# Buggy code
def extract_text_candidates(
    boxes,
    page_bbox,
    avg_font_pts,
    width,
    char_width,
    page_num,
    ref_page_seen,
    boxes_figures,
    page_width,
    page_height,
):
    # Too many "." in the Table of Content pages - ignore because it takes a lot of time
    if len(boxes) == 0 or len(boxes) > 3500:
        return {}, False
    plane = Plane(page_bbox)
    plane.extend(boxes)

    # Row level clustering - identify objects that have same horizontal alignment
    rid2obj = [set([i]) for i in range(len(boxes))]  # initialize clusters
    obj2rid = list(
        range(len(boxes))
    )  # default object map to cluster with its own index
    prev_clusters = obj2rid
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2rid[i1] == obj2rid[i2]):
                    continue
                box1 = b1.bbox
                box2 = b2.bbox
                if (
                    (abs(box1[1] - box2[1]) < 0.11 * avg_font_pts)
                    or (abs(box1[3] - box2[3]) < 0.11 * avg_font_pts)
                    or (
                        round((box1[1] + box1[3]) / 2) == round((box2[1] + box2[3]) / 2)
                    )
                ):
                    min_i = min(i1, i2)
                    max_i = max(i1, i2)
                    rid1 = obj2rid[min_i]
                    rid2 = obj2rid[max_i]
                    for obj_iter in rid2obj[rid2]:
                        rid2obj[rid1].add(obj_iter)
                        obj2rid[obj_iter] = rid1
                    rid2obj[rid2] = set()
        if prev_clusters == obj2rid:
            break
        prev_clusters = obj2rid

    cid2obj = [set([i]) for i in range(len(boxes))]  # initialize clusters
    obj2cid = list(
        range(len(boxes))
    )  # default object map to cluster with its own index
    prev_clusters = obj2cid

    # add the code for merging close text boxes in particular row
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2cid[i1] == obj2cid[i2]):
                    continue
                box1 = b1.bbox
                box2 = b2.bbox
                if obj2rid[i1] == obj2rid[i2]:
                    if (
                        (b1.bbox[0] < b2.bbox[0])
                        and ((b2.bbox[0] - b1.bbox[2]) <= 2 * char_width)
                    ) or (
                        (b2.bbox[0] < b1.bbox[0])
                        and ((b1.bbox[0] - b2.bbox[2]) <= 2 * char_width)
                    ):
                        min_i = min(i1, i2)
                        max_i = max(i1, i2)
                        cid1 = obj2cid[min_i]
                        cid2 = obj2cid[max_i]
                        for obj_iter in cid2obj[cid2]:
                            cid2obj[cid1].add(obj_iter)
                            obj2cid[obj_iter] = cid1
                        cid2obj[cid2] = set()
        if prev_clusters == obj2cid:
            break
        prev_clusters = obj2cid

    # vertical alignment code
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2cid[i1] == obj2cid[i2]):
                    continue
                if b1.bbox[1] < b2.bbox[1]:
                    box1 = b1.bbox
                    box2 = b2.bbox
                elif b2.bbox[1] < b1.bbox[1]:
                    box1 = b2.bbox
                    box2 = b1.bbox
                else:
                    # horizontally aligned
                    continue
                if abs((box2[3] - box2[1]) - (box1[3] - box1[1])) > 0.5 * avg_font_pts:
                    continue
                if (
                    box2[1] < box1[3]
                    or (box2[1] - box1[1] < 1.5 * avg_font_pts)
                    or (box2[3] - box1[3] < 1.5 * avg_font_pts)
                ):  # can probably do better if we find the average space between words
                    if (
                        abs(box1[0] - box2[0]) < 3 * char_width
                        or abs(box1[2] - box2[2]) < 3 * char_width
                        or (((box1[0] + box1[2]) / 2) == ((box2[0] + box2[2]) / 2))
                    ):
                        min_i = min(i1, i2)
                        max_i = max(i1, i2)
                        cid1 = obj2cid[min_i]
                        cid2 = obj2cid[max_i]
                        # move all objects from cluster cid2 to cid1
                        # reassign cluster ids for all such objects as well
                        for obj_iter in cid2obj[cid2]:
                            cid2obj[cid1].add(obj_iter)
                            obj2cid[obj_iter] = cid1
                        cid2obj[cid2] = set()
        if prev_clusters == obj2cid:
            break
        prev_clusters = obj2cid

