docling 2.12.0__py3-none-any.whl → 2.14.0__py3-none-any.whl

docling/utils/layout_utils.py

@@ -1,812 +0,0 @@
-import copy
-import logging
-
-import networkx as nx
-from docling_core.types.doc import DocItemLabel
-
-logger = logging.getLogger("layout_utils")
-
-
-## -------------------------------
-## Geometric helper functions
-## The coordinates grow left to right, and bottom to top.
-## The bounding box list elements 0 to 3 are x_left, y_bottom, x_right, y_top.
-
-
-def area(bbox):
-    return (bbox[2] - bbox[0]) * (bbox[3] - bbox[1])
-
-
-def contains(bbox_i, bbox_j):
-    ## Returns True if bbox_i contains bbox_j, else False
-    return (
-        bbox_i[0] <= bbox_j[0]
-        and bbox_i[1] <= bbox_j[1]
-        and bbox_i[2] >= bbox_j[2]
-        and bbox_i[3] >= bbox_j[3]
-    )
-
-
-def is_intersecting(bbox_i, bbox_j):
-    return not (
-        bbox_i[2] < bbox_j[0]
-        or bbox_i[0] > bbox_j[2]
-        or bbox_i[3] < bbox_j[1]
-        or bbox_i[1] > bbox_j[3]
-    )
-
-
-def bb_iou(boxA, boxB):
-    # determine the (x, y)-coordinates of the intersection rectangle
-    xA = max(boxA[0], boxB[0])
-    yA = max(boxA[1], boxB[1])
-    xB = min(boxA[2], boxB[2])
-    yB = min(boxA[3], boxB[3])
-    # compute the area of intersection rectangle
-    interArea = max(0, xB - xA + 1) * max(0, yB - yA + 1)
-    # compute the area of both the prediction and ground-truth
-    # rectangles
-    boxAArea = (boxA[2] - boxA[0] + 1) * (boxA[3] - boxA[1] + 1)
-    boxBArea = (boxB[2] - boxB[0] + 1) * (boxB[3] - boxB[1] + 1)
-    # compute the intersection over union by taking the intersection
-    # area and dividing it by the sum of prediction + ground-truth
-    # areas - the interesection area
-    iou = interArea / float(boxAArea + boxBArea - interArea)
-    # return the intersection over union value
-    return iou
-
-
-def compute_intersection(bbox_i, bbox_j):
-    ## Returns the size of the intersection area of the two boxes
-    if not is_intersecting(bbox_i, bbox_j):
-        return 0
-    ## Determine the (x, y)-coordinates of the intersection rectangle:
-    xA = max(bbox_i[0], bbox_j[0])
-    yA = max(bbox_i[1], bbox_j[1])
-    xB = min(bbox_i[2], bbox_j[2])
-    yB = min(bbox_i[3], bbox_j[3])
-    ## Compute the area of intersection rectangle:
-    interArea = (xB - xA) * (yB - yA)
-    if interArea < 0:
-        logger.debug("Warning: Negative intersection detected!")
-        return 0
-    return interArea
-
-
-def surrounding(bbox_i, bbox_j):
-    ## Computes minimal box that contains both input boxes
-    sbox = []
-    sbox.append(min(bbox_i[0], bbox_j[0]))
-    sbox.append(min(bbox_i[1], bbox_j[1]))
-    sbox.append(max(bbox_i[2], bbox_j[2]))
-    sbox.append(max(bbox_i[3], bbox_j[3]))
-    return sbox
-
-
-def surrounding_list(bbox_list):
-    ## Computes minimal box that contains all boxes in the input list
-    ## The list should be non-empty, but just in case it's not:
-    if len(bbox_list) == 0:
-        sbox = [0, 0, 0, 0]
-    else:
-        sbox = []
-        sbox.append(min([bbox[0] for bbox in bbox_list]))
-        sbox.append(min([bbox[1] for bbox in bbox_list]))
-        sbox.append(max([bbox[2] for bbox in bbox_list]))
-        sbox.append(max([bbox[3] for bbox in bbox_list]))
-    return sbox
-
-
-def vertical_overlap(bboxA, bboxB):
-    ## bbox[1] is the lower bound, bbox[3] the upper bound (larger number)
-    if bboxB[3] < bboxA[1]:  ## B below A
-        return False
-    elif bboxA[3] < bboxB[1]:  ## A below B
-        return False
-    else:
-        return True
-
-
-def vertical_overlap_fraction(bboxA, bboxB):
-    ## Returns the vertical overlap as fraction of the lower bbox height.
