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Fix mpes incomplete files #523

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Fix mpes incomplete files #523

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ebd1234
catch OSError for incomplete files
rettigl Nov 19, 2024
a783232
fix get_count_rate and get_elapsed_time
rettigl Nov 19, 2024
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101 changes: 62 additions & 39 deletions sed/loader/mpes/loader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,20 +88,27 @@ def hdf5_to_dataframe(
)

# Delay-read all files
arrays = [
da.from_delayed(
dask.delayed(hdf5_to_array)(
h5file=h5py.File(f),
group_names=group_names,
time_stamps=time_stamps,
ms_markers_group=ms_markers_group,
first_event_time_stamp_key=first_event_time_stamp_key,
),
dtype=test_array.dtype,
shape=(test_array.shape[0], np.nan),
)
for f in files
]
arrays = []
for f in files:
try:
arrays.append(
da.from_delayed(
dask.delayed(hdf5_to_array)(
h5file=h5py.File(f),
group_names=group_names,
time_stamps=time_stamps,
ms_markers_group=ms_markers_group,
first_event_time_stamp_key=first_event_time_stamp_key,
),
dtype=test_array.dtype,
shape=(test_array.shape[0], np.nan),
),
)
except OSError as exc:
if "Unable to synchronously open file" in str(exc):
print(f"Unable to open file {f}: {str(exc)}")
pass

array_stack = da.concatenate(arrays, axis=1).T

return ddf.from_dask_array(array_stack, columns=column_names)
Expand Down Expand Up @@ -169,20 +176,26 @@ def hdf5_to_timed_dataframe(
)

# Delay-read all files
arrays = [
da.from_delayed(
dask.delayed(hdf5_to_timed_array)(
h5file=h5py.File(f),
group_names=group_names,
time_stamps=time_stamps,
ms_markers_group=ms_markers_group,
first_event_time_stamp_key=first_event_time_stamp_key,
),
dtype=test_array.dtype,
shape=(test_array.shape[0], np.nan),
)
for f in files
]
arrays = []
for f in files:
try:
arrays.append(
da.from_delayed(
dask.delayed(hdf5_to_timed_array)(
h5file=h5py.File(f),
group_names=group_names,
time_stamps=time_stamps,
ms_markers_group=ms_markers_group,
first_event_time_stamp_key=first_event_time_stamp_key,
),
dtype=test_array.dtype,
shape=(test_array.shape[0], np.nan),
),
)
except OSError as exc:
if "Unable to synchronously open file" in str(exc):
pass

array_stack = da.concatenate(arrays, axis=1).T

return ddf.from_dask_array(array_stack, columns=column_names)
Expand Down Expand Up @@ -914,13 +927,18 @@ def get_count_rate(
count_rate_list = []
accumulated_time = 0
for fid in fids:
count_rate_, secs_ = get_count_rate(
h5py.File(self.files[fid]),
ms_markers_group=ms_markers_group,
)
secs_list.append((accumulated_time + secs_).T)
count_rate_list.append(count_rate_.T)
accumulated_time += secs_[-1]
try:
count_rate_, secs_ = get_count_rate(
h5py.File(self.files[fid]),
ms_markers_group=ms_markers_group,
)
secs_list.append((accumulated_time + secs_).T)
count_rate_list.append(count_rate_.T)
accumulated_time += secs_[-1]
except OSError as exc:
if "Unable to synchronously open file" in str(exc):
print(f"Unable to open file {fid}: {str(exc)}")
pass

count_rate = np.concatenate(count_rate_list)
secs = np.concatenate(secs_list)
Expand Down Expand Up @@ -954,10 +972,15 @@ def get_elapsed_time(self, fids: Sequence[int] = None, **kwds) -> float:

secs = 0.0
for fid in fids:
secs += get_elapsed_time(
h5py.File(self.files[fid]),
ms_markers_group=ms_markers_group,
)
try:
secs += get_elapsed_time(
h5py.File(self.files[fid]),
ms_markers_group=ms_markers_group,
)
except OSError as exc:
if "Unable to synchronously open file" in str(exc):
print(f"Unable to open file {fid}: {str(exc)}")
pass

return secs

Expand Down