Python core.Block类代码示例

    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])

    def read_block(self, lazy=False, group=None, reader=None):
        """
        Read a Block from the file

        :param lazy: Enables lazy reading
        :param group: HDF5 Group representing the block in NSDF model tree (optional)
        :param reader: NSDFReader instance (optional)
        :return: Read block
        """
        assert not lazy, 'Do not support lazy'

        block = Block()
        group, reader = self._select_first_container(group, reader, 'block')

        if group is None:
            return None

        attrs = group.attrs

        self._read_block_children(block, group, reader)
        block.create_many_to_one_relationship()

        self._read_container_metadata(attrs, block)

        return block

    def read_block(self, lazy=False, cascade=True, channel_index=None):
        """
        Arguments:
            Channel_index: can be int, iterable or None to select one, many or all channel(s)

        """

        blk = Block()
        if cascade:
            seg = Segment(file_origin=self._filename)
            blk.segments += [seg]

            if channel_index:
                if type(channel_index) is int:
                    channel_index = [channel_index]
                if type(channel_index) is list:
                    channel_index = np.array(channel_index)
            else:
                channel_index = np.arange(0, self._attrs["shape"][1])

            chx = ChannelIndex(name="all channels", index=channel_index)
            blk.channel_indexes.append(chx)

            ana = self.read_analogsignal(channel_index=channel_index, lazy=lazy, cascade=cascade)
            ana.channel_index = chx
            seg.duration = (self._attrs["shape"][0] / self._attrs["kwik"]["sample_rate"]) * pq.s

            # neo.tools.populate_RecordingChannel(blk)
        blk.create_many_to_one_relationship()
        return blk

 def _block_to_neo(self, nix_block):
     neo_attrs = self._nix_attr_to_neo(nix_block)
     neo_block = Block(**neo_attrs)
     neo_block.rec_datetime = datetime.fromtimestamp(
         nix_block.created_at
     )
     self._neo_map[nix_block.name] = neo_block
     return neo_block

def proc_dam(filename):
    '''Load an dam file that has already been processed by the official matlab
    file converter.  That matlab data is saved to an m-file, which is then
    converted to a numpy '.npz' file.  This numpy file is the file actually
    loaded.  This function converts it to a neo block and returns the block.
    This block can be compared to the block produced by BrainwareDamIO to
    make sure BrainwareDamIO is working properly

    block = proc_dam(filename)

    filename: The file name of the numpy file to load.  It should end with
    '*_dam_py?.npz'. This will be converted to a neo 'file_origin' property
    with the value '*.dam', so the filename to compare should fit that pattern.
    'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
    for the python 3 version of the numpy file.

    example: filename = 'file1_dam_py2.npz'
             dam file name = 'file1.dam'
    '''
    with np.load(filename) as damobj:
        damfile = damobj.items()[0][1].flatten()

    filename = os.path.basename(filename[:-12]+'.dam')

    signals = [res.flatten() for res in damfile['signal']]
    stimIndexes = [int(res[0, 0].tolist()) for res in damfile['stimIndex']]
    timestamps = [res[0, 0] for res in damfile['timestamp']]

    block = Block(file_origin=filename)

    chx = ChannelIndex(file_origin=filename,
                       index=np.array([0]),
                       channel_ids=np.array([1]),
                       channel_names=np.array(['Chan1'], dtype='S'))

    block.channel_indexes.append(chx)

    params = [res['params'][0, 0].flatten() for res in damfile['stim']]
    values = [res['values'][0, 0].flatten() for res in damfile['stim']]
    params = [[res1[0] for res1 in res] for res in params]
    values = [[res1 for res1 in res] for res in values]
    stims = [dict(zip(param, value)) for param, value in zip(params, values)]

    fulldam = zip(stimIndexes, timestamps, signals, stims)
    for stimIndex, timestamp, signal, stim in fulldam:
        sig = AnalogSignal(signal=signal*pq.mV,
                           t_start=timestamp*pq.d,
                           file_origin=filename,
                           sampling_period=1.*pq.s)
        segment = Segment(file_origin=filename,
                          index=stimIndex,
                          **stim)
        segment.analogsignals = [sig]
        block.segments.append(segment)

    block.create_many_to_one_relationship()

    return 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)
            
