diff --git a/bob/bio/base/database/filelist/query.py b/bob/bio/base/database/filelist/query.py
index f1e5a0511c401d78b40c4030b09d7eb451275f99..09ae85f89744affd70295a832909cb92ec4c7af6 100644
--- a/bob/bio/base/database/filelist/query.py
+++ b/bob/bio/base/database/filelist/query.py
@@ -125,6 +125,7 @@ class FileListBioDatabase(ZTBioDatabase):
and the given sub-directories and file names (which default to useful values if not given)."""
super(FileListBioDatabase, self).__init__(
+ filelists_directory=filelists_directory,
name=name,
protocol=protocol,
original_directory=original_directory,
@@ -150,10 +151,8 @@ class FileListBioDatabase(ZTBioDatabase):
# self.original_directory = original_directory
# self.original_extension = original_extension
self.bio_file_class = bio_file_class
-
- self.m_annotation_directory = annotation_directory
- self.m_annotation_extension = annotation_extension
- self.m_annotation_type = annotation_type
+ self.keep_read_lists_in_memory=keep_read_lists_in_memory
+ self.list_readers = {}
self.m_base_dir = os.path.abspath(filelists_directory)
if not os.path.isdir(self.m_base_dir):
@@ -183,72 +182,45 @@ class FileListBioDatabase(ZTBioDatabase):
# Z-Norm files format: filename client_id
self.m_znorm_filename = znorm_filename if znorm_filename is not None else 'for_znorm.lst'
- # decide, which scoring type we have:
- if probes_filename is not None and scores_filename is None:
- self.m_use_dense_probes = True
- elif probes_filename is None and scores_filename is not None:
- self.m_use_dense_probes = False
- elif use_dense_probe_file_list is not None:
- self.m_use_dense_probes = use_dense_probe_file_list
- # Then direct path to a given protocol
- elif os.path.isdir(os.path.join(self.get_base_directory(), self.m_dev_subdir)) or os.path.isfile(
- os.path.join(self.get_base_directory(), self.m_world_filename)):
- if os.path.exists(self.get_list_file('dev', 'for_probes')) and not os.path.exists(
- self.get_list_file('dev', 'for_scores')):
- self.m_use_dense_probes = True
- elif not os.path.exists(self.get_list_file('dev', 'for_probes')) and os.path.exists(
- self.get_list_file('dev', 'for_scores')):
- self.m_use_dense_probes = False
- else:
- raise ValueError("Unable to determine, which way of probing should be used. Please specify.")
- # Then path to a directory that contains several subdirectories (one for each protocol)
- else:
- # Look at subdirectories for each protocol
- protocols = [p for p in os.listdir(self.get_base_directory()) if
- os.path.isdir(os.path.join(self.get_base_directory(), p))]
- if len(protocols) == 0:
- raise ValueError(
- "Unable to determine, which way of probing should be used (no protocol directories found). Please specify.")
- list_use_dense_probes = []
- for p in protocols:
- if os.path.exists(self.get_list_file('dev', 'for_probes', p)) and not os.path.exists(
- self.get_list_file('dev', 'for_scores', p)):
- use_dense_probes = True
- elif not os.path.exists(self.get_list_file('dev', 'for_probes', p)) and os.path.exists(
- self.get_list_file('dev', 'for_scores', p)):
- use_dense_probes = False
- else:
- raise ValueError(
- "Unable to determine, which way of probing should be used, looking at the protocol (directory) '%s'. Please specify." % p)
- list_use_dense_probes.append(use_dense_probes)
- if len(set(list_use_dense_probes)) == 1:
- self.m_use_dense_probes = list_use_dense_probes[0]
- else:
- raise ValueError(
- "Unable to determine, which way of probing should be used, since this is not consistent accross protocols. Please specify.")
+ self.m_use_dense_probe_file_list = use_dense_probe_file_list
+
+
+ def _list_reader(self, protocol):
+ if protocol not in self.list_readers:
+ if protocol is not None:
+ protocol_dir = os.path.join(self.get_base_directory(), protocol)
+ if not os.path.isdir(protocol_dir):
+ raise ValueError("The directory %s for the given protocol '%s' does not exist" % (protocol_dir, protocol))
+ self.list_readers[protocol] = ListReader(self.keep_read_lists_in_memory)
- self.m_list_reader = ListReader(keep_read_lists_in_memory)
+ return self.list_readers[protocol]
def _make_bio(self, files):
return [self.bio_file_class(client_id=f.client_id, path=f.path, file_id=f.id) for f in files]
def all_files(self, groups=['dev']):
- files = self.objects(groups, self.protocol, None, None, **self.all_files_options)
+ files = self.objects(groups, self.protocol, **self.all_files_options)
# add all files that belong to the ZT-norm
for group in groups:
if group == 'world':
continue
if self.implements_zt(self.protocol, group):
- files += self.tobjects(group, self.protocol, None)
+ files += self.tobjects(group, self.protocol)
files += self.zobjects(group, self.protocol, **self.z_probe_options)
return self.sort(self._make_bio(files))
- def groups(self, protocol=None):
+ def groups(self, protocol=None, add_world=True, add_subworld=True):
"""This function returns the list of groups for this database.
protocol : str or ``None``
The protocol for which the groups should be retrieved.
