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Implement data skip in samples #13269

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papadop wants to merge 3 commits into from
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Implement data skip in samples #13269

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c52dbdf
Do not ignore the file_id.
papadop Jun 1, 2025
873ec22
Implement FIFF_DATA_SKIP_SAMP.
papadop Jun 1, 2025
03cefe4
Also handle multiple skip at start. Small simplification.
papadop Jun 1, 2025
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4 changes: 2 additions & 2 deletions mne/_fiff/tag.py
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Original file line number Diff line number Diff line change
Expand Up @@ -361,9 +361,9 @@ def _read_old_pack(fid, tag, shape, rlims):

def _read_dir_entry_struct(fid, tag, shape, rlims):
"""Read dir entry struct tag."""
pos = tag.pos + 16
pos = tag.pos
entries = list()
for offset in range(1, tag.size // 16):
for offset in range(tag.size // 16):
ent = _read_tag_header(fid, pos + offset * 16)
# The position of the real tag on disk is stored in the "next" entry within the
# directory, so we need to overwrite ent.pos. For safety let's also overwrite
Expand Down
41 changes: 21 additions & 20 deletions mne/io/fiff/raw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -231,7 +231,6 @@ def _read_raw_file(
nchan = int(info["nchan"])
first = 0
first_samp = 0
first_skip = 0

# Get first sample tag if it is there
if directory[first].kind == FIFF.FIFF_FIRST_SAMPLE:
Expand All @@ -240,14 +239,6 @@ def _read_raw_file(
first += 1
_check_entry(first, nent)

# Omit initial skip
if directory[first].kind == FIFF.FIFF_DATA_SKIP:
# This first skip can be applied only after we know the bufsize
tag = read_tag(fid, directory[first].pos)
first_skip = int(tag.data.item())
first += 1
_check_entry(first, nent)

raw = _RawShell()
raw.first_samp = first_samp
if info["meas_date"] is None and annotations is not None:
Expand Down Expand Up @@ -281,6 +272,9 @@ def _read_raw_file(
FIFF.FIFFT_COMPLEX_DOUBLE: "double",
}

nskip = 0
nskip_in_samples = 0
first_data_buffer = True
for k in range(first, nent):
ent = directory[k]
# There can be skips in the data (e.g., if the user unclicked)
Expand All @@ -297,24 +291,28 @@ def _read_raw_file(
if orig_format is None:
orig_format = _orig_format_dict[ent.type]

# Do we have an initial skip pending?
if first_skip > 0:
first_samp += nsamp * first_skip
raw.first_samp = first_samp
first_skip = 0

# Do we have a skip pending?
if nskip > 0:
nskip_in_samples += nskip * nsamp
nskip = 0

if nskip_in_samples > 0:
raw_extras.append(
dict(
ent=None,
first=first_samp,
nsamp=nskip * nsamp,
last=first_samp + nskip * nsamp - 1,
nsamp=nskip_in_samples,
last=first_samp + nskip_in_samples - 1,
)
)
first_samp += nskip * nsamp
nskip = 0
first_samp += nskip_in_samples
nskip_in_samples = 0

# Handle an initial skip.

if first_data_buffer:
raw.first_samp = first_samp
first_data_buffer = False

# Add a data buffer
raw_extras.append(
Expand All @@ -328,7 +326,10 @@ def _read_raw_file(
first_samp += nsamp
elif ent.kind == FIFF.FIFF_DATA_SKIP:
tag = read_tag(fid, ent.pos)
nskip = int(tag.data.item())
nskip += int(tag.data.item())
elif ent.kind == FIFF.FIFF_DATA_SKIP_SAMP:
tag = read_tag(fid, ent.pos)
nskip_in_samples += int(tag.data.item())

next_fname = _get_next_fname(fid, _path_from_fname(fname), tree)

Expand Down
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