Add atvskeystroke/3 (api change: beat.backend.python v1.4.1)

advanced/databases/atvskeystroke/3.json

+{
+  "description": "The ATVS Keystroke database",
+  "root_folder": "/idiap/group/biometric/databases/atvs_keystroke",
+  "protocols": [
+    {
+      "name": "A",
+      "template": "simple_keystroke_recognition",
+      "sets": [
+        {
+          "name": "templates",
+          "template": "templates",
+          "view": "Templates",
+          "parameters": {
+            "protocol": "A"
+          },
+          "outputs": {
+            "file_id": "{{ system_user.username }}/uint64/1",
+            "client_id": "{{ system_user.username }}/text/1",
+            "template_id": "{{ system_user.username }}/text/1",
+            "keystroke": "{{ user.username }}/atvs_keystroke/1"
+          }
+        },
+        {
+          "name": "probes",
+          "template": "probes",
+          "view": "Probes",
+          "parameters": {
+            "protocol": "A"
+          },
+          "outputs": {
+            "file_id": "{{ system_user.username }}/uint64/1",
+            "probe_id": "{{ system_user.username }}/uint64/1",
+            "client_id": "{{ system_user.username }}/text/1",
+            "template_ids": "{{ system_user.username }}/array_1d_text/1",
+            "keystroke": "{{ user.username }}/atvs_keystroke/1"
+          }
+        }
+      ]
+    }
+  ]
+}
\ No newline at end of file

advanced/databases/atvskeystroke/3.py

+###############################################################################
+#                                                                             #
+# Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/           #
+# Contact: beat.support@idiap.ch                                              #
+#                                                                             #
+# This file is part of the beat.examples module of the BEAT platform.         #
+#                                                                             #
+# Commercial License Usage                                                    #
+# Licensees holding valid commercial BEAT licenses may use this file in       #
+# accordance with the terms contained in a written agreement between you      #
+# and Idiap. For further information contact tto@idiap.ch                     #
+#                                                                             #
+# Alternatively, this file may be used under the terms of the GNU Affero      #
+# Public License version 3 as published by the Free Software and appearing    #
+# in the file LICENSE.AGPL included in the packaging of this file.            #
+# The BEAT platform 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.                                        #
+#                                                                             #
+# You should have received a copy of the GNU Affero Public License along      #
+# with the BEAT platform. If not, see http://www.gnu.org/licenses/.           #
+#                                                                             #
+###############################################################################
+
+import numpy as np
+import bob.db.atvskeystroke
+
+
+keystroke_feature = ['', 'holdtime', 'rplatency', 'pplatency', 'rrlatency', 'prlatency']
+keystroke_type = ['', 'given_name', 'family_name', 'email', 'nationality', 'id_number']
+
+
+#----------------------------------------------------------
+
+
+def keystroke_reader(filename):
+    counter = 0
+    feat = 0
+
+    data = {}
+    for line in open(filename, 'r').readlines():
+        if not line.strip(): continue
+        if counter % 6 == 0:
+            feat += 1
+            label = line.strip()
+            data[keystroke_feature[feat]] = {}
+        else:
+            values = [np.int32(v) for v in line.strip().split(' ')]
+            data[keystroke_feature[feat]][keystroke_type[counter % 6]] = np.array(values)
+        counter += 1
+
+    return data
+
+
+#----------------------------------------------------------
+
+
+def get_client_end_index(objs, client_id, client_start_index,
+                         start_index, end_index):
+    client_end_index = client_start_index
+
+    while client_end_index + 1 <= end_index:
+        obj = objs[client_end_index + 1 - start_index]
+
+        if isinstance(obj, tuple):
+            obj = obj[1]
+
+        if obj.client_id != client_id:
+            return client_end_index
+
+        client_end_index += 1
+
+    return end_index
+
+
+#----------------------------------------------------------
+
+
+def get_template_end_index(objs, template_id, template_start_index,
+                           start_index, end_index):
+    template_end_index = template_start_index
+
+    while template_end_index + 1 <= end_index:
+        id = objs[template_end_index + 1 - start_index][0]
+
+        if id != template_id:
+            return template_end_index
+
+        template_end_index += 1
+
+    return end_index
+
+
+#----------------------------------------------------------
+
+
+class Templates:
+    """Outputs:
+        - keystroke: "{{ user.username }}/atvs_keystroke/1
+        - file_id: "{{ system_user.username }}/uint64/1"
+        - client_id: "{{ system_user.username }}/text/1"
+        - template_id: "{{ system_user.username }}/text/1"
+
+    One "file_id" is associated with a given "keystroke".
+    Several "keystroke" are associated with a given "client_id".
+    Several "client_id" are associated with a given "template_id".
