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PyMVPA: Python MultiVariate Pattern Analysis
Package mvpa :: Package misc :: Package io :: Module base :: Class ColumnData
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Class ColumnData

source code

Read data that is stored in columns of text files.

All read data is available via a dictionary-like interface. If column headers are available, the column names serve as dictionary keys. If no header exists an articfical key is generated: str(number_of_column).

Splitting of text file lines is performed by the standard split() function (which gets passed the sep argument as separator string) and each element is converted into the desired datatype.

Because data is read into a dictionary no two columns can have the same name in the header! Each column is stored as a list in the dictionary.

Instance Methods [hide private] 
new empty dictionary
__init__(self, source, header=True, sep=None, headersep=None, dtype=float, skiplines=0)
Read data from file into a dictionary.		 source code
 
_getAttrib(self, key)
Return corresponding value if given key is known to current instance		 source code
 
__str__(self)
str(x)		 source code
 
_check(self)
Performs some checks for data integrity.		 source code
 
_fromFile(self, filename, header, sep, headersep, dtype, skiplines)
Loads column data from file -- clears object first.		 source code
 
__iadd__(self, other)
Merge column data.		 source code
 
selectSamples(self, selection)
Return new ColumnData with selected samples		 source code
 
getNColumns(self)
Returns the number of columns.		 source code
 
tofile(self, filename, header=True, header_order=None, sep=' ')
Write column data to a text file.		 source code
 
getNRows(self)
Returns the number of rows.		 source code

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __getitem__, __gt__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __setitem__, __sizeof__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values, viewitems, viewkeys, viewvalues

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables [hide private]
  __doc__ = enhancedDocString('ColumnData', locals())
  ncolumns = property(fget= getNColumns)
  nrows = property(fget= getNRows)

Inherited from dict: __hash__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, source, header=True, sep=None, headersep=None, dtype=float, skiplines=0)
(Constructor)

source code 
Read data from file into a dictionary.
Parameters:
  • source (basestring or dict) - If values is given as a string all data is read from the file and additonal keyword arguments can be sued to customize the read procedure. If a dictionary is passed a deepcopy is performed.
  • header (bool or list of basestring) - Indicates whether the column names should be read from the first line (header=True). If header=False unique column names will be generated (see class docs). If header is a python list, it's content is used as column header names and its length has to match the number of columns in the file.
  • sep (basestring or None) - Separator string. The actual meaning depends on the output format (see class docs).
  • headersep (basestring or None) - Separator string used in the header. The actual meaning depends on the output format (see class docs).
  • dtype (type or list(types)) - Desired datatype(s). Datatype per column get be specified by passing a list of types.
  • skiplines (int) - Number of lines to skip at the beginning of the file.
Returns: 
new empty dictionary
Overrides: object.__init__

_getAttrib(self, key)

source code 

Return corresponding value if given key is known to current instance

Is used for automatically added properties to the class.

Returns:
Value if key is known

__str__(self)
(Informal representation operator)

source code 
str(x)
Overrides: object.__str__
(inherited documentation)

tofile(self, filename, header=True, header_order=None, sep=' ')

source code 
Write column data to a text file.
Parameters:
  • filename (basestring) - Target filename
  • header (bool) - If True a column header is written, using the column keys. If False no header is written.
  • header_order (None or list of basestring) - If it is a list of strings, they will be used instead of simply asking for the dictionary keys. However these strings must match the dictionary keys in number and identity. This argument type can be used to determine the order of the columns in the output file. The default value is None. In this case the columns will be in an arbitrary order.
  • sep (basestring) - String that is written as a separator between to data columns.

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PyMVPA: Python MultiVariate Pattern Analysis
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