    # get cluster spans
    cid2span = {}
    for cid in range(len(cid2obj)):
        cid2span[cid] = {}
        cid2span[cid]["min_x"] = float("Inf")
        cid2span[cid]["min_y"] = float("Inf")
        cid2span[cid]["max_x"] = float("-Inf")
        cid2span[cid]["max_y"] = float("-Inf")
        for obj in cid2obj[cid]:
            cid2span[cid]["min_x"] = min(cid2span[cid]["min_x"], boxes[obj].bbox[0])
            cid2span[cid]["max_x"] = max(cid2span[cid]["max_x"], boxes[obj].bbox[2])
            cid2span[cid]["min_y"] = min(cid2span[cid]["min_y"], boxes[obj].bbox[1])
            cid2span[cid]["max_y"] = max(cid2span[cid]["max_y"], boxes[obj].bbox[3])

    # Don't split up references
    references_bbox = []
    references_cid = set()
    for cid in range(len(cid2obj)):
        if len(cid2obj[cid]) == 1:
            if boxes[list(cid2obj[cid])[0]].get_text().lower() == "references":
                references_bbox = [
                    cid2span[cid]["min_x"],
                    cid2span[cid]["min_y"],
                    cid2span[cid]["max_x"],
                    cid2span[cid]["max_y"],
                ]
                for cid2 in range(len(cid2obj)):
                    if (
                        round(cid2span[cid]["min_x"]) == round(cid2span[cid2]["min_x"])
                        and cid2span[cid]["max_y"] < cid2span[cid2]["min_y"]
                    ):
                        references_cid.add(cid2)
                        cid2span[cid2]["min_x"] = cid2span[cid]["min_x"]
                        cid2span[cid2]["max_x"] = cid2span[cid]["max_x"]

    # get a list of empty cids
    empty_cids = [cid for cid in range(len(cid2obj)) if len(cid2obj[cid]) == 0]
    empty_idx = 0

    # Split paras based on whitespaces - seems to work
    if ref_page_seen == False:
        for cid in range(len(cid2obj)):
            if (
                len(cid2obj[cid]) > 0
                and cid not in empty_cids
                and cid not in references_cid
            ):
                cid_maxx = max([boxes[obj].bbox[2] for obj in cid2obj[cid]])
                cid_minx = min([boxes[obj].bbox[0] for obj in cid2obj[cid]])
                rid_list = set([obj2rid[obj] for obj in cid2obj[cid]])
                # Get min_y for each row
                rid_miny = {}
                for rid in rid_list:
                    rid_miny[rid] = min(
                        [
                            boxes[obj].bbox[1] if obj in cid2obj[cid] else 10000
                            for obj in rid2obj[rid]
                        ]
                    )
                sorted_rid_miny = sorted(
                    list(rid_miny.items()), key=operator.itemgetter(1)
                )
                last_rid = 0
                for i in range(len(sorted_rid_miny) - 1):
                    row1 = sorted_rid_miny[i][0]
                    row2 = sorted_rid_miny[i + 1][0]
                    row1_maxx = max(
                        [
                            boxes[obj].bbox[2] if obj in cid2obj[cid] else -1
                            for obj in rid2obj[row1]
                        ]
                    )
                    row2_minx = min(
                        [
                            boxes[obj].bbox[0] if obj in cid2obj[cid] else 10000
                            for obj in rid2obj[row2]
                        ]
                    )
                    if row1_maxx <= cid_maxx and (row2_minx - char_width) > cid_minx:
                        # split cluster cid
                        new_cid_idx = empty_cids[empty_idx]
                        empty_idx += 1
                        for i_iter in range(last_rid, i + 1):
                            obj_list = [
                                obj
                                for obj in rid2obj[sorted_rid_miny[i_iter][0]]
                                if obj2cid[obj] == cid
                            ]
                            for obj in obj_list:
                                cid2obj[cid].remove(obj)
                                cid2obj[new_cid_idx].add(obj)
                                obj2cid[obj] = new_cid_idx
                        last_rid = i + 1

