diff --git a/bob/bio/base/algorithm/LDA.py b/bob/bio/base/algorithm/LDA.py
index 83bcc4c770a6dd1d8110e9fce39c99740719496f..9689f9987d0a9b8470c740f2b74e8a33a87c8d24 100644
--- a/bob/bio/base/algorithm/LDA.py
+++ b/bob/bio/base/algorithm/LDA.py
@@ -14,7 +14,7 @@ import logging
logger = logging.getLogger("bob.bio.base")
class LDA (Algorithm):
- """Tool for computing linear discriminant analysis (so-called Fisher faces)"""
+ """Computes linear discriminant analysis"""
def __init__(
self,
diff --git a/bob/bio/base/algorithm/PCA.py b/bob/bio/base/algorithm/PCA.py
index 708216e930dcd46c98b7d73497ce43ea6ab64db4..515eb88bbe1b6502415641aa7925f7ce0b18e011 100644
--- a/bob/bio/base/algorithm/PCA.py
+++ b/bob/bio/base/algorithm/PCA.py
@@ -14,7 +14,7 @@ import logging
logger = logging.getLogger("bob.bio.base")
class PCA (Algorithm):
- """Tool for computing eigenfaces"""
+ """Performs PCA on the given data"""
def __init__(
self,
diff --git a/bob/bio/base/script/enroll.py b/bob/bio/base/script/enroll.py
new file mode 100644
index 0000000000000000000000000000000000000000..842c9347d4b8de68bfa1371e5c12bd0530777273
--- /dev/null
+++ b/bob/bio/base/script/enroll.py
@@ -0,0 +1,62 @@
+"""This script can be used to enroll a model from several features using the given algorithm.
+"""
+
+import argparse
+import bob.core
+logger = bob.core.log.setup("bob.bio.base")
+
+import bob.bio.base
+
+
+def command_line_arguments(command_line_parameters):
+ """Parse the program options"""
+
+ # set up command line parser
+ parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', required = True, help = 'Biometric recognition; registered algorithms are: %s' % bob.bio.base.resource_keys('algorithm'))
+ parser.add_argument('-e', '--extractor', metavar = 'x', nargs = '+', required = True, help = 'Feature extraction; registered feature extractors are: %s' % bob.bio.base.resource_keys('extractor'))
+ parser.add_argument('-P', '--projector-file', metavar = 'FILE', help = 'The pre-trained extractor file, if the algorithm performs projection')
+ parser.add_argument('-E', '--enroller-file', metavar = 'FILE', help = 'The pre-trained enroller file, if the extractor requires enroller training')
+ parser.add_argument('-i', '--input-files', metavar = 'FEATURE', nargs='+', required = True, help = "A list of feature files to enroll the model from")
+ parser.add_argument('-o', '--output-file', metavar = 'MODEL', default = 'model.hdf5', help = "The file to write the enrolled model into (should be of type HDF5)")
+
+ # add verbose option
+ bob.core.log.add_command_line_option(parser)
+ # parse arguments
+ args = parser.parse_args(command_line_parameters)
+ # set verbosity level
+ bob.core.log.set_verbosity_level(logger, args.verbose)
+
+ return args
+
+
+def main(command_line_parameters=None):
+ """Preprocesses the given image with the given preprocessor."""
