316 lines
11 KiB
Python
316 lines
11 KiB
Python
# -*- coding: UTF-8 no BOM -*-
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# $Id$
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class ASCIItable():
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'''
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There should be a doc string here :)
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'''
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import sys,numpy
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__slots__ = ['__IO__',
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'info',
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'labels',
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'data',
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]
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# ------------------------------------------------------------------
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def __init__(self,
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fileIn = sys.stdin,
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fileOut = sys.stdout,
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buffered = False, # flush writes
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labels = True): # assume table has labels
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self.__IO__ = {'in': fileIn,
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'out':fileOut,
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'output':[],
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'buffered':buffered,
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'labels':labels,
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'validReadSize': 0,
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'readBuffer': [], # buffer to hold non-advancing reads
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'dataStart': 0,
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}
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self.info = []
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self.labels = []
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self.data = []
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# ------------------------------------------------------------------
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def _transliterateToFloat(self,x):
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try:
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return float(x)
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except:
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return 0.0
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# ------------------------------------------------------------------
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def output_write(self,
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what):
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'''
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aggregate a single row (string) or list of (possibly containing further lists of) rows into output
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'''
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if not isinstance(what, (str, unicode)):
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try:
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for item in what: self.output_write(item)
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except:
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self.__IO__['output'] += [str(what)]
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else:
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self.__IO__['output'] += [what]
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return self.__IO__['buffered'] or self.output_flush()
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# ------------------------------------------------------------------
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def output_flush(self,
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clear = True):
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import sys
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try:
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self.__IO__['output'] == [] or self.__IO__['out'].write('\n'.join(self.__IO__['output']) + '\n')
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except(IOError) as e:
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return False
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if clear: self.output_clear()
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return True
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# ------------------------------------------------------------------
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def output_clear(self):
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self.__IO__['output'] = []
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# ------------------------------------------------------------------
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def head_read(self):
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'''
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get column labels by either read the first row, or
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--if keyword "head[*]" is present-- the last line of the header
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'''
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import re
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try:
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self.__IO__['in'].seek(0)
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except:
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pass
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firstline = self.__IO__['in'].readline()
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m = re.search('(\d+)\s*head', firstline.lower())
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if self.__IO__['labels']: # table features labels
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if m: # found header info
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self.info = [self.__IO__['in'].readline().strip() for i in xrange(1,int(m.group(1)))]
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self.labels = self.__IO__['in'].readline().split()
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else: # no header info (but labels)
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self.labels = firstline.split()
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self.__IO__['validReadSize'] = len(self.labels)
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else: # no labels present in table
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if m: # found header info
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self.info = [self.__IO__['in'].readline().strip() for i in xrange(0,int(m.group(1)))] # all header is info
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# ... without any labels
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try:
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self.__IO__['dataStart'] = self.__IO__['in'].tell() # current file position is at start of data
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except(IOError):
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pass
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if self.__IO__['validReadSize'] == 0: # in case no valid data length is known
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self.data_read(advance = False)
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self.__IO__['validReadSize'] = len(self.data) # assume constant data width from first line
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# ------------------------------------------------------------------
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def head_write(self):
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'''
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write current header information (info + labels)
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'''
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if self.__IO__['labels']:
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return self.output_write ([
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'%i\theader'%(len(self.info)+1),
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self.info,
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'\t'.join(self.labels),
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])
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else:
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return self.output_write ([
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'%i\theader'%(len(self.info)),
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self.info,
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])
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# ------------------------------------------------------------------
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def labels_append(self,
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what):
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'''
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add item or list to existing set of labels (and switch on labeling)
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'''
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if not isinstance(what, (str, unicode)):
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try:
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for item in what: self.labels_append(item)
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except:
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self.labels += [str(what)]
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else:
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self.labels += [what]
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self.__IO__['labels'] = True # switch on processing (in particular writing) of labels
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# ------------------------------------------------------------------
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def labels_clear(self):
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'''
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delete existing labels and switch to no labeling
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'''
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self.labels = []
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self.__IO__['labels'] = False
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# ------------------------------------------------------------------
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def labels_index(self,
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labels):
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'''
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tell index of column label(s)
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'''
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if isinstance(labels,list):
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idx = []
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for label in labels:
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try:
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idx.append(label+0)
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except TypeError:
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try:
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idx.append(self.labels.index(label))
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except ValueError:
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idx.append(-1)
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else:
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try:
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idx = labels+0
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except TypeError:
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try:
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idx = self.labels.index(labels)
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except(ValueError):
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idx = -1
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return idx
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# ------------------------------------------------------------------
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def info_append(self,
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what):
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'''
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add item or list to existing set of infos
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'''
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if not isinstance(what, (str, unicode)):
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try:
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for item in what: self.info_append(item)
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except:
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self.info += [str(what)]
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else:
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self.info += [what]
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# ------------------------------------------------------------------
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def info_clear(self):
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'''
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delete any info block
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'''
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self.info = []
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# ------------------------------------------------------------------
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def data_rewind(self):
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self.__IO__['in'].seek(self.__IO__['dataStart']) # position file to start of data section
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self.__IO__['readBuffer'] = [] # delete any non-advancing data reads
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# ------------------------------------------------------------------
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def data_skipLines(self,count):
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'''
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wind forward by count number of lines
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'''
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for i in xrange(count):
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alive = self.data_read()
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return alive
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# ------------------------------------------------------------------
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def data_read(self,advance = True):
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'''
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read next line (possibly buffered) and parse it into data array
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'''
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if len(self.__IO__['readBuffer']) > 0:
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line = self.__IO__['readBuffer'].pop(0) # take buffered content
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else:
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line = self.__IO__['in'].readline() # get next data row from file
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if not advance:
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self.__IO__['readBuffer'].append(line) # keep line just read in buffer
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if self.__IO__['labels']:
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items = line.split()[:self.__IO__['validReadSize']] # use up to valid size (label count)
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self.data = items if len(items) == self.__IO__['validReadSize'] else [] # take if correct number of entries
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else:
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self.data = line.split() # take all
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return self.data != []
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# ------------------------------------------------------------------
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def data_readLine(self,line):
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'''
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seek beginning of data and wind forward to selected line
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'''
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self.__IO__['in'].seek(self.__IO__['dataStart'])
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for i in xrange(line-1):
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self.__IO__['in'].readline()
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self.data_read()
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# ------------------------------------------------------------------
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def data_readArray(self,
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labels = []):
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import numpy
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'''
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read whole data of all (given) labels as numpy array
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'''
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if labels == []: indices = range(self.__IO__['validReadSize']) # use all columns
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else: indices = self.labels_index(labels) # use specified columns
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try:
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self.data_rewind() # try to wind back to start of data
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except:
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pass # assume/hope we are at data start already...
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self.data = numpy.loadtxt(self.__IO__['in'], usecols=indices)
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if len(self.data.shape) < 2: # single column
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self.data = self.data.reshape(self.data.shape[0],1)
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return self.data.shape
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# ------------------------------------------------------------------
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def data_write(self,delimiter = '\t'):
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'''
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write current data array and report alive output back
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'''
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if len(self.data) == 0: return True
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if isinstance(self.data[0],list):
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return self.output_write([delimiter.join(map(str,items)) for items in self.data])
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else:
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return self.output_write(delimiter.join(map(str,self.data)))
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# ------------------------------------------------------------------
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def data_writeArray(self,format = '%g',delimiter = '\t'):
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import numpy
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'''
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write whole numpy array data
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'''
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return numpy.savetxt(self.__IO__['out'],self.data,fmt = format,delimiter = delimiter)
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# ------------------------------------------------------------------
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def data_append(self,
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what):
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if not isinstance(what, (str, unicode)):
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try:
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for item in what: self.data_append(item)
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except:
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self.data += [str(what)]
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else:
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self.data += [what]
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# ------------------------------------------------------------------
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def data_set(self,
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what,where):
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idx = -1
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try:
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idx = self.labels.index(where)
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if len(self.data) <= idx:
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self.data_append(['n/a' for i in xrange(idx+1-len(self.data))]) # grow data if too short
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self.data[idx] = str(what)
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except(ValueError):
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pass
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return idx
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# ------------------------------------------------------------------
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def data_clear(self):
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self.data = []
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# ------------------------------------------------------------------
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def data_asFloat(self):
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return map(self._transliterateToFloat,self.data)
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