[Scipy-svn] r4094 - trunk/scipy/io/arff
scipy-svn@scip...
scipy-svn@scip...
Mon Apr 7 14:10:16 CDT 2008
Author: cdavid
Date: 2008-04-07 14:10:10 -0500 (Mon, 07 Apr 2008)
New Revision: 4094
Added:
trunk/scipy/io/arff/arffread.py
Log:
Add arff reader implementation.
Added: trunk/scipy/io/arff/arffread.py
===================================================================
--- trunk/scipy/io/arff/arffread.py 2008-04-07 19:09:50 UTC (rev 4093)
+++ trunk/scipy/io/arff/arffread.py 2008-04-07 19:10:10 UTC (rev 4094)
@@ -0,0 +1,519 @@
+#! /usr/bin/env python
+# Last Change: Mon Aug 20 08:00 PM 2007 J
+import re
+import itertools
+import sys
+
+import numpy as N
+
+from scipy.io.arff.utils import partial
+
+"""A module to read arff files."""
+
+# An Arff file is basically two parts:
+# - header
+# - data
+#
+# A header has each of its components starting by @META where META is one of
+# the keyword (attribute of relation, for now).
+
+# TODO:
+# - both integer and reals are treated as numeric -> the integer info is lost !
+# - Replace ValueError by ParseError or something
+
+# We know can handle the following:
+# - numeric and nominal attributes
+# - missing values for numeric attributes
+
+r_meta = re.compile('^\s*@')
+# Match a comment
+r_comment = re.compile(r'^%')
+# Match an empty line
+r_empty = re.compile(r'^\s+$')
+# Match a header line, that is a line which starts by @ + a word
+r_headerline = re.compile(r'^@\S*')
+r_datameta = re.compile(r'^@[Dd][Aa][Tt][Aa]')
+r_relation = re.compile(r'^@[Rr][Ee][Ll][Aa][Tt][Ii][Oo][Nn]\s*(\S*)')
+r_attribute = re.compile(r'^@[Aa][Tt][Tt][Rr][Ii][Bb][Uu][Tt][Ee]\s*(..*$)')
+
+# To get attributes name enclosed with ''
+r_comattrval = re.compile(r"'(..+)'\s+(..+$)")
+# To get attributes name enclosed with '', possibly spread accross multilines
+r_mcomattrval = re.compile(r"'([..\n]+)'\s+(..+$)")
+# To get normal attributes
+r_wcomattrval = re.compile(r"(\S+)\s+(..+$)")
+
+#-------------------------
+# Module defined exception
+#-------------------------
+class ArffError(IOError):
+ pass
+
+class ParseArffError(ArffError):
+ pass
+
+#------------------
+# Various utilities
+#------------------
+
+# An attribute is defined as @attribute name value
+def parse_type(attrtype):
+ """Given an arff attribute value (meta data), returns its type.
+
+ Expect the value to be a name."""
+ uattribute = attrtype.lower().strip()
+ if uattribute[0] == '{':
+ return 'nominal'
+ elif uattribute[:len('real')] == 'real':
+ return 'numeric'
+ elif uattribute[:len('integer')] == 'integer':
+ return 'numeric'
+ elif uattribute[:len('numeric')] == 'numeric':
+ return 'numeric'
+ elif uattribute[:len('string')] == 'string':
+ return 'string'
+ elif uattribute[:len('relational')] == 'relational':
+ return 'relational'
+ else:
+ raise ValueError("unknown attribute %s" % uattribute)
+
+
+def get_nominal(attribute):
+ """If attribute is nominal, returns a list of the values"""
+ return attribute.split(',')
+
+def read_data_list(ofile):
+ """Read each line of the iterable and put it in a list."""
+ data = [ofile.next()]
+ if data[0].strip()[0] == '{':
+ raise ValueError("This looks like a sparse ARFF: not supported yet")
+ data.extend([i for i in ofile])
+ return data
+
+def get_ndata(ofile):
+ """Read the whole file to get number of data attributes."""
+ data = [ofile.next()]
+ loc = 1
+ if data[0].strip()[0] == '{':
+ raise ValueError("This looks like a sparse ARFF: not supported yet")
+ for i in ofile:
+ loc += 1
+ return loc
+
+def maxnomlen(atrv):
+ """Given a string contening a nominal type definition, returns the string
+ len of the biggest component.
+
+ A nominal type is defined as seomthing framed between brace ({}).
+
+ Example: maxnomlen("{floup, bouga, fl, ratata}") returns 6 (the size of
+ ratata, the longest nominal value)."""
