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When reading edf, decode all strings using 'iso8859-1'. #429

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merged 1 commit into from
Oct 28, 2022
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When reading edf, decode all strings using 'iso8859-1'. #429

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50 changes: 29 additions & 21 deletions wfdb/io/convert/edf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ def read_edf(
header_only=False,
verbose=False,
rdedfann_flag=False,
encoding="iso8859-1",
):
"""
Read a EDF format file into a WFDB Record.
Expand Down Expand Up @@ -61,6 +62,9 @@ def read_edf(
is being called by the user and the file has annotations, then warn
them that the EDF file has annotations and that they should use
`rdedfann` instead.
encoding : str, optional
The encoding to use for strings in the header. Although the edf
specification requires ascii strings, some files do not adhere to it.

Returns
-------
Expand Down Expand Up @@ -139,7 +143,7 @@ def read_edf(
edf_file = open(record_name, mode="rb")

# Version of this data format (8 bytes)
version = struct.unpack("<8s", edf_file.read(8))[0].decode()
version = struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)

# Check to see that the input is an EDF file. (This check will detect
# most but not all other types of files.)
Expand All @@ -152,7 +156,7 @@ def read_edf(
print("EDF version number: {}".format(version.strip()))

# Local patient identification (80 bytes)
patient_id = struct.unpack("<80s", edf_file.read(80))[0].decode()
patient_id = struct.unpack("<80s", edf_file.read(80))[0].decode(encoding)
if verbose:
print("Patient ID: {}".format(patient_id))

Expand All @@ -161,12 +165,12 @@ def read_edf(
# including an abbreviated month name in English and a full (4-digit)
# year, as is done here if this information is available in the input
# record. EDF+ requires this.
record_id = struct.unpack("<80s", edf_file.read(80))[0].decode()
record_id = struct.unpack("<80s", edf_file.read(80))[0].decode(encoding)
if verbose:
print("Recording ID: {}".format(record_id))

# Start date of recording (dd.mm.yy) (8 bytes)
start_date = struct.unpack("<8s", edf_file.read(8))[0].decode()
start_date = struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)
if verbose:
print("Recording Date: {}".format(start_date))
start_day, start_month, start_year = [int(i) for i in start_date.split(".")]
Expand All @@ -177,21 +181,21 @@ def read_edf(
start_year += 100

# Start time of recording (hh.mm.ss) (8 bytes)
start_time = struct.unpack("<8s", edf_file.read(8))[0].decode()
start_time = struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)
if verbose:
print("Recording Time: {}".format(start_time))
start_hour, start_minute, start_second = [
int(i) for i in start_time.split(".")
]

# Number of bytes in header (8 bytes)
header_bytes = int(struct.unpack("<8s", edf_file.read(8))[0].decode())
header_bytes = int(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding))
if verbose:
print("Number of bytes in header record: {}".format(header_bytes))

# Reserved (44 bytes)
reserved_notes = (
struct.unpack("<44s", edf_file.read(44))[0].decode().strip()
struct.unpack("<44s", edf_file.read(44))[0].decode(encoding).strip()
)
if reserved_notes[:5] == "EDF+C":
# The file is EDF compatible and will work without issue
Expand All @@ -209,7 +213,7 @@ def read_edf(
print("Free Space: {}".format(reserved_notes))

# Number of blocks (-1 if unknown) (8 bytes)
num_blocks = int(struct.unpack("<8s", edf_file.read(8))[0].decode())
num_blocks = int(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding))
if verbose:
print("Number of data records: {}".format(num_blocks))
if num_blocks == -1:
Expand All @@ -218,7 +222,7 @@ def read_edf(
)

# Duration of a block, in seconds (8 bytes)
block_duration = float(struct.unpack("<8s", edf_file.read(8))[0].decode())
block_duration = float(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding))
if verbose:
print(
"Duration of each data record in seconds: {}".format(block_duration)
Expand All @@ -227,7 +231,7 @@ def read_edf(
block_duration = 1.0

