def uploadToGNode(self):
self.csvData = extractCSVMetaData(self.csvFile, self.expName)
self.dataBlockToUpload = Block(name=self.blockName, file_origin=self.expName)
raw_seg = Segment(name='rawData', index=0)
self.vibrationSignal.name = 'Vibration Stimulus'
self.vibrationSignal.description = 'Vibration Stimulus applied to the honey bee antenna'
self.voltageSignal.name = 'Membrane Potential'
self.voltageSignal.description = 'Vibration Sensitive inter-neuron membrane potential'
self.vibrationSignal.segment = raw_seg
self.voltageSignal.segment = raw_seg
raw_seg.analogsignals.append(self.vibrationSignal)
raw_seg.analogsignals.append(self.voltageSignal)
if len(self.dataBlock.segments[0].analogsignals) > 2:
self.currentSignal.name = 'Current Signal'
self.currentSignal.description = 'Indicates whether a current is being injected or not. The magnitudes ' \
'are given in an event array'
self.currentSignal.segment = raw_seg
raw_seg.analogsignals.append(self.currentSignal)
if len(self.dataBlock.segments[0].eventarrays) == 2:
raw_seg.eventarrays.append(self.dataBlock.segments[0].eventarrays[1])
self.dataBlock.segments[0].eventarrays[1].segment = raw_seg
raw_seg.block = self.dataBlockToUpload
self.dataBlockToUpload.segments.append(raw_seg)
self.doc = odml.Document(author="Ajayrama K.", version="1.0")
self.mainSec = odml.Section(name=self.expName, type='experiment')
self.doc.append(self.mainSec)
expSummary = odml.Section(name='VibrationStimulus', type='experiment/electrophysiology')
quantity_parser = lambda lst: [odml.Value(data=float(x), unit=x.dimensionality.string) for x in lst]
frequencies = quantity_parser(self.csvData['freqs'])
if frequencies:
expSummary.append(odml.Property(name='FrequenciesUsed', value=frequencies))
durations = quantity_parser(self.csvData['pulse'][0])
if durations:
expSummary.append(odml.Property(name='PulseInputDurations', value=durations))
intervals = quantity_parser(self.csvData['pulse'][1])
if intervals:
expSummary.append(odml.Property(name='PulseInputIntervals', value=intervals))
expSummary.append(odml.Property(name='SpontaneousActivityPresence', value=self.csvData['spont']))
if not self.csvData['resp'] == '':
expSummary.append(odml.Property(name='NatureOfResponse', value=self.csvData['resp']))
self.mainSec.append(expSummary)
print asctime() + ' : Uploading metadata'
doc = self.session.set_all(self.doc)
print asctime() + ' : Uploading metadata Done'
print asctime() + ' : Refreshing metadata'
mainSec = self.session.get(doc.sections[0].location, refresh=True, recursive=True)
print asctime() + ' : Refreshing metadata Done'
self.dataBlockToUpload.section = mainSec
print asctime() + ' : Uploading Data'
blkLoc = self.session.set_all(self.dataBlockToUpload)
print asctime() + ' : Uploading Data Done'
def test_section_proxy(self):
s = odml.Section("sec1")
p = odml.Property(name="p", value="1")
s.append(p)
ps = proxy.MappedSection(s)
# forward attributes
ps.name = "sec2"
self.assertEqual(s.name, "sec2")
p2 = odml.Property(name="p2", value="2")
# append to proxy section, creates a proxy in ps
# and the original object in s
ps.append(p2)
self.assertIn(p2, s)
self.assertIn(p2, ps)
self.assertIs(s.contains(p2), p2)
self.assertIsInstance(ps.contains(p2), proxy.Proxy)
# removing from proxy section, removes both
ps.remove(p2)
self.assertNotIn(p2, s)
self.assertNotIn(p2, ps)
# appending to section, creates a proxy in ps
s.append(p2)
self.assertIn(p2, s)
self.assertIn(p2, ps)
self.assertIs(s.contains(p2), p2)
self.assertIsInstance(ps.contains(p2), proxy.Proxy)
# removing removes from ps too
s.remove(p2)
self.assertNotIn(p2, s)
self.assertNotIn(p2, ps)
# appending creates in both, removing in ps removes in both
s.append(p2)
ps.remove(p2)
self.assertNotIn(p2, s)
self.assertNotIn(p2, ps)
# append a proxy to ps, both original and proxy compare to
# be 'in' ps
pp = proxy.PropertyProxy(p)
# you can use proxy_append to add an explicit proxy obj (without affecting
# the original section) or you can append the object to the original section
# so that the proxy object is created in the proxy section, too
ps.proxy_append(pp) # this one is only in ps
self.assertIn(pp, ps)
self.assertIn(p, ps) # as p == pp, this also holds true
# even if the name is changed
ps.name = "p3"
self.assertEqual(p.name, "p") # does not change the name of p
self.assertEqual(ps.name, "p3") # but the one of ps
self.assertIn(pp, ps) # both are in ps though
self.assertIn(p, ps)
# and we can remove it again
ps.remove(p)
self.assertNotIn(p, ps)
self.assertNotIn(pp, ps)
self.assertNotIn(p, s)
s2 = odml.Section("sec3")
# a mapped section added to another mapped section
# will only appear there
ps2 = proxy.MappedSection(s2)
ps.proxy_append(ps2)
self.assertIn(ps2, ps)
self.assertIn(s2, ps)
self.assertNotIn(s2, s)
# and we can remove it again
ps.remove(s2)
self.assertNotIn(ps2, ps)
def get_odml_doc(dtypes):
# CREATE A DOCUMENT
doc = odml.Document(version='0.0.1')
doc.author = 'Author1'
doc.date = datetime.date.today()
doc.version = '0.0.1'
doc.repository = ''
# APPEND MAIN SECTIONS
doc.append(
odml.Section(name='Animal',
definition='Information about the animal used'))
parent = doc['Animal']
parent.append(
odml.Section(
'Development',
definition='Information about the development of the animal'))
parent = doc['Animal']['Development']
parent.append(
odml.Section('dev_measures_template',
type='template',
definition='Developmental data of a single day'))
parent = doc['Animal']
parent.append(
odml.Property(name='AnimalID',
definition='ID of the animal used for this experiment'))
parent.append(
odml.Property(name='Species', definition='Species of the animal'))
parent.append(
odml.Property(name='Strain', definition='Strain of the animal'))
parent.append(odml.Property(name='Sex', definition='Sex of the animal'))
parent.append(
odml.Property(name='Birthdate', definition='Birthdate of the animal'))
parent.append(
odml.Property(name='BirthAge',
unit='days',
definition='Time of birth after conception'))
parent.append(
odml.Property(name='MotherID', definition='AnimalID of the mother'))
parent = doc['Animal']['Development']
parent.append(
odml.Property(name='EyeOpening',
definition='Date of first eye opening'))
parent.append(
odml.Property(
name='GraspingReflex',
definition='Date of first observation of grasping reflex'))
parent = doc['Animal']['Development']['dev_measures_template']
parent.append(
odml.Property(name='Weight',
unit='g',
definition='Weight of the animal'))
parent.append(
odml.Property(name='BodyLength',
unit='cm',
definition='Distance from nose to tail tip [cm]'))
parent.append(
odml.Property(name='TailLength',
unit='cm',
definition='Length of the tail'))
parent.append(
odml.Property(
name='Date',
definition='Date of recording of this set of developmental measures'
))
parent.append(
odml.Property(
name='CliffAvoidance',
unit='s',
definition='Time after which cliff aversion reflex is observed'))
parent.append(
odml.Property(
name='DevelopmentalAge',
definition=
'Developmental age of the animal in days after birth (P_)'))
return doc
parent.append(
odml.Section(name="Tricia Marie McMillan",
type="crew/person",
definition="Information on Trillian Astra"))
parent.append(
odml.Section(name="Ford Prefect",
type="crew/person",
definition="Information on Ford Prefect"))
# APPEND PROPERTIES WITH VALUES
parent.append(
odml.Property(name="NameCrewMembers",
value=[
"Arthur Philip Dent", "Zaphod Beeblebrox",
"Tricia Marie McMillan", "Ford Prefect"
],
dtype=odml.DType.person,
definition="List of crew members names"))
parent.append(
odml.Property(name="NoCrewMembers",
value=4,
dtype=odml.DType.int,
definition="Number of crew members",
uncertainty=1,
reference="The Hitchhiker's guide to the Galaxy (novel)"))
# SET NEW PARENT NODE
parent = doc['TheCrew']['Arthur Philip Dent']
def setup_tutorodml():
doc = odml.Document(version='0.0.x')
doc.author = 'FirstName LastName'
doc.date = datetime.date.today()
doc.version = '0.0.x'
doc.repository = '/myserver/myrepo'
# APPEND MAIN SECTIONS
doc.append(odml.Section(name='MySection',
type='<Enter the type of data this section is'
' associated with, e.g. hardware>',
definition='<Describe the purpose of sections '
'in short statements in this '
'column.>'))
doc.append(odml.Section(name='OneMoreSection',
type='<Enter the type of data this section is'
' associated with, e.g. software>',
definition='<Use only the first cell in this '
'column to for the section '
'description.>'))
parent = doc['OneMoreSection']
parent.append(odml.Section('MySubsection',
type='<Enter the type of data this section'
' is associated with, e.g. settings>',
definition='<Describe the purpose of this '
'section here (eg. everything '
'concerning the amplifier '
'used...)'))
