diff --git a/bob/bio/base/test/test_config_file.py b/bob/bio/base/test/test_config_file.py
new file mode 100644
index 0000000000000000000000000000000000000000..39e6c347ccd2d97edf48e6bcf57a771f1ee25d40
--- /dev/null
+++ b/bob/bio/base/test/test_config_file.py
@@ -0,0 +1,229 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+
+'''Tests for the configuration-file command line options'''
+
+import os
+import shutil
+import tempfile
+
+from ..script.verify import parse_arguments
+
+
+def tmp_file(contents):
+ '''Generates a temporary configuration file with the contents on the input'''
+
+ retval = tempfile.NamedTemporaryFile('w')
+ retval.write('\n'.join(contents) + '\n')
+ retval.flush()
+ return retval
+
+
+def check_parameters(args_file, args_cmdline):
+ '''Checks parameters generated from a configuration file or command-line
+ are as similar they can be'''
+
+ from bob.bio.base.test.dummy.database import DummyDatabase
+ assert isinstance(args_file.database, DummyDatabase)
+ assert isinstance(args_cmdline.database, DummyDatabase)
+ from bob.bio.base.test.dummy.preprocessor import DummyPreprocessor
+ assert isinstance(args_file.preprocessor, DummyPreprocessor)
+ assert isinstance(args_cmdline.preprocessor, DummyPreprocessor)
+ from bob.bio.base.test.dummy.extractor import DummyExtractor
+ assert isinstance(args_file.extractor, DummyExtractor)
+ assert isinstance(args_cmdline.extractor, DummyExtractor)
+ from bob.bio.base.test.dummy.algorithm import DummyAlgorithm
+ assert isinstance(args_file.algorithm, DummyAlgorithm)
+ assert isinstance(args_cmdline.algorithm, DummyAlgorithm)
+
+ # elements checked otherwise or not comparable between the two settings
+ skip_check = (
+ 'configuration_file',
+ 'imports',
+ 'database',
+ 'preprocessor',
+ 'extractor',
+ 'algorithm',
+ )
+
+ for attr in [k for k in dir(args_file) if not k.startswith('_')]:
+ if attr in skip_check: continue
+ assert hasattr(args_cmdline, attr)
+ attr_cmdline = getattr(args_cmdline, attr)
+ attr_file = getattr(args_file, attr)
+ if (isinstance(attr_file, (bool, str, int, list))) or (attr_file is None):
+ assert attr_cmdline == attr_file, '(%s) %r != %r' % \
+ (attr, attr_cmdline, attr_file)
+ else:
+ assert False, '(%s) %r == %r?' % (attr, attr_cmdline, attr_file)
+
+
+def test_basic():
+
+ test_dir = None
+ test_config_file = None
+ try:
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ test_config_file = tmp_file([
+ 'from bob.bio.base.test.dummy.database import database',
+ 'from bob.bio.base.test.dummy.preprocessor import preprocessor',
+ 'from bob.bio.base.test.dummy.extractor import extractor',
+ 'from bob.bio.base.test.dummy.algorithm import algorithm',
+ 'zt_norm = True',
+ 'verbose = 1',
+ 'sub_directory = "test_config"',
+ 'temp_directory = "%s"' % test_dir,
+ 'result_directory = "%s"' % test_dir,
+ ])
+
+ args = parse_arguments(['-c', test_config_file.name])
+
+ assert args.zt_norm is True
+ assert args.verbose == 1
+ assert args.sub_directory.endswith('test_config')
+ assert args.temp_directory.startswith(test_dir)
+ assert args.result_directory.startswith(test_dir)
+ assert args.allow_missing_files is False
+
+ from bob.bio.base.test.dummy.database import DummyDatabase
+ assert isinstance(args.database, DummyDatabase)
+ from bob.bio.base.test.dummy.preprocessor import DummyPreprocessor
+ assert isinstance(args.preprocessor, DummyPreprocessor)
+ from bob.bio.base.test.dummy.extractor import DummyExtractor
+ assert isinstance(args.extractor, DummyExtractor)
+ from bob.bio.base.test.dummy.algorithm import DummyAlgorithm
+ assert isinstance(args.algorithm, DummyAlgorithm)
+
+ finally:
+ if test_dir: shutil.rmtree(test_dir)
+ if test_config_file: del test_config_file
+
+
+def test_compare_to_cmdline_basic():
+
+ test_dir = None
+ test_config_file = None
+ try:
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ test_config_file = tmp_file([
+ 'from bob.bio.base.test.dummy.database import database',
+ 'from bob.bio.base.test.dummy.preprocessor import preprocessor',
+ 'from bob.bio.base.test.dummy.extractor import extractor',
+ 'from bob.bio.base.test.dummy.algorithm import algorithm',
+ 'zt_norm = True',
+ 'verbose = 1',
+ 'sub_directory = "test_config"',
+ 'temp_directory = "%s"' % test_dir,
+ 'result_directory = "%s"' % test_dir,
+ ])
+
+ args_file = parse_arguments(['-c', test_config_file.name])
+
+ # now do the same with command-line arguments, ensure result is equal
+ args_cmdline = parse_arguments([
+ '-d', 'bob.bio.base.test.dummy.database.DummyDatabase()',
+ '-p', 'bob.bio.base.test.dummy.preprocessor.DummyPreprocessor()',
+ '-e', 'bob.bio.base.test.dummy.extractor.DummyExtractor()',
+ '-a', 'bob.bio.base.test.dummy.algorithm.DummyAlgorithm()',
+ '--zt-norm',
+ '-vs', 'test_config',
+ '--temp-directory', test_dir,
+ '--result-directory', test_dir,
+ '--imports', 'bob.bio.base.test.dummy',
+ ])
+
+ check_parameters(args_file, args_cmdline)
+
+ finally:
+ if test_dir: shutil.rmtree(test_dir)
+ if test_config_file: del test_config_file
+
+
+def test_compare_to_cmdline_resources():
+
+ test_dir = None
+ test_config_file = None
+ try:
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ test_config_file = tmp_file([
+ 'database = "dummy"',
+ 'preprocessor = "dummy"',
+ 'extractor = "dummy"',
+ 'algorithm = "dummy"',
+ 'zt_norm = True',
+ 'allow_missing_files = True',
+ 'verbose = 1',
+ 'sub_directory = "test_config"',
+ 'temp_directory = "%s"' % test_dir,
+ 'result_directory = "%s"' % test_dir,
+ 'preferred_package = "bob.bio.base"',
+ ])
+
+ args_file = parse_arguments(['-c', test_config_file.name])
+
+ # now do the same with command-line arguments, ensure result is equal
+ args_cmdline = parse_arguments([
+ '-d', 'dummy',
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-a', 'dummy',
+ '--zt-norm',
+ '--allow-missing-files',
+ '-vs', 'test_config',
+ '--temp-directory', test_dir,
+ '--result-directory', test_dir,
+ '--preferred-package', 'bob.bio.base',
+ ])
+
+ check_parameters(args_file, args_cmdline)
+
+ finally:
+ if test_dir: shutil.rmtree(test_dir)
+ if test_config_file: del test_config_file
+
+
+def test_compare_to_cmdline_skip():
+
+ test_dir = None
+ test_config_file = None
+ try:
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ test_config_file = tmp_file([
+ 'database = "dummy"',
+ 'preprocessor = "dummy"',
+ 'extractor = "dummy"',
+ 'skip_preprocessing = True',
+ 'skip_extraction = True',
+ 'algorithm = "dummy"',
+ 'zt_norm = True',
+ 'allow_missing_files = True',
+ 'verbose = 1',
+ 'sub_directory = "test_config"',
+ 'temp_directory = "%s"' % test_dir,
+ 'result_directory = "%s"' % test_dir,
+ 'preferred_package = "bob.bio.base"',
+ ])
+
+ args_file = parse_arguments(['-c', test_config_file.name])
+
+ # now do the same with command-line arguments, ensure result is equal
+ args_cmdline = parse_arguments([
+ '-d', 'dummy',
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-a', 'dummy',
+ '--zt-norm',
+ '--allow-missing-files',
+ '--skip-preprocessing',
+ '--skip-extraction',
+ '-vs', 'test_config',
+ '--temp-directory', test_dir,
+ '--result-directory', test_dir,
+ '--preferred-package', 'bob.bio.base',
+ ])
+
+ check_parameters(args_file, args_cmdline)
+
+ finally:
+ if test_dir: shutil.rmtree(test_dir)
+ if test_config_file: del test_config_file
diff --git a/bob/bio/base/test/test_scripts.py b/bob/bio/base/test/test_scripts.py
index 0141aeb34b47ec36c18814298968529d5d370547..cfaddc437f3b59fc6efb0518635424fdbbea2009 100644
--- a/bob/bio/base/test/test_scripts.py
+++ b/bob/bio/base/test/test_scripts.py
@@ -9,7 +9,6 @@ import shutil
import tempfile
import numpy
-import bob.io.base.test_utils
import bob.io.image
import bob.bio.base
from . import utils
diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index 3749b36e29f7cb224371e75bcad321c7c55cce5e..ba4379960571bdf35e23f117b5c34c3e0e94a56d 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -47,13 +47,15 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
#######################################################################################
############## options that are required to be specified #######################
config_group = parser.add_argument_group('\nParameters defining the experiment. Most of these parameters can be a registered resource, a configuration file, or even a string that defines a newly created object')
- config_group.add_argument('-d', '--database', metavar = 'x', nargs = '+', required = True,
+ config_group.add_argument('-c', '--configuration-file',
+ help = 'A configuration file containing one or more of "database", "preprocessor", "extractor", "algorithm" and/or "grid"')
+ config_group.add_argument('-d', '--database', metavar = 'x', nargs = '+',
help = 'Database and the protocol; registered databases are: %s' % utils.resource_keys('database', exclude_resources_from))
- config_group.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+', required = True,
+ config_group.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+',
help = 'Data preprocessing; registered preprocessors are: %s' % utils.resource_keys('preprocessor', exclude_resources_from))
- config_group.add_argument('-e', '--extractor', metavar = 'x', nargs = '+', required = True,
+ config_group.add_argument('-e', '--extractor', metavar = 'x', nargs = '+',
help = 'Feature extraction; registered feature extractors are: %s' % utils.resource_keys('extractor', exclude_resources_from))
- config_group.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', required = True,
+ config_group.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+',
help = 'Biometric recognition; registered algorithms are: %s' % utils.resource_keys('algorithm', exclude_resources_from))
config_group.add_argument('-g', '--grid', metavar = 'x', nargs = '+',
help = 'Configuration for the grid setup; if not specified, the commands are executed sequentially on the local machine.')
@@ -61,7 +63,7 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
help = 'If one of your configuration files is an actual command, please specify the lists of required libraries (imports) to execute this command')
config_group.add_argument('-W', '--preferred-package', metavar = 'LIB',
help = 'If resources with identical names are defined in several packages, prefer the one from the given package')
- config_group.add_argument('-s', '--sub-directory', metavar = 'DIR', required = True,
+ config_group.add_argument('-s', '--sub-directory', metavar = 'DIR',
help = 'The sub-directory where the files of the current experiment should be stored. Please specify a directory name with a name describing your experiment')
config_group.add_argument('--groups', metavar = 'GROUP', nargs = '+', default = ['dev'],
help = "The groups (i.e., 'dev', 'eval') for which the models and scores should be generated; by default, only the 'dev' group is evaluated")
@@ -132,7 +134,7 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
help = 'Runs the local scheduler with the given nice value')
flag_group.add_argument('-D', '--delete-jobs-finished-with-status', choices = ('all', 'failure', 'success'),
help = 'If selected, local scheduler jobs that finished with the given status are deleted from the --gridtk-database-file; otherwise the jobs remain in the database')
- flag_group.add_argument('-c', '--calibrate-scores', action='store_true',
+ flag_group.add_argument('-C', '--calibrate-scores', action='store_true',
help = 'Performs score calibration after the scores are computed.')
flag_group.add_argument('-z', '--zt-norm', action='store_true',
help = 'Enable the computation of ZT norms')
@@ -153,6 +155,22 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
}
+def _take_from_config_or_command_line(args, config, keyword, default, required=True, is_resource=True):
+
+ if getattr(args, keyword) != default:
+ if is_resource:
+ setattr(args, keyword, utils.load_resource(' '.join(getattr(args, keyword)), keyword, imports = args.imports, preferred_package = args.preferred_package))
+
+ elif config is not None and hasattr(config, keyword):
+
+ val = getattr(config, keyword)
+ if isinstance(val, str) and is_resource:
+ val = utils.load_resource(val, keyword, imports = args.imports, preferred_package = args.preferred_package)
+ setattr(args, keyword, val)
+
+ elif required:
+ raise ValueError("Please specify a %s either on command line (via --%s) or in the configuration file (via --configuration-file)" %(keyword, keyword))
+
def initialize(parsers, command_line_parameters = None, skips = []):
"""initialize(parsers, command_line_parameters = None, skips = []) -> args
@@ -185,7 +203,7 @@ def initialize(parsers, command_line_parameters = None, skips = []):
.. note:: The database, preprocessor, extractor, algorithm and grid (if specified) are actual instances of the according classes.
"""
- # execute-only
+ # add execute-only flags to command line options
if skips is not None:
#######################################################################################
################# options for skipping parts of the toolchain #########################
@@ -194,16 +212,70 @@ def initialize(parsers, command_line_parameters = None, skips = []):
skip_group.add_argument('--skip-%s' % skip, action='store_true', help = 'Skip the %s step.' % skip)
skip_group.add_argument('-o', '--execute-only', nargs = '+', choices = skips, help = 'If specified, executes only the given parts of the tool chain.')
- args = parsers['main'].parse_args(command_line_parameters)
+ # parse the arguments
+ parser = parsers['main']
+ args = parser.parse_args(command_line_parameters)
+
+ # first, read the configuration file and set everything from the config file to the args -- as long as not overwritten on command line
+ config = utils.read_config_file(args.configuration_file) if args.configuration_file is not None else None
+ for keyword in ("database", "preprocessor", "extractor", "algorithm"):
+ _take_from_config_or_command_line(args, config, keyword,
+ parser.get_default(keyword))
+
+ _take_from_config_or_command_line(args, config, "grid",
+ parser.get_default(keyword), required=False)
+
+ _take_from_config_or_command_line(args, config, "sub_directory",
+ parser.get_default(keyword), is_resource=False)
+
+ skip_keywords = tuple(['skip_' + k.replace('-', '_') for k in skips])
+
+ for keyword in (
+ "protocol",
+ "groups",
+ "parallel",
+ "preferred_package",
+ "temp_directory",
+ "result_directory",
+ "extractor_file",
+ "projector_file",
+ "enroller_file",
+ "gridtk_database_file",
+ "experiment_info_file",
+ "database_directories_file",
+ "preprocessed_directory",
+ "extracted_directory",
+ "projected_directory",
+ "model_directories",
+ "score_directories",
+ "zt_directories",
+ "grid_log_directory",
+ "verbose",
+ "dry_run",
+ "force",
+ "write_compressed_score_files",
+ "stop_on_failure",
+ "run_local_scheduler",
+ "external_dependencies",
+ "timer",
+ "nice",
+ "delete_jobs_finished_with_status",
+ "calibrate_scores",
+ "zt_norm",
+ "allow_missing_files",
+ "env",
+ ) + skip_keywords:
+ _take_from_config_or_command_line(args, config, keyword,
+ parser.get_default(keyword), required=False, is_resource=False)
# evaluate skips
if skips is not None and args.execute_only is not None:
for skip in skips:
if skip not in args.execute_only:
- exec("args.skip_%s = True" % (skip.replace("-", "_")))
+ setattr("args", "skip_%s" % skip.replace("-", "_"), True)
if args.parallel is not None:
- args.grid = ['bob.bio.base.grid.Grid("local", number_of_parallel_processes = %d)' % args.parallel]
+ args.grid = bob.bio.base.grid.Grid("local", number_of_parallel_processes = args.parallel)
args.run_local_scheduler = True
args.stop_on_failure = True
@@ -214,13 +286,6 @@ def initialize(parsers, command_line_parameters = None, skips = []):
if args.timer is not None and not len(args.timer):
args.timer = ('real', 'system', 'user')
- # load configuration resources
- args.database = utils.load_resource(' '.join(args.database), 'database', imports = args.imports, preferred_package = args.preferred_package)
- args.preprocessor = utils.load_resource(' '.join(args.preprocessor), 'preprocessor', imports = args.imports, preferred_package = args.preferred_package)
- args.extractor = utils.load_resource(' '.join(args.extractor), 'extractor', imports = args.imports, preferred_package = args.preferred_package)
- args.algorithm = utils.load_resource(' '.join(args.algorithm), 'algorithm', imports = args.imports, preferred_package = args.preferred_package)
- if args.grid is not None:
- args.grid = utils.load_resource(' '.join(args.grid), 'grid', imports = args.imports, preferred_package = args.preferred_package)
# set base directories
if args.temp_directory is None:
@@ -232,7 +297,6 @@ def initialize(parsers, command_line_parameters = None, skips = []):
args.result_directory = os.path.join(args.result_directory, args.sub_directory)
args.grid_log_directory = os.path.join(args.temp_directory, args.grid_log_directory)
-
# protocol command line override
if args.protocol is not None:
args.database.protocol = args.protocol