How to use the circus.shared.files.load_data function in circus

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github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
N_total         = params.getint('data', 'N_total')
    sampling_rate   = params.getint('data', 'sampling_rate')
    do_temporal_whitening = params.getboolean('whitening', 'temporal')
    do_spatial_whitening  = params.getboolean('whitening', 'spatial')
    spike_thresh     = params.getfloat('detection', 'spike_thresh')
    file_out_suff    = params.get('data', 'file_out_suff')
    N_t              = params.getint('detection', 'N_t')
    nodes, edges     = get_nodes_and_edges(params)
    chunk_size       = N_t
    
    if do_spatial_whitening:
        spatial_whitening  = load_data(params, 'spatial_whitening')
    if do_temporal_whitening:
        temporal_whitening = load_data(params, 'temporal_whitening')

    thresholds       = load_data(params, 'thresholds')    
    
    try:
        result    = load_data(params, 'results')
    except Exception:
        result    = {'spiketimes' : {}, 'amplitudes' : {}}

    curve     = numpy.zeros((len(triggers), len(result['spiketimes'].keys()), lims[1]+lims[0]), dtype=numpy.int32)
    count     = 0
    
    for count, t_spike in enumerate(triggers):
        for key in result['spiketimes'].keys():
            elec  = int(key.split('_')[1])
            idx   = numpy.where((result['spiketimes'][key] > t_spike - lims[0]) & (result['spiketimes'][key] <  t_spike + lims[0]))
            curve[count, elec, t_spike - result['spiketimes'][key][idx]] += 1
    pylab.subplot(111)
    pylab.imshow(numpy.mean(curve, 0), aspect='auto')
github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
do_spatial_whitening  = params.getboolean('whitening', 'spatial')
    spike_thresh     = params.getfloat('detection', 'spike_thresh')
    file_out_suff    = params.get('data', 'file_out_suff')
    N_t              = params.getint('detection', 'N_t')
    nodes, edges     = get_nodes_and_edges(params)
    chunk_size       = N_t
    
    if do_spatial_whitening:
        spatial_whitening  = load_data(params, 'spatial_whitening')
    if do_temporal_whitening:
        temporal_whitening = load_data(params, 'temporal_whitening')

    thresholds       = load_data(params, 'thresholds')    
    
    try:
        result    = load_data(params, 'results')
    except Exception:
        result    = {'spiketimes' : {}, 'amplitudes' : {}}

    curve     = numpy.zeros((len(triggers), len(result['spiketimes'].keys()), lims[1]+lims[0]), dtype=numpy.int32)
    count     = 0
    
    for count, t_spike in enumerate(triggers):
        for key in result['spiketimes'].keys():
            elec  = int(key.split('_')[1])
            idx   = numpy.where((result['spiketimes'][key] > t_spike - lims[0]) & (result['spiketimes'][key] <  t_spike + lims[0]))
            curve[count, elec, t_spike - result['spiketimes'][key][idx]] += 1
    pylab.subplot(111)
    pylab.imshow(numpy.mean(curve, 0), aspect='auto') 
    return curve
github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
N_e             = params.getint('data', 'N_e')
    N_t             = params.getint('detection', 'N_t')
    N_total         = params.nb_channels
    sampling_rate   = params.rate
    do_temporal_whitening = params.getboolean('whitening', 'temporal')
    do_spatial_whitening  = params.getboolean('whitening', 'spatial')
    spike_thresh     = params.getfloat('detection', 'spike_thresh')
    file_out_suff    = params.get('data', 'file_out_suff')
    template_shift   = params.getint('detection', 'template_shift')
    nodes, edges     = get_nodes_and_edges(params)
    chunk_size       = (t_stop - t_start)*sampling_rate
    padding          = (t_start*sampling_rate, t_start*sampling_rate)
    suff             = params.get('data', 'suffix')

    if do_spatial_whitening:
        spatial_whitening  = load_data(params, 'spatial_whitening')
    if do_temporal_whitening:
        temporal_whitening = load_data(params, 'temporal_whitening')

    thresholds       = load_data(params, 'thresholds')
    data = data_file.get_data(0, chunk_size, padding=padding, chunk_size=chunk_size, nodes=nodes)
    data_shape = len(data)

    data_file.close()
    if do_spatial_whitening:
        data = numpy.dot(data, spatial_whitening)
    if do_temporal_whitening:
        data = scipy.ndimage.filters.convolve1d(data, temporal_whitening, axis=0, mode='constant')

    try:
        result    = load_data(params, 'results')
    except Exception:
github spyking-circus / spyking-circus / circus / shared / algorithms.py View on Github external
def delete_mixtures(params, nb_cpu, nb_gpu, use_gpu):

