Python Block.annotate方法代码示例

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
    def test_block_write(self):
        block = Block(name=self.rword(),
                      description=self.rsentence())
        self.write_and_compare([block])

        block.annotate(**self.rdict(5))
        self.write_and_compare([block])

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
    def read_block(self, lazy=False, cascade=True):

        if self.filename is not None:
            self.stfio_rec = stfio.read(self.filename)

        bl = Block()
        bl.description = self.stfio_rec.file_description
        bl.annotate(comment=self.stfio_rec.comment)
        try:
            bl.rec_datetime = self.stfio_rec.datetime
        except:
            bl.rec_datetime = None

        if not cascade:
            return bl

        dt = np.round(self.stfio_rec.dt * 1e-3, 9) * pq.s  # ms to s
        sampling_rate = 1.0/dt
        t_start = 0 * pq.s

        # iterate over sections first:
        for j, recseg in enumerate(self.stfio_rec[0]):
            seg = Segment(index=j)
            length = len(recseg)

            # iterate over channels:
            for i, recsig in enumerate(self.stfio_rec):
                name = recsig.name
                unit = recsig.yunits
                try:
                    pq.Quantity(1, unit)
                except:
                    unit = ''

                if lazy:
                    signal = pq.Quantity([], unit)
                else:
                    signal = pq.Quantity(recsig[j], unit)
                anaSig = AnalogSignal(signal, sampling_rate=sampling_rate,
                                      t_start=t_start, name=str(name),
                                      channel_index=i)
                if lazy:
                    anaSig.lazy_shape = length
                seg.analogsignals.append(anaSig)

            bl.segments.append(seg)
            t_start = t_start + length * dt

        bl.create_many_to_one_relationship()

        return bl

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
 def read_block(self,
                lazy = False,
                cascade = True,
                group = 0):
     blo = Block(name = 'test')
     if cascade:
         tree = getbyroute(self.pul.tree,[0,group])
         for i,child in enumerate(tree['children']):
             blo.segments.append(self.read_segment(group=group,series = i))
         annotations = tree['contents'].__dict__.keys()
         annotations.remove('readlist')
         for a in annotations:
             d = {a:str(tree['contents'].__dict__[a])}
             blo.annotate(**d)
     create_many_to_one_relationship(blo)
     return blo

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
    def test_context_write(self):
        neoblock = Block(name=self.rword(), description=self.rsentence())
        with NixIO(self.filename, "ow") as iofile:
            iofile.write_block(neoblock)

        nixfile = nix.File.open(self.filename, nix.FileMode.ReadOnly,
                                backend="h5py")
        self.compare_blocks([neoblock], nixfile.blocks)
        nixfile.close()

        neoblock.annotate(**self.rdict(5))
        with NixIO(self.filename, "rw") as iofile:
            iofile.write_block(neoblock)
        nixfile = nix.File.open(self.filename, nix.FileMode.ReadOnly,
                                backend="h5py")
        self.compare_blocks([neoblock], nixfile.blocks)
        nixfile.close()

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
    def create_all_annotated(cls):
        times = cls.rquant(1, pq.s)
        signal = cls.rquant(1, pq.V)
        blk = Block()
        blk.annotate(**cls.rdict(3))

        seg = Segment()
        seg.annotate(**cls.rdict(4))
        blk.segments.append(seg)

        asig = AnalogSignal(signal=signal, sampling_rate=pq.Hz)
        asig.annotate(**cls.rdict(2))
        seg.analogsignals.append(asig)

        isig = IrregularlySampledSignal(times=times, signal=signal,
                                        time_units=pq.s)
        isig.annotate(**cls.rdict(2))
        seg.irregularlysampledsignals.append(isig)

        epoch = Epoch(times=times, durations=times)
        epoch.annotate(**cls.rdict(4))
        seg.epochs.append(epoch)

        event = Event(times=times)
        event.annotate(**cls.rdict(4))
        seg.events.append(event)

        spiketrain = SpikeTrain(times=times, t_stop=pq.s, units=pq.s)
        d = cls.rdict(6)
        d["quantity"] = pq.Quantity(10, "mV")
        d["qarray"] = pq.Quantity(range(10), "mA")
        spiketrain.annotate(**d)
        seg.spiketrains.append(spiketrain)

        chx = ChannelIndex(name="achx", index=[1, 2], channel_ids=[0, 10])
        chx.annotate(**cls.rdict(5))
        blk.channel_indexes.append(chx)

        unit = Unit()
        unit.annotate(**cls.rdict(2))
        chx.units.append(unit)

        return blk

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]
    def read_block(self, lazy=False, cascade=True):

        header = self.read_header()
        version = header['fFileVersionNumber']

        bl = Block()
        bl.file_origin = os.path.basename(self.filename)
        bl.annotate(abf_version=str(version))

