def configure(self, time_series, sw, sp): """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. :param time_series: the input time-series for which fcd matrix should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window """ """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. """ self.input_shape = time_series.read_data_shape() log_debug_array(self.log, time_series, "time_series") actual_sp = float(sp) / time_series.sample_period actual_sw = float(sw) / time_series.sample_period actual_ts_length = self.input_shape[0] if actual_sw >= actual_ts_length or actual_sp >= actual_ts_length or actual_sp >= actual_sw: raise LaunchException( "Spanning (Sp) and Sliding (Sw) window size parameters need to be less than the TS length, " "and Sp < Sw. After calibration with sampling period, current values are: Sp=%d, Sw=%d, Ts=%d). " "Please configure valid input parameters." % (actual_sp, actual_sw, actual_ts_length)) # -------------------- Fill Algorithm for Analysis -------------------## self.algorithm = FcdCalculator(time_series=time_series, sw=sw, sp=sp)
def configure(self, time_series, sw, sp): """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. :param time_series: the input time-series for which fcd matrix should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window """ """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. """ self.input_shape = time_series.read_data_shape() log_debug_array(self.log, time_series, "time_series") ##-------------------- Fill Algorithm for Analysis -------------------## self.algorithm = FcdCalculator(time_series=time_series, sw=sw, sp=sp)
def get_input_tree(self): """ Return a list of lists describing the interface to the analyzer. This is used by the GUI to generate the menus and fields necessary for defining a simulation. """ algorithm = FcdCalculator() algorithm.trait.bound = self.INTERFACE_ATTRIBUTES_ONLY tree = algorithm.interface[self.INTERFACE_ATTRIBUTES] tree[0]['conditions'] = FilterChain( fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[4]) return tree
class FunctionalConnectivityDynamicsAdapter(ABCAsynchronous): """ TVB adapter for calling the Pearson CrossCorrelation algorithm. """ _ui_name = "FCD matrix" _ui_description = "Functional Connectivity Dynamics metric" _ui_subsection = "fcd_calculator" def get_input_tree(self): """ Return a list of lists describing the interface to the analyzer. This is used by the GUI to generate the menus and fields necessary for defining a simulation. """ algorithm = FcdCalculator() algorithm.trait.bound = self.INTERFACE_ATTRIBUTES_ONLY tree = algorithm.interface[self.INTERFACE_ATTRIBUTES] tree[0]['conditions'] = FilterChain( fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[4]) return tree def get_output(self): return [Fcd, ConnectivityMeasure] def configure(self, time_series, sw, sp): """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. :param time_series: the input time-series for which fcd matrix should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window """ """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. """ self.input_shape = time_series.read_data_shape() log_debug_array(self.log, time_series, "time_series") ##-------------------- Fill Algorithm for Analysis -------------------## self.algorithm = FcdCalculator(time_series=time_series, sw=sw, sp=sp) def get_required_memory_size(self, **kwargs): # We do not know how much memory is needed. return -1 def get_required_disk_size(self, **kwargs): return 0 def launch(self, time_series, sw, sp): """ Launch algorithm and build results. :param time_series: the input time-series for which correlation coefficient should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window :returns: the fcd matrix for the given time-series, with that sw and that sp :rtype: `Fcd`,`ConnectivityMeasure` """ result = [ ] # where fcd, fcd_segmented (eventually), and connectivity measures will be stored [fcd, fcd_segmented, eigvect_dict, eigval_dict, Connectivity] = self.algorithm.evaluate() # Create a Fcd dataType object. result_fcd = Fcd(storage_path=self.storage_path, source=time_series, sw=sw, sp=sp) result_fcd.array_data = fcd result.append(result_fcd) if np.amax(fcd_segmented) == 1.1: result_fcd_segmented = Fcd(storage_path=self.storage_path, source=time_series, sw=sw, sp=sp) result_fcd_segmented.array_data = fcd_segmented result.append(result_fcd_segmented) for mode in eigvect_dict.keys(): for var in eigvect_dict[mode].keys(): for ep in eigvect_dict[mode][var].keys(): for eig in range(3): result_eig = ConnectivityMeasure( storage_path=self.storage_path) result_eig.connectivity = Connectivity result_eig.array_data = eigvect_dict[mode][var][ep][ eig] result_eig.title = "Epoch # %d, \n eigenvalue = %s,\n variable = %s,\n mode = %s." % ( ep, eigval_dict[mode][var][ep][eig], var, mode) result.append(result_eig) return result
class FunctionalConnectivityDynamicsAdapter(ABCAsynchronous): """ TVB adapter for calling the Pearson CrossCorrelation algorithm. """ _ui_name = "FCD matrix" _ui_description = "Functional Connectivity Dynamics metric" _ui_subsection = "fcd_calculator" def get_input_tree(self): """ Return a list of lists describing the interface to the analyzer. This is used by the GUI to generate the menus and fields necessary for defining a simulation. """ algorithm = FcdCalculator() algorithm.trait.bound = self.INTERFACE_ATTRIBUTES_ONLY tree = algorithm.interface[self.INTERFACE_ATTRIBUTES] tree[0]['conditions'] = FilterChain(fields=[FilterChain.datatype + '._nr_dimensions'], operations=["=="], values=[4]) return tree def get_output(self): return [Fcd, ConnectivityMeasure] def configure(self, time_series, sw, sp): """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. :param time_series: the input time-series for which fcd matrix should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window """ """ Store the input shape to be later used to estimate memory usage. Also create the algorithm instance. """ self.input_shape = time_series.read_data_shape() log_debug_array(self.log, time_series, "time_series") ##-------------------- Fill Algorithm for Analysis -------------------## self.algorithm = FcdCalculator(time_series=time_series, sw=sw, sp=sp) def get_required_memory_size(self, **kwargs): # We do not know how much memory is needed. return -1 def get_required_disk_size(self, **kwargs): return 0 def launch(self, time_series, sw, sp): """ Launch algorithm and build results. :param time_series: the input time-series for which correlation coefficient should be computed :param sw: length of the sliding window :param sp: spanning time: distance between two consecutive sliding window :returns: the fcd matrix for the given time-series, with that sw and that sp :rtype: `Fcd`,`ConnectivityMeasure` """ result = [] # where fcd, fcd_segmented (eventually), and connectivity measures will be stored [fcd, fcd_segmented, eigvect_dict, eigval_dict, Connectivity] = self.algorithm.evaluate() # Create a Fcd dataType object. result_fcd = Fcd(storage_path=self.storage_path, source=time_series, sw=sw, sp=sp) result_fcd.array_data = fcd result.append(result_fcd) if np.amax(fcd_segmented)==1.1 : result_fcd_segmented = Fcd(storage_path=self.storage_path, source=time_series, sw=sw, sp=sp) result_fcd_segmented.array_data = fcd_segmented result.append(result_fcd_segmented) for mode in eigvect_dict.keys(): for var in eigvect_dict[mode].keys(): for ep in eigvect_dict[mode][var].keys(): for eig in range(3): result_eig = ConnectivityMeasure(storage_path=self.storage_path) result_eig.connectivity = Connectivity result_eig.array_data = eigvect_dict[mode][var][ep][eig] result_eig.title = "Epoch # %d, \n eigenvalue = %s,\n variable = %s,\n mode = %s." % (ep,eigval_dict[mode][var][ep][eig], var, mode) result.append(result_eig) return result