parquetTable.py

Go to the documentation of this file.

# This file is part of pipe_tasks.
#
# Developed for the LSST Data Management System.
# This product includes software developed by the LSST Project
# (http://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.
"""
Implementation of thin wrappers to pyarrow.ParquetFile.
"""
 
import re
import json
from itertools import product
import pyarrow
import pyarrow.parquet
import numpy as np
import pandas as pd
 
 
class ParquetTable(object):
    """Thin wrapper to pyarrow's ParquetFile object
 
    Call `toDataFrame` method to get a `pandas.DataFrame` object,
    optionally passing specific columns.
 
    The main purpose of having this wrapper rather than directly
    using `pyarrow.ParquetFile` is to make it nicer to load
    selected subsets of columns, especially from dataframes with multi-level
    column indices.
 
    Instantiated with either a path to a parquet file or a dataFrame
 
    Parameters
    ----------
    filename : str, optional
        Path to Parquet file.
    dataFrame : dataFrame, optional
    """
 
    def __init__(self, filename=None, dataFrame=None):
        self.filenamefilename = filename
        if filename is not None:
            self._pf_pf = pyarrow.parquet.ParquetFile(filename)
            self._df_df = None
            self._pandasMd_pandasMd = None
        elif dataFrame is not None:
            self._df_df = dataFrame
            self._pf_pf = None
        else:
            raise ValueError("Either filename or dataFrame must be passed.")
 
        self._columns_columns = None
        self._columnIndex_columnIndex = None
 
    def write(self, filename):
        """Write pandas dataframe to parquet
 
        Parameters
        ----------
        filename : str
            Path to which to write.
        """
        if self._df_df is None:
            raise ValueError("df property must be defined to write.")
        table = pyarrow.Table.from_pandas(self._df_df)
        pyarrow.parquet.write_table(table, filename, compression="none")
 
    @property
    def pandasMd(self):
        if self._pf_pf is None:
            raise AttributeError("This property is only accessible if ._pf is set.")
        if self._pandasMd_pandasMd is None:
            self._pandasMd_pandasMd = json.loads(self._pf_pf.metadata.metadata[b"pandas"])
        return self._pandasMd_pandasMd
 
    @property
    def columnIndex(self):
        """Columns as a pandas Index
        """
        if self._columnIndex_columnIndex is None:
            self._columnIndex_columnIndex = self._getColumnIndex_getColumnIndex()
        return self._columnIndex_columnIndex
 
    def _getColumnIndex(self):
        if self._df_df is not None:
            return self._df_df.columns
        else:
            return pd.Index(self.columnscolumns)
 
    @property
    def columns(self):
        """List of column names (or column index if df is set)
 
        This may either be a list of column names, or a
        pandas.Index object describing the column index, depending
        on whether the ParquetTable object is wrapping a ParquetFile
        or a DataFrame.
        """
        if self._columns_columns is None:
            self._columns_columns = self._getColumns_getColumns()
        return self._columns_columns
 
    def _getColumns(self):
        if self._df_df is not None:
            return self._sanitizeColumns_sanitizeColumns(self._df_df.columns)
        else:
            return self._pf_pf.metadata.schema.names
 
    def _sanitizeColumns(self, columns):
        return [c for c in columns if c in self.columnIndexcolumnIndex]
 
    def toDataFrame(self, columns=None):
        """Get table (or specified columns) as a pandas DataFrame
 
        Parameters
        ----------
        columns : list, optional
            Desired columns.  If `None`, then all columns will be
            returned.
        """
        if self._pf_pf is None:
            if columns is None:
                return self._df_df
            else:
                return self._df_df[columns]
 
        if columns is None:
            return self._pf_pf.read().to_pandas()
 
        df = self._pf_pf.read(columns=columns, use_pandas_metadata=True).to_pandas()
        return df
 
 
class MultilevelParquetTable(ParquetTable):
    """Wrapper to access dataframe with multi-level column index from Parquet
 
    This subclass of `ParquetTable` to handle the multi-level is necessary
    because there is not a convenient way to request specific table subsets
    by level via Parquet through pyarrow, as there is with a `pandas.DataFrame`.
 
    Additionally, pyarrow stores multilevel index information in a very strange
    way. Pandas stores it as a tuple, so that one can access a single column
    from a pandas dataframe as `df[('ref', 'HSC-G', 'coord_ra')]`.  However, for
    some reason pyarrow saves these indices as "stringified" tuples, such that
    in order to read thissame column from a table written to Parquet, you would
    have to do the following:
 
        pf = pyarrow.ParquetFile(filename)
        df = pf.read(columns=["('ref', 'HSC-G', 'coord_ra')"])
 
    See also https://github.com/apache/arrow/issues/1771, where we've raised
    this issue.
 
    As multilevel-indexed dataframes can be very useful to store data like
    multiple filters' worth of data in the same table, this case deserves a
    wrapper to enable easier access;
    that's what this object is for.  For example,
 
        parq = MultilevelParquetTable(filename)
        columnDict = {'dataset':'meas',
                      'filter':'HSC-G',
                      'column':['coord_ra', 'coord_dec']}
        df = parq.toDataFrame(columns=columnDict)
 
    will return just the coordinate columns; the equivalent of calling
    `df['meas']['HSC-G'][['coord_ra', 'coord_dec']]` on the total dataframe,
    but without having to load the whole frame into memory---this reads just
    those columns from disk.  You can also request a sub-table; e.g.,
 
        parq = MultilevelParquetTable(filename)
        columnDict = {'dataset':'meas',
                      'filter':'HSC-G'}
        df = parq.toDataFrame(columns=columnDict)
 
    and this will be the equivalent of `df['meas']['HSC-G']` on the total dataframe.
 
