def _handleEvents(self, events):
# saves many events to pytables table at once.
# EVENTS MUST ALL BE OF SAME TYPE!!!!!
try:
#ioHub.print2err("_handleEvent: ",self.active_experiment_id,self.active_session_id)
if self.checkForExperimentAndSessionIDs(len(events)) is False:
return False
event=events[0]
etype=event[DeviceEvent.EVENT_TYPE_ID_INDEX]
#ioHub.print2err("etype: ",etype)
eventClass=EventConstants.getClass(etype)
etable=self.TABLES[eventClass.IOHUB_DATA_TABLE]
#ioHub.print2err("eventClass: etable",eventClass,etable)
np_events=[]
for event in events:
event[DeviceEvent.EVENT_EXPERIMENT_ID_INDEX]=self.active_experiment_id
event[DeviceEvent.EVENT_SESSION_ID_INDEX]=self.active_session_id
np_events.append(tuple(event))
np_array= N.array(np_events,dtype=eventClass.NUMPY_DTYPE)
#ioHub.print2err('np_array:',np_array)
etable.append(np_array)
self.bufferedFlush(len(np_events))
except ioHubError, e:
print2err(e)
def _handleEvents(self, events):
# saves many events to pytables table at once.
# EVENTS MUST ALL BE OF SAME TYPE!!!!!
try:
#ioHub.print2err("_handleEvent: ",self.active_experiment_id,self.active_session_id)
if self.checkForExperimentAndSessionIDs(len(events)) is False:
return False
event = events[0]
etype = event[DeviceEvent.EVENT_TYPE_ID_INDEX]
#ioHub.print2err("etype: ",etype)
eventClass = EventConstants.getClass(etype)
etable = self.TABLES[eventClass.IOHUB_DATA_TABLE]
#ioHub.print2err("eventClass: etable",eventClass,etable)
np_events = []
for event in events:
event[DeviceEvent.
EVENT_EXPERIMENT_ID_INDEX] = self.active_experiment_id
event[DeviceEvent.
EVENT_SESSION_ID_INDEX] = self.active_session_id
np_events.append(tuple(event))
np_array = N.array(np_events, dtype=eventClass.NUMPY_DTYPE)
#ioHub.print2err('np_array:',np_array)
etable.append(np_array)
self.bufferedFlush(len(np_events))
except ioHubError, e:
print2err(e)
def _handleEvent(self, event):
try:
eventClass = None
if self.checkForExperimentAndSessionIDs(event) is False:
return False
etype = event[DeviceEvent.EVENT_TYPE_ID_INDEX]
# print2err("*** ",DeviceEvent.EVENT_TYPE_ID_INDEX, '_handleEvent: ',etype,' : event list: ',event)
eventClass = EventConstants.getClass(etype)
etable = self.TABLES[eventClass.IOHUB_DATA_TABLE]
event[DeviceEvent.
EVENT_EXPERIMENT_ID_INDEX] = self.active_experiment_id
event[DeviceEvent.EVENT_SESSION_ID_INDEX] = self.active_session_id
np_array = N.array([
tuple(event),
], dtype=eventClass.NUMPY_DTYPE)
etable.append(np_array)
self.bufferedFlush()
except:
print2err("Error saving event: ", event)
printExceptionDetailsToStdErr()
def getEventTable(self, event_type):
"""
Returns the DataStore table that contains events of the specified type.
**Docstr TBC.**
"""
if self.hdfFile:
klassTables = self.hdfFile.root.class_table_mapping
deviceEventTable = None
event_column = None
event_value = None
if isinstance(event_type, basestring):
if event_type.find('Event') >= 0:
event_column = 'class_name'
event_value = event_type
else:
event_value = ''
tokens = event_type.split('_')
for t in tokens:
event_value += t[0].upper() + t[1:].lower()
event_value = event_type + 'Event'
event_value = '"%s"' % (event_value)
elif isinstance(event_type, (int, long)):
event_column = 'class_id'
event_value = event_type
else:
iohub.print2err(
"getEventTable error: event_type arguement must be a string or and int"
)
return None
result = [
row.fetch_all_fields() for row in klassTables.where(
'({0} == {1}) & (class_type_id == 1)'.format(
event_column, event_value))
]
if len(result) != 1:
iohub.print2err(
"event_type_id passed to getEventAttribute can only return one row from CLASS_MAPPINGS: ",
len(result))
return None
tablePathString = result[0][3]
return self.hdfFile.getNode(tablePathString)
return None
def addClassMappings(cls,device_class,device_event_ids,event_classes):
if cls._classes is None:
cls._classes={}
#import iohub
#iohub.print2err("Adding Device Event Mappings for device: ",device_class.__name__)
for event_id in device_event_ids:
event_constant_string=cls.getName(event_id)
import iohub
event_class=None
for event_class in event_classes.values():
if event_class.EVENT_TYPE_ID == event_id:
cls._classes[event_id]=event_class
cls._classes[event_class]=event_id
#iohub.print2err("\tAdding Event Class Mapping: ",event_constant_string, " = ",event_id)
break
if event_id not in cls._classes.keys():
iohub.print2err("\t*** ERROR ADDING EVENT CLASSS MAPPING: Could not find class: ",event_constant_string, " = ",event_id)
def getEventTable(self,event_type):
"""
Returns the DataStore table that contains events of the specified type.