    data_file      = params.data_file
    N_e            = params.getint('data', 'N_e')
    N_total        = params.nb_channels
    N_t            = params.getint('detection', 'N_t')
    template_shift = params.getint('detection', 'template_shift')
    cc_merge       = params.getfloat('clustering', 'cc_merge')
    mixtures       = []
    to_remove      = []

    filename         = params.get('data', 'file_out_suff') + '.overlap-mixtures.hdf5'
    norm_templates   = load_data(params, 'norm-templates')
    best_elec        = load_data(params, 'electrodes')
    limits           = load_data(params, 'limits')
    nodes, edges     = get_nodes_and_edges(params)
    inv_nodes        = numpy.zeros(N_total, dtype=numpy.int32)
    inv_nodes[nodes] = numpy.arange(len(nodes))
    decimation       = params.getboolean('clustering', 'decimation')

    overlap = get_overlaps(params, extension='-mixtures', erase=True, normalize=False, maxoverlap=False, verbose=False, half=True, use_gpu=use_gpu, nb_cpu=nb_cpu, nb_gpu=nb_gpu, decimation=decimation)
    overlap.close()

    SHARED_MEMORY = get_shared_memory_flag(params)

    if SHARED_MEMORY:
        c_overs    = load_data_memshared(params, 'overlaps', extension='-mixtures', use_gpu=use_gpu, nb_cpu=nb_cpu, nb_gpu=nb_gpu)
    else:
        c_overs    = load_data(params, 'overlaps', extension='-mixtures')
github spyking-circus / spyking-circus / circus / shared / algorithms.py View on Github external
N_e            = params.getint('data', 'N_e')
    N_t            = params.getint('data', 'N_t')
    cc_merge       = params.getfloat('clustering', 'cc_merge')
    x,        N_tm = templates.shape
    nb_temp        = N_tm/2
    merged         = [nb_temp, 0]
    mixtures       = []
    to_remove      = []

    overlap  = get_overlaps(comm, params, extension='-mixtures', erase=True, parallel_hdf5=parallel_hdf5, normalize=False, maxoverlap=False, verbose=False, half=True)
    filename = params.get('data', 'file_out_suff') + '.overlap-mixtures.hdf5'
    result   = []
    
    norm_templates   = load_data(params, 'norm-templates')
    templates        = load_data(params, 'templates')
    result           = load_data(params, 'clusters')
    best_elec        = load_data(params, 'electrodes')
    limits           = load_data(params, 'limits')
    N_total          = params.getint('data', 'N_total')
    nodes, edges     = get_nodes_and_edges(params)
    inv_nodes        = numpy.zeros(N_total, dtype=numpy.int32)
    inv_nodes[nodes] = numpy.argsort(nodes)

    distances = numpy.zeros((nb_temp, nb_temp), dtype=numpy.float32)

    over_x     = overlap.get('over_x')[:]
    over_y     = overlap.get('over_y')[:]
    over_data  = overlap.get('over_data')[:]
    over_shape = overlap.get('over_shape')[:]
    overlap.close()

    overlap    = scipy.sparse.csr_matrix((over_data, (over_x, over_y)), shape=over_shape)
github spyking-circus / spyking-circus / circus / shared / algorithms.py View on Github external
best_elec        = load_data(params, 'electrodes')
    limits           = load_data(params, 'limits')
    nodes, edges     = get_nodes_and_edges(params)
    inv_nodes        = numpy.zeros(N_total, dtype=numpy.int32)
    inv_nodes[nodes] = numpy.arange(len(nodes))
    decimation       = params.getboolean('clustering', 'decimation')

    overlap = get_overlaps(params, extension='-mixtures', erase=True, normalize=False, maxoverlap=False, verbose=False, half=True, use_gpu=use_gpu, nb_cpu=nb_cpu, nb_gpu=nb_gpu, decimation=decimation)
    overlap.close()

    SHARED_MEMORY = get_shared_memory_flag(params)

    if SHARED_MEMORY:
        c_overs    = load_data_memshared(params, 'overlaps', extension='-mixtures', use_gpu=use_gpu, nb_cpu=nb_cpu, nb_gpu=nb_gpu)
    else:
        c_overs    = load_data(params, 'overlaps', extension='-mixtures')

    if SHARED_MEMORY:
        templates  = load_data_memshared(params, 'templates', normalize=False)
    else:
        templates  = load_data(params, 'templates')

    x,        N_tm = templates.shape
    nb_temp        = int(N_tm//2)
    merged         = [nb_temp, 0]

    supports = {}
    for t in range(N_e):
        elecs = numpy.take(inv_nodes, edges[nodes[t]])
        supports[t] = elecs

    overlap_0 = numpy.zeros(nb_temp, dtype=numpy.float32)
github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
# print("tprs: {}".format(tprs))
    ##### end temporary zone
    
    fpers = load_data(params, 'false-positive-error-rates')
    fners = load_data(params, 'false-negative-error-rates')
    ##### TODO: remove temporary zone
    # print("fpers: {}".format(fpers))
    # print("fners: {}".format(fners))
    ##### end temporary zone
    fpers = 100.0 * fpers
    fners = 100.0 * fners
    
