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Commit 349c90fd authored by Tiago de Freitas Pereira's avatar Tiago de Freitas Pereira
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Merge branch 'p1' into 'master' 

[Automatic] update links and the ci mostly



See merge request !4
parents 85dd1fef f535c004
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bob/learn/boosting/ExponentialLoss.py
View file @ 349c90fd
from .LossFunction import LossFunction
import numpy
from . import LossFunction
class ExponentialLoss (LossFunction):
""" The class implements the exponential loss function for the boosting framework."""
def loss(self, targets, scores):
"""The function computes the exponential loss values using prediction scores and targets.
It can be used in classification tasks, e.g., in combination with the StumpTrainer.
Keyword parameters:
class ExponentialLoss(LossFunction):
""" The class implements the exponential loss function for the boosting framework."""
targets (float <#samples, #outputs>): The target values that should be reached.
def loss(self, targets, scores):
"""The function computes the exponential loss values using prediction scores and targets.
It can be used in classification tasks, e.g., in combination with the StumpTrainer.
scores (float <#samples, #outputs>): The scores provided by the classifier.
Keyword parameters:
Returns
(float <#samples, #outputs>): The loss values for the samples, always >= 0
"""
return numpy.exp(-(targets * scores))
targets (float <#samples, #outputs>): The target values that should be reached.
scores (float <#samples, #outputs>): The scores provided by the classifier.
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the exponential loss function using prediction scores and targets.
Returns
(float <#samples, #outputs>): The loss values for the samples, always >= 0
"""
return numpy.exp(-(targets * scores))
Keyword parameters:
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the exponential loss function using prediction scores and targets.
targets (float <#samples, #outputs>): The target values that should be reached.
Keyword parameters:
scores (float <#samples, #outputs>): The scores provided by the classifier.
targets (float <#samples, #outputs>): The target values that should be reached.
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
loss = numpy.exp(-(targets * scores))
return -targets * loss
scores (float <#samples, #outputs>): The scores provided by the classifier.
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
loss = numpy.exp(-(targets * scores))
return -targets * loss
bob/learn/boosting/LogitLoss.py
View file @ 349c90fd
from .LossFunction import LossFunction
from . import LossFunction
import numpy
class LogitLoss(LossFunction):
""" The class to implement the logit loss function for the boosting framework."""
def loss(self, targets, scores):
"""The function computes the logit loss values using prediction scores and targets.
class LogitLoss(LossFunction):
""" The class to implement the logit loss function for the boosting framework."""
Keyword parameters:
def loss(self, targets, scores):
"""The function computes the logit loss values using prediction scores and targets.
targets (float <#samples, #outputs>): The target values that should be reached.
Keyword parameters:
scores (float <#samples, #outputs>): The scores provided by the classifier.
targets (float <#samples, #outputs>): The target values that should be reached.
Returns
(float <#samples, #outputs>): The loss values for the samples, which is always >= 0
"""
e = numpy.exp(-(targets * scores))
return numpy.log(1. + e)
scores (float <#samples, #outputs>): The scores provided by the classifier.
Returns
(float <#samples, #outputs>): The loss values for the samples, which is always >= 0
"""
e = numpy.exp(-(targets * scores))
return numpy.log(1. + e)
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the logit loss function using prediction scores and targets.
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the logit loss function using prediction scores and targets.
Keyword parameters:
Keyword parameters:
targets (float <#samples, #outputs>): The target values that should be reached.
targets (float <#samples, #outputs>): The target values that should be reached.
scores (float <#samples, #outputs>): The scores provided by the classifier.
scores (float <#samples, #outputs>): The scores provided by the classifier.
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
e = numpy.exp(-(targets * scores))
denom = 1./(1. + e)
return -targets * e * denom
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
e = numpy.exp(-(targets * scores))
denom = 1. / (1. + e)
return -targets * e * denom
bob/learn/boosting/LossFunction.py
View file @ 349c90fd
import numpy
class LossFunction:
"""This is a base class for all loss functions implemented in pure python.
It is simply a python re-implementation of the :py:class:`bob.learn.boosting.LossFunction` class.
This class provides the interface for the L-BFGS optimizer.
Please overwrite the loss() and loss_gradient() function (see below) in derived loss classes.
"""
class LossFunction(object):
"""This is a base class for all loss functions implemented in pure python.
It is simply a python re-implementation of the :py:class:`bob.learn.boosting.LossFunction` class.
def loss(self, targets, scores):
"""This function is to compute the loss for the given targets and scores.
Keyword parameters:
This class provides the interface for the L-BFGS optimizer.
Please overwrite the loss() and loss_gradient() function (see below) in derived loss classes.
"""
targets (float <#samples, #outputs>): The target values that should be reached.
def __init__(self):
pass
scores (float <#samples, #outputs>): The scores provided by the classifier.
def loss(self, targets, scores):
"""This function is to compute the loss for the given targets and scores.
Returns
(float <#samples, #outputs>) or (float <#samples, 1>): The loss based on the given scores and targets.
Depending on the intended task, one of the two output variants should be chosen.
For classification tasks, please use the former way (#samples, #outputs), while for regression tasks, use the latter (#samples, 1).
"""
raise NotImplementedError("This is a pure abstract function. Please implement that in your derived class.")
Keyword parameters:
targets (float <#samples, #outputs>): The target values that should be reached.
def loss_gradient(self, targets, scores):
"""This function is to compute the gradient of the loss for the given targets and scores.
scores (float <#samples, #outputs>): The scores provided by the classifier.
Keyword parameters:
Returns
(float <#samples, #outputs>) or (float <#samples, 1>): The loss based on the given scores and targets.
Depending on the intended task, one of the two output variants should be chosen.
For classification tasks, please use the former way (#samples, #outputs), while for regression tasks, use the latter (#samples, 1).
"""
raise NotImplementedError("This is a pure abstract function. Please implement that in your derived class.")
targets (float <#samples, #outputs>): The target values that should be reached.
def loss_gradient(self, targets, scores):
"""This function is to compute the gradient of the loss for the given targets and scores.
scores (float <#samples, #outputs>): The scores provided by the classifier.
Keyword parameters:
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
raise NotImplementedError("This is a pure abstract function. Please implement that in your derived class.")
targets (float <#samples, #outputs>): The target values that should be reached.
scores (float <#samples, #outputs>): The scores provided by the classifier.
def loss_sum(self, alpha, targets, previous_scores, current_scores):
"""The function computes the sum of the loss which is used to find the optimized values of alpha (x).
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
raise NotImplementedError("This is a pure abstract function. Please implement that in your derived class.")
The functions computes sum of loss values which is required during the line search step for the optimization of the alpha.
This function is given as the input for the L-BFGS optimization function.
def loss_sum(self, alpha, targets, previous_scores, current_scores):
"""The function computes the sum of the loss which is used to find the optimized values of alpha (x).
Keyword parameters:
The functions computes sum of loss values which is required during the line search step for the optimization of the alpha.
This function is given as the input for the L-BFGS optimization function.
alpha (float): The current value of the alpha.
Keyword parameters:
targets (float <#samples, #outputs>): The targets for the samples
alpha (float): The current value of the alpha.
previous_scores (float <#samples, #outputs>): The cumulative prediction scores of the samples until the previous round of the boosting.
targets (float <#samples, #outputs>): The targets for the samples
current_scores (float <#samples, #outputs>): The prediction scores of the samples for the current round of the boosting.
previous_scores (float <#samples, #outputs>): The cumulative prediction scores of the samples until the previous round of the boosting.
Returns
current_scores (float <#samples, #outputs>): The prediction scores of the samples for the current round of the boosting.
