Closed ethho closed 3 years ago
Census ZCTA and the vertex
index are not identical:
$ PYTHONPATH='.' poetry run python scripts/20210512_partition_model.py
Traceback (most recent call last):
File "scripts/20210512_partition_model.py", line 69, in <module>
main(**opts)
File "scripts/20210512_partition_model.py", line 48, in main
out_ds = input_ds.xsimlab.run(model=model, decoding=dict(mask_and_scale=False))
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/xr_accessor.py", line 860, in run
driver.run_model()
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/drivers.py", line 478, in run_model
_run(
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/drivers.py", line 342, in _run
model.execute("initialize", rt_context, **execute_kwargs)
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/model.py", line 1023, in execute
_, (_, signal_process) = self._execute_process(p_obj, *execute_args)
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/model.py", line 842, in _execute_process
state_out, signal_out = executor.execute(
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/process.py", line 530, in execute
signal_out = executor.execute(p_obj, runtime_context, state=state)
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xsimlab/process.py", line 394, in execute
signal = self.meth(p_obj, *args)
File "/Users/TASethanho/tacc/projects/meyers/covid/episimlab/episimlab/setup/counts.py", line 62, in initialize
da[dict()] = self.read_census_csv()
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xarray/core/dataarray.py", line 718, in __setitem__
assert_coordinate_consistent(value, obj.coords.variables)
File "/Users/TASethanho/Library/Caches/pypoetry/virtualenvs/episimlab-aT2Erjcy-py3.8/lib/python3.8/site-packages/xarray/core/coordinates.py", line 382, in assert_coordinate_consistent
raise IndexError(
IndexError: dimension coordinate 'vertex' conflicts between indexed and indexing objects:
<xarray.DataArray 'vertex' (vertex: 1935)>
array([75001, 75002, 75006, ..., 79936, 79938, 79942])
Coordinates:
* vertex (vertex) int64 75001 75002 75006 75007 ... 79935 79936 79938 79942
vs.
<xarray.IndexVariable 'vertex' (vertex: 87)>
array([76511, 76527, 76530, 76537, 76574, 76578, 78602, 78610, 78612, 78613,
78615, 78616, 78617, 78619, 78620, 78621, 78626, 78628, 78632, 78633,
78634, 78640, 78641, 78642, 78644, 78645, 78648, 78650, 78652, 78653,
78654, 78655, 78659, 78660, 78662, 78664, 78665, 78666, 78669, 78676,
78681, 78701, 78702, 78703, 78704, 78705, 78712, 78717, 78719, 78721,
78722, 78723, 78724, 78725, 78726, 78727, 78728, 78729, 78730, 78731,
78732, 78733, 78734, 78735, 78736, 78737, 78738, 78739, 78741, 78742,
78744, 78745, 78746, 78747, 78748, 78749, 78750, 78751, 78752, 78753,
78754, 78756, 78757, 78758, 78759, 78953, 78957], dtype=int32)
$ PYTHONPATH='.' poetry run python scripts/20210512_partition_model.py
# opens pyplot like below...
As of ddb72e9, the partitioning model ingests contact_xr
as a file (tests/data/20200311_contact_matrix.nc
) via PartitionFromNC
, instead of taking travel_fp
and contacts_fp
and processing via Partition
. This was for the purposes of local development, since running Partition
on realistic travel and contacts data takes ~45 minutes serially on Frontera.
Possible next step is to replace PartitionFromNC
with Partition
, pass travel_fp
and contacts_fp
, and run on Frontera.
Fixes #12