            # RC and RCG
            rc_list = [ ]
            for i, xml_rcg in  enumerate(root.find('anatomicalDescription').find('channelGroups').findall('group')):
                rcg = RecordingChannelGroup(name = 'Group {0}'.format(i))
                bl.recordingchannelgroups.append(rcg)
                for xml_rc in xml_rcg:
                    rc = RecordingChannel(index = int(xml_rc.text))
                    rc_list.append(rc)
                    rcg.recordingchannels.append(rc)
                    rc.recordingchannelgroups.append(rcg)
                rcg.channel_indexes = np.array([rc.index for rc in rcg.recordingchannels], dtype = int)
                rcg.channel_names = np.array(['Channel{0}'.format(rc.index) for rc in rcg.recordingchannels], dtype = 'S')
        
            # 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)
                rc_list[s].analogsignals.append(sig)
            
        bl.create_many_to_one_relationship()
        return bl

def proc_src(filename):
    '''Load an src file that has already been processed by the official matlab
    file converter.  That matlab data is saved to an m-file, which is then
    converted to a numpy '.npz' file.  This numpy file is the file actually
    loaded.  This function converts it to a neo block and returns the block.
    This block can be compared to the block produced by BrainwareSrcIO to
    make sure BrainwareSrcIO is working properly

    block = proc_src(filename)

    filename: The file name of the numpy file to load.  It should end with
    '*_src_py?.npz'. This will be converted to a neo 'file_origin' property
    with the value '*.src', so the filename to compare should fit that pattern.
    'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
    for the python 3 version of the numpy file.

    example: filename = 'file1_src_py2.npz'
             src file name = 'file1.src'
    '''
    with np.load(filename) as srcobj:
        srcfile = srcobj.items()[0][1]

    filename = os.path.basename(filename[:-12]+'.src')

    block = Block(file_origin=filename)

    NChannels = srcfile['NChannels'][0, 0][0, 0]
    side = str(srcfile['side'][0, 0][0])
    ADperiod = srcfile['ADperiod'][0, 0][0, 0]

    comm_seg = proc_src_comments(srcfile, filename)
    block.segments.append(comm_seg)

    rcg = proc_src_units(srcfile, filename)
    chan_nums = np.arange(NChannels, dtype='int')
    chan_names = []
    for i in chan_nums:
        name = 'Chan'+str(i)
        chan_names.append(name)
        chan = RecordingChannel(file_origin='filename',
                                name=name,
                                index=int(i))
        rcg.recordingchannels.append(chan)
    rcg.channel_indexes = chan_nums
    rcg.channel_names = np.array(chan_names, dtype='string_')
    block.recordingchannelgroups.append(rcg)

    for rep in srcfile['sets'][0, 0].flatten():
        proc_src_condition(rep, filename, ADperiod, side, block)

    block.create_many_to_one_relationship()

    return block

    def read_block(self, lazy=False, cascade=True):
        bl = Block()
        tankname = os.path.basename(self.dirname)
        bl.file_origin = tankname

        if not cascade : return bl

        for blockname in os.listdir(self.dirname):
            seg = self.read_segment(blockname, lazy, cascade)
            bl.segments.append(seg)

        bl.create_many_to_one_relationship()
        return bl

    def test__children(self):
        blk = Block(name='block1')
        blk.recordingchannelgroups = [self.rcg1]
        blk.create_many_to_one_relationship()

        self.assertEqual(self.rcg1._container_child_objects, ('Unit',))
        self.assertEqual(self.rcg1._data_child_objects, ('AnalogSignalArray',))
        self.assertEqual(self.rcg1._single_parent_objects, ('Block',))
        self.assertEqual(self.rcg1._multi_child_objects, ('RecordingChannel',))
        self.assertEqual(self.rcg1._multi_parent_objects, ())
        self.assertEqual(self.rcg1._child_properties, ())