**Docstr TBC.**
"""
if self.hdfFile:
klassTables=self.hdfFile.root.class_table_mapping
deviceEventTable=None
event_column=None
event_value=None
if isinstance(event_type,basestring):
if event_type.find('Event')>=0:
event_column='class_name'
event_value=event_type
else:
event_value=''
tokens=event_type.split('_')
for t in tokens:
event_value+=t[0].upper()+t[1:].lower()
event_value=event_type+'Event'
event_value='"%s"'%(event_value)
elif isinstance(event_type,(int,long)):
event_column='class_id'
event_value=event_type
else:
iohub.print2err("getEventTable error: event_type arguement must be a string or and int")
return None
result=[row.fetch_all_fields() for row in klassTables.where('({0} == {1}) & (class_type_id == 1)'.format(event_column,event_value))]
if len(result)!= 1:
iohub.print2err("event_type_id passed to getEventAttribute can only return one row from CLASS_MAPPINGS: ",len(result))
return None
tablePathString=result[0][3]
return self.hdfFile.getNode(tablePathString)
return None
def addClassMappings(cls, device_class, device_event_ids,
event_classes):
if cls._classes is None:
cls._classes = {}
#import iohub
#iohub.print2err("Adding Device Event Mappings for device: ",device_class.__name__)
for event_id in device_event_ids:
event_constant_string = cls.getName(event_id)
import iohub
event_class = None
for event_class in event_classes.values():
if event_class.EVENT_TYPE_ID == event_id:
cls._classes[event_id] = event_class
cls._classes[event_class] = event_id
#iohub.print2err("\tAdding Event Class Mapping: ",event_constant_string, " = ",event_id)
break
if event_id not in cls._classes.keys():
iohub.print2err(
"\t*** ERROR ADDING EVENT CLASSS MAPPING: Could not find class: ",
event_constant_string, " = ", event_id)
def _handleEvent(self, event):
try:
eventClass=None
if self.checkForExperimentAndSessionIDs(event) is False:
return False
etype=event[DeviceEvent.EVENT_TYPE_ID_INDEX]
# print2err("*** ",DeviceEvent.EVENT_TYPE_ID_INDEX, '_handleEvent: ',etype,' : event list: ',event)
eventClass=EventConstants.getClass(etype)
etable=self.TABLES[eventClass.IOHUB_DATA_TABLE]
event[DeviceEvent.EVENT_EXPERIMENT_ID_INDEX]=self.active_experiment_id
event[DeviceEvent.EVENT_SESSION_ID_INDEX]=self.active_session_id
np_array= N.array([tuple(event),],dtype=eventClass.NUMPY_DTYPE)
etable.append(np_array)
self.bufferedFlush()
except:
print2err("Error saving event: ",event)
printExceptionDetailsToStdErr()
class ioHubpyTablesFile():
def __init__(self, fileName, folderPath, fmode='a', ioHubsettings=None):
self.fileName = fileName
self.folderPath = folderPath
self.filePath = os.path.join(folderPath, fileName)
self.settings = ioHubsettings
self.active_experiment_id = None
self.active_session_id = None
self.flushCounter = self.settings.get('flush_interval', 32)
self._eventCounter = 0
self.TABLES = dict()
self._eventGroupMappings = dict()
self.emrtFile = openFile(self.filePath, mode=fmode)
atexit.register(close_open_data_files, False)
if len(self.emrtFile.title) == 0:
self.buildOutTemplate()
self.flush()
else:
self.loadTableMappings()
def updateDataStoreStructure(self, device_instance, event_class_dict):
dfilter = Filters(complevel=0,
complib='zlib',
shuffle=False,
fletcher32=False)
def eventTableLabel2ClassName(event_table_label):
tokens = str(event_table_label[0] + event_table_label[1:].lower() +
'Event').split('_')
return ''.join([t[0].upper() + t[1:] for t in tokens])
for event_cls_name, event_cls in event_class_dict.iteritems():
if event_cls.IOHUB_DATA_TABLE:
event_table_label = event_cls.IOHUB_DATA_TABLE
if event_table_label not in self.TABLES:
self.TABLES[event_table_label] = self.emrtFile.createTable(
self._eventGroupMappings[event_table_label],
eventTableLabel2ClassName(event_table_label),
event_cls.NUMPY_DTYPE,
title="%s %s Data" %
(device_instance.__class__.__name__,
eventTableLabel2ClassName(event_table_label)),
filters=dfilter.copy())
self.flush()
self.addClassMapping(event_cls, self.TABLES[event_table_label])
def loadTableMappings(self):
