diff --git a/bob/bio/base/baseline/Baseline.py b/bob/bio/base/baseline/Baseline.py
index bb3a9ee7de6ccab4d8e6accb85d94082ce390b08..40459ccad63c444709e6092b37d20b29e9048d33 100644
--- a/bob/bio/base/baseline/Baseline.py
+++ b/bob/bio/base/baseline/Baseline.py
@@ -1,32 +1,75 @@
#!/usr/bin/env python
# vim: set fileencoding=utf-8 :
# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
+from .. import resource_keys, load_resource
+
+
+def search_preprocessor(db_name, keys):
+ """
+ Wrapper that searches for preprocessors for specific databases.
+ If not found, the default preprocessor is returned
+ """
+ for k in keys:
+ if db_name.startswith(k):
+ return k
+ else:
+ return "default"
+
+
+def get_available_databases():
+ """
+ Get all the available databases through the database entry-points
+ """
+
+ available_databases = dict()
+ all_databases = resource_keys('database', strip=[])
+ for database in all_databases:
+ try:
+ database_entry_point = load_resource(database, 'database')
+
+ available_databases[database] = dict()
+
+ # Checking if the database has data for the ZT normalization
+ available_databases[database]["has_zt"] = hasattr(database_entry_point, "zobjects") and hasattr(database_entry_point, "tobjects")
+ available_databases[database]["groups"] = []
+ # Searching for database groups
+ try:
+ groups = list(database_entry_point.groups())
+ for g in ["dev", "eval"]:
+ available_databases[database]["groups"] += [g] if g in groups else []
+ except Exception:
+ # In case the method groups is not implemented
+ available_databases[database]["groups"] = ["dev"]
+ except Exception:
+ pass
+ return available_databases
class Baseline(object):
- """
- Base class to define baselines
-
- A Baseline is composed by the triplet :any:`bob.bio.base.preprocessor.Preprocessor`,
- :any:`bob.bio.base.extractor.Extractor` and :any:`bob.bio.base.algorithm.Algorithm`
-
- Attributes
- ----------
-
- name: str
- Name of the baseline. This name will be displayed in the command line interface
- preprocessors: dict
- Dictionary containing all possible preprocessors
- extractor: str
- Registered resource or a config file containing the feature extractor
- algorithm: str
- Registered resource or a config file containing the algorithm
-
- """
-
- def __init__(self, name="", preprocessors=dict(), extractor="", algorithm="", **kwargs):
- super(Baseline, self).__init__(**kwargs)
- self.name = name
- self.preprocessors = preprocessors
- self.extractor = extractor
- self.algorithm = algorithm
+ """
+ Base class to define baselines
+
+ A Baseline is composed by the triplet
+ :any:`bob.bio.base.preprocessor.Preprocessor`,
+ :any:`bob.bio.base.extractor.Extractor`, and
+ :any:`bob.bio.base.algorithm.Algorithm`
+
+ Attributes
+ ----------
+ name : str
+ Name of the baseline. This name will be displayed in the command line
+ interface.
+ preprocessors : dict
+ Dictionary containing all possible preprocessors
+ extractor : str
+ Registered resource or a config file containing the feature extractor
+ algorithm : str
+ Registered resource or a config file containing the algorithm
+ """
+
+ def __init__(self, name, preprocessors, extractor, algorithm, **kwargs):
+ super(Baseline, self).__init__(**kwargs)
+ self.name = name
+ self.preprocessors = preprocessors
+ self.extractor = extractor
+ self.algorithm = algorithm
diff --git a/bob/bio/base/baseline/__init__.py b/bob/bio/base/baseline/__init__.py
index 12d6273762f59edcb51f6e7858d4f5b02c58f759..8e510bd3ea4dee434a12a3817a1c4769862d1fcd 100755
--- a/bob/bio/base/baseline/__init__.py
+++ b/bob/bio/base/baseline/__init__.py
@@ -1,43 +1,31 @@
-from .Baseline import Baseline
-import bob.bio.base
-
-
-def get_available_databases():
- """
- Get all the available databases through the database entry-points
- """
-
- available_databases = dict()
- all_databases = bob.bio.base.resource_keys('database', strip=[])
- for database in all_databases:
- try:
- database_entry_point = bob.bio.base.load_resource(database, 'database')
-
- available_databases[database] = dict()
-
- # Checking if the database has data for the ZT normalization
- available_databases[database]["has_zt"] = hasattr(database_entry_point, "zobjects") and hasattr(database_entry_point, "tobjects")
- available_databases[database]["groups"] = []
- # Searching for database groups
- try:
- groups = list(database_entry_point.groups())
- for g in ["dev", "eval"]:
- available_databases[database]["groups"] += [g] if g in groups else []
- except:
- # In case the method groups is not implemented
- available_databases[database]["groups"] = ["dev"]
- except:
- pass
- return available_databases
+from .Baseline import Baseline, search_preprocessor, get_available_databases
def get_config():
"""Returns a string containing the configuration information.
"""
-
import bob.extension
return bob.extension.get_config(__name__)
# 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:
+
+ *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__(
+ Baseline,
+)
+
__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/base/script/baseline.py b/bob/bio/base/script/baseline.py
index 3b8be66b7caf6c257e4ad0a1d7eb55be6c5dd044..74c219446b86748e2f5b0ce343f46c1332236e3b 100644
--- a/bob/bio/base/script/baseline.py
+++ b/bob/bio/base/script/baseline.py
@@ -3,77 +3,71 @@
# Tiago de Freitas Pereira <tiago.pereira@idiap.ch>
"""
-This script runs some face recognition baselines under some face databases
-
-Examples:
-
-This command line will run the facenet from David Sandberg using the ATnT dataset:
- `bob bio baseline --baseline facenet_msceleba_inception_v1 --database atnt`
-
+A script to run biometric recognition baselines
"""
-import bob.bio.base
-import bob.io.base
+from .. import load_resource
import os
-from bob.bio.base.script.verify import main as verify
-from bob.bio.base.baseline import get_available_databases
-from bob.extension.scripts.click_helper import (
- verbosity_option, ConfigCommand, ResourceOption)
+from .verify import main as verify
+from ..baseline import get_available_databases, search_preprocessor
+from bob.extension.scripts.click_helper import verbosity_option
import click
-@click.command(entry_point_group='bob.bio.config', cls=ConfigCommand)
-@click.option('--database', '-d', required=True, cls=ResourceOption, help="Registered database. Check it out `resources.py --types database` for ready to be used databases")
-@click.option('--baseline', '-b', required=True, cls=ResourceOption, help="Registered baseline. Check it out `resources.py --types baseline` for ready to be used baseline")
-@click.option('--temp-dir', '-T', required=False, cls=ResourceOption, help="The directory for temporary files")
-@click.option('--result-dir', '-R', required=False, cls=ResourceOption, help="The directory for resulting score files")
-@click.option('--grid', '-g', help="Execute the algorithm in the SGE grid.", is_flag=True)
-@click.option('--zt-norm', '-z', help="Enable the computation of ZT norms (if the database supports it).", is_flag=True)
-@verbosity_option(cls=ResourceOption)
+@click.command(context_settings={'ignore_unknown_options': True,
+ 'allow_extra_args': True})
+@click.argument('baseline', required=True)
+@click.argument('database', required=True)
+@verbosity_option()
+@click.pass_context
+def baseline(ctx, baseline, database):
+ """Run a biometric recognition baseline.
-def baseline(baseline, database, temp_dir, result_dir, grid, zt_norm, **kwargs):
- """
- Run a biometric recognition baselines
+ \b
+ Example:
+ $ bob bio baseline eigenface atnt -vvv
- Check it out all baselines available by typing `resource.py --types baseline`
+ which will run the eigenface baseline (from bob.bio.face) on the atnt
+ database.
- """
+ \b
+ Check out all baselines available by running:
+ `resource.py --types baseline`
+ and all available databases by running:
+ `resource.py --types database`
+
+ This script accepts parameters accepted by verify.py as well.
+ See `verify.py --help` for the extra options that you can pass.
+
+ Hint: pass `--grid demanding` to run the baseline on the SGE grid.
- def search_preprocessor(key, keys):
- """
- Wrapper that searches for preprocessors for specific databases.
- If not found, the default preprocessor is returned
- """
- for k in keys:
- if key.startswith(k):
- return k
- else:
- return "default"
+ Hint: pass `--temp-directory <dir>` to set the directory for temporary files
- # Triggering training for each baseline/database
- loaded_baseline = bob.bio.base.load_resource(baseline, 'baseline', package_prefix="bob.bio.")
+ Hint: pass `--result-directory <dir>` to set the directory for resulting score files
+
+ """
+ # Triggering training for each baseline/database
+ loaded_baseline = load_resource(
+ baseline, 'baseline', package_prefix="bob.bio.")
# this is the default sub-directory that is used
sub_directory = os.path.join(database, baseline)
+
+ # find the compatible preprocessor for this database
database_data = get_available_databases()[database]
+ db = search_preprocessor(database, loaded_baseline.preprocessors.keys())
+ preprocessor = loaded_baseline.preprocessors[db]
+
+ # call verify with all parameters
parameters = [
- '-p', loaded_baseline.preprocessors[search_preprocessor(database, loaded_baseline.preprocessors.keys())],
+ '-p', preprocessor,
'-e', loaded_baseline.extractor,
'-d', database,
'-a', loaded_baseline.algorithm,
- '-vvv',
- '--temp-directory', temp_dir,
- '--result-directory', result_dir,
'--sub-directory', sub_directory
- ]
-
- parameters += ['--groups'] + database_data["groups"]
-
- if grid:
- parameters += ['-g', 'demanding']
+ ] + ['-v'] * ctx.meta['verbosity']
- if zt_norm and 'has_zt' in database_data:
- parameters += ['--zt-norm']
+ parameters += ['--groups'] + database_data["groups"]
- verify(parameters)
+ verify(parameters + ctx.args)
diff --git a/bob/bio/base/test/dummy/baseline.py b/bob/bio/base/test/dummy/baseline.py
index e52717ec9eceb24911c4c24706553b5e12021509..e52d4b59992c160aa3a3a2b0c1874709968637a4 100644
--- a/bob/bio/base/test/dummy/baseline.py
+++ b/bob/bio/base/test/dummy/baseline.py
@@ -2,14 +2,8 @@ from bob.bio.base.baseline import Baseline
import pkg_resources
import os
-
dummy_dir = pkg_resources.resource_filename('bob.bio.base', 'test/dummy')
-class DummyBaseline(Baseline):
-
- def __init__(self, **kwargs):
- super(DummyBaseline, self).__init__(**kwargs)
-
-baseline = DummyBaseline(name="dummy",
+baseline = Baseline(name="dummy",
preprocessors={"default": os.path.join(dummy_dir, 'preprocessor.py')},
extractor=os.path.join(dummy_dir, 'extractor.py'),
algorithm=os.path.join(dummy_dir, 'algorithm.py'))
diff --git a/bob/bio/base/test/test_baselines.py b/bob/bio/base/test/test_baselines.py
index 42760e9d5e958496699d1b071c9e7573f40bc4b2..27dd5749b5eab5a7cbef8853753e25e41c218731 100644
--- a/bob/bio/base/test/test_baselines.py
+++ b/bob/bio/base/test/test_baselines.py
@@ -8,7 +8,7 @@ def test_baselines():
try:
tmp_dir = tempfile.mkdtemp(prefix="bobtest_")
runner = CliRunner()
- result = runner.invoke(baseline, args=('-d', 'dummy', '-b', 'dummy', '-T', tmp_dir, '-R', tmp_dir))
+ result = runner.invoke(baseline, args=('dummy', 'dummy', '-T', tmp_dir, '-R', tmp_dir))
assertion_error_message = (
'Command exited with this output: `{}\' \n'
'If the output is empty, you can run this script locally to see '
@@ -16,6 +16,6 @@ def test_baselines():
'bin/bob bio baseline -d dummy -a dummy -o /tmp/temp_annotations'
''.format(result.output))
assert result.exit_code == 0, assertion_error_message
-
+
finally:
shutil.rmtree(tmp_dir)
diff --git a/doc/baseline.rst b/doc/baseline.rst
index 2996e7baafe8c1f58664fc88f445a3e4c871b56f..2e6da391465c2c217906ea450c3a1d415a407b6e 100644
--- a/doc/baseline.rst
+++ b/doc/baseline.rst
@@ -5,72 +5,81 @@ Defining baselines
==================
-Once you have a biometric system well established, tuned and working for a particular database (or a particular set of databases), you may want to provide **an easier to reproduce** way to share it.
-For this purpose, we defined something called baseline.
+Once you have a biometric system well established, tuned and working for a
+particular database (or a particular set of databases), you may want to provide
+**an easier to reproduce** way to share it. For this purpose, we defined
+something called baseline.
-A baseline is composed by the triplet :any:`bob.bio.base.preprocessor.Preprocessor`, :any:`bob.bio.base.extractor.Extractor` and :any:`bob.bio.base.algorithm.Algorithm`.
