Source code for snudda.utils.reposition_neurons

import h5py




class RepositionNeurons(object):
    """ Reposition neurons in the network file. """

    def __init__(self, position_file):

        """ Constructor.

        Args:
            position_file : network position file
        """

        self.position_file = position_file
        self.hdf5_file = h5py.File(position_file, "r+")

        assert "synapses" not in self.hdf5_file["network"], "This code should not be used after detection."

    def __del__(self):
        self.close()



    def close(self):

        """ Close file."""

        if self.hdf5_file:
            self.hdf5_file.close()
            self.hdf5_file = None




    def place(self, neuron_id, position, rotation=None, verbose=True):

        """ Reposition neuron neuron_id to position with rotation.

        Args:
            neuron_id : Neuron ID affected
            position : New position of neuron
            rotation : New rotatoin of neuron
            verbose : Print info?
        """

        info = (f"Moving neuron {neuron_id} from {self.hdf5_file['network/neurons/position'][neuron_id]} "
                f"to {position}")
        if rotation is not None:
            info += f" setting rotation to {rotation}"

        if verbose:
            print(info)

        self.hdf5_file["network/neurons/position"][neuron_id] = position

        if rotation is not None:
            self.hdf5_file["network/neurons/rotation"][neuron_id] = rotation.reshape((9,))


    def set_morphology_id(self, neuron_id, morphology_id):

        raise DeprecationWarning("morpology_id is replaced by morphology_key ")

        """ Set morphologyID for neuron with neuron_id (neuron_id = None means all neurons) """
        if neuron_id is not None:
            self.hdf5_file["network/neurons/morphology_id"][neuron_id] = morphology_id
        else:
            self.hdf5_file["network/neurons/morphology_id"][:] = morphology_id



    def set_morphology_key(self, neuron_id, morphology_key):

        """ Set morphologyKey for neuron with neuron_id (neuron_id = None means all neurons) """
        if neuron_id is not None:
            self.hdf5_file["network/neurons/morphology_key"][neuron_id] = morphology_key
        else:
            self.hdf5_file["network/neurons/morphology_key"][:] = morphology_key




    def set_parameter_key(self, neuron_id, parameter_key):

        """ Set parameterKey for neuron with neuron_id (neuron_id = None means all neurons) """

        if neuron_id is not None:
            self.hdf5_file["network/neurons/parameter_key"][neuron_id] = parameter_key
        else:
            self.hdf5_file["network/neurons/parameter_key"][:] = parameter_key


    def set_parameter_id(self, neuron_id, parameter_id):

        raise DeprecationWarning("parameter_id is replaced by parameter_key")

        """ Set parameterID for neuron with neuron_id (neuron_id = None means all neurons) """

        if neuron_id is not None:
            self.hdf5_file["network/neurons/parameter_id"][neuron_id] = parameter_id
        else:
            self.hdf5_file["network/neurons/parameter_id"][:] = parameter_id

    def set_modulation_id(self, neuron_id, modulation_id):

        raise DeprecationWarning("modulation_id is replaced by modulation_key")

        """ Set modulationID for neuron with neuron_id (neuron_id = None means all neurons) """

        if neuron_id is not None:
            self.hdf5_file["network/neurons/modulation_id"][neuron_id] = modulation_id
        else:
            self.hdf5_file["network/neurons/modulation_id"][:] = modulation_id



    def set_modulation_key(self, neuron_id, modulation_key):

        """ Set modulationKey for neuron with neuron_id (neuron_id = None means all neurons) """

        if neuron_id is not None:
            self.hdf5_file["network/neurons/modulation_key"][neuron_id] = modulation_key
        else:
            self.hdf5_file["network/neurons/modulation_key"][:] = modulation_key