-    ## bbox[1] is the lower bound, bbox[3] the upper bound (larger number)
-    ## Height 0 is permitted in the input.
-    heightA = bboxA[3] - bboxA[1]
-    heightB = bboxB[3] - bboxB[1]
-    min_height = min(heightA, heightB)
-    if bboxA[3] >= bboxB[3]:  ## A starts higher or equal
-        if (
-            bboxA[1] <= bboxB[1]
-        ):  ## B is completely in A; this can include height of B = 0:
-            fraction = 1
-        else:
-            overlap = max(bboxB[3] - bboxA[1], 0)
-            fraction = overlap / max(min_height, 0.001)
-    else:
-        if (
-            bboxB[1] <= bboxA[1]
-        ):  ## A is completely in B; this can include height of A = 0:
-            fraction = 1
-        else:
-            overlap = max(bboxA[3] - bboxB[1], 0)
-            fraction = overlap / max(min_height, 0.001)
-    return fraction
-
-
-## -------------------------------
-## Cluster-and-cell relations
-
-
-def compute_enclosed_cells(
-    cluster_bbox, raw_cells, min_cell_intersection_with_cluster=0.2
-):
-    cells_in_cluster = []
-    cells_in_cluster_int = []
-    for ix, cell in enumerate(raw_cells):
-        cell_bbox = cell["bbox"]
-        intersection = compute_intersection(cell_bbox, cluster_bbox)
-        frac_area = area(cell_bbox) * min_cell_intersection_with_cluster
-
-        if (
-            intersection > frac_area and frac_area > 0
-        ):  # intersect > certain fraction of cell
-            cells_in_cluster.append(ix)
-            cells_in_cluster_int.append(intersection)
-        elif contains(
-            cluster_bbox,
-            [cell_bbox[0] + 3, cell_bbox[1] + 3, cell_bbox[2] - 3, cell_bbox[3] - 3],
-        ):
-            cells_in_cluster.append(ix)
-    return cells_in_cluster, cells_in_cluster_int
-
-
-def find_clusters_around_cells(cell_count, clusters):
-    ## Per raw cell, find to which clusters it belongs.
-    ## Return list of these indices in the raw-cell order.
-    clusters_around_cells = [[] for _ in range(cell_count)]
-    for cl_ix, cluster in enumerate(clusters):
-        for ix in cluster["cell_ids"]:
-            clusters_around_cells[ix].append(cl_ix)
-    return clusters_around_cells
-
-
-def find_cell_index(raw_ix, cell_array):
-    ## "raw_ix" is a rawcell_id.
-    ## "cell_array" has the structure of an (annotation) cells array.
-    ## Returns index of cell in cell_array that has this rawcell_id.
-    for ix, cell in enumerate(cell_array):
-        if cell["rawcell_id"] == raw_ix:
-            return ix
-
-
-def find_cell_indices(cluster, cell_array):
-    ## "cluster" must have the structure as in a clusters array in a prediction,
-    ## "cell_array" that of a cells array.
-    ## Returns list of indices of cells in cell_array that have the rawcell_ids as in the cluster,
-    ## in the order of the rawcell_ids.
-    result = []
-    for raw_ix in sorted(cluster["cell_ids"]):
-        ## Find the cell with this rawcell_id (if any)
-        for ix, cell in enumerate(cell_array):
-            if cell["rawcell_id"] == raw_ix:
-                result.append(ix)
-    return result
-
-
-def find_first_cell_index(cluster, cell_array):
-    ## "cluster" must be a dict with key "cell_ids"; it can also be a line.
-    ## "cell_array" has the structure of a cells array in an annotation.
-    ## Returns index of cell in cell_array that has the lowest rawcell_id from the cluster.
-    result = []  ## We keep it a list as it can be empty (picture without text cells)
-    if len(cluster["cell_ids"]) == 0:
-        return result
-    raw_ix = min(cluster["cell_ids"])
-    ## Find the cell with this rawcell_id (if any)
-    for ix, cell in enumerate(cell_array):
-        if cell["rawcell_id"] == raw_ix:
-            result.append(ix)
-            break  ## One is enough; should be only one anyway.
-    if result == []:
-        logger.debug(
-            "  Warning: Raw cell " + str(raw_ix) + " not found in annotation cells"
-        )
-    return result
-
-
-## -------------------------------
-## Cluster labels and text
-
-
-def relabel_cluster(cluster, cl_ix, new_label, target_pred):
-    ## "cluster" must have the structure as in a clusters array in a prediction,
-    ## "cl_ix" is its index in target_pred,
-    ## "new_label" is the intended new label,
-    ## "target_pred" is the entire current target prediction.