    clusters = [[boxes[i] for i in cluster] for cluster in filter(bool, cid2obj)]
    nodes = [Node(elems) for elems in clusters]
    node_indices = [i for i, x in enumerate(cid2obj) if x]
    merge_indices = [i for i in range(len(node_indices))]
    page_stat = Node(boxes)
    nodes, merge_indices = merge_nodes(nodes, plane, page_stat, merge_indices)

    ##Merging Nodes
    new_nodes = []
    new_node_indices = []
    for idx in range(len(merge_indices)):
        if merge_indices[idx] == idx:
            new_nodes.append(nodes[idx])
            new_node_indices.append(node_indices[idx])

    # Heuristics for Node type
    ref_nodes = []
    new_ref_page_seen = False
    if len(references_cid) > 0 or ref_page_seen or references_bbox != []:
        new_ref_page_seen = True
    ref_seen_in_node = False or ref_page_seen
    all_boxes = boxes + boxes_figures
    min_y_page = float("Inf")
    for idx, box in enumerate(all_boxes):
        min_y_page = min(min_y_page, box.bbox[1])
    if page_num == -1:
        # handle title, authors and abstract here
        log.error("TODO: no way to handle title authors abstract yet.")
    else:
        # eliminate header, footer, page number
        # sort other text and classify as header/paragraph
        new_nodes.sort(key=cmp_to_key(xy_reading_order))
        for idx, node in enumerate(new_nodes):
            if idx < len(new_nodes) - 1:
                if (
                    round(node.y0) == round(min_y_page)
                    or math.floor(node.y0) == math.floor(min_y_page)
                ) and node.y1 - node.y0 < 2 * avg_font_pts:  # can be header
                    idx_new = idx + 1
                    if idx_new < len(new_nodes) - 1:
                        while (
                            idx_new < len(new_nodes) - 1
                            and (round(node.y0) == round(new_nodes[idx_new].y0))
                            or (
                                math.floor(node.y0) == math.floor(new_nodes[idx_new].y0)
                            )
                        ):
                            idx_new += 1
                    if idx_new < len(new_nodes) - 1:
                        if new_nodes[idx_new].y0 - node.y0 > 1.5 * avg_font_pts:
                            node.type = "Header"
                            continue
            # get captions - first word is fig/figure/table
            first_elem = None
            for elem in node.elems:
                if round(elem.bbox[0]) == round(node.x0) and round(
                    elem.bbox[1]
                ) == round(node.y0):
                    first_elem = elem
                    break
            if first_elem != None:
                text = first_elem.get_text()
                if len(text) > 10:
                    text = first_elem.get_text()[0:10]
                if "Table" in text:
                    node.type = "Table Caption"
                    continue
                if "Fig" in text or "Figure" in text:
                    node.type = "Figure Caption"
                    continue
                if first_elem.get_text().lower() == "references":
                    node.type = "Section Header"
                    ref_seen_in_node = True
                    continue
            if ref_seen_in_node:
                node.type = "List"
                continue
            if references_bbox != [] or ref_seen_in_node:
                if (
                    node.y0 > references_bbox[3]
                    and node.x0 <= references_bbox[0]
                    and node.x1 > references_bbox[2]
                ):
                    node.type = "List"
                    continue
            if node.y1 - node.y0 <= 2.0 * avg_font_pts:  # one lines - section
                node.type = "Section Header"
            else:  # multiple lines - para
                node.type = "Paragraph"

