The SciDB Query Interface

scidbpy provides python wrappers for many useful SciDB operations, but the SciDB AFL query language can provide even more customization of operations (For more information on SciDB’s AFL and AQL languages, see the SciDB Manual). The query() function provides a useful interface for generating raw queries by exploiting Python’s String Formatting syntax. Through automatic insertion of the server-side identifiers of SciDB arrays, attributes, and dimensions, the query interface makes constructing complicated queries very convenient.

The general approach first creates a new SciDBArray object and then issues a query to populate data. For example, to build an array of zeros similar to the result of the zeros() function shown above, the query can be constructed in the following way:

>>> # first define an empty array to hold the result
>>> zeros = sdb.new_array(shape=(5, 5), dtype='double')
>>> # now execute a query to fill the array
>>> sdb.query('store(build({A}, 0), {A})', A=zeros)
>>> zeros.toarray()
array([[ 0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.]])

The result is that zeros is a 10x10 array filled with zeros. Here the format statement {A} is replaced by the name of the desired array on the SciDB server.

We can use this interface to quickly build more complex arrays. For example, to create an identity matrix similar to the result of the identity() function shown above, we add a boolean check:

>>> ident = sdb.new_array((5, 5), dtype='double')
>>> sdb.query('store(build({A}, iif({A.d0}={A.d1}, 1, 0)), {A})',
...           A=ident)
>>> ident.toarray()
array([[ 1.,  0.,  0.,  0.,  0.],
       [ 0.,  1.,  0.,  0.,  0.],
       [ 0.,  0.,  1.,  0.,  0.],
       [ 0.,  0.,  0.,  1.,  0.],
       [ 0.,  0.,  0.,  0.,  1.]])

Here the substitutions {A.d0} and {A.d1} are replaced by the first and second dimension names of the array referenced by A.

Things can become even more complicated. The following example creates a 5x5 tridiagonal array, similar to the one used in the above examples:

>>> tridiag = sdb.new_array((5, 5))
>>> sdb.query('store(build({A}, \
...               iif({A.d0}={A.d1}, 2, iif({A.d0} <= {A.d1}+1 and {A.d0} >= {A.d1}-1, -1, 0))), {A})', A=tridiag)
>>> tridiag.toarray()
array([[ 2., -1.,  0.,  0.,  0.],
       [-1.,  2., -1.,  0.,  0.],
       [ 0., -1.,  2., -1.,  0.],
       [ 0.,  0., -1.,  2., -1.],
       [ 0.,  0.,  0., -1.,  2.]])

The query builds a tridiagonal array with 2 on the diagonal and -1 on the sub- and super-diagonals. This shows how the query-formatting syntax provided by the scidbpy package can be used to generate extremely powerful AFL queries.

The full replacement syntax is outlined in the documentation of the query() function. It is a useful way to help streamline the process of writing SciDB queries if and when it becomes necessary.

Working with the Array Functional Language

In addtion to the SciDBArray class and query interface, SciDB-Py provides a direct binding to SciDB’s Array Functional Language, or AFL.

The AFL consists of approximately 100 functions to perform array analysis. You can access these operators through the afl attribute of a SciDB instance. More information on these operators can be found on the SciDB documentation.

AFL operators accept and return SciDBArray objects, and thus can be used interchangeably with methods on the SciDBArray class itself.

Usage Example

>>> from scidbpy import connect
>>> sdb = connect()
>>> x = sdb.random((3, 4))
>>> afl =
>>> # the number of elements greater than 0.5
>>> cts = afl.aggregate(afl.filter(x, 'f0 > 0.5'), 'count(*)')
>>> cts.query
'aggregate(filter(py1100918363281_00001,f0 > 0.5),count(*))'
>>> cts.toarray()
array([8], dtype=uint64)

Note that each AFL operator includes documentation from the official SciDB manual:

In [37]: afl.filter?
Type:        function
String form: <function filter at 0x104eb1c08>
File:        /Users/beaumont/scidbpy/scidbpy/
Definition:  afl.filter(*args)
filter( srcArray, expression )

Produces a result array by filtering out (mark as empty) the cells in the source array     for which the expression evaluates to False.


    - srcArray: a source array with srcAttrs and srcDims.
    - expression: an expression which takes a cell in the source array
      as input and evaluates to either True or False.


Some AFL functions, like list(), expect single-quoted strings as input. These quotes must be explicitly provided (e.g. afl.list("'arrays'")).

Chaining AFL Operators

Many SciDB queries involve nesting several AFL calls, with the result of an inner call included as the first argument of an outer call. For example:

afl.filter(afl.project(afl.apply(x, 'y', 'f0+1'), 'y'), 'y > 3')

SciDB-py includes some syntactic sugar for building queries like this: for AFL operators whose names don’t collide with another SciDBArray method, x.operator(...) is equivalent to afl.operator(x, ...). Thus, the above query can be re-written as:

x.apply('y', 'f0+1').project('y').filter('y > 3')

These two syntaxes are equivalent.


This syntax only applies to AFL operators that don’t collide with a SciDBArray method name.