From 7b54bbaa07623868233be6c5bfaba146f5393a99 Mon Sep 17 00:00:00 2001
From: Amir MOHAMMADI <amir.mohammadi@idiap.ch>
Date: Wed, 27 Apr 2016 16:39:19 +0200
Subject: [PATCH] Generate documentation
---
bob/fusion/base/fusion.py | 138 -----------------------
bob/fusion/base/tools/command_line.py | 4 +-
doc/bob.fusion.base.algorithm.rst | 62 ++++++++++
doc/bob.fusion.base.config.algorithm.rst | 54 +++++++++
doc/bob.fusion.base.config.rst | 17 +++
doc/bob.fusion.base.rst | 20 ++++
doc/bob.fusion.base.script.rst | 30 +++++
doc/bob.fusion.base.tools.rst | 30 +++++
doc/bob.fusion.rst | 17 +++
doc/bob.rst | 17 +++
doc/{fusion.rst => guide.rst} | 12 +-
doc/index.rst | 15 +--
doc/modules.rst | 7 ++
doc/py_api.rst | 10 --
14 files changed, 264 insertions(+), 169 deletions(-)
delete mode 100644 bob/fusion/base/fusion.py
create mode 100644 doc/bob.fusion.base.algorithm.rst
create mode 100644 doc/bob.fusion.base.config.algorithm.rst
create mode 100644 doc/bob.fusion.base.config.rst
create mode 100644 doc/bob.fusion.base.rst
create mode 100644 doc/bob.fusion.base.script.rst
create mode 100644 doc/bob.fusion.base.tools.rst
create mode 100644 doc/bob.fusion.rst
create mode 100644 doc/bob.rst
rename doc/{fusion.rst => guide.rst} (65%)
create mode 100644 doc/modules.rst
delete mode 100644 doc/py_api.rst
diff --git a/bob/fusion/base/fusion.py b/bob/fusion/base/fusion.py
deleted file mode 100644
index 62c9372..0000000
--- a/bob/fusion/base/fusion.py
+++ /dev/null
@@ -1,138 +0,0 @@
-#!/usr/bin/env python
-
-import os
-import numpy
-import matplotlib.pyplot as plt
-from bob.measure.load import load_score, get_all_scores,\
- get_negatives_positives_all
-from bob.fusion.base.algorithm import LLR, Weighted_Sum, MLP
-from bob.fusion.base.normalizer import ZNorm
-
-
-def main():
- '''
-/home/amir/idiap/remote/user/mobio-male/baselines/gmm/male/nonorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/baselines/gmm/male/nonorm/scores-eval
-/home/amir/idiap/remote/user/mobio-male/baselines/gmm/male/ztnorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/baselines/gmm/male/ztnorm/scores-eval
-
-/home/amir/idiap/remote/user/mobio-male/baselines/gabor-graph/male/nonorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/baselines/gabor-graph/male/nonorm/scores-eval
-/home/amir/idiap/remote/user/mobio-male/baselines/gabor-graph/male/ztnorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/baselines/gabor-graph/male/ztnorm/scores-eval
-
-
-/home/amir/idiap/remote/user/mobio-male/voice/gmm/male/nonorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/voice/gmm/male/nonorm/scores-eval
-/home/amir/idiap/remote/user/mobio-male/voice/gmm/male/ztnorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/voice/gmm/male/ztnorm/scores-eval
-
-/home/amir/idiap/remote/user/mobio-male/voice/isv/male/nonorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/voice/isv/male/nonorm/scores-eval
-/home/amir/idiap/remote/user/mobio-male/voice/isv/male/ztnorm/scores-dev
-/home/amir/idiap/remote/user/mobio-male/voice/isv/male/ztnorm/scores-eval
- # = ['/home/amir/idiap/remote/scores-dev_gmm',
- # '/home/amir/idiap/remote/scores-dev_isv']
- # s_eval_paths = ['/home/amir/idiap/remote/scores-eval_gmm',
- # '/home/amir/idiap/remote/scores-eval_isv']
-
-
-
- '''
- score_path_mask = '/home/amir/idiap/remote/user/mobio-male/{}/male/{}/scores-{}'
- fusion_lists = [
- (('baselines/gmm', 'voice/isv'), 'face-voice/F-gmm-S-isv{}'),
- (('baselines/gmm', 'baselines/gabor-graph'), 'baselines/gmm-gabor-graph{}'),
- (('voice/gmm', 'voice/isv'), 'voice/gmm-isv{}'),
- # (('baselines/gmm', 'baselines/gabor-graph', 'voice/gmm', 'voice/isv'), 'face-voice/F-gmm-gabor-graph-S-gmm-isv{}'),
- ]
- for norm in ['ztnorm']:
- for scores_paths_param, save_path_param in fusion_lists:
- save_path_dev = score_path_mask.format(save_path_param, norm, 'dev')
- save_path_eval = score_path_mask.format(save_path_param, norm, 'eval')
- # for path in [save_path_dev, save_path_eval]:
- # for tag in [
- # '_Weighted_Sum',
- # '_LLR',
- # '_MLP'
- # ]:
- # try:
- # os.makedirs(os.path.split(path.format(tag))[0])
- # except Exception:
- # pass
- s_dev_paths = [
- score_path_mask.format(a, norm, 'dev') for a in scores_paths_param]
- s_eval_paths = [
- score_path_mask.format(a, norm, 'eval') for a in scores_paths_param]
-
- score_lines_list = [load_score(path) for path in s_dev_paths]
- scores = get_all_scores(score_lines_list)
- trainer_scores = get_negatives_positives_all(score_lines_list)
- score_lines_list_eval = [load_score(path) for path in s_eval_paths]
- scores_eval = get_all_scores(score_lines_list_eval)
- plt.figure()
- for i, (fuse, tag) in enumerate([
- (Weighted_Sum(normalizer=ZNorm(), scores=numpy.array(scores), trainer_scores=trainer_scores), '_Weighted_Sum'),
- (LLR(normalizer=ZNorm(), scores=numpy.array(scores), trainer_scores=trainer_scores), '_LLR'),
- (MLP(normalizer=ZNorm(), scores=numpy.array(scores), trainer_scores=trainer_scores, verbose=True,
- mlp_shape=(2, 3, 1), batch_size=1, seed=0), '_MLP'),
- ]):
- plt.subplot(2,2,i+1)
- fuse.train()
- # import ipdb; ipdb.set_trace()
- fused_scores_dev = fuse()
- score_lines = numpy.array(score_lines_list[0])
- score_lines['score'] = fused_scores_dev
- # import ipdb
- # ipdb.set_trace()
- # numpy.savetxt(save_path_dev.format(tag), score_lines, fmt='%s %s %s %.6f')
-
- fuse.scores = numpy.array(scores_eval)
- fused_scores_eval = fuse()
- fuse.scores = numpy.array(scores_eval)
-
- score_lines = numpy.array(score_lines_list_eval[0])
- score_lines['score'] = fused_scores_eval
- # numpy.savetxt(save_path_eval.format(tag), score_lines, fmt='%s %s %s %.6f')
-
- # plot the decision boundary
- from bob.measure import eer_threshold, min_hter_threshold
- from bob.measure.load import get_negatives_positives
-
- score_labels = score_lines['claimed_id'] == score_lines['real_id']
- threshold = eer_threshold(*get_negatives_positives(score_lines))
- thres_system1 = min_hter_threshold(
- *get_negatives_positives(score_lines_list[0]))
- thres_system2 = min_hter_threshold(
- *get_negatives_positives(score_lines_list[1]))
- fuse.plot_boundary_decision(
- score_labels, threshold,
- scores_paths_param[0], scores_paths_param[1],
- thres_system1, thres_system2,
- True,
- seed=0
- )
- plt.title(tag[1:])
- # print(thres_system1, thres_system2)
- # thres_system1, thres_system2 = (3.51670052, 3.19892205)
- # plt.axvline(thres_system1, color='red')
- # plt.axhline(thres_system2, color='red')
- # plt.show()
- plt.savefig('scatter_{}_{}.pdf'.format(norm, '_'.join([a.replace('/','-') for a in scores_paths_param])))
- plt.close()
- # return
-
- # fuse = LLR(scores=scores, trainer_scores=trainer_scores)
- # fuse.train()
- # print('LLR', fuse()[:10])
- # fuse = Weighted_Sum(scores=scores)
- # print('Weighted_Sum', fuse()[:10])
- # fuse = MEAN(scores=scores)
- # print('MEAN', fuse()[:10])
- # fuse = MLP(scores=scores, trainer_scores=trainer_scores,
- # verbose=True, max_iter=0, batch_size=1)
- # fuse.train()
- # print('MLP', fuse()[:10])
-
-if __name__ == '__main__':
- main()
diff --git a/bob/fusion/base/tools/command_line.py b/bob/fusion/base/tools/command_line.py
index a72a12b..f9662df 100644
--- a/bob/fusion/base/tools/command_line.py
+++ b/bob/fusion/base/tools/command_line.py
@@ -119,7 +119,7 @@ def write_info(args, command_line_parameters):
command_line_parameters : [str] or ``None``
The command line parameters that have been interpreted.
If ``None``, the parameters specified by the user on command line
- are considered.
+ are considered.
executable : str
The name of the executable (such as ``'./bin/verify.py'``) that is used
@@ -161,7 +161,7 @@ def load_resource(resource, keyword, imports=['bob.fusion.base'],
1. a resource as defined in the setup.py
2. a configuration file
3. a string defining the construction of an object. If imports are required
- for the construction of this object, they can be given as list of strings.
+ for the construction of this object, they can be given as list of strings.
**Parameters:**
diff --git a/doc/bob.fusion.base.algorithm.rst b/doc/bob.fusion.base.algorithm.rst
new file mode 100644
index 0000000..bd1c60c
--- /dev/null
+++ b/doc/bob.fusion.base.algorithm.rst
@@ -0,0 +1,62 @@
+bob.fusion.base.algorithm package
+=================================
+
+Submodules
+----------
+
+bob.fusion.base.algorithm.Algorithm module
+------------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.Algorithm
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.algorithm.AlgorithmBob module
+---------------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.AlgorithmBob
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.algorithm.LLR module
+------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.LLR
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.algorithm.MLP module
+------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.MLP
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.algorithm.Weighted_Sum module
+---------------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.Weighted_Sum
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.algorithm.mlp_train_helper module
+-------------------------------------------------
+
+.. automodule:: bob.fusion.base.algorithm.mlp_train_helper
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base.algorithm
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.base.config.algorithm.rst b/doc/bob.fusion.base.config.algorithm.rst
new file mode 100644
index 0000000..696ffe5
--- /dev/null
+++ b/doc/bob.fusion.base.config.algorithm.rst
@@ -0,0 +1,54 @@
+bob.fusion.base.config.algorithm package
+========================================
+
+Submodules
+----------
+
+bob.fusion.base.config.algorithm.llr module
+-------------------------------------------
+
+.. automodule:: bob.fusion.base.config.algorithm.llr
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.config.algorithm.llr_skl module
+-----------------------------------------------
+
+.. automodule:: bob.fusion.base.config.algorithm.llr_skl
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.config.algorithm.mean module
+--------------------------------------------
+
+.. automodule:: bob.fusion.base.config.algorithm.mean
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.config.algorithm.mlp module
+-------------------------------------------
+
+.. automodule:: bob.fusion.base.config.algorithm.mlp
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.config.algorithm.plr_2 module
+---------------------------------------------
+
+.. automodule:: bob.fusion.base.config.algorithm.plr_2
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base.config.algorithm
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.base.config.rst b/doc/bob.fusion.base.config.rst
new file mode 100644
index 0000000..7a31f5d
--- /dev/null
+++ b/doc/bob.fusion.base.config.rst
@@ -0,0 +1,17 @@
+bob.fusion.base.config package
+==============================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ bob.fusion.base.config.algorithm
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base.config
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.base.rst b/doc/bob.fusion.base.rst
new file mode 100644
index 0000000..d0812d8
--- /dev/null
+++ b/doc/bob.fusion.base.rst
@@ -0,0 +1,20 @@
+bob.fusion.base package
+=======================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ bob.fusion.base.algorithm
+ bob.fusion.base.config
+ bob.fusion.base.script
+ bob.fusion.base.tools
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.base.script.rst b/doc/bob.fusion.base.script.rst
new file mode 100644
index 0000000..638fb52
--- /dev/null
+++ b/doc/bob.fusion.base.script.rst
@@ -0,0 +1,30 @@
+bob.fusion.base.script package
+==============================
+
+Submodules
+----------
+
+bob.fusion.base.script.bob_fuse module
+--------------------------------------
+
+.. automodule:: bob.fusion.base.script.bob_fuse
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.script.plot_fusion_decision_boundary module
+-----------------------------------------------------------
+
+.. automodule:: bob.fusion.base.script.plot_fusion_decision_boundary
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base.script
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.base.tools.rst b/doc/bob.fusion.base.tools.rst
new file mode 100644
index 0000000..31e5409
--- /dev/null
+++ b/doc/bob.fusion.base.tools.rst
@@ -0,0 +1,30 @@
+bob.fusion.base.tools package
+=============================
+
+Submodules
+----------
+
+bob.fusion.base.tools.command_line module
+-----------------------------------------
+
+.. automodule:: bob.fusion.base.tools.command_line
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+bob.fusion.base.tools.plotting module
+-------------------------------------
+
+.. automodule:: bob.fusion.base.tools.plotting
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion.base.tools
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.fusion.rst b/doc/bob.fusion.rst
new file mode 100644
index 0000000..ad8d408
--- /dev/null
+++ b/doc/bob.fusion.rst
@@ -0,0 +1,17 @@
+bob.fusion package
+==================
+
+Subpackages
+-----------
+
+.. toctree::
+
+ bob.fusion.base
+
+Module contents
+---------------
+
+.. automodule:: bob.fusion
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/bob.rst b/doc/bob.rst
new file mode 100644
index 0000000..86625e7
--- /dev/null
+++ b/doc/bob.rst
@@ -0,0 +1,17 @@
+bob package
+===========
+
+Subpackages
+-----------
+
+.. toctree::
+
+ bob.fusion
+
+Module contents
+---------------
+
+.. automodule:: bob
+ :members:
+ :undoc-members:
+ :show-inheritance:
diff --git a/doc/fusion.rst b/doc/guide.rst
similarity index 65%
rename from doc/fusion.rst
rename to doc/guide.rst
index a3c2b76..8074927 100644
--- a/doc/fusion.rst
+++ b/doc/guide.rst
@@ -8,18 +8,18 @@
Running Score Fusion in Biometric Recognition Experiments
==========================================================
-There are two scripts available in the package as of now and they work for verification scenarios.