        # date and time
        if version < 2.:
            YY = 1900
            MM = 1
            DD = 1
            hh = int(header['lFileStartTime'] / 3600.)
            mm = int((header['lFileStartTime'] - hh * 3600) / 60)
            ss = header['lFileStartTime'] - hh * 3600 - mm * 60
            ms = int(np.mod(ss, 1) * 1e6)
            ss = int(ss)
        elif version >= 2.:
            YY = int(header['uFileStartDate'] / 10000)
            MM = int((header['uFileStartDate'] - YY * 10000) / 100)
            DD = int(header['uFileStartDate'] - YY * 10000 - MM * 100)
            hh = int(header['uFileStartTimeMS'] / 1000. / 3600.)
            mm = int((header['uFileStartTimeMS'] / 1000. - hh * 3600) / 60)
            ss = header['uFileStartTimeMS'] / 1000. - hh * 3600 - mm * 60
            ms = int(np.mod(ss, 1) * 1e6)
            ss = int(ss)
        bl.rec_datetime = datetime.datetime(YY, MM, DD, hh, mm, ss, ms)

        if not cascade:
            return bl

        # file format
        if header['nDataFormat'] == 0:
            dt = np.dtype('i2')
        elif header['nDataFormat'] == 1:
            dt = np.dtype('f4')

        if version < 2.:
            nbchannel = header['nADCNumChannels']
            head_offset = header['lDataSectionPtr'] * BLOCKSIZE + header[
                'nNumPointsIgnored'] * dt.itemsize
            totalsize = header['lActualAcqLength']
        elif version >= 2.:
            nbchannel = header['sections']['ADCSection']['llNumEntries']
            head_offset = header['sections']['DataSection'][
                'uBlockIndex'] * BLOCKSIZE
            totalsize = header['sections']['DataSection']['llNumEntries']

        data = np.memmap(self.filename, dt, 'r',
                         shape=(totalsize,), offset=head_offset)

        # 3 possible modes
        if version < 2.:
            mode = header['nOperationMode']
        elif version >= 2.:
            mode = header['protocol']['nOperationMode']

        if (mode == 1) or (mode == 2) or (mode == 5) or (mode == 3):
            # event-driven variable-length mode (mode 1)
            # event-driven fixed-length mode (mode 2 or 5)
            # gap free mode (mode 3) can be in several episodes

            # read sweep pos
            if version < 2.:
                nbepisod = header['lSynchArraySize']
                offset_episode = header['lSynchArrayPtr'] * BLOCKSIZE
            elif version >= 2.:
                nbepisod = header['sections']['SynchArraySection'][
                    'llNumEntries']
                offset_episode = header['sections']['SynchArraySection'][
                    'uBlockIndex'] * BLOCKSIZE
            if nbepisod > 0:
                episode_array = np.memmap(
                    self.filename, [('offset', 'i4'), ('len', 'i4')], 'r',
                    shape=nbepisod, offset=offset_episode)
            else:
                episode_array = np.empty(1, [('offset', 'i4'), ('len', 'i4')])
                episode_array[0]['len'] = data.size
                episode_array[0]['offset'] = 0

            # sampling_rate
            if version < 2.:
                sampling_rate = 1. / (header['fADCSampleInterval'] *
                                      nbchannel * 1.e-6) * pq.Hz
            elif version >= 2.:
                sampling_rate = 1.e6 / \
                    header['protocol']['fADCSequenceInterval'] * pq.Hz

            # construct block
            # one sweep = one segment in a block
            pos = 0
            for j in range(episode_array.size):
                seg = Segment(index=j)

                length = episode_array[j]['len']

                if version < 2.:
                    fSynchTimeUnit = header['fSynchTimeUnit']
#.........这里部分代码省略.........

