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Refactor of LH5 I/O routines, deprecation of existing methods #24

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merged 13 commits into from
Nov 24, 2023
Merged

Refactor of LH5 I/O routines, deprecation of existing methods #24

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94c944d
Moved lh5_store.py and renamed
MoritzNeuberger Nov 24, 2023
0827ffb
Overwrite content of store.py
MoritzNeuberger Nov 24, 2023
4c930a7
Added other files
MoritzNeuberger Nov 24, 2023
76e892b
Added other files
MoritzNeuberger Nov 24, 2023
b55ae45
Moved test files
MoritzNeuberger Nov 24, 2023
6c4acfc
Changed test files
MoritzNeuberger Nov 24, 2023
063fdb9
Everything adjusted and passes tests
MoritzNeuberger Nov 24, 2023
e1ac279
Also updated the docs agian
MoritzNeuberger Nov 24, 2023
c6a82c6
Renamed and back to and
MoritzNeuberger Nov 24, 2023
9a05121
Renamed and back to and
MoritzNeuberger Nov 24, 2023
6df838c
Adjusted warning messages to be individual for each function.
MoritzNeuberger Nov 24, 2023
72cd1a3
Fixed docs
MoritzNeuberger Nov 24, 2023
ff8d627
Apply suggestions from code review
MoritzNeuberger Nov 24, 2023
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2 changes: 1 addition & 1 deletion docs/source/extensions/numbadoc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,7 @@ def import_object(self) -> bool:
"""
success = super().import_object()
if success:
# Store away numba wrapper
# store away numba wrapper
self.jitobj = self.object
# And bend references to underlying python function
if hasattr(self.object, "py_func"):
Expand Down
44 changes: 21 additions & 23 deletions docs/source/notebooks/DataCompression.ipynb
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Expand Up @@ -61,8 +61,8 @@
"metadata": {},
"outputs": [],
"source": [
"store = lgdo.LH5Store()\n",
"store.write_object(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"store = lgdo.lh5.LH5Store()\n",
"store.write(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"lgdo.show(\"data.lh5\")"
]
},
Expand Down Expand Up @@ -110,7 +110,7 @@
"metadata": {},
"outputs": [],
"source": [
"lgdo.lh5_store.DEFAULT_HDF5_SETTINGS"
"lgdo.lh5.store.DEFAULT_HDF5_SETTINGS"
]
},
{
Expand All @@ -131,18 +131,18 @@
"outputs": [],
"source": [
"# use another built-in filter\n",
"lgdo.lh5_store.DEFAULT_HDF5_SETTINGS = {\"compression\": \"lzf\"}\n",
"lgdo.lh5.store.DEFAULT_HDF5_SETTINGS = {\"compression\": \"lzf\"}\n",
"\n",
"# specify filter name and options\n",
"lgdo.lh5_store.DEFAULT_HDF5_SETTINGS = {\"compression\": \"gzip\", \"compression_opts\": 7}\n",
"lgdo.lh5.store.DEFAULT_HDF5_SETTINGS = {\"compression\": \"gzip\", \"compression_opts\": 7}\n",
"\n",
"# specify a registered filter provided by hdf5plugin\n",
"import hdf5plugin\n",
"\n",
"lgdo.lh5_store.DEFAULT_HDF5_SETTINGS = {\"compression\": hdf5plugin.Blosc()}\n",
"lgdo.lh5.store.DEFAULT_HDF5_SETTINGS = {\"compression\": hdf5plugin.Blosc()}\n",
"\n",
"# shuffle bytes before compressing (typically better compression ratio with no performance penalty)\n",
"lgdo.lh5_store.DEFAULT_HDF5_SETTINGS = {\"shuffle\": True, \"compression\": \"lzf\"}"
"lgdo.lh5.store.DEFAULT_HDF5_SETTINGS = {\"shuffle\": True, \"compression\": \"lzf\"}"
]
},
{
Expand All @@ -166,7 +166,7 @@
"metadata": {},
"outputs": [],
"source": [
"store.write_object(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"store.write(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"show_h5ds_opts(\"data/col1\")"
]
},
Expand All @@ -175,7 +175,7 @@
"id": "f597a9e2",
"metadata": {},
"source": [
"Nice. Shuffling bytes before compressing significantly reduced size on disk. Last but not least, `create_dataset()` keyword arguments can be passed to `write_object()`. They will be forwarded as is, overriding default settings."
"Nice. Shuffling bytes before compressing significantly reduced size on disk. Last but not least, `create_dataset()` keyword arguments can be passed to `write()`. They will be forwarded as is, overriding default settings."
]
},
{
Expand All @@ -185,9 +185,7 @@
"metadata": {},
"outputs": [],
"source": [
"store.write_object(\n",
" data, \"data\", \"data.lh5\", wo_mode=\"of\", shuffle=True, compression=\"gzip\"\n",
")\n",
"store.write(data, \"data\", \"data.lh5\", wo_mode=\"of\", shuffle=True, compression=\"gzip\")\n",
"show_h5ds_opts(\"data/col1\")"
]
},
Expand All @@ -207,7 +205,7 @@
"outputs": [],
"source": [
"data[\"col2\"].attrs[\"hdf5_settings\"] = {\"compression\": \"gzip\"}\n",
"store.write_object(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"store.write(data, \"data\", \"data.lh5\", wo_mode=\"of\")\n",
"\n",
"show_h5ds_opts(\"data/col1\")\n",
"show_h5ds_opts(\"data/col2\")"
Expand All @@ -221,7 +219,7 @@
"We are now storing table columns with different compression settings.\n",
"\n",
"<div class=\"alert alert-info\">\n",
"**Note:** since any [h5py.Group.create_dataset()](https://docs.h5py.org/en/stable/high/group.html#h5py.Group.create_dataset) keyword argument can be used in `write_object()` or set in the `hdf5_settings` attribute, other HDF5 dataset settings can be configured, like the chunk size.\n",
"**Note:** since any [h5py.Group.create_dataset()](https://docs.h5py.org/en/stable/high/group.html#h5py.Group.create_dataset) keyword argument can be used in `write()` or set in the `hdf5_settings` attribute, other HDF5 dataset settings can be configured, like the chunk size.\n",
"</div>"
]
},
Expand All @@ -232,7 +230,7 @@
"metadata": {},
"outputs": [],
"source": [
"store.write_object(data, \"data\", \"data.lh5\", wo_mode=\"of\", chunks=2)"
"store.write(data, \"data\", \"data.lh5\", wo_mode=\"of\", chunks=2)"
]
},
{
Expand All @@ -257,7 +255,7 @@
"from legendtestdata import LegendTestData\n",
"\n",
"ldata = LegendTestData()\n",
"wfs, n_rows = store.read_object(\n",
"wfs, n_rows = store.read(\n",
" \"geds/raw/waveform\",\n",
" ldata.get_path(\"lh5/LDQTA_r117_20200110T105115Z_cal_geds_raw.lh5\"),\n",
")\n",
Expand Down Expand Up @@ -347,7 +345,7 @@
" t0=wfs.t0,\n",
" dt=wfs.dt,\n",
")\n",
"store.write_object(enc_wfs, \"waveforms\", \"data.lh5\", wo_mode=\"o\")\n",
"store.write(enc_wfs, \"waveforms\", \"data.lh5\", wo_mode=\"o\")\n",
"lgdo.show(\"data.lh5\", attrs=True)"
]
},
Expand All @@ -372,7 +370,7 @@
"metadata": {},
"outputs": [],
"source": [
"obj, _ = store.read_object(\"waveforms\", \"data.lh5\")\n",
"obj, _ = store.read(\"waveforms\", \"data.lh5\")\n",
"obj.values"
]
},
Expand All @@ -391,7 +389,7 @@
"metadata": {},
"outputs": [],
"source": [
"obj, _ = store.read_object(\"waveforms\", \"data.lh5\", decompress=False)\n",
"obj, _ = store.read(\"waveforms\", \"data.lh5\", decompress=False)\n",
"obj.values"
]
},
Expand Down Expand Up @@ -433,9 +431,9 @@
"from lgdo.compression import ULEB128ZigZagDiff\n",
"\n",
"wfs.values.attrs[\"compression\"] = ULEB128ZigZagDiff()\n",
"store.write_object(wfs, \"waveforms\", \"data.lh5\", wo_mode=\"of\")\n",
"store.write(wfs, \"waveforms\", \"data.lh5\", wo_mode=\"of\")\n",
"\n",
"obj, _ = store.read_object(\"waveforms\", \"data.lh5\", decompress=False)\n",
"obj, _ = store.read(\"waveforms\", \"data.lh5\", decompress=False)\n",
"obj.values.attrs[\"codec\"]"
]
},
Expand All @@ -447,8 +445,8 @@
"Further reading:\n",
"\n",
"- [Available waveform compression algorithms](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.compression.html)\n",
"- [read_object() docstring](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5_store.LH5Store.read_object)\n",
"- [write_object() docstring](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5_store.LH5Store.write_object)"
"- [read() docstring](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5.store.LH5Store.read)\n",
"- [write() docstring](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5_store.LH5Store.write)"
]
}
],
Expand Down
22 changes: 9 additions & 13 deletions docs/source/notebooks/LH5Files.ipynb
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Expand Up @@ -38,7 +38,7 @@
"id": "c136b537",
"metadata": {},
"source": [
"We can use `lgdo.lh5_store.ls()` [[docs]](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5_store.ls) to inspect the file contents:"
"We can use `lgdo.lh5.ls()` [[docs]](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5.ls) to inspect the file contents:"
]
},
{
Expand Down Expand Up @@ -131,7 +131,7 @@
"metadata": {},
"outputs": [],
"source": [
"store.read_object(\"geds/raw\", lh5_file)"
"store.read(\"geds/raw\", lh5_file)"
]
},
{
Expand All @@ -149,7 +149,7 @@
"metadata": {},
"outputs": [],
"source": [
"obj, n_rows = store.read_object(\"geds/raw/timestamp\", lh5_file)\n",
"obj, n_rows = store.read(\"geds/raw/timestamp\", lh5_file)\n",
"obj"
]
},
Expand All @@ -170,7 +170,7 @@
"metadata": {},
"outputs": [],
"source": [
"obj, n_rows = store.read_object(\"geds/raw/timestamp\", lh5_file, start_row=15, n_rows=10)\n",
"obj, n_rows = store.read(\"geds/raw/timestamp\", lh5_file, start_row=15, n_rows=10)\n",
"print(obj)"
]
},
Expand All @@ -189,7 +189,7 @@
"metadata": {},
"outputs": [],
"source": [
"obj, n_rows = store.read_object(\n",
"obj, n_rows = store.read(\n",
" \"geds/raw\", lh5_file, field_mask=(\"timestamp\", \"energy\"), idx=[1, 3, 7, 9, 10, 15]\n",
")\n",
"print(obj)"
Expand All @@ -200,7 +200,7 @@
"id": "b3f52d77",
"metadata": {},
"source": [
"As you might have noticed, `read_object()` loads all the requested data in memory at once. This can be a problem when dealing with large datasets. `LH5Iterator` [[docs]](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5_store.LH5Iterator) makes it possible to handle data one chunk at a time (sequentially) to avoid running out of memory:"
"As you might have noticed, `read_object()` loads all the requested data in memory at once. This can be a problem when dealing with large datasets. `LH5Iterator` [[docs]](https://legend-pydataobj.readthedocs.io/en/stable/api/lgdo.html#lgdo.lh5.iterator.LH5Iterator) makes it possible to handle data one chunk at a time (sequentially) to avoid running out of memory:"
]
},
{
Expand Down Expand Up @@ -260,9 +260,7 @@
"source": [
"store = LH5Store()\n",
"\n",
"store.write_object(\n",
" scalar, name=\"message\", lh5_file=\"my_objects.lh5\", wo_mode=\"overwrite_file\"\n",
")"
"store.write(scalar, name=\"message\", lh5_file=\"my_objects.lh5\", wo_mode=\"overwrite_file\")"
]
},
{
Expand Down Expand Up @@ -300,10 +298,8 @@
"metadata": {},
"outputs": [],
"source": [
"store.write_object(array, name=\"numbers\", group=\"closet\", lh5_file=\"my_objects.lh5\")\n",
"store.write_object(\n",
" wf_table, name=\"waveforms\", group=\"closet\", lh5_file=\"my_objects.lh5\"\n",
")\n",
"store.write(array, name=\"numbers\", group=\"closet\", lh5_file=\"my_objects.lh5\")\n",
"store.write(wf_table, name=\"waveforms\", group=\"closet\", lh5_file=\"my_objects.lh5\")\n",
"show(\"my_objects.lh5\")"
]
},
Expand Down
4 changes: 2 additions & 2 deletions src/lgdo/__init__.py
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Expand Up @@ -66,11 +66,11 @@
"VectorOfVectors",
"VectorOfEncodedVectors",
"WaveformTable",
"LH5Iterator",
"LH5Store",
"load_dfs",
"load_nda",
"ls",
"show",
"LH5Iterator",
"LH5Store",
"__version__",
]
2 changes: 1 addition & 1 deletion src/lgdo/cli.py
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Expand Up @@ -9,7 +9,7 @@


def lh5ls():
""":func:`.show` command line interface."""
""":func:`.lh5.show` command line interface."""
parser = argparse.ArgumentParser(
prog="lh5ls", description="Inspect LEGEND HDF5 (LH5) file contents"
)
Expand Down
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