+ args = command_line_arguments(command_line_parameters)
+
+ logger.debug("Loading extractor")
+ extractor = bob.bio.base.load_resource(' '.join(args.extractor), "extractor")
+
+ logger.debug("Loading algorithm")
+ algorithm = bob.bio.base.load_resource(' '.join(args.algorithm), "algorithm")
+ if algorithm.requires_projector_training:
+ if args.projector_file is None:
+ raise ValueError("The desired algorithm requires a pre-trained projector file, but it was not specified")
+ algorithm.load_projector(args.projector_file)
+
+ if algorithm.requires_enroller_training:
+ if args.enroller_file is None:
+ raise ValueError("The desired algorithm requires a pre-trained enroller file, but it was not specified")
+ algorithm.load_enroller(args.enroller_file)
+
+ logger.debug("Loading %d features for enrollment", len(args.input_files))
+ features = [extractor.read_feature(f) for f in args.input_files]
+ if algorithm.use_projected_features_for_enrollment:
+ logger.debug("Projecting enrollment features")
+ features = [algorithm.project(f) for f in features]
+
+ logger.debug("Enrolling model")
+ model = algorithm.enroll(features)
+ algorithm.write_model(model, args.output_file)
+ logger.info("Wrote model to file '%s'", args.output_file)
diff --git a/bob/bio/base/script/evaluate.py b/bob/bio/base/script/evaluate.py
index 9b1afb7a768c37470a163fee569019267e4f797d..b85f6138b6645d171d9545599d066d7ae18aa068 100644
--- a/bob/bio/base/script/evaluate.py
+++ b/bob/bio/base/script/evaluate.py
@@ -67,9 +67,7 @@ def command_line_arguments(command_line_parameters):
parser.add_argument('-R', '--roc', help = "If given, ROC curves will be plotted into the given pdf file.")
parser.add_argument('-D', '--det', help = "If given, DET curves will be plotted into the given pdf file.")
parser.add_argument('-C', '--cmc', help = "If given, CMC curves will be plotted into the given pdf file.")
- parser.add_argument('-p', '--parser', default = '4column', choices = ('4column', '5column'), help="The style of the resulting score files. The default fits to the usual output of FaceRecLib score files.")
-
- parser.add_argument('--self-test', action='store_true', help=argparse.SUPPRESS)
+ parser.add_argument('--parser', default = '4column', choices = ('4column', '5column'), help="The style of the resulting score files. The default fits to the usual output of FaceRecLib score files.")
# add verbose option
bob.core.log.add_command_line_option(parser)
diff --git a/bob/bio/base/script/extract.py b/bob/bio/base/script/extract.py
new file mode 100644
index 0000000000000000000000000000000000000000..549d0579d86d329e0d144037a6604886fa979f14
--- /dev/null
+++ b/bob/bio/base/script/extract.py
@@ -0,0 +1,52 @@
+"""This script can be used to extract features using the given extractor from the given preprocessed image.
+"""
+
+import argparse
+import bob.core
+logger = bob.core.log.setup("bob.bio.base")
+
+import bob.bio.base
+
+
+def command_line_arguments(command_line_parameters):
+ """Parse the program options"""
+
+ # set up command line parser
+ parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument('-e', '--extractor', metavar = 'x', nargs = '+', required = True, help = 'Feature extraction; registered feature extractors are: %s' % bob.bio.base.resource_keys('extractor'))
+ parser.add_argument('-E', '--extractor-file', metavar = 'FILE', help = "The pre-trained extractor file, if the extractor requires training")
+ parser.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+', required = True, help = 'Data preprocessing; registered preprocessors are: %s' % bob.bio.base.resource_keys('preprocessor'))
+ parser.add_argument('-i', '--input-file', metavar = 'PREPROCESSED', required = True, help = "The preprocessed data file to read.")
+ parser.add_argument('-o', '--output-file', metavar = 'FEATURE', default = 'extracted.hdf5', help = "The file to write the extracted features into (should be of type HDF5)")
+
+ # add verbose option
+ bob.core.log.add_command_line_option(parser)
+ # parse arguments
+ args = parser.parse_args(command_line_parameters)
+ # set verbosity level
+ bob.core.log.set_verbosity_level(logger, args.verbose)
+
+ return args
+
+
+def main(command_line_parameters=None):
+ """Preprocesses the given image with the given preprocessor."""