# 需要导入模块: from neo.core import Block [as 别名]
# 或者: from neo.core.Block import annotate [as 别名]

#.........这里部分代码省略.........

            # step 4: compute the length (number of samples) of the channels
            chan_len = np.zeros(len(list_data), dtype = np.int)
            for ind_chan, list_blocks in enumerate(list_data):
                for ind_block in list_blocks:
                    chan_len[ind_chan] += count_samples(
                                          file_blocks[ind_block]['m_length'])

            # step 5: find channels for which data are available
            ind_valid_chan = np.nonzero(chan_len)[0]

            # step 6: load the data
            # TODO give the possibility to load data as AnalogSignalArrays
            for ind_chan in ind_valid_chan:
                list_blocks = list_data[ind_chan]
                ind = 0 # index in the data vector

                # read time stamp for the beginning of the signal
                form = '<l' # reading format
                ind_block = list_blocks[0]
                count = count_samples(file_blocks[ind_block]['m_length'])
                fid.seek(file_blocks[ind_block]['pos']+6+count*2)
                buf = fid.read(struct.calcsize(form))
                val = struct.unpack(form , buf)
                start_index = val[0]

                # WARNING: in the following blocks are read supposing taht they
                # are all contiguous and sorted in time. I don't know if it's
                # always the case. Maybe we should use the time stamp of each
                # data block to choose where to put the read data in the array.
                if not lazy:
                    temp_array = np.empty(chan_len[ind_chan], dtype = np.int16)
                    # NOTE: we could directly create an empty AnalogSignal and
                    # load the data in it, but it is much faster to load data
                    # in a temporary numpy array and create the AnalogSignals
                    # from this temporary array
                    for ind_block in list_blocks:
                        count = count_samples(
                                file_blocks[ind_block]['m_length'])
                        fid.seek(file_blocks[ind_block]['pos']+6)
                        temp_array[ind:ind+count] = \
                            np.fromfile(fid, dtype = np.int16, count = count)
                        ind += count

                sampling_rate = \
                    file_blocks[list_chan[ind_chan]]['m_SampleRate'] * pq.kHz
                t_start = (start_index / sampling_rate).simplified
                if lazy:
                    ana_sig = AnalogSignal([],
                                           sampling_rate = sampling_rate,
                                           t_start = t_start,
                                           name = file_blocks\
                                               [list_chan[ind_chan]]['m_Name'],
                                           file_origin = \
                                               os.path.basename(self.filename),
                                           units = pq.dimensionless)
                    ana_sig.lazy_shape = chan_len[ind_chan]
                else:
                    ana_sig = AnalogSignal(temp_array,
                                           sampling_rate = sampling_rate,
                                           t_start = t_start,
                                           name = file_blocks\
                                               [list_chan[ind_chan]]['m_Name'],
                                           file_origin = \
                                               os.path.basename(self.filename),
                                           units = pq.dimensionless)
# todo apibreak: create ChannelIndex for each signals
#                ana_sig.channel_index = \
#                            file_blocks[list_chan[ind_chan]]['m_numChannel']
                ana_sig.annotate(channel_name = \
                            file_blocks[list_chan[ind_chan]]['m_Name'])
                ana_sig.annotate(channel_type = \
                            file_blocks[list_chan[ind_chan]]['type_subblock'])
                seg.analogsignals.append(ana_sig)

        fid.close()

        if file_blocks[0]['m_TypeBlock'] == 'h': # this should always be true
            blck.rec_datetime = datetime.datetime(\
                file_blocks[0]['m_date_year'],
                file_blocks[0]['m_date_month'],
                file_blocks[0]['m_date_day'],
                file_blocks[0]['m_time_hour'],
                file_blocks[0]['m_time_minute'],
                file_blocks[0]['m_time_second'],
                10000 * file_blocks[0]['m_time_hsecond'])
                # the 10000 is here to convert m_time_hsecond from centisecond
                # to microsecond
            version = file_blocks[0]['m_version']
            blck.annotate(alphamap_version = version)
            if cascade:
                seg.rec_datetime = blck.rec_datetime.replace()
                # I couldn't find a simple copy function for datetime,
                # using replace without arguments is a twisted way to make a
                # copy
                seg.annotate(alphamap_version = version)
        if cascade:
            blck.create_many_to_one_relationship()

        return blck