(float <#outputs>) The sum of the loss values for the current value of the alpha
"""
Returns
# compute the scores and loss for the current alpha
scores = previous_scores + alpha * current_scores
losses = self.loss(targets, scores)
(float <#outputs>) The sum of the loss values for the current value of the alpha
"""
# compute the sum of the loss
return numpy.sum(losses, 0)
# compute the scores and loss for the current alpha
scores = previous_scores + alpha * current_scores
losses = self.loss(targets, scores)
# compute the sum of the loss
return numpy.sum(losses, 0)
def loss_gradient_sum(self, alpha, targets, previous_scores, current_scores):
"""The function computes the gradient as the sum of the derivatives per sample which is used to find the optimized values of alpha.
def loss_gradient_sum(self, alpha, targets, previous_scores, current_scores):
"""The function computes the gradient as the sum of the derivatives per sample which is used to find the optimized values of alpha.
The functions computes sum of loss values which is required during the line search step for the optimization of the alpha.
This function is given as the input for the L-BFGS optimization function.
The functions computes sum of loss values which is required during the line search step for the optimization of the alpha.
This function is given as the input for the L-BFGS optimization function.
Keyword parameters:
Keyword parameters:
alpha (float): The current value of the alpha.
alpha (float): The current value of the alpha.
targets (float <#samples, #outputs>): The targets for the samples
targets (float <#samples, #outputs>): The targets for the samples
previous_scores (float <#samples, #outputs>): The cumulative prediction scores of the samples until the previous round of the boosting.
previous_scores (float <#samples, #outputs>): The cumulative prediction scores of the samples until the previous round of the boosting.
current_scores (float <#samples, #outputs>): The prediction scores of the samples for the current round of the boosting.
current_scores (float <#samples, #outputs>): The prediction scores of the samples for the current round of the boosting.
Returns
(float <#outputs>) The sum of the loss gradient for the current value of the alpha.
"""
Returns
(float <#outputs>) The sum of the loss gradient for the current value of the alpha.
"""
# compute the loss gradient for the updated score
scores = previous_scores + alpha * current_scores
loss_gradients = self.loss_gradient(targets, scores)
# compute the loss gradient for the updated score
scores = previous_scores + alpha * current_scores
loss_gradients = self.loss_gradient(targets, scores)
# take the sum of the loss gradient values
return numpy.sum(loss_gradients * current_scores, 0)
# take the sum of the loss gradient values
return numpy.sum(loss_gradients * current_scores, 0)
bob/learn/boosting/TangentialLoss.py
View file @ 349c90fd
from .LossFunction import LossFunction
from . import LossFunction
import numpy
class TangentialLoss (LossFunction):
"""Tangent loss function, as described in http://www.svcl.ucsd.edu/projects/LossDesign/TangentBoost.html."""
def loss(self, targets, scores):
"""The function computes the logit loss values using prediction scores and targets.
class TangentialLoss(LossFunction):
"""Tangent loss function, as described in http://www.svcl.ucsd.edu/projects/LossDesign/TangentBoost.html."""
Keyword parameters:
def loss(self, targets, scores):
"""The function computes the logit loss values using prediction scores and targets.
targets (float <#samples, #outputs>): The target values that should be reached.
Keyword parameters:
scores (float <#samples, #outputs>): The scores provided by the classifier.
targets (float <#samples, #outputs>): The target values that should be reached.
Returns
(float <#samples, #outputs>): The loss values for the samples, always >= 0
"""
return (2. * numpy.arctan(targets * scores) - 1.)**2
scores (float <#samples, #outputs>): The scores provided by the classifier.
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the tangential loss function using prediction scores and targets.
Returns
(float <#samples, #outputs>): The loss values for the samples, always >= 0
"""
return (2. * numpy.arctan(targets * scores) - 1.) ** 2
Keyword parameters:
def loss_gradient(self, targets, scores):
"""The function computes the gradient of the tangential loss function using prediction scores and targets.
targets (float <#samples, #outputs>): The target values that should be reached.
Keyword parameters:
scores (float <#samples, #outputs>): The scores provided by the classifier.
targets (float <#samples, #outputs>): The target values that should be reached.