# ADDING PROPERTIES
parent = doc['MySection']
parent.append(odml.Property(name='MyFirstProperty',
values='MyFirstValue',
dtype='str',
unit=None,
uncertainty=None,
definition='<Enter a short definition of '
'the property and the associated '
'value described here>'))
parent.append(odml.Property(name='MultiValuedProperty',
values=[2.001, 4],
dtype='float',
unit='mm',
uncertainty=0.02,
definition='A section can have multiple properties attached and '
'a property can contain multiple values.'))
parent = doc['OneMoreSection']
parent.append(odml.Property(name='MyEmptyProperty',
values=None,
dtype='int',
unit='mV',
uncertainty=None,
definition='This property contains an empty value.'
'Empty values can be highlighted using odmltables.'))
parent = doc['OneMoreSection']['MySubsection']
parent.append(odml.Property(name='MyLastProperty',
values=datetime.datetime.today().date(),
dtype='date',
unit='AD',
uncertainty=None,
definition='You can define the hierarchical'
' location of a section via the'
' "path to section" column.'
'The value contains todays date.'))
return doc
def create_datatype_test_odml():
"""
create an odml-document using every odml datatype at least once
"""
# data that will be written in the odml-document
int_values = [-10, 0, 10]
float_values = [-1.234, 0.0, 1.234]
bool_values = ['true', 'false', 'True', 'False', 't', 'f', 'T', 'F', 1, 0]
text_value = "this is a text. It is longer than a string and contains " + \
"punctuation marks!"
datetime_value = datetime.datetime(2014, 12, 11, 15, 2, 0)
date_value = datetime.date(2014, 12, 11)
time_value = datetime.time(15, 2, 0)
# create a new odml document
doc = odml.Document(version='0.1')
# create sections
doc.append(odml.Section(name='numbers'))
doc.append(odml.Section(name='texts'))
doc.append(odml.Section(name='other'))
# add subsections and properties
parent = doc['numbers']
parent.append(
odml.Property(name='Integer',
values=int_values,
definition='contains different int-values'))
parent.append(
odml.Property(name='Float',
values=float_values,
definition='contains different float-values'))
parent = doc['texts']
parent.append(odml.Section(name='datetime'))
parent.append(odml.Section(name='string-like'))
parent = doc['texts']['datetime']
parent.append(
odml.Property(name='Datetime',
values=datetime_value,
dtype=odml.DType.datetime))
parent.append(
odml.Property(name='Date', values=date_value, dtype=odml.DType.date))
parent.append(
odml.Property(name='Time', values=time_value, dtype=odml.DType.time))
parent = doc['texts']['string-like']
parent.append(
odml.Property(name='String',
values='this is a string',
dtype=odml.DType.string))
parent.append(
odml.Property(name='Text', values=text_value, dtype=odml.DType.text))
parent.append(
odml.Property(name='Person',
values='Jana Pick',
dtype=odml.DType.person))
parent = doc['other']
parent.append(
odml.Property(name='Boolean',
values=bool_values,
dtype=odml.DType.boolean))
return doc
def test_children(self):
"""
This test checks the correct saving and loading of Section children of a Document.
"""
s_type = "type"
# Lvl 1 child Sections
sec_lvl_11 = odml.Section(name="sec_11", type=s_type, parent=self.doc)
_ = odml.Section(name="sec_12", type=s_type, parent=self.doc)
# Lvl 2 child Sections
sec_lvl_21 = odml.Section(name="sec_21",
type=s_type,
parent=sec_lvl_11)
_ = odml.Section(name="sec_22", type=s_type, parent=sec_lvl_11)
_ = odml.Section(name="sec_23", type=s_type, parent=sec_lvl_11)
# Lvl 2 child Properties
_ = odml.Property(name="prop_21", parent=sec_lvl_11)
_ = odml.Property(name="prop_22", parent=sec_lvl_11)
_ = odml.Property(name="prop_23", parent=sec_lvl_11)
# Lvl 3 child Sections
_ = odml.Section(name="sec_31", type=s_type, parent=sec_lvl_21)
_ = odml.Section(name="sec_32", type=s_type, parent=sec_lvl_21)
_ = odml.Section(name="sec_33", type=s_type, parent=sec_lvl_21)
_ = odml.Section(name="sec_34", type=s_type, parent=sec_lvl_21)
# Lvl 3 child Properties
_ = odml.Property(name="prop_31", parent=sec_lvl_21)
_ = odml.Property(name="prop_32", parent=sec_lvl_21)
_ = odml.Property(name="prop_33", parent=sec_lvl_21)
_ = odml.Property(name="prop_34", parent=sec_lvl_21)
jdoc, xdoc, ydoc = self.save_load()
# Test correct JSON save and load.
self.assertEqual(len(jdoc.sections), 2)
jsec_lvl_1 = jdoc[sec_lvl_11.name]
self.assertEqual(len(jsec_lvl_1.sections), 3)
self.assertEqual(len(jsec_lvl_1.properties), 3)
jsec_lvl_2 = jsec_lvl_1[sec_lvl_21.name]
self.assertEqual(len(jsec_lvl_2.sections), 4)
self.assertEqual(len(jsec_lvl_2.properties), 4)
# Test correct XML save and load.
self.assertEqual(len(xdoc.sections), 2)
xsec_lvl_1 = xdoc[sec_lvl_11.name]
self.assertEqual(len(xsec_lvl_1.sections), 3)
self.assertEqual(len(xsec_lvl_1.properties), 3)
xsec_lvl_2 = xsec_lvl_1[sec_lvl_21.name]
self.assertEqual(len(xsec_lvl_2.sections), 4)
self.assertEqual(len(xsec_lvl_2.properties), 4)