    Parameters
    ----------
    filename : str, optional
        Path to Parquet file.
    dataFrame : dataFrame, optional
    """
 
    def __init__(self, *args, **kwargs):
        super(MultilevelParquetTable, self).__init__(*args, **kwargs)
 
        self._columnLevelNames_columnLevelNames = None
 
    @property
    def columnLevelNames(self):
        if self._columnLevelNames_columnLevelNames is None:
            self._columnLevelNames_columnLevelNames = {
                level: list(np.unique(np.array(self.columnscolumns)[:, i]))
                for i, level in enumerate(self.columnLevelscolumnLevels)
            }
        return self._columnLevelNames_columnLevelNames
 
    @property
    def columnLevels(self):
        """Names of levels in column index
        """
        return self.columnIndexcolumnIndex.names
 
    def _getColumnIndex(self):
        if self._df_df is not None:
            return super()._getColumnIndex()
        else:
            levelNames = [f["name"] for f in self.pandasMdpandasMd["column_indexes"]]
            return pd.MultiIndex.from_tuples(self.columnscolumns, names=levelNames)
 
    def _getColumns(self):
        if self._df_df is not None:
            return super()._getColumns()
        else:
            columns = self._pf_pf.metadata.schema.names
            n = len(self.pandasMdpandasMd["column_indexes"])
            pattern = re.compile(", ".join(["'(.*)'"] * n))
            matches = [re.search(pattern, c) for c in columns]
            return [m.groups() for m in matches if m is not None]
 
    def toDataFrame(self, columns=None, droplevels=True):
        """Get table (or specified columns) as a pandas DataFrame
 
        To get specific columns in specified sub-levels:
 
            parq = MultilevelParquetTable(filename)
            columnDict = {'dataset':'meas',
                      'filter':'HSC-G',
                      'column':['coord_ra', 'coord_dec']}
            df = parq.toDataFrame(columns=columnDict)
 
        Or, to get an entire subtable, leave out one level name:
 
            parq = MultilevelParquetTable(filename)
            columnDict = {'dataset':'meas',
                          'filter':'HSC-G'}
            df = parq.toDataFrame(columns=columnDict)
 
        Parameters
        ----------
        columns : list or dict, optional
            Desired columns.  If `None`, then all columns will be
            returned.  If a list, then the names of the columns must
            be *exactly* as stored by pyarrow; that is, stringified tuples.
            If a dictionary, then the entries of the dictionary must
            correspond to the level names of the column multi-index
            (that is, the `columnLevels` attribute).  Not every level
            must be passed; if any level is left out, then all entries
            in that level will be implicitly included.
        droplevels : bool
            If True drop levels of column index that have just one entry
 
        """
        if columns is None:
            if self._pf_pf is None:
                return self._df_df
            else:
                return self._pf_pf.read().to_pandas()
 
        if isinstance(columns, dict):
            columns = self._colsFromDict_colsFromDict(columns)
 
        if self._pf_pf is None:
            try:
                df = self._df_df[columns]
            except (AttributeError, KeyError):
                newColumns = [c for c in columns if c in self.columnIndexcolumnIndex]
                if not newColumns:
                    raise ValueError("None of the requested columns ({}) are available!".format(columns))
                df = self._df_df[newColumns]
        else:
            pfColumns = self._stringify_stringify(columns)
            try:
                df = self._pf_pf.read(columns=pfColumns, use_pandas_metadata=True).to_pandas()
            except (AttributeError, KeyError):
                newColumns = [c for c in columns if c in self.columnIndexcolumnIndex]
                if not newColumns:
                    raise ValueError("None of the requested columns ({}) are available!".format(columns))
                pfColumns = self._stringify_stringify(newColumns)
                df = self._pf_pf.read(columns=pfColumns, use_pandas_metadata=True).to_pandas()
 
        if droplevels:
            # Drop levels of column index that have just one entry
            levelsToDrop = [n for lev, n in zip(df.columns.levels, df.columns.names) if len(lev) == 1]
 
            # Prevent error when trying to drop *all* columns
            if len(levelsToDrop) == len(df.columns.names):
                levelsToDrop.remove(df.columns.names[-1])
 
            df.columns = df.columns.droplevel(levelsToDrop)
 
        return df
 
    def _colsFromDict(self, colDict):
        new_colDict = {}
        for i, lev in enumerate(self.columnLevelscolumnLevels):
            if lev in colDict:
                if isinstance(colDict[lev], str):
                    new_colDict[lev] = [colDict[lev]]
                else:
                    new_colDict[lev] = colDict[lev]
            else:
                new_colDict[lev] = self.columnIndexcolumnIndex.levels[i]
 
        levelCols = [new_colDict[lev] for lev in self.columnLevelscolumnLevels]
        cols = product(*levelCols)
        return list(cols)
 
    def _stringify(self, cols):
        return [str(c) for c in cols]