+ nomtp = get_nom_val(atrv)
+ return max(len(i) for i in nomtp)
+
+def get_nom_val(atrv):
+ """Given a string contening a nominal type, returns a tuple of the possible
+ values.
+
+ A nominal type is defined as something framed between brace ({}).
+
+ Example: get_nom_val("{floup, bouga, fl, ratata}") returns ("floup",
+ "bouga", "fl", "ratata")."""
+ r_nominal = re.compile('{(..+)}')
+ m = r_nominal.match(atrv)
+ if m:
+ return tuple(i.strip() for i in m.group(1).split(','))
+ else:
+ raise ValueError("This does not look like a nominal string")
+
+def go_data(ofile):
+ """Skip header.
+
+ the first next() call of the returned iterator will be the @data line"""
+ return itertools.dropwhile(lambda x : not r_datameta.match(x), ofile)
+
+#----------------
+# Parsing header
+#----------------
+def tokenize_attribute(iterable, attribute):
+ """Parse a raw string in header (eg starts by @attribute).
+
+ Given a raw string attribute, try to get the name and type of the
+ attribute. Constraints:
+ - The first line must start with @attribute (case insensitive, and
+ space like characters begore @attribute are allowed)
+ - Works also if the attribute is spread on multilines.
+ - Works if empty lines or comments are in between
+
+ :Parameters:
+ attribute : str
+ the attribute string.
+
+ :Returns:
+ name : str
+ name of the attribute
+ value : str
+ value of the attribute
+ next : str
+ next line to be parsed
+
+ Example:
+ - if attribute is a string defined in python as r"floupi real", will
+ return floupi as name, and real as value.
+ - if attribute is r"'floupi 2' real", will return 'floupi 2' as name,
+ and real as value. """
+ sattr = attribute.strip()
+ mattr = r_attribute.match(sattr)
+ if mattr:
+ # atrv is everything after @attribute
+ atrv = mattr.group(1)
+ if r_comattrval.match(atrv):
+ name, type = tokenize_single_comma(atrv)
+ next = iterable.next()
+ elif r_wcomattrval.match(atrv):
+ name, type = tokenize_single_wcomma(atrv)
+ next = iterable.next()
+ else:
+ # Not sure we should support this, as it does not seem supported by
+ # weka.
+ raise ValueError("multi line not supported yet")
+ #name, type, next = tokenize_multilines(iterable, atrv)
+ else:
+ raise ValueError("First line unparsable: %s" % sattr)
+
+ if type == 'relational':
+ raise ValueError("relational attributes not supported yet")
+ return name, type, next
+
+def tokenize_multilines(iterable, val):
+ """Can tokenize an attribute spread over several lines."""
+ # If one line does not match, read all the following lines up to next
+ # line with meta character, and try to parse everything up to there.
+ if not r_mcomattrval.match(val):
+ all = [val]
+ i = iterable.next()
+ while not r_meta.match(i):
+ all.append(i)
+ i = iterable.next()
+ if r_mend.search(i):
+ raise ValueError("relational attribute not supported yet")
+ print "".join(all[:-1])
+ m = r_comattrval.match("".join(all[:-1]))
+ return m.group(1), m.group(2), i
+ else:
+ raise ValueError("Cannot parse attribute names spread over multi "\
+ "lines yet")
+
+def tokenize_single_comma(val):
+ # XXX we match twice the same string (here and at the caller level). It is
+ # stupid, but it is easier for now...
+ m = r_comattrval.match(val)
+ if m:
+ try:
+ name = m.group(1).strip()
+ type = m.group(2).strip()
+ except IndexError:
+ raise ValueError("Error while tokenizing attribute")
+ else:
+ raise ValueError("Error while tokenizing single %s" % val)
+ return name, type
+
+def tokenize_single_wcomma(val):
+ # XXX we match twice the same string (here and at the caller level). It is
+ # stupid, but it is easier for now...
+ m = r_wcomattrval.match(val)
+ if m:
+ try:
+ name = m.group(1).strip()
+ type = m.group(2).strip()
+ except IndexError:
+ raise ValueError("Error while tokenizing attribute")
+ else:
+ raise ValueError("Error while tokenizing single %s" % val)
+ return name, type
+
+def read_header(ofile):
+ """Read the header of the iterable ofile."""
+ i = ofile.next()
+
+ # Pass first comments
+ while r_comment.match(i):
+ i = ofile.next()
+
+ # Header is everything up to DATA attribute ?