        self.assertEqual(self.rcg1._single_child_objects,
                         ('Unit', 'AnalogSignalArray',))

        self.assertEqual(self.rcg1._container_child_containers, ('units',))
        self.assertEqual(self.rcg1._data_child_containers,
                         ('analogsignalarrays',))
        self.assertEqual(self.rcg1._single_child_containers,
                         ('units', 'analogsignalarrays'))
        self.assertEqual(self.rcg1._single_parent_containers, ('block',))
        self.assertEqual(self.rcg1._multi_child_containers,
                         ('recordingchannels',))
        self.assertEqual(self.rcg1._multi_parent_containers, ())

        self.assertEqual(self.rcg1._child_objects,
                         ('Unit', 'AnalogSignalArray', 'RecordingChannel'))
        self.assertEqual(self.rcg1._child_containers,
                         ('units', 'analogsignalarrays', 'recordingchannels'))
        self.assertEqual(self.rcg1._parent_objects, ('Block',))
        self.assertEqual(self.rcg1._parent_containers, ('block',))

        self.assertEqual(len(self.rcg1.children),
                         (len(self.units1) +
                          len(self.rchan1) +
                          len(self.sigarr1)))
        self.assertEqual(self.rcg1.children[0].name, self.unitnames1[0])
        self.assertEqual(self.rcg1.children[1].name, self.unitnames1[1])
        self.assertEqual(self.rcg1.children[2].name, self.sigarrnames1[0])
        self.assertEqual(self.rcg1.children[3].name, self.sigarrnames1[1])
        self.assertEqual(self.rcg1.children[4].name, self.rchannames1[0])
        self.assertEqual(self.rcg1.children[5].name, self.rchannames1[1])
        self.assertEqual(len(self.rcg1.parents), 1)
        self.assertEqual(self.rcg1.parents[0].name, 'block1')

        self.rcg1.create_many_to_one_relationship()
        self.rcg1.create_many_to_many_relationship()
        self.rcg1.create_relationship()
        assert_neo_object_is_compliant(self.rcg1)

 def read(self, lazy=False, cascade=True, **kargs):
     if Block in self.readable_objects:
         if hasattr(self, "read_all_blocks") and callable(getattr(self, "read_all_blocks")):
             return self.read_all_blocks(lazy=lazy, cascade=cascade, **kargs)
         return [self.read_block(lazy=lazy, cascade=cascade, **kargs)]
     elif Segment in self.readable_objects:
         bl = Block(name="One segment only")
         if not cascade:
             return bl
         seg = self.read_segment(lazy=lazy, cascade=cascade, **kargs)
         bl.segments.append(seg)
         bl.create_many_to_one_relationship()
         return [bl]
     else:
         raise NotImplementedError

 def read(self, lazy=False, **kargs):
     if lazy:
         assert self.support_lazy, 'This IO do not support lazy loading'
     if Block in self.readable_objects:
         if (hasattr(self, 'read_all_blocks') and
                 callable(getattr(self, 'read_all_blocks'))):
             return self.read_all_blocks(lazy=lazy, **kargs)
         return [self.read_block(lazy=lazy, **kargs)]
     elif Segment in self.readable_objects:
         bl = Block(name='One segment only')
         seg = self.read_segment(lazy=lazy, **kargs)
         bl.segments.append(seg)
         bl.create_many_to_one_relationship()
         return [bl]
     else:
         raise NotImplementedError

 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

    def test__construct_subsegment_by_unit(self):
        nb_seg = 3
        nb_unit = 7
        unit_with_sig = np.array([0, 2, 5])
        signal_types = ['Vm', 'Conductances']
        sig_len = 100

        # channelindexes
        chxs = [ChannelIndex(name='Vm',
                             index=unit_with_sig),
                ChannelIndex(name='Conductance',
                             index=unit_with_sig)]