# create meta-data tables
self._buildEventGroupMappingDict()
self.TABLES[
'EXPERIMENT_METADETA'] = self.emrtFile.root.data_collection.experiment_meta_data
self.TABLES[
'SESSION_METADETA'] = self.emrtFile.root.data_collection.session_meta_data
self.TABLES[
'CLASS_TABLE_MAPPINGS'] = self.emrtFile.root.class_table_mapping
# create tables dict of hdf5 path mappings
try:
self.TABLES[
'KEYBOARD_KEY'] = self.emrtFile.root.data_collection.events.keyboard.KeyboardKeyEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'KEYBOARD_CHAR'] = self.emrtFile.root.data_collection.events.keyboard.KeyboardCharEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'MOUSE_INPUT'] = self.emrtFile.root.data_collection.events.mouse.MouseInputEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'GAMEPAD_STATE_CHANGE'] = self.emrtFile.root.data_collection.events.gamepad.GamepadStateChangeEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'MESSAGE'] = self.emrtFile.root.data_collection.events.experiment.MessageEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'LOG'] = self.emrtFile.root.data_collection.events.experiment.LogEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'MULTI_CHANNEL_ANALOG_INPUT'] = self.emrtFile.root.data_collection.events.analog_input.MultiChannelAnalogInputEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'MONOCULAR_EYE_SAMPLE'] = self.emrtFile.root.data_collection.events.eyetracker.MonocularEyeSampleEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'BINOCULAR_EYE_SAMPLE'] = self.emrtFile.root.data_collection.events.eyetracker.BinocularEyeSampleEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'FIXATION_START'] = self.emrtFile.root.data_collection.events.eyetracker.FixationStartEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'FIXATION_END'] = self.emrtFile.root.data_collection.events.eyetracker.FixationEndEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'SACCADE_START'] = self.emrtFile.root.data_collection.events.eyetracker.SaccadeStartEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'SACCADE_END'] = self.emrtFile.root.data_collection.events.eyetracker.SaccadeEndEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'BLINK_START'] = self.emrtFile.root.data_collection.events.eyetracker.BlinkStartEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
try:
self.TABLES[
'BLINK_END'] = self.emrtFile.root.data_collection.events.eyetracker.BlinkEndEvent
except:
# Just means the table for this event type has not been created as the event type is not being recorded
pass
def buildOutTemplate(self):
self.emrtFile.title = DATA_FILE_TITLE
self.emrtFile.FILE_VERSION = FILE_VERSION
self.emrtFile.SCHEMA_DESIGNER = SCHEMA_AUTHORS
self.emrtFile.SCHEMA_MODIFIED = SCHEMA_MODIFIED_DATE
#CREATE GROUPS
self.emrtFile.createGroup(
self.emrtFile.root,
'analysis',
title=
'Data Analysis Files, notebooks, scripts and saved results tables.'
)
self.emrtFile.createGroup(
self.emrtFile.root,
'data_collection',
title='Data Collected from Experiment Sessions')
self.flush()
self.emrtFile.createGroup(
self.emrtFile.root.data_collection,
'events',
title='Events that occurred and were saved during the experiments.'
)
self.emrtFile.createGroup(
self.emrtFile.root.data_collection,
'condition_variables',
title=
'Experiment DV and IVs used during and experiment session, or calculated and stored. In general, each row represents one trial of an experiment session.'
)
self.flush()
self.TABLES['CLASS_TABLE_MAPPINGS'] = self.emrtFile.createTable(
self.emrtFile.root,
'class_table_mapping',
ClassTableMappings,
title='Mapping of ioObjects Classes to ioHub tables')
self.TABLES['EXPERIMENT_METADETA'] = self.emrtFile.createTable(
self.emrtFile.root.data_collection,
'experiment_meta_data',
ExperimentMetaData,
title='Different Experiments Paradigms that have been run')
self.TABLES['SESSION_METADETA'] = self.emrtFile.createTable(
self.emrtFile.root.data_collection,
'session_meta_data',
SessionMetaData,
title='Session run for the various experiments.')
