ConnectomeView

NodeSet

Set of nodes (each of which can contain single cells or lists of cells) to use in a ConnectomeView. An optional text description can be provided, and the color, shape, position or size of the NodeSets to use in graphical depictions can be set.

Source code in cect/ConnectomeView.py

class NodeSet:
    """Set of nodes (each of which can contain single cells or lists of cells) to use in a ``ConnectomeView``.
    An optional text `description` can be provided, and the `color`, `shape`, `position` or `size` of the NodeSets to use in graphical depictions can be set."""

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

    def is_one_cell(self):
        """
        Returns True if the NodeSet contains only one cell, and the name of the NodeSet is the same as that cell.
        """
        return len(self.cells) == 1 and self.name == self.cells[0]

    def __repr__(self):
        """
        Returns a string representation of the NodeSet, including its name, description, color, shape, position, and the list of cells it contains.
        """
        info = "NodeSet: %s" % self.name
        if self.description is not None:
            info += " (%s)" % self.description
        info += "\t"
        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):
        """
        Returns a HTML <span> element for use in markdown or HTML for a representation of the NodeSet, including its name colored by the set color.
        """
        return (
            f'<span style="color:{self.color};">{self.name}</span>'
            if self.color
            else self.name
        )

__repr__()

Returns a string representation of the NodeSet, including its name, description, color, shape, position, and the list of cells it contains.

Source code in cect/ConnectomeView.py

def __repr__(self):
    """
    Returns a string representation of the NodeSet, including its name, description, color, shape, position, and the list of cells it contains.
    """
    info = "NodeSet: %s" % self.name
    if self.description is not None:
        info += " (%s)" % self.description
    info += "\t"
    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

is_one_cell()

Returns True if the NodeSet contains only one cell, and the name of the NodeSet is the same as that cell.

Source code in cect/ConnectomeView.py

def is_one_cell(self):
    """
    Returns True if the NodeSet contains only one cell, and the name of the NodeSet is the same as that cell.
    """
    return len(self.cells) == 1 and self.name == self.cells[0]

to_markdown()

Returns a HTML element for use in markdown or HTML for a representation of the NodeSet, including its name colored by the set color.

Source code in cect/ConnectomeView.py

def to_markdown(self):
    """
    Returns a HTML <span> element for use in markdown or HTML for a representation of the NodeSet, including its name colored by the set color.
    """
    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,
        text_scale=1.0,
    ):
        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
        self.text_scale = text_scale  # scale for text size for nodes in plots etc.

    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