# Test correct YAML save and load.
self.assertEqual(len(ydoc.sections), 2)
ysec_lvl_1 = ydoc[sec_lvl_11.name]
self.assertEqual(len(ysec_lvl_1.sections), 3)
self.assertEqual(len(ysec_lvl_1.properties), 3)
ysec_lvl_2 = ysec_lvl_1[sec_lvl_21.name]
self.assertEqual(len(ysec_lvl_2.sections), 4)
self.assertEqual(len(ysec_lvl_2.properties), 4)
def test_value_float(self):
p = odml.Property("test", value="1.5", dtype="float")
self.assertEqual(p.values[0], 1.5)
def setUp(self):
self.p = odml.Property(name="test", value=1)
def test_value_int(self):
p = odml.Property("test", 1, dtype="int")
self.assertEqual(p.values[0], 1)
def test_conversion_float_to_int(self):
p = odml.Property("test", "1.5", dtype="float")
self.assertEqual(p.dtype, "float")
p.dtype = "int"
self.assertEqual(p.dtype, "int")
self.assertEqual(p.values[0], 1)
def rg_subsession_tree(tasktype=None, trialids=[]):
"""
Builds an odML Document for reach-to-grasp subsession metadata
Returns:
(odml.doc.BaseDocument)
odML Document with default reach-to-grasp subsession metadata
"""
# CREATE A DOCUMENT
doc = odml.Document(version='0.1')
# APPEND MAIN SECTION
doc.append(
odml.Section(name='Subsession',
type='subsession',
definition='Information on the subsession'))
# SET PARENT NODE
parent = doc['Subsession']
# APPEND SUBSECTIONS
if tasktype:
parent.append(get_task_subsection(tasktype=tasktype,
trialids=trialids))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Session',
value=default_value(odml.DType.string),
definition='Session name'))
parent.append(
odml.Property(name='Subsession',
value=default_value(odml.DType.string),
definition='Subsession name'))
parent.append(
odml.Property(name='Date',
value=default_value(odml.DType.date),
definition='Date of session'))
parent.append(
odml.Property(name='Weekday',
value=default_value(odml.DType.string),
definition='Weekday of session'))
parent.append(
odml.Property(name='Time',
value=default_value(odml.DType.time),
definition='Time of subsession'))
parent.append(
odml.Property(name='Duration',
value=default_value(odml.DType.int, unit='sec'),
definition='Duration of subsession'))
parent.append(
odml.Property(name='IsSpikeSorted',
value=default_value(odml.DType.boolean),
definition='States if a spike sorting was '
'performed for this subsession '))
value = default_value(odml.DType.string)
if tasktype:
value.data = tasktype
parent.append(
odml.Property(name='TaskType',
value=value,
definition='Performed task type'))
parent.append(
odml.Property(name='Noisy',
value=default_value(odml.DType.boolean),
definition='States if subsession is noisy'))
parent.append(
odml.Property(name='Comment',
value=default_value(odml.DType.string),
definition='Comment about the subsession'))
return doc
def get_task_subsection(tasktype, trialids=[]):
"""
Constructs a Section describing the given task type including Properties,
Values and (possibly default) data
Args:
tasktype (string):
Type of performed task (OneCue, TwoCues, Observation, Sleep, or
Mapping)
trialids (list of int):
trial ids (only possible for OneCue, TwoCues, Observation)
Returns:
(odml.section.BaseSection)
Section describing the specified task type
Note:
Valid task types: OneCue, TwoCues, Observation, Sleep, Mapping
"""
# CREATE MAIN SECTION
main = odml.Section(name='TaskSettings',
type='subsession/task',
definition='Information on task settings')
if tasktype in ['OneCue', 'TwoCues', 'Observation']:
# APPEND SUBSECTIONS
main.append(
odml.Section(name='TrialTypeSettings',
type='subsession/task/trial',
definition='Information on trial type '
'parameters'))
trial_section_names = get_trial_section_names(trialids)
for sname in trial_section_names:
main.append(
odml.Section(name=sname,
type='subsession/task/trial',
definition='Information on trial '
'parameters'))
# APPEND PROPERTIES WITH DEFAULT VALUES
main.append(
odml.Property(name='TotalTrialCount',
value=default_value(odml.DType.int),
definition='Total number of trials'))
main.append(
odml.Property(name='CorrectTrialCount',
value=default_value(odml.DType.int),
definition='Number of correctly performed '
'trials'))
main.append(
odml.Property(name='GripErrorTrialCount',
value=default_value(odml.DType.int),
definition='Number of error trials'))
main.append(
odml.Property(name='StandardSettings',
value=default_value(odml.DType.boolean),
definition='States if subsession was '
'performed under standard '
'settings'))
# SET PARENT NODE
parent = main['TrialTypeSettings']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Condition',
value=default_value(odml.DType.int),
definition='Trial type combination of '
'subsession was condition'))
parent.append(
odml.Property(name='OrderForce',
value=default_value(odml.DType.string),
definition='Trial order of force '
'conditions (random or block)'))
parent.append(
odml.Property(name='OrderGrip',
value=default_value(odml.DType.string),
definition='Trial order of grip '
'conditions (random or block)'))
parent.append(
odml.Property(name='BlockSize',
value=default_value(odml.DType.int),
definition='Order of trial type '
'combination was of block '
'size'))
# SET PARENT NODE
for sname in trial_section_names:
parent = main[sname]
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='DigitalEvents',
type='subsession/task/trial/events',
definition='Information on digital '
'trial events'))
parent.append(
odml.Section(name='AnalogEvents',
type='subsession/task/trial/events',
definition='Information on analogue '
'trial events'))
parent.append(
odml.Section(name='Periods',
type='subsession/task/trial/periods',
definition='Information on trial '
'periods'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='ID',
value=default_value(odml.DType.int),
definition='Trial ID'))
parent.append(
odml.Property(name='PerformanceCode',
value=default_value(odml.DType.int),
definition='States if this was an '
'error or a correct trial'))
parent.append(
odml.Property(name='TrialType',
value=default_value(odml.DType.int),
definition='Trial type of trial'))
parent.append(
odml.Property(name='ForceType',
value=default_value(odml.DType.string),
definition='Force type measured in '
'trial'))
# SET PARENT NODE
parent = main[sname]['DigitalEvents']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='TS',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when trial start is '
'activated'))
parent.append(
odml.Property(name='FP-ON',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when fixation point '
'is activated'))
parent.append(
odml.Property(name='CUE-ON',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when (first) CUE is '
'activated '))
parent.append(
odml.Property(name='CUE-OFF',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when (first) CUE is '
'deactivated '))
parent.append(
odml.Property(name='GO-ON',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when (second cue) GO '
'is activated '))
parent.append(
odml.Property(name='SR',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when switch is '
'released'))
parent.append(
odml.Property(name='GO-OFF',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when (second cue) GO '
'is deactivated '))
parent.append(
odml.Property(name='RW',
value=default_value(odml.DType.int,
unit='1./30000*s'),
definition='Time when reward is '
'given'))
# SET PARENT NODE
parent = main[sname]['AnalogEvents']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='GripForceSignals',
type='subsession/task/trial/events',
definition='Information on analogue '
'events detected with grip '
'force signals'))
parent.append(
odml.Section(name='DisplacementSignal',
type='subsession/task/trial/events',
definition='Information on analogue '
'events detected with '
'object displacement '
'signal'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='UsedForceSensor',
value=default_value(odml.DType.int),
definition='Channel ID index of force '
'sensor used in grip force '
'detection'))
parent.append(
odml.Property(name='ManuallyControlled',
value=default_value(odml.DType.boolean),
definition='States if analogue event '
'detection of this trial '
'was manually controlled'))
# SET PARENT NODE
parent = main[sname]['AnalogEvents']['GripForceSignals']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='OT',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when target object '
'is touched'))
parent.append(
odml.Property(name='HS',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when holding '
'position of target object '
'is reached and holding '
