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Set correct checksums and samps_per_frame in Record.wrsamp #424

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Merged
tompollard merged 5 commits into from
Nov 9, 2022
Merged

Set correct checksums and samps_per_frame in Record.wrsamp #424

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cac2af6
SignalMixin.wr_dats: acknowledge that optional fields aren't checked.
Sep 22, 2022
768d833
Record.wrsamp: ignore samps_per_frame when expanded is false.
Sep 22, 2022
fc4cfec
Record.wrsamp: always set checksums to correct values.
Sep 22, 2022
9a0d086
Test writing an originally-multi-frequency record with expanded=False.
Sep 22, 2022
489aa62
check_sig_cohesion: fix error when expanded signal lengths mismatch.
Sep 23, 2022
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16 changes: 16 additions & 0 deletions tests/test_record.py
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Original file line number Diff line number Diff line change
Expand Up @@ -633,6 +633,22 @@ def test_4d(self):

assert np.array_equal(sig_round, sig_target)

def test_write_smoothed(self):
"""
Test writing a record after reading with smooth_frames
"""
record = wfdb.rdrecord(
"sample-data/drive02",
physical=False,
smooth_frames=True,
)
record.wrsamp(write_dir=self.temp_path)
record2 = wfdb.rdrecord(
os.path.join(self.temp_path, "drive02"),
physical=False,
)
np.testing.assert_array_equal(record.d_signal, record2.d_signal)

def test_to_dataframe(self):
record = wfdb.rdrecord("sample-data/test01_00s")
df = record.to_dataframe()
Expand Down
8 changes: 7 additions & 1 deletion wfdb/io/_header.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,7 +278,7 @@ def set_defaults(self):
for f in sfields:
self.set_default(f)

def wrheader(self, write_dir=""):
def wrheader(self, write_dir="", expanded=True):
"""
Write a WFDB header file. The signals are not used. Before
writing:
Expand All @@ -290,6 +290,10 @@ def wrheader(self, write_dir=""):
----------
write_dir : str, optional
The output directory in which the header is written.
expanded : bool, optional
Whether the header file should include `samps_per_frame` (this
should only be true if the signal files are written using
`expanded=True`).

Returns
-------
Expand All @@ -305,6 +309,8 @@ def wrheader(self, write_dir=""):
# sig_write_fields is a dictionary of
# {field_name:required_channels}
rec_write_fields, sig_write_fields = self.get_write_fields()
if not expanded:
sig_write_fields.pop("samps_per_frame", None)

# Check the validity of individual fields used to write the header
# Record specification fields (and comments)
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14 changes: 7 additions & 7 deletions wfdb/io/_signal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -142,7 +142,7 @@ def wr_dats(self, expanded, write_dir):
# Get all the fields used to write the header
# Assuming this method was called through wrsamp,
# these will have already been checked in wrheader()
write_fields = self.get_write_fields()
_, _ = self.get_write_fields()

if expanded:
# Using list of arrays e_d_signal
Expand All @@ -152,8 +152,10 @@ def wr_dats(self, expanded, write_dir):
self.check_field("d_signal")

# Check the cohesion of the d_signal field against the other
# fields used to write the header
self.check_sig_cohesion(write_fields, expanded)
# fields used to write the header. (Note that for historical
# reasons, this doesn't actually check any of the optional
# header fields.)
self.check_sig_cohesion([], expanded)

# Write each of the specified dat files
self.wr_dat_files(expanded=expanded, write_dir=write_dir)
Expand Down Expand Up @@ -192,10 +194,8 @@ def check_sig_cohesion(self, write_fields, expanded):
for ch in range(self.n_sig):
if len(self.e_d_signal[ch]) != spf[ch] * self.sig_len:
raise ValueError(
"Length of channel "
+ str(ch)
+ "does not match samps_per_frame["
+ str(ch + "]*sig_len")
f"Length of channel {ch} does not match "
f"samps_per_frame[{ch}]*sig_len"
)

# For each channel (if any), make sure the digital format has no values out of bounds
Expand Down
12 changes: 11 additions & 1 deletion wfdb/io/record.py
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Original file line number Diff line number Diff line change
Expand Up @@ -922,9 +922,19 @@ def wrsamp(self, expanded=False, write_dir=""):
N/A

"""
# Update the checksum field (except for channels that did not have
# a checksum to begin with, or where the checksum was already
# valid.)
if self.checksum is not None:
checksums = self.calc_checksum(expanded=expanded)
for ch, old_val in enumerate(self.checksum):
if old_val is None or (checksums[ch] - old_val) % 65536 == 0:
checksums[ch] = old_val
self.checksum = checksums

# Perform field validity and cohesion checks, and write the
# header file.
self.wrheader(write_dir=write_dir)
self.wrheader(write_dir=write_dir, expanded=expanded)
if self.n_sig > 0:
# Perform signal validity and cohesion checks, and write the
# associated dat files.
Expand Down