Downloading SciDBArrays

It is often advantageous to convert small arrays into “normal” python data structures, for further analysis in python. SciDB-Py provides several conversion routines:

SciDB supports a wide variety of data types and array schemas, including several concepts that don’t have obvious analogs in NumPy. These include:

  • Nonzero array origins
  • Unbounded array dimensions
  • Null values for all datatypes (including integers)

The exact shape and datatype of the result of SciDBArray.toarray() depends on these details. Below we outline the various possibilities, starting with the easiest cases.

Single attribute, non-sparse, non-nullable array

An array with a single non-nullable attribute is converted into a NumPy array of equivalent datatype:

SciDB datatype NumPy datatype (typecode)
bool bool (‘<b1’)
int8 int8 (‘<b’)
uint8 uint8 (‘<B’)
int16 int16 (‘<h’)
uint16 uint16 (‘<H’)
int32 int32 (‘<i’)
uint32 uint32 (‘<I’)
int64 int64 (‘<l’)
uint64 uint64 (‘<L’)
float float32 (‘<float32’)
double double (‘<d’)
char S1 (‘c’)
datetime datetime64 (‘<M8[s]’)
datetimetz datetime64 (‘<M8[s]’)
string object

Note that strings are converted into python object arrays, since NumPy string arrrays are otherwise required to have the same string length in each element

Single attribute, nullable array

NumPy does not support the notion of missing values for datatypes like integers and boolean. Thus, when downloading an array with a nullable attribute, these datatypes are “promoted” to a datatype with a dedicated missing value holder:

SciDB datatype Null-promoted datatype
bool double
int8 double
uint8 double
int16 double
uint16 double
int32 double
uint32 double
int64 double
uint64 double
float float32
double double
char S1 (‘c’)
datetime datetime64 (‘<M8[s]’)
datetimetz datetime64 (‘<M8[s]’)
string object

In the NumPy array, each masked element is assigned the default null value for its datatype:

NumPy Datatype Default masked value
float, double NaN
char '\0'
object None
datetime NaT

Another way to deal with missing values is to substitute a manually-defined missing value. This converts the array to a non-nullable array:

>>> from scidbpy import connect
>>> sdb = connect()

>>> x ='<a:int8 NULL>[i=0:5,10,0]', 'iif(i>0, i, null)')
>>> x.toarray()
array([ nan,   1.,   2.,   3.,   4.,   5.])

>>> x.substitute(-1).toarray()
array([-1,  1,  2,  3,  4,  5], dtype=int8)

SciDB allows several different “missing-data” codes to be assigned to a masked cell. At the moment SciDB-Py doesn’t distinguish between these: either a cell has data, or it is considered masked.

Arrays with empty cells

In addition to masked values, SciDBArrays can have empty cells. These cells are treated as zero-valued when converting to a NumPy array. The zero-value for non-numeric datatypes is determined from the NumPy.zeros function:

>>> x ='<a:int8>[i=0:3,10,0]', 10)
>>> x = x.redimension('<a:int8>[i=0:5,10,0]')
>>> x.toarray()
array([10, 10, 10, 10,  0,  0], dtype=int8)

>>> x ='<a:char>[i=0:3,10,0]', "'a'")
>>> x = x.redimension('<a:char>[i=0:5,10,0]')
>>> x.toarray()
array(['a', 'a', 'a', 'a', '', ''], dtype='|S1')

Nonzero Origins

SciDBArray.toarray() shifts any non-zero origin to the 0-position in the NumPy array:

>>> x ='<a:int8>[i=5:10,10,0]', 'i')
>>> x.toarray()
array([ 5,  6,  7,  8,  9, 10], dtype=int8)

The original array indices can be extracted using the unpack operator:

>>> x.unpack('_idx').toarray()
array([(5, 5), (6, 6), (7, 7), (8, 8), (9, 9), (10, 10)],
       dtype=[('i', '<i8'), ('a', 'i1')])

Unbound Arrays

When a SciDBArray is unbound, the resulting NumPy array is truncated to the region containing data.

Multiattribute arrays

Arrays with multiple attributes are handled analogously to single-attribute arrays as discussed above. However, the output is returned as a NumPy record array, with record labels matching the SciDB attribute labels.

Efficient Transfer for Dense Arrays

SciDB arrays are internally sparse. To preserve the location of nonempty cells when downloading, SciDB-Py has to explicitly transfer the multidimensional index of each nonempty cell, along with the values of that cell. This adds processing and bandwidth overhead.

SciDB-Py v14.10 introduced a new dense transfer option for more efficient downloading of arrays with no empty cells. If you specify method=dense to methods like toarray(), SciDB-Py will avoid transferring indices.

It is up to the user to set method=dense, as well as to verify that the array is fully dense (has no empty cells).


``method=dense’’ is an experimental feature of SciDB-Py v14.10. Please report any bugs.

Compressed Transfer

Starting in v14.10, SciDB-Py has experimental support for gzipped-compressed transfer. This requires a version of Shim more recent than Nov 3, 2014.

To explicitly enable compression for a particular transfer, specify compression=1-9 in a method like toarray(). compression=1 corresponds to fast compression, ``compression=9’’ corresponds to best compression.

To implicitly enable compression for all transfers, set the default_compression attribute of the SciDBInterface to 1-9:

sdb.default_compression = 1
sdb.zeros(10).toarray()  # implicitly uses toarray(compression=1)