-Spoofing and Anti-spoofing scenarios are not considered yet in the scripts however the Python API allows for easy extension.
-
Each score fusion experiment requires at least a classifier.
-The ``bob.fusion.base`` package itself implements two such classifiers: ``MLP`` and ``WeightedSum``.
+The ``bob.fusion.base`` package itself implements three such classifiers: ``MLP``, ``LLR`` and ``WeightedSum``.
You can also use any class as a classifier that implements a ``fit(X[, y])`` and a ``decision_function(X)`` method.
An example is `sklearn.linear_model.LogisticRegression <http://scikit-learn.org/stable/modules/generated/sklearn.linear_model.LogisticRegression.html>`_.
You can also use pre-processors to pre-process your data. The pre-processor class should implement a ``fit_transform(X[, y])`` and a ``transform(X[, y, copy])`` methods. An example is `sklearn.preprocessing.StandardScaler <http://scikit-learn.org/stable/modules/generated/sklearn.preprocessing.StandardScaler.html>`_.
-Using ``sklearn`` classifiers and pre-processors you can different fusion algorithms. Please take a look at some examples in ``bob.fusion.base.config.algorithm`` to see how it is done.
+Using ``sklearn`` classifiers and pre-processors you can implement different fusion algorithms. Please take a look at some examples in ``bob.fusion.base.config.algorithm`` to see how it is done.
+
+There are two scripts available in the package as of now and they work for verification scenarios.
+Spoofing and Anti-spoofing scenarios are not considered yet **in the scripts** however the Python API allows for easy extension.
-Also take a look at the scripts ``fuse.py`` and ``plot_fusion_decision_boundary.py`` and use them for your actual fusion experiments.
+Also take a look at the scripts ``bob_fuse.py`` and ``plot_fusion_decision_boundary.py`` and use them for your actual fusion experiments.
.. include:: links.rst
diff --git a/doc/index.rst b/doc/index.rst
index 2d22471..85f9bba 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -19,7 +19,7 @@ Users Guide
.. toctree::
:maxdepth: 2
- fusion
+ guide
================
Reference Manual
@@ -28,7 +28,7 @@ Reference Manual
.. toctree::
:maxdepth: 2
- py_api
+* :ref:`modindex`
==========
@@ -36,22 +36,11 @@ References
==========
-=========
-ToDo-List
-=========
-
-This documentation is still under development.
-Here is a list of things that needs to be done:
-
-.. todolist::
- testing
-
==================
Indices and tables
==================
* :ref:`genindex`
-* :ref:`modindex`
* :ref:`search`
.. include:: links.rst
diff --git a/doc/modules.rst b/doc/modules.rst
new file mode 100644
index 0000000..8dc34ff
--- /dev/null
+++ b/doc/modules.rst
@@ -0,0 +1,7 @@
+bob.fusion.base
+===============
+
+.. toctree::
+ :maxdepth: 4
+
+ bob
diff --git a/doc/py_api.rst b/doc/py_api.rst
deleted file mode 100644
index 951e069..0000000
--- a/doc/py_api.rst
+++ /dev/null
@@ -1,10 +0,0 @@
-
-===========================
-Python API for bob.fusion.base
-===========================
-
-
-Details
--------
-
-.. include:: links.rst
--
GitLab