    ##### TODO: clean temporary zone
    # res = None
    # error = None
    sc_fpers = load_data(params, 'sc-false-positive-error-rates')
    sc_fners = load_data(params, 'sc-false-negative-error-rates')
    sc_fper = load_data(params, 'sc-best-false-positive-error-rate')
    sc_fner = load_data(params, 'sc-best-false-negative-error-rate')
    selection = load_data(params, 'selection')
    ##### TODO: remove temporary zone
    # print("sc_fpers: {}".format(sc_fpers))
    # print("sc_fners: {}".format(sc_fners))
    # print("sc_fper: {}".format(sc_fper))
    # print("sc_fner: {}".format(sc_fner))
    # print("selection: {}".format(selection))
    ##### end temporary zone
    sc_fpers = 100.0 * sc_fpers
    sc_fners = 100.0 * sc_fners
    sc_fper = 100.0 * sc_fper
    sc_fner = 100.0 * sc_fner
    ##### end temporary zone
github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
def view_roc_curve_(params, save=None):
    '''Plot ROC curve.'''
    
    fprs = load_data(params, 'false-positive-rates')
    tprs = load_data(params, 'true-positive-rates')
    ##### TODO: remove temporary zone
    # print("fprs: {}".format(fprs))
    # print("tprs: {}".format(tprs))
    ##### end temporary zone
    
    fpers = load_data(params, 'false-positive-error-rates')
    fners = load_data(params, 'false-negative-error-rates')
    ##### TODO: remove temporary zone
    # print("fpers: {}".format(fpers))
    # print("fners: {}".format(fners))
    ##### end temporary zone
    fpers = 100.0 * fpers
    fners = 100.0 * fners
    
    ##### TODO: clean temporary zone
github spyking-circus / spyking-circus / circus / shared / algorithms.py View on Github external
templates      = load_data(params, 'templates')
    N_e            = params.getint('data', 'N_e')
    N_t            = params.getint('data', 'N_t')
    cc_merge       = params.getfloat('clustering', 'cc_merge')
    x,        N_tm = templates.shape
    nb_temp        = N_tm/2
    merged         = [nb_temp, 0]
    mixtures       = []
    to_remove      = []

    overlap  = get_overlaps(comm, params, extension='-mixtures', erase=True, parallel_hdf5=parallel_hdf5, normalize=False, maxoverlap=False, verbose=False, half=True)
    filename = params.get('data', 'file_out_suff') + '.overlap-mixtures.hdf5'
    result   = []
    
    norm_templates   = load_data(params, 'norm-templates')
    templates        = load_data(params, 'templates')
    result           = load_data(params, 'clusters')
    best_elec        = load_data(params, 'electrodes')
    limits           = load_data(params, 'limits')
    N_total          = params.getint('data', 'N_total')
    nodes, edges     = get_nodes_and_edges(params)
    inv_nodes        = numpy.zeros(N_total, dtype=numpy.int32)
    inv_nodes[nodes] = numpy.argsort(nodes)

    distances = numpy.zeros((nb_temp, nb_temp), dtype=numpy.float32)

    over_x     = overlap.get('over_x')[:]
    over_y     = overlap.get('over_y')[:]
    over_data  = overlap.get('over_data')[:]
    over_shape = overlap.get('over_shape')[:]
    overlap.close()
github spyking-circus / spyking-circus / circus / shared / plot.py View on Github external
def view_roc_curve_(params, save=None):
    '''Plot ROC curve.'''
    
    fprs = load_data(params, 'false-positive-rates')
    tprs = load_data(params, 'true-positive-rates')
    ##### TODO: remove temporary zone
    # print("fprs: {}".format(fprs))
    # print("tprs: {}".format(tprs))
    ##### end temporary zone
    
    fpers = load_data(params, 'false-positive-error-rates')
    fners = load_data(params, 'false-negative-error-rates')
    ##### TODO: remove temporary zone
    # print("fpers: {}".format(fpers))
    # print("fners: {}".format(fners))
    ##### end temporary zone
    fpers = 100.0 * fpers
    fners = 100.0 * fners
    
    ##### TODO: clean temporary zone