diff --git a/bob/bio/base/__init__.py b/bob/bio/base/__init__.py
index adf87109095c9c436917098995b9252c7bef93d7..a81db5cd825633417b6f1a2e24a37380e4120bd0 100644
--- a/bob/bio/base/__init__.py
+++ b/bob/bio/base/__init__.py
@@ -1,7 +1,12 @@
from .utils import *
from . import database
-from . import algorithm
+from . import preprocessor
from . import extractor
+from . import algorithm
+from . import tools
+from . import grid # only one file, not complete directory
+
+from . import test
diff --git a/bob/bio/base/database/DatabaseFileList.py b/bob/bio/base/database/DatabaseFileList.py
new file mode 100644
index 0000000000000000000000000000000000000000..a423442521c9305f94525aeda9a844f5691e2e3b
--- /dev/null
+++ b/bob/bio/base/database/DatabaseFileList.py
@@ -0,0 +1,83 @@
+#!/usr/bin/env python
+# vim: set fileencoding=utf-8 :
+# @author: Manuel Guenther <Manuel.Guenther@idiap.ch>
+# @date: Wed Oct 3 10:31:51 CEST 2012
+#
+# Copyright (C) 2011-2012 Idiap Research Institute, Martigny, Switzerland
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, version 3 of the License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+
+from .DatabaseBob import DatabaseBobZT
+
+class DatabaseFileList (DatabaseBobZT):
+ """This class should be used whenever you have an :py:class:`bob.db.verification.filelist.Database``."""
+
+ def __init__(
+ self,
+ database, # The bob database that is used
+ **kwargs # The default parameters of the base class
+ ):
+ """
+ Parameters of the constructor of this database:
+
+ database : :py:class:`bob.db.verification.filelist.Database`
+ The database that provides the actual interface
+
+ kwargs
+ Keyword arguments directly passed to the :py:class:`DatabaseBobZT` base class constructor
+ """
+
+ DatabaseBobZT.__init__(
+ self,
+ database = database,
+ **kwargs
+ )
+
+
+ def all_files(self, groups = ['dev']):
+ """Returns all File objects of the database for the current protocol. If the current protocol is 'None' (a string), None (NoneType) will be used instead"""
+ files = self.database.objects(protocol = self.protocol if self.protocol != 'None' else None, groups = groups, **self.all_files_options)
+
+ # add all files that belong to the ZT-norm
+ for group in groups:
+ if group == 'world': continue
+ if self.database.implements_zt(protocol = self.protocol if self.protocol != 'None' else None, groups = group):
+ files += self.database.tobjects(protocol = self.protocol if self.protocol != 'None' else None, groups = group, model_ids = None)
+ files += self.database.zobjects(protocol = self.protocol if self.protocol != 'None' else None, groups = group, **self.m_z_probe_options)
+ return self.sort(files)
+
+
+ def uses_probe_file_sets(self):
+ """Defines if, for the current protocol, the database uses several probe files to generate a score."""
+ return False
+
+
+ def model_ids(self, group = 'dev'):
+ """Returns the model ids for the given group and the current protocol."""
+ return sorted(self.database.model_ids(protocol = self.protocol if self.protocol != 'None' else None, groups = group))
+
+
+ def client_id_from_model_id(self, model_id, group = 'dev'):
+ """Returns the client id for the given model id."""
+ return self.database.get_client_id_from_model_id(model_id, groups = group, protocol = self.protocol if self.protocol != 'None' else None)
+
+
+ def client_id_from_t_model_id(self, t_model_id, group = 'dev'):
+ """Returns the client id for the given T-model id."""
+ return self.database.get_client_id_from_tmodel_id(t_model_id, groups=group, protocol=self.protocol if self.protocol != 'None' else None)
+
+
+ def t_model_ids(self, group = 'dev'):
+ """Returns the T-Norm model ids for the given group and the current protocol."""
+ return sorted(self.database.tmodel_ids(protocol = self.protocol if self.protocol != 'None' else None, groups = group))
diff --git a/bob/bio/base/database/__init__.py b/bob/bio/base/database/__init__.py
index 4be83f81fd87a662ebeb2a93be4fc6b149a9b5ed..e40749ee493def073b3bad13699846e9596112b5 100644
--- a/bob/bio/base/database/__init__.py
+++ b/bob/bio/base/database/__init__.py
@@ -1,5 +1,6 @@
from .Database import Database, DatabaseZT
from .DatabaseBob import DatabaseBob, DatabaseBobZT
+from .DatabaseFileList import DatabaseFileList
# gets sphinx autodoc done right - don't remove it
__all__ = [_ for _ in dir() if not _.startswith('_')]
diff --git a/bob/bio/base/grid.py b/bob/bio/base/grid.py
index e9170a11668441ece86da4f903a057a48a96bae4..aba9ca30950fa1a429d283cfb317fe52bcea7820 100644
--- a/bob/bio/base/grid.py
+++ b/bob/bio/base/grid.py
@@ -32,7 +32,7 @@ PREDEFINED_QUEUES = {
'Week' : {'queue' : 'q1wm', 'memfree' : '32G', 'pe_opt' : 'pe_mth 4', 'hvmem' : '8G'}
}
-class GridParameters:
+class Grid:
"""This class is defining the options that are required to submit parallel jobs to the SGE grid.
"""
diff --git a/bob/bio/base/script/verify.py b/bob/bio/base/script/verify.py
index 577064c6c176643f09db7a58a07f9df87fccd8b2..4df60e4ee3790cacba340e912d4ba6b4b7aeca56 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):
+def add_jobs(args, submitter = None):
"""Adds all (desired) jobs of the tool chain to the grid, or to the local list to be executed."""
# collect the job ids
@@ -50,8 +50,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('preprocess',))
else:
- job_ids['preprocessing'] = self.submit_grid_job(
- 'preprocess',
+ job_ids['preprocessing'] = submitter.submit(
+ '--sub-task preprocess',
number_of_parallel_jobs = args.grid.number_of_preprocessing_jobs,
dependencies = deps,
**args.grid.preprocessing_queue)
@@ -62,8 +62,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('train-extractor',))
else:
- job_ids['extractor-training'] = self.submit_grid_job(
- 'train-extractor',
+ job_ids['extractor-training'] = submitter.submit(
+ '--sub-task train-extractor',
name = 'train-f',
dependencies = deps,
**args.grid.training_queue)
@@ -74,8 +74,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('extract',))
else:
- job_ids['extraction'] = self.submit_grid_job(
- 'extract',
+ job_ids['extraction'] = submitter.submit(
+ '--sub-task extract',
number_of_parallel_jobs = args.grid.number_of_extraction_jobs,
dependencies = deps,
**args.grid.extraction_queue)
@@ -86,8 +86,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('train-projector',))
else:
- job_ids['projector_training'] = self.submit_grid_job(
- 'train-projector',
+ job_ids['projector_training'] = submitter.submit(
+ '--sub-task train-projector',
name="train-p",
dependencies = deps,
**args.grid.training_queue)
@@ -98,8 +98,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('project',))
else:
- job_ids['projection'] = self.submit_grid_job(
- 'project',
+ job_ids['projection'] = submitter.submit(
+ '--sub-task project',
number_of_parallel_jobs = args.grid.number_of_projection_jobs,
dependencies = deps,
**args.grid.projection_queue)
@@ -110,8 +110,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('train-enroller',))
else:
- job_ids['enroller_training'] = self.submit_grid_job(
- 'train-enroller',
+ job_ids['enroller_training'] = submitter.submit(
+ '--sub-task train-enroller',
name = "train-e",
dependencies = deps,
**args.grid.training_queue)
@@ -129,8 +129,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('enroll', group, 'N'))
else:
- job_ids['enroll_%s_N'%group] = self.submit_grid_job(
- 'enroll --group %s --model-type N'%group,
+ job_ids['enroll_%s_N'%group] = submitter.submit(
+ '--sub-task enroll --group %s --model-type N'%group,
name = "enr-N-%s"%group,
number_of_parallel_jobs = args.grid.number_of_enrollment_jobs,
dependencies = deps,
@@ -141,8 +141,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('enroll', group, 'T'))
else:
- job_ids['enroll_%s_T'%group] = self.submit_grid_job(
- 'enroll --group %s --model-type T'%group,
+ job_ids['enroll_%s_T'%group] = submitter.submit(
+ '--sub-task enroll --group %s --model-type T'%group,
name = "enr-T-%s"%group,
number_of_parallel_jobs = args.grid.number_of_enrollment_jobs,
dependencies = deps,
@@ -154,8 +154,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('compute-scores', group, None, 'A'))
else:
- job_ids['score_%s_A'%group] = self.submit_grid_job(
- 'compute-scores --group %s --score-type A'%group,
+ job_ids['score_%s_A'%group] = submitter.submit(
+ '--sub-task compute-scores --group %s --score-type A'%group,
name = "score-A-%s"%group,
number_of_parallel_jobs = args.grid.number_of_scoring_jobs,
dependencies = enroll_deps_n[group],
@@ -169,22 +169,22 @@ def add_jobs(args):
jobs_to_execute.append(('compute-scores', group, None, 'D'))
jobs_to_execute.append(('compute-scores', group, None, 'Z'))
else:
- job_ids['score_%s_B'%group] = self.submit_grid_job(
- 'compute-scores --group %s --score-type B'%group,
+ job_ids['score_%s_B'%group] = submitter.submit(
+ '--sub-task compute-scores --group %s --score-type B'%group,
name = "score-B-%s"%group,
number_of_parallel_jobs = args.grid.number_of_scoring_jobs,
dependencies = enroll_deps_n[group],
**args.grid.scoring_queue)
- job_ids['score_%s_C'%group] = self.submit_grid_job(
- 'compute-scores --group %s --score-type C'%group,
+ job_ids['score_%s_C'%group] = submitter.submit(
+ '--sub-task compute-scores --group %s --score-type C'%group,
name = "score-C-%s"%group,
number_of_parallel_jobs = args.grid.number_of_scoring_jobs,
dependencies = enroll_deps_t[group],
**args.grid.scoring_queue)
- job_ids['score_%s_D'%group] = self.submit_grid_job(
- 'compute-scores --group %s --score-type D'%group,
+ job_ids['score_%s_D'%group] = submitter.submit(
+ '--sub-task compute-scores --group %s --score-type D'%group,
name = "score-D-%s"%group,
number_of_parallel_jobs = args.grid.number_of_scoring_jobs,
dependencies = enroll_deps_t[group],
@@ -192,8 +192,8 @@ def add_jobs(args):
# compute zt-norm
score_deps[group] = [job_ids['score_%s_A'%group], job_ids['score_%s_B'%group], job_ids['score_%s_C'%group], job_ids['score_%s_D'%group]]
- job_ids['score_%s_Z'%group] = self.submit_grid_job(
- 'compute-scores --group %s --score-type Z'%group,
+ job_ids['score_%s_Z'%group] = submitter.submit(
+ '--sub-task compute-scores --group %s --score-type Z'%group,
name = "score-Z-%s"%group,
dependencies = score_deps[group])
concat_deps[group].extend([job_ids['score_%s_B'%group], job_ids['score_%s_C'%group], job_ids['score_%s_D'%group], job_ids['score_%s_Z'%group]])
@@ -205,8 +205,8 @@ def add_jobs(args):
if args.grid is None:
jobs_to_execute.append(('concatenate', group))
else:
- job_ids['concat_%s'%group] = self.submit_grid_job(
- 'concatenate --group %s'%group,
+ job_ids['concat_%s'%group] = submitter.submit(
+ '--sub-task concatenate --group %s'%group,
name = "concat-%s"%group,
dependencies = concat_deps[group])
@@ -216,8 +216,8 @@ def add_jobs(args):
jobs_to_execute.append(('calibrate',))
else:
calib_deps = [job_ids['concat_%s'%g] for g in args.groups if 'concat_%s'%g in job_ids]
- job_ids['calibrate'] = self.submit_grid_job(
- 'calibrate',
+ job_ids['calibrate'] = submitter.submit(
+ '--sub-task calibrate',
dependencies = calib_deps)
@@ -230,7 +230,8 @@ def add_jobs(args):
def execute(args):
- """Run the desired job of the ZT tool chain that is specified on command line."""
+ """Run the desired job of the tool chain that is specified on command line.
+ This job might be executed either in the grid, or locally."""
# the file selector object
fs = tools.FileSelector.instance()
@@ -341,12 +342,11 @@ def execute(args):
# Test if the keyword was processed
else:
return False
- raise ValueError("The given subtask '%s' could not be processed. THIS IS A BUG. Please report this to the authors." % args.sub_task)
return True
-def verify(args, command_line_parameters, external_dependencies = [], external_fake_job_id = 0):
+def verify(args, command_line_parameters, external_fake_job_id = 0):
"""This is the main entry point for computing verification experiments.
You just have to specify configurations for any of the steps of the toolchain, which are:
-- the database
@@ -362,17 +362,28 @@ def verify(args, command_line_parameters, external_dependencies = [], external_f
# as the main entry point, check whether the sub-task is specified
if args.sub_task is not None:
# execute the desired sub-task
- execute_grid_job(args)
+ execute(args)
return {}
else:
# add jobs
- retval = add_jobs(args)
+ submitter = tools.GridSubmission(args, command_line_parameters, first_fake_job_id = 0) if args.grid else None
+ retval = add_jobs(args, submitter)
tools.write_info(args, command_line_parameters)
- if args.grid:
- pass
+ if args.grid is not None:
+ if args.grid.is_local() and args.run_local_scheduler:
+ if args.dry_run:
+ print ("Would have started the local scheduler to run the experiments with parallel jobs")
+ else:
+ # start the jman local deamon
+ submitter.execute_local()
+ return {}
+
+ else:
+ # return job ids as a dictionary
+ return retval
else:
- # not in a grid, use default tool chain sequentially
+ # not in a grid, execute tool chain sequentially
if args.timer:
logger.info("- Timer: Starting timer")
start_time = os.times()
@@ -395,35 +406,6 @@ def verify(args, command_line_parameters, external_dependencies = [], external_f
return {}
- """
- else:
- # no other parameter given, so deploy new jobs
-
- # get the name of this file
- this_file = __file__
- if this_file[-1] == 'c':
- this_file = this_file[0:-1]
-
- executor.write_info(command_line_parameters)
-
- # initialize the executor to submit the jobs to the grid
- executor.set_common_parameters(calling_file = this_file, parameters = command_line_parameters, fake_job_id = external_fake_job_id)
-
- # add the jobs
- job_ids = executor.add_jobs_to_grid(external_dependencies)
-
- if executor.m_grid.is_local() and args.run_local_scheduler:
- if args.dry_run:
- print ("Would have started the local scheduler to finally run the experiments with parallel jobs")
- else:
- # start the jman local deamon
- executor.execute_local_deamon()
- return {}
-
- else:
- return job_ids
- """
-
def main(command_line_parameters = sys.argv):
"""Executes the main function"""
try:
diff --git a/bob/bio/base/test/__init__.py b/bob/bio/base/test/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..77d1ede44a3aed0ce4bfde00a6288787622a17c7 100644
--- a/bob/bio/base/test/__init__.py
+++ b/bob/bio/base/test/__init__.py
@@ -0,0 +1 @@
+from . import dummy
diff --git a/bob/bio/base/test/data/atnt/models.lst b/bob/bio/base/test/data/atnt/models.lst
new file mode 100644
index 0000000000000000000000000000000000000000..eeaa42baeedf51060b920b00dc53fa65d68eed20
--- /dev/null
+++ b/bob/bio/base/test/data/atnt/models.lst
@@ -0,0 +1,100 @@
+s3/9 3 3
+s3/2 3 3
+s3/4 3 3
+s3/5 3 3
+s3/7 3 3
+s4/9 4 4
+s4/2 4 4
+s4/4 4 4
+s4/5 4 4
+s4/7 4 4
+s7/9 7 7
+s7/2 7 7
+s7/4 7 7
+s7/5 7 7
+s7/7 7 7
+s8/9 8 8
+s8/2 8 8
+s8/4 8 8
+s8/5 8 8
+s8/7 8 8
+s9/9 9 9
+s9/2 9 9
+s9/4 9 9
+s9/5 9 9
+s9/7 9 9
+s13/9 13 13
+s13/2 13 13
+s13/4 13 13
+s13/5 13 13
+s13/7 13 13
+s15/9 15 15
+s15/2 15 15
+s15/4 15 15
+s15/5 15 15
+s15/7 15 15
+s18/9 18 18
+s18/2 18 18
+s18/4 18 18
+s18/5 18 18
+s18/7 18 18
+s19/9 19 19
+s19/2 19 19
+s19/4 19 19
+s19/5 19 19
+s19/7 19 19
+s22/9 22 22
+s22/2 22 22
+s22/4 22 22
+s22/5 22 22
+s22/7 22 22
+s23/9 23 23
+s23/2 23 23
+s23/4 23 23
+s23/5 23 23
+s23/7 23 23
+s25/9 25 25
+s25/2 25 25
+s25/4 25 25
+s25/5 25 25
+s25/7 25 25
+s28/9 28 28
+s28/2 28 28
+s28/4 28 28
+s28/5 28 28
+s28/7 28 28
+s30/9 30 30
+s30/2 30 30
+s30/4 30 30
+s30/5 30 30
+s30/7 30 30
+s31/9 31 31
+s31/2 31 31
+s31/4 31 31
+s31/5 31 31
+s31/7 31 31
+s32/9 32 32
+s32/2 32 32
+s32/4 32 32
+s32/5 32 32
+s32/7 32 32
+s35/9 35 35
+s35/2 35 35
+s35/4 35 35
+s35/5 35 35
+s35/7 35 35
+s37/9 37 37
+s37/2 37 37
+s37/4 37 37
+s37/5 37 37
+s37/7 37 37
+s38/9 38 38
+s38/2 38 38
+s38/4 38 38
+s38/5 38 38
+s38/7 38 38
+s40/9 40 40
+s40/2 40 40
+s40/4 40 40
+s40/5 40 40
+s40/7 40 40
diff --git a/bob/bio/base/test/data/atnt/probes.lst b/bob/bio/base/test/data/atnt/probes.lst
new file mode 100644
index 0000000000000000000000000000000000000000..9423e365d09fc3fa51c3b2a0f0125cd59352281a
--- /dev/null
+++ b/bob/bio/base/test/data/atnt/probes.lst
@@ -0,0 +1,100 @@
+s3/8 3
+s3/1 3
+s3/10 3
+s3/3 3
+s3/6 3
+s4/8 4
+s4/1 4
+s4/10 4
+s4/3 4
+s4/6 4
+s7/8 7
+s7/1 7
+s7/10 7
+s7/3 7
+s7/6 7
+s8/8 8
+s8/1 8
+s8/10 8
+s8/3 8
+s8/6 8
+s9/8 9
+s9/1 9
+s9/10 9
+s9/3 9
+s9/6 9
+s13/8 13
+s13/1 13
+s13/10 13
+s13/3 13
+s13/6 13
+s15/8 15
+s15/1 15
+s15/10 15
+s15/3 15
+s15/6 15
+s18/8 18
+s18/1 18
+s18/10 18
+s18/3 18
+s18/6 18
+s19/8 19
+s19/1 19
+s19/10 19
+s19/3 19
+s19/6 19
+s22/8 22
+s22/1 22
+s22/10 22
+s22/3 22
+s22/6 22
+s23/8 23
+s23/1 23
+s23/10 23
+s23/3 23
+s23/6 23
+s25/8 25
+s25/1 25
+s25/10 25
+s25/3 25
+s25/6 25
+s28/8 28
+s28/1 28
+s28/10 28
+s28/3 28
+s28/6 28
+s30/8 30
+s30/1 30
+s30/10 30
+s30/3 30
+s30/6 30
+s31/8 31
+s31/1 31
+s31/10 31
+s31/3 31
+s31/6 31
+s32/8 32
+s32/1 32
+s32/10 32
+s32/3 32
+s32/6 32
+s35/8 35
+s35/1 35
+s35/10 35
+s35/3 35
+s35/6 35
+s37/8 37
+s37/1 37
+s37/10 37
+s37/3 37
+s37/6 37
+s38/8 38
+s38/1 38
+s38/10 38
+s38/3 38
+s38/6 38
+s40/8 40
+s40/1 40
+s40/10 40
+s40/3 40
+s40/6 40
diff --git a/bob/bio/base/test/data/atnt/world.lst b/bob/bio/base/test/data/atnt/world.lst
new file mode 100644
index 0000000000000000000000000000000000000000..0a526ead3d5e5d0930ed2234bd577161c30dfe2b
--- /dev/null
+++ b/bob/bio/base/test/data/atnt/world.lst
@@ -0,0 +1,200 @@
+s1/9 1
+s1/2 1
+s1/4 1
+s1/5 1
+s1/7 1
+s1/8 1
+s1/1 1
+s1/10 1
+s1/3 1
+s1/6 1
+s2/9 2
+s2/2 2
+s2/4 2
+s2/5 2
+s2/7 2
+s2/8 2
+s2/1 2
+s2/10 2
+s2/3 2
+s2/6 2
+s5/9 5
+s5/2 5
+s5/4 5
+s5/5 5
+s5/7 5
+s5/8 5
+s5/1 5
+s5/10 5
+s5/3 5
+s5/6 5
+s6/9 6
+s6/2 6
+s6/4 6
+s6/5 6
+s6/7 6
+s6/8 6
+s6/1 6
+s6/10 6
+s6/3 6
+s6/6 6
+s10/9 10
+s10/2 10
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diff --git a/bob/bio/base/test/data/scores-nonorm-calibrated-dev b/bob/bio/base/test/data/scores-nonorm-calibrated-dev
new file mode 100644
index 0000000000000000000000000000000000000000..4e8e60f5db6ff05340938302ca093fce231d3a72
--- /dev/null
+++ b/bob/bio/base/test/data/scores-nonorm-calibrated-dev
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diff --git a/bob/bio/base/test/data/scores-ztnorm-calibrated-dev b/bob/bio/base/test/data/scores-ztnorm-calibrated-dev
new file mode 100644
index 0000000000000000000000000000000000000000..cb022a1cc9b2c1b25d3cf1736544a644d8929095
--- /dev/null
+++ b/bob/bio/base/test/data/scores-ztnorm-calibrated-dev
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diff --git a/bob/bio/base/test/dummy/__init__.py b/bob/bio/base/test/dummy/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..fc3eb09b2ff61ff843e299a42a11c9c48b20cef8 100644
--- a/bob/bio/base/test/dummy/__init__.py
+++ b/bob/bio/base/test/dummy/__init__.py
@@ -0,0 +1,4 @@
+from . import database
+from . import preprocessor
+from . import extractor
+from . import algorithm
diff --git a/bob/bio/base/test/dummy/algorithm.py b/bob/bio/base/test/dummy/algorithm.py
index c73b5282d5dfa5162c8e4cda5ca8e065e66dbfb9..61c874b25a626112706eef9051abfcdb6f3a45b2 100644
--- a/bob/bio/base/test/dummy/algorithm.py
+++ b/bob/bio/base/test/dummy/algorithm.py
@@ -1,16 +1,18 @@
-import bob.bio.base
import scipy.spatial
+import bob.io.base
+
+from bob.bio.base.algorithm import Algorithm
_data = [5., 6., 7., 8., 9.]
-class DummyAlgorithm (bob.bio.base.algorithm.Algorithm):
+class DummyAlgorithm (Algorithm):
"""This class is used to test all the possible functions of the tool chain, but it does basically nothing."""
def __init__(self):
"""Generates a test value that is read and written"""
# call base class constructor registering that this tool performs everything.
- bob.bio.base.algorithm.Algorithm.__init__(
+ Algorithm.__init__(
self,
performs_projection = True,
use_projected_features_for_enrollment = True,
diff --git a/bob/bio/base/test/dummy/database.py b/bob/bio/base/test/dummy/database.py
index 04bdb44f4d3af4e393e051d94a9031fff3c315d2..748b5123dd468763389886a64ac9195491134101 100644
--- a/bob/bio/base/test/dummy/database.py
+++ b/bob/bio/base/test/dummy/database.py
@@ -1,15 +1,17 @@
import bob.db.atnt
-import bob.bio.base
import os
-class DummyDatabase (bob.bio.base.database.DatabaseBobZT):
+from bob.bio.base.database import DatabaseBob, DatabaseBobZT
+from bob.bio.base.test.utils import atnt_database_directory
+
+class DummyDatabase (DatabaseBobZT):
def __init__(self):
# call base class constructor with useful parameters
- bob.bio.base.database.DatabaseBobZT.__init__(
+ DatabaseBobZT.__init__(
self,
database = bob.db.atnt.Database(
- original_directory = bob.bio.base.test.utils.atnt_database_directory()
+ original_directory = atnt_database_directory()
),
name = 'test',
check_original_files_for_existence = True,
@@ -17,19 +19,15 @@ class DummyDatabase (bob.bio.base.database.DatabaseBobZT):
models_depend_on_protocol = False
)
-
def all_files(self, groups = ['dev']):
- return bob.bio.base.database.DatabaseBob.all_files(self, groups)
-
+ return DatabaseBob.all_files(self, groups)
def t_model_ids(self, group = 'dev'):
return self.model_ids(group)
-
def t_enroll_files(self, model_id, group = 'dev'):
return self.enroll_files(model_id, group)
-
def z_probe_files(self, group = 'dev'):
return self.probe_files(None, group)
diff --git a/bob/bio/base/test/dummy/extractor.py b/bob/bio/base/test/dummy/extractor.py
index ad3a798f6df30e9ed42e2cbc7694c0cc23eb7a00..0b95e046717a087fa4bb897b161340a1dff42541 100644
--- a/bob/bio/base/test/dummy/extractor.py
+++ b/bob/bio/base/test/dummy/extractor.py
@@ -1,19 +1,21 @@
-import bob.bio.base
import numpy
+import bob.io.base
+
+from bob.bio.base.extractor import Extractor
_data = [0., 1., 2., 3., 4.]
-class DummyExtractor (bob.bio.base.extractor.Extractor):
+class DummyExtractor (Extractor):
def __init__(self):
- bob.bio.base.extractor.Extractor.__init__(self, requires_training=True)
+ Extractor.__init__(self, requires_training=True)
self.model = False
def train(self, train_data, extractor_file):
assert isinstance(train_data, list)
- bob.bio.base.save(_data, extractor_file)
+ bob.io.base.save(_data, extractor_file)
def load(self, extractor_file):
- data = bob.bio.base.load(extractor_file)
+ data = bob.io.base.load(extractor_file)
assert (_data == data).all()
self.model = True
diff --git a/bob/bio/base/test/dummy/filelist.py b/bob/bio/base/test/dummy/filelist.py
new file mode 100644
index 0000000000000000000000000000000000000000..dc59e4a170147bf32fe1e3f274668127df248f32
--- /dev/null
+++ b/bob/bio/base/test/dummy/filelist.py
@@ -0,0 +1,25 @@
+import bob.db.verification.filelist
+from bob.bio.base.database import DatabaseFileList
+from bob.bio.base.test.utils import atnt_database_directory
+import pkg_resources
+
+database = DatabaseFileList(
+ database = bob.db.verification.filelist.Database(
+ base_dir = pkg_resources.resource_filename('bob.bio.base.test', 'data/atnt'),
+ original_directory = atnt_database_directory(),
+ original_extension = ".pgm",
+ dev_subdir = '.',
+ eval_subdir = '.',
+ world_filename = 'world.lst',
+ models_filename = 'models.lst',
+ probes_filename = 'probes.lst',
+ tnorm_filename = 'models.lst',
+ znorm_filename = 'probes.lst',
+ keep_read_lists_in_memory = True
+ ),
+ name = 'test_filelist',
+ protocol = None,
+ check_original_files_for_existence = True,
+ training_depends_on_protocol = False,
+ models_depend_on_protocol = False
+)
diff --git a/bob/bio/base/test/dummy/fileset.py b/bob/bio/base/test/dummy/fileset.py
new file mode 100644
index 0000000000000000000000000000000000000000..e4de45f962daa943b72fde8f7ce8401de324caea
--- /dev/null
+++ b/bob/bio/base/test/dummy/fileset.py
@@ -0,0 +1,52 @@
+import bob.db.atnt
+import os
+
+from bob.bio.base.database import DatabaseBob, DatabaseBobZT
+from bob.bio.base.test.utils import atnt_database_directory
+
+class FileSetDatabase (DatabaseBobZT):
+
+ def __init__(self):
+ # call base class constructor with useful parameters
+ facereclib.databases.DatabaseBobZT.__init__(
+ self,
+ database = bob.db.atnt.Database(
+ original_directory = atnt_database_directory(),
+ ),
+ name = 'test_fileset',
+ check_original_files_for_existence = True,
+ training_depends_on_protocol = False,
+ models_depend_on_protocol = False
+ )
+
+ def uses_probe_file_sets(self):
+ return True
+
+ def probe_file_sets(self, model_id = None, group = 'dev'):
+ """Returns the list of probe File objects (for the given model id, if given)."""
+ files = self.arrange_by_client(self.sort(self.database.objects(protocol = None, groups = group, purposes = 'probe')))
+ # arrange files by clients
+ file_sets = []
+ for client_files in files:
+ # generate file set for each client
+ file_set = facereclib.databases.FileSet(client_files[0].client_id, client_files[0].client_id, client_files[0].path)
+ file_set.files = client_files
+ file_sets.append(file_set)
+ return file_sets
+
+ def all_files(self, groups = ['dev']):
+ return DatabaseBob.all_files(self, groups)
+
+ def t_model_ids(self, group = 'dev'):
+ return self.model_ids(group)
+
+ def t_enroll_files(self, model_id, group = 'dev'):
+ return self.enroll_files(model_id, group)
+
+ def z_probe_files(self, group = 'dev'):
+ return self.probe_files(None, group)
+
+ def z_probe_file_sets(self, group = 'dev'):
+ return self.probe_file_sets(None, group)
+
+database = FileSetDatabase()
diff --git a/bob/bio/base/test/dummy/preprocessor.py b/bob/bio/base/test/dummy/preprocessor.py
index 9f525a3368fc4fa6215eab7dc45562f14c541891..2770e2fe37fcb66053da2eba02cca3bc1ad71b27 100644
--- a/bob/bio/base/test/dummy/preprocessor.py
+++ b/bob/bio/base/test/dummy/preprocessor.py
@@ -1,9 +1,8 @@
+from bob.bio.base.preprocessor import Preprocessor
-import bob.bio.base
-
-class DummyPreprocessor (bob.bio.base.preprocessor.Preprocessor):
+class DummyPreprocessor (Preprocessor):
def __init__(self):
- bob.bio.base.preprocessor.Preprocessor.__init__(self)
+ Preprocessor.__init__(self)
def __call__(self, data, annotation):
"""Does nothing, simply converts the data type of the data, ignoring any annotation."""
diff --git a/bob/bio/base/test/test_scripts.py b/bob/bio/base/test/test_scripts.py
index 6ae497bc5cba3d4143a99a50c6e8b38b06ca092d..582dc4abe12818867c8c5740544998fbf5dafad1 100644
--- a/bob/bio/base/test/test_scripts.py
+++ b/bob/bio/base/test/test_scripts.py
@@ -13,12 +13,14 @@ import numpy
import bob.io.base.test_utils
import bob.io.image
import bob.bio.base
+from . import utils
from nose.plugins.skip import SkipTest
import pkg_resources
-regenerate_reference = True
+regenerate_reference = False
+
dummy_dir = pkg_resources.resource_filename('bob.bio.base', 'test/dummy')
@@ -62,14 +64,7 @@ def _verify(parameters, test_dir, sub_dir, ref_modifier="", score_modifier=('sco
shutil.rmtree(test_dir)
-def grid_available():
- try:
- import gridtk
- except ImportError:
- raise SkipTest("Skipping test since gridtk is not available")
-
-
-def test_faceverify_local():
+def test_verify_local():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
@@ -87,7 +82,8 @@ def test_faceverify_local():
_verify(parameters, test_dir, 'test_local')
-def test_faceverify_resources():
+
+def test_verify_resources():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
@@ -106,7 +102,7 @@ def test_faceverify_resources():
_verify(parameters, test_dir, 'test_resource')
-def test_faceverify_commandline():
+def test_verify_commandline():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
@@ -125,275 +121,141 @@ def test_faceverify_commandline():
_verify(parameters, test_dir, 'test_commandline')
-"""
-def test01c_faceverify_parallel(self):
- self.grid_available()
+@utils.grid_available
+def test_verify_parallel():
test_dir = tempfile.mkdtemp(prefix='frltest_')
test_database = os.path.join(test_dir, "database.sql3")
# define dummy parameters
parameters = [
- '-d', os.path.join(base_dir, 'scripts', 'atnt_Test.py'),
- '-p', 'face-crop',
- '-f', 'facereclib.features.Eigenface(subspace_dimension', '=', '100)',
- '-t', 'facereclib.tools.Dummy()',
+ '-d', os.path.join(dummy_dir, 'database.py'),
+ '-p', 'dummy',
+ '-e', 'bob.bio.base.test.dummy.extractor.DummyExtractor()',
+ '-a', 'dummy',
'--zt-norm',
- '-b', 'test_c',
+ '-s', 'test_parallel',
'--temp-directory', test_dir,
- '--user-directory', test_dir,
- '-g', 'facereclib.utils.GridParameters(grid = "local", number_of_parallel_processes = 2, scheduler_sleep_time = 0.1)', '-G', test_database, '--run-local-scheduler'
+ '--result-directory', test_dir,
+ '-g', 'bob.bio.base.grid.Grid(grid = "local", number_of_parallel_processes = 2, scheduler_sleep_time = 0.1)', '-G', test_database, '--run-local-scheduler', '-R',
+ '--import', 'bob.io.image'
]
- print (facereclib.utils.command_line(parameters))
+ print (bob.bio.base.tools.command_line(parameters))
- self.__face_verify__(parameters, test_dir, 'test_c')
+ _verify(parameters, test_dir, 'test_parallel')
-def test01d_faceverify_compressed(self):
+def test_verify_compressed():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
- '-d', os.path.join(base_dir, 'scripts', 'atnt_Test.py'),
- '-p', 'face-crop',
- '-f', 'facereclib.features.Eigenface(subspace_dimension', '=', '100)',
- '-t', 'facereclib.tools.Dummy()',
+ '-d', 'dummy',
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-a', 'dummy',
'--zt-norm',
- '-b', 'test_d',
+ '-s', 'test_compressed',
'--temp-directory', test_dir,
- '--user-directory', test_dir,
+ '--result-directory', test_dir,
'--write-compressed-score-files'
]
- print (facereclib.utils.command_line(parameters))
+ print (bob.bio.base.tools.command_line(parameters))
- self.__face_verify__(parameters, test_dir, 'test_d', score_modifier=('scores', '.tar.bz2'))
+ _verify(parameters, test_dir, 'test_compressed', score_modifier=('scores', '.tar.bz2'))
-def test01m_faceverify_calibrate(self):
+def test_verify_calibrate():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
- '-d', os.path.join(base_dir, 'scripts', 'atnt_Test.py'),
- '-p', os.path.join(config_dir, 'preprocessing', 'face_crop.py'),
- '-f', os.path.join(config_dir, 'features', 'eigenfaces.py'),
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
+ '-d', 'dummy',
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-a', 'dummy',
'--zt-norm',
- '-b', 'test',
+ '-s', 'test_calibrate',
'--temp-directory', test_dir,
- '--user-directory', test_dir,
+ '--result-directory', test_dir,
'--calibrate-scores'
]
- print (facereclib.utils.command_line(parameters))
+ print (bob.bio.base.tools.command_line(parameters))
- # check that the calibrated scores are as expected
- self.__face_verify__(parameters, test_dir, 'test', '-calibrated', score_modifier=('calibrated', ''))
+ _verify(parameters, test_dir, 'test_calibrate', '-calibrated', score_modifier=('calibrated', ''))
-def test01x_faceverify_filelist(self):
- try:
- import bob.db.verification.filelist
- except ImportError:
- raise SkipTest("Skipping test since bob.db.verification.filelist is not available")
+def test_verify_fileset():
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
- '-d', os.path.join(base_dir, 'databases', 'atnt_fl', 'atnt_fl_database.py'),
-# '--protocol', 'None',
- '-p', os.path.join(config_dir, 'preprocessing', 'face_crop.py'),
- '-f', os.path.join(config_dir, 'features', 'eigenfaces.py'),
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
+ '-d', os.path.join(dummy_dir, 'database.py'),
+ '-p', 'dummy',
+ '-e', 'bob.bio.base.test.dummy.extractor.DummyExtractor()',
+ '-a', 'dummy',
'--zt-norm',
- '-b', 'test_x',
+ '-s', 'test_fileset',
'--temp-directory', test_dir,
- '--user-directory', test_dir
- ]
-
- print (facereclib.utils.command_line(parameters))
-
- from facereclib.script.faceverify import main
- main([sys.argv[0]] + parameters)
-
- # assert that the score file exists
- score_files = (os.path.join(test_dir, 'test_x', 'scores', 'nonorm', 'scores-dev'), os.path.join(test_dir, 'test_x', 'scores', 'ztnorm', 'scores-dev'))
- self.assertTrue(os.path.exists(score_files[0]))
- self.assertTrue(os.path.exists(score_files[1]))
-
- # assert that the scores are are identical
- reference_files = (os.path.join(base_dir, 'scripts', 'scores-nonorm-dev'), os.path.join(base_dir, 'scripts', 'scores-ztnorm-dev'))
-
- for i in (0,1):
-
- a1, b1 = bob.measure.load.split_four_column(score_files[i])
- a2, b2 = bob.measure.load.split_four_column(reference_files[i])
-
- a1 = sorted(a1); a2 = sorted(a2); b1 = sorted(b1); b2 = sorted(b2)
-
- for i in range(len(a1)):
- self.assertAlmostEqual(a1[i], a2[i], 6)
- for i in range(len(b1)):
- self.assertAlmostEqual(b1[i], b2[i], 6)
-
- shutil.rmtree(test_dir)
-
-
-
-def test02_faceverify_grid(self):
- self.grid_available()
- test_dir = tempfile.mkdtemp(prefix='frltest_')
- # define dummy parameters including the dry-run
- parameters = [
- sys.argv[0],
- '-d', os.path.join(base_dir, 'scripts', 'atnt_Test.py'),
- '-p', 'face-crop',
- '-f', 'eigenfaces',
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '-g', 'grid',
- '--zt-norm',
- '--dry-run',
- '--user-directory', test_dir,
- '-b', 'dummy'
- ]
-
- print (facereclib.utils.command_line(parameters))
-
- # run the test; should not execute anything...
- from facereclib.script.faceverify import main
- main(parameters)
- shutil.rmtree(test_dir)
-
-
-def test03_faceverify_lfw_local(self):
- # try to import the lfw database
- try:
- facereclib.utils.resources.load_resource('lfw','database')
- except Exception as e:
- raise SkipTest("The resource for database 'lfw' could not be loaded; probably you didn't define the 'bob.db.lfw' in your *buildout.cfg*. Here is the import error: '%s'" % e)
-
- test_dir = tempfile.mkdtemp(prefix='frltest_')
- # define dummy parameters
- parameters = [
- sys.argv[0],
- '-p', 'face-crop',
- '-f', 'eigenfaces',
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '--dry-run',
- '--user-directory', test_dir,
- '-b', 'dummy'
+ '--result-directory', test_dir
]
- print (facereclib.utils.command_line(parameters))
-
- # run the test; should not execute anything...
- from facereclib.script.faceverify_lfw import main
- main(parameters)
- shutil.rmtree(test_dir)
-
-
-def test04_faceverify_lfw_grid(self):
- self.grid_available()
- # try to import the lfw database
- try:
- facereclib.utils.resources.load_resource('lfw','database')
- except Exception as e:
- raise SkipTest("The resource for database 'lfw' could not be loaded; probably you didn't define the 'bob.db.lfw' in your *buildout.cfg*. Here is the import error: '%s'" % e)
-
- test_dir = tempfile.mkdtemp(prefix='frltest_')
- # define dummy parameters
- parameters = [
- sys.argv[0],
- '-p', 'face-crop',
- '-f', 'eigenfaces',
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '-g', 'grid',
- '--dry-run',
- '--user-directory', test_dir,
- '-b', 'dummy'
- ]
+ print (bob.bio.base.tools.command_line(parameters))
- print (facereclib.utils.command_line(parameters))
+ _verify(parameters, test_dir, 'test_fileset', ref_modifier="-fileset")
- # run the test; should not execute anything...
- from facereclib.script.faceverify_lfw import main
- main(parameters)
- shutil.rmtree(test_dir)
-def test05_faceverify_gbu_local(self):
- # try to import the gbu database
+def test_verify_filelist():
try:
- facereclib.utils.resources.load_resource('gbu','database')
- except Exception as e:
- raise SkipTest("The resource for database 'gbu' could not be loaded; probably you didn't define the 'bob.db.gbu' in your *buildout.cfg*. Here is the import error: '%s'" % e)
-
+ import bob.db.verification.filelist
+ except ImportError:
+ raise SkipTest("Skipping test since bob.db.verification.filelist is not available")
test_dir = tempfile.mkdtemp(prefix='frltest_')
# define dummy parameters
parameters = [
- sys.argv[0],
- '-p', 'face-crop',
- '-f', 'eigenfaces',
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '--dry-run',
- '--user-directory', test_dir,
- '-b', 'dummy'
+ '-d', os.path.join(dummy_dir, 'filelist.py'),
+ '-p', 'dummy',
+ '-e', 'dummy',
+ '-a', 'dummy',
+ '--zt-norm',
+ '-s', 'test_filelist',
+ '--temp-directory', test_dir,
+ '--result-directory', test_dir
]
- print (facereclib.utils.command_line(parameters))
-
- # run the test; should not execute anything...
- from facereclib.script.faceverify_gbu import main
- main(parameters)
- shutil.rmtree(test_dir)
-
+ print (bob.bio.base.tools.command_line(parameters))
-def test06_faceverify_gbu_grid(self):
- self.grid_available()
- # try to import the gbu database
try:
- facereclib.utils.resources.load_resource('gbu','database')
- except Exception as e:
- raise SkipTest("The resource for database 'gbu' could not be loaded; probably you didn't define the 'bob.db.gbu' in your *buildout.cfg*. Here is the import error: '%s'" % e)
-
- test_dir = tempfile.mkdtemp(prefix='frltest_')
- # define dummy parameters
- parameters = [
- sys.argv[0],
- '-p', 'face-crop',
- '-f', 'eigenfaces',
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '-g', 'grid',
- '--dry-run',
- '--user-directory', test_dir,
- '-b', 'dummy'
- ]
-
- print (facereclib.utils.command_line(parameters))
+ from bob.bio.base.script.verify import main
+ main([sys.argv[0]] + parameters)
- # run the test; should not execute anything...
- from facereclib.script.faceverify_gbu import main
- main(parameters)
- shutil.rmtree(test_dir)
+ # assert that the score file exists
+ score_files = [os.path.join(test_dir, 'test_filelist', 'None', norm, 'scores-dev') for norm in ('nonorm', 'ztnorm')]
+ assert os.path.exists(score_files[0]), "Score file %s does not exist" % score_files[0]
+ assert os.path.exists(score_files[1]), "Score file %s does not exist" % score_files[1]
+ # assert that the scores are are identical (might be in a different order, though
+ reference_files = [os.path.join(data_dir, 'scores-%s-dev' % norm) for norm in ('nonorm', 'ztnorm')]
-def test10_faceverify_file_set(self):
- test_dir = tempfile.mkdtemp(prefix='frltest_')
- # define dummy parameters
- parameters = [
- '-d', os.path.join(base_dir, 'scripts', 'fileset_Test.py'),
- '-p', os.path.join(config_dir, 'preprocessing', 'face_crop.py'),
- '-f', os.path.join(config_dir, 'features', 'eigenfaces.py'),
- '-t', os.path.join(config_dir, 'tools', 'dummy.py'),
- '--zt-norm',
- '-b', 'test',
- '--temp-directory', test_dir,
- '--user-directory', test_dir
- ]
+ for i in (0,1):
+ # load scores
+ a1, b1 = bob.measure.load.split_four_column(score_files[i])
+ a2, b2 = bob.measure.load.split_four_column(reference_files[i])
+ # sort scores
+ a1 = sorted(a1); a2 = sorted(a2); b1 = sorted(b1); b2 = sorted(b2)
+
+ # assert that scores are almost equal
+ for i in range(len(a1)):
+ abs(a1[i] - a2[i]) < 1e-6
+ for i in range(len(b1)):
+ abs(b1[i] - b2[i]) < 1e-6
- print (facereclib.utils.command_line(parameters))
+ finally:
+ shutil.rmtree(test_dir)
- self.__face_verify__(parameters, test_dir, 'test', ref_modifier="-fileset")
+"""
def test11_baselines_api(self):
self.grid_available()
# test that all of the baselines would execute
diff --git a/bob/bio/base/test/utils.py b/bob/bio/base/test/utils.py
index 7359ba0e296ff45680cb3d65eb622ecad57c8019..15a1f9c5295d582bf3913cf8d71f5f42469eb059 100644
--- a/bob/bio/base/test/utils.py
+++ b/bob/bio/base/test/utils.py
@@ -19,6 +19,9 @@
import numpy
import os
+import functools
+from nose.plugins.skip import SkipTest
+
import logging
logger = logging.getLogger("bob.bio.base")
@@ -37,6 +40,17 @@ def random_training_set_by_id(shape, count = 50, minimum = 0, maximum = 1):
train_set.append([numpy.random.random(shape) * (maximum - minimum) + minimum for j in range(count)])
return train_set
+def grid_available(test):
+ '''Decorator to check if the gridtk is present, before running the test'''
+ @functools.wraps(test)
+ def wrapper(*args, **kwargs):
+ try:
+ import gridtk
+ return test(*args, **kwargs)
+ except ImportError:
+ raise SkipTest("Skipping test since gridtk is not available")
+ return wrapper
+
atnt_default_directory = os.environ['ATNT_DATABASE_DIRECTORY'] if 'ATNT_DATABASE_DIRECTORY' in os.environ else "/idiap/group/biometric/databases/orl/"
global atnt_downloaded_directory
diff --git a/bob/bio/base/tools/command_line.py b/bob/bio/base/tools/command_line.py
index dc533e52a2a1a32f372b17708e17ea8abe37fc0d..03b52e391fcd790de5efbb3e1ce243da0506ffb3 100644
--- a/bob/bio/base/tools/command_line.py
+++ b/bob/bio/base/tools/command_line.py
@@ -80,6 +80,8 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
help = 'Name of the directory (relative to --result-directory) where to write the results to')
sub_dir_group.add_argument('--zt-directories', metavar = 'DIR', nargs = 5, default = ['zt_norm_A', 'zt_norm_B', 'zt_norm_C', 'zt_norm_D', 'zt_norm_D_sameValue'],
help = 'Name of the directories (of --temp-directory) where to write the ZT-norm values; only used with --zt-norm')
+ sub_dir_group.add_argument('--grid-log-directory', metavar = 'DIR', default = 'grid_tk_logs',
+ help = 'Name of the directory (relative to --temp-directory) where to log files are written; only used with --grid')
flag_group = parser.add_argument_group('\nFlags that change the behavior of the experiment')
bob.core.log.add_command_line_option(flag_group)
@@ -97,6 +99,8 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
help = 'Measure and report the time required by the execution of the tool chain (only on local machine)')
flag_group.add_argument('-L', '--run-local-scheduler', action='store_true',
help = 'Starts the local scheduler after submitting the jobs to the local queue (by default, local jobs must be started by hand, e.g., using ./bin/jman --local -vv run-scheduler -x)')
+ flag_group.add_argument('-N', '--nice', type=int, default=10,
+ help = 'Runs the local scheduler with the given nice value')
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',
@@ -112,21 +116,6 @@ def command_line_parser(description=__doc__, exclude_resources_from=[]):
}
-def zt_options(parsers):
- """Adds options for ZT score normalization to the parsers."""
-
- #######################################################################################
- #################### sub-tasks being executed by this script ##########################
- parser.add_argument('--sub-task',
- choices = ('preprocess', 'train-extractor', 'extract', 'train-projector', 'project', 'train-enroller', 'enroll', 'compute-scores', 'concatenate', 'calibrate'),
- help = argparse.SUPPRESS) #'Executes a subtask (FOR INTERNAL USE ONLY!!!)'
- parser.add_argument('--model-type', choices = ['N', 'T'],
- help = argparse.SUPPRESS) #'Which type of models to generate (Normal or TModels)'
- parser.add_argument('--score-type', choices = ['A', 'B', 'C', 'D', 'Z'],
- help = argparse.SUPPRESS) #'The type of scores that should be computed'
- parser.add_argument('--group',
- help = argparse.SUPPRESS) #'The group for which the current action should be performed'
-
def initialize(parsers, command_line_parameters = None, skips = []):
"""Parses the command line and arranges the arguments accordingly, and returns the arguments.
@@ -157,6 +146,10 @@ def initialize(parsers, command_line_parameters = None, skips = []):
if args.timer is not None and not len(args.timer):
args.timer = ('real', 'system', 'user')
+ # set base directories
+ args.temp_directory = os.path.join(args.temp_directory, args.sub_directory)
+ args.result_directory = os.path.join(args.result_directory, args.sub_directory)
+
# load configuration resources
args.database = load_resource(' '.join(args.database), 'database', imports = args.imports)
args.preprocessor = load_resource(' '.join(args.preprocessor), 'preprocessor', imports = args.imports)
@@ -164,6 +157,7 @@ def initialize(parsers, command_line_parameters = None, skips = []):
args.algorithm = load_resource(' '.join(args.algorithm), 'algorithm', imports = args.imports)
if args.grid is not None:
args.grid = load_resource(' '.join(args.grid), 'grid', imports = args.imports)
+ args.grid_log_dir = os.path.join(args.temp_directory, args.grid_log_directory)
# protocol command line override
if args.protocol is not None:
@@ -171,9 +165,6 @@ def initialize(parsers, command_line_parameters = None, skips = []):
protocol = 'None' if args.database.protocol is None else args.database.protocol
- args.temp_directory = os.path.join(args.temp_directory, args.sub_directory)
- args.result_directory = os.path.join(args.result_directory, args.sub_directory)
-
# result files
args.info_file = os.path.join(args.result_directory, protocol, args.experiment_info_file)
@@ -196,7 +187,7 @@ def initialize(parsers, command_line_parameters = None, skips = []):
model_directories = [os.path.join(args.temp_directory, protocol, m) for m in args.model_directories],
score_directories = [os.path.join(args.temp_directory, protocol, z) for z in args.score_directories],
zt_score_directories = [os.path.join(args.result_directory, protocol, s) for s in args.zt_directories],
- compressed_extension = 'tar.bz2' if args.write_compressed_score_files else '',
+ compressed_extension = '.tar.bz2' if args.write_compressed_score_files else '',
default_extension = '.hdf5',
)
diff --git a/bob/bio/base/tools/grid.py b/bob/bio/base/tools/grid.py
index b8760845c7a91657735b41ff00b32c128959b214..45eb5cf0a6bb3c4285d83f7e6352516de4f92969 100644
--- a/bob/bio/base/tools/grid.py
+++ b/bob/bio/base/tools/grid.py
@@ -1,3 +1,15 @@
+from __future__ import print_function
+
+import sys
+import os
+import math
+from ..grid import Grid
+from .command_line import command_line
+
+import bob.core
+import logging
+logger = logging.getLogger("bob.bio.base")
+
def indices(list_to_split, number_of_parallel_jobs, task_id=None):
"""This function returns the first and last index for the files for the current job ID.
If no job id is set (e.g., because a sub-job is executed locally), it simply returns all indices."""
@@ -18,3 +30,79 @@ def indices(list_to_split, number_of_parallel_jobs, task_id=None):
start = job_id * number_of_objects_per_job
end = min((job_id + 1) * number_of_objects_per_job, len(list_to_split))
return (start, end)
+
+
+class GridSubmission:
+ def __init__(self, args, command_line_parameters, executable = './bin/verify.py', first_fake_job_id = 0):
+ assert os.path.isfile(executable)
+ assert isinstance(args.grid, Grid)
+ 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')]
+ 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_db_file)
+ 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.
+ If the name is not given, it will take the second parameter of the ``command`` as name.
+ """
+ dependencies = dependencies + self.args.external_dependencies
+
+ # create the command to be executed
+ cmd = [self.executable] + self.command_line
+ cmd += command.split()
+
+ # if no job name is specified, create one
+ if name is None:
+ name = command.split()[1]
+ # generate log directory
+ log_dir = os.path.join(self.args.grid_log_directory, name)
+
+ # generate job array
+ if number_of_parallel_jobs > 1:
+ array = (1,number_of_parallel_jobs,1)
+ else:
+ array = None
+
+ # submit the job to the job manager
+ if not self.args.dry_run:
+ job_id = self.job_manager.submit(
+ command_line = cmd,
+ name = name,
+ array = array,
+ dependencies = dependencies,
+ log_dir = log_dir,
+ stop_on_failure = self.args.delete_dependent_jobs_on_failure,
+ **kwargs
+ )
+ logger.info("submitted: job '%s' with id '%d' and dependencies '%s'" % (name, job_id, dependencies))
+ self.submitted_job_ids.append(job_id)
+ return job_id
+ else:
+ self.fake_job_id += 1
+ print ('would have submitted job', name, 'with id', self.fake_job_id, 'with parameters', kwargs, end='')
+ if array:
+ print (' using', array[1], 'parallel jobs', end='')
+ print (' as:', command_line(cmd), '\nwith dependencies', dependencies)
+ return self.fake_job_id
+
+
+ def grid_job_id(self):
+ id = os.getenv('JOB_ID')
+ if id is not None:
+ return int(id)
+ return id
+
+ def execute_local(self):
+ """Starts the local deamon and waits until it has finished."""
+ logger.info("Starting jman deamon to run the jobs on the local machine.")
+ failures = self.job_manager.run_scheduler(job_ids=self.submitted_job_ids, parallel_jobs=self.args.grid.number_of_parallel_processes, sleep_time=self.args.grid.scheduler_sleep_time, die_when_finished=True, nice=self.args.nice)
+ if failures:
+ logger.error("The jobs with the following IDS did not finish successfully: '%s'.", ', '.join([str(f) for f in failures]))
+ self.job_manager.report(job_ids = failures[:1], output=False)
diff --git a/bob/bio/base/tools/scoring.py b/bob/bio/base/tools/scoring.py
index b8c902963dddd843a1b1780fe17cfdfda925044f..d14cb4fecf5db794eefb20b51875d7e5b5a6b762 100644
--- a/bob/bio/base/tools/scoring.py
+++ b/bob/bio/base/tools/scoring.py
@@ -140,7 +140,7 @@ def _scores_b(algorithm, model_ids, group, force):
# test if the file is already there
score_file = fs.b_file(model_id, group)
if utils.check_file(score_file, force):
- Logger.warn("Score file '%s' already exists.", score_file)
+ logger.warn("Score file '%s' already exists.", score_file)
else:
model = algorithm.read_model(fs.model_file(model_id, group))
b = _scores(algorithm, model, z_probe_files)
@@ -399,11 +399,12 @@ def calibrate(norms = ['nonorm', 'ztnorm'], groups = ['dev', 'eval'], prior = 0.
logger.info(" - Calibration: calibrating scores from '%s' to '%s'", score_file, calibrated_file)
# iterate through the score file and calibrate scores
- scores = _open_to_read(score_file)
+ scores = bob.measure.load.four_column(_open_to_read(score_file))
+
f = _open_to_write(calibrated_file, write_compressed)
for line in scores:
- assert len(line) == 4
+ assert len(line) == 4, "The line %s of score file %s cannot be interpreted" % (line, score_file)
calibrated_score = llr_machine([line[3]])
f.write('%s %s %s %3.8f\n' % (line[0], line[1], line[2], calibrated_score[0]))
_close_written(calibrated_file, f, write_compressed)
diff --git a/bob/bio/base/utils/io.py b/bob/bio/base/utils/io.py
index a7327f2dc2bb102f164f2c11f0439cb8c1a55fdd..8af99ced9ff41a534a2b43d4757ad31ca5fdf720 100644
--- a/bob/bio/base/utils/io.py
+++ b/bob/bio/base/utils/io.py
@@ -1,6 +1,9 @@
import os
import tempfile, tarfile
+import logging
+logger = logging.getLogger("bob.bio.base")
+
import bob.io.base
def check_file(filename, force, expected_file_size = 1):