load.py 13.9 KB
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#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Andre Anjos <andre.anjos@idiap.ch>
# Mon 23 May 2011 16:23:05 CEST

"""A set of utilities to load score files with different formats.
"""

import numpy
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import tarfile
import os

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def open_file(filename, mode='rt'):
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  """open_file(filename) -> file_like

  Opens the given score file for reading.
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  Score files might be raw text files, or a tar-file including a single score file inside.

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  **Parameters:**
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  ``filename`` : str or file-like
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    The name of the score file to open, or a file-like object open for reading.
    If a file name is given, the according file might be a raw text file or a (compressed) tar file containing a raw text file.
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  **Returns:**

  ``file_like`` : file-like
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    A read-only file-like object as it would be returned by open().
  """
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  if not isinstance(filename, str) and hasattr(filename, 'read'):
    # It seems that this is an open file
    return filename

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  if not os.path.isfile(filename):
    raise IOError("Score file '%s' does not exist." % filename)
  if not tarfile.is_tarfile(filename):
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    return open(filename, mode)
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  # open the tar file for reading
  tar = tarfile.open(filename, 'r')
  # get the first file in the tar file
  tar_info = tar.next()
  while tar_info is not None and not tar_info.isfile():
    tar_info = tar.next()
  # check that one file was found in the archive
  if tar_info is None:
    raise IOError("The given file is a .tar file, but it does not contain any file.")

  # open the file for reading
  return tar.extractfile(tar_info)

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def four_column(filename):
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  """four_column(filename) -> claimed_id, real_id, test_label, score

  Loads a score set from a single file and yield its lines (to avoid loading the score file at once into memory).
  This function verifies that all fields are correctly placed and contain valid fields.
  The score file must contain the following information in each line:

    claimed_id real_id test_label score

  **Parametes:**

  ``filename`` : str or file-like
    The file object that will be opened with :py:func:`open_file` containing the scores.
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  **Yields:**
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  ``claimed_id`` : str
    The claimed identity -- the client name of the model that was used in the comparison
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  ``real_id`` : str
    The real identity -- the client name of the probe that was used in the comparison

  ``test_label`` : str
    A label of the probe -- usually the probe file name, or the probe id

  ``score`` : float
    The result of the comparison of the model and the probe
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  """

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  for i, l in enumerate(open_file(filename)):
    if isinstance(l, bytes): l = l.decode('utf-8')
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    s = l.strip()
    if len(s) == 0 or s[0] == '#': continue #empty or comment
    field = [k.strip() for k in s.split()]
    if len(field) < 4:
      raise SyntaxError('Line %d of file "%s" is invalid: %s' % (i, filename, l))
    try:
      score = float(field[3])
    except:
      raise SyntaxError('Cannot convert score to float at line %d of file "%s": %s' % (i, filename, l))
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    yield (field[0], field[1], field[2], score)
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def split_four_column(filename):
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  """split_four_column(filename) -> negatives, positives

  Loads a score set from a single file and splits the scores
  between negatives and positives. The score file has to respect the 4 column
  format as defined in the method :py:func:`four_column`.
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  This method avoids loading and allocating memory for the strings present in
  the file. We only keep the scores.

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  **Parameters:**

  ``filename`` : str or file-like
    The file that will be opened with :py:func:`open_file` containing the scores.
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  **Returns:**

  ``negatives`` : array_like(1D, float)
    The list of ``score``'s, for which the ``claimed_id`` and the ``real_id`` differed (see :py:func:`four_column`).

  ``positives`` : array_like(1D, float)
    The list of ``score``'s, for which the ``claimed_id`` and the ``real_id`` are identical (see :py:func:`four_column`).
  """
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  score_lines = load_score(filename, 4)
  return get_negatives_positives(score_lines)
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def cmc_four_column(filename):
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  """cmc_four_column(filename) -> cmc_scores
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  Loads scores to compute CMC curves from a file in four column format.
  The four column file needs to be in the same format as described in :py:func:`four_column`,
  and the ``test_label`` (column 3) has to contain the test/probe file name or a probe id.
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  This function returns a list of tuples.
  For each probe file, the tuple consists of a list of negative scores and a list of positive scores.
  Usually, the list of positive scores should contain only one element, but more are allowed.
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  The result of this function can directly be passed to, e.g., the :py:func:`bob.measure.cmc` function.
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  **Parameters:**

  ``filename`` : str or file-like
    The file that will be opened with :py:func:`open_file` containing the scores.