    # handle references
    newer_nodes = []
    ref_indices = [False for idx in range(len(new_nodes))]
    for idx1, node1 in enumerate(new_nodes):
        if ref_indices[idx1] == True:
            continue
        if node1.type != "List":
            newer_nodes.append(node1)
            continue
        x0, y0, x1, y1 = node1.x0, node1.y0, node1.x1, node1.y1
        newer_node = node1
        ref_indices[idx1] = True
        for idx2, node2 in enumerate(new_nodes):
            if idx1 != idx2:
                if node2.type == "List" and ref_indices[idx2] == False:
                    if (node2.x0 <= x0 and node2.x1 >= x0) or (
                        x0 <= node2.x0 and x1 >= node2.x0
                    ):
                        newer_node.merge(node2)
                        ref_indices[idx2] = True
        newer_nodes.append(newer_node)

    # handle figures
    for fig_box in boxes_figures:
        node_fig = Node(fig_box)
        node_fig.type = "Figure"
        newer_nodes.append(node_fig)

    tree = {}
    tree["section_header"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Section Header"
    ]
    tree["header"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Header"
    ]
    tree["paragraph"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Paragraph"
    ]
    # tree["figure"] = [(page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1) for node in newer_nodes if node.type=="Figure"]
    tree["figure_caption"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Figure Caption"
    ]
    tree["table_caption"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Table Caption"
    ]
    tree["list"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "List"
    ]
    return tree, new_ref_page_seen


# Traceback (IndexError)
$ pdftotree test.pdf
Traceback (most recent call last):
File "/home/lwhsiao/repos/pdftotree/.venv/bin/pdftotree", line 6, in <module>
exec(compile(open(__file__).read(), __file__, 'exec'))
File "/home/lwhsiao/repos/pdftotree/bin/pdftotree", line 82, in <module>
args.favor_figures, args.visualize)
File "/home/lwhsiao/repos/pdftotree/pdftotree/core.py", line 58, in parse
pdf_tree = extractor.get_tree_structure(model, favor_figures)
File "/home/lwhsiao/repos/pdftotree/pdftotree/TreeExtract.py", line 188, in get_tree_structure
favor_figures)
File "/home/lwhsiao/repos/pdftotree/pdftotree/utils/pdf/pdf_parsers.py", line 734, in parse_tree_structure
ref_page_seen, boxes_figures, page_width, page_height)
File "/home/lwhsiao/repos/pdftotree/pdftotree/utils/pdf/pdf_parsers.py", line 1001, in extract_text_candidates
new_nodes[idx_new].y0))):
IndexError: list index out of range

# Fixed code
def extract_text_candidates(
    boxes,
    page_bbox,
    avg_font_pts,
    width,
    char_width,
    page_num,
    ref_page_seen,
    boxes_figures,
    page_width,
    page_height,
):
    # Too many "." in the Table of Content pages - ignore because it takes a lot of time
    if len(boxes) == 0 or len(boxes) > 3500:
        return {}, False
    plane = Plane(page_bbox)
    plane.extend(boxes)

    # Row level clustering - identify objects that have same horizontal alignment
    rid2obj = [set([i]) for i in range(len(boxes))]  # initialize clusters
    obj2rid = list(
        range(len(boxes))
    )  # default object map to cluster with its own index
    prev_clusters = obj2rid
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2rid[i1] == obj2rid[i2]):
                    continue
                box1 = b1.bbox
                box2 = b2.bbox
                if (
                    (abs(box1[1] - box2[1]) < 0.11 * avg_font_pts)
                    or (abs(box1[3] - box2[3]) < 0.11 * avg_font_pts)
                    or (
                        round((box1[1] + box1[3]) / 2) == round((box2[1] + box2[3]) / 2)
                    )
                ):
                    min_i = min(i1, i2)
                    max_i = max(i1, i2)
                    rid1 = obj2rid[min_i]
                    rid2 = obj2rid[max_i]
                    for obj_iter in rid2obj[rid2]:
                        rid2obj[rid1].add(obj_iter)
                        obj2rid[obj_iter] = rid1
                    rid2obj[rid2] = set()
        if prev_clusters == obj2rid:
            break
        prev_clusters = obj2rid

    cid2obj = [set([i]) for i in range(len(boxes))]  # initialize clusters
    obj2cid = list(
        range(len(boxes))
    )  # default object map to cluster with its own index
    prev_clusters = obj2cid

    # add the code for merging close text boxes in particular row
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2cid[i1] == obj2cid[i2]):
                    continue
                box1 = b1.bbox
                box2 = b2.bbox
                if obj2rid[i1] == obj2rid[i2]:
                    if (
                        (b1.bbox[0] < b2.bbox[0])
                        and ((b2.bbox[0] - b1.bbox[2]) <= 2 * char_width)
                    ) or (
                        (b2.bbox[0] < b1.bbox[0])
                        and ((b1.bbox[0] - b2.bbox[2]) <= 2 * char_width)
                    ):
                        min_i = min(i1, i2)
                        max_i = max(i1, i2)
                        cid1 = obj2cid[min_i]
                        cid2 = obj2cid[max_i]
                        for obj_iter in cid2obj[cid2]:
                            cid2obj[cid1].add(obj_iter)
                            obj2cid[obj_iter] = cid1
                        cid2obj[cid2] = set()
        if prev_clusters == obj2cid:
            break
        prev_clusters = obj2cid

    # vertical alignment code
    while True:
        for i1, b1 in enumerate(boxes):
            for i2, b2 in enumerate(boxes):
                if (i1 == i2) or (obj2cid[i1] == obj2cid[i2]):
                    continue
                if b1.bbox[1] < b2.bbox[1]:
                    box1 = b1.bbox
                    box2 = b2.bbox
                elif b2.bbox[1] < b1.bbox[1]:
                    box1 = b2.bbox
                    box2 = b1.bbox
                else:
                    # horizontally aligned
                    continue
                if abs((box2[3] - box2[1]) - (box1[3] - box1[1])) > 0.5 * avg_font_pts:
                    continue
                if (
                    box2[1] < box1[3]
                    or (box2[1] - box1[1] < 1.5 * avg_font_pts)
                    or (box2[3] - box1[3] < 1.5 * avg_font_pts)
                ):  # can probably do better if we find the average space between words
                    if (
                        abs(box1[0] - box2[0]) < 3 * char_width
                        or abs(box1[2] - box2[2]) < 3 * char_width
                        or (((box1[0] + box1[2]) / 2) == ((box2[0] + box2[2]) / 2))
                    ):
                        min_i = min(i1, i2)
                        max_i = max(i1, i2)
                        cid1 = obj2cid[min_i]
                        cid2 = obj2cid[max_i]
                        # move all objects from cluster cid2 to cid1
                        # reassign cluster ids for all such objects as well
                        for obj_iter in cid2obj[cid2]:
                            cid2obj[cid1].add(obj_iter)
                            obj2cid[obj_iter] = cid1
                        cid2obj[cid2] = set()
        if prev_clusters == obj2cid:
            break
        prev_clusters = obj2cid

    # get cluster spans
    cid2span = {}
    for cid in range(len(cid2obj)):
        cid2span[cid] = {}
        cid2span[cid]["min_x"] = float("Inf")
        cid2span[cid]["min_y"] = float("Inf")
        cid2span[cid]["max_x"] = float("-Inf")
        cid2span[cid]["max_y"] = float("-Inf")
        for obj in cid2obj[cid]:
            cid2span[cid]["min_x"] = min(cid2span[cid]["min_x"], boxes[obj].bbox[0])
            cid2span[cid]["max_x"] = max(cid2span[cid]["max_x"], boxes[obj].bbox[2])
            cid2span[cid]["min_y"] = min(cid2span[cid]["min_y"], boxes[obj].bbox[1])
            cid2span[cid]["max_y"] = max(cid2span[cid]["max_y"], boxes[obj].bbox[3])

    # Don't split up references
    references_bbox = []
    references_cid = set()
    for cid in range(len(cid2obj)):
        if len(cid2obj[cid]) == 1:
            if boxes[list(cid2obj[cid])[0]].get_text().lower() == "references":
                references_bbox = [
                    cid2span[cid]["min_x"],
                    cid2span[cid]["min_y"],
                    cid2span[cid]["max_x"],
                    cid2span[cid]["max_y"],
                ]
                for cid2 in range(len(cid2obj)):
                    if (
                        round(cid2span[cid]["min_x"]) == round(cid2span[cid2]["min_x"])
                        and cid2span[cid]["max_y"] < cid2span[cid2]["min_y"]
                    ):
                        references_cid.add(cid2)
                        cid2span[cid2]["min_x"] = cid2span[cid]["min_x"]
                        cid2span[cid2]["max_x"] = cid2span[cid]["max_x"]

    # get a list of empty cids
    empty_cids = [cid for cid in range(len(cid2obj)) if len(cid2obj[cid]) == 0]
    empty_idx = 0

    # Split paras based on whitespaces - seems to work
    if ref_page_seen == False:
        for cid in range(len(cid2obj)):
            if (
                len(cid2obj[cid]) > 0
                and cid not in empty_cids
                and cid not in references_cid
            ):
                cid_maxx = max([boxes[obj].bbox[2] for obj in cid2obj[cid]])
                cid_minx = min([boxes[obj].bbox[0] for obj in cid2obj[cid]])
                rid_list = set([obj2rid[obj] for obj in cid2obj[cid]])
                # Get min_y for each row
                rid_miny = {}
                for rid in rid_list:
                    rid_miny[rid] = min(
                        [
                            boxes[obj].bbox[1] if obj in cid2obj[cid] else 10000
                            for obj in rid2obj[rid]
                        ]
                    )
                sorted_rid_miny = sorted(
                    list(rid_miny.items()), key=operator.itemgetter(1)
                )
                last_rid = 0
                for i in range(len(sorted_rid_miny) - 1):
                    row1 = sorted_rid_miny[i][0]
                    row2 = sorted_rid_miny[i + 1][0]
                    row1_maxx = max(
                        [
                            boxes[obj].bbox[2] if obj in cid2obj[cid] else -1
                            for obj in rid2obj[row1]
                        ]
                    )
                    row2_minx = min(
                        [
                            boxes[obj].bbox[0] if obj in cid2obj[cid] else 10000
                            for obj in rid2obj[row2]
                        ]
                    )
                    if row1_maxx <= cid_maxx and (row2_minx - char_width) > cid_minx:
                        # split cluster cid
                        new_cid_idx = empty_cids[empty_idx]
                        empty_idx += 1
                        for i_iter in range(last_rid, i + 1):
                            obj_list = [
                                obj
                                for obj in rid2obj[sorted_rid_miny[i_iter][0]]
                                if obj2cid[obj] == cid
                            ]
                            for obj in obj_list:
                                cid2obj[cid].remove(obj)
                                cid2obj[new_cid_idx].add(obj)
                                obj2cid[obj] = new_cid_idx
                        last_rid = i + 1

    clusters = [[boxes[i] for i in cluster] for cluster in filter(bool, cid2obj)]
    nodes = [Node(elems) for elems in clusters]
    node_indices = [i for i, x in enumerate(cid2obj) if x]
    merge_indices = [i for i in range(len(node_indices))]
    page_stat = Node(boxes)
    nodes, merge_indices = merge_nodes(nodes, plane, page_stat, merge_indices)

    ##Merging Nodes
    new_nodes = []
    new_node_indices = []
    for idx in range(len(merge_indices)):
        if merge_indices[idx] == idx:
            new_nodes.append(nodes[idx])
            new_node_indices.append(node_indices[idx])

