Commit 75077dec authored by Theophile GENTILHOMME's avatar Theophile GENTILHOMME
Browse files

fix documentation

parent 79a2177f
Pipeline #17723 failed with stage
in 35 minutes and 21 seconds
from .load import (open_file, split, cmc, split_four_column, four_column,
split_five_column, five_column, scores, load_score,
dump_score
dump_score, cmc_four_column, cmc_five_column
)
from .openbr import (write_matrix, write_score_file)
......@@ -268,7 +268,9 @@ def scores(filename, ncolumns=None):
"""scores(filename, ncolumns=None) -> tuple
Loads the scores from the given score file and yield its lines.
Depending on the score file format, four or five elements are yielded, see :py:func:`bob.bio.base.score.four_column` and :py:func:`bob.bio.base.score.five_column` for details.
Depending on the score file format, four or five elements are yielded, see
:py:func:`bob.bio.base.score.load.four_column` and
:py:func:`bob.bio.base.score.load.five_column` for details.
Parameters:
......@@ -281,7 +283,8 @@ def scores(filename, ncolumns=None):
Yields:
tuple:
see :py:func:`bob.bio.base.score.four_column` or :py:func:`bob.bio.base.score.five_column`
see :py:func:`bob.bio.base.score.load.four_column` or
:py:func:`bob.bio.base.score.load.five_column`
"""
return _iterate_score_file(filename)
......@@ -291,7 +294,8 @@ def split(filename, ncolumns=None):
Loads the scores from the given score file and splits them into positives and negatives.
Depending on the score file format, it calls see :py:func:`bob.bio.base.score.split_four_column` and `:py:func:`bob.bio.base.score.split_five_column` for details.
Depending on the score file format, it calls see :py:func:`split_four_column`
and :py:func:`split_five_column` for details.
Parameters:
......@@ -324,7 +328,9 @@ def cmc(filename, ncolumns=None):
Loads scores to compute CMC curves.
Depending on the score file format, it calls see :py:func:`bob.bio.base.score.cmc_four_column` and `:py:func:`bob.bio.base.score.cmc_five_column` for details.
Depending on the score file format, it calls see
:py:func:`bob.bio.base.score.load.cmc_four_column` and
`:py:func:`bob.bio.base.score.load.cmc_five_column` for details.
Parameters:
......
......@@ -62,7 +62,7 @@ def _scores(algorithm, reader, model, probe_objects, allow_missing_files):
def _open_to_read(score_file):
"""Checks for the existence of the normal and the compressed version of the file, and calls :py:func:`score.open_file` for the existing one."""
"""Checks for the existence of the normal and the compressed version of the file, and calls :py:func:`bob.bio.base.score.open_file` for the existing one."""
if not os.path.exists(score_file):
score_file += '.tar.bz2'
if not os.path.exists(score_file):
......@@ -115,7 +115,8 @@ def _delete(score_file, write_compressed):
def _save_scores(score_file, scores, probe_objects, client_id, write_compressed):
"""Saves the scores of one model into a text file that can be interpreted by :py:func:`score.split_four_column`."""
"""Saves the scores of one model into a text file that can be interpreted by
:py:func:`bob.bio.base.score.split_four_column`."""
assert len(probe_objects) == scores.shape[1]
# open file for writing
......@@ -493,7 +494,9 @@ def _concat(score_files, output, write_compressed, model_ids):
def concatenate(compute_zt_norm, groups = ['dev', 'eval'], write_compressed = False, add_model_id = False):
"""Concatenates all results into one (or two) score files per group.
Score files, which were generated per model, are concatenated into a single score file, which can be interpreter by :py:func:`score.split_four_column`.
Score files, which were generated per model, are concatenated into a single
score file, which can be interpreter by
:py:func:`bob.bio.base.score.load.split_four_column`.
The score files are always re-computed, regardless if they exist or not.
**Parameters:**
......
......@@ -78,6 +78,7 @@ Users Guide
filelist-guide
more
annotations
openbr
Reference Manual
......
.. _bob.bio.base.openbr:
=====================
Score file conversion
=====================
Sometimes, it is required to export the score files generated by Bob to a
different format, e.g., to be able to generate a plot comparing Bob's systems
with other systems. In this package, we provide source code to convert between
different types of score files.
Bob to OpenBR
-------------
One of the supported formats is the matrix format that the National Institute
of Standards and Technology (NIST) uses, and which is supported by OpenBR_.
The scores are stored in two binary matrices, where the first matrix (usually
with a ``.mtx`` filename extension) contains the raw scores, while a second
mask matrix (extension ``.mask``) contains information, which scores are
positives, and which are negatives.
To convert from Bob's four column or five column score file to a pair of these
matrices, you can use the :py:func:`bob.bio.base.score.openbr.write_matrix` function.
