AlignedDyanmicTable does not support [int, str] type slicing #651
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oruebel
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Jul 21, 2021
Smplify interacting with DynamicTables that reference other tables via DynamicTableRegion, creating a collection of linked tables. In the ICEphys case this is a "simple" linear hierarchy of tables, but in principle a table may contain any number of DynamicTableRegion columns. This PR adds several functions to simplify introspection of linked DynamicTables and conversion to pandas DataFrames. - [X] Fix #646 by adding ``AlignedDynamicTable.get`` - [X] Fix #651 by updating ``AlignedDynamicTable.get`` to support slicing with ``[int, (str, str)]``, ``[int, str, str]``, and ``[int, str]`` to select a single cell or row of a category table, repectively - [X] Add ``AlignedDynamicTable.get_colnames(...)`` functions to allow us to keep compliance of the ``colnames`` property with ``DynamicTable`` while providing an easy way to get the full list of column names. - [X] Set name of DataFrame in ``DynamicTable.to_dataframe()`` and ``DynamicTable.get`` - [X] Add helper functions to ``DynamicTable`` to deal with foreign columns: - [X] ``DynamicTable.get_foreign_columns`` to identify if the table contains ``DynamicTableRegion`` columns - [X] ``DynamicTable.has_foreign_columns`` to identify which columns are``DynamicTableRegion`` columns - [X] ``DynamicTable.get_linked_tables`` to retrieve all tables linked to either directly or indirectly from the current table via ``DynamicTableRegion`` - [x] Implement the same helper functions also for ``AlignedDynamicTable`` - [x] ``DynamicTable.get_foreign_columns`` to identify if the table contains ``DynamicTableRegion`` columns - [X] ``DynamicTable.has_foreign_columns`` to identify which columns are``DynamicTableRegion`` columns - [x] ``DynamicTable.get_linked_tables`` to retrieve all tables linked to either directly or indirectly from the current table via ``DynamicTableRegion`` - [X] Add new module ``hdmf.common.hierarchicaltable`` with helper functions to facilitate conversion of linked tables to a single Pandas dataframe. - [X] ``to_hierarchical_dataframe`` to merge linked tables into a single consolidated pandas DataFrame. - [X] ``drop_id_columns`` to remove "id" columns from a DataFrame. - [X] ``flatten_column_index`` to replace a ``pandas.MultiIndex`` with a regular ``pandas.Index`` - [x] Add test for DyanmicTableRegion pointing to AlignedDynamicTable to check that the all columns are used - [x] Add tests for hierarchicaltable.py for - [X] to_hierarchical_dataframe - [x] drop_id_columns - [x] flatten_column_index functions - [X] File issue tickets for open TODO items for future PRs - [X] ``to_hierarchical_dataframe`` should be updated to support resolution of more than one DynamicTableRegion column. See #649 - [x] Add tutorial for DynamicTableRegion and how to use for linking to tables and for creating linked tables. See #648
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Description
DynamicTable
uses the syntaxdt[int, str](i.e.,dt[row_index, column_name]) to select a single cell from the table.AlignedDynamicTablehowever currently only supports slicing with tuples of strings to select whole tables or columns, e.g.at[category_name, columns_name]. To retrieve a single cell,AlignedDynamicTablecurrently requires that the row index be listed last, e.g.,at[category_name, columns_name, 0]For consistency withDynamicTable,AlignedDynamicTable`` should be updated to allow for selections of the form:[int, str](i.e.,[row_index, category_name]) to select a single row of a category table[int, (str, str)](i.e., [row_index, category_name, column_name]``) to select a single cell of the table.[int, str, str]should work the same as[int, (str, str)]Checklist
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