def save_metadata(self):
trial_name = 'trial_{0:04d}'.format(self.trial_counter)
file_list = [f for f in os.listdir(self.data_dir) if f.startswith(trial_name)]
""" create a document """
doc = odml.Document()
""" create dataset section """
ds = odml.Section('datasets', 'dataset')
p = odml.Property('files', None)
ds.append(p)
for f in file_list:
p.append('{0:s}/{1:s}'.format(self.data_dir, f))
doc.append(ds)
for t in list(self.metadata_tabs.values()):
m = t.metadata()
if m.type == 'recording':
v = odml.Value(self.record_timestamp, dtype='datetime')
m.append(odml.Property('StartTime', v))
doc.append(m)
for cam_name, cam in list(self.cameras.items()):
s = odml.Section(cam_name,'hardware/camera')
if not cam.is_raspicam():
v = odml.Value(frames_per_second, unit="Hz")
s.append(odml.Property('Framerate', v))
for p, v in list(cam.get_properties().items()):
prop = odml.Property(p, v)
s.append(prop)
doc.append(s)
doc.append(self.event_list)
print(self.event_list)
from odml.tools.xmlparser import XMLWriter
writer = XMLWriter(doc)
writer.write_file('{0}/{1}.xml'.format(self.data_dir, trial_name))
def test_int(self):
v = odml.Value(value="123456789012345678901", dtype="int")
self.assertEqual(v.data, 123456789012345678901)
self.assertEqual(v.value, "123456789012345678901")
v = odml.Value(value="-123456789012345678901", dtype="int")
self.assertEqual(v.data, -123456789012345678901)
v = odml.Value(value="123.45", dtype="int")
self.assertEqual(v.data, 123)
def get_location(location):
if location == 'old':
loc = odml.Value(data='Inst. de Neurosciences Cognitives de la '
'Mediterranee (INCM), GLM, CNRS - Aix Marseille '
'Univ., Marseille, France',
dtype=odml.DType.string)
elif location == 'new':
loc = odml.Value(data='Inst. de Neurosciences de la Timone (INT), '
'UMR 7289, CNRS - Aix Marseille Univ., '
'Marseille, France',
dtype=odml.DType.string)
else:
loc = default_value(odml.DType.url)
return loc
def clicked_tag(self):
ts = str(datetime.now()).split('.')[0]
text, ok = QtWidgets.QInputDialog.getText(self, 'Tag data with Event', 'Enter tag comment:')
""" write tags into .xml (odML) file """
if ok:
tag_name = 'event_{0:02d}'.format(len(self.event_list))
e = odml.Section(tag_name, 'event')
e.append(odml.Property('timestamp', odml.Value(ts, dtype='datetime')))
e.append(odml.Property('comment', odml.Value(text, dtype='string')))
self.event_list.append(e)
""" write tags into the .dat file as pure text """
trial_info_filename = '{0:s}/trial_{1:04d}_info.dat'.format(self.data_dir, self.trial_counter)
with open(trial_info_filename, 'a') as f:
timestamp = datetime.now().strftime(("tag-time:" + "\t" + "%Y-%m-%d %H:%M:%S:%f")[:-3] + "\t" + text)
f.write(timestamp + '\n')
def test_dependence(self):
a = self.p
b = self.p
self.assertEqual(a, b)
a.value = odml.Value(5)
self.assertEqual(a, b)
self.assertEqual(a.value, b.value)
def test_8bit_binary(self):
data = ''.join([chr(i) for i in xrange(256)])
v = odml.Value(data, dtype="binary")
v.encoder = "base64"
b64_data = 'AAECAwQFBgcICQoLDA0ODxAREhMUFRYXGBkaGxwdHh8gISIjJCUmJygpKissLS4vMDEyMzQ1Njc4OTo7PD0+P0BBQkNERUZHSElKS0xNTk9QUVJTVFVWV1hZWltcXV5fYGFiY2RlZmdoaWprbG1ub3BxcnN0dXZ3eHl6e3x9fn+AgYKDhIWGh4iJiouMjY6PkJGSk5SVlpeYmZqbnJ2en6ChoqOkpaanqKmqq6ytrq+wsbKztLW2t7i5uru8vb6/wMHCw8TFxsfIycrLzM3Oz9DR0tPU1dbX2Nna29zd3t/g4eLj5OXm5+jp6uvs7e7v8PHy8/T19vf4+fr7/P3+/w=='
self.assertEqual(v.value, b64_data)
v.value = b64_data
self.assertEqual(v.data, data)
