def __getattr__(self, name):
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
if TraceMethodCtrl.has_method(self.__class__, name):
func = TraceMethodCtrl.get_method(self.__class__, name)
return functools.partial(func, self)
raise AttributeError('No Such method for trace type: %s.%s'
% (self.__class__.__name__, name))
def __getattr__(self, name):
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
if TraceMethodCtrl.has_method(self.__class__, name):
func = TraceMethodCtrl.get_method(self.__class__, name)
return functools.partial(func, self)
raise AttributeError('No Such method for trace type: %s.%s' %
(self.__class__.__name__, name))
def __getattr__(self, name):
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
if TraceMethodCtrl.has_method(self.__class__, name):
func = TraceMethodCtrl.get_method(self.__class__, name)
return functools.partial(func, self)
available_methods = ','.join( [s[1] for s in TraceMethodCtrl.registered_methods.keys()] )
raise AttributeError('No Such method for trace type: %s.%s (Maybe:%s)'
% (self.__class__.__name__, name,available_methods))
from morphforge.traces.traceobjpluginctrl import copy_trace_attrs
# Shifting:
#############
def _shift_pt_trace(trace, offset):
tr_type = type(trace)
tr_new = tr_type(
time=trace.time_pts + offset,
data=trace.data_pts,)
copy_trace_attrs(trace, tr_new, comment='+(Shifted %2.2f)' % offset)
return tr_new
TraceMethodCtrl.register(TraceFixedDT, 'shift', _shift_pt_trace)
TraceMethodCtrl.register(TraceVariableDT, 'shift', _shift_pt_trace)
# Windowing:
###############
def _window_fixed_trace(trace, time_window):
# Dirty Pre-processing
if isinstance(time_window, Quantity):
assert len(time_window) == 2
time_window = (time_window[0], time_window[1])
# print time_window, type(time_window)
from morphforge.traces.tracetypes import TraceVariableDT
from morphforge.traces.tracetypes import TracePiecewise
from morphforge.traces.tracetypes import TraceFixedDT
def _get_piecewise_linear_points(tr):
x_unit = tr.pieces[0].get_min_time().units
y_unit = tr.pieces[0].get_start_value().units
x_points = []
y_points = []
for piece in tr.pieces:
x_points.append(float(piece.get_min_time().rescale(x_unit).magnitude))
x_points.append(float(piece.get_max_time().rescale(x_unit).magnitude))
y_points.append(
float(piece.get_start_value().rescale(y_unit).magnitude))
y_points.append(float(piece.get_end_value().rescale(y_unit).magnitude))
return (np.array(x_points) * x_unit, np.array(y_points) * y_unit)
# Plotting:
TraceMethodCtrl.register(TraceFixedDT, 'plotpoints', lambda tr:
(tr.time_pts, tr.data_pts))
TraceMethodCtrl.register(TraceVariableDT, 'plotpoints', lambda tr:
(tr.time_pts, tr.data_pts))
TraceMethodCtrl.register(TracePiecewise, 'plotpoints',
_get_piecewise_linear_points)
def _fft(tr, normalise=True):
fft_values = np.fft.fft(tr.data_pts)
if normalise:
fft_values /= fft_values.max()
dt_in_s = tr.get_dt_new().rescale('s').magnitude
ftfreq = np.fft.fftfreq(tr.data_pts.size, dt_in_s)
return (ftfreq, fft_values)
def _psd(tr, normalise=True):
fft_values = np.fft.fft(tr.data_pts)
fft_values = fft_values.real()**2 + fft_values.imag()**2
if normalise:
fft_values /= fft_values.max()
dt_in_s = tr.get_dt_new().rescale('s').magnitude
ftfreq = np.fft.fftfreq(tr.data_pts.size, dt_in_s)
return (ftfreq, fft_values)
TraceMethodCtrl.register(TraceFixedDT,
'fft',
_fft,
can_fallback_to_fixed_trace=True)
TraceMethodCtrl.register(TraceFixedDT,
'psd',
_psd,
can_fallback_to_fixed_trace=True)
import numpy as np
from morphforge.traces.tracetypes import TraceVariableDT
from morphforge.traces.tracetypes import TracePiecewise
from morphforge.traces.tracetypes import TraceFixedDT
import copy
def _clone_fixed(tr):
tr_new = TraceFixedDT(
time = np.copy( tr.time_pts_np) * tr.time_units,
data = np.copy( tr.data_pts_np) * tr.data_units )
copy_trace_attrs(tr, tr_new, comment='+(cloned)')
return tr_new
def _clone_variable(tr):
tr_new = TraceVariableDT(
time = np.copy( tr.time_pts_np) * tr.time_units,
data = np.copy( tr.data_pts_np) * tr.data_units )
copy_trace_attrs(tr, tr_new, comment='+(cloned)')
return tr_new
def _clone_piecewise(tr):
tr_new = TracePiecewise(pieces = [copy.copy(piece) for piece in tr.pieces])
copy_trace_attrs(tr, tr_new, comment='+(cloned)')
return tr_new
TraceMethodCtrl.register(TraceFixedDT, 'clone', _clone_fixed)
TraceMethodCtrl.register(TraceVariableDT, 'clone', _clone_variable)
TraceMethodCtrl.register(TracePiecewise, 'clone', _clone_piecewise)
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
import numpy as np
from morphforge.traces.tracetypes import TraceVariableDT
from morphforge.traces.tracetypes import TracePiecewise
from morphforge.traces.tracetypes import TraceFixedDT
def _get_piecewise_linear_points(tr):
x_unit = tr.pieces[0].get_min_time().units
y_unit = tr.pieces[0].get_start_value().units
x_points = []
y_points = []
for piece in tr.pieces:
x_points.append(float(piece.get_min_time().rescale(x_unit).magnitude))
x_points.append(float(piece.get_max_time().rescale(x_unit).magnitude))
y_points.append(float(piece.get_start_value().rescale(y_unit).magnitude))
y_points.append(float(piece.get_end_value().rescale(y_unit).magnitude))
return (np.array(x_points) * x_unit, np.array(y_points) * y_unit)
# Plotting:
TraceMethodCtrl.register(TraceFixedDT, 'plotpoints', lambda tr: (tr.time_pts, tr.data_pts))
TraceMethodCtrl.register(TraceVariableDT, 'plotpoints', lambda tr: (tr.time_pts, tr.data_pts))
TraceMethodCtrl.register(TracePiecewise, 'plotpoints', _get_piecewise_linear_points)
# Shifting:
#############
def _shift_pt_trace(trace, offset):
tr_type = type(trace)
tr_new = tr_type(
time=trace.time_pts + offset,
data=trace.data_pts,
)
copy_trace_attrs(trace, tr_new, comment='+(Shifted %2.2f)' % offset)
return tr_new
TraceMethodCtrl.register(TraceFixedDT, 'shift', _shift_pt_trace)
TraceMethodCtrl.register(TraceVariableDT, 'shift', _shift_pt_trace)
# Windowing:
###############
def _window_fixed_trace(trace, time_window):
# Dirty Pre-processing
if isinstance(time_window, Quantity):
assert len(time_window) == 2
time_window = (time_window[0], time_window[1])
# print time_window, type(time_window)
def _butterworthfilter(tr, filterorder, cutoff_frequency):
cutoff_frequency.rescale('Hz')
import scipy.signal
frequency_hz = 1 / float(tr.get_dt_new().rescale('s'))
n_frq_hz = frequency_hz / 2.0
cuttoff_norm = cutoff_frequency / n_frq_hz
(coeff_num, coeff_denom) = scipy.signal.filter_design.butter(filterorder, cuttoff_norm)
filteredsignal = scipy.signal.lfilter(coeff_num, coeff_denom, tr.data_pts_np)
tr_new = TraceFixedDT(time=tr.time_pts, data=filteredsignal * tr.data_unit,)
copy_trace_attrs(tr, tr_new, comment="+(Butterworth Filtered)" )
return tr_new
TraceMethodCtrl.register(TraceFixedDT, 'filterbutterworth', _butterworthfilter, can_fallback_to_fixed_trace=True)
def _besselfilter(tr, filterorder, cutoff_frequency):
cutoff_frequency.rescale('Hz')
import scipy.signal
frequency_hz = 1 / float(tr.get_dt_new().rescale('s'))
n_frq_hz = frequency_hz / 2.0
cuttoff_norm = cutoff_frequency / n_frq_hz
(coeff_num, coeff_denom) = scipy.signal.filter_design.bessel(filterorder, cuttoff_norm)
filteredsignal = scipy.signal.lfilter(coeff_num, coeff_denom, tr.data_pts_np)
time_shift = tr.get_dt_new() * max(len(coeff_denom), len(coeff_num))
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl, copy_trace_attrs
from morphforge.traces import TraceFixedDT, TraceVariableDT, TracePiecewise
import numpy as np
# Mean, rms, stddev, variance functions:
##############################
# For FixedDT traces, these are simple:
TraceMethodCtrl.register(TraceFixedDT, 'mean', lambda tr: np.mean(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, 'stddev',
lambda tr: np.std(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, 'var', lambda tr: np.var(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, 'rms',
lambda tr: np.sqrt(np.mean(tr.data_pts**2)))
# For VariableDT traces
def _variabledt_mean(tr):
import scipy.integrate
# Calculate the mean with simpsons rule:
integral = scipy.integrate.simps(y=tr.data_pts_np, x=tr.time_pts_s)
mean = integral / tr.get_duration().rescale('s').magnitude * tr.data_unit
return mean
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
from morphforge.traces import TraceFixedDT
import numpy as np
def _fft(tr, normalise=True):
fft_values = np.fft.fft(tr.data_pts)
if normalise:
fft_values /= fft_values.max()
dt_in_s = tr.get_dt_new().rescale('s').magnitude
ftfreq = np.fft.fftfreq(tr.data_pts.size, dt_in_s)
return (ftfreq, fft_values)
def _psd(tr, normalise=True):
fft_values = np.fft.fft(tr.data_pts)
fft_values = fft_values.real() ** 2 + fft_values.imag() ** 2
if normalise:
fft_values /= fft_values.max()
dt_in_s = tr.get_dt_new().rescale('s').magnitude
ftfreq = np.fft.fftfreq(tr.data_pts.size, dt_in_s)
return (ftfreq, fft_values)
TraceMethodCtrl.register(TraceFixedDT, 'fft', _fft, can_fallback_to_fixed_trace=True)
TraceMethodCtrl.register(TraceFixedDT, 'psd', _psd, can_fallback_to_fixed_trace=True)
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
from morphforge.traces import TraceFixedDT
from morphforge.traces.tracetypes import TracePiecewise, PieceWiseComponentVisitor
def _integrate_pointbased(tr, ):
import scipy.integrate
return scipy.integrate.simps(y=tr.data_pts_np, x=tr.time_pts_np) * tr.data_unit * tr.time_unit
TraceMethodCtrl.register(TraceFixedDT, 'integrate', _integrate_pointbased)
class PiecewiseIntegrator(PieceWiseComponentVisitor):
@classmethod
def visit_linear(cls, o):
return 0.5 * (o.time_window[1]-o.time_window[0]) * (o.x1-o.x0)
@classmethod
def visit_flat(cls, o ):
return (o.time_window[1]-o.time_window[0]) * o.x
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.traces.traceobjpluginctrl import copy_trace_attrs
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
from morphforge.traces import TraceFixedDT
from morphforge.traces import TraceVariableDT
from morphforge.traces import TracePiecewise
from MMtrace_conversion import TraceConverter, TraceApproximator
# Conversion to: FixedDT:
#########################
TraceMethodCtrl.register(
TraceFixedDT, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(
tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
TraceMethodCtrl.register(