+ args = command_line_arguments(command_line_parameters)
+
+ logger.debug("Loading preprocessor")
+ preprocessor = bob.bio.base.load_resource(' '.join(args.preprocessor), "preprocessor")
+ logger.debug("Loading extractor")
+ extractor = bob.bio.base.load_resource(' '.join(args.extractor), "extractor")
+ if extractor.requires_training:
+ if args.extractor_file is None:
+ raise ValueError("The desired extractor requires a pre-trained extractor file, but it was not specified")
+ extractor.load(args.extractor_file)
+
+ logger.debug("Loading preprocessed data from file '%s'", args.input_file)
+ preprocessed = preprocessor.read_data(args.input_file)
+
+ logger.info("Extracting features")
+ extracted = extractor(preprocessed)
+ extractor.write_feature(extracted, args.output_file)
+ logger.info("Wrote extracted features to file '%s'", args.output_file)
diff --git a/bob/bio/base/script/grid_search.py b/bob/bio/base/script/grid_search.py
index 2216eed3d3ab829e1834cc85e71b55f9331a40c2..62379c5f195cee599b2cb3402bde3cb412e1639f 100755
--- a/bob/bio/base/script/grid_search.py
+++ b/bob/bio/base/script/grid_search.py
@@ -18,7 +18,7 @@ global configuration
global place_holder_key
# the extracted command line arguments
global args
-# the job ids as returned by the call to the faceverify function
+# the job ids as returned by the call to the verify function
global job_ids
# first fake job id (useful for the --dry-run option)
global fake_job_id
@@ -74,7 +74,7 @@ def command_line_options(command_line_parameters):
help = 'Split the gridtk databases after the following level -1 - never split; 0 - preprocess; 1 - extract; 2 -- project; 3 -- enroll; 4 -- score;')
parser.add_argument('-x', '--executable',
- help = '(optional) The executable to be executed instead of facereclib/script/faceverify.py (taken *always* from the facereclib, not from the bin directory)')
+ help = '(optional) The executable to be executed instead of bob/bio/base/verify.py (taken *always* from bob.bio.base, not from the bin directory)')
parser.add_argument('-R', '--result-directory', default = os.path.join("/idiap/user", os.environ["USER"]),
help = 'The directory where to write the resulting score files to.')
@@ -101,7 +101,7 @@ def command_line_options(command_line_parameters):
help = 'Use the given variable instead of the "replace" keyword in the configuration file')
parser.add_argument('parameters', nargs = argparse.REMAINDER,
- help = "Parameters directly passed to the face verify script. Use -- to separate this parameters from the parameters of this script. See 'bin/verify.py --help' for a complete list of options.")
+ help = "Parameters directly passed to the verify script. Use -- to separate this parameters from the parameters of this script. See 'bin/verify.py --help' for a complete list of options.")
bob.core.log.add_command_line_option(parser)
@@ -168,7 +168,7 @@ def replace(string, replacements):
def create_command_line(replacements):
- """Creates the parameters for the function call that will be given to the faceverify script."""
+ """Creates the parameters for the function call that will be given to the verify script."""
# get the values to be replaced with
values = {}
for key in configuration.replace:
@@ -200,7 +200,7 @@ dependency_keys = ['DUMMY', 'preprocess', 'extract', 'project', 'enroll']
def directory_parameters(directories):
- """This function generates the faceverify parameters that define the directories, where the data is stored.
+ """This function generates the verify parameters that define the directories, where the data is stored.
The directories are set such that data is reused whenever possible, but disjoint if needed."""
def _join_dirs(index, subdir):
# collect sub-directories
@@ -318,7 +318,7 @@ def execute_dependent_task(command_line, directories, dependency_level):
if args.verbose:
print ("Would have executed job", utils.command_line(command_line))
else:
- # execute the face verification experiment
+ # execute the verification experiment
global fake_job_id
new_job_ids = verify.verify(verif_args, command_line, external_fake_job_id = fake_job_id)
else:
@@ -379,7 +379,7 @@ def create_recursive(replace_dict, step_index, directories, dependency_level, ke
new_dependency_level = step_index
-def main(command_line_parameters = sys.argv):
+def main(command_line_parameters = None):
"""Main entry point for the parameter test. Try --help to see the parameters that can be specified."""
global task_count, job_count, job_ids, score_directories
@@ -388,7 +388,7 @@ def main(command_line_parameters = sys.argv):
job_ids = {}
score_directories = []
- command_line_options(command_line_parameters[1:])
+ command_line_options(command_line_parameters)
global configuration, place_holder_key
configuration = utils.read_config_file(args.configuration_file)
diff --git a/bob/bio/base/script/preprocess.py b/bob/bio/base/script/preprocess.py
new file mode 100644
index 0000000000000000000000000000000000000000..ddc175402497ef13e8c673174c42d1fb31035097
--- /dev/null
+++ b/bob/bio/base/script/preprocess.py
@@ -0,0 +1,60 @@
+"""This script can be used to preprocess a single data file with a given preprocessor.
+"""
+
+import argparse
+import bob.core
+logger = bob.core.log.setup("bob.bio.base")
+
+import bob.bio.base
+import bob.db.verification.utils
+import numpy
+
+import bob.core
+import bob.io.base
+import bob.io.image
+
+
+def command_line_arguments(command_line_parameters):
+ """Parse the program options"""
+
+ # set up command line parser
+ parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+', required = True, help = 'Data preprocessing; registered preprocessors are: %s' % bob.bio.base.resource_keys('preprocessor'))
+ parser.add_argument('-i', '--input-file', metavar = 'FILE', required = True, help = "The data file to be preprocessed.")
+# parser.add_argument('-a', '--annotations', nargs='+', help = "Key=value-pairs for the annotations")
+ parser.add_argument('-a', '--annotation-file', metavar = 'FILE', help = "The annotation file for the given data file, if applicable and/or available; currently the only supported format is the 'named' annotation format.")
+ parser.add_argument('-o', '--output-file', metavar = 'PREPROCESSED', default = 'preprocessed.hdf5', help = "Write the preprocessed data into this file (should be of type HDF5)")
+ parser.add_argument('-c', '--convert-as-image', metavar = 'IMAGE', help = "Write the preprocessed data into this image file, converting it to an image, if possible")
+
+ # add verbose option
+ bob.core.log.add_command_line_option(parser)
+
+ # parse arguments
+ args = parser.parse_args(command_line_parameters)
+
+ # set verbosity level
+ bob.core.log.set_verbosity_level(logger, args.verbose)
+
+ return args
+
+def main(command_line_parameters=None):
+ """Preprocesses the given image with the given preprocessor."""
+ args = command_line_arguments(command_line_parameters)
+
+ logger.debug("Loading preprocessor")
+ preprocessor = bob.bio.base.load_resource(' '.join(args.preprocessor), "preprocessor")
+
+ logger.debug("Loading input data from file '%s'%s", args.input_file, " and '%s'" % args.annotation_file if args.annotation_file is not None else "")
+ data = preprocessor.read_original_data(args.input_file)
+ annotations = bob.db.verification.utils.read_annotation_file(args.annotation_file, 'named') if args.annotation_file is not None else None
+
+ logger.info("Preprocessing data")
+ preprocessed = preprocessor(data, annotations)
+ preprocessor.write_data(preprocessed, args.output_file)
+ logger.info("Wrote preprocessed data to file '%s'", args.output_file)
+
+ if args.convert_as_image is not None:
+ converted = bob.core.convert(preprocessed, 'uint8', dest_range=(0,255), source_range=(numpy.min(preprocessed), numpy.max(preprocessed)))
+ bob.io.base.save(converted, args.convert_as_image)
+ logger.info("Wrote preprocessed data to image file '%s'", args.convert_as_image)
diff --git a/bob/bio/base/script/score.py b/bob/bio/base/script/score.py
new file mode 100644
index 0000000000000000000000000000000000000000..2e617e09cdbc7218c3c44ecfb951c7632cd83f8b
--- /dev/null
+++ b/bob/bio/base/script/score.py
@@ -0,0 +1,62 @@
+"""This script can be used to compute scores between a list of enrolled models and a list of probe files.
+"""
+
+from __future__ import print_function
+
+import argparse
+import bob.core
+logger = bob.core.log.setup("bob.bio.base")
+
+import bob.bio.base
+
+
+def command_line_arguments(command_line_parameters):
+ """Parse the program options"""
+
+ # set up command line parser
+ parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+ parser.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', required = True, help = 'Biometric recognition; registered algorithms are: %s' % bob.bio.base.resource_keys('algorithm'))
+ parser.add_argument('-P', '--projector-file', metavar = 'FILE', help = 'The pre-trained extractor file, if the algorithm performs projection')
+ parser.add_argument('-E', '--enroller-file' , metavar = 'FILE', help = 'The pre-trained enroller file, if the extractor requires enroller training')
+ parser.add_argument('-m', '--model-files', metavar = 'MODEL', nargs='+', required = True, help = "A list of enrolled model files")
+ parser.add_argument('-p', '--probe-files', metavar = 'PROBE', nargs='+', required = True, help = "A list of extracted feature files used as probes")
+
+ # add verbose option
+ bob.core.log.add_command_line_option(parser)
+ # parse arguments
+ args = parser.parse_args(command_line_parameters)
+ # set verbosity level
+ bob.core.log.set_verbosity_level(logger, args.verbose)
+
+ return args
+
+
+def main(command_line_parameters=None):
+ """Preprocesses the given image with the given preprocessor."""
+ args = command_line_arguments(command_line_parameters)
+
+ logger.debug("Loading algorithm")
+ algorithm = bob.bio.base.load_resource(' '.join(args.algorithm), "algorithm")
+ if algorithm.requires_projector_training:
+ if args.projector_file is None:
+ raise ValueError("The desired algorithm requires a pre-trained projector file, but it was not specified")
+ algorithm.load_projector(args.projector_file)
+
+ if algorithm.requires_enroller_training:
+ if args.enroller_file is None:
+ raise ValueError("The desired algorithm requires a pre-trained enroller file, but it was not specified")
+ algorithm.load_enroller(args.enroller_file)
+
+ logger.debug("Loading %d models", len(args.model_files))
+ models = {m : algorithm.read_model(m) for m in args.model_files}
+ logger.debug("Loading %d probes", len(args.probe_files))
+ probes = {p : algorithm.read_probe(p) for p in args.probe_files}
+ if algorithm.performs_projection:
+ logger.debug("Projecting %d probes", len(args.probe_files))
+ probes = {p : algorithm.project(probes[p]) for p in probes}
+
+ logger.info("Computing scores")
+ for p in args.probe_files:
+ for m in args.model_files:
+ print("Score between model '%s' and probe '%s' is %3.8f" % (m, p, algorithm.score(models[m], probes[p])))
diff --git a/bob/bio/base/script/verify.py b/bob/bio/base/script/verify.py
index a699f13d685605790f478aede29354f8c6c2594d..869e88a29e1b3494f5fee7e47f1b30a6adb823fc 100644
--- a/bob/bio/base/script/verify.py
+++ b/bob/bio/base/script/verify.py
@@ -34,7 +34,7 @@ def parse_arguments(command_line_parameters, exclude_resources_from = []):
skips = ['preprocessing', 'extractor-training', 'extraction', 'projector-training', 'projection', 'enroller-training', 'enrollment', 'score-computation', 'concatenation', 'calibration'])
-def add_jobs(args, submitter = None):
+def add_jobs(args, submitter):
"""Adds all (desired) jobs of the tool chain to the grid, or to the local list to be executed."""
# collect the job ids
@@ -378,9 +378,9 @@ def verify(args, command_line_parameters, external_fake_job_id = 0):
return {}
else:
# add jobs
- submitter = tools.GridSubmission(args, command_line_parameters, first_fake_job_id = external_fake_job_id) if args.grid else None
+ submitter = tools.GridSubmission(args, command_line_parameters, first_fake_job_id = external_fake_job_id)
retval = add_jobs(args, submitter)
- tools.write_info(args, command_line_parameters)
+ tools.write_info(args, command_line_parameters, submitter.executable)
if args.grid is not None:
if args.grid.is_local() and args.run_local_scheduler:
@@ -419,11 +419,11 @@ def verify(args, command_line_parameters, external_fake_job_id = 0):
return {}
-def main(command_line_parameters = sys.argv):
+def main(command_line_parameters = None):
"""Executes the main function"""
try:
# do the command line parsing
- args = parse_arguments(command_line_parameters[1:])
+ args = parse_arguments(command_line_parameters)
# perform face verification test
verify(args, command_line_parameters)
diff --git a/bob/bio/base/test/test_scripts.py b/bob/bio/base/test/test_scripts.py
index cb5acba33fba78da2fa690aa5e1bd297db0952b5..7d40bc34f8ec1cc30da108ce4aceaac0df2ad3fb 100644
--- a/bob/bio/base/test/test_scripts.py
+++ b/bob/bio/base/test/test_scripts.py
@@ -5,7 +5,6 @@ from __future__ import print_function
import bob.measure
import os
-import sys
import shutil
import tempfile
import numpy
@@ -29,7 +28,7 @@ data_dir = pkg_resources.resource_filename('bob.bio.base', 'test/data')
def _verify(parameters, test_dir, sub_dir, ref_modifier="", score_modifier=('scores','')):
from bob.bio.base.script.verify import main
try:
- main([sys.argv[0]] + parameters)
+ main(parameters)
# assert that the score file exists
score_files = [os.path.join(test_dir, sub_dir, 'Default', norm, '%s-dev%s'%score_modifier) for norm in ('nonorm', 'ztnorm')]
@@ -227,7 +226,7 @@ def test_verify_filelist():
try:
from bob.bio.base.script.verify import main
- main([sys.argv[0]] + parameters)
+ main(parameters)
# assert that the score file exists
score_files = [os.path.join(test_dir, 'test_filelist', 'None', norm, 'scores-dev') for norm in ('nonorm', 'ztnorm')]
@@ -300,7 +299,6 @@ def test_grid_search():
try:
# first test without grid option
parameters = [
- sys.argv[0],
'-c', os.path.join(dummy_dir, 'grid_search.py'),
'-d', 'dummy',
'-e', 'dummy',
@@ -319,7 +317,6 @@ def test_grid_search():
# now, in the grid...
parameters = [
- sys.argv[0],
'-c', os.path.join(dummy_dir, 'grid_search.py'),
'-d', 'dummy',
'-s', 'test_grid_search',
@@ -340,7 +337,6 @@ def test_grid_search():
# and now, finally run locally
parameters = [
- sys.argv[0],
'-c', os.path.join(dummy_dir, 'grid_search.py'),
'-d', 'dummy',
'-s', 'test_grid_search',
@@ -359,6 +355,96 @@ def test_grid_search():
# number of jobs in the grid: 36 (including best possible re-use of files; minus preprocessing)
assert bob.bio.base.script.grid_search.job_count == 0
+ finally:
+ shutil.rmtree(test_dir)
+
+
+def test_scripts():
+ # Tests the bin/preprocess.py, bin/extract.py, bin/enroll.py and bin/score.py scripts
+ test_dir = tempfile.mkdtemp(prefix='bobtest_')
+ data_file = os.path.join(test_dir, "data.hdf5")
+ annotation_file = os.path.join(test_dir, "annotatations.txt")
+ preprocessed_file = os.path.join(test_dir, "preprocessed.hdf5")
+ preprocessed_image = os.path.join(test_dir, "preprocessed.png")
+ extractor_file = os.path.join(test_dir, "extractor.hdf5")
+ extracted_file = os.path.join(test_dir, "extracted.hdf5")
+ projector_file = os.path.join(test_dir, "projector.hdf5")
+ enroller_file = os.path.join(test_dir, "enroller.hdf5")
+ model_file = os.path.join(test_dir, "model.hdf5")
+
+ # tests that the parameter_test.py script works properly
+ try:
+ # create test data
+ test_data = utils.random_array((20,20), 0., 255., seed=84)
+ test_data[0,0] = 0.
+ test_data[19,19] = 255.
+ bob.io.base.save(test_data, data_file)
+ with open(annotation_file, 'w') as a:
+ a.write("leye 100 200\nreye 100 100")
+
+ extractor = bob.bio.base.load_resource("dummy", "extractor")
+ extractor.train([], extractor_file)
+
+ algorithm = bob.bio.base.load_resource("dummy", "algorithm")
+ algorithm.train_projector([], projector_file)
+ algorithm.train_enroller([], enroller_file)
+
+ from bob.bio.base.script.preprocess import main as preprocess
+ from bob.bio.base.script.extract import main as extract
+ from bob.bio.base.script.enroll import main as enroll
+ from bob.bio.base.script.score import main as score
+
+ # preprocessing
+ parameters = [
+ '-i', data_file,
+ '-a', annotation_file,
+ '-p', 'dummy',
+ '-o', preprocessed_file,
+ '-c', preprocessed_image
+ ]
+ preprocess(parameters)
+
+ assert os.path.isfile(preprocessed_file)
+ assert os.path.isfile(preprocessed_image)
+ assert numpy.allclose(bob.io.base.load(preprocessed_file), test_data)
+ assert numpy.allclose(bob.io.base.load(preprocessed_image), test_data, rtol=1., atol=1.)
+
+ # feature extraction
+ parameters = [
+ '-i', preprocessed_file,
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-E', extractor_file,
+ '-o', extracted_file,
+ ]
+ extract(parameters)
+
+ assert os.path.isfile(extracted_file)
+ assert numpy.allclose(bob.io.base.load(extracted_file), test_data.flatten())
+
+ # enrollment
+ parameters = [
+ '-i', extracted_file, extracted_file,
+ '-e', 'dummy',
+ '-a', 'dummy',
+ '-P', projector_file,
+ '-E', enroller_file,
+ '-o', model_file
+ ]
+ enroll(parameters)
+
+ assert os.path.isfile(model_file)
+ assert numpy.allclose(bob.io.base.load(model_file), test_data.flatten())
+
+ # scoring
+ parameters = [
+ '-m', model_file, model_file,
+ '-p', extracted_file, extracted_file,
+ '-a', 'dummy',
+ '-P', projector_file,
+ '-E', enroller_file,
+ ]
+ score(parameters)
finally:
shutil.rmtree(test_dir)
diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index b2da327edcea91e476037c8f16df50936aece3f1..0a49bd75b6550ac5ba63f00b8947b944e350fe58 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -25,11 +25,11 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
config_group.add_argument('-d', '--database', metavar = 'x', nargs = '+', required = True,
help = 'Database and the protocol; registered databases are: %s' % resource_keys('database', exclude_resources_from))
config_group.add_argument('-p', '--preprocessor', metavar = 'x', nargs = '+', required = True,
- help = 'Image preprocessing; registered preprocessors are: %s' % resource_keys('preprocessor', exclude_resources_from))
+ help = 'Data preprocessing; registered preprocessors are: %s' % resource_keys('preprocessor', exclude_resources_from))
config_group.add_argument('-e', '--extractor', metavar = 'x', nargs = '+', required = True,
help = 'Feature extraction; registered feature extractors are: %s' % resource_keys('extractor', exclude_resources_from))
config_group.add_argument('-a', '--algorithm', metavar = 'x', nargs = '+', required = True,
- help = 'Face recognition; registered face recognition algorithms are: %s' % resource_keys('algorithm', exclude_resources_from))
+ help = 'Biometric recognition; registered algorithms are: %s' % 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.')
config_group.add_argument('--imports', metavar = 'LIB', nargs = '+', default = ['bob.bio.base'],
@@ -249,13 +249,24 @@ def groups(args):
return groups
-def write_info(args, command_line_parameters):
+def command_line(cmdline):
+ """Converts the given options to a string that can be executed on command line."""
+ c = ""
+ for cmd in cmdline:
+ if cmd[0] in '/-':
+ c += "%s " % cmd
+ else:
+ c += "'%s' " % cmd
+ return c
+
+
+def write_info(args, command_line_parameters, executable):
# write configuration
try:
bob.io.base.create_directories_safe(os.path.dirname(args.info_file))
f = open(args.info_file, 'w')
f.write("Command line:\n")
- f.write(" ".join(command_line_parameters) + "\n\n")
+ f.write(command_line([executable] + command_line_parameters) + "\n\n")
f.write("Configuration:\n")
f.write("Database:\n%s\n\n" % args.database)
f.write("Preprocessing:\n%s\n\n" % args.preprocessor)
@@ -263,14 +274,3 @@ def write_info(args, command_line_parameters):
f.write("Algorithm:\n%s\n\n" % args.algorithm)
except IOError:
logger.error("Could not write the experimental setup into file '%s'", args.info_file)
-
-
-def command_line(cmdline):
- """Converts the given options to a string that can be executed on command line."""
- c = ""
- for cmd in cmdline:
- if cmd[0] in '/-':
- c += "%s " % cmd
- else:
- c += "'%s' " % cmd
- return c
diff --git a/bob/bio/base/tools/grid.py b/bob/bio/base/tools/grid.py
index 2eaf27ca598bfd790e3bb4060e3503d88f14894c..5306f93cb03f07e8a0d916acf8bde541e6b651fb 100644
--- a/bob/bio/base/tools/grid.py
+++ b/bob/bio/base/tools/grid.py
@@ -34,30 +34,37 @@ def indices(list_to_split, number_of_parallel_jobs, task_id=None):
class GridSubmission:
def __init__(self, args, command_line_parameters, executable = 'verify.py', first_fake_job_id = 0):
- assert isinstance(args.grid, Grid)
- # find, where jman and the executable are installed
+ # find, where the executable is installed
import bob.extension
- jmans = bob.extension.find_executable('jman', prefixes = ['bin'])
- if not len(jmans):
- raise IOError("Could not find the 'jman' executable. Have you installed GridTK?")
executables = bob.extension.find_executable(executable, prefixes = ['bin'])
if not len(executables):
raise IOError("Could not find the '%s' executable." % executable)
- jman, executable = jmans[0], executables[0]
- assert os.path.isfile(jman) and os.path.isfile(executable)
-
- self.args = args
- self.command_line = [p for p in command_line_parameters[1:] if not p.startswith('--skip') and p not in ('-q', '--dry-run', '-o', '--execute-only')]
+ executable = executables[0]
+ assert os.path.isfile(executable)
self.executable = executable
- self.fake_job_id = first_fake_job_id
-
- import gridtk
- # setup logger
- bob.core.log.set_verbosity_level(bob.core.log.setup("gridtk"), args.verbose)
- Manager = gridtk.local.JobManagerLocal if args.grid.is_local() else gridtk.sge.JobManagerSGE
- self.job_manager = Manager(database = args.gridtk_database_file, wrapper_script=jman)
- self.submitted_job_ids = []
+
+ if args.grid is not None:
+ assert isinstance(args.grid, Grid)
+
+ # find, where jman is installed
+ jmans = bob.extension.find_executable('jman', prefixes = ['bin'])
+ if not len(jmans):
+ raise IOError("Could not find the 'jman' executable. Have you installed GridTK?")
+ jman = jmans[0]
+ assert os.path.isfile(jman)
+
+ self.args = args
+ self.command_line = [p for p in command_line_parameters if not p.startswith('--skip') and p not in ('-q', '--dry-run', '-o', '--execute-only')]
+ self.fake_job_id = first_fake_job_id
+
+ import gridtk
+ # setup logger
+ bob.core.log.set_verbosity_level(bob.core.log.setup("gridtk"), args.verbose)
+ Manager = gridtk.local.JobManagerLocal if args.grid.is_local() else gridtk.sge.JobManagerSGE
+ self.job_manager = Manager(database = args.gridtk_database_file, wrapper_script=jman)
+ self.submitted_job_ids = []
+
def submit(self, command, number_of_parallel_jobs = 1, dependencies=[], name = None, **kwargs):
"""Submit a grid job with the given command, which is added to the default command line.
diff --git a/setup.py b/setup.py
index 95a244d32826b17b629ace4736f8e5b0138a6635..3746ff5e6249c1f376ee73cd8099e90b0375de80 100644
--- a/setup.py
+++ b/setup.py
@@ -107,6 +107,10 @@ setup(
'resources.py = bob.bio.base.script.resources:main',
'evaluate.py = bob.bio.base.script.evaluate:main',
'grid_search.py = bob.bio.base.script.grid_search:main',
+ 'preprocess.py = bob.bio.base.script.preprocess:main',
+ 'extract.py = bob.bio.base.script.extract:main',
+ 'enroll.py = bob.bio.base.script.enroll:main',
+ 'score.py = bob.bio.base.script.score:main',
],
'bob.bio.database': [