ConnectomeView

NONPHARYNGEAL_NEURONS_HERM_VIEW = View('NonpharyngealH', 'Nonpharyngeal Neurons (herm)', 'All **hermaphrodite** neurons except those in the pharynx', [], EXC_INH_GJ_FUNC_CONT_SYN_CLASSES, only_show_existing_nodes=False) module-attribute

NONPHARYNGEAL_NEURONS_HM_VIEW = View( "NonpharyngealHM", "Nonpharyngeal Neurons", "All neurons (herm. & male) except those in the pharynx", [], EXC_INH_GJ_FUNC_CONT_SYN_CLASSES, only_show_existing_nodes=False, )

NodeSet

Set of nodes (can be single cells or lists of cells) to use in a View. Can specify the color, shape, position or size to use in graphical depictions.

Source code in cect/ConnectomeView.py

class NodeSet:
    """Set of nodes (can be single cells or lists of cells) to use in a ``View``. Can specify the `color`, `shape`, `position` or `size` to use in graphical depictions."""

    def __init__(self, name, cells, color=None, shape=None, position=None, size=None):
        self.name = name
        self.color = color
        self.cells = cells
        self.shape = shape
        self.position = position
        self.size = size

    def is_one_cell(self):
        return len(self.cells) == 1 and self.name == self.cells[0]

    def __repr__(self):
        info = "NodeSet: %s\t(" % self.name
        if self.color is not None:
            info += "%s " % self.color
        if self.shape is not None:
            info += "%s " % self.shape
        if self.position is not None:
            info += "%s " % (str(self.position))
        info += "\t%s" % self.cells

        return info

    def to_markdown(self):
        return (
            f'<span style="color:{self.color};">{self.name}</span>'
            if self.color
            else self.name
        )

View

A view of a ConnectomeDataset specifying subsets of cells (or lists of cells) as NodeSets, e.g. can be used to just show the connections between the pharyngeal neurons in a whole connectome dataset, or to group the sensory neurons, interneuron, etc. together.

Source code in cect/ConnectomeView.py

class View:
    """A view of a ``ConnectomeDataset`` specifying subsets of cells (or lists of cells) as ``NodeSet``s, e.g. can be used to just show the connections between the pharyngeal neurons in a whole connectome dataset, or to group the sensory neurons, interneuron, etc. together."""

    def __init__(
        self,
        id,
        name,
        description,
        node_sets,
        synclass_sets={},
        colormap=DEFAULT_COLORMAP,
        only_show_existing_nodes=False,
    ):
        self.id = id
        self.name = name
        self.description = description
        self.node_sets = node_sets
        self.synclass_sets = synclass_sets
        self.colormap = colormap
        self.only_show_existing_nodes = only_show_existing_nodes

    def __repr__(self):
        info = "ConnectomeView: %s (%s)" % (
            self.name,
            self.id,
        )
        if self.description is not None:
            info += "\n  %s" % self.description
        for n in self.node_sets:
            info += "\n    %s" % n
        for s in self.synclass_sets:
            info += "\n    Synclass set: %s (%s)" % (s, self.synclass_sets[s])
        return info

    def to_markdown(self):
        info = "**%s** (%s)\n" % (
            self.name,
            self.id,
        )
        if self.description is not None:
            info += "_%s_\n\n" % self.description

        total_cells = sum([len(n.cells) for n in self.node_sets])
        info += f"| Nodes ({len(self.node_sets)} total)| Num cells in node | Cells ({total_cells} total)|\n| --- | --- | --- |\n"

        for n in self.node_sets:
            node_colored = f'<span style="color:{n.color};">{n.name}</span>'
            cells_linked = [
                get_cell_internal_link(
                    c, individual_cell_page=True, html=True, use_color=True
                )
                for c in n.cells
            ]
            info += "|**%s** |%i | %s|\n" % (
                node_colored,
                len(n.cells),
                ", ".join(cells_linked),
            )
        return info

    def has_color(self):
        for ns in self.node_sets:
            if ns.color is not None:
                return True
        return False

    def has_multicell_nodes(self):
        for ns in self.node_sets:
            if not ns.is_one_cell():
                return True
        return False

    def get_node_set(self, node_set_name):
        for ns in self.node_sets:
            if ns.name == node_set_name:
                return ns
        return None

    def get_index_of_cell(self, cell):
        for i in range(len(self.node_sets)):
            if cell in self.node_sets[i].cells:
                return i
        return -1