+ add_world : bool
+ Add the world groups?
+
+ add_subworld : bool
+ Add the sub-world groups? Only valid, when ``add_world=True``
+
Returns: a list of groups
"""
@@ -259,23 +231,27 @@ class FileListBioDatabase(ZTBioDatabase):
groups.append('dev')
if os.path.isdir(os.path.join(self.get_base_directory(), protocol, self.m_eval_subdir)):
groups.append('eval')
- if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_world_filename)):
- groups.append('world')
- if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_optional_world_1_filename)):
- groups.append('optional_world_1')
- if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_optional_world_2_filename)):
- groups.append('optional_world_2')
+ if add_world:
+ if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_world_filename)):
+ groups.append('world')
+ if add_world and add_subworld:
+ if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_optional_world_1_filename)):
+ groups.append('optional_world_1')
+ if os.path.isfile(os.path.join(self.get_base_directory(), protocol, self.m_optional_world_2_filename)):
+ groups.append('optional_world_2')
else:
if os.path.isdir(os.path.join(self.get_base_directory(), self.m_dev_subdir)):
groups.append('dev')
if os.path.isdir(os.path.join(self.get_base_directory(), self.m_eval_subdir)):
groups.append('eval')
- if os.path.isfile(os.path.join(self.get_base_directory(), self.m_world_filename)):
- groups.append('world')
- if os.path.isfile(os.path.join(self.get_base_directory(), self.m_optional_world_1_filename)):
- groups.append('optional_world_1')
- if os.path.isfile(os.path.join(self.get_base_directory(), self.m_optional_world_2_filename)):
- groups.append('optional_world_2')
+ if add_world:
+ if os.path.isfile(os.path.join(self.get_base_directory(), self.m_world_filename)):
+ groups.append('world')
+ if add_world and add_subworld:
+ if os.path.isfile(os.path.join(self.get_base_directory(), self.m_optional_world_1_filename)):
+ groups.append('optional_world_1')
+ if os.path.isfile(os.path.join(self.get_base_directory(), self.m_optional_world_2_filename)):
+ groups.append('optional_world_2')
return groups
def implements_zt(self, protocol=None, groups=None):
@@ -292,16 +268,36 @@ class FileListBioDatabase(ZTBioDatabase):
Returns:
``True`` if the all file lists for ZT score normalization exist, otherwise ``False``.
"""
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
-
protocol = protocol or self.protocol
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
+
for group in groups:
for t in ['for_tnorm', 'for_znorm']:
- if not os.path.exists(self.get_list_file(group, t, protocol)):
+ if not os.path.exists(self._get_list_file(group, t, protocol)):
return False
# all files exist
return True
+ def uses_dense_probe_file(self, protocol):
+ """Determines if a dense probe file list is used based on the existence of parameters."""
+ # return, whatever was specified in constructor, if not None
+ if self.m_use_dense_probe_file_list is not None:
+ return self.m_use_dense_probe_file_list
+
+ # check the existence of the files
+ probes = True
+ scores = True
+ for group in self.groups(protocol, add_world=False):
+ probes = probes and os.path.exists(self._get_list_file(group, type='for_probes', protocol=protocol))
+ scores = probes and os.path.exists(self._get_list_file(group, type='for_scores', protocol=protocol))
+ # decide, which score files are available
+ if probes and not scores:
+ return True
+ if not probes and scores:
+ return False
+ raise ValueError("Unable to determine, which way of probing should be used. Please specify.")
+
+
def get_base_directory(self):
"""Returns the base directory where the filelists defining the database
are located."""
@@ -314,7 +310,7 @@ class FileListBioDatabase(ZTBioDatabase):
if not os.path.isdir(self.filelists_directory):
raise RuntimeError('Invalid directory specified %s.' % (self.filelists_directory))
- def get_list_file(self, group, type=None, protocol=None):
+ def _get_list_file(self, group, type=None, protocol=None):
if protocol:
base_directory = os.path.join(self.get_base_directory(), protocol)
else:
@@ -353,15 +349,13 @@ class FileListBioDatabase(ZTBioDatabase):
Returns: The client id for the given model id, if found.
