir_name=dir_name,
pn_dir=pn_dir,
fmt=fmt,
sample_offset=byte_offset,
n_sig=n_sig,
samps_per_frame=samps_per_frame,
start_frame=sampfrom,
end_frame=sampto,
)
else:
data_to_read = _rd_dat_file(
file_name, dir_name, pn_dir, fmt, start_byte, n_read_samples, sig_stream
data_to_read = _rd_compressed_stream(
buf,
fmt=fmt,
sample_offset=byte_offset,
n_sig=n_sig,
samps_per_frame=samps_per_frame,
start_frame=sampfrom,
end_frame=sampto,
)
else:
data_to_read = _rd_dat_stream(buf, fmt, start_byte, n_read_samples)

if extra_flat_samples:
if fmt in UNALIGNED_FMTS:
Expand Down Expand Up @@ -1591,7 +1552,7 @@ def _required_byte_num(mode, fmt, n_samp):
return int(n_bytes)


def _rd_dat_file(file_name, dir_name, pn_dir, fmt, start_byte, n_samp, sig_stream):
def _rd_dat_stream(buf, fmt, start_byte, n_samp):
"""
Read data from a dat file, either local or remote, into a 1d numpy
array.
Expand All @@ -1602,14 +1563,6 @@ def _rd_dat_file(file_name, dir_name, pn_dir, fmt, start_byte, n_samp, sig_strea
Parameters
----------
file_name : str
The name of the dat file.
dir_name : str
The full directory where the dat file(s) are located, if the dat
file(s) are local.
pn_dir : str
The PhysioNet directory where the dat file(s) are located, if
the dat file(s) are remote.
fmt : str
The format of the dat file.
start_byte : int
Expand Down Expand Up @@ -1649,27 +1602,11 @@ def _rd_dat_file(file_name, dir_name, pn_dir, fmt, start_byte, n_samp, sig_strea
element_count = n_samp
byte_count = n_samp * BYTES_PER_SAMPLE[fmt]

# Memory Stream
if sig_stream is not None:
sig_stream.seek(start_byte)
sig_data = np.frombuffer(
sig_stream.read(), dtype=np.dtype(DATA_LOAD_TYPES[fmt]), count=element_count
)
# Local dat file
elif pn_dir is None:
with open(os.path.join(dir_name, file_name), "rb") as fp:
fp.seek(start_byte)
sig_data = np.fromfile(
fp, dtype=np.dtype(DATA_LOAD_TYPES[fmt]), count=element_count
)
# Stream dat file from Physionet
else:
dtype_in = np.dtype(DATA_LOAD_TYPES[fmt])
sig_data = download._stream_dat(
file_name, pn_dir, byte_count, start_byte, dtype_in
)
buf.seek(start_byte)
return np.frombuffer(
buf.read(byte_count), dtype=np.dtype(DATA_LOAD_TYPES[fmt]), count=element_count
)

return sig_data

def _blocks_to_samples(sig_data, n_samp, fmt):
"""
Expand Down Expand Up @@ -1790,20 +1727,28 @@ def _blocks_to_samples(sig_data, n_samp, fmt):


def _rd_compressed_stream(
fp,
buf,
fmt,
sample_offset,
n_sig,
samps_per_frame,
start_frame,
end_frame,
):
signature = fp.read(4)
import soundfile

if any(spf != samps_per_frame[0] for spf in samps_per_frame):
raise ValueError(
"All channels in a FLAC signal file must have the same "
"sampling rate and samples per frame"
)

signature = buf.read(4)
if signature != b"fLaC":
raise ValueError(f"{fp.name} is not a FLAC file")
fp.seek(0)
raise ValueError(f"{buf.name} is not a FLAC file")
buf.seek(0)

with soundfile.SoundFile(fp) as sf:
with soundfile.SoundFile(buf) as sf:
# Determine the actual resolution of the FLAC stream and the
# data type will use when reading it. Note that soundfile
# doesn't support int8.
Expand All @@ -1817,18 +1762,18 @@ def _rd_compressed_stream(
format_bits = 24
read_dtype = "int32"
else:
raise ValueError(f"unknown subtype in {fp.name} ({sf.subtype})")
raise ValueError(f"unknown subtype in {buf.name} ({sf.subtype})")

max_bits = int(fmt) - 500
if format_bits > max_bits:
raise ValueError(
f"wrong resolution in {fp.name} "
f"wrong resolution in {buf.name} "
f"({format_bits}, expected <= {max_bits})"
)

if sf.channels != n_sig:
raise ValueError(
f"wrong number of channels in {fp.name} "
f"wrong number of channels in {buf.name} "
f"({sf.channels}, expected {n_sig})"
)

Expand Down Expand Up @@ -1906,73 +1851,6 @@ def _rd_compressed_stream(
return sig_data.reshape(-1)


def _rd_compressed_file(
file_name,
dir_name,
pn_dir,
fmt,
sample_offset,
n_sig,
samps_per_frame,
start_frame,
end_frame,
):
"""
Read data from a compressed file into a 1D numpy array.
Parameters
----------
file_name : str
The name of the signal file.
dir_name : str
The full directory where the signal file is located, if local.
This argument is ignored if `pn_dir` is not None.
pn_dir : str or None
The PhysioNet database directory where the signal file is located.
fmt : str
The format code of the signal file.
sample_offset : int
The sample number in the signal file corresponding to sample 0 of
the WFDB record.
n_sig : int
The number of signals in the file.
samps_per_frame : list
The number of samples per frame for each signal in the file.
start_frame : int
The starting frame number to read.
end_frame : int
The ending frame number to read.
Returns
-------
signal : ndarray
The data read from the signal file. This is a one-dimensional
array in the same order the samples would be stored in a binary
signal file; `signal[(i*n_sig+j)*samps_per_frame[0]+k]` is sample
number `i*samps_per_frame[0]+k` of signal `j`.
Notes
-----
Converting the output array into "dat file order" here is inefficient,
but necessary to match the behavior of _rd_dat_file. It would be
better to reorganize _rd_dat_signals to make the reshaping unnecessary.
"""
import soundfile

if any(spf != samps_per_frame[0] for spf in samps_per_frame):
raise ValueError(
"All channels in a FLAC signal file must have the same "
"sampling rate and samples per frame"
)

if pn_dir is None:
file_name = os.path.join(dir_name, file_name)

with _coreio._open_file(pn_dir, file_name, "rb") as fp:
return _rd_compressed_stream(fp, fmt, sample_offset, n_sig, samps_per_frame, start_frame, end_frame)


def _skew_sig(
sig, skew, n_sig, read_len, fmt, nan_replace, samps_per_frame=None
):
Expand Down
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