self.assertEqual(v.value, b64_data)
v.encoder = "quoted-printable"
qp_data = '=00=01=02=03=04=05=06=07=08=09\n=0B=0C\r=0E=0F=10=11=12=13=14=15=16=17=18=19=1A=1B=1C=1D=1E=1F !"#$%&\'()*+,-=\n./0123456789:;<=3D>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghijklmnopqrstuv=\nwxyz{|}~=7F=80=81=82=83=84=85=86=87=88=89=8A=8B=8C=8D=8E=8F=90=91=92=93=94=\n=95=96=97=98=99=9A=9B=9C=9D=9E=9F=A0=A1=A2=A3=A4=A5=A6=A7=A8=A9=AA=AB=AC=AD=\n=AE=AF=B0=B1=B2=B3=B4=B5=B6=B7=B8=B9=BA=BB=BC=BD=BE=BF=C0=C1=C2=C3=C4=C5=C6=\n=C7=C8=C9=CA=CB=CC=CD=CE=CF=D0=D1=D2=D3=D4=D5=D6=D7=D8=D9=DA=DB=DC=DD=DE=DF=\n=E0=E1=E2=E3=E4=E5=E6=E7=E8=E9=EA=EB=EC=ED=EE=EF=F0=F1=F2=F3=F4=F5=F6=F7=F8=\n=F9=FA=FB=FC=FD=FE=FF'
self.assertEqual(v.value, qp_data)
v.value = qp_data
self.assertEqual(v.data, data)
self.assertEqual(v.value, qp_data)
v.encoder = "hexadecimal"
hex_data = '000102030405060708090a0b0c0d0e0f101112131415161718191a1b1c1d1e1f202122232425262728292a2b2c2d2e2f303132333435363738393a3b3c3d3e3f404142434445464748494a4b4c4d4e4f505152535455565758595a5b5c5d5e5f606162636465666768696a6b6c6d6e6f707172737475767778797a7b7c7d7e7f808182838485868788898a8b8c8d8e8f909192939495969798999a9b9c9d9e9fa0a1a2a3a4a5a6a7a8a9aaabacadaeafb0b1b2b3b4b5b6b7b8b9babbbcbdbebfc0c1c2c3c4c5c6c7c8c9cacbcccdcecfd0d1d2d3d4d5d6d7d8d9dadbdcdddedfe0e1e2e3e4e5e6e7e8e9eaebecedeeeff0f1f2f3f4f5f6f7f8f9fafbfcfdfeff'
self.assertEqual(v.value, hex_data)
v.value = hex_data
self.assertEqual(v.data, data)
self.assertEqual(v.value, hex_data)
self.assertEqual(v.checksum, 'crc32$29058c73')
v.checksum = "md5"
self.assertEqual(v.checksum, 'md5$e2c865db4162bed963bfaa9ef6ac18f0')
v.encoder = ''
v.data = v.data[:127] # chrs > 128 cannot be converted to ascii
v.dtype = "string"
self.assertIsNone(v.encoder)
self.assertIsNone(v.checksum)
self.assertEqual(v.value, data[:127])
def test_pre_post_change(self):
res = []
func = lambda context: res.append(
(context.preChange, context.postChange))
odml.getImplementation().Value._Changed += func
a = odml.Value(1)
a.value = 2
odml.getImplementation().Value._Changed -= func
self.assertEqual(res, [(True, False), (False, True)])
def test_event_passing(self):
s = odml.Section(name="section")
v = odml.Value(1)
p = odml.Property(name="prop", value=v)
s.append(p)
v.data = 4
self.assertEqual(v._modified, [v])
self.assertEqual(p._modified, [v, p])
self.assertEqual(s._modified, [v, p, s])
self.assertEqual(v.data, 4)
def test_empty_binary(self):
v = odml.Value("", dtype="string")
v.dtype = "binary"
v.encoding = "base64"
self.assertIsNone(v.value)
v.encoding = "quoted-printable"
self.assertIsNone(v.value)
v.encoding = "hexadecimal"
self.assertIsNone(v.value)
self.assertEqual(v.checksum, 'crc32$00000000')
v.checksum = "md5"
self.assertEqual(v.checksum, 'md5$d41d8cd98f00b204e9800998ecf8427e')
def test_simple_events(self):
a = odml.Value(1)
a._value = 2
self.assertEqual(a.data, 2)
# modifying a protected attribute should not make a call,
# thus the _modified property won't be set
self.assertRaises(AttributeError, lambda: a._modified)
a.data = 3
self.assertEqual(a.data, 3)
self.assertIs(a._modified[0], a)
self.assertEqual(a._context.val, ("data", 3))
self.assertTrue(a._context.postChange)
def append(self, value):
"""
adds a value to the list of values
If *value* is not an odml.Value instance, such an instance will be created
given the addition function arguments (see :ref:`__init__` for their description).
