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Fix: Avoid _like function in Chunking #340

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Merged
RemiLehe merged 1 commit into from
Apr 14, 2022
Merged

Fix: Avoid _like function in Chunking #340

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6 changes: 5 additions & 1 deletion openpmd_viewer/openpmd_timeseries/data_reader/io_reader/utilities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,17 +56,21 @@ def get_data(series, record_component, i_slice=None, pos_slice=None,
if i_slice is not None and not isinstance(i_slice, list):
i_slice = [i_slice]

# ADIOS2: Actual chunks, all other: one chunk
chunks = record_component.available_chunks()

# read whole data set
if pos_slice is None:
# mask invalid regions with NaN
data = np.full_like(record_component, np.nan)
# note: full_like triggers a full read, thus we avoid it #340
data = np.full(record_component.shape, np.nan, record_component.dtype)
for chunk in chunks:
chunk_slice = chunk_to_slice(chunk)
# read only valid region
x = record_component[chunk_slice]
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@ax3l ax3l Apr 13, 2022

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I wonder if this is related to openPMD/openPMD-api#1225
Prior to #332 we did not copy an extra time.

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@ax3l ax3l Apr 13, 2022

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actually, @AlexanderSinn found that x = record_component[()] is fast, but it becomes slow the moment we have the data = np.full_like(record_component, np.nan) above.

We could try to make the above line a np.full with shape and dtype.

series.flush()
data[chunk_slice] = x
# slice: read only part of the data set
else:
full_shape = record_component.shape

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