'period starts'))
parent.append(
odml.Property(name='OR',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when target object '
'is released'))
parent.append(
odml.Property(name='BTB',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when object moved '
'back to its baseline'))
# SET PARENT NODE
parent = main[sname]['AnalogEvents']['DisplacementSignal']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='OT',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when target object '
'is touched'))
parent.append(
odml.Property(name='HS',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when holding '
'position of target object '
'is reached and holding '
'period starts'))
parent.append(
odml.Property(name='OR',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when target object '
'is released'))
parent.append(
odml.Property(name='BTB',
value=default_value(odml.DType.int, unit='ms'),
definition='Time when object moved '
'back to its baseline'))
# SET PARENT NODE
parent = main[sname]['Periods']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='GripForceSignals',
type='subsession/task/trial/events',
definition='Information on periods '
'calculated with analogue '
'events detected with grip '
'force signals'))
parent.append(
odml.Section(name='DisplacementSignal',
type='subsession/task/trial/events',
definition='Information on periods '
'calculated with analogue '
'events detected with '
'object displacement '
'signal'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='RT',
value=default_value(odml.DType.int, unit='ms'),
definition='Reaction time (period '
'between GO and SR)'))
parent.append(
odml.Property(name='ITI',
value=default_value(odml.DType.int, unit='ms'),
definition='Inter-trial-interval '
'(period until next '
'trial)'))
# SET PARENT NODE
parent = main[sname]['Periods']['GripForceSignals']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='RGT',
value=default_value(odml.DType.int, unit='ms'),
definition='Reach-to-grasp time '
'(period between SR and '
'OT)'))
parent.append(
odml.Property(name='PT',
value=default_value(odml.DType.int, unit='ms'),
definition='Pull time (period between '
'OT and HS)'))
parent.append(
odml.Property(name='MT',
value=default_value(odml.DType.int, unit='ms'),
definition='Movement time (period '
'between GO-ON and HS)'))
parent.append(
odml.Property(name='HT',
value=default_value(odml.DType.int, unit='ms'),
definition='Hold time (period between '
'HS and RW)'))
parent.append(
odml.Property(name='ORT',
value=default_value(odml.DType.int, unit='ms'),
definition='Time until object is '
'released (period between '
'RW an OR '))
# SET PARENT NODE
parent = main[sname]['Periods']['DisplacementSignal']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='RGT',
value=default_value(odml.DType.int, unit='ms'),
definition='Reach-to-grasp time '
'(period between SR and '
'OT)'))
parent.append(
odml.Property(name='PT',
value=default_value(odml.DType.int, unit='ms'),
definition='Pull time (period between '
'OT and HS)'))
parent.append(
odml.Property(name='MT',
value=default_value(odml.DType.int, unit='ms'),
definition='Movement time (period '
'between GO-ON and HS)'))
parent.append(
odml.Property(name='HT',
value=default_value(odml.DType.int, unit='ms'),
definition='Hold time (period between '
'HS and RW)'))
parent.append(
odml.Property(name='ORT',
value=default_value(odml.DType.int, unit='ms'),
definition='Time until object is '
'released (period between '
'RW an OR '))
elif tasktype == 'Sleep':
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
main.append(
odml.Property(name='SleepStart',
value=default_value(odml.DType.int, unit='samples'),
definition='Start time(s) of sleep '
'interval(s)'))
main.append(
odml.Property(name='SleepEnd',
value=default_value(odml.DType.int, unit='samples'),
definition='End time(s) of sleep '
'interval(s)'))
elif tasktype == 'Mapping':
# APPEND SUBSECTIONS
main.append(
odml.Section(name='Shoulder',
type='subsession/task/RF',
definition='Information on shoulder mapping'))
main.append(
odml.Section(name='Elbow',
type='subsession/task/RF',
definition='Information on elbow mapping'))
main.append(
odml.Section(name='Wrist',
type='subsession/task/RF',
definition='Information on wrist mapping'))
main.append(
odml.Section(name='Thumb',
type='subsession/task/RF',
definition='Information on wrist mapping'))
main.append(
odml.Section(name='Index',
type='subsession/task/RF',
definition='Information on wrist mapping'))
main.append(
odml.Section(name='Digit2to5',
type='subsession/task/RF',
definition='Information on wrist mapping'))
main.append(
odml.Section(name='Digit5',
type='subsession/task/RF',
definition='Information on wrist mapping'))
# APPEND PROPERTIES WITH DEFAULT VALUES
main.append(
odml.Property(name='PassivePG',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval where a '
'passively precision grip was '
'mimicked'))
main.append(
odml.Property(name='UlnarDeviation',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval where Ulnar was '
'deviated'))
main.append(
odml.Property(name='Digit2to3Extension',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval where digits 2 '
'and 3 were extended'))
main.append(
odml.Property(name='TouchPalm',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval where palm was '
'touched'))
main.append(
odml.Property(name='TouchCheek',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval where cheek was '
'touched'))
# SET PARENT NODE
parent = main['Shoulder']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='MoveForward',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was moved forward'))
parent.append(
odml.Property(name='Lowering',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was lowered down'))
# SET PARENT NODE
parent = main['Elbow']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Flexion',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was flexed'))
parent.append(
odml.Property(name='Extension',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was extended'))
# SET PARENT NODE
parent = main['Wrist']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Flexion',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was flexed'))
parent.append(
odml.Property(name='Pronation',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was pronated'))
# SET PARENT NODE
parent = main['Thumb']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Abduction',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was abducted'))
parent.append(
odml.Property(name='Adduction',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was adducted'))
parent.append(
odml.Property(name='Extension',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body '
'part was extended'))
parent.append(
odml.Property(name='TouchEnd',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which end of '
'body part was touched'))
parent.append(
odml.Property(name='TouchInterior',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which '
'interior body part was '
'touched'))
# SET PARENT NODE
parent = main['Index']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Abduction',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body part was '
'abducted'))
parent.append(
odml.Property(name='Flexion',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body part was '
'flexed'))
parent.append(
odml.Property(name='Extension',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body part was '
'extended'))
parent.append(
odml.Property(
name='TouchInteriorFace',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which interior body part '
'was touched'))
# SET PARENT NODE
parent = main['Digit2to5']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Flexion',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body part was '
'flexed'))
parent.append(
odml.Property(
name='TouchInteriorFace',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which interior body part '
'was touched'))
# SET PARENT NODE
parent = main['Digit5']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Flexion',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which body part was '
'flexed'))
parent.append(
odml.Property(
name='TouchLateralFace',
value=default_value(odml.DType.int, unit='samples'),
definition='Time interval in which lateral body part '
'was touched'))
return main
def rg_project_tree(tasktype='TwoCues'):
"""
Builds an odML Document for reach-to-grasp project metadata
Args:
used_taskdesign (string, optional):
States the task design used in this subsession
Returns:
(odml.doc.BaseDocument)
odML Document with default reach-to-grasp project metadata
Note:
Valid used_taskdesign: OneCue, TwoCues, Observation, Sleep, Mapping
"""
# CREATE A DOCUMENT
doc = odml.Document(version='0.1')
# CREATE A MAIN SECTION
doc.append(odml.Section(name='Project',
type='project',
definition='Information on the experimental '
'project'))
# SET PARENT NODE
parent = doc['Project']
# APPEND SUBSECTIONS
parent.append(odml.Section(name='TaskDesigns',
type='project',
definition='Information on tasks'))
parent.append(odml.Section(name='TrialTypeCodes',
type='codes',
definition='Information on trial type codes'))
parent.append(odml.Section(name='ConditionCodes',
type='codes',
definition='Information on condition codes '
'(trial type combination codes)'))
parent.append(odml.Section(name='PerformanceCodes',
type='codes',
definition='Information on trial performance '
'codes'))
parent.append(odml.Section(name='TrialSettings',
type='setup/control',
definition='Information on the programmed '
'trial settings'))
parent.append(odml.Section(name='TargetObjectSettings',
type='setup/control',
definition='Information on the settings of the '
'target object'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='Name',
value=odml.Value(data='reach-to-grasp',
dtype=odml.DType.string),
definition='Name of project'))
parent.append(odml.Property(name='Type',
value=odml.Value(data='electrophysiology',
dtype=odml.DType.string),
definition='Type of project'))
parent.append(odml.Property(name='Subtype',
value=odml.Value(data='motor behavior',
dtype=odml.DType.string),
definition='Name of the project'))
parent.append(odml.Property(name='Description',
value=default_value(odml.DType.url),
definition='Project description URL'))
parent.append(odml.Property(name='Collaborators',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in rg_collaborators()],
definition='Affilitations of involved '
'collaborators'))
# SET PARENT NODE
parent = doc['Project']['TaskDesigns']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='Designs',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['OneCue', 'TwoCues',
'Observation', 'Sleep',
'Mapping']],
definition='Names of possible task designs'))
parent.append(odml.Property(name='UsedDesign',
value=odml.Value(data=tasktype,
dtype=odml.DType.string)
if tasktype
else default_value(odml.DType.string),
definition='Name of used task design'))
parent.append(odml.Property(name='Description',
value=default_value(odml.DType.url),
definition='Task designs descriptions URL'))
# SET PARENT NODE
parent = doc['Project']['TrialTypeCodes']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='SGLF',
value=odml.Value(data=89,
dtype=odml.DType.int),
definition='Side grip / low force code'))
parent.append(odml.Property(name='SGHF',
value=odml.Value(data=86,
dtype=odml.DType.int),
definition='Side grip / high force code'))
parent.append(odml.Property(name='PGLF',
value=odml.Value(data=169,
dtype=odml.DType.int),
definition='Precision grip / low force code'))
parent.append(odml.Property(name='PGHF',
value=odml.Value(data=166,
dtype=odml.DType.int),
definition='Precision grip / high force code'))
parent.append(odml.Property(name='LFSG',
value=odml.Value(data=149,
dtype=odml.DType.int),
definition='Low force / side grip code'))
parent.append(odml.Property(name='LFPG',
value=odml.Value(data=154,
dtype=odml.DType.int),
definition='Low force / precision grip code'))
parent.append(odml.Property(name='HFSG',
value=odml.Value(data=101,
dtype=odml.DType.int),
definition='High force / side grip code'))
parent.append(odml.Property(name='HFPG',
value=odml.Value(data=106,
dtype=odml.DType.int),
definition='High force / precision grip code'))
parent.append(odml.Property(name='SGSG',
value=odml.Value(data=85,
dtype=odml.DType.int),
definition='Side grip / side grip code'))
parent.append(odml.Property(name='PGPG',
value=odml.Value(data=170,
dtype=odml.DType.int),
definition='Precision grip / precision grip '
'code'))
parent.append(odml.Property(name='n.d.',
value=odml.Value(data=0,
dtype=odml.DType.int),
definition='Code for not detectable trial '
'type'))
# SET PARENT NODE
parent = doc['Project']['ConditionCodes']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='cnd_1',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGLF', 'SGHF',
'PGLF', 'PGHF']],
definition='Grip first trials, all grip and '
'force types'))
parent.append(odml.Property(name='cnd_2',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGLF', 'SGHF',
'PGLF', 'PGHF']],
definition='Force first trials, all force and '
'grip types'))
parent.append(odml.Property(name='cnd_11',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGLF', 'PGLF']],
definition='Grip first trials, all grip '
'types, but only low force'))
parent.append(odml.Property(name='cnd_12',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGHF', 'PGHF']],
definition='Grip first trials, all grip '
'types, but only high force'))
parent.append(odml.Property(name='cnd_13',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGHF', 'SGLF']],
definition='Grip first trials, only side '
'grip, but all force types'))
parent.append(odml.Property(name='cnd_14',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['PGHF', 'PGLF']],
definition='Grip first trials, only precision '
'grip, but all force types'))
parent.append(odml.Property(name='cnd_21',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['LFSG', 'LFPG']],
definition='Force first trials, only low '
'force, but all grip types'))
parent.append(odml.Property(name='cnd_22',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['HFSG', 'HFPG']],
definition='Force first trials, only high '
'force, but all grip types'))
parent.append(odml.Property(name='cnd_23',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['HFSG', 'LFSG']],
definition='Force first trials, all force '
'types, but only side grip'))
parent.append(odml.Property(name='cnd_24',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['HFPG', 'LFPG']],
definition='Force first trials, all force '
'types, but only side grip'))
parent.append(odml.Property(name='cnd_131',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGLF']],
definition='Grip first trials, only side '
'grip, only low force'))
parent.append(odml.Property(name='cnd_132',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGHF']],
definition='Grip first trials, only side '
'grip, only high force'))
parent.append(odml.Property(name='cnd_133',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['SGSG']],
definition='Grip first trials, only side '
'grip, force needs to be guessed'))
parent.append(odml.Property(name='cnd_141',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['PGLF']],
definition='Grip first trials, only precision '
'grip, only low force'))
parent.append(odml.Property(name='cnd_142',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['PGHF']],
definition='Grip first trials, only precision '
'grip, only high force'))
parent.append(odml.Property(name='cnd_144',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['PGPG']],
definition='Grip first trials, only precision '
'grip, force needs to be guessed'))
parent.append(odml.Property(name='cnd_213',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['LFSG']],
definition='Force first trials, only low '
'force, only side grip'))
parent.append(odml.Property(name='cnd_214',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['LFPG']],
definition='Force first trials, only low '
'force, only precision grip'))
parent.append(odml.Property(name='cnd_223',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['HFSG']],
definition='Force first trials, only high '
'force, only side grip'))
parent.append(odml.Property(name='cnd_224',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['HFPG']],
definition='Force first trials, only high '
'force, only precision grip'))
# SET PARENT NODE
parent = doc['Project']['PerformanceCodes']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='pc_127',
value=odml.Value(data='correct trial',
dtype=odml.DType.string),
definition='Performance code of a correctly '
'completed trial'))
parent.append(odml.Property(name='pc_64',
value=odml.Value(data='SR < FP-ON',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'switch is released too early '
'(before fixation point)'))
parent.append(odml.Property(name='pc_96',