If *value* is not an odml.Value instance and *unit*, *dtype* or *uncertainty* are
missing, the values will be copied from the last value in this properties
value-list if *copy_attributes* is True. If there is no value present to be
copied from, an IndexError will be raised.
"""
if not isinstance(value, odml_value.Value):
value = odml.Value(value)
self._values.append(value)
value._property = self
def __init__(self,
name,
value,
definition=None,
dependency=None,
dependency_value=None,
mapping=None):
"""
Create a new Property with one single or multiple values. If something is passed as value that
is not a Value object, the method will try to infer the values dtype from the type of the
parameter.
Example for a property with a single value
>>> Property("property1", odml.Value(2)) #or
>>> Property("property1", 2)
Example for a property with multiple values
>>> Property("property2", [odml.Value(data=1), odml.Value(data=2)]) #or
>>> Property("property2", [1, 2])
:param name: The mane of the property
:param value: Either a Value or some type a Value can be created from or a list of values.
:param definition: The definition of the property.
:param dependency: Another property this property depends on.
:param dependency_value: Dependency on a certain value.
:param mapping: Mapping information of the property.
"""
#TODO doc description for arguments
#TODO validate arguments
self._name = name
self._section = None
self._reset_values()
self.definition = definition
self.dependency = dependency
self.dependency_value = dependency_value
self._mapping = mapping
if isinstance(value, list):
for v in value:
if not isinstance(v, odml_value.Value):
v = odml.Value(v)
self.append(v)
elif value is not None:
self.append(value)
def fill_odml_with_xls(doc, xls, source_filename):
"""
"""
for d in xls:
prop_path = ':'.join([d['Path'], d['Property Name']])
prop = doc.get_property_by_path(prop_path)
if len(d['Value']) == 1 and len(prop.values) == 1:
prop.value.data = d['Value'][0]
prop.value.dtype = d['odML Data Type'][0]
prop.value.filename = source_filename
if len(d['Data Unit']) > 0:
prop.value.unit = d['Data Unit'][0]
if len(d['Data Uncertainty']) > 0:
prop.value.uncertainty = d['Data Uncertainty'][0]
elif len(d['Value']) > 1 and len(prop.values) == 1:
for i, v in enumerate(d['Value']):
if i == 0:
prop.value.data = v
prop.value.filename = source_filename
if len(d['Data Unit']) > 0:
prop.value.unit = d['Data Unit'][i]
if len(d['Data Uncertainty']) > 0:
prop.value.uncertainty = d['Data Uncertainty'][i]
else:
prop.values.append(
odml.Value(data=v,
dtype=d['odML Data Type'][i],
unit=d['Data Unit'][i]
if len(d['Data Unit']) > 0 else '',
uncertainty=d['Data Uncertainty']
if len(d['Data Uncertainty']) > 0 else '',
filename=source_filename))
elif len(prop.values) == len(d['Value']):
for i, v in enumerate(d['Value']):
prop.values[i].data = d['Value'][i]
prop.values[i].dtype = d['odML Data Type'][i]
prop.values[i].filename = source_filename
if len(d['Data Unit']) > 0:
prop.values[i].unit = d['Data Unit'][i]
if len(d['Data Uncertainty']) > 0:
prop.values[i].uncertainty = d['Data Uncertainty'][i]
def propcsv2odmltree(load_from, document):
"""
Writing odml properties within an csv to an odml tree.
