From b8efca2376b36a45aace8676242852f71f97d1e0 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Wed, 11 Oct 2017 16:48:39 +0200
Subject: [PATCH] Add sequential and parallel processors, pre-processors, and
extractors
---
bob/bio/base/extractor/__init__.py | 17 +++-
bob/bio/base/extractor/stacks.py | 125 ++++++++++++++++++++++++++
bob/bio/base/preprocessor/__init__.py | 16 +++-
bob/bio/base/preprocessor/stacks.py | 61 +++++++++++++
bob/bio/base/test/test_stacks.py | 45 ++++++++++
bob/bio/base/utils/__init__.py | 1 +
bob/bio/base/utils/processors.py | 84 +++++++++++++++++
doc/implemented.rst | 6 ++
doc/py_api.rst | 11 +++
9 files changed, 358 insertions(+), 8 deletions(-)
create mode 100644 bob/bio/base/extractor/stacks.py
create mode 100644 bob/bio/base/preprocessor/stacks.py
create mode 100644 bob/bio/base/test/test_stacks.py
create mode 100644 bob/bio/base/utils/processors.py
diff --git a/bob/bio/base/extractor/__init__.py b/bob/bio/base/extractor/__init__.py
index 7b55d421..03851247 100644
--- a/bob/bio/base/extractor/__init__.py
+++ b/bob/bio/base/extractor/__init__.py
@@ -1,11 +1,14 @@
from .Extractor import Extractor
from .Linearize import Linearize
+from .stacks import (SequentialExtractor, ParallelExtractor,
+ CallableExtractor, MultipleExtractor)
+
# gets sphinx autodoc done right - don't remove it
def __appropriate__(*args):
"""Says object was actually declared here, and not in the import module.
- Fixing sphinx warnings of not being able to find classes, when path is shortened.
- Parameters:
+ Fixing sphinx warnings of not being able to find classes, when path is
+ shortened. Parameters:
*args: An iterable of objects to modify
@@ -13,10 +16,16 @@ def __appropriate__(*args):
<https://github.com/sphinx-doc/sphinx/issues/3048>`
"""
- for obj in args: obj.__module__ = __name__
+ for obj in args:
+ obj.__module__ = __name__
+
__appropriate__(
Extractor,
Linearize,
- )
+ SequentialExtractor,
+ ParallelExtractor,
+ CallableExtractor,
+ MultipleExtractor,
+)
__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/base/extractor/stacks.py b/bob/bio/base/extractor/stacks.py
new file mode 100644
index 00000000..511b7d04
--- /dev/null
+++ b/bob/bio/base/extractor/stacks.py
@@ -0,0 +1,125 @@
+from ..utils.processors import SequentialProcessor, ParallelProcessor
+from .Extractor import Extractor
+
+
+class MultipleExtractor(Extractor):
+ """Base class for SequentialExtractor and ParallelExtractor. This class is
+ not meant to be used directly."""
+
+ def get_attributes(self, processors):
+ requires_training = any((p.requires_training for p in processors))
+ split_training_data_by_client = any(
+ (p.split_training_data_by_client for p in processors))
+ min_extractor_file_size = min(
+ (p.min_extractor_file_size for p in processors))
+ min_feature_file_size = min(
+ (p.min_feature_file_size for p in processors))
+ return (requires_training, split_training_data_by_client,
+ min_extractor_file_size, min_feature_file_size)
+
+ def get_extractor_files(self, extractor_file):
+ paths = [extractor_file]
+ paths += [extractor_file +
+ '_{}.hdf5'.format(i) for i in range(1, len(self.processors))]
+ return paths
+
+ def train_one(self, e, training_data, extractor_file, apply=False):
+ if not e.requires_training:
+ return
+ if e.split_training_data_by_client:
+ e.train(training_data, extractor_file)
+ if not apply:
+ return
+ training_data = [[e(d) for d in datalist] for datalist in training_data]
+ elif not self.split_training_data_by_client:
+ e.train(training_data, extractor_file)
+ if not apply:
+ return
+ training_data = [e(d) for d in training_data]
+ else:
+ # make training_data flat
+ training_data_len = [len(datalist) for datalist in training_data]
+ training_data = [d for datalist in training_data for d in datalist]
+ e.train(training_data, extractor_file)
+ if not apply:
+ return
+ # split training data
+ new_training_data, i = [], 0
+ for length in training_data_len:
+ class_data = []
+ for _ in range(length):
+ class_data.append(e(training_data[i]))
+ i += 1
+ new_training_data.append(class_data)
+ training_data = new_training_data
+ return training_data
+
+ def load(self, extractor_file):
+ paths = self.get_extractor_files(extractor_file)
+ for e, path in zip(self.processors, paths):
+ e.load(path)
+
+
+class SequentialExtractor(SequentialProcessor, MultipleExtractor):
+ __doc__ = SequentialProcessor.__doc__
+
+ def __init__(self, processors):
+
+ (requires_training, split_training_data_by_client,
+ min_extractor_file_size, min_feature_file_size) = self.get_attributes(
+ processors)
+
+ SequentialProcessor.__init__(self, processors)
+ MultipleExtractor.__init__(
+ self,
+ requires_training=requires_training,
+ split_training_data_by_client=split_training_data_by_client,
+ min_extractor_file_size=min_extractor_file_size,
+ min_feature_file_size=min_feature_file_size)
+
+ def train(self, training_data, extractor_file):
+ paths = self.get_extractor_files(extractor_file)
+ for e, path in zip(self.processors, paths):
+ training_data = self.train_one(e, training_data, path, apply=True)
+
+
+class ParallelExtractor(ParallelProcessor, MultipleExtractor):
+ __doc__ = ParallelProcessor.__doc__
+
+ def __init__(self, processors):
+
+ (requires_training, split_training_data_by_client,
+ min_extractor_file_size, min_feature_file_size) = self.get_attributes(
+ processors)
+
+ ParallelProcessor.__init__(self, processors)
+ MultipleExtractor.__init__(
+ self,
+ requires_training=requires_training,
+ split_training_data_by_client=split_training_data_by_client,
+ min_extractor_file_size=min_extractor_file_size,
+ min_feature_file_size=min_feature_file_size)
+
+ def train(self, training_data, extractor_file):
+ paths = self.get_extractor_files(extractor_file)
+ for e, path in zip(self.processors, paths):
+ self.train_one(e, training_data, path)
+
+
+class CallableExtractor(Extractor):
+ """A simple extractor that takes a callable and applies that callable to the
+ input.
+
+ Attributes
+ ----------
+ callable : object
+ Anything that is callable. It will be used as an extractor in
+ bob.bio.base.
+ """
+
+ def __init__(self, callable, **kwargs):
+ super(CallableExtractor, self).__init__(**kwargs)
+ self.callable = callable
+
+ def __call__(self, data):
+ return self.callable(data)
diff --git a/bob/bio/base/preprocessor/__init__.py b/bob/bio/base/preprocessor/__init__.py
index 0f981ce2..8c0a0567 100644
--- a/bob/bio/base/preprocessor/__init__.py
+++ b/bob/bio/base/preprocessor/__init__.py
@@ -1,11 +1,14 @@
from .Preprocessor import Preprocessor
from .Filename import Filename
+from .stacks import (SequentialPreprocessor,
+ ParallelPreprocessor, CallablePreprocessor)
+
# gets sphinx autodoc done right - don't remove it
def __appropriate__(*args):
"""Says object was actually declared here, and not in the import module.
- Fixing sphinx warnings of not being able to find classes, when path is shortened.