        # Unit
        all_unit = []
        for u in range(nb_unit):
            un = Unit(name='Unit #%d' % u, channel_indexes=np.array([u]))
            assert_neo_object_is_compliant(un)
            all_unit.append(un)

        blk = Block()
        blk.channel_indexes = chxs
        for s in range(nb_seg):
            seg = Segment(name='Simulation %s' % s)
            for j in range(nb_unit):
                st = SpikeTrain([1, 2], units='ms',
                                t_start=0., t_stop=10)
                st.unit = all_unit[j]

            for t in signal_types:
                anasigarr = AnalogSignal(np.zeros((sig_len,
                                                        len(unit_with_sig))),
                                              units='nA',
                                              sampling_rate=1000.*pq.Hz,
                                              channel_indexes=unit_with_sig)
                seg.analogsignals.append(anasigarr)

        blk.create_many_to_one_relationship()
        for unit in all_unit:
            assert_neo_object_is_compliant(unit)
        for chx in chxs:
            assert_neo_object_is_compliant(chx)
        assert_neo_object_is_compliant(blk)

        # what you want
        newseg = seg.construct_subsegment_by_unit(all_unit[:4])
        assert_neo_object_is_compliant(newseg)

    def read_block(self, lazy=False, cascade=True, **kargs):
        """
        Reads a block from the raw data file "fname" generated
        with BrainWare
        """

        # there are no keyargs implemented to so far.  If someone tries to pass
        # them they are expecting them to do something or making a mistake,
        # neither of which should pass silently
        if kargs:
            raise NotImplementedError("This method does not have any " "argument implemented yet")
        self._fsrc = None

        block = Block(file_origin=self._filename)

        # if we aren't doing cascade, don't load anything
        if not cascade:
            return block

        # create the objects to store other objects
        rcg = RecordingChannelGroup(file_origin=self._filename)
        rchan = RecordingChannel(file_origin=self._filename, index=1, name="Chan1")

        # load objects into their containers
        rcg.recordingchannels.append(rchan)
        block.recordingchannelgroups.append(rcg)
        rcg.channel_indexes = np.array([1])
        rcg.channel_names = np.array(["Chan1"], dtype="S")

        # open the file
        with open(self._path, "rb") as fobject:
            # while the file is not done keep reading segments
            while True:
                seg = self._read_segment(fobject, lazy)
                # if there are no more Segments, stop
                if not seg:
                    break

                # store the segment and signals
                block.segments.append(seg)
                rchan.analogsignals.append(seg.analogsignals[0])

        # remove the file object
        self._fsrc = None

        block.create_many_to_one_relationship()
        return block

    def read_block(self, lazy=False, cascade=True, **kargs):
        '''
        Reads a block from the raw data file "fname" generated
        with BrainWare
        '''

        # there are no keyargs implemented to so far.  If someone tries to pass
        # them they are expecting them to do something or making a mistake,
        # neither of which should pass silently
        if kargs:
            raise NotImplementedError('This method does not have any '
                                      'arguments implemented yet')
        self._fsrc = None

        block = Block(file_origin=self._filename)

        # if we aren't doing cascade, don't load anything
        if not cascade:
            return block

        # create the objects to store other objects
        chx = ChannelIndex(file_origin=self._filename,
                                    channel_ids=np.array([1]),
                                    index=np.array([0]),
                                    channel_names=np.array(['Chan1'], dtype='S'))

        # load objects into their containers
        block.channel_indexes.append(chx)

        # open the file
        with open(self._path, 'rb') as fobject:
            # while the file is not done keep reading segments
            while True:
                seg = self._read_segment(fobject, lazy)
                # if there are no more Segments, stop
                if not seg:
                    break

                # store the segment and signals
                seg.analogsignals[0].channel_index = chx
                block.segments.append(seg)

        # remove the file object
        self._fsrc = None

        block.create_many_to_one_relationship()
        return block