Merge branch 'issue-8-remove-database-configuration' into 'master'

Issue 8 remove database configuration

Solving issue #37  (some database tests are missing)


See merge request !38

bob/bio/base/preprocessor/Preprocessor.py

@@ -22,7 +22,7 @@ class Preprocessor:
     A list of keyword arguments to be written in the :py:meth:`__str__` function.
   """
 
-  def __init__(self, writes_data = True, read_original_data = lambda biofile,directory,extension : biofile.load(directory,extension), **kwargs):
+  def __init__(self, writes_data = True, read_original_data = utils.read_original_data, **kwargs):
     # Each class needs to have a constructor taking
     # all the parameters that are required for the preprocessing as arguments
     self.writes_data = writes_data

bob/bio/base/test/test_database_implementations.py

+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# Amir Mohammadi <amir.mohammadi@idiap.ch>
+# Wed 20 July 16:20:12 CEST 2016
+#
+
+"""
+Very simple tests for Implementations
+"""
+
+import os
+from bob.bio.base.database import BioDatabase, ZTBioDatabase
+
+
+def check_database(database, groups=('dev',), protocol=None, training_depends=False, models_depend=False):
+    assert isinstance(database, BioDatabase)
+
+    # load the directories
+    if 'HOME' in os.environ:
+        database.replace_directories(os.path.join(os.environ['HOME'], '.bob_bio_databases.txt'))
+
+    if protocol: database.protocol = protocol
+    if protocol is None: protocol = database.protocol
+
+    assert len(database.all_files()) > 0
+    assert len(database.training_files('train_extractor')) > 0
+    assert len(database.arrange_by_client(database.training_files('train_enroller'))) > 0
+
+    for group in groups:
+        model_ids = database.model_ids_with_protocol(group, protocol=protocol)
+        assert len(model_ids) > 0
+        assert database.client_id_from_model_id(model_ids[0]) is not None
+        assert len(database.enroll_files(model_ids[0], group)) > 0
+        assert len(database.probe_files(model_ids[0], group)) > 0
+
+    assert database.training_depends_on_protocol == training_depends
+    assert database.models_depend_on_protocol == models_depend
+
+
+def check_database_zt(database, groups=('dev', 'eval'), protocol=None, training_depends=False, models_depend=False):
+    check_database(database, groups, protocol, training_depends, models_depend)
+    assert isinstance(database, ZTBioDatabase)
+    for group in groups:
+        t_model_ids = database.t_model_ids(group)
+        assert len(t_model_ids) > 0
+        assert database.client_id_from_model_id(t_model_ids[0]) is not None
+        assert len(database.t_enroll_files(t_model_ids[0], group)) > 0
+        assert len(database.z_probe_files(group)) > 0
+
+

bob/bio/base/utils/io.py

@@ -4,6 +4,7 @@ import tempfile, tarfile
 import logging
 logger = logging.getLogger("bob.bio.base")
 
+from .. import database
 import bob.io.base
 
 def filter_missing_files(file_names, split_by_client=False, allow_missing_files=True):
@@ -51,6 +52,33 @@ def check_file(filename, force, expected_file_size = 1):
   return False
 
 
+def read_original_data(biofile, directory, extension):
+  """read_original_data(biofile, directory, extension) -> data
+
+  This function reads the original data using the given ``biofile`` instance.
+  It simply calls ``load(directory, extension)`` from :py:class:`bob.bio.base.database.BioFile` or one of its derivatives.
+
+  **Parameters:**
+
+  ``biofile`` : :py:class:`bob.bio.base.database.BioFile` or one of its derivatives
+    The file to read the original data.
+
+  ``directory`` : str
+    The base directory of the database.
+
+  ``extension`` : str or ``None``
+    The extension of the original data.
+    Might be ``None`` if the ``biofile`` itself has the extension stored.
+
+  **Returns**
+
+  ``data`` : object
+    Whatver ``biofile.load`` returns; usually a :py:class:`numpy.ndarray`
+  """
+  assert isinstance(biofile, database.BioFile)
+  return biofile.load(directory, extension)
+
+
 def load(file):
   """Loads data from file. The given file might be an HDF5 file open for reading or a string."""
   if isinstance(file, bob.io.base.HDF5File):