def test_channel_index_write(self):
block = Block(name=self.rword())
chx = ChannelIndex(name=self.rword(),
description=self.rsentence(),
index=[1, 2, 3, 5, 8, 13])
block.channel_indexes.append(chx)
self.write_and_compare([block])
chx.annotate(**self.rdict(3))
self.write_and_compare([block])
chx.channel_names = ["one", "two", "three", "five", "eight", "xiii"]
self.write_and_compare([block])
def read_block(self,
lazy = False,
cascade = True,
):
"""
"""
tree = ElementTree.parse(self.filename)
root = tree.getroot()
acq = root.find('acquisitionSystem')
nbits = int(acq.find('nBits').text)
nbchannel = int(acq.find('nChannels').text)
sampling_rate = float(acq.find('samplingRate').text)*pq.Hz
voltage_range = float(acq.find('voltageRange').text)
#offset = int(acq.find('offset').text)
amplification = float(acq.find('amplification').text)
bl = Block(file_origin = os.path.basename(self.filename).replace('.xml', ''))
if cascade:
seg = Segment()
bl.segments.append(seg)
# RCG
for i, xml_chx in enumerate(root.find('anatomicalDescription').find('channelGroups').findall('group')):
n_channels = len(xml_chx)
chx = ChannelIndex(name='Group {0}'.format(i),
index=np.arange(n_channels, dtype = int))
chx.channel_ids = np.array([int(xml_rc.text) for xml_rc in xml_chx])
chx.channel_names = np.array(['Channel{0}'.format(id) for id in chx.channel_ids], dtype = 'S')
bl.channel_indexes.append(chx)
# AnalogSignals
reader = RawBinarySignalIO(filename = self.filename.replace('.xml', '.dat'))
seg2 = reader.read_segment(cascade = True, lazy = lazy,
sampling_rate = sampling_rate,
t_start = 0.*pq.s,
unit = pq.V, nbchannel = nbchannel,
bytesoffset = 0,
dtype = np.int16 if nbits<=16 else np.int32,
rangemin = -voltage_range/2.,
rangemax = voltage_range/2.,)
for s, sig in enumerate(seg2.analogsignals):
if not lazy:
sig /= amplification
sig.segment = seg
seg.analogsignals.append(sig)
chx.analogsignals.append(sig)
bl.create_many_to_one_relationship()
return bl
def test_channel_index_write(self):
block = Block(name=self.rword())
chx = ChannelIndex(name=self.rword(),
description=self.rsentence(),
index=[1, 2, 3, 5, 8, 13])
block.channel_indexes.append(chx)
self.write_and_compare([block])
chx.annotate(**self.rdict(3))
self.write_and_compare([block])
chx.channel_names = ["one", "two", "three", "five",
"eight", "xiii"]
self.write_and_compare([block])
def test_channel_index_write(self):
block = Block(name=self.rword())
chx = ChannelIndex(name=self.rword(),
description=self.rsentence(),
channel_ids=[10, 20, 30, 50, 80, 130],
index=[1, 2, 3, 5, 8, 13])
block.channel_indexes.append(chx)
self.write_and_compare([block])
chx.annotate(**self.rdict(3))
self.write_and_compare([block])
chx.channel_names = ["one", "two", "three", "five", "eight", "xiii"]
chx.coordinates = self.rquant((6, 3), pq.um)
self.write_and_compare([block])
# add an empty channel index and check again
newchx = ChannelIndex(np.array([]))
block.channel_indexes.append(newchx)
self.write_and_compare([block])