    # Heuristics for Node type
    ref_nodes = []
    new_ref_page_seen = False
    if len(references_cid) > 0 or ref_page_seen or references_bbox != []:
        new_ref_page_seen = True
    ref_seen_in_node = False or ref_page_seen
    all_boxes = boxes + boxes_figures
    min_y_page = float("Inf")
    for idx, box in enumerate(all_boxes):
        min_y_page = min(min_y_page, box.bbox[1])
    if page_num == -1:
        # handle title, authors and abstract here
        log.error("TODO: no way to handle title authors abstract yet.")
    else:
        # eliminate header, footer, page number
        # sort other text and classify as header/paragraph
        new_nodes.sort(key=cmp_to_key(xy_reading_order))
        for idx, node in enumerate(new_nodes):
            if idx < len(new_nodes) - 1:
                if (
                    round(node.y0) == round(min_y_page)
                    or math.floor(node.y0) == math.floor(min_y_page)
                ) and node.y1 - node.y0 < 2 * avg_font_pts:  # can be header
                    idx_new = idx + 1
                    if idx_new < len(new_nodes) - 1:
                        while idx_new < len(new_nodes) - 1 and (
                            (round(node.y0) == round(new_nodes[idx_new].y0))
                            or (
                                math.floor(node.y0) == math.floor(new_nodes[idx_new].y0)
                            )
                        ):
                            idx_new += 1
                    if idx_new < len(new_nodes) - 1:
                        if new_nodes[idx_new].y0 - node.y0 > 1.5 * avg_font_pts:
                            node.type = "Header"
                            continue
            # get captions - first word is fig/figure/table
            first_elem = None
            for elem in node.elems:
                if round(elem.bbox[0]) == round(node.x0) and round(
                    elem.bbox[1]
                ) == round(node.y0):
                    first_elem = elem
                    break
            if first_elem != None:
                text = first_elem.get_text()
                if len(text) > 10:
                    text = first_elem.get_text()[0:10]
                if "Table" in text:
                    node.type = "Table Caption"
                    continue
                if "Fig" in text or "Figure" in text:
                    node.type = "Figure Caption"
                    continue
                if first_elem.get_text().lower() == "references":
                    node.type = "Section Header"
                    ref_seen_in_node = True
                    continue
            if ref_seen_in_node:
                node.type = "List"
                continue
            if references_bbox != [] or ref_seen_in_node:
                if (
                    node.y0 > references_bbox[3]
                    and node.x0 <= references_bbox[0]
                    and node.x1 > references_bbox[2]
                ):
                    node.type = "List"
                    continue
            if node.y1 - node.y0 <= 2.0 * avg_font_pts:  # one lines - section
                node.type = "Section Header"
            else:  # multiple lines - para
                node.type = "Paragraph"

    # handle references
    newer_nodes = []
    ref_indices = [False for idx in range(len(new_nodes))]
    for idx1, node1 in enumerate(new_nodes):
        if ref_indices[idx1] == True:
            continue
        if node1.type != "List":
            newer_nodes.append(node1)
            continue
        x0, y0, x1, y1 = node1.x0, node1.y0, node1.x1, node1.y1
        newer_node = node1
        ref_indices[idx1] = True
        for idx2, node2 in enumerate(new_nodes):
            if idx1 != idx2:
                if node2.type == "List" and ref_indices[idx2] == False:
                    if (node2.x0 <= x0 and node2.x1 >= x0) or (
                        x0 <= node2.x0 and x1 >= node2.x0
                    ):
                        newer_node.merge(node2)
                        ref_indices[idx2] = True
        newer_nodes.append(newer_node)

    # handle figures
    for fig_box in boxes_figures:
        node_fig = Node(fig_box)
        node_fig.type = "Figure"
        newer_nodes.append(node_fig)

    tree = {}
    tree["section_header"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Section Header"
    ]
    tree["header"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Header"
    ]
    tree["paragraph"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Paragraph"
    ]
    # tree["figure"] = [(page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1) for node in newer_nodes if node.type=="Figure"]
    tree["figure_caption"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Figure Caption"
    ]
    tree["table_caption"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "Table Caption"
    ]
    tree["list"] = [
        (page_num, page_width, page_height) + (node.y0, node.x0, node.y1, node.x1)
        for node in newer_nodes
        if node.type == "List"
    ]
    return tree, new_ref_page_seen