"""
- # compatibility reasons
- groups = group
- groups = self.check_parameters_for_validity(groups, "group",
- ('dev', 'eval', 'world', 'optional_world_1', 'optional_world_2'),
- default_parameters=('dev', 'eval', 'world'))
-
protocol = self.protocol
+ groups = self.check_parameters_for_validity(group, "group",
+ self.groups(protocol),
+ default_parameters=self.groups(protocol, add_subworld=False))
+
for group in groups:
- model_dict = self.m_list_reader.read_models(self.get_list_file(group, 'for_models', protocol), group,
+ model_dict = self._list_reader(protocol).read_models(self._get_list_file(group, 'for_models', protocol), group,
'for_models')
if model_id in model_dict:
return model_dict[model_id]
@@ -386,12 +380,11 @@ class FileListBioDatabase(ZTBioDatabase):
Returns: The client id for the given model id of a T-Norm model, if found.
"""
- groups = group
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
-
protocol = self.protocol
+ groups = self.check_parameters_for_validity(group, "group", self.groups(protocol, add_world=False))
+
for group in groups:
- model_dict = self.m_list_reader.read_models(self.get_list_file(group, 'for_tnorm', protocol), group,
+ model_dict = self._list_reader(protocol).read_models(self._get_list_file(group, 'for_tnorm', protocol), group,
'for_tnorm')
if t_model_id in model_dict:
return model_dict[t_model_id]
@@ -456,7 +449,7 @@ class FileListBioDatabase(ZTBioDatabase):
protocol = protocol or self.protocol
# read all lists for all groups and extract the model ids
for group in groups:
- files = self.m_list_reader.read_list(self.get_list_file(group, type, protocol), group, type)
+ files = self._list_reader(protocol).read_list(self._get_list_file(group, type, protocol), group, type)
for file in files:
ids.add(file.client_id)
return ids
@@ -477,8 +470,8 @@ class FileListBioDatabase(ZTBioDatabase):
protocol = protocol or self.protocol
groups = self.check_parameters_for_validity(groups, "group",
- ('dev', 'eval', 'world', 'optional_world_1', 'optional_world_2'),
- default_parameters=('dev', 'eval', 'world'))
+ self.groups(protocol),
+ default_parameters=self.groups(protocol, add_subworld=False))
return self.__client_id_list__(groups, 'for_models', protocol)
@@ -497,7 +490,7 @@ class FileListBioDatabase(ZTBioDatabase):
"""
protocol = protocol or self.protocol
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
return self.__client_id_list__(groups, 'for_tnorm', protocol)
@@ -516,7 +509,7 @@ class FileListBioDatabase(ZTBioDatabase):
"""
protocol = protocol or self.protocol
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
return self.__client_id_list__(groups, 'for_znorm', protocol)
@@ -525,7 +518,7 @@ class FileListBioDatabase(ZTBioDatabase):
protocol = protocol or self.protocol
# read all lists for all groups and extract the model ids
for group in groups:
- dict = self.m_list_reader.read_models(self.get_list_file(group, type, protocol), group, type)
+ dict = self._list_reader(protocol).read_models(self._get_list_file(group, type, protocol), group, type)
ids.update(dict.keys())
return list(ids)
@@ -543,10 +536,7 @@ class FileListBioDatabase(ZTBioDatabase):
Returns: A list containing all the model ids which have the given properties.
"""
protocol = protocol or self.protocol
-
- groups = self.check_parameters_for_validity(groups, "group",
- ('dev', 'eval', 'world', 'optional_world_1', 'optional_world_2'),
- default_parameters=('dev', 'eval', 'world'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol=protocol))
return self.__model_id_list__(groups, 'for_models', protocol)
@@ -564,8 +554,7 @@ class FileListBioDatabase(ZTBioDatabase):
Returns: A list containing all the T-Norm model ids belonging to the given group.
"""
protocol = protocol or self.protocol
-
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
return self.__model_id_list__(groups, 'for_tnorm', protocol)
@@ -590,8 +579,7 @@ class FileListBioDatabase(ZTBioDatabase):
groups : str or [str] or ``None``
One of the groups ("dev", "eval", "world", "optional_world_1", "optional_world_2") or a tuple with several of them.
- If 'None' is given (this is the default), it is considered the same as a
- tuple with all possible values.