value=odml.Value(data='SR < CUE-ON',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'switch is released too early '
'(before delay cue is turned on)'))
parent.append(odml.Property(name='pc_112',
value=odml.Value(data='SR < CUE-OFF',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'switch is released too early '
'(before delay cue is turned off)'))
parent.append(odml.Property(name='pc_120',
value=odml.Value(data='SR < GO-ON',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'switch is released too early '
'(before GO cue turns on)'))
parent.append(odml.Property(name='pc_124',
value=odml.Value(data='no SR',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'switch is not released'))
parent.append(odml.Property(name='pc_126',
value=odml.Value(data='grip error',
dtype=odml.DType.string),
definition='Performance code of a trial where '
'the wrong grip type is used'))
# SET PARENT NODE
parent = doc['Project']['TrialSettings']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='DigitalEvents',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['TS', 'FP-ON', 'CUE-ON',
'CUE-OFF', 'GO-ON', 'SR',
'RW', 'GO-OFF']],
definition='Digital recorded trial events'))
parent.append(odml.Property(name='AnalogEvents',
value=[odml.Value(data=data,
dtype=odml.DType.string)
for data in ['OT', 'HS', 'OR', 'BTB']],
definition='Analog recorded trial events'))
parent.append(odml.Property(name='TSP',
value=odml.Value(data=400.0,
dtype=odml.DType.float,
unit='ms'),
definition='Duration of trial start period '
'(period between TS and FP)'))
parent.append(odml.Property(name='FPP',
value=odml.Value(data=400.0,
dtype=odml.DType.float,
unit='ms'),
definition='Duration of fixation point period '
'(period between FP and CUE-ON)'))
parent.append(odml.Property(name='CUE',
value=odml.Value(data=300.0,
dtype=odml.DType.float,
unit='ms'),
definition='Duration of CUE period (period '
'between CUE-ON and CUE-OFF'))
parent.append(odml.Property(name='DELAY',
value=odml.Value(data=1000.0,
dtype=odml.DType.float,
unit='ms'),
definition='Duration of delay period (period '
'between CUE-OFF and GO)'))
parent.append(odml.Property(name='HT',
value=odml.Value(data=500.0,
dtype=odml.DType.float,
unit='ms'),
definition='Duration of holding time (period '
'between HS and RW)'))
parent.append(odml.Property(name='MTLimit',
value=odml.Value(data=700.0,
dtype=odml.DType.float,
unit='ms'),
definition='Time limit for movement (period '
'between GO-ON and HS)'))
parent.append(odml.Property(name='RTLimit',
value=odml.Value(data=1000.0,
dtype=odml.DType.float,
unit='ms'),
definition='Time limit for reaction time '
'(period between GO-ON and SR)'))
parent.append(odml.Property(name='PTLimits',
value=default_value(odml.DType.float,
unit='ms'),
definition='Min and max time to pull the '
'object into the holding position '
'(period between OT and HS)'))
# SET PARENT NODE
parent = doc['Project']['TargetObjectSettings']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(odml.Property(name='HoldPosRange',
value=[odml.Value(data=data,
dtype=odml.DType.int,
unit='mm')
for data in [4.0, 14.0]],
definition='Distance window for holding the '
'object in place'))
parent.append(odml.Property(name='LowForceWeight',
value=odml.Value(data=100.0,
dtype=odml.DType.float,
unit='g'),
definition='Weight of object in low force '
'modus'))
parent.append(odml.Property(name='HighForceWeight',
value=odml.Value(data=200.0,
dtype=odml.DType.float,
unit='g'),
definition='Weight of object in high force '
'modus'))
return doc
def rej_tree(rej_names=[]):
"""
Builds an odML Document for reach-to-grasp preprocessing metadata
Returns:
(odml.doc.BaseDocument)
odML Document with default reach-to-grasp preprocessing metadata
"""
# CREATE A DOCUMENT
doc = odml.Document(version='0.1')
# APPEND MAIN SECTION
doc.append(
odml.Section(name='RejectionsLFP',
type='preprocessing',
definition='Information on rejection of '
'experimental LFP signals'))
# SET PARENT NODE
parent = doc['RejectionsLFP']
# APPEND SUBSECTIONS
for rejn in rej_names:
parent.append(
odml.Section(name=rejn,
type='subject/preparation',
definition='Information on rejection '
'performed on this LFP band'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(
name='LFPBands',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in rej_names
] if len(rej_names) > 0 else default_value(odml.DType.string),
definition='Information on which LFP bands '
'the rejection was performed'))
if len(rej_names) > 0:
for rejn in rej_names:
# SET PARENT NODE
parent = doc['RejectionsLFP'][rejn]
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Highcut',
value=default_value(odml.DType.float),
definition='High cut frequency of '
'rejection filter'))
parent.append(
odml.Property(name='Lowcut',
value=default_value(odml.DType.float),
definition='Low cut frequency of '
'rejection filter'))
parent.append(
odml.Property(name='Order',
value=default_value(odml.DType.int),
definition='Order of rejection filter'))
parent.append(
odml.Property(name='RejElectrodes',
value=default_value(odml.DType.int),
definition='ID list of rejected '
'electrodes'))
parent.append(
odml.Property(name='RejTrials',
value=default_value(odml.DType.int),
definition='ID list of rejected '
'trials'))
return doc
def create_property(self, name):
return odml.Property(name=name.replace("sec", "prop"),
value=name.replace("sec", "val"))
def rg_setup_tree(location='-'):
"""
Builds an odML Document for reach-to-grasp setup metadata
Returns:
(odml.doc.BaseDocument)
odML Document with default reach-to-grasp setup metadata
"""
# CREATE A DOCUMENT
doc = odml.Document(version='0.1')
# APPEND MAIN SECTION
doc.append(
odml.Section(name='Setup',
type='setup',
definition='Information on the experimental '
'setup'))
# SET PARENT NODE
parent = doc['Setup']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='Apparatus',
type='setup',
definition='Information on the experimental '
'apparatus'))
parent.append(
odml.Section(name='ControlComputer',
type='setup/software',
definition='Information on the experimental '
'control'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Location',
value=get_location(location),
definition='Location of the setup'))
parent.append(
odml.Property(name='Description',
value=default_value(odml.DType.url),
definition='Setup description URL'))
parent.append(
odml.Property(name='DAQSystem',
value=odml.Value(data='Cerebus',
dtype=odml.DType.string),
definition='DAQ system used'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='StartSwitch',
type='setup',
definition='Information on the start switch'))
parent.append(
odml.Section(name='TargetObject',
type='setup',
definition='Information on the target object'))
parent.append(
odml.Section(name='CueSystem',
type='setup',
definition='Information on the cue system'))
parent.append(
odml.Section(name='RewardSystem',
type='setup',
definition='Information on the reward system'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Manufacturer',
value=odml.Value(data='NI A/D Card (ref?)',
dtype=odml.DType.string),
definition='Owner of the setup'))
parent.append(
odml.Property(name='Creator',
value=odml.Value(data='Thomas Brochier',
dtype=odml.DType.string),
definition='Full name of person who created '
'the setup'))
parent.append(
odml.Property(name='Maintainer',
value=odml.Value(data='Thomas Brochier',
dtype=odml.DType.string),
definition='Full name of person who maintains '
'the setup'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['StartSwitch']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='activates start trial',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Type',
value=odml.Value(data='table switch',
dtype=odml.DType.string),
definition='Type of apparatus'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='analog', dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='Events',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in ['TS', 'SR']
],
definition='Names of events extracted from '
'this signal'))
parent.append(
odml.Property(name='SamplingRate',
value=odml.Value(data=30000,
dtype=odml.DType.int,
unit='samples/sec'),
definition='Sampling rate of data'))
parent.append(
odml.Property(name='ConnectedTo',
value=odml.Value(data='NeuralSignalProcessor',
dtype=odml.DType.string),
definition='Target device of apparatus'))
parent.append(
odml.Property(name='MonitoredBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='nev', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