TraceVariableDT, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(
tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
TraceMethodCtrl.register(
TracePiecewise, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(
tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
# Conversion to VariableDT:
###########################
TraceMethodCtrl.register(
TraceFixedDT, 'convert_to_variable', lambda tr, eps: copy_trace_attrs(
tr_old=tr,
tr_new=TraceConverter.reduce_to_variable_dt_trace(original_trace=tr,
epsilon=eps)))
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl, copy_trace_attrs
from morphforge.traces import TraceFixedDT, TraceVariableDT, TracePiecewise
import numpy as np
# Mean, rms, stddev, variance functions:
##############################
# For FixedDT traces, these are simple:
TraceMethodCtrl.register(TraceFixedDT, "mean", lambda tr: np.mean(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, "stddev", lambda tr: np.std(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, "var", lambda tr: np.var(tr.data_pts))
TraceMethodCtrl.register(TraceFixedDT, "rms", lambda tr: np.sqrt(np.mean(tr.data_pts ** 2)))
# For VariableDT traces
def _variabledt_mean(tr):
import scipy.integrate
# Calculate the mean with simpsons rule:
integral = scipy.integrate.simps(y=tr.data_pts_np, x=tr.time_pts_s)
mean = integral / tr.get_duration().rescale("s").magnitude * tr.data_unit
return mean
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.traces.traceobjpluginctrl import copy_trace_attrs
from morphforge.traces.traceobjpluginctrl import TraceMethodCtrl
from morphforge.traces import TraceFixedDT
from morphforge.traces import TraceVariableDT
from morphforge.traces import TracePiecewise
from MMtrace_conversion import TraceConverter, TraceApproximator
# Conversion to: FixedDT:
#########################
TraceMethodCtrl.register(TraceFixedDT, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
TraceMethodCtrl.register(TraceVariableDT, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
TraceMethodCtrl.register(TracePiecewise, 'convert_to_fixed', lambda tr, dt: copy_trace_attrs(tr_old=tr, tr_new=TraceConverter.rebase_to_fixed_dt(tr, dt)))
# Conversion to VariableDT:
###########################
TraceMethodCtrl.register(
TraceFixedDT,
'convert_to_variable',
lambda tr, eps: copy_trace_attrs(tr_old=tr, tr_new=TraceConverter.reduce_to_variable_dt_trace(original_trace=tr, epsilon=eps)))
TraceMethodCtrl.register(
TraceVariableDT,
from morphforge.traces import TraceFixedDT
#import numpy as np
#import quantities as pq
#import operator
from morphforge.traces.tracetypes import TracePiecewise, PieceWiseComponentVisitor
#from morphforge.traces.tracetypes.tracepiecewise import TracePieceFunctionLinear
#from morphforge.traces.tracetypes.tracepiecewise import TracePieceFunctionFlat
def _integrate_pointbased(tr, ):
import scipy.integrate
return scipy.integrate.simps(
y=tr.data_pts_np, x=tr.time_pts_np) * tr.data_unit * tr.time_unit
TraceMethodCtrl.register(TraceFixedDT, 'integrate', _integrate_pointbased)
class PiecewiseIntegrator(PieceWiseComponentVisitor):
@classmethod
def visit_linear(cls, o):
return 0.5 * (o.time_window[1] - o.time_window[0]) * (o.x1 - o.x0)
@classmethod
def visit_flat(cls, o):
return (o.time_window[1] - o.time_window[0]) * o.x
def _integrate_piecewise(tr):
pieces = [PiecewiseIntegrator.visit(piece) for piece in tr.pieces]
tot = None