+ If 'None' is given (this is the default), it is considered to be the existing subset of ``("world", "dev", "eval")``.
classes : str or [str] or ``None``
The classes (types of accesses) to be retrieved ('client', 'impostor')
@@ -603,13 +591,13 @@ class FileListBioDatabase(ZTBioDatabase):
"""
protocol = protocol or self.protocol
- if self.m_use_dense_probes and classes is not None:
+ if self.uses_dense_probe_file(protocol) and classes is not None:
raise ValueError("To be able to use the 'classes' keyword, please use the 'for_scores.lst' list file.")
purposes = self.check_parameters_for_validity(purposes, "purpose", ('enroll', 'probe'))
groups = self.check_parameters_for_validity(groups, "group",
- ('dev', 'eval', 'world', 'optional_world_1', 'optional_world_2'),
- default_parameters=('dev', 'eval', 'world'))
+ self.groups(protocol),
+ default_parameters=self.groups(protocol, add_subworld=False))
classes = self.check_parameters_for_validity(classes, "class", ('client', 'impostor'))
if isinstance(model_ids, six.string_types):
@@ -619,29 +607,26 @@ class FileListBioDatabase(ZTBioDatabase):
lists = []
probe_lists = []
if 'world' in groups:
- lists.append(self.m_list_reader.read_list(self.get_list_file('world', protocol=protocol), 'world'))
+ lists.append(self._list_reader(protocol).read_list(self._get_list_file('world', protocol=protocol), 'world'))
if 'optional_world_1' in groups:
- lists.append(self.m_list_reader.read_list(self.get_list_file('optional_world_1', protocol=protocol),
+ lists.append(self._list_reader(protocol).read_list(self._get_list_file('optional_world_1', protocol=protocol),
'optional_world_1'))
if 'optional_world_2' in groups:
- lists.append(self.m_list_reader.read_list(self.get_list_file('optional_world_2', protocol=protocol),
+ lists.append(self._list_reader(protocol).read_list(self._get_list_file('optional_world_2', protocol=protocol),
'optional_world_2'))
for group in ('dev', 'eval'):
if group in groups:
if 'enroll' in purposes:
lists.append(
- self.m_list_reader.read_list(self.get_list_file(group, 'for_models', protocol=protocol), group,
- 'for_models'))
+ self._list_reader(protocol).read_list(self._get_list_file(group, 'for_models', protocol=protocol), group, 'for_models'))
if 'probe' in purposes:
- if self.m_use_dense_probes:
+ if self.uses_dense_probe_file(protocol):
probe_lists.append(
- self.m_list_reader.read_list(self.get_list_file(group, 'for_probes', protocol=protocol),
- group, 'for_probes'))
+ self._list_reader(protocol).read_list(self._get_list_file(group, 'for_probes', protocol=protocol), group, 'for_probes'))
else:
probe_lists.append(
- self.m_list_reader.read_list(self.get_list_file(group, 'for_scores', protocol=protocol),
- group, 'for_scores'))
+ self._list_reader(protocol).read_list(self._get_list_file(group, 'for_scores', protocol=protocol), group, 'for_scores'))
# now, go through the lists and filter the elements
@@ -660,7 +645,7 @@ class FileListBioDatabase(ZTBioDatabase):
# probe files; filter by model id and by class
for list in probe_lists:
- if self.m_use_dense_probes:
+ if self.uses_dense_probe_file(protocol):
# dense probing is used; do not filter over the model ids and not over the classes
# -> just add all probe files
for file in list:
@@ -702,8 +687,7 @@ class FileListBioDatabase(ZTBioDatabase):
Returns: A list of :py:class:`BioFile` objects considering all the filtering criteria.
"""
protocol = protocol or self.protocol
-
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
if (isinstance(model_ids, six.string_types)):
model_ids = (model_ids,)
@@ -712,7 +696,7 @@ class FileListBioDatabase(ZTBioDatabase):
# we assume that there is no duplicate file here...
retval = []
for group in groups:
- for file in self.m_list_reader.read_list(self.get_list_file(group, 'for_tnorm', protocol), group,
+ for file in self._list_reader(protocol).read_list(self._get_list_file(group, 'for_tnorm', protocol), group,
'for_tnorm'):
if model_ids is None or file._model_id in model_ids:
retval.append(file)
@@ -734,14 +718,14 @@ class FileListBioDatabase(ZTBioDatabase):
"""
protocol = protocol or self.protocol
- groups = self.check_parameters_for_validity(groups, "group", ('dev', 'eval'))
+ groups = self.check_parameters_for_validity(groups, "group", self.groups(protocol, add_world=False))