+ relation = None
+ attributes = []
+ while not r_datameta.match(i):
+ m = r_headerline.match(i)
+ if m:
+ isattr = r_attribute.match(i)
+ if isattr:
+ name, type, i = tokenize_attribute(ofile, i)
+ attributes.append((name, type))
+ else:
+ isrel = r_relation.match(i)
+ if isrel:
+ relation = isrel.group(1)
+ else:
+ raise ValueError("Error parsing line %s" % i)
+ i = ofile.next()
+ else:
+ i = ofile.next()
+
+ return relation, attributes
+
+#--------------------
+# Parsing actual data
+#--------------------
+def safe_float(x):
+ """given a string x, convert it to a float. If the stripped string is a ?,
+ return a Nan (missing value)."""
+ if x.strip() == '?':
+ return N.nan
+ else:
+ return N.float(x)
+
+def safe_nominal(value, pvalue):
+ svalue = value.strip()
+ if svalue in pvalue:
+ return svalue
+ elif svalue == '?':
+ return svalue
+ else:
+ raise ValueError("%s value not in %s" % (str(svalue), str(pvalue)))
+
+def get_delim(line):
+ """Given a string representing a line of data, check whether the
+ delimiter is ',' or space."""
+ l = line.split(',')
+ if len(l) > 1:
+ return ','
+ else:
+ l = line.split(' ')
+ if len(l) > 1:
+ return ' '
+ else:
+ raise ValueError("delimiter not understood: " + line)
+
+class MetaData:
+ """Small container to keep useful informations on a ARFF dataset.
+
+ Also maintains the list of attributes in order, i.e. doing for i in meta,
+ where meta is an instance of MetaData, will return the different attribute
+ names in the order they were defined."""
+ def __init__(self, rel, attr):
+ self.name = rel
+ # We need the dictionary to be ordered
+ # XXX: may be better to implement an ordered dictionary
+ self._attributes = {}
+ self._attrnames = []
+ for name, value in attr:
+ tp = parse_type(value)
+ self._attrnames.append(name)
+ if tp == 'nominal':
+ self._attributes[name] = (tp, get_nom_val(value))
+ else:
+ self._attributes[name] = (tp, None)
+
+ def __repr__(self):
+ msg = ""
+ msg += "Dataset: %s\n" % self.name
+ for i in self._attrnames:
+ msg += "\t%s's type is %s" % (i, self._attributes[i][0])
+ if self._attributes[i][1]:
+ msg += ", range is %s" % str(self._attributes[i][1])
+ msg += '\n'
+ return msg
+
+ def __iter__(self):
+ return iter(self._attrnames)
+
+ def __getitem__(self, key):
+ return self._attributes[key]
+
+def read_arff(filename):
+ ofile = open(filename)
+
+ # Parse the header file
+ try:
+ rel, attr = read_header(ofile)
+ except ValueError, e:
+ msg = "Error while parsing header, error was: " + str(e)
+ raise ParseArffError(msg)
+
+ # Check whether we have a string attribute (not supported yet)
+ hasstr = False
+ for name, value in attr:
+ type = parse_type(value)
+ if type == 'string':
+ hasstr = True
+
+ meta = MetaData(rel, attr)
+
+ # XXX The following code is not great
+ # Build the type descriptor descr and the list of convertors to convert
+ # each attribute to the suitable type (which should match the one in
+ # descr).
+
+ # This can be used once we want to support integer as integer values and
+ # not as numeric anymore (using masked arrays ?).
+ acls2dtype = {'real' : N.float, 'integer' : N.float, 'numeric' : N.float}
+ acls2conv = {'real' : safe_float, 'integer' : safe_float, 'numeric' : safe_float}
+ descr = []
+ convertors = []
+ if not hasstr:
+ for name, value in attr:
+ type = parse_type(value)
+ if type == 'date':
+ raise ValueError("date type not supported yet, sorry")
+ elif type == 'nominal':
+ n = maxnomlen(value)
+ descr.append((name, 'S%d' % n))
+ pvalue = get_nom_val(value)
+ convertors.append(partial(safe_nominal, pvalue = pvalue))
+ else:
+ descr.append((name, acls2dtype[type]))
+ convertors.append(safe_float)
+ #dc.append(acls2conv[type])
+ #sdescr.append((name, acls2sdtype[type]))
+ else:
+ # How to support string efficiently ? Ideally, we should know the max
+ # size of the string before allocating the numpy array.
+ raise NotImplementedError("String attributes not supported yet, sorry")
+
+ ni = len(convertors)
+
+ # Get the delimiter from the first line of data:
+ def next_data_line(row_iter):
+ """Assumes we are already in the data part (eg after @data)."""