parent.append(
odml.Property(name='Length',
value=default_value(odml.DType.float, unit='cm'),
definition='Length of apparatus'))
parent.append(
odml.Property(name='Width',
value=default_value(odml.DType.float, unit='cm'),
definition='Length of apparatus'))
parent.append(
odml.Property(name='Height',
value=default_value(odml.DType.float, unit='mm'),
definition='Length of apparatus'))
parent.append(
odml.Property(name='PosX',
value=odml.Value(data=5.0,
dtype=odml.DType.float,
unit='cm'),
definition='X position of apparatus'))
parent.append(
odml.Property(name='PosY',
value=odml.Value(data=0.0,
dtype=odml.DType.float,
unit='cm'),
definition='Y position of apparatus'))
parent.append(
odml.Property(name='PosZ',
value=odml.Value(data=0.0,
dtype=odml.DType.float,
unit='cm'),
definition='Z position of apparatus'))
parent.append(
odml.Property(name='PosOrigin',
value=odml.Value(data='midline, waist-level',
dtype=odml.DType.string),
definition='Origin for xyz position of '
'apparatus'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['TargetObject']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='FSRSensor',
type='setup/daq',
definition='Information on the FSR sensors'))
parent.append(
odml.Section(name='HESensor',
type='setup/daq',
definition='Information on the hall-effect '
'sensor'))
parent.append(
odml.Section(name='LoadForce',
type='setup/daq',
definition='Information on the load force '
'signal'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='object to grasp, pull '
'and hold',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Type',
value=odml.Value(data='stainless steel '
'parallelpiped',
dtype=odml.DType.string),
definition='Type of apparatus'))
parent.append(
odml.Property(name='Length',
value=odml.Value(data=40.0,
dtype=odml.DType.float,
unit='mm'),
definition='Length of apparatus'))
parent.append(
odml.Property(name='Width',
value=odml.Value(data=16.0,
dtype=odml.DType.float,
unit='mm'),
definition='Width of apparatus'))
parent.append(
odml.Property(name='Height',
value=odml.Value(data=10.0,
dtype=odml.DType.float,
unit='mm'),
definition='Height of apparatus'))
parent.append(
odml.Property(name='AttachedTo',
value=odml.Value(data='anterior end of a low- '
'friction horizontal '
'shuttle',
dtype=odml.DType.string),
definition='Device apparatus is attached to'))
parent.append(
odml.Property(name='Rotation',
value=odml.Value(data=45.0,
dtype=odml.DType.float,
unit='degree'),
definition='Rotation of apparatus from '
'vertical axis'))
parent.append(
odml.Property(name='PosX',
value=odml.Value(data=5.0,
dtype=odml.DType.float,
unit='cm'),
definition='X position of apparatus'))
parent.append(
odml.Property(name='PosY',
value=odml.Value(data=13.0,
dtype=odml.DType.float,
unit='cm'),
definition='Y position of apparatus'))
parent.append(
odml.Property(name='PosZ',
value=odml.Value(data=14.0,
dtype=odml.DType.float,
unit='cm'),
definition='Z position of apparatus'))
parent.append(
odml.Property(name='PosOrigin',
value=odml.Value(data='midline, waist-level',
dtype=odml.DType.string),
definition='Origin for xyz position of '
'apparatus'))
parent.append(
odml.Property(name='PullRange',
value=[
odml.Value(data=data,
dtype=odml.DType.float,
unit='mm') for data in [0.0, 15.0]
],
definition='Minimum and maximum pull range '
'of target object'))
parent.append(
odml.Property(name='WeightRange',
value=[
odml.Value(data=data,
dtype=odml.DType.float,
unit='g') for data in [0.0, 800.0]
],
definition='Minimum and maximum weight range '
'of target object'))
parent.append(
odml.Property(name='WeightSwitch',
value=odml.Value(data='activation of magnet',
dtype=odml.DType.string),
definition='Mechanism to switch weight '
'configuration'))
parent.append(
odml.Property(name='Sensors',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in ['FSRSensor', 'HESensor', 'LoadForce']
],
definition='Sensors providing additional '
'analogue signals to monitor '
'task and behavior'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['TargetObject']['FSRSensor']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='measures grip and '
'pulling load forces by '
'means of force '
'sensitive resistances '
'(FSR)',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='SGChannelIDs',
value=[
odml.Value(data=data, dtype=odml.DType.int)
for data in [138, 140]
],
definition='Channel IDs of FSR sensors to '
'measure load forces of side grip'))
parent.append(
odml.Property(name='PGChannelIDs',
value=[
odml.Value(data=data, dtype=odml.DType.int)
for data in [137, 139]
],
definition='Channel IDs of FSR sensors to '
'measure load forces of precision '
'grip'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='analog', dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='Events',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in ['OT', 'OR', 'HS', 'BTB']
],
definition='Names of events extracted from '
'this signal'))
parent.append(
odml.Property(name='SamplingRate',
value=odml.Value(data=1000,
dtype=odml.DType.int,
unit='samples/sec'),
definition='Sampling rate of data'))
parent.append(
odml.Property(name='ConnectedTo',
value=odml.Value(data='NeuralSignalProcessor',
dtype=odml.DType.string),
definition='Target device of apparatus'))
parent.append(
odml.Property(name='MonitoredBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='ControlledBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='ns2', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['TargetObject']['HESensor']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='hall effect (HE) sensor'
' measures horizontal '
'displacement',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Count',
value=odml.Value(data=1, dtype=odml.DType.int),
definition='Number of hall-effect sensors'))
parent.append(
odml.Property(name='ChannelID',
value=odml.Value(data=143, dtype=odml.DType.int),
definition='Channel ID of HESensor to '
'measure horizontal object '
'displacement'))
parent.append(
odml.Property(name='Events',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in ['OT', 'OR', 'HS', 'BTB']
],
definition='Names of events extracted from '
'this signal'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='analog', dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='ns2', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['TargetObject']['LoadForce']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='used to detect load '
'force of the target '
'object',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Count',
value=odml.Value(data=1, dtype=odml.DType.int),
definition='Number of load force signals'))
parent.append(
odml.Property(name='ChannelID',
value=odml.Value(data=141, dtype=odml.DType.int),
definition='Channel ID of load force signal'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='analog', dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='ns2', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['CueSystem']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='CueCodes',
type='setup/daq',
definition='Information on cue codes'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='instructing movement '
'configurations of each '
'trial',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Type',
value=odml.Value(data='visual, LED cube',
dtype=odml.DType.string),
definition='Type of apparatus'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='digital',
dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='EventNames',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in [
'FP-ON', 'CUE-ON', 'CUE-OFF', 'GO-ON', 'GO-OFF',
'ERROR-FLASH', 'VALIDATION-FLASH'
]
],
definition='Names of events extracted from '
'this signal'))
parent.append(
odml.Property(name='Length',
value=default_value(odml.DType.float, unit='mm'),
definition='Length of apparatus'))
parent.append(
odml.Property(name='Width',
value=default_value(odml.DType.float, unit='mm'),
definition='Width of apparatus'))
parent.append(
odml.Property(name='Height',
value=default_value(odml.DType.float, unit='mm'),
definition='Height of apparatus'))
parent.append(
odml.Property(name='PosX',
value=odml.Value(data=5.0,
dtype=odml.DType.float,
unit='cm'),
definition='X position of apparatus'))
parent.append(
odml.Property(name='PosY',
value=odml.Value(data=13.0,
dtype=odml.DType.float,
unit='cm'),
definition='Y position of apparatus'))
parent.append(
odml.Property(name='PosZ',
value=default_value(odml.DType.float, unit='cm'),
definition='Z position of apparatus'))