+A baseline (:any:`bob.bio.base.baseline.Baseline`) is composed by the triplet
+of :any:`bob.bio.base.preprocessor.Preprocessor`,
+:any:`bob.bio.base.extractor.Extractor` and
+:any:`bob.bio.base.algorithm.Algorithm`.
-First, check it out the baselines ready to be triggered in your environment by doing:
+First, check it out the baselines ready to be triggered in your environment by
+doing:
.. code-block:: sh
$ bob bio baseline --help
+For example, if you run ``bob bio baseline -vvv eigenface atnt``, it will run
+the eigenface face recognition baseline on the atnt database (assuming you have
+installed ``bob.bio.face`` and ``bob.db.atnt``).
-To create your own baseline, you just need to define it like in the recipe below:
+
+To create your own baseline, you just need to define it like in the recipe
+below:
.. code-block:: py
from bob.bio.base.baseline import Baseline
- class DummyBaseline(Baseline):
-
- def __init__(self):
-
- self.preprocessors = dict() # SHOULD BE DEFINED AS A DICTIONARY
- self.preprocessors["default"] = 'my-preprocessor'
- self.extractor = 'my-extractor'
- self.algorithm = 'my-algorithm'
- baseline = DummyBaseline()
+ baseline = Baseline(name="my-baseline",
+ preprocessors={"default": 'my-preprocessor'},
+ extractor='my-extractor'),
+ algorithm='my-algorithm'))
-Some databases may require some especific preprocessors depending on the type of meta-informations provided.
-For instance, for some face recognition databases, faces should be cropped in a particular way depending on the annotations provided.
-To approach this issue, the preprocessors are defined in a dictionary, with a generic preprocessor defined as **default** and the database specific preprocessor defined by database name as in the example below:
+Some databases may require some specific preprocessors depending on the type
+of meta-informations provided. For instance, for some face recognition
+databases, faces should be cropped in a particular way depending on the
+annotations provided. To approach this issue, the preprocessors are defined in
+a dictionary, with a generic preprocessor defined as **default** and the
+database specific preprocessor defined by database name as in the example
+below:
.. code-block:: py
self.preprocessors = dict()
self.preprocessors["default"] = 'my-preprocessor'
self.preprocessors["database_name"] = 'my-specific-preprocessor'
-
-Follow below a full example on how to define a baseline with database specific preprocessors.
+
+Follow below a full example on how to define a baseline with database specific
+preprocessors.
.. code-block:: py
from bob.bio.base.baseline import Baseline
- class AnotherBaseline(Baseline):
-
- def __init__(self):
-
- self.preprocessors = dict() # SHOULD BE DEFINED AS A DICTIONARY
- self.preprocessors["default"] = 'my-preprocessor'
- self.preprocessors["database_name"] = 'my-specific-preprocessor'
- self.extractor = 'my-extractor'
- self.algorithm = 'my-algorithm'
- baseline = AnotherBaseline()
+ preprocessors = {"default": 'my-preprocessor'}
+ preprocessors["database_name"] = 'my-specific-preprocessor'
+ baseline = Baseline(name="another-baseline",
+ preprocessors=preprocessors,
+ extractor='my-extractor'),
+ algorithm='my-algorithm'))
.. note::
- The triplet can be a resource or a configuration file.
- This works in the same way as in :ref:`Running Experiments <running_part_1>`.
+ The triplet can be a resource or a configuration file. This works in the
+ same way as in :ref:`Running Experiments <running_part_1>`.
.. note::
- Baselines are also registered as resources under the keyworkd `bob.bio.baseline`.
+ Baselines are also registered as resources under the keyword
+ `bob.bio.baseline`.
-You can find the list of readily available baselines using the ``resources.py`` command:
+You can find the list of readily available baselines using the ``resources.py``
+command:
.. code-block:: sh
diff --git a/doc/implemented.rst b/doc/implemented.rst
index 052e56deb9b1f7c0bb0f8fb12aafc59215c1cb82..80a4ab1ee8a35d73c98bafae3c2261ac66184d01 100644
--- a/doc/implemented.rst
+++ b/doc/implemented.rst
@@ -16,6 +16,7 @@ Base Classes
bob.bio.base.algorithm.Algorithm
bob.bio.base.grid.Grid
bob.bio.base.annotator.Annotator
+ bob.bio.base.baseline.Baseline
Implementations
@@ -80,4 +81,10 @@ Annotators
.. automodule:: bob.bio.base.annotator
+Baselines
+---------
+
+.. automodule:: bob.bio.base.baseline
+
+
.. include:: links.rst