Small refactors in particlefile.py
#1843
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VeckoTheGecko
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Feb 10, 2025
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| if len(indices_to_write) == 0: | ||
| return | ||
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| pids = pset.particledata.getvardata("id", indices_to_write) | ||
| to_add = sorted(set(pids) - set(self._pids_written.keys())) | ||
| for i, pid in enumerate(to_add): | ||
| self._pids_written[pid] = self._maxids + i | ||
| ids = np.array([self._pids_written[p] for p in pids], dtype=int) | ||
| self._maxids = len(self._pids_written) | ||
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| once_ids = np.where(pset.particledata.getvardata("obs_written", indices_to_write) == 0)[0] | ||
| if len(once_ids) > 0: | ||
| ids_once = ids[once_ids] | ||
| indices_to_write_once = indices_to_write[once_ids] | ||
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| if self.create_new_zarrfile: | ||
| if self.chunks is None: | ||
| self._chunks = (len(pset), 1) | ||
| if pset._repeatpclass is not None and self.chunks[0] < 1e4: # type: ignore[index] | ||
| warnings.warn( | ||
| f"ParticleFile chunks are set to {self.chunks}, but this may lead to " | ||
| f"a significant slowdown in Parcels when many calls to repeatdt. " | ||
| f"Consider setting a larger chunk size for your ParticleFile (e.g. chunks=(int(1e4), 1)).", | ||
| FileWarning, | ||
| stacklevel=2, | ||
| ) | ||
| attrs = self._create_variables_attribute_dict() | ||
| obs = np.zeros((self._maxids), dtype=np.int32) | ||
| for var in self.vars_to_write: | ||
| varout = self._convert_varout_name(var) | ||
| if varout not in ["trajectory"]: # because 'trajectory' is written as coordinate | ||
| if self._write_once(var): | ||
| data = np.full( | ||
| (arrsize[0],), | ||
| self._fill_value_map[self.vars_to_write[var]], | ||
| dtype=self.vars_to_write[var], | ||
| ) | ||
| data[ids_once] = pset.particledata.getvardata(var, indices_to_write_once) | ||
| dims = ["trajectory"] | ||
| else: | ||
| data = np.full( | ||
| arrsize, self._fill_value_map[self.vars_to_write[var]], dtype=self.vars_to_write[var] | ||
| ) | ||
| data[ids, 0] = pset.particledata.getvardata(var, indices_to_write) | ||
| dims = ["trajectory", "obs"] | ||
| ds[varout] = xr.DataArray(data=data, dims=dims, attrs=attrs[varout]) | ||
| ds[varout].encoding["chunks"] = self.chunks[0] if self._write_once(var) else self.chunks # type: ignore[index] | ||
| ds.to_zarr(self.fname, mode="w") | ||
| self._create_new_zarrfile = False | ||
| if (self._maxids > len(ids)) or (self._maxids > self.chunks[0]): # type: ignore[index] | ||
| arrsize = (self._maxids, self.chunks[1]) # type: ignore[index] | ||
| else: | ||
| # Either use the store that was provided directly or create a DirectoryStore: | ||
| if issubclass(type(self.fname), zarr.storage.Store): | ||
| store = self.fname | ||
| else: | ||
| store = zarr.DirectoryStore(self.fname) | ||
| Z = zarr.group(store=store, overwrite=False) | ||
| obs = pset.particledata.getvardata("obs_written", indices_to_write) | ||
| for var in self.vars_to_write: | ||
| varout = self._convert_varout_name(var) | ||
| if self._maxids > Z[varout].shape[0]: | ||
| self._extend_zarr_dims(Z[varout], store, dtype=self.vars_to_write[var], axis=0) | ||
| arrsize = (len(ids), self.chunks[1]) # type: ignore[index] | ||
| ds = xr.Dataset( | ||
| attrs=self.metadata, | ||
