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perform flattening as necessary in test suite (#130)
* move methods for flattening netcdf and hdf group structures to separate module * feature/PODAAC-5065 (#129) * fix way xarray open granules that have as a time unit * fix pylint * change function to use original function if can parse only change units if we can not parse * make xarray override into its own function * add test for override_decode_cf_datetime function * disable pyline one line instead of global * Update podaac/subsetter/subset.py Co-authored-by: Frank Greguska <[email protected]> * add missing parameter to docstring * typo in docstring * extract netcdf opening procedure from beginning of `subset() into a new function * update tests to use netcdf opening wrapper function, to prevent errors with tempo data * /version 2.3.0-alpha.5 * update `test_specified_variables()` to use netcdf opening wrapper function in multiple places to prevent errors with tempo data * cosmetic * clean up comment and use 'decode_times'=True for test * feature/issue 126 (#131) * Add variable leading slash flexibility * Add tests back to test file * changelog added and updated * Update podaac/subsetter/subset.py Co-authored-by: Frank Greguska <[email protected]> * update Syntax * resolve conflict Co-authored-by: nlensse1 <[email protected]> Co-authored-by: Frank Greguska <[email protected]> * /version 2.3.0-alpha.6 * Update build-pipeline.yml * /version 2.3.0-alpha.7 * Merge changes from origin/develop * Merge changes from issues/127 Co-authored-by: sliu008 <[email protected]> Co-authored-by: Frank Greguska <[email protected]> Co-authored-by: l2ss-py bot <[email protected]> Co-authored-by: Nick Lenssen <[email protected]> Co-authored-by: nlensse1 <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,232 @@ | ||
| from shutil import copy | ||
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| import h5py | ||
| import netCDF4 as nc | ||
| import numpy as np | ||
| import xarray as xr | ||
|
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| GROUP_DELIM = '__' | ||
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| def transform_grouped_dataset(nc_dataset, file_to_subset): | ||
| """ | ||
| Transform a netCDF4 Dataset that has groups to an xarray compatible | ||
| dataset. xarray does not work with groups, so this transformation | ||
| will flatten the variables in the dataset and use the group path as | ||
| the new variable name. For example, data_01 > km > sst would become | ||
| 'data_01__km__sst', where GROUP_DELIM is __. | ||
| This same pattern is applied to dimensions, which are located under | ||
| the appropriate group. They are renamed and placed in the root | ||
| group. | ||
| Parameters | ||
| ---------- | ||
| nc_dataset : nc.Dataset | ||
| netCDF4 Dataset that contains groups | ||
| file_to_subset : str | ||
| Returns | ||
| ------- | ||
| nc.Dataset | ||
| netCDF4 Dataset that does not contain groups and that has been | ||
| flattened. | ||
| """ | ||
|
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| # Close the existing read-only dataset and reopen in append mode | ||
| nc_dataset.close() | ||
| nc_dataset = nc.Dataset(file_to_subset, 'r+') | ||
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| dimensions = {} | ||
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| def walk(group_node, path): | ||
| for key, item in group_node.items(): | ||
| group_path = f'{path}{GROUP_DELIM}{key}' | ||
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| # If there are variables in this group, copy to root group | ||
| # and then delete from current group | ||
| if item.variables: | ||
| # Copy variables to root group with new name | ||
| for var_name, var in item.variables.items(): | ||
| var_group_name = f'{group_path}{GROUP_DELIM}{var_name}' | ||
| nc_dataset.variables[var_group_name] = var | ||
| # Delete variables | ||
| var_names = list(item.variables.keys()) | ||
| for var_name in var_names: | ||
| del item.variables[var_name] | ||
|
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| if item.dimensions: | ||
| dims = list(item.dimensions.keys()) | ||
| for dim_name in dims: | ||
| new_dim_name = f'{group_path.replace("/", GROUP_DELIM)}{GROUP_DELIM}{dim_name}' | ||
| item.dimensions[new_dim_name] = item.dimensions[dim_name] | ||
| dimensions[new_dim_name] = item.dimensions[dim_name] | ||
| item.renameDimension(dim_name, new_dim_name) | ||
|
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| # If there are subgroups in this group, call this function | ||
| # again on that group. | ||
| if item.groups: | ||
| walk(item.groups, group_path) | ||
|
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| # Delete non-root groups | ||
| group_names = list(group_node.keys()) | ||
| for group_name in group_names: | ||
| del group_node[group_name] | ||
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| for var_name in list(nc_dataset.variables.keys()): | ||
| new_var_name = f'{GROUP_DELIM}{var_name}' | ||
| nc_dataset.variables[new_var_name] = nc_dataset.variables[var_name] | ||
| del nc_dataset.variables[var_name] | ||
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| walk(nc_dataset.groups, '') | ||
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| # Update the dimensions of the dataset in the root group | ||
| nc_dataset.dimensions.update(dimensions) | ||
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| return nc_dataset | ||
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| def recombine_grouped_datasets(datasets, output_file, start_date): # pylint: disable=too-many-branches | ||
| """ | ||
| Given a list of xarray datasets, combine those datasets into a | ||
| single netCDF4 Dataset and write to the disk. Each dataset has been | ||
| transformed using its group path and needs to be un-transformed and | ||
| placed in the appropriate group. | ||
| Parameters | ||
| ---------- | ||
| datasets : list (xr.Dataset) | ||
| List of xarray datasets to be combined | ||
| output_file : str | ||
| Name of the output file to write the resulting NetCDF file to. | ||
| """ | ||
|