+
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  |
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    |   file_id   | |   file_id   | |   file_id   | |   file_id   | |   file_id   | |   file_id   |
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    ----------------------------------------------- -----------------------------------------------
+    |                   client_id                 | |                   client_id                 |
+    ----------------------------------------------- -----------------------------------------------
+    -----------------------------------------------------------------------------------------------
+    |                                        template_id                                          |
+    -----------------------------------------------------------------------------------------------
+
+    Note: for this particular database, there is only one "client_id"
+    per "template_id".
+    """
+
+    def setup(self, root_folder, outputs, parameters, force_start_index=None,
+              force_end_index=None):
+
+        # Initialisations
+        self.root_folder = root_folder
+        self.outputs = outputs
+        self.parameters = parameters
+
+        # Open the database and load the objects to provide via the outputs
+        self.db = bob.db.atvskeystroke.Database()
+
+        template_ids = sorted(self.db.model_ids(groups='eval',
+                                                protocol=parameters['protocol']),
+                              key=lambda x: int(x))
+
+        self.objs = []
+
+        for template_id in template_ids:
+            objs = sorted(self.db.objects(groups='eval',
+                                          protocol=self.parameters['protocol'],
+                                          purposes='enrol',
+                                          model_ids=[template_id]),
+                          key=lambda x: (x.client_id, x.id))
+
+            self.objs.extend([ (template_id, obj) for obj in objs ])
+
+        # Determine the range of indices that must be provided
+        self.start_index = force_start_index if force_start_index is not None else 0
+        self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
+
+        self.objs = self.objs[self.start_index : self.end_index + 1]
+
+        self.next_index = self.start_index
+
+        return True
+
+
+    def done(self, last_data_index):
+        return last_data_index >= self.end_index
+
+
+    def next(self):
+        (template_id, obj) = self.objs[self.next_index - self.start_index]
+
+
+        # Output: template_id (only provide data when the template_id change)
+        if self.outputs['template_id'].isConnected() and \
+           self.outputs['template_id'].last_written_data_index < self.next_index:
+
+            template_end_index = get_template_end_index(self.objs, template_id,
+                                                        self.next_index,
+                                                        self.start_index,
+                                                        self.end_index)
+
+            self.outputs['template_id'].write(
+                {
+                    'text': str(template_id)
+                },
+                template_end_index
+            )
+
+
+        # Output: client_id (only provide data when the client_id change)
+        if self.outputs['client_id'].isConnected() and \
+           self.outputs['client_id'].last_written_data_index < self.next_index:
+
+            client_end_index = get_client_end_index(self.objs, obj.client_id,
+                                                    self.next_index,
+                                                    self.start_index,
+                                                    self.end_index)
+
+            self.outputs['client_id'].write(
+                {
+                    'text': str(obj.client_id)
+                },
+                client_end_index
+            )
+
+
+        # Output: file_id (provide data at each iteration)
+        if self.outputs['file_id'].isConnected():
+            self.outputs['file_id'].write(
+                {
+                    'value': np.uint64(obj.id)
+                },
+                self.next_index
+            )
+
+
+        # Output: image (provide data at each iteration)
+        if self.outputs['keystroke'].isConnected():
+            self.outputs['keystroke'].write(
+                keystroke_reader(obj.make_path(self.root_folder, '.txt')),
+                self.next_index
+            )
+
+
+        # Determine the next data index that must be provided
+        self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+                                                              if x.isConnected() ]
+        )
+
+        return True
+
+
+#----------------------------------------------------------
+
+
+class Probes:
+    """Outputs:
+        - keystroke: "{{ user.username }}/atvs_keystroke/1
+        - file_id: "{{ system_user.username }}/uint64/1"
+        - client_id: "{{ system_user.username }}/text/1"
+        - probe_id: "{{ system_user.username }}/uint64/1",
+        - template_ids: "{{ system_user.username }}/array_1d_text/1",
+
+    One "file_id" is associated with a given "keystroke".
+    One "probe_id" is associated with a given "keystroke".
+    Several "keystroke" are associated with a given "client_id".
+    Several "client_id" are associated with a given "template_ids".