| coords={"trajectory": ("trajectory", pids), "obs": ("obs", np.arange(arrsize[1], dtype=np.int32))}, | ||
| ) | ||
| attrs = self._create_variables_attribute_dict() | ||
| obs = np.zeros((self._maxids), dtype=np.int32) | ||
| for var in self.vars_to_write: | ||
| varout = self._convert_varout_name(var) | ||
| if varout not in ["trajectory"]: # because 'trajectory' is written as coordinate | ||
| if self._write_once(var): | ||
| if len(once_ids) > 0: | ||
| Z[varout].vindex[ids_once] = pset.particledata.getvardata(var, indices_to_write_once) | ||
| data = np.full( | ||
| (arrsize[0],), | ||
| self._fill_value_map[self.vars_to_write[var]], | ||
| dtype=self.vars_to_write[var], | ||
| ) | ||
| data[ids_once] = pset.particledata.getvardata(var, indices_to_write_once) | ||
| dims = ["trajectory"] | ||
| else: | ||
| if max(obs) >= Z[varout].shape[1]: # type: ignore[type-var] | ||
| self._extend_zarr_dims(Z[varout], store, dtype=self.vars_to_write[var], axis=1) | ||
| Z[varout].vindex[ids, obs] = pset.particledata.getvardata(var, indices_to_write) | ||
| data = np.full( | ||
| arrsize, self._fill_value_map[self.vars_to_write[var]], dtype=self.vars_to_write[var] | ||
| ) | ||
| data[ids, 0] = pset.particledata.getvardata(var, indices_to_write) | ||
| dims = ["trajectory", "obs"] | ||
| ds[varout] = xr.DataArray(data=data, dims=dims, attrs=attrs[varout]) | ||
| ds[varout].encoding["chunks"] = self.chunks[0] if self._write_once(var) else self.chunks # type: ignore[index] | ||
| ds.to_zarr(self.fname, mode="w") | ||
| self._create_new_zarrfile = False | ||
| else: | ||
| # Either use the store that was provided directly or create a DirectoryStore: | ||
| if isinstance(self.fname, zarr.storage.Store): | ||
| store = self.fname | ||
| else: | ||
| store = zarr.DirectoryStore(self.fname) | ||
| Z = zarr.group(store=store, overwrite=False) | ||
| obs = pset.particledata.getvardata("obs_written", indices_to_write) | ||
| for var in self.vars_to_write: | ||
| varout = self._convert_varout_name(var) | ||
| if self._maxids > Z[varout].shape[0]: | ||
| self._extend_zarr_dims(Z[varout], store, dtype=self.vars_to_write[var], axis=0) | ||
| if self._write_once(var): | ||
| if len(once_ids) > 0: | ||
| Z[varout].vindex[ids_once] = pset.particledata.getvardata(var, indices_to_write_once) | ||
| else: | ||
| if max(obs) >= Z[varout].shape[1]: # type: ignore[type-var] | ||
| self._extend_zarr_dims(Z[varout], store, dtype=self.vars_to_write[var], axis=1) | ||
| Z[varout].vindex[ids, obs] = pset.particledata.getvardata(var, indices_to_write) | ||
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| pset.particledata.setvardata("obs_written", indices_to_write, obs + 1) | ||
| pset.particledata.setvardata("obs_written", indices_to_write, obs + 1) |
Contributor
Author
There was a problem hiding this comment.
This is just a reversal of the clause and a de-indentation.
| self._create_new_zarrfile = False | ||
| else: | ||
| # Either use the store that was provided directly or create a DirectoryStore: | ||
| if isinstance(self.fname, zarr.storage.Store): |
Contributor
Author
There was a problem hiding this comment.
Previously was issubclass(type(self.fname), zarr.storage.Store):, this is equivalent
Some errors due to grid iheritence hierarchy which aren't trivial to fix
VeckoTheGecko
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erikvansebille
approved these changes
Feb 10, 2025
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