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Commit edae49e1 authored by Amir Mohammadi's avatar Amir Mohammadi
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move some functionality of bob.bio.base.database.BioDatabase to bob.db.base

parent 2e7ac534
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1 merge request!56makes the annotations method implementation mandatory
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bob/bio/base/database/database.py
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......@@ -154,76 +154,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
###########################################################################
# Helper functions that you might want to use in derived classes
###########################################################################
def replace_directories(self, replacements=None):
"""This helper function replaces the ``original_directory`` and the ``annotation_directory`` of the database with the directories read from the given replacement file.
This function is provided for convenience, so that the database configuration files do not need to be modified.
Instead, this function uses the given dictionary of replacements to change the original directory and the original extension (if given).
The given ``replacements`` can be of type ``dict``, including all replacements, or a file name (as a ``str``), in which case the file is read.
The structure of the file should be:
.. code-block:: text
# Comments starting with # and empty lines are ignored
[YOUR_..._DATA_DIRECTORY] = /path/to/your/data
[YOUR_..._ANNOTATION_DIRECTORY] = /path/to/your/annotations
If no annotation files are available (e.g. when they are stored inside the ``database``), the annotation directory can be left out.
**Parameters:**
replacements : dict or str
A dictionary with replacements, or a name of a file to read the dictionary from.
If the file name does not exist, no directories are replaced.
"""
if replacements is None:
return
if isinstance(replacements, str):
if not os.path.exists(replacements):
return
# Open the database replacement file and reads its content
with open(replacements) as f:
replacements = {}
for line in f:
if line.strip() and not line.startswith("#"):
splits = line.split("=")
assert len(splits) == 2
replacements[splits[0].strip()] = splits[1].strip()
assert isinstance(replacements, dict)
if self.original_directory in replacements:
self.original_directory = replacements[self.original_directory]
try:
if self.annotation_directory in replacements:
self.annotation_directory = replacements[self.annotation_directory]
except AttributeError:
pass
def sort(self, files):
"""sort(files) -> sorted
Returns a sorted version of the given list of File's (or other structures that define an 'id' data member).
The files will be sorted according to their id, and duplicate entries will be removed.
**Parameters:**
files : [:py:class:`bob.bio.base.database.BioFile`]
The list of files to be uniquified and sorted.
**Returns:**
sorted : [:py:class:`bob.bio.base.database.BioFile`]
The sorted list of files, with duplicate `BioFile.id`\s being removed.
"""
# sort files using their sort function
sorted_files = sorted(files)
# remove duplicates
return [f for i, f in enumerate(sorted_files) if not i or sorted_files[i - 1].id != f.id]
def uses_probe_file_sets(self, protocol=None):
"""Defines if, for the current protocol, the database uses several probe files to generate a score.
Returns True if the given protocol specifies file sets for probes, instead of a single probe file.
......@@ -313,26 +243,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
# List of files, do not remove duplicates
return [f.make_path(directory, extension) for f in files]
def original_file_names(self, files):
"""original_file_names(files) -> paths
Returns the full path of the original data of the given File objects.
**Parameters:**
files : [:py:class:`bob.bio.base.database.BioFile`]
The list of file object to retrieve the original data file names for.
**Returns:**
paths : [str] or [[str]]
The paths extracted for the files, in the same order.
If this database provides file sets, a list of lists of file names is returned, one sub-list for each file set.
"""
assert self.original_directory is not None
assert self.original_extension is not None
return self.file_names(files, self.original_directory, self.original_extension)
#################################################################
###### Methods to be overwritten by derived classes #############
#################################################################
......@@ -405,28 +315,6 @@ class BioDatabase(six.with_metaclass(abc.ABCMeta, bob.db.base.Database)):
######### Methods to provide common functionality ###############
#################################################################
def original_file_name(self, file):
"""This function returns the original file name for the given File object.
Keyword parameters:
file : :py:class:`bob.bio.base.database.BioFile` or a derivative
The File objects for which the file name should be retrieved
Return value : str
The original file name for the given File object
"""
# check if directory is set
if not self.original_directory or not self.original_extension:
raise ValueError(
"The original_directory and/or the original_extension were not specified in the constructor.")
# extract file name
file_name = file.make_path(self.original_directory, self.original_extension)
if not self.check_existence or os.path.exists(file_name):
return file_name
raise ValueError("The file '%s' was not found. Please check the original directory '%s' and extension '%s'?" % (
file_name, self.original_directory, self.original_extension))
def all_files(self, groups=None):
"""all_files(groups=None) -> files
......
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