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| base_dataset = nc.Dataset(output_file, mode='w') | ||
|
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| for dataset in datasets: | ||
| group_lst = [] | ||
| for var_name in dataset.variables.keys(): # need logic if there is data in the top level not in a group | ||
| group_lst.append('/'.join(var_name.split(GROUP_DELIM)[:-1])) | ||
| group_lst = ['/' if group == '' else group for group in group_lst] | ||
| groups = set(group_lst) | ||
| for group in groups: | ||
| base_dataset.createGroup(group) | ||
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| for dim_name in list(dataset.dims.keys()): | ||
| new_dim_name = dim_name.split(GROUP_DELIM)[-1] | ||
| dim_group = _get_nested_group(base_dataset, dim_name) | ||
| dim_group.createDimension(new_dim_name, dataset.dims[dim_name]) | ||
|
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| # Rename variables | ||
| _rename_variables(dataset, base_dataset, start_date) | ||
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| # Remove group vars from base dataset | ||
| for var_name in list(base_dataset.variables.keys()): | ||
| if GROUP_DELIM in var_name: | ||
| del base_dataset.variables[var_name] | ||
|
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| # Remove group dims from base dataset | ||
| for dim_name in list(base_dataset.dimensions.keys()): | ||
| if GROUP_DELIM in dim_name: | ||
| del base_dataset.dimensions[dim_name] | ||
|
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| # Copy global attributes | ||
| base_dataset.setncatts(datasets[0].attrs) | ||
| # Write and close | ||
| base_dataset.close() | ||
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| def _get_nested_group(dataset, group_path): | ||
| nested_group = dataset | ||
| for group in group_path.strip(GROUP_DELIM).split(GROUP_DELIM)[:-1]: | ||
| nested_group = nested_group.groups[group] | ||
| return nested_group | ||
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| def _rename_variables(dataset, base_dataset, start_date): | ||
| for var_name in list(dataset.variables.keys()): | ||
| new_var_name = var_name.split(GROUP_DELIM)[-1] | ||
| var_group = _get_nested_group(base_dataset, var_name) | ||
| variable = dataset.variables[var_name] | ||
| var_dims = [x.split(GROUP_DELIM)[-1] for x in dataset.variables[var_name].dims] | ||
| if np.issubdtype( | ||
| dataset.variables[var_name].dtype, np.dtype(np.datetime64) | ||
| ) or np.issubdtype( | ||
| dataset.variables[var_name].dtype, np.dtype(np.timedelta64) | ||
| ): | ||
| if start_date: | ||
| dataset.variables[var_name].values = (dataset.variables[var_name].values - np.datetime64(start_date))/np.timedelta64(1, 's') | ||
| variable = dataset.variables[var_name] | ||
| else: | ||
| cf_dt_coder = xr.coding.times.CFDatetimeCoder() | ||
| encoded_var = cf_dt_coder.encode(dataset.variables[var_name]) | ||
| variable = encoded_var | ||
|
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| var_attrs = variable.attrs | ||
| fill_value = var_attrs.get('_FillValue') | ||
| var_attrs.pop('_FillValue', None) | ||
| comp_args = {"zlib": True, "complevel": 1} | ||
|
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| if variable.dtype == object: | ||
| var_group.createVariable(new_var_name, 'S1', var_dims, fill_value=fill_value, **comp_args) | ||
| elif variable.dtype == 'timedelta64[ns]': | ||
| var_group.createVariable(new_var_name, 'i4', var_dims, fill_value=fill_value, **comp_args) | ||
| else: | ||
| var_group.createVariable(new_var_name, variable.dtype, var_dims, fill_value=fill_value, **comp_args) | ||
|
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| # Copy attributes | ||
| var_group.variables[new_var_name].setncatts(var_attrs) | ||
|
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| # Copy data | ||
| var_group.variables[new_var_name].set_auto_maskandscale(False) | ||
| var_group.variables[new_var_name][:] = variable.data | ||
|
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| def h5file_transform(finput): | ||
| """ | ||
| Transform a h5py Dataset that has groups to an xarray compatible | ||
| dataset. xarray does not work with groups, so this transformation | ||
| will flatten the variables in the dataset and use the group path as | ||
| the new variable name. For example, data_01 > km > sst would become | ||
| 'data_01__km__sst', where GROUP_DELIM is __. | ||
| Returns | ||
| ------- | ||
| nc.Dataset | ||
| netCDF4 Dataset that does not contain groups and that has been | ||
| flattened. | ||
| """ | ||
| data_new = h5py.File(finput, 'r+') | ||
| del_group_list = list(data_new.keys()) | ||
| has_groups = bool(data_new['/']) | ||
|
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| def walk_h5py(data_new, group): | ||
| # flattens h5py file | ||
| for key, item in data_new[group].items(): | ||
| group_path = f'{group}{key}' | ||
| if isinstance(item, h5py.Dataset): | ||
| new_var_name = group_path.replace('/', '__') | ||
|
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| data_new[new_var_name] = data_new[group_path] | ||
| del data_new[group_path] | ||
|
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| elif isinstance(item, h5py.Group): | ||
| if len(list(item.keys())) == 0: | ||
| new_group_name = group_path.replace('/', '__') | ||
| data_new[new_group_name] = data_new[group_path] | ||
|
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| walk_h5py(data_new, data_new[group_path].name + '/') | ||
|
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| walk_h5py(data_new, data_new.name) | ||
|
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| for del_group in del_group_list: | ||
| del data_new[del_group] | ||
|
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| finputnc = '.'.join(finput.split('.')[:-1]) + '.nc' | ||
|
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| data_new.close() # close the h5py dataset | ||
| copy(finput, finputnc) # copy to a nc file | ||
|
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| nc_dataset = nc.Dataset(finputnc, mode='r') | ||
|
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| return nc_dataset, has_groups |
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