+
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  | |  keystroke  |
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    |   file_id   | |   file_id   | |   file_id   | |   file_id   | |   file_id   | |   file_id   |
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    |   probe_id  | |   probe_id  | |   probe_id  | |   probe_id  | |   probe_id  | |   probe_id  |
+    --------------- --------------- --------------- --------------- --------------- ---------------
+    ----------------------------------------------- -----------------------------------------------
+    |                   client_id                 | |                   client_id                 |
+    ----------------------------------------------- -----------------------------------------------
+    -----------------------------------------------------------------------------------------------
+    |                                        template_ids                                         |
+    -----------------------------------------------------------------------------------------------
+    """
+
+    def setup(self, root_folder, outputs, parameters, force_start_index=None,
+              force_end_index=None):
+
+        # Initialisations
+        self.root_folder = root_folder
+        self.outputs = outputs
+        self.parameters = parameters
+
+        # Open the database and load the objects to provide via the outputs
+        self.db = bob.db.atvskeystroke.Database()
+
+        template_ids = sorted(self.db.model_ids(groups='eval',
+                                                protocol=parameters['protocol']),
+                              key=lambda x: int(x))
+
+        self.objs = []
+
+        for template_id in template_ids:
+            objs = sorted(self.db.objects(groups='eval',
+                                          protocol=self.parameters['protocol'],
+                                          purposes='probe',
+                                          model_ids=[template_id]),
+                          key=lambda x: (x.client_id, x.id))
+
+            self.objs.extend([ (template_id, obj) for obj in objs ])
+
+        # Determine the range of indices that must be provided
+        self.start_index = force_start_index if force_start_index is not None else 0
+        self.end_index = force_end_index if force_end_index is not None else len(self.objs) - 1
+
+        self.objs = self.objs[self.start_index : self.end_index + 1]
+
+        self.next_index = self.start_index
+
+        return True
+
+
+    def done(self, last_data_index):
+        return last_data_index >= self.end_index
+
+
+    def next(self):
+        (template_id, obj) = self.objs[self.next_index - self.start_index]
+
+
+        # Output: template_ids (only provide data when the template_ids change)
+        if self.outputs['template_ids'].isConnected() and \
+           self.outputs['template_ids'].last_written_data_index < self.next_index:
+
+            template_end_index = get_template_end_index(self.objs, template_id,
+                                                        self.next_index,
+                                                        self.start_index,
+                                                        self.end_index)
+
+            self.outputs['template_ids'].write(
+                {
+                    'text': [ str(template_id) ]
+                },
+                template_end_index
+            )
+
+
+        # Output: client_id (only provide data when the client_id change)
+        if self.outputs['client_id'].isConnected() and \
+           self.outputs['client_id'].last_written_data_index < self.next_index:
+
+            client_end_index = get_client_end_index(self.objs, obj.client_id,
+                                                    self.next_index,
+                                                    self.start_index,
+                                                    self.end_index)
+
+            self.outputs['client_id'].write(
+                {
+                    'text': str(obj.client_id)
+                },
+                client_end_index
+            )
+
+
+        # Output: probe_id (provide data at each iteration)
+        if self.outputs['probe_id'].isConnected():
+            self.outputs['probe_id'].write(
+                {
+                    'value': np.uint64(obj.id)
+                },
+                self.next_index
+            )
+
+        # Output: file_id (provide data at each iteration)
+        if self.outputs['file_id'].isConnected():
+            self.outputs['file_id'].write(
+                {
+                    'value': np.uint64(obj.id)
+                },
+                self.next_index
+            )
+
+
+        # Output: image (provide data at each iteration)
+        if self.outputs['keystroke'].isConnected():
+            self.outputs['keystroke'].write(
+                keystroke_reader(obj.make_path(self.root_folder, '.txt')),
+                self.next_index
+            )
+
+
+        # Determine the next data index that must be provided
+        self.next_index = 1 + min([ x.last_written_data_index for x in self.outputs
+                                                              if x.isConnected() ]
+        )
+
+        return True
+
+
+#----------------------------------------------------------
+
+
+# Test the behavior of the views (on fake data)
+if __name__ == '__main__':
+
+    # Install a mock load method for the keystrokes
+    def mock_keystroke_reader(filename):
+        return {}
+
+    keystroke_reader = mock_keystroke_reader
+
+
+    # Mock output class
+    class MockOutput:
+
+        def __init__(self, name, connected):
+            self.name = name
+            self.connected = connected
+            self.last_written_data_index = -1
+            self.written_data = []
+
+        def write(self, data, end_data_index):
+            self.written_data.append(( self.last_written_data_index + 1, end_data_index, data ))
+            self.last_written_data_index = end_data_index
+
+        def isConnected(self):
+            return self.connected
+
+
+    # Tester utility class
+    from beat.backend.python.outputs import OutputList
+    import itertools
+
+    class Tester:
+
+        def __init__(self, name, view_class, outputs_declaration, parameters,
