# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import itertools
import math
import numpy
from . import base_classes as _base_classes
from . import utils
from actin_dynamics.numerical import interpolation, measurements
from actin_dynamics import logger as _logger
_log = _logger.getLogger(__file__)
class PyreneSEM(_base_classes.Analysis):
def __init__(self, sample_period=None, stop_time=None, label=None,
**kwargs):
self.sample_period = float(sample_period)
self.stop_time = float(stop_time)
self.weights = dict((k, float(v)) for k, v in kwargs.iteritems())
_base_classes.Analysis.__init__(self, label=label, **kwargs)
def perform(self, simulation_results, result_factory):
pyrene_measurements = [self._get_pyrene_measurements(s)
for s in simulation_results]
resulting_measurement = _calculate_concentration_sem(pyrene_measurements)
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
from .base_classes import Objective as _Objective
from actin_dynamics.numerical import residuals as _residuals
from actin_dynamics.numerical import interpolation as _interpolation
from actin_dynamics.numerical import measurements as _measurements
import itertools as _itertools
from actin_dynamics import logger
log = logger.getLogger(__file__)
class SimpleDataFit(_Objective):
def __init__(self,
measurement=None,
residual_type=None,
interpolate_simulation=False,
label=None,
skip_beginning=0,
scale_simulation_by=1):
self.residual_function = getattr(_residuals, residual_type)
self.measurement_name = measurement
self.interpolate_simulation = bool(interpolate_simulation)
self.scale_simulation_by = float(scale_simulation_by)
self.skip_beginning = float(skip_beginning)
