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Refactored
EchoData.update_platform to improve readability (OSOcean…
…Acoustics#1209) * refactored update_platform method * removed extra print statements
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| import numpy as np | ||
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| def _extvar_properties(ds, name): | ||
| """Test the external variable for presence and all-nan values, | ||
| and extract its time dimension name. | ||
| Returns <presence>, <valid values>, <time dim name> | ||
| """ | ||
| if name in ds: | ||
| # Assumes the only dimension in the variable is a time dimension | ||
| time_dim_name = ds[name].dims[0] if len(ds[name].dims) > 0 else "scalar" | ||
| if not ds[name].isnull().all(): | ||
| return True, True, time_dim_name | ||
| else: | ||
| return True, False, time_dim_name | ||
| else: | ||
| return False, False, None | ||
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| def _clip_by_time_dim(external_ds, ext_time_dim_name, ping_time): | ||
| """ | ||
| Clip incoming time to 1 less than min of EchoData["Sonar/Beam_group1"]["ping_time"] | ||
| and 1 greater than max of EchoData["Sonar/Beam_group1"]["ping_time"]. | ||
| Accounts for unsorted external time by checking whether each time value is between | ||
| min and max ping_time instead of finding the 2 external times corresponding to the | ||
| min and max ping_time and taking all the times between those indices. | ||
| """ | ||
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| sorted_external_time = external_ds[ext_time_dim_name].data | ||
| sorted_external_time.sort() | ||
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| min_index = max( | ||
| np.searchsorted(sorted_external_time, ping_time.min(), side="left") - 1, | ||
| 0, | ||
| ) | ||
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| max_index = min( | ||
| np.searchsorted( | ||
| sorted_external_time, | ||
| ping_time.max(), | ||
| side="right", | ||
| ), | ||
| len(sorted_external_time) - 1, | ||
| ) | ||
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| return external_ds.sel( | ||
| { | ||
| ext_time_dim_name: np.logical_and( | ||
| sorted_external_time[min_index] <= external_ds[ext_time_dim_name], | ||
| external_ds[ext_time_dim_name] <= sorted_external_time[max_index], | ||
| ) | ||
| } | ||
| ) | ||
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| def get_mappings_expanded(logger, extra_platform_data, variable_mappings, platform): | ||
| """ | ||
| Generate a dictionary of mappings between Platform group variables and external variables. | ||
| Parameters | ||
| ---------- | ||
| logger : logging.Logger | ||
| A logger object to log warnings and errors. | ||
| extra_platform_data : xr.Dataset | ||
| An `xr.Dataset` containing the additional platform data to be added | ||
| to the `EchoData["Platform"]` group. | ||
| variable_mappings: Dict[str,str] | ||
| A dictionary mapping Platform variable names (dict key) to the | ||
| external-data variable name (dict value). | ||
| platform: xr.Dataset | ||
| An `xr.Dataset` containing the original Platform data. | ||
| Returns | ||
| ------- | ||
| mappings_expanded: Dict[str, Dict[str, Any]] | ||
| A dictionary containing mappings between Platform group variables and external variables. | ||
| Raises | ||
| ------ | ||
| ValueError: If only one of latitude and longitude are specified. | ||
| If the external latitude and longitude use different time dimensions. | ||
| """ | ||
|
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| mappings_expanded = {} | ||
| for platform_var, external_var in variable_mappings.items(): | ||
| # TODO: instead of using existing Platform group variables, a better practice is to | ||
| # define a set of allowable Platform variables (sonar_model dependent) for this check. | ||
| # This set can be dynamically generated from an external source like a CDL or yaml. | ||
| if platform_var in platform: | ||
| platform_validvalues = not platform[platform_var].isnull().all() | ||
| ext_present, ext_validvalues, ext_time_dim_name = _extvar_properties( | ||
| extra_platform_data, external_var | ||
| ) | ||
| if ext_present and ext_validvalues: | ||
| mappings_expanded[platform_var] = dict( | ||
| external_var=external_var, | ||
| ext_time_dim_name=ext_time_dim_name, | ||
| platform_validvalues=platform_validvalues, | ||
| ) | ||
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| # Generate warning if mappings_expanded is empty | ||
| if not mappings_expanded: | ||
| logger.warning( | ||
| "No variables will be updated, " | ||
| "check variable_mappings to ensure variable names are correctly specified!" | ||
| ) | ||
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| # If longitude or latitude are requested, verify that both are present | ||
| # and they share the same external time dimension | ||
| if "longitude" in mappings_expanded or "latitude" in mappings_expanded: | ||
| if "longitude" not in mappings_expanded or "latitude" not in mappings_expanded: | ||
| raise ValueError( | ||
| "Only one of latitude and longitude are specified. Please include both, or neither." # noqa | ||
| ) | ||
| if ( | ||
| mappings_expanded["longitude"]["ext_time_dim_name"] | ||
| != mappings_expanded["latitude"]["ext_time_dim_name"] | ||
| ): | ||
| raise ValueError( | ||
| "The external latitude and longitude use different time dimensions. " | ||
| "They must share the same time dimension." | ||
| ) | ||
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| # Generate warnings regarding variables that will be updated | ||
| vars_not_handled = set(variable_mappings.keys()).difference(mappings_expanded.keys()) | ||
| if len(vars_not_handled) > 0: | ||
| logger.warning( | ||
| f"The following requested variables will not be updated: {', '.join(vars_not_handled)}" # noqa | ||
| ) | ||
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| vars_notnan_replaced = [ | ||
| platform_var for platform_var, v in mappings_expanded.items() if v["platform_validvalues"] | ||
| ] | ||
| if len(vars_notnan_replaced) > 0: | ||
| logger.warning( | ||
| f"Some variables with valid data in the original Platform group will be overwritten: {', '.join(vars_notnan_replaced)}" # noqa | ||
| ) | ||
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| return mappings_expanded |