# Number of signals (4 bytes)
n_sig = int(struct.unpack("<4s", edf_file.read(4))[0].decode())
n_sig = int(struct.unpack("<4s", edf_file.read(4))[0].decode(encoding))
if verbose:
print("Number of signals: {}".format(n_sig))
if n_sig < 1:
Expand All @@ -236,7 +240,7 @@ def read_edf(
# Label (e.g., EEG FpzCz or Body temp) (16 bytes each)
sig_name = []
for _ in range(n_sig):
temp_sig = struct.unpack("<16s", edf_file.read(16))[0].decode().strip()
temp_sig = struct.unpack("<16s", edf_file.read(16))[0].decode(encoding).strip()
if temp_sig == "EDF Annotations" and not rdedfann_flag:
print(
"*** This may be an EDF+ Annotation file instead, please see "
Expand All @@ -250,7 +254,7 @@ def read_edf(
transducer_types = []
for _ in range(n_sig):
transducer_types.append(
struct.unpack("<80s", edf_file.read(80))[0].decode().strip()
struct.unpack("<80s", edf_file.read(80))[0].decode(encoding).strip()
)
if verbose:
print("Transducer Types: {}".format(transducer_types))
Expand All @@ -259,7 +263,7 @@ def read_edf(
physical_dims = []
for _ in range(n_sig):
physical_dims.append(
struct.unpack("<8s", edf_file.read(8))[0].decode().strip()
struct.unpack("<8s", edf_file.read(8))[0].decode(encoding).strip()
)
if verbose:
print("Physical Dimensions: {}".format(physical_dims))
Expand All @@ -269,7 +273,7 @@ def read_edf(
for _ in range(n_sig):
physical_min = np.append(
physical_min,
float(struct.unpack("<8s", edf_file.read(8))[0].decode()),
float(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)),
)
if verbose:
print("Physical Minimums: {}".format(physical_min))
Expand All @@ -279,7 +283,7 @@ def read_edf(
for _ in range(n_sig):
physical_max = np.append(
physical_max,
float(struct.unpack("<8s", edf_file.read(8))[0].decode()),
float(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)),
)
if verbose:
print("Physical Maximums: {}".format(physical_max))
Expand All @@ -289,7 +293,7 @@ def read_edf(
for _ in range(n_sig):
digital_min = np.append(
digital_min,
float(struct.unpack("<8s", edf_file.read(8))[0].decode()),
float(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)),
)
if verbose:
print("Digital Minimums: {}".format(digital_min))
Expand All @@ -299,7 +303,7 @@ def read_edf(
for _ in range(n_sig):
digital_max = np.append(
digital_max,
float(struct.unpack("<8s", edf_file.read(8))[0].decode()),
float(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding)),
)
if verbose:
print("Digital Maximums: {}".format(digital_max))
Expand All @@ -308,7 +312,7 @@ def read_edf(
prefilter_info = []
for _ in range(n_sig):
prefilter_info.append(
struct.unpack("<80s", edf_file.read(80))[0].decode().strip()
struct.unpack("<80s", edf_file.read(80))[0].decode(encoding).strip()
)
if verbose:
print("Prefiltering Information: {}".format(prefilter_info))
Expand All @@ -317,14 +321,14 @@ def read_edf(
samps_per_block = []
for _ in range(n_sig):
samps_per_block.append(
int(struct.unpack("<8s", edf_file.read(8))[0].decode())
int(struct.unpack("<8s", edf_file.read(8))[0].decode(encoding))
)
if verbose:
print("Number of Samples per Record: {}".format(samps_per_block))

# The last 32*nsig bytes in the header are unused
for _ in range(n_sig):
struct.unpack("<32s", edf_file.read(32))[0].decode()
struct.unpack("<32s", edf_file.read(32))[0].decode(encoding)

# Pre-process the acquired data before creating the record
record_name_out = (
Expand Down Expand Up @@ -997,6 +1001,7 @@ def rdedfann(
info_only=True,
record_only=False,
verbose=False,
encoding="iso8859-1",
):
"""
This program returns the annotation information from an EDF+ file
Expand Down Expand Up @@ -1038,6 +1043,9 @@ def rdedfann(
verbose : bool, optional
Whether to print all the information read about the file (True) or
not (False).
encoding : str, optional
The encoding to use for strings in the header. Although the edf
specification requires ascii strings, some files do not adhere to it.

Returns
-------
Expand Down Expand Up @@ -1110,7 +1118,7 @@ def rdedfann(
adjusted_hex = hex(
struct.unpack("<H", struct.pack(">H", chunk + 1))[0]
)
annotation_string += bytes.fromhex(adjusted_hex[2:]).decode("ascii")
annotation_string += bytes.fromhex(adjusted_hex[2:]).decode(encoding)
# Remove all of the whitespace
for rep in ["\x00", "\x14", "\x15"]:
annotation_string = annotation_string.replace(rep, " ")
Expand Down