HDFStore Term memory efficient way to check for membership in list

Question

I have a pandas HDFStore that I am try to select from. I would like to select data between a two timestamps with an id in a large np.array. The following code works but takes up too much memory only when queried for membership in a list. If I use a datetimeindex and a range, the memory footprint is 95% less.

#start_ts, end_ts are timestamps
#instruments is an array of python objects

not_memory_efficient = adj_data.select("US", [Term("date",">=", start_ts),
                              Term("date", "<=", end_ts),
                              Term("id", "=", instruments)])
memory_efficient = adj_data.select("US", [Term("date",">=", start_ts),
                              Term("date", "<=", end_ts),)

Is there a more memory efficient way to do this in HDFStore? Should I set the index to the "sec_id"? (I can also use the chunksize option and concat myself, but that seems to be a bit of a hack.)

Edits:

The hdfstore is created by pd.HDFStore creating a dataframe and storing such as this. I made a mistake earlier

def write_data(country_data, store_file):
    for country in country_data:
        if len(country_data[country]) == 0:
            continue
        df = pd.concat(country_data[country], ignore_index=True)
        country_data[country] = []
        store_file.append(country, df, format="t")

As requested, here is the ptdump for this table: https://gist.github.com/MichaelWS/7980846 also, here is the df: https://gist.github.com/MichaelWS/7981451

Answer 1

To memorialize this for other users.

In HDFStore, is required to designate certain columns as data_columns if they are not the index in order to later query then.

Docs are here

Create a frame

In [23]: df = DataFrame(dict(date = pd.date_range('20130101',periods=10), id = list('abcabcabcd'), C = np.random.randn(10)))


In [28]: df
Out[28]: 
          C                date id
0  0.605701 2013-01-01 00:00:00  a
1  0.451346 2013-01-02 00:00:00  b
2  0.479483 2013-01-03 00:00:00  c
3 -0.012589 2013-01-04 00:00:00  a
4 -0.028552 2013-01-05 00:00:00  b
5  0.737100 2013-01-06 00:00:00  c
6 -1.050292 2013-01-07 00:00:00  a
7  0.137444 2013-01-08 00:00:00  b
8 -0.327491 2013-01-09 00:00:00  c
9 -0.660220 2013-01-10 00:00:00  d

[10 rows x 3 columns]

Save to hdf WITHOUT data_columns

In [24]: df.to_hdf('test.h5','df',mode='w',format='table')

0.13 will report this error (0.12 will just silently ignore)

In [25]: pd.read_hdf('test.h5','df',where='date>20130101 & date<20130105 & id=["b","c"]')
 ValueError: The passed where expression: date>20130101 & date<20130105 & id=["b","c"]
            contains an invalid variable reference
            all of the variable refrences must be a reference to
            an axis (e.g. 'index' or 'columns'), or a data_column
            The currently defined references are: index,columns

Set all the columns as data columns (can also be a specific list of columns)

In [26]: df.to_hdf('test.h5','df',mode='w',format='table',data_columns=True)

In [27]: pd.read_hdf('test.h5','df',where='date>20130101 & date<20130105 & id=["b","c"]')
Out[27]: 
          C                date id
1  0.451346 2013-01-02 00:00:00  b
2  0.479483 2013-01-03 00:00:00  c

[2 rows x 3 columns]

Here is a the Table node of ptdump -av of the file:

/df/table (Table(10,)) ''
  description := {
  "index": Int64Col(shape=(), dflt=0, pos=0),
  "C": Float64Col(shape=(), dflt=0.0, pos=1),
  "date": Int64Col(shape=(), dflt=0, pos=2),
  "id": StringCol(itemsize=1, shape=(), dflt='', pos=3)}
  byteorder := 'little'
  chunkshape := (2621,)
  autoindex := True
  colindexes := {
    "date": Index(6, medium, shuffle, zlib(1)).is_csi=False,
    "index": Index(6, medium, shuffle, zlib(1)).is_csi=False,
    "C": Index(6, medium, shuffle, zlib(1)).is_csi=False,
    "id": Index(6, medium, shuffle, zlib(1)).is_csi=False}
  /df/table._v_attrs (AttributeSet), 19 attributes:
   [CLASS := 'TABLE',
    C_dtype := 'float64',
    C_kind := ['C'],
    FIELD_0_FILL := 0,
    FIELD_0_NAME := 'index',
    FIELD_1_FILL := 0.0,
    FIELD_1_NAME := 'C',
    FIELD_2_FILL := 0,
    FIELD_2_NAME := 'date',
    FIELD_3_FILL := '',
    FIELD_3_NAME := 'id',
    NROWS := 10,
    TITLE := '',
    VERSION := '2.7',
    date_dtype := 'datetime64',
    date_kind := ['date'],
    id_dtype := 'string8',
    id_kind := ['id'],
    index_kind := 'integer']

The key thing to note is that the data_columns are separate in the 'description', AND they are setup as indexes.

Answer 2

You cannot supply a large list to be selected through and not have the entire pandas object loaded into memory. This is a limit in how numexpr operates.

pandas issue: https://github.com/pydata/pandas/issues/5717

pytables issue: http://sourceforge.net/mailarchive/message.php?msg_id=30390757