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
m = targets * scores
numer = 4. * (2. * numpy.arctan(m) - 1.)
denom = 1. + m**2
return numer/denom
scores (float <#samples, #outputs>): The scores provided by the classifier.
Returns
loss (float <#samples, #outputs>): The gradient of the loss based on the given scores and targets.
"""
m = targets * scores
numer = 4. * (2. * numpy.arctan(m) - 1.)
denom = 1. + m ** 2
return numer / denom
bob/learn/boosting/__init__.py
View file @ 349c90fd
......@@ -11,7 +11,7 @@ from bob.learn.boosting.version import module as __version__
from bob.learn.boosting.version import api as __api_version__
# include loss functions
from bob.learn.boosting import LossFunction # Just to get the documentation for it
from bob.learn.boosting.LossFunction import LossFunction # Just to get the documentation for it
from bob.learn.boosting.ExponentialLoss import ExponentialLoss
from bob.learn.boosting.LogitLoss import LogitLoss
from bob.learn.boosting.TangentialLoss import TangentialLoss
......@@ -34,5 +34,19 @@ def get_config():
return bob.extension.get_config(__name__, version.externals, version.api)
# gets sphinx autodoc done right - don't remove it
def __appropriate__(*args):
"""Says object was actually declared here, an not on the import module.
Parameters:
*args: An iterable of objects to modify
Resolves `Sphinx referencing issues
<https://github.com/sphinx-doc/sphinx/issues/3048>`
"""
for obj in args: obj.__module__ = __name__
__appropriate__(
LossFunction,
)
# gets sphinx autodoc done right - don't remove it
__all__ = [_ for _ in dir() if not _.startswith('_')]
bob/learn/boosting/boosted_machine.cpp
View file @ 349c90fd
......@@ -245,7 +245,7 @@ static PyObject* boostedMachine_add(
static auto boostedMachine_forward_doc = bob::extension::FunctionDoc(
"forward",
"Returns the prediction for the given feature vector(s)",
".. note:: The :py:func:`__call__` function is an alias for this function.\n\n"
".. note:: The ``__call__`` function is an alias for this function.\n\n"
"This function can be called in six different ways:\n\n"
"1. ``(uint16 <#inputs>)`` will compute and return the uni-variate prediction for a single feature vector.\n"
"2. ``(uint16 <#samples,#inputs>, float <#samples>)`` will compute the uni-variate prediction for several feature vectors.\n"
......
bob/learn/boosting/lut_machine.cpp
View file @ 349c90fd
......@@ -157,7 +157,7 @@ static PyObject* lutMachine_lut(
static auto lutMachine_forward_doc = bob::extension::FunctionDoc(
"forward",
"Returns the prediction for the given feature vector(s)",
".. note:: The :py:func:`__call__` function is an alias for this function.\n\n"
".. note:: The ``__call__`` function is an alias for this function.\n\n"
"This function can be called in four different ways:\n\n"
"1. ``(uint16 <#inputs>)`` will compute and return the uni-variate prediction for a single feature vector.\n"
"2. ``(uint16 <#samples,#inputs>, float <#samples>)`` will compute the uni-variate prediction for several feature vectors.\n"
......
bob/learn/boosting/stump_machine.cpp
View file @ 349c90fd
......@@ -115,9 +115,8 @@ static PyObject* stumpMachine_threshold(
static auto stumpMachine_polarity_doc = bob::extension::VariableDoc(
"polarity",
"float",
"The polarity of the comparison: -1 if the values lower than the threshold should be accepted, +1 otherwise"
"The polarity of the comparison -1 if the values lower than the threshold should be accepted, +1 otherwise."