# iterate over the lists and extract the files
# we assume that there is no duplicate file here...
retval = []
for group in groups:
retval.extend([file for file in
- self.m_list_reader.read_list(self.get_list_file(group, 'for_znorm', protocol), group,
+ self._list_reader(protocol).read_list(self._get_list_file(group, 'for_znorm', protocol), group,
'for_znorm')])
return self._make_bio(retval)
@@ -759,14 +743,14 @@ class FileListBioDatabase(ZTBioDatabase):
Return value
The annotations as a dictionary: {'reye':(re_y,re_x), 'leye':(le_y,le_x)}
"""
- if self.m_annotation_directory is None:
+ if self.annotation_directory is None:
return None
# since the file id is equal to the file name, we can simply use it
- annotation_file = os.path.join(self.m_annotation_directory, file.id + self.m_annotation_extension)
+ annotation_file = os.path.join(self.annotation_directory, file.id + self.annotation_extension)
# return the annotations as read from file
- return bob.db.base.read_annotation_file(annotation_file, self.m_annotation_type)
+ return bob.db.base.read_annotation_file(annotation_file, self.annotation_type)
def original_file_name(self, file, check_existence=True):
"""Returns the original file name of the given file.
diff --git a/bob/bio/base/test/data/example_fielist/data/model4_session1_sample2.pos b/bob/bio/base/test/data/example_filelist/data/model4_session1_sample2.pos
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/data/model4_session1_sample2.pos
rename to bob/bio/base/test/data/example_filelist/data/model4_session1_sample2.pos
diff --git a/bob/bio/base/test/data/example_fielist/dev/for_models.lst b/bob/bio/base/test/data/example_filelist/dev/for_models.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/dev/for_models.lst
rename to bob/bio/base/test/data/example_filelist/dev/for_models.lst
diff --git a/bob/bio/base/test/data/example_fielist/dev/for_probes.lst b/bob/bio/base/test/data/example_filelist/dev/for_probes.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/dev/for_probes.lst
rename to bob/bio/base/test/data/example_filelist/dev/for_probes.lst
diff --git a/bob/bio/base/test/data/example_fielist/dev/for_scores.lst b/bob/bio/base/test/data/example_filelist/dev/for_scores.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/dev/for_scores.lst
rename to bob/bio/base/test/data/example_filelist/dev/for_scores.lst
diff --git a/bob/bio/base/test/data/example_fielist/dev/for_tnorm.lst b/bob/bio/base/test/data/example_filelist/dev/for_tnorm.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/dev/for_tnorm.lst
rename to bob/bio/base/test/data/example_filelist/dev/for_tnorm.lst
diff --git a/bob/bio/base/test/data/example_fielist/dev/for_znorm.lst b/bob/bio/base/test/data/example_filelist/dev/for_znorm.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/dev/for_znorm.lst
rename to bob/bio/base/test/data/example_filelist/dev/for_znorm.lst
diff --git a/bob/bio/base/test/data/example_fielist/eval/for_models.lst b/bob/bio/base/test/data/example_filelist/eval/for_models.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/eval/for_models.lst
rename to bob/bio/base/test/data/example_filelist/eval/for_models.lst
diff --git a/bob/bio/base/test/data/example_fielist/eval/for_probes.lst b/bob/bio/base/test/data/example_filelist/eval/for_probes.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/eval/for_probes.lst
rename to bob/bio/base/test/data/example_filelist/eval/for_probes.lst
diff --git a/bob/bio/base/test/data/example_fielist/eval/for_scores.lst b/bob/bio/base/test/data/example_filelist/eval/for_scores.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/eval/for_scores.lst
rename to bob/bio/base/test/data/example_filelist/eval/for_scores.lst
diff --git a/bob/bio/base/test/data/example_fielist/eval/for_tnorm.lst b/bob/bio/base/test/data/example_filelist/eval/for_tnorm.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/eval/for_tnorm.lst
rename to bob/bio/base/test/data/example_filelist/eval/for_tnorm.lst
diff --git a/bob/bio/base/test/data/example_fielist/eval/for_znorm.lst b/bob/bio/base/test/data/example_filelist/eval/for_znorm.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/eval/for_znorm.lst
rename to bob/bio/base/test/data/example_filelist/eval/for_znorm.lst
diff --git a/bob/bio/base/test/data/example_fielist/norm/train_optional_world_1.lst b/bob/bio/base/test/data/example_filelist/norm/train_optional_world_1.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/norm/train_optional_world_1.lst
rename to bob/bio/base/test/data/example_filelist/norm/train_optional_world_1.lst
diff --git a/bob/bio/base/test/data/example_fielist/norm/train_optional_world_2.lst b/bob/bio/base/test/data/example_filelist/norm/train_optional_world_2.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/norm/train_optional_world_2.lst
rename to bob/bio/base/test/data/example_filelist/norm/train_optional_world_2.lst
diff --git a/bob/bio/base/test/data/example_fielist/norm/train_world.lst b/bob/bio/base/test/data/example_filelist/norm/train_world.lst
similarity index 100%
rename from bob/bio/base/test/data/example_fielist/norm/train_world.lst
rename to bob/bio/base/test/data/example_filelist/norm/train_world.lst
diff --git a/bob/bio/base/test/data/example_filelist2/dev/for_models.lst b/bob/bio/base/test/data/example_filelist2/dev/for_models.lst
new file mode 100644
index 0000000000000000000000000000000000000000..7bdbf751bd8c6f432f780199a77a8d60a45fa388
--- /dev/null
+++ b/bob/bio/base/test/data/example_filelist2/dev/for_models.lst
@@ -0,0 +1,12 @@
+data/model3_session1_sample1 3 3
+data/model3_session1_sample2 3 3
+data/model3_session1_sample3 3 3
+data/model3_session2_sample1 3 3
+data/model4_session1_sample1 4 4
+data/model4_session1_sample2 4 4
+data/model4_session1_sample3 4 4
+data/model4_session2_sample1 4 4
+data/model5_session1_sample1 5 5
+data/model5_session1_sample2 5 5
+data/model5_session1_sample3 5 5
+data/model5_session2_sample1 5 5
diff --git a/bob/bio/base/test/data/example_filelist2/dev/for_scores.lst b/bob/bio/base/test/data/example_filelist2/dev/for_scores.lst
new file mode 100644
index 0000000000000000000000000000000000000000..340e7ec1d87af20168035baf5d3ade33a9908ada
--- /dev/null
+++ b/bob/bio/base/test/data/example_filelist2/dev/for_scores.lst
@@ -0,0 +1,14 @@
+data/model3_session3_sample1 3 3 3
+data/model3_session3_sample2 3 3 3
+data/model3_session3_sample3 3 3 3
+data/model3_session4_sample1 3 3 3
+data/model4_session3_sample1 3 3 4
+data/model4_session3_sample2 3 3 4
+data/model4_session3_sample1 4 4 4
+data/model4_session3_sample2 4 4 4
+data/model4_session3_sample3 4 4 4
+data/model4_session4_sample1 4 4 4
+data/model3_session3_sample1 4 4 3
+data/model3_session3_sample2 4 4 3
+data/model5_session3_sample1 5 3 5
+data/model5_session3_sample1 5 5 5
diff --git a/bob/bio/base/test/test_filelist.py b/bob/bio/base/test/test_filelist.py
index 15a8d5aee0311acb3b90dbf9308046807c66571f..405591a866ba3e7bc2c630a27b533d2e5a39dbb6 100644
--- a/bob/bio/base/test/test_filelist.py
+++ b/bob/bio/base/test/test_filelist.py
@@ -22,9 +22,10 @@
import os
import bob.io.base.test_utils
from bob.bio.base.database import FileListBioDatabase
+import nose.tools
-example_dir = os.path.realpath(bob.io.base.test_utils.datafile('.', __name__, 'data/example_fielist'))
+example_dir = os.path.realpath(bob.io.base.test_utils.datafile('.', __name__, 'data/example_filelist'))
def test_query():
@@ -77,7 +78,7 @@ def test_query():
def test_query_protocol():
- db = FileListBioDatabase(os.path.dirname(example_dir), 'test', protocol='example_fielist', use_dense_probe_file_list=False)
+ db = FileListBioDatabase(os.path.dirname(example_dir), 'test', protocol='example_filelist', use_dense_probe_file_list=False)
assert len(db.groups()) == 5 # 5 groups (dev, eval, world, optional_world_1, optional_world_2)
@@ -125,8 +126,18 @@ def test_query_protocol():
assert db.client_id_from_t_model_id('7', group=None) == '7'
+ # check other protocols
+ assert len(db.objects(protocol='non-existent')) == 0
+
+ prot = 'example_filelist2'
+ assert len(db.model_ids_with_protocol(protocol=prot)) == 3 # 3 model ids for dev only
+ nose.tools.assert_raises(ValueError, db.model_ids_with_protocol, protocol=prot, groups='eval') # eval does not exist for this protocol
+ assert len(db.objects(protocol=prot, groups='dev', purposes='enroll')) == 12
+ assert len(db.objects(protocol=prot, groups='dev', purposes='probe')) == 9
+
+
def test_query_dense():
- db = FileListBioDatabase(example_dir, 'test', probes_filename='for_probes.lst')
