From 87b41c41fa90ccccb6c5a6e886ce81f58fa3d776 Mon Sep 17 00:00:00 2001
From: Manuel Gunther <siebenkopf@googlemail.com>
Date: Tue, 4 Apr 2017 19:23:53 -0600
Subject: [PATCH] Implemented skipping of ZT files if not wanted
---
bob/bio/base/database/database.py | 20 +++++++++++++-------
bob/bio/base/database/filelist/query.py | 6 ++++--
bob/bio/base/tools/FileSelector.py | 14 ++++++++------
bob/bio/base/tools/command_line.py | 1 +
4 files changed, 26 insertions(+), 15 deletions(-)
diff --git a/bob/bio/base/database/database.py b/bob/bio/base/database/database.py
index 5bfb7978..2ab51564 100644
--- a/bob/bio/base/database/database.py
+++ b/bob/bio/base/database/database.py
@@ -370,7 +370,7 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
"""
return sorted(self.model_ids_with_protocol(groups=groups, protocol=self.protocol))
- def all_files(self, groups=None):
+ def all_files(self, groups=None, **kwargs):
"""all_files(groups=None) -> files
Returns all files of the database, respecting the current protocol.
@@ -382,6 +382,8 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
The groups to get the data for.
If ``None``, data for all groups is returned.
+ kwargs: ignored
+
**Returns:**
files : [:py:class:`bob.bio.base.database.BioFile`]
@@ -640,7 +642,7 @@ class ZTBioDatabase(BioDatabase):
"""
raise NotImplementedError("This function must be implemented in your derived class.")
- def all_files(self, groups=['dev']):
+ def all_files(self, groups=['dev'], add_zt_files=True):
"""all_files(groups=None) -> files
Returns all files of the database, including those for ZT norm, respecting the current protocol.
@@ -652,6 +654,9 @@ class ZTBioDatabase(BioDatabase):
The groups to get the data for.
If ``None``, data for all groups is returned.
+ add_zt_files: bool
+ If set (the default), files for ZT score normalization are added.
+
**Returns:**
files : [:py:class:`bob.bio.base.database.BioFile`]
@@ -660,11 +665,12 @@ class ZTBioDatabase(BioDatabase):
files = self.objects(protocol=self.protocol, groups=groups, **self.all_files_options)
# add all files that belong to the ZT-norm
- for group in groups:
- if group == 'world':
- continue
- files += self.tobjects(protocol=self.protocol, groups=group, model_ids=None)
- files += self.zobjects(protocol=self.protocol, groups=group, **self.z_probe_options)
+ if add_zt_files:
+ for group in groups:
+ if group == 'world':
+ continue
+ files += self.tobjects(protocol=self.protocol, groups=group, model_ids=None)
+ files += self.zobjects(protocol=self.protocol, groups=group, **self.z_probe_options)
return self.sort(files)
@abc.abstractmethod
diff --git a/bob/bio/base/database/filelist/query.py b/bob/bio/base/database/filelist/query.py
index dcaad932..3d3c4f11 100644
--- a/bob/bio/base/database/filelist/query.py
+++ b/bob/bio/base/database/filelist/query.py
@@ -198,13 +198,15 @@ class FileListBioDatabase(ZTBioDatabase):
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']):
+ def all_files(self, groups=['dev'], add_zt_files=True):
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):
+ if add_zt_files:
+ if not self.implements_zt(self.protocol, group):
+ raise ValueError("ZT score files are requested, but no such files are defined in group %s for protocol %s", group, self.protocol)
files += self.tobjects(group, self.protocol)
files += self.zobjects(group, self.protocol, **self.z_probe_options)
return self.sort(self._make_bio(files))
diff --git a/bob/bio/base/tools/FileSelector.py b/bob/bio/base/tools/FileSelector.py
index 0870ee71..3f1a9bae 100644
--- a/bob/bio/base/tools/FileSelector.py
+++ b/bob/bio/base/tools/FileSelector.py
@@ -68,7 +68,8 @@ class FileSelector(object):
score_directories,
zt_score_directories = None,
default_extension = '.hdf5',
- compressed_extension = ''
+ compressed_extension = '',
+ zt_norm = False
):
"""Initialize the file selector object with the current configuration."""
@@ -89,6 +90,7 @@ class FileSelector(object):
'extracted' : extracted_directory,
'projected' : projected_directory
}
+ self.zt_norm = zt_norm
def uses_probe_file_sets(self):
@@ -108,7 +110,7 @@ class FileSelector(object):
### List of files that will be used for all files
def original_data_list(self, groups = None):
"""Returns the list of original ``BioFile`` objects that can be used for preprocessing."""
- return self.database.all_files(groups=groups)
+ return self.database.all_files(groups=groups,add_zt_files=self.zt_norm)
def original_directory_and_extension(self):
"""Returns the directory and extension of the original files."""
@@ -116,7 +118,7 @@ class FileSelector(object):
def annotation_list(self, groups = None):
"""Returns the list of annotations objects."""
- return self.database.all_files(groups=groups)
+ return self.database.all_files(groups=groups,add_zt_files=self.zt_norm)
def get_annotations(self, annotation_file):
"""Returns the annotations of the given file."""
@@ -124,15 +126,15 @@ class FileSelector(object):
def preprocessed_data_list(self, groups = None):
"""Returns the list of preprocessed data files."""
- return self.get_paths(self.database.all_files(groups=groups), "preprocessed")
+ return self.get_paths(self.database.all_files(groups=groups,add_zt_files=self.zt_norm), "preprocessed")
def feature_list(self, groups = None):
"""Returns the list of extracted feature files."""
- return self.get_paths(self.database.all_files(groups=groups), "extracted")
+ return self.get_paths(self.database.all_files(groups=groups,add_zt_files=self.zt_norm), "extracted")
def projected_list(self, groups = None):
"""Returns the list of projected feature files."""
- return self.get_paths(self.database.all_files(groups=groups), "projected")
+ return self.get_paths(self.database.all_files(groups=groups,add_zt_files=self.zt_norm), "projected")
### Training lists
diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index 5ddd7150..2cdc11f9 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -460,6 +460,7 @@ def initialize(parsers, command_line_parameters=None, skips=[]):
zt_score_directories=[os.path.join(args.temp_directory, protocol, s) for s in args.zt_directories],
compressed_extension='.tar.bz2' if args.write_compressed_score_files else '',
default_extension='.hdf5',
+ zt_norm = args.zt_norm
)
return args
--
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