- Parameters:
+ Fixing sphinx warnings of not being able to find classes, when path is
+ shortened. Parameters:
*args: An iterable of objects to modify
@@ -13,10 +16,15 @@ def __appropriate__(*args):
<https://github.com/sphinx-doc/sphinx/issues/3048>`
"""
- for obj in args: obj.__module__ = __name__
+ for obj in args:
+ obj.__module__ = __name__
+
__appropriate__(
Preprocessor,
Filename,
- )
+ SequentialPreprocessor,
+ ParallelPreprocessor,
+ CallablePreprocessor,
+)
__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/base/preprocessor/stacks.py b/bob/bio/base/preprocessor/stacks.py
new file mode 100644
index 00000000..1c8be13d
--- /dev/null
+++ b/bob/bio/base/preprocessor/stacks.py
@@ -0,0 +1,61 @@
+from ..utils.processors import SequentialProcessor, ParallelProcessor
+from .Preprocessor import Preprocessor
+
+
+class SequentialPreprocessor(SequentialProcessor, Preprocessor):
+ __doc__ = SequentialProcessor.__doc__
+
+ def __init__(self, processors, **kwargs):
+ min_preprocessed_file_size = 1000
+ try:
+ min_preprocessed_file_size = min(
+ (p.min_preprocessed_file_size for p in processors))
+ except AttributeError:
+ pass
+
+ SequentialProcessor.__init__(self, processors)
+ Preprocessor.__init__(
+ self, min_preprocessed_file_size=min_preprocessed_file_size, **kwargs)
+
+ def __call__(self, data, annotations):
+ return super(SequentialPreprocessor, self).__call__(
+ data, annotations=annotations)
+
+
+class ParallelPreprocessor(ParallelProcessor, Preprocessor):
+ __doc__ = ParallelProcessor.__doc__
+
+ def __init__(self, processors, **kwargs):
+ min_preprocessed_file_size = 1000
+ try:
+ min_preprocessed_file_size = min(
+ (p.min_preprocessed_file_size for p in processors))
+ except AttributeError:
+ pass
+
+ ParallelProcessor.__init__(self, processors)
+ Preprocessor.__init__(
+ self, min_preprocessed_file_size=min_preprocessed_file_size, **kwargs)
+
+ def __call__(self, data, annotations):
+ return super(ParallelPreprocessor, self).__call__(
+ data, annotations=annotations)
+
+
+class CallablePreprocessor(Preprocessor):
+ """A simple preprocessor that takes a callable and applies that callable to
+ the input.
+
+ Attributes
+ ----------
+ callable : object
+ Anything that is callable. It will be used as a preprocessor in
+ bob.bio.base.
+ """
+
+ def __init__(self, callable, **kwargs):
+ super(CallablePreprocessor, self).__init__(**kwargs)
+ self.callable = callable
+
+ def __call__(self, data, annotations):
+ return self.callable(data)
diff --git a/bob/bio/base/test/test_stacks.py b/bob/bio/base/test/test_stacks.py
new file mode 100644
index 00000000..3db57f56
--- /dev/null
+++ b/bob/bio/base/test/test_stacks.py
@@ -0,0 +1,45 @@
+from functools import partial
+import numpy as np
+from bob.bio.base.utils.processors import (
+ SequentialProcessor, ParallelProcessor)
+from bob.bio.base.preprocessor import (
+ SequentialPreprocessor, ParallelPreprocessor, CallablePreprocessor)
+from bob.bio.base.extractor import (
+ SequentialExtractor, ParallelExtractor, CallableExtractor)
+
+DATA = [0, 1, 2, 3, 4]
+PROCESSORS = [partial(np.power, 2), np.mean]
+SEQ_DATA = PROCESSORS[1](PROCESSORS[0](DATA))
+PAR_DATA = np.hstack([PROCESSORS[0](DATA), PROCESSORS[1](DATA)])
+
+
+def test_processors():
+ proc = SequentialProcessor(PROCESSORS)
+ data = proc(DATA)
+ assert np.allclose(data, SEQ_DATA)
+
+ proc = ParallelProcessor(PROCESSORS)
+ data = proc(DATA)
+ assert np.allclose(data, PAR_DATA)
+
+
+def test_preprocessors():
+ processors = [CallablePreprocessor(p) for p in PROCESSORS]
+ proc = SequentialPreprocessor(processors)
+ data = proc(DATA, None)
+ assert np.allclose(data, SEQ_DATA)
+
+ proc = ParallelPreprocessor(processors)
+ data = proc(DATA, None)
+ assert np.allclose(data, PAR_DATA)
+
+
+def test_extractors():
+ processors = [CallableExtractor(p) for p in PROCESSORS]
+ proc = SequentialExtractor(processors)
+ data = proc(DATA)
+ assert np.allclose(data, SEQ_DATA)
+
+ proc = ParallelExtractor(processors)
+ data = proc(DATA)
+ assert np.allclose(data, PAR_DATA)
diff --git a/bob/bio/base/utils/__init__.py b/bob/bio/base/utils/__init__.py
index 4f1b2967..b65569cb 100644
--- a/bob/bio/base/utils/__init__.py
+++ b/bob/bio/base/utils/__init__.py
@@ -6,6 +6,7 @@
from .resources import *
from .io import *
from .singleton import *
+from . import processors
import numpy
diff --git a/bob/bio/base/utils/processors.py b/bob/bio/base/utils/processors.py
new file mode 100644
index 00000000..64549d76
--- /dev/null
+++ b/bob/bio/base/utils/processors.py
@@ -0,0 +1,84 @@
+import numpy
+
+
+class SequentialProcessor(object):
+ """A helper class which takes several processors and applies them one by one
+ sequentially
+
+ Attributes
+ ----------
+ processors : list
+ A list of processors to apply.
+ """
+
+ def __init__(self, processors):
+ super(SequentialProcessor, self).__init__()
+ self.processors = processors
+
+ def __call__(self, data, **kwargs):
+ """Applies the processors on the data sequentially. The output of the first
+ one goes as input to the next one.
+
+ Parameters
+ ----------
+ data : object
+ The data that needs to be processed.
+ **kwargs
+ Any kwargs are passed to the processors.
+
+ Returns
+ -------
+ object
+ The processed data.
+ """
+ for processor in self.processors:
+ try:
+ data = processor(data, **kwargs)
+ except ValueError:
+ data = processor(data)
+ return data
+
+
+class ParallelProcessor(object):
+ """A helper class which takes several processors and applies them on each
+ processor separately and outputs a list of their outputs in the end.
+
+ Attributes
+ ----------
+ processors : list
+ A list of processors to apply.
+ stack : bool
+ If True (default), :any:`numpy.hstack` is called on the list of outputs.
+ """
+
+ def __init__(self, processors, stack=True):
+ super(ParallelProcessor, self).__init__()
+ self.processors = processors
+ self.stack = stack
+
+ def __call__(self, data, **kwargs):
+ """Applies the processors on the data independently and outputs a list of
+ their outputs.
+
+ Parameters
+ ----------
+ data : object
+ The data that needs to be processed.
+ **kwargs
+ Any kwargs are passed to the processors.
+
+ Returns
+ -------
+ object
+ The processed data.
+ """
+ output = []
+ for processor in self.processors:
+ try:
+ out = processor(data, **kwargs)
+ except ValueError:
+ out = processor(data)
+ output.append(out)
+ if self.stack:
+ output = numpy.hstack(output)
+ return output
diff --git a/doc/implemented.rst b/doc/implemented.rst
index 8ceb9fe9..84b358bf 100644
--- a/doc/implemented.rst
+++ b/doc/implemented.rst
@@ -22,6 +22,12 @@ Implementations
.. autosummary::
bob.bio.base.preprocessor.Filename
+ bob.bio.base.preprocessor.SequentialPreprocessor
+ bob.bio.base.preprocessor.ParallelPreprocessor
+ bob.bio.base.preprocessor.CallablePreprocessor
+ bob.bio.base.extractor.SequentialExtractor
+ bob.bio.base.extractor.ParallelExtractor
+ bob.bio.base.extractor.CallableExtractor
bob.bio.base.extractor.Linearize
bob.bio.base.algorithm.Distance
bob.bio.base.algorithm.PCA
diff --git a/doc/py_api.rst b/doc/py_api.rst
index c9841b2b..13daaa8f 100644
--- a/doc/py_api.rst
+++ b/doc/py_api.rst
@@ -42,6 +42,14 @@ Miscellaneous functions
bob.bio.base.selected_indices
+Generic classes
+---------------
+
+.. autosummary::
+ bob.bio.base.utils.processors.SequentialProcessor
+ bob.bio.base.utils.processors.ParallelProcessor
+
+
Tools to run recognition experiments
------------------------------------
@@ -109,4 +117,7 @@ Details
.. autoclass:: FileSelector
+.. automodule:: bob.bio.base.utils.processors
+
+
.. include:: links.rst
--
GitLab