+ db = FileListBioDatabase(example_dir, 'test', use_dense_probe_file_list=True)
assert len(db.objects(groups='world')) == 8 # 8 samples in the world set
@@ -162,13 +173,7 @@ def test_multiple_extensions():
assert file_name == os.path.join(example_dir, file.path + '.pos')
file = bob.bio.base.database.BioFile(4, "data/model4_session1_sample1", "data/model4_session1_sample1")
- try:
- file_name = db.original_file_name(file, False)
- raised = False
- except IOError as e:
- raised = True
-
- assert raised
+ nose.tools.assert_raises(IOError, db.original_file_name, file, False)
def test_driver_api():
diff --git a/doc/filelist-guide.rst b/doc/filelist-guide.rst
index 96287eb549859e5504e61562d286875607c31857..547ac79767b12d6fafe8f64333a4675056bc6144 100644
--- a/doc/filelist-guide.rst
+++ b/doc/filelist-guide.rst
@@ -15,24 +15,28 @@ All functions defined in that interface are properly instantiated, as soon as th
Creating File Lists
-------------------
-The initial step for using this package is to provide file lists specifying the ``'world'`` (training), ``'dev'`` (development) and ``'eval'`` (evaluation) set to be used by the biometric verification algorithm.
+The initial step for using this package is to provide file lists specifying the ``'world'`` (training; optional), ``'dev'`` (development; required) and ``'eval'`` (evaluation; optional) set to be used by the biometric verification algorithm.
The summarized complete structure of the list base directory (here denoted as ``basedir``) containing all the files should be like this::
- basedir -- norm -- train_world.lst
- | |-- train_optional_world_1.lst
- | |-- train_optional_world_2.lst
+ filelists_directory
+ |-- norm
+ |-- train_world.lst
+ |-- train_optional_world_1.lst
+ |-- train_optional_world_2.lst
|
- |-- dev -- for_models.lst
- | |-- for_probes.lst
- | |-- for_scores.lst
- | |-- for_tnorm.lst
- | |-- for_znorm.lst
+ |-- dev
+ |-- for_models.lst
+ |-- for_probes.lst
+ |-- for_scores.lst
+ |-- for_tnorm.lst
+ |-- for_znorm.lst
|
- |-- eval -- for_models.lst
- |-- for_probes.lst
- |-- for_scores.lst
- |-- for_tnorm.lst
- |-- for_znorm.lst
+ |-- eval
+ |-- for_models.lst
+ |-- for_probes.lst
+ |-- for_scores.lst
+ |-- for_tnorm.lst
+ |-- for_znorm.lst
The file lists contain several information that need to be available for the biometric recognition experiment to run properly.
@@ -53,7 +57,7 @@ A complete list of possible information is:
The following list files need to be created:
-- **For training**:
+- **For training** (optional):
* *world file*, with default name ``train_world.lst``, in the default sub-directory ``norm``.
It is a 2-column file with format:
@@ -62,14 +66,14 @@ The following list files need to be created:
filename client_id
- * two (optional) *world files*, with default names ``train_optional_world_1.lst`` and ``train_optional_world_2.lst``, in default sub-directory ``norm``.
+ * two *world files*, with default names ``train_optional_world_1.lst`` and ``train_optional_world_2.lst``, in default sub-directory ``norm``.
The format is the same as for the world file.
These files are not needed for most of biometric recognition algorithms, hence, they need to be specified only if the algorithm uses them.
- **For enrollment**:
- * two *model files* for the development and evaluation set, with default name ``for_models.lst`` in the default sub-directories ``dev`` and ``eval``, respectively.
- They are 3-column files with format::
+ * one or two *model files* for the development (and evaluation) set, with default name ``for_models.lst`` in the default sub-directories ``dev`` (and ``eval``).
+ They are 3-column files with format:
.. code-block:: text
@@ -80,45 +84,45 @@ The following list files need to be created:
There exist two different ways to implement file lists used for scoring.
* The first (and simpler) variant is to define a file list of probe files, where all probe files will be tested against all models.
- Hence, you need to specify two *probe files* for the development and evaluation set, with default name ``for_probes.lst`` in the default sub-directories ``dev`` and ``eval``, respectively.
+ Hence, you need to specify one or two *probe files* for the development (and evaluation) set, with default name ``for_probes.lst`` in the default sub-directories ``dev`` (and ``eval``).