+ raw = row_iter.next()
+ while r_empty.match(raw):
+ raw = row_iter.next()
+ while r_comment.match(raw):
+ raw = row_iter.next()
+ return raw
+
+ try:
+ dtline = next_data_line(ofile)
+ delim = get_delim(dtline)
+ except ValueError, e:
+ raise ParseArffError("Error while parsing delimiter: " + str(e))
+ finally:
+ ofile.seek(0, 0)
+ ofile = go_data(ofile)
+ # skip the @data line
+ ofile.next()
+
+ def generator(row_iter, delim = ','):
+ # TODO: this is where we are spending times (~80%). I think things
+ # could be made more efficiently:
+ # - We could for example "compile" the function, because some values
+ # do not change here.
+ # - The function to convert a line to dtyped values could also be
+ # generated on the fly from a string and be executed instead of
+ # looping.
+ # - The regex are overkill: for comments, checking that a line starts
+ # by % should be enough and faster, and for empty lines, same thing
+ # --> this does not seem to change anything.
+
+ # We do not abstract skipping comments and empty lines for performances
+ # reason.
+ raw = row_iter.next()
+ while r_empty.match(raw):
+ raw = row_iter.next()
+ while r_comment.match(raw):
+ raw = row_iter.next()
+
+ row = raw.split(delim)
+ yield tuple([convertors[i](row[i]) for i in range(ni)])
+ for raw in row_iter:
+ while r_comment.match(raw):
+ raw = row_iter.next()
+ while r_empty.match(raw):
+ raw = row_iter.next()
+ row = raw.split(delim)
+ yield tuple([convertors[i](row[i]) for i in range(ni)])
+
+ a = generator(ofile, delim = delim)
+ # No error should happen here: it is a bug otherwise
+ data = N.fromiter(a, descr)
+ return data, meta
+
+#-----
+# Misc
+#-----
+def basic_stats(data):
+ nbfac = data.size * 1. / (data.size - 1)
+ return N.nanmin(data), N.nanmax(data), N.mean(data), N.std(data) * nbfac
+
+def print_attribute(name, tp, data):
+ type = tp[0]
+ if type == 'numeric' or type == 'real' or type == 'integer':
+ min, max, mean, std = basic_stats(data)
+ print "%s,%s,%f,%f,%f,%f" % (name, type, min, max, mean, std)
+ else:
+ msg = name + ",{"
+ for i in range(len(tp[1])-1):
+ msg += tp[1][i] + ","
+ msg += tp[1][-1]
+ msg += "}"
+ print msg
+
+def test_weka(filename):
+ data, meta = read_arff(filename)
+ print len(data.dtype)
+ print data.size
+ for i in meta:
+ print_attribute(i,meta[i],data[i])
+
+def floupi(filename):
+ data, meta = read_arff(filename)
+ from attrselect import print_dataset_info
+ print_dataset_info(data)
+ print "relation %s, has %d instances" % (meta.name, data.size)
+ itp = iter(types)
+ for i in data.dtype.names:
+ print_attribute(i,itp.next(),data[i])
+ #tp = itp.next()
+ #if tp == 'numeric' or tp == 'real' or tp == 'integer':
+ # min, max, mean, std = basic_stats(data[i])
+ # print "\tinstance %s: min %f, max %f, mean %f, std %f" % \
+ # (i, min, max, mean, std)
+ #else:
+ # print "\tinstance %s is non numeric" % i
+
+if __name__ == '__main__':
+ #import glob
+ #for i in glob.glob('arff.bak/data/*'):
+ # relation, attributes = read_header(open(i))
+ # print "Parsing header of %s: relation %s, %d attributes" % (i,
+ # relation, len(attributes))
+
+ import sys
+ filename = sys.argv[1]
+ #filename = 'arff.bak/data/pharynx.arff'
+ #floupi(filename)
+ test_weka(filename)
+
+ #gf = []
+ #wf = []
+ #for i in glob.glob('arff.bak/data/*'):
+ # try:
+ # print "=============== reading %s ======================" % i
+ # floupi(i)
+ # gf.append(i)
+ # except ValueError, e:
+ # print "!!!! Error parsing the file !!!!!"
+ # print e
+ # wf.append(i)
+ # except IndexError, e:
+ # print "!!!! Error parsing the file !!!!!"
+ # print e
+ # wf.append(i)
+ # except ArffError, e:
+ # print "!!!! Error parsing the file !!!!!"
+ # print e
+ # wf.append(i)
+
+ #print "%d good files" % len(gf)
+ #print "%d bad files" % len(wf)
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