self.flush()
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'experiment',
title='Experiment Generated Events')
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'keyboard',
title='Keyboard Created Events')
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'mouse',
title='Mouse Device Created Events')
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'gamepad',
title='GamePad Created Events')
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'analog_input',
title='AnalogInput Device Created Events')
self.emrtFile.createGroup(self.emrtFile.root.data_collection.events,
'eyetracker',
title='Eye Tracker Generated Events')
self.flush()
self._buildEventGroupMappingDict()
def _buildEventGroupMappingDict(self):
self._eventGroupMappings[
'KEYBOARD_KEY'] = self.emrtFile.root.data_collection.events.keyboard
self._eventGroupMappings[
'KEYBOARD_CHAR'] = self.emrtFile.root.data_collection.events.keyboard
self._eventGroupMappings[
'MOUSE_INPUT'] = self.emrtFile.root.data_collection.events.mouse
self._eventGroupMappings[
'GAMEPAD_STATE_CHANGE'] = self.emrtFile.root.data_collection.events.gamepad
self._eventGroupMappings[
'MULTI_CHANNEL_ANALOG_INPUT'] = self.emrtFile.root.data_collection.events.analog_input
self._eventGroupMappings[
'MESSAGE'] = self.emrtFile.root.data_collection.events.experiment
self._eventGroupMappings[
'LOG'] = self.emrtFile.root.data_collection.events.experiment
self._eventGroupMappings[
'MONOCULAR_EYE_SAMPLE'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'BINOCULAR_EYE_SAMPLE'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'FIXATION_START'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'FIXATION_END'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'SACCADE_START'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'SACCADE_END'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'BLINK_START'] = self.emrtFile.root.data_collection.events.eyetracker
self._eventGroupMappings[
'BLINK_END'] = self.emrtFile.root.data_collection.events.eyetracker
def addClassMapping(self, ioClass, ctable):
names = [
x['class_id'] for x in self.TABLES['CLASS_TABLE_MAPPINGS'].where(
"(class_id == %d)" % (ioClass.EVENT_TYPE_ID))
]
if len(names) == 0:
trow = self.TABLES['CLASS_TABLE_MAPPINGS'].row
trow['class_id'] = ioClass.EVENT_TYPE_ID
trow['class_type_id'] = 1 # Device or Event etc.
trow['class_name'] = ioClass.__name__
trow['table_path'] = ctable._v_pathname
trow.append()
self.flush()
def createOrUpdateExperimentEntry(self, experimentInfoList):
#ioHub.print2err("createOrUpdateExperimentEntry called with: ",experimentInfoList)
experiment_metadata = self.TABLES['EXPERIMENT_METADETA']
result = [
row for row in experiment_metadata.iterrows()
if row['code'] == experimentInfoList[1]
]
if len(result) > 0:
result = result[0]
self.active_experiment_id = result['experiment_id']
return self.active_experiment_id
max_id = 0
id_col = experiment_metadata.col('experiment_id')
if len(id_col) > 0:
max_id = N.amax(id_col)
self.active_experiment_id = max_id + 1
experimentInfoList[0] = self.active_experiment_id
experiment_metadata.append([
experimentInfoList,
])
self.flush()
#ioHub.print2err("Experiment ID set to: ",self.active_experiment_id)
return self.active_experiment_id
def createExperimentSessionEntry(self, sessionInfoDict):
#ioHub.print2err("createExperimentSessionEntry called with: ",sessionInfoDict)
session_metadata = self.TABLES['SESSION_METADETA']
max_id = 0
id_col = session_metadata.col('session_id')
if len(id_col) > 0:
max_id = N.amax(id_col)
self.active_session_id = int(max_id + 1)
values = (self.active_session_id, self.active_experiment_id,
sessionInfoDict['code'], sessionInfoDict['name'],
sessionInfoDict['comments'],
sessionInfoDict['user_variables'])
session_metadata.append([
values,
])
self.flush()
#ioHub.print2err("Session ID set to: ",self.active_session_id)
return self.active_session_id
def _initializeConditionVariableTable(self, experiment_id, np_dtype):
experimentConditionVariableTable = None
self._EXP_COND_DTYPE = N.dtype(np_dtype)
try:
expCondTableName = "EXP_CV_%d" % (experiment_id)
experimentConditionVariableTable = self.emrtFile.root.data_collection.condition_variables._f_getChild(
expCondTableName)
self.TABLES['EXP_CV'] = experimentConditionVariableTable
except NoSuchNodeError, nsne:
try:
experimentConditionVariableTable = self.emrtFile.createTable(
self.emrtFile.root.data_collection.condition_variables,
expCondTableName,
self._EXP_COND_DTYPE,
title='Condition Variables for Experiment id %d' %
(experiment_id))
self.TABLES['EXP_CV'] = experimentConditionVariableTable
self.emrtFile.flush()
except:
printExceptionDetailsToStdErr()
return False
except Exception:
print2err(
'Error getting experimentConditionVariableTable for experiment %d, table name: %s'
% (experiment_id, expCondTableName))
printExceptionDetailsToStdErr()
return False