Skip to content

ConnectomeView

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 
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
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

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 
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
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
        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