d2_path.py

import networkx as nx
from collections import Counter
import sys


""" Represent an udg path into a d2g graph
"""
class Path(list):

    def __init__(self, d2g):
        super(Path, self).__init__()
        self.d2g = d2g
        self.covering_variables = {x: 0 for x in self.d2g.barcode_edge_idxs.values()}
        self.covering_value = 0
        # a succession of Counter (multiset)
        self.barcode_order = []
        self.lcp_per_multiset = []
        self.barcode_score = 0
        self.size_score = 0

    def append(self, obj) -> None:
        lcp = self.d2g.get_lcp(obj)

        # Update the covering variables
        for barcode_edge in lcp.edges:
            edge_idx = self.d2g.barcode_edge_idxs[barcode_edge]
            if self.covering_variables[edge_idx] == 0:
                self.covering_value += 1
            self.covering_variables[edge_idx] += 1

        self._append_barcodes(lcp)

        super(Path, self).append(lcp)

    def _append_barcodes(self, lcp):
        set_idx = len(self.barcode_order) - 1
        remaining_barcodes = Counter(lcp.nodes)

        while set_idx >= 0:
            current_multiset = self.barcode_order[set_idx]
            intersection = remaining_barcodes & current_multiset

            if intersection == current_multiset:
                remaining_barcodes -= intersection
                self.lcp_per_multiset[set_idx].add(lcp)
                self.barcode_score += 1
            else:
                if len(intersection) == 0:
                    break
                # Split the multiset in two parts
                left = current_multiset - intersection
                right = intersection
                self.barcode_order[set_idx] = right
                self.barcode_order.insert(set_idx, left)
                # Split the lcp appearance
                self.lcp_per_multiset.insert(set_idx, self.lcp_per_multiset[set_idx].copy())
                self.lcp_per_multiset[set_idx+1].add(lcp)
                self.barcode_score += len(self.lcp_per_multiset[set_idx+1])
                # Update remaining barcodes
                remaining_barcodes -= intersection
                break
            set_idx -= 1

        if len(remaining_barcodes) > 0:
            self.barcode_order.append(remaining_barcodes)
            self.lcp_per_multiset.append({lcp})
            self.barcode_score += 1

    def pop(self, index=-1):
        if index != -1:
            print("Warning: pop on other values than -1 have side effects here. The code will be adapted soon", file=sys.stderr)
            exit(1)
        index = -1
        lcp = super(Path, self).pop(index)
        self._pop_barcodes(lcp)

        # Update the covering variables
        for barcode_edge in lcp.edges:
            edge_idx = self.d2g.barcode_edge_idxs[barcode_edge]
            self.covering_variables[edge_idx] -= 1
            if self.covering_variables[edge_idx] == 0:
                self.covering_value -= 1

        return lcp

    def _pop_barcodes(self, lcp):
        set_idx = len(self.barcode_order) - 1

        while set_idx >= 0 and lcp in self.lcp_per_multiset[set_idx]:
            lcp_list = self.lcp_per_multiset[set_idx]
            lcp_list.remove(lcp)
            self.barcode_score -= 1
            if len(lcp_list) == 0:
                self.lcp_per_multiset.pop(set_idx)
                self.barcode_order.pop(set_idx)
            set_idx -= 1

        if 0 <= set_idx < len(self.lcp_per_multiset) - 1 and self.lcp_per_multiset[set_idx] == self.lcp_per_multiset[set_idx+1]:
            rmv = self.lcp_per_multiset.pop(set_idx)
            self.barcode_score -= len(rmv)
            self.barcode_order[set_idx+1] += self.barcode_order[set_idx]
            self.barcode_order.pop(set_idx)

    def copy(self):
        copy = Path(self.d2g)

        # Copy the list
        for x in self:
            super(Path, copy).append(x)

        # Copy the variables
        for key, val in self.covering_variables.items():
            copy.covering_variables[key] = val
        copy.covering_value = self.covering_value

        # Copy barcode structures
        for lcp_list in self.lcp_per_multiset:
            copy.lcp_per_multiset.append(lcp_list.copy())
        for barcodes in self.barcode_order:
            copy.barcode_order.append(barcodes.copy())
        copy.barcode_score = self.barcode_score

        return copy

    def add_path(self, path):
        for lcp in path:
            self.append(lcp)

    def covering_score(self):
        return self.covering_value / len(self.covering_variables)

    def save_gexf(self, filename):
        d2p = nx.Graph()
        # Add the nodes
        for udg in self:
            d2p.add_node(udg.idx)
            d2p.nodes[udg.idx]["center"] = udg.center
            d2p.nodes[udg.idx]["udg"] = str(udg)
            d2p.nodes[udg.idx]["score"] = f"{udg.score}/{udg.get_optimal_score()}"
            barcode_edges = " ".join([str(self.d2g.barcode_edge_idxs[x]) for x in udg.edges])
            d2p.nodes[udg.idx]["barcode_edges"] = barcode_edges

        # add the edges
        for idx in range(len(self)-1):
            udg1 = self[idx]
            udg2 = self[idx+1]

            d2p.add_edge(udg1.idx, udg2.idx)

        nx.write_gexf(d2p, filename)