They are 2-column files with format:
.. code-block:: text
filename client_id
- * The other option is to specify a detailed list, which probe file should be be compared with which client model, i.e., two *score files* for the development and evaluation set, with default name ``for_scores.lst`` in the sub-directories ``dev`` and ``eval``, respectively.
+ * The other option is to specify a detailed list, which probe file should be be compared with which client model, i.e., one or two *score files* for the development (and evaluation) set, with default name ``for_scores.lst`` in the sub-directories ``dev`` (and ``eval``).
These files need to be provided only if the scoring is to be done selectively, meaning by creating a sparse probe/model scoring matrix.
- They are 4-column files with format::
+ They are 4-column files with format:
.. code-block:: text
filename model_id claimed_client_id client_id
-- **For ZT score normalization**:
+ .. note:: The verification queries will use either only the probe or only the score files, so only one of them is mandatory.
+ If only one of the two files is available, the scoring technique will be automatically determined.
+ In case both probe and score files are provided, the user should set the parameter ``use_dense_probe_file_list``, which specifies the files to consider, when creating the object of the ``Database`` class.
+
+
+- **For ZT score normalization** (optional):
Optionally, file lists for ZT score normalization can be added.
- These are
+ These are:
- * two *files for t-score normalization* for the development and evaluation set, with default name ``for_tnorm.lst`` in both sub-directories ``dev`` and ``eval``, respectively.
- They are 3-column files with format::
+ * one or two *files for t-score normalization* for the development (and evaluation) set, with default name ``for_tnorm.lst`` in both sub-directories ``dev`` (and ``eval``).
+ They are 3-column files with format:
.. code-block:: text
filename model_id client_id
- * two *files for z-score normalization* for the development and evaluation set, with default name ``for_znorm.lst`` in both sub-directories ``dev`` and ``eval``, respectively.
- They are 2-column files with format::
+ * one or two *files for z-score normalization* for the development (and evaluation) set, with default name ``for_znorm.lst`` in both sub-directories ``dev`` (and ``eval``).
+ They are 2-column files with format:
.. code-block:: text
filename client_id
-.. note:: The verification queries will use either only the probe or only the score files, so only one of them is mandatory.
- In case both probe and score files are provided, the user should set the parameter ``use_dense_probe_file_list``, which specifies the files to consider, when creating the object of the ``Database`` class.
-
-.. note:: If the database does not provide an evaluation set, the scoring files can be omitted.
- Similarly, if the user only define **for scoring** files and omit the remaining ones, the only valid queries will be scoring-related ones.
@@ -145,17 +149,24 @@ Alternatively, if you have more protocols, you could do the following:
>>> db = bob.bio.base.database.FileListBioDatabase('basedir', 'mydb', protocol='protocol')
>>> db.objects()
+or specify the protocol while querying the database:
+
+.. code-block:: python
+
+ >>> db = bob.bio.base.database.FileListBioDatabase('basedir', 'mydb')
+ >>> db.objects(protocol='protocol')
+
When a protocol is specified, it is appended to the base directory that contains the file lists.
-If you need to use another protocol, the best option is to create another instance.
-For instance, given two protocols 'P1' and 'P2' (with filelists contained in 'basedir/P1' and 'basedir/P2', respectively), the following would work:
+You can query the database with ``another`` protocol, simply as:
.. code-block:: python
- >>> db1 = bob.bio.base.database.FileListBioDatabase('basedir', 'mydb', protocol='P1')
- >>> db2 = bob.bio.base.database.FileListBioDatabase('basedir', 'mydb', protocol='P2')
- >>> db1.objects() # Get the objects for the protocol P1
- >>> db2.objects() # Get the objects for the protocol P2
+ >>> db = bob.bio.base.database.FileListBioDatabase('basedir', 'mydb')
+ >>> db.objects(protocol='protocol')
+ >>> db.objects(protocol='another')
+
+and you retrieve the files stored in `basedir/protocol` and `basedir/another`, respectively.
-Note that if you use several protocols as explained above, the scoring part should be defined in the same way for all the protocols, either by using ``for_probes.lst`` or ``for_scores.lst``.
-This means that at the time of the database instantiation, it will be determined (or specified using the ``use_dense_probe_file_list`` optional argument), whether the protocols should use the content of ``for_probes.lst`` or ``for_scores.lst``.
-In particular, it is not possible to use a mixture of those for different protocols, once the database object has been created.
+.. note::
+ If you use several protocols as explained above, the ``use_dense_probe_file_list`` parameter is global for all protocols.
+ In case you have ``for_scores.lst`` in one and ``for_probes.lst`` in another protocol, it will automatically switch between the scoring strategies -- as long as you leave ``use_dense_probe_file_list=None``.