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  **Returns:**

  ``cmc_scores`` : [(array_like(1D, float), array_like(1D, float))]
    A list of tuples, where each tuple contains the ``negative`` and ``positive`` scores for one probe of the database
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  """
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  # extract positives and negatives
  pos_dict = {}
  neg_dict = {}
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  # read four column list  
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  for (client_id, probe_id, probe_name, score_str) in four_column(filename):
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    try:
      score = float(score_str)
      # check in which dict we have to put the score
      if client_id == probe_id:
        correct_dict = pos_dict
      else:
        correct_dict = neg_dict
      # append score
      if probe_name in correct_dict:
        correct_dict[probe_name].append(score)
      else:
        correct_dict[probe_name] = [score]
    except:
      raise SyntaxError("Cannot convert score '%s' to float" % score_str)

  # convert to lists of tuples of ndarrays
  retval = []
  import logging
  logger = logging.getLogger('bob')
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  for probe_name in sorted(pos_dict.keys()):
    if probe_name in neg_dict:
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      retval.append((numpy.array(neg_dict[probe_name], numpy.float64), numpy.array(pos_dict[probe_name], numpy.float64)))
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    else:
      logger.warn('For probe name "%s" there are only positive scores. This probe name is ignored.' % probe_name)

  #test if there are probes for which only negatives exist
  for probe_name in sorted(neg_dict.keys()):
    if not probe_name in pos_dict.keys():
      logger.warn('For probe name "%s" there are only negative scores. This probe name is ignored.' % probe_name)
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  return retval
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def five_column(filename):
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  """five_column(filename) -> claimed_id, model_label, real_id, test_label, score

  Loads a score set from a single file and yield its lines (to avoid loading the score file at once into memory).
  This function verifies that all fields are correctly placed and contain valid fields.
  The score file must contain the following information in each line:

    claimed_id model_label real_id test_label score

  **Parametes:**

  ``filename`` : str or file-like
    The file object that will be opened with :py:func:`open_file` containing the scores.

  **Yields:**

  ``claimed_id`` : str
    The claimed identity -- the client name of the model that was used in the comparison

  ``model_label`` : str
    A label for the model -- usually the model file name, or the model id

  ``real_id`` : str
    The real identity -- the client name of the probe that was used in the comparison

  ``test_label`` : str
    A label of the probe -- usually the probe file name, or the probe id

  ``score`` : float
    The result of the comparison of the model and the probe.
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  """

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  for i, l in enumerate(open_file(filename)):
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    if isinstance(l, bytes): l = l.decode('utf-8')
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    s = l.strip()
    if len(s) == 0 or s[0] == '#': continue #empty or comment
    field = [k.strip() for k in s.split()]
    if len(field) < 5:
      raise SyntaxError('Line %d of file "%s" is invalid: %s' % (i, filename, l))
    try:
      score = float(field[4])
    except:
      raise SyntaxError('Cannot convert score to float at line %d of file "%s": %s' % (i, filename, l))
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    yield (field[0], field[1], field[2], field[3], score)
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def split_five_column(filename):
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  """split_five_column(filename) -> negatives, positives

  Loads a score set from a single file in five column format and splits the scores
  between negatives and positives. The score file has to respect the 4 column
  format as defined in the method :py:func:`five_column`.
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  This method avoids loading and allocating memory for the strings present in
  the file. We only keep the scores.

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  **Parameters:**

  ``filename`` : str or file-like
    The file that will be opened with :py:func:`open_file` containing the scores.

  **Returns:**

  ``negatives`` : array_like(1D, float)
    The list of ``score``'s, for which the ``claimed_id`` and the ``real_id`` differed (see :py:func:`five_column`).

  ``positives`` : array_like(1D, float)
    The list of ``score``'s, for which the ``claimed_id`` and the ``real_id`` are identical (see :py:func:`five_column`).
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  """
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  score_lines = load_score(filename, 5)
  return get_negatives_positives(score_lines)
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def cmc_five_column(filename):
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  """cmc_four_column(filename) -> cmc_scores
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  Loads scores to compute CMC curves from a file in five column format.
  The four column file needs to be in the same format as described in :py:func:`five_column`,
  and the ``test_label`` (column 4) has to contain the test/probe file name or a probe id.
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  This function returns a list of tuples.
  For each probe file, the tuple consists of a list of negative scores and a list of positive scores.
  Usually, the list of positive scores should contain only one element, but more are allowed.
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  The result of this function can directly be passed to, e.g., the :py:func:`bob.measure.cmc` function.
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  **Parameters:**

  ``filename`` : str or file-like
    The file that will be opened with :py:func:`open_file` containing the scores.