"""
pdict = propcsv2dict(load_from)
for pname in pdict.keys():
values = []
for i in range(len(pdict[pname]['Value'])):
values.append(
odml.Value(data=pdict[pname]['Value'][i],
dtype=pdict[pname]['odML Data Type'][i],
unit=pdict[pname]['Data Unit'],
uncertainty=pdict[pname]['Data Uncertainty'],
definition=pdict[pname]['Value Definition']))
prop = document.get_property_by_path(pdict[pname]['Path 2 Property'])
prop.definition = pdict[pname]['Property Definition']
prop.values = values
def default_value(dtype, unit=None):
"""
Returns an odML Value with default data of the given DType
Args:
dtype (odml.DType):
DType of the default data
unit (string, optional):
Unit of the default data
Returns:
(odml.value.BaseValue):
odML Value with default data, dtype and unit
Note:
Valid DTypes: odml.DType.text, odml.DType.string, odml.DType.person,
odml.DType.url, odml.DType.binary, odml.DType.boolean, odml.DType.int,
odml.DType.date, odml.DType.datetime
"""
if dtype in [
odml.DType.text, odml.DType.string, odml.DType.person,
odml.DType.binary
]:
data = '-'
elif dtype == odml.DType.url:
data = 'file://-'
elif dtype == odml.DType.boolean:
data = False
elif dtype == odml.DType.int:
data = -1
elif dtype == odml.DType.float:
data = -1.0
elif dtype == odml.DType.date:
data = datetime.date(1111, 11, 11)
elif dtype == odml.DType.datetime:
data = datetime.datetime(1111, 11, 11, 11, 11, 11)
elif dtype == odml.DType.time:
data = datetime.time(11, 11, 11)
else:
raise TypeError('Unknown DType')
return odml.Value(data=data, dtype=dtype, unit=unit)
def create_value(self, content):
return odml.Value(content)
def test_independence(self):
a = self.p.clone()
b = self.p.clone()
self.assertEqual(a, b)
a.value = odml.Value(5)
self.assertNotEqual(a, b)
def test_value_float(self):
v = odml.Value(value="1.5", dtype="float")
self.assertEqual(v.data, 1.5)
def test_conversion_float_to_int(self):
v = odml.Value(value="1.5", dtype="float")
v.dtype = "int"
self.assertEqual(v.dtype, "int")
self.assertEqual(v.data, 1)
def test_conversion_int_to_float(self):
v = odml.Value(value="1", dtype="int")
v.dtype = "float" # change dtype
self.assertEqual(v.dtype, "float")
self.assertEqual(v.data, 1.0)
self.assertEqual(v.value, "1.0")
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 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 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
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=[
odml.Value(data="Arthur Philip Dent",
dtype=odml.DType.person),
odml.Value(data="Zaphod Beeblebrox",
dtype=odml.DType.person),
odml.Value(data="Tricia Marie McMillan",
dtype=odml.DType.person),
odml.Value(data="Ford Prefect", dtype=odml.DType.person)
],
definition="List of crew members names"))
parent.append(
odml.Property(name="NoCrewMembers",
value=odml.Value(data=4, dtype=odml.DType.int),
definition="Number of crew members"))
# SET NEW PARENT NODE
parent = doc['TheCrew']['Arthur Philip Dent']
def test_value_int(self):
v = odml.Value(value="1", dtype="int")
self.assertEqual(v.data, 1)
"""
popup menu action: reset property
"""
dst = prop.get_merged_equivalent().clone()
cmd = commands.ReplaceObject(obj=prop, repl=dst)
self.execute(cmd)
def set_value(self, widget, (prop, val)):
"""
popup menu action: set value
set the curr
"""
model, path, obj = self.popup_data
if val is None:
val = odml.Value("")
else:
val = val.clone()
if obj is prop:
obj = prop.values[0]
prop = obj._property
# first append, then remove to keep the constraint that a property
# will always hold at least one value
cmd = commands.Multiple(cmds=[
commands.AppendValue(obj=prop, val=val),
commands.DeleteObject(obj=obj)
])
self.execute(cmd)
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