parent.append(
odml.Property(name='PosOrigin',
value=odml.Value(data='midline, waist-level',
dtype=odml.DType.string),
definition='Origin for xyz position of '
'apparatus'))
parent.append(
odml.Property(name='LEDCount',
value=odml.Value(data=5, dtype=odml.DType.int),
definition='Number of LEDs'))
parent.append(
odml.Property(name='LEDConfiguration',
value=odml.Value(data='2-1-2', dtype=odml.DType.string),
definition='Arrangement of LEDs'))
parent.append(
odml.Property(name='CornerLEDColor',
value=odml.Value(data='red', dtype=odml.DType.string),
definition='Color of the corner LEDs'))
parent.append(
odml.Property(name='CenterLEDColor',
value=odml.Value(data='yellow', dtype=odml.DType.string),
definition='Color of the center LEDs'))
parent.append(
odml.Property(name='SamplingRate',
value=odml.Value(data=30000,
dtype=odml.DType.int,
unit='samples/sec'),
definition='Sampling rate of data'))
parent.append(
odml.Property(name='ConnectedTo',
value=odml.Value(data='NeuralSignalProcessor',
dtype=odml.DType.string),
definition='Target device of apparatus'))
parent.append(
odml.Property(name='MonitoredBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='ControlledBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='nev', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['CueSystem']['CueCodes']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='LeftLEDs',
value=odml.Value(data='side grip',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
parent.append(
odml.Property(name='RightLEDs',
value=odml.Value(data='precision grip',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
parent.append(
odml.Property(name='BottomLEDs',
value=odml.Value(data='low force',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
parent.append(
odml.Property(name='TopLEDs',
value=odml.Value(data='high force',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
parent.append(
odml.Property(name='CenterLED',
value=odml.Value(data='fixation point',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
parent.append(
odml.Property(name='CornerLEDs',
value=odml.Value(data='grip error',
dtype=odml.DType.string),
definition='LEDs coding this trial '
'instruction'))
# SET PARENT NODE
parent = doc['Setup']['Apparatus']['RewardSystem']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Function',
value=odml.Value(data='rewards subject if '
'trial was performed '
'correctly',
dtype=odml.DType.string),
definition='Function of apparatus'))
parent.append(
odml.Property(name='Type',
value=odml.Value(data='reward pipe',
dtype=odml.DType.string),
definition='Type of apparatus'))
parent.append(
odml.Property(name='SignalType',
value=odml.Value(data='digital',
dtype=odml.DType.string),
definition='Signal type of apparatus (digital '
'or analog)'))
parent.append(
odml.Property(name='EventNames',
value=[
odml.Value(data=data, dtype=odml.DType.string)
for data in ['RW']
],
definition='Names of events extracted from '
'this signal'))
parent.append(
odml.Property(name='RewardFood',
value=odml.Value(data='apple sauce',
dtype=odml.DType.string),
definition='Food used for reward'))
parent.append(
odml.Property(name='RewardAmount',
value=odml.Value(data=0.5,
dtype=odml.DType.float,
unit='ml/200ms'),
definition='Food amount used for reward per '
'trial'))
parent.append(
odml.Property(name='SamplingRate',
value=odml.Value(data=30000,
dtype=odml.DType.int,
unit='samples/sec'),
definition='Sampling rate of data'))
parent.append(
odml.Property(name='ConnectedTo',
value=odml.Value(data='NeuralSignalProcessor',
dtype=odml.DType.string),
definition='Target device of apparatus'))
parent.append(
odml.Property(name='MonitoredBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='ControlledBy',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Control software of apparatus'))
parent.append(
odml.Property(name='SavedIn',
value=odml.Value(data='nev', dtype=odml.DType.string),
definition='File in which apparatus signals '
'are saved'))
# SET PARENT NODE
parent = doc['Setup']['ControlComputer']
# APPEND SUBSECTIONS
parent.append(
odml.Section(name='ControlSoftware',
type='setup/daq',
definition='Information on the control software'
' of the Cerebus^TM system'))
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='CPU',
value=default_value(odml.DType.string),
definition='CPU model'))
parent.append(
odml.Property(name='RAM',
value=default_value(odml.DType.float, unit='GB'),
definition='Amount of RAM'))
parent.append(
odml.Property(name='Mainboard',
value=default_value(odml.DType.string),
definition='Mainboard type'))
parent.append(
odml.Property(name='HarddiskCapacity',
value=default_value(odml.DType.float, unit='GB'),
definition='Disk capacity of data storage'))
parent.append(
odml.Property(name='OSType',
value=default_value(odml.DType.string),
definition='Type of operating system'))
parent.append(
odml.Property(name='OSVersion',
value=default_value(odml.DType.string),
definition='Version of operating system'))
# SET PARENT NODE
parent = doc['Setup']['ControlComputer']['ControlSoftware']
# APPEND SUBSECTIONS
# APPEND PROPERTIES WITH DEFAULT VALUES
parent.append(
odml.Property(name='Name',
value=odml.Value(data='LabVIEW',
dtype=odml.DType.string),
definition='Name of software'))
parent.append(
odml.Property(name='Manufacturer',
value=odml.Value(data='National Instruments',
dtype=odml.DType.string),
definition='Manufacturer of software'))
parent.append(
odml.Property(name='Version',
value=default_value(odml.DType.string),
definition='Software version'))
return doc
def test_property_values_cardinality(self):
# -- Test assignment validation warnings
doc = odml.Document()
sec = odml.Section(name="sec", type="sec_type", parent=doc)
# Making sure only the required warnings are tested
self._clear_output()
# -- Test cardinality validation warnings on Property init
# Test warning when setting invalid minimum
_ = odml.Property(name="prop_card_min",
values=[1],
val_cardinality=(2, None),
parent=sec)
output = self._get_captured_output()
test_msg = "%s (minimum %s values, %s found)" % (self.msg_base, 2, 1)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test warning when setting invalid maximum
_ = odml.Property(name="prop_card_max",
values=[1, 2, 3],
val_cardinality=2,
parent=sec)
output = self._get_captured_output()
test_msg = "%s (maximum %s values, %s found)" % (self.msg_base, 2, 3)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test no warning on valid init
prop_card = odml.Property(name="prop_card",
values=[1, 2],
val_cardinality=(1, 5),
parent=sec)
output = self._get_captured_output()
self.assertEqual(output, [])
# -- Test cardinality validation warnings on cardinality updates
# Test warning when setting minimally required values cardinality
prop_card.val_cardinality = (3, None)
output = self._get_captured_output()
test_msg = "%s (minimum %s values, %s found)" % (self.msg_base, 3, 2)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test warning when setting maximally required values cardinality
prop_card.values = [1, 2, 3]
prop_card.val_cardinality = 2
output = self._get_captured_output()
test_msg = "%s (maximum %s values, %s found)" % (self.msg_base, 2, 3)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test no warning on valid cardinality
prop_card.val_cardinality = (1, 10)
output = self._get_captured_output()
self.assertEqual(output, [])
# Test no warning when setting cardinality to None
prop_card.val_cardinality = None
output = self._get_captured_output()
self.assertEqual(output, [])
# -- Test cardinality validation warnings on values updates
# Test warning when violating minimally required values cardinality
prop_card.val_cardinality = (3, None)
prop_card.values = [1, 2]
output = self._get_captured_output()
test_msg = "%s (minimum %s values, %s found)" % (self.msg_base, 3, 2)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test warning when violating maximally required values cardinality
prop_card.val_cardinality = (None, 2)
prop_card.values = [1, 2, 3]
output = self._get_captured_output()
test_msg = "%s (maximum %s values, %s found)" % (self.msg_base, 2, 3)
self.assertEqual(len(output), 1)
self.assertIn(test_msg, output[0])
# Test no warning when setting correct number of values
prop_card.values = [1, 2]
output = self._get_captured_output()
self.assertEqual(output, [])
# Test no warning when setting values to None
prop_card.values = None
output = self._get_captured_output()
self.assertEqual(output, [])
