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Better error message upon failure in loading OpenEphysBinary folder #1389

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Better error message upon failure in loading OpenEphysBinary folder #1389

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1590420
Better error message upon failure in loading OE binary folder
alejoe91 Jan 31, 2024
084945c
Fix conflicts
alejoe91 Apr 5, 2024
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187 changes: 95 additions & 92 deletions neo/rawio/openephysbinaryrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -496,102 +496,105 @@ def explore_folder(dirname, experiment_names=None):
folder_structure = {}
possible_experiment_names = []

for root, dirs, files in os.walk(dirname):
for file in files:
if not file == "structure.oebin":
continue
root = Path(root)

node_folder = root.parents[1]
node_name = node_folder.stem
if not node_name.startswith("Record"):
# before version 5.x.x there was not multi Node recording
# so no node_name
node_name = ""

if node_name not in folder_structure:
folder_structure[node_name] = {}
folder_structure[node_name]["experiments"] = {}

# here we skip if experiment_names is not None
experiment_folder = root.parents[0]
experiment_name = experiment_folder.stem
experiment_id = int(experiment_name.replace("experiment", ""))
if experiment_name not in possible_experiment_names:
possible_experiment_names.append(experiment_name)
if experiment_names is not None and experiment_name not in experiment_names:
continue
if experiment_id not in folder_structure[node_name]["experiments"]:
experiment = {}
experiment["name"] = experiment_name
if experiment_name == "experiment1":
settings_file = node_folder / "settings.xml"
else:
settings_file = node_folder / f"settings_{experiment_id}.xml"
experiment["settings_file"] = settings_file
experiment["recordings"] = {}
folder_structure[node_name]["experiments"][experiment_id] = experiment

recording_folder = root
recording_name = root.stem
recording_id = int(recording_name.replace("recording", ""))
# add recording
recording = {}
recording["name"] = recording_name
recording["streams"] = {}

# metadata
with open(recording_folder / "structure.oebin", encoding="utf8", mode="r") as f:
rec_structure = json.load(f)

if (recording_folder / "continuous").exists() and len(rec_structure["continuous"]) > 0:
recording["streams"]["continuous"] = {}
for info in rec_structure["continuous"]:
# when multi Record Node the stream name also contains
# the node name to make it unique
oe_stream_name = Path(info["folder_name"]).name # remove trailing slash
if len(node_name) > 0:
stream_name = node_name + "#" + oe_stream_name
try:
for root, dirs, files in os.walk(dirname):
for file in files:
if not file == "structure.oebin":
continue
root = Path(root)

node_folder = root.parents[1]
node_name = node_folder.stem
if not node_name.startswith("Record"):
# before version 5.x.x there was not multi Node recording
# so no node_name
node_name = ""

if node_name not in folder_structure:
folder_structure[node_name] = {}
folder_structure[node_name]["experiments"] = {}

# here we skip if experiment_names is not None
experiment_folder = root.parents[0]
experiment_name = experiment_folder.stem
experiment_id = int(experiment_name.replace("experiment", ""))
if experiment_name not in possible_experiment_names:
possible_experiment_names.append(experiment_name)
if experiment_names is not None and experiment_name not in experiment_names:
continue
if experiment_id not in folder_structure[node_name]["experiments"]:
experiment = {}
experiment["name"] = experiment_name
if experiment_name == "experiment1":
settings_file = node_folder / "settings.xml"
else:
stream_name = oe_stream_name
raw_filename = recording_folder / "continuous" / info["folder_name"] / "continuous.dat"
settings_file = node_folder / f"settings_{experiment_id}.xml"
experiment["settings_file"] = settings_file
experiment["recordings"] = {}
folder_structure[node_name]["experiments"][experiment_id] = experiment

recording_folder = root
recording_name = root.stem
recording_id = int(recording_name.replace("recording", ""))
# add recording
recording = {}
recording["name"] = recording_name
recording["streams"] = {}

# metadata
with open(recording_folder / "structure.oebin", encoding="utf8", mode="r") as f:
rec_structure = json.load(f)

if (recording_folder / "continuous").exists() and len(rec_structure["continuous"]) > 0:
recording["streams"]["continuous"] = {}
for info in rec_structure["continuous"]:
# when multi Record Node the stream name also contains
# the node name to make it unique
oe_stream_name = Path(info["folder_name"]).name # remove trailing slash
if len(node_name) > 0:
stream_name = node_name + "#" + oe_stream_name
else:
stream_name = oe_stream_name
raw_filename = recording_folder / "continuous" / info["folder_name"] / "continuous.dat"

# Updates for OpenEphys v0.6:
# In new vesion (>=0.6) timestamps.npy is now called sample_numbers.npy
# see https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Binary-format.html#continuous
sample_numbers = recording_folder / "continuous" / info["folder_name"] / "sample_numbers.npy"
if sample_numbers.is_file():
timestamp_file = sample_numbers
else:
timestamp_file = recording_folder / "continuous" / info["folder_name"] / "timestamps.npy"
timestamps = np.load(str(timestamp_file), mmap_mode="r")
timestamp0 = timestamps[0]
t_start = timestamp0 / info["sample_rate"]

# TODO for later : gap checking
signal_stream = info.copy()
signal_stream["raw_filename"] = str(raw_filename)
signal_stream["dtype"] = "int16"
signal_stream["timestamp0"] = timestamp0
signal_stream["t_start"] = t_start

recording["streams"]["continuous"][stream_name] = signal_stream

if (root / "events").exists() and len(rec_structure["events"]) > 0:
recording["streams"]["events"] = {}
for info in rec_structure["events"]:
oe_stream_name = Path(info["folder_name"]).name # remove trailing slash
stream_name = node_name + "#" + oe_stream_name

# Updates for OpenEphys v0.6:
# In new vesion (>=0.6) timestamps.npy is now called sample_numbers.npy
# see https://open-ephys.github.io/gui-docs/User-Manual/Recording-data/Binary-format.html#continuous
sample_numbers = recording_folder / "continuous" / info["folder_name"] / "sample_numbers.npy"
if sample_numbers.is_file():
timestamp_file = sample_numbers
else:
timestamp_file = recording_folder / "continuous" / info["folder_name"] / "timestamps.npy"
timestamps = np.load(str(timestamp_file), mmap_mode="r")
timestamp0 = timestamps[0]
t_start = timestamp0 / info["sample_rate"]

# TODO for later : gap checking
signal_stream = info.copy()
signal_stream["raw_filename"] = str(raw_filename)
signal_stream["dtype"] = "int16"
signal_stream["timestamp0"] = timestamp0
signal_stream["t_start"] = t_start

recording["streams"]["continuous"][stream_name] = signal_stream

if (root / "events").exists() and len(rec_structure["events"]) > 0:
recording["streams"]["events"] = {}
for info in rec_structure["events"]:
oe_stream_name = Path(info["folder_name"]).name # remove trailing slash
stream_name = node_name + "#" + oe_stream_name

event_stream = info.copy()
for name in _possible_event_stream_names:
npy_filename = root / "events" / info["folder_name"] / f"{name}.npy"
if npy_filename.is_file():
event_stream[f"{name}_npy"] = str(npy_filename)
event_stream = info.copy()
for name in _possible_event_stream_names:
npy_filename = root / "events" / info["folder_name"] / f"{name}.npy"
if npy_filename.is_file():
event_stream[f"{name}_npy"] = str(npy_filename)

recording["streams"]["events"][stream_name] = event_stream
recording["streams"]["events"][stream_name] = event_stream

folder_structure[node_name]["experiments"][experiment_id]["recordings"][recording_id] = recording
folder_structure[node_name]["experiments"][experiment_id]["recordings"][recording_id] = recording
except Exception as e:
raise Exception(f"Error while exploring Open Ephys folder {dirname}. Invalid folder structure?")
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# now create all_streams, nb_block, nb_segment_per_block
# nested dictionary: block_index > seg_index > data_type > stream_name
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