);
static PyObject* stumpMachine_polarity(
StumpMachineObject* self,
void* )
......@@ -130,7 +129,7 @@ static PyObject* stumpMachine_polarity(
static auto stumpMachine_forward_doc = bob::extension::FunctionDoc(
"forward",
"Returns the prediction for the given feature vector(s)",
".. note:: The :py:func:`__call__` function is an alias for this function.\n\n"
".. note:: The ``__call__`` function is an alias for this function.\n\n"
".. todo:: write more detailed documentation",
true
)
......
doc/conf.py
View file @ 349c90fd
......@@ -30,9 +30,29 @@ extensions = [
import sphinx
if sphinx.__version__ >= "1.4.1":
extensions.append('sphinx.ext.imgmath')
imgmath_image_format = 'svg'
else:
extensions.append('sphinx.ext.pngmath')
# Be picky about warnings
nitpicky = True
# Ignores stuff we can't easily resolve on other project's sphinx manuals
nitpick_ignore = []
# Allows the user to override warnings from a separate file
if os.path.exists('nitpick-exceptions.txt'):
for line in open('nitpick-exceptions.txt'):
if line.strip() == "" or line.startswith("#"):
continue
dtype, target = line.split(None, 1)
target = target.strip()
try: # python 2.x
target = unicode(target)
except NameError:
pass
nitpick_ignore.append((dtype, target))
# Always includes todos
todo_include_todos = True
......@@ -216,8 +236,13 @@ autodoc_default_flags = [
]
# For inter-documentation mapping:
from bob.extension.utils import link_documentation
intersphinx_mapping = link_documentation()
from bob.extension.utils import link_documentation, load_requirements
sphinx_requirements = "extra-intersphinx.txt"
if os.path.exists(sphinx_requirements):
intersphinx_mapping = link_documentation(additional_packages=load_requirements(sphinx_requirements))
else:
intersphinx_mapping = link_documentation()
# We want to remove all private (i.e. _. or __.__) members
# that are not in the list of accepted functions
......
doc/py_api.rst
View file @ 349c90fd
......@@ -26,7 +26,7 @@ Available trainers in :py:mod:`bob.learn.boosting` are:
* :py:class:`bob.learn.boosting.Boosting` : Trains a strong machine of type :py:class:`bob.learn.boosting.BoostedMachine`.
* :py:class:`bob.learn.boosting.LUTTrainer` : Trains a weak machine of type :py:class:`bob.learn.boosting.LUTMachine`.
* :py:class:`bob.learn.boosting.StrumTrainer` : Trains a weak machine of type :py:class:`bob.learn.boosting.StumpMachine`.
* :py:class:`bob.learn.boosting.StumpTrainer` : Trains a weak machine of type :py:class:`bob.learn.boosting.StumpMachine`.
Loss functions
......@@ -40,9 +40,9 @@ A base class loss function :py:class:`bob.learn.boosting.LossFunction` is called
Not all combinations of loss functions and weak trainers make sense.
Here is a list of useful combinations:
1. :py:class:`bob.learn.boosting.ExponentialLoss` with :py:class:`bob.learn.boosting.StrumTrainer` (uni-variate classification only).
2. :py:class:`bob.learn.boosting.LogitLoss` with :py:class:`bob.learn.boosting.StrumTrainer` or :py:class:`bob.learn.boosting.LUTTrainer` (uni-variate or multi-variate classification).
3. :py:class:`bob.learn.boosting.TangentialLoss` with :py:class:`bob.learn.boosting.StrumTrainer` or :py:class:`bob.learn.boosting.LUTTrainer` (uni-variate or multi-variate classification).
1. :py:class:`bob.learn.boosting.ExponentialLoss` with :py:class:`bob.learn.boosting.StumpTrainer` (uni-variate classification only).
2. :py:class:`bob.learn.boosting.LogitLoss` with :py:class:`bob.learn.boosting.StumpTrainer` or :py:class:`bob.learn.boosting.LUTTrainer` (uni-variate or multi-variate classification).
3. :py:class:`bob.learn.boosting.TangentialLoss` with :py:class:`bob.learn.boosting.StumpTrainer` or :py:class:`bob.learn.boosting.LUTTrainer` (uni-variate or multi-variate classification).
4. :py:class:`bob.learn.boosting.JesorskyLoss` with :py:class:`bob.learn.boosting.LUTTrainer` (multi-variate regression only).
Details
......
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