+                     irregular_outputs=[]):
+            self.name = name
+            self.view_class = view_class
+            self.outputs_declaration = {}
+            self.parameters = parameters
+            self.irregular_outputs = irregular_outputs
+
+            self.determine_increments(outputs_declaration)
+
+            for L in range(0, len(self.outputs_declaration) + 1):
+                for subset in itertools.combinations(self.outputs_declaration.keys(), L):
+                    self.run(subset)
+
+        def determine_increments(self, outputs_declaration):
+            outputs = OutputList()
+            for name in outputs_declaration:
+                outputs.add(MockOutput(name, True))
+
+            view = self.view_class()
+            view.setup('', outputs, self.parameters)
+
+            view.next()
+
+            print "View '%s', increments found:" % self.name
+            for output in outputs:
+                self.outputs_declaration[output.name] = output.last_written_data_index + 1
+                print '  - %s: %d' % (output.name, output.last_written_data_index + 1)
+
+
+        def run(self, connected_outputs):
+            if len(connected_outputs) == 0:
+                return
+
+            print "Testing '%s', with %d output(s): %s" % (self.name, len(connected_outputs),
+                                                           ', '.join(connected_outputs))
+
+            connected_outputs = dict([ x for x in self.outputs_declaration.items()
+                                         if x[0] in connected_outputs ])
+
+            not_connected_outputs = dict([ x for x in self.outputs_declaration.items()
+                                             if x[0] not in connected_outputs ])
+
+            outputs = OutputList()
+            for name in self.outputs_declaration.keys():
+                outputs.add(MockOutput(name, name in connected_outputs))
+
+            parameters = dict()
+
+            view = self.view_class()
+            view.setup('', outputs, self.parameters)
+
+            next_expected_indices = {}
+            for name, increment in connected_outputs.items():
+                next_expected_indices[name] = 0
+
+            next_index = 0
+
+            def _done():
+                for output in outputs:
+                    if output.isConnected() and not view.done(output.last_written_data_index):
+                        return False
+                return True
+
+            while not(_done()):
+                view.next()
+
+                for name in connected_outputs.keys():
+                    if name not in self.irregular_outputs:
+                        assert(outputs[name].written_data[-1][0] == next_expected_indices[name])
+                        assert(outputs[name].written_data[-1][1] == next_expected_indices[name] + connected_outputs[name] - 1)
+                    else:
+                        assert(outputs[name].written_data[-1][0] == next_expected_indices[name])
+                        assert(outputs[name].written_data[-1][1] >= next_expected_indices[name])
+
+                for name in not_connected_outputs.keys():
+                    assert(len(outputs[name].written_data) == 0)
+
+                next_index = 1 + min([ x.written_data[-1][1] for x in outputs if x.isConnected() ])
+
+                for name in connected_outputs.keys():
+                    if name not in self.irregular_outputs:
+                        if next_index == next_expected_indices[name] + connected_outputs[name]:
+                            next_expected_indices[name] += connected_outputs[name]
+                    else:
+                        if next_index > outputs[name].written_data[-1][1]:
+                            next_expected_indices[name] = outputs[name].written_data[-1][1] + 1
+
+            for name in connected_outputs.keys():
+                if name not in self.irregular_outputs:
+                    assert(len(outputs[name].written_data) == next_index / connected_outputs[name])
+                else:
+                    print "  Irregular output '%s': %s" % (name, str([ (x[0], x[1]) for x in outputs[name].written_data ]))
+
+
+    # The actual tests
+    Tester('Templates', Templates,
+        [
+            'template_id',
+            'client_id',
+            'file_id',
+            'keystroke',
+        ],
+        dict(
+            protocol = 'A',
+        )
+    )
+
+    Tester('Probes', Probes,
+        [
+            'template_ids',
+            'client_id',
+            'probe_id',
+            'file_id',
+            'keystroke',
+        ],
+        dict(
+            protocol = 'A',
+        ),
+        irregular_outputs = [
+            'client_id',
+        ]
+    )

advanced/databases/atvskeystroke/3.rst

+.. Copyright (c) 2017 Idiap Research Institute, http://www.idiap.ch/          ..
+.. Contact: beat.support@idiap.ch                                             ..
+..                                                                            ..
+.. This file is part of the beat.examples module of the BEAT platform.        ..
+..                                                                            ..
+.. Commercial License Usage                                                   ..
+.. Licensees holding valid commercial BEAT licenses may use this file in      ..
+.. accordance with the terms contained in a written agreement between you     ..
+.. and Idiap. For further information contact tto@idiap.ch                    ..
+..                                                                            ..
+.. Alternatively, this file may be used under the terms of the GNU Affero     ..
+.. Public License version 3 as published by the Free Software and appearing   ..
+.. in the file LICENSE.AGPL included in the packaging of this file.           ..
+.. The BEAT platform 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.                                       ..
+..                                                                            ..
+.. You should have received a copy of the GNU Affero Public License along     ..
+.. with the BEAT platform. If not, see http://www.gnu.org/licenses/.          ..
+
+
+The ATVS-Keystroke Database
+---------------------------
+
+Changelog
+=========
+
+* **Version 3**, 27/Oct/2017: