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Update to documents_to_xarray #471

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Update to documents_to_xarray #471

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0df1b2c
replaced documents_to_xarray
gwbischof Nov 27, 2019
9597e55
fixed some tests
gwbischof Feb 3, 2020
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55 changes: 32 additions & 23 deletions databroker/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1339,19 +1339,26 @@ def __repr__(self):
out = f"<Intake catalog: Stream *REPR_RENDERING_FAILURE* {exc!r}>"
return out

def _to_xarray(self, fill='yes'):

def stream_gen():
for i in itertools.count():
partition = self.read_partition({'index': i, 'fill': fill,
'partition_size': 'auto'})
if not partition:
break
yield from partition

stream = stream_gen()

array_pages = [eventpage_to_arraypage(doc) for name, doc
in stream if name == 'event_page']
array_page = concat_arraypages(array_pages)
dataset_page = arraypage_to_datasetpage(array_page)
return dataset_page

def _open_dataset(self):
self._load_header()
self._ds = documents_to_xarray(
start_doc=self._run_start_doc,
stop_doc=self._run_stop_doc,
descriptor_docs=self._descriptors,
get_event_pages=self._get_event_pages,
filler=self.fillers['delayed'],
get_resource=self._get_resource,
lookup_resource_for_datum=self._lookup_resource_for_datum,
get_datum_pages=self._get_datum_pages,
include=self.include,
exclude=self.exclude)
self._ds = self._to_xarray()['data']

def read(self):
"""
Expand Down Expand Up @@ -1756,7 +1763,7 @@ def parse_transforms(transforms):
intake.container.container_map['bluesky-event-stream'] = RemoteBlueskyEventStream


def concat_dataarray_pages(dataarray_pages):
def concat_arraypages(dataarray_pages):
"""
Combines a iterable of dataarray_pages to a single dataarray_page.

Expand All @@ -1777,6 +1784,7 @@ def concat_dataarray_pages(dataarray_pages):

array_keys = ['seq_num', 'time', 'uid']
data_keys = dataarray_pages[0]['data'].keys()
filled_keys = dataarray_pages[0]['filled'].keys()

return {'descriptor': pages[0]['descriptor'],
**{key: list(itertools.chain.from_iterable(
Expand All @@ -1789,10 +1797,10 @@ def concat_dataarray_pages(dataarray_pages):
for key in data_keys},
'filled': {key: xarray.concat([page['filled'][key]
for page in pages], dim='concat_dim')
for key in data_keys}}
for key in filled_keys}}


def event_page_to_dataarray_page(event_page, dims=None, coords=None):
def eventpage_to_arraypage(event_page, dims=None, coords=None):
"""
Converts the event_page's data, timestamps, and filled to xarray.DataArray.

Expand All @@ -1817,21 +1825,22 @@ def event_page_to_dataarray_page(event_page, dims=None, coords=None):

array_keys = ['seq_num', 'time', 'uid']
data_keys = event_page['data'].keys()
filled_keys = event_page['filled'].keys()

return {'descriptor': event_page['descriptor'],
**{key: event_page[key] for key in array_keys},
'data': {key: xarray.DataArray(
event_page['data'][key], dims=dims, coords=coords, name=key)
'data': {key: xarray.DataArray(event_page['data'][key], dims=dims,
coords=coords, name=key)
for key in data_keys},
'timestamps': {key: xarray.DataArray(
event_page['timestamps'][key], dims=dims, coords=coords, name=key)
'timestamps': {key: xarray.DataArray(event_page['timestamps'][key],
dims=dims, coords=coords, name=key)
for key in data_keys},
'filled': {key: xarray.DataArray(
event_page['filled'][key], dims=dims, coords=coords, name=key)
for key in data_keys}}
'filled': {key: xarray.DataArray(event_page['filled'][key],
dims=dims, coords=coords, name=key)
for key in filled_keys}}


def dataarray_page_to_dataset_page(dataarray_page):
def arraypage_to_datasetpage(dataarray_page):

"""
Converts the dataarray_page's data, timestamps, and filled to xarray.DataSet.
Expand Down