cobra/sampling/hr_sampler.py
def generate_fva_warmup(self):
        """Generate the warmup points for the sampler.

        Generates warmup points by setting each flux as the sole objective
        and minimizing/maximizing it. Also caches the projection of the
        warmup points into the nullspace for non-homogeneous problems (only
        if necessary).

        """

        self.n_warmup = 0
        reactions = self.model.reactions
        self.warmup = np.zeros((2 * len(reactions), len(self.model.variables)))
        self.model.objective = Zero

        for sense in ("min", "max"):
            self.model.objective_direction = sense

            for i, r in enumerate(reactions):
                variables = (self.model.variables[self.fwd_idx[i]],
                             self.model.variables[self.rev_idx[i]])

                # Omit fixed reactions if they are non-homogeneous
                if r.upper_bound - r.lower_bound < self.bounds_tol:
                    LOGGER.info("skipping fixed reaction %s" % r.id)
                    continue

                self.model.objective.set_linear_coefficients(
                    {variables[0]: 1, variables[1]: -1})

                self.model.slim_optimize()

                if not self.model.solver.status == OPTIMAL:
                    LOGGER.info("can not maximize reaction %s, skipping it" %
                                r.id)
                    continue

                primals = self.model.solver.primal_values
                sol = [primals[v.name] for v in self.model.variables]
                self.warmup[self.n_warmup, ] = sol
                self.n_warmup += 1

                # Reset objective
                self.model.objective.set_linear_coefficients(
                    {variables[0]: 0, variables[1]: 0})

        # Shrink to measure
        self.warmup = self.warmup[0:self.n_warmup, :]

        # Remove redundant search directions
        keep = np.logical_not(self._is_redundant(self.warmup))
        self.warmup = self.warmup[keep, :]
        self.n_warmup = self.warmup.shape[0]

        # Catch some special cases
        if len(self.warmup.shape) == 1 or self.warmup.shape[0] == 1:
            raise ValueError("Your flux cone consists only of a single point!")
        elif self.n_warmup == 2:
            if not self.problem.homogeneous:
                raise ValueError("Can not sample from an inhomogenous problem"
                                 " with only 2 search directions :(")
            LOGGER.info("All search directions on a line, adding another one.")
            newdir = self.warmup.T.dot([0.25, 0.25])
            self.warmup = np.vstack([self.warmup, newdir])
            self.n_warmup += 1

        # Shrink warmup points to measure
        self.warmup = shared_np_array(
            (self.n_warmup, len(self.model.variables)), self.warmup)
def generate_fva_warmup(self):
        """Generate the warmup points for the sampler.

        Generates warmup points by setting each flux as the sole objective
        and minimizing/maximizing it. Also caches the projection of the
        warmup points into the nullspace for non-homogeneous problems (only
        if necessary).

        """

        self.n_warmup = 0
        reactions = self.model.reactions
        self.warmup = np.zeros((2 * len(reactions), len(self.model.variables)))
        self.model.objective = Zero

        for sense in ("min", "max"):
            self.model.objective_direction = sense

            for i, r in enumerate(reactions):
                variables = (self.model.variables[self.fwd_idx[i]],
                             self.model.variables[self.rev_idx[i]])

                # Omit fixed reactions if they are non-homogeneous
                if r.upper_bound - r.lower_bound < self.bounds_tol:
                    LOGGER.info("skipping fixed reaction %s" % r.id)
                    continue

                self.model.objective.set_linear_coefficients(
                    {variables[0]: 1, variables[1]: -1})

                self.model.slim_optimize()

                if not self.model.solver.status == OPTIMAL:
                    LOGGER.info("can not maximize reaction %s, skipping it" %
                                r.id)
                    continue

                primals = self.model.solver.primal_values
                sol = [primals[v.name] for v in self.model.variables]
                self.warmup[self.n_warmup, ] = sol
                self.n_warmup += 1

                # Reset objective
                self.model.objective.set_linear_coefficients(
                    {variables[0]: 0, variables[1]: 0})

        # Shrink to measure
        self.warmup = self.warmup[0:self.n_warmup, :]

        # Remove redundant search directions
        keep = np.logical_not(self._is_redundant(self.warmup))
        self.warmup = self.warmup[keep, :]
        self.n_warmup = self.warmup.shape[0]

        # Catch some special cases
        if len(self.warmup.shape) == 1 or self.warmup.shape[0] == 1:
            raise ValueError("Your flux cone consists only of a single point!")
        elif self.n_warmup == 2:
            if not self.problem.homogeneous:
                raise ValueError("Can not sample from an inhomogenous problem"
                                 " with only 2 search directions :(")
            LOGGER.info("All search directions on a line, adding another one.")
            newdir = self.warmup.T.dot([0.25, 0.25])
            self.warmup = np.vstack([self.warmup, newdir])
            self.n_warmup += 1

        # Shrink warmup points to measure
        self.warmup = shared_np_array(
            (self.n_warmup, len(self.model.variables)), self.warmup)
def generate_fva_warmup ( self ) : self . n_warmup = 0 reactions = self . model . reactions self . warmup = np . zeros ( ( 2 * len ( reactions ) , len ( self . model . variables ) ) ) self . model . objective = Zero for sense in ( "min" , "max" ) : self . model . objective_direction = sense for i , r in enumerate ( reactions ) : variables = ( self . model . variables [ self . fwd_idx [ i ] ] , self . model . variables [ self . rev_idx [ i ] ] ) # Omit fixed reactions if they are non-homogeneous if r . upper_bound - r . lower_bound < self . bounds_tol : LOGGER . info ( "skipping fixed reaction %s" % r . id ) continue self . model . objective . set_linear_coefficients ( { variables [ 0 ] : 1 , variables [ 1 ] : - 1 } ) self . model . slim_optimize ( ) if not self . model . solver . status == OPTIMAL : LOGGER . info ( "can not maximize reaction %s, skipping it" % r . id ) continue primals = self . model . solver . primal_values sol = [ primals [ v . name ] for v in self . model . variables ] self . warmup [ self . n_warmup , ] = sol self . n_warmup += 1 # Reset objective self . model . objective . set_linear_coefficients ( { variables [ 0 ] : 0 , variables [ 1 ] : 0 } ) # Shrink to measure self . warmup = self . warmup [ 0 : self . n_warmup , : ] # Remove redundant search directions keep = np . logical_not ( self . _is_redundant ( self . warmup ) ) self . warmup = self . warmup [ keep , : ] self . n_warmup = self . warmup . shape [ 0 ] # Catch some special cases if len ( self . warmup . shape ) == 1 or self . warmup . shape [ 0 ] == 1 : raise ValueError ( "Your flux cone consists only of a single point!" ) elif self . n_warmup == 2 : if not self . problem . homogeneous : raise ValueError ( "Can not sample from an inhomogenous problem" " with only 2 search directions :(" ) LOGGER . info ( "All search directions on a line, adding another one." ) newdir = self . warmup . T . dot ( [ 0.25 , 0.25 ] ) self . warmup = np . vstack ( [ self . warmup , newdir ] ) self . n_warmup += 1 # Shrink warmup points to measure self . warmup = shared_np_array ( ( self . n_warmup , len ( self . model . variables ) ) , self . warmup )
Generate the warmup points for the sampler.

        Generates warmup points by setting each flux as the sole objective
        and minimizing/maximizing it. Also caches the projection of the
        warmup points into the nullspace for non-homogeneous problems (only
        if necessary).
Generate the warmup points for the sampler .