  **Returns:**

  ``cmc_scores`` : [(array_like(1D, float), array_like(1D, float))]
    A list of tuples, where each tuple contains the ``negative`` and ``positive`` scores for one probe of the database
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  """
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  # extract positives and negatives
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  pos_dict = {}
  neg_dict = {}
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  # read four column list
  for (client_id, _, probe_id, probe_name, score) in five_column(filename):
    # check in which dict we have to put the score
    if client_id == probe_id:
      correct_dict = pos_dict
    else:
      correct_dict = neg_dict
    # append score
    if probe_name in correct_dict:
      correct_dict[probe_name].append(score)
    else:
      correct_dict[probe_name] = [score]
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  # convert to lists of tuples of ndarrays
  retval = []
  import logging
  logger = logging.getLogger('bob')
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  for probe_name in sorted(pos_dict.keys()):
    if probe_name in neg_dict:
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      retval.append((numpy.array(neg_dict[probe_name], numpy.float64), numpy.array(pos_dict[probe_name], numpy.float64)))
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    else:
      logger.warn('For probe name "%s" there are only positive scores. This probe name is ignored.' % probe_name)
  # test if there are probes for which only negatives exist
  for probe_name in sorted(neg_dict.keys()):
    if not probe_name in pos_dict.keys():
       logger.warn('For probe name "%s" there are only negative scores. This probe name is ignored.' % probe_name)
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  return retval
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def load_score(filename, ncolumns=None):
  """Load scores using numpy.loadtxt and return the data as a numpy array.

  **Parameters:**

  ``filename`` : str or file-like
    A path or file-like object that will be read with :py:func:`numpy.loadtxt`
    containing the scores.

  ``ncolumns`` : 4 or 5 [default is 4]
    Specifies the number of columns in the score file.

  **Returns:**

  ``score_lines`` : numpy array
    An array which contains not only the actual scores but also the
    'claimed_id', 'real_id', 'test_label', and ['model_label']

  """
  if ncolumns is None:
    ncolumns = 4

  def convertfunc(x):
    return x

  if ncolumns == 4:
    names = ('claimed_id', 'real_id', 'test_label', 'score')
    converters = {
      0: convertfunc,
      1: convertfunc,
      2: convertfunc,
      3: float}

  elif ncolumns == 5:
    names = ('claimed_id', 'model_label', 'real_id', 'test_label', 'score')
    converters = {
      0: convertfunc,
      1: convertfunc,
      2: convertfunc,
      3: convertfunc,
      4: float}
  else:
    raise ValueError("ncolumns of 4 and 5 are supported only.")

  score_lines = numpy.genfromtxt(
    open_file(filename, mode='rb'), dtype=None, names=names,
    converters=converters, invalid_raise=True)
  new_dtype = []
  for name in score_lines.dtype.names[:-1]:
    new_dtype.append((name, str(score_lines.dtype[name]).replace('S', 'U')))
  new_dtype.append(('score', float))
  score_lines = numpy.array(score_lines, new_dtype)
  return score_lines


def get_negatives_positives(score_lines):
  """Take the output of load_score and return negatives and positives.
  This function aims to replace split_four_column and split_five_column
  but takes a different input. It's up to you to use which one.
  """
  pos_mask = score_lines['claimed_id'] == score_lines['real_id']
  positives = score_lines['score'][pos_mask]
  negatives = score_lines['score'][numpy.logical_not(pos_mask)]
  return (negatives, positives)


def get_negatives_positives_all(score_lines_list):
  """Take a list of outputs of load_score and return stacked negatives and
  positives."""
  negatives, positives = [], []
  for score_lines in score_lines_list:
    neg_pos = get_negatives_positives(score_lines)
    negatives.append(neg_pos[0])
    positives.append(neg_pos[1])
  negatives = numpy.vstack(negatives).T
  positives = numpy.vstack(positives).T
  return (negatives, positives)


def get_all_scores(score_lines_list):
  """Take a list of outputs of load_score and return stacked scores"""
  return numpy.vstack([score_lines['score']
                       for score_lines in score_lines_list]).T


def dump_score(filename, score_lines):
  """Dump scores that were loaded using :py:func:`load_score`
  The number of columns is automatically detected.
  """
  if len(score_lines.dtype) == 5:
    fmt = '%s %s %s %s %.9f'
  elif len(score_lines.dtype) == 4:
    fmt = '%s %s %s %.9f'
  else:
    raise ValueError("Only scores with 4 and 5 columns are supported.")
  numpy.savetxt(filename, score_lines, fmt=fmt)