In the simplest way, this function takes a score file
``'five-column-sore-file'`` and writes the pair ``'openbr.mtx', 'openbr.mask'``
of OpenBR_ compatible files:
.. code-block:: py
>>> bob.bio.base.score.openbr.write_matrix('five-column-sore-file', 'openbr.mtx', 'openbr.mask', score_file_format = '5column')
In this way, the score file will be parsed and the matrices will be written in
the same order that is obtained from the score file.
For most of the applications, this should be sufficient, but as the identity
information is lost in the matrix files, no deeper analysis is possible anymore
when just using the matrices. To enforce an order of the models and probes
inside the matrices, you can use the ``model_names`` and ``probe_names``
parameters of :py:func:`bob.bio.base.score.openbr.write_matrix`:
* The ``probe_names`` parameter lists the ``path`` elements stored in the score
files, which are the fourth column in a ``5column`` file, and the third
column in a ``4column`` file, see :py:func:`bob.bio.base.score.load.five_column` and
:py:func:`bob.bio.base.score.load.four_column`.
* The ``model_names`` parameter is a bit more complicated. In a ``5column``
format score file, the model names are defined by the second column of that
file, see :py:func:`bob.bio.base.score.load.five_column`. In a ``4column`` format
score file, the model information is not contained, but only the client
information of the model. Hence, for the ``4column`` format, the
``model_names`` actually lists the client ids found in the first column, see
:py:func:`bob.bio.base.score.load.four_column`.
.. warning::
The model information is lost, but required to write the matrix files. In
the ``4column`` format, we use client ids instead of the model
information. Hence, when several models exist per client, this function
will not work as expected.
Additionally, there are fields in the matrix files, which define the gallery
and probe list files that were used to generate the matrix. These file names
can be selected with the ``gallery_file_name`` and ``probe_file_name`` keyword
parameters of :py:func:`bob.bio.base.score.openbr.write_matrix`.
Finally, OpenBR defines a specific ``'search'`` score file format, which is
designed to be used to compute CMC curves. The score matrix contains
descendingly sorted and possibly truncated list of scores, i.e., for each
probe, a sorted list of all scores for the models is generated. To generate
these special score file format, you can specify the ``search`` parameter. It
specifies the number of highest scores per probe that should be kept. If the
``search`` parameter is set to a negative value, all scores will be kept. If
the ``search`` parameter is higher as the actual number of models, ``NaN``
scores will be appended, and the according mask values will be set to ``0``
(i.e., to be ignored).
OpenBR to Bob
-------------
On the other hand, you might also want to generate a Bob-compatible (four or
five column) score file based on a pair of OpenBR matrix and mask files. This
is possible by using the :py:func:`bob.bio.base.score.openbr.write_score_file`
function. At the basic, it takes the given pair of matrix and mask files, as
well as the desired output score file:
.. code-block:: py
>>> bob.bio.base.score.openbr.write_score_file('openbr.mtx', 'openbr.mask', 'four-column-sore-file')
This score file is sufficient to compute a CMC curve (see `bob.measure`), however it
does not contain relevant client ids or paths for models and probes.
Particularly, it assumes that each client has exactly one associated model.
To add/correct these information, you can use additional parameters to
:py:func:`bob.bio.base.score.openbr.write_score_file`. Client ids of models and
probes can be added using the ``models_ids`` and ``probes_ids`` keyword
arguments. The length of these lists must be identical to the number of models
and probes as given in the matrix files, **and they must be in the same order
as used to compute the OpenBR matrix**. This includes that the same
same-client and different-client pairs as indicated by the OpenBR mask will be
generated, which will be checked inside the function.
To add model and probe path information, the ``model_names`` and
``probe_names`` parameters, which need to have the same size and order as the
``models_ids`` and ``probes_ids``. These information are simply stored in the
score file, and no further check is applied.
.. note:: The ``model_names`` parameter is used only when writing score files in ``score_file_format='5column'``, in the ``'4column'`` format, this parameter is ignored.
.. Place youre references here:
.. _openbr: http://openbiometrics.org
......@@ -94,6 +94,26 @@ Scoring
bob.bio.base.tools.concatenate
bob.bio.base.tools.calibrate
Loading data
------------
.. autosummary::
bob.bio.base.score.load.open_file
bob.bio.base.score.load.scores
bob.bio.base.score.load.split
bob.bio.base.score.load.cmc
bob.bio.base.score.load.four_column
bob.bio.base.score.load.split_four_column
bob.bio.base.score.load.cmc_four_column
bob.bio.base.score.load.five_column
bob.bio.base.score.load.split_five_column
bob.bio.base.score.load.cmc_five_column
OpenBR conversions
------------------
.. autosummary::
bob.bio.base.score.openbr.write_matrix
bob.bio.base.score.openbr.write_score_file
Details
-------
......@@ -108,5 +128,6 @@ Details
.. autoclass:: FileSelector
.. automodule:: bob.bio.base.score.load
.. automodule:: bob.bio.base.score.openbr
.. include:: links.rst
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment