How to use the histomicstk.annotations_and_masks.masks_to_annotations_handler._parse_annot_coords function in histomicstk

def _merge_leafs(self, leafs):
        nest_polygons = []
        for leaf in leafs:
            leafidx = int(leaf.split('polygon-')[1])
            nest = dict(self.contours_slice.loc[leafidx, :])
            coords = _parse_annot_coords(nest)
            nest_polygons.append(Polygon(coords))
        return self._merge_polygons(nest_polygons)

# Nests of the same label. The nest IDs are using the index of the
        # roi dataframe from the edge_nests dictionary
        Nests1 = _get_nests_slice(1)
        Nests2 = _get_nests_slice(2)

        # to avoid redoing things, keep all polygons in a list
        polygons1 = []
        nno1 = 0
        nno1Max = Nests1.shape[0]
        for nid1, nest1 in Nests1.iterrows():
            nno1 += 1
            self._print2("%s: edge1-nest %d of %d" % (
                monitorPrefix, nno1, nno1Max))
            try:
                coords = np.array(_parse_annot_coords(nest1))
                coords[:, 0] = coords[:, 0] + self.roiinfos[
                    edgepair['roi1-name']]['left']
                coords[:, 1] = coords[:, 1] + self.roiinfos[
                    edgepair['roi1-name']]['top']
                polygons1.append((nid1, Polygon(coords)))
            except Exception as e:
                self._print2(
                    "%s: edge1-nest %d of %d: Shapely Error (below)" % (
                        monitorPrefix, nno1, nno1Max))
                self._print2(e)

        # go through the "other" polygons to get merge list
        to_merge = DataFrame(columns=[
            'nest1-roiname', 'nest1-nid', 'nest2-roiname', 'nest2-nid'])
        nno2 = 0
        nno2Max = Nests2.shape[0]

"""Merge polygons using shapely (Internal).

        Given a single cluster from _get_merge_clusters_from_df(), This creates
        and merges polygons into a single cascaded union. It first dilates the
        polygons by buffer_size pixels to make them overlap, merges them,
        then erodes back by buffer_size to get the merged polygon.

        """
        buffer_size = self.merge_thresh + 3
        nest_polygons = []
        for nestinfo in cluster:
            nest = dict(self.edge_contours[nestinfo['roiname']].loc[
                nestinfo['nid'], :])
            roitop = self.roiinfos[nestinfo['roiname']]['top']
            roileft = self.roiinfos[nestinfo['roiname']]['left']
            coords = _parse_annot_coords(
                nest, x_offset=roileft, y_offset=roitop)
            nest_polygons.append(Polygon(coords).buffer(buffer_size))
        merged_polygon = cascaded_union(nest_polygons).buffer(-buffer_size)
        return merged_polygon

def _add_roi_offset_to_contours(self, roi_df, roiname):
        """Add roi offset to coordinates of polygons (Internal)."""
        for idx, annot in roi_df.iterrows():
            coords = np.int32(_parse_annot_coords(dict(annot)))
            coords[:, 0] = coords[:, 0] + self.roiinfos[roiname]['left']
            coords[:, 1] = coords[:, 1] + self.roiinfos[roiname]['top']
            roi_df.loc[idx, 'coords_x'] = ",".join(
                [str(j) for j in coords[:, 0]])
            roi_df.loc[idx, 'coords_y'] = ",".join(
                [str(j) for j in coords[:, 1]])
        return roi_df

polygons1.append((nid1, Polygon(coords)))
            except Exception as e:
                self._print2(
                    "%s: edge1-nest %d of %d: Shapely Error (below)" % (
                        monitorPrefix, nno1, nno1Max))
                self._print2(e)

        # go through the "other" polygons to get merge list
        to_merge = DataFrame(columns=[
            'nest1-roiname', 'nest1-nid', 'nest2-roiname', 'nest2-nid'])
        nno2 = 0
        nno2Max = Nests2.shape[0]
        for nid2, nest2 in Nests2.iterrows():
            nno2 += 1
            try:
                coords = np.array(_parse_annot_coords(nest2))
                coords[:, 0] = coords[:, 0] + self.roiinfos[
                    edgepair['roi2-name']]['left']
                coords[:, 1] = coords[:, 1] + self.roiinfos[
                    edgepair['roi2-name']]['top']
                polygon2 = Polygon(coords)
            except Exception as e:
                self._print2(
                    "%s: edge2-nest %d of %d: Shapely Error (below)" % (
                        monitorPrefix, nno2, nno2Max))
                self._print2(e)
                continue

            nno1Max = len(polygons1)-1
            for nno1, poly1 in enumerate(polygons1):
                self._print2(
                    "%s: edge2-nest %d of %d: vs. edge1-nest %d of %d" % (