-    ## Sets label on the cluster itself, and on the cells in the target_pred.
-    ## Returns new_label so that also the cl_label variable in the main code is easily set.
-    target_pred["clusters"][cl_ix]["type"] = new_label
-    cluster_target_cells = find_cell_indices(cluster, target_pred["cells"])
-    for ix in cluster_target_cells:
-        target_pred["cells"][ix]["label"] = new_label
-    return new_label
-
-
-def find_cluster_text(cluster, raw_cells):
-    ## "cluster" must be a dict with "cell_ids"; it can also be a line.
-    ## "raw_cells" must have the format of item["raw"]["cells"]
-    ## Returns the text of the cluster, with blanks between the cell contents
-    ## (which seem to be words or phrases without starting or trailing blanks).
-    ## Note that in formulas, this may give a lot more blanks than originally
-    cluster_text = ""
-    for raw_ix in sorted(cluster["cell_ids"]):
-        cluster_text = cluster_text + raw_cells[raw_ix]["text"] + " "
-    return cluster_text.rstrip()
-
-
-def find_cluster_text_without_blanks(cluster, raw_cells):
-    ## "cluster" must be a dict with "cell_ids"; it can also be a line.
-    ## "raw_cells" must have the format of item["raw"]["cells"]
-    ## Returns the text of the cluster, without blanks between the cell contents
-    ## Interesting in formula analysis.
-    cluster_text = ""
-    for raw_ix in sorted(cluster["cell_ids"]):
-        cluster_text = cluster_text + raw_cells[raw_ix]["text"]
-    return cluster_text.rstrip()
-
-
-## -------------------------------
-## Clusters and lines
-## (Most line-oriented functions are only needed in TextAnalysisGivenClusters,
-##  but this one also in FormulaAnalysis)
-
-
-def build_cluster_from_lines(lines, label, id):
-    ## Lines must be a non-empty list of dicts (lines) with elements "cell_ids" and "bbox"
-    ## (There is no condition that they are really geometrically lines)
-    ## A cluster in standard format is returned with given label and id
-    local_lines = copy.deepcopy(
-        lines
-    )  ## without this, it changes "lines" also outside this function
-    first_line = local_lines.pop(0)
-    cluster = {
-        "id": id,
-        "type": label,
-        "cell_ids": first_line["cell_ids"],
-        "bbox": first_line["bbox"],
-        "confidence": 0,
-        "created_by": "merged_cells",
-    }
-    confidence = 0
-    counter = 0
-    for line in local_lines:
-        new_cell_ids = cluster["cell_ids"] + line["cell_ids"]
-        cluster["cell_ids"] = new_cell_ids
-        cluster["bbox"] = surrounding(cluster["bbox"], line["bbox"])
-        counter += 1
-        confidence += line["confidence"]
-    confidence = confidence / counter
-    cluster["confidence"] = confidence
-    return cluster
-
-
-## -------------------------------
-## Reading order
-
-
-def produce_reading_order(clusters, cluster_sort_type, cell_sort_type, sort_ids):
-    ## In:
-    ##   Clusters: list as in predictions.
-    ##   cluster_sort_type: string, currently only "raw_cells".
-    ##   cell_sort_type: string, currently only "raw_cells".
-    ##   sort_ids: Boolean, whether the cluster ids should be adapted to their new position
-    ## Out: Another clusters list, sorted according to the type.
-
-    logger.debug("---- Start cluster sorting ------")
-
-    if cell_sort_type == "raw_cell_ids":
-        for cl in clusters:
-            sorted_cell_ids = sorted(cl["cell_ids"])
-            cl["cell_ids"] = sorted_cell_ids
-    else:
-        logger.debug(
-            "Unknown cell_sort_type `"
-            + cell_sort_type
-            + "`, no cell sorting will happen."
-        )
-
-    if cluster_sort_type == "raw_cell_ids":
-        clusters_with_cells = [cl for cl in clusters if cl["cell_ids"] != []]
-        clusters_without_cells = [cl for cl in clusters if cl["cell_ids"] == []]
-        logger.debug(
-            "Clusters with cells: " + str([cl["id"] for cl in clusters_with_cells])
-        )
-        logger.debug(
-            "  Their first cell ids: "
-            + str([cl["cell_ids"][0] for cl in clusters_with_cells])
-        )
-        logger.debug(
-            "Clusters without cells: "
-            + str([cl["id"] for cl in clusters_without_cells])
-        )
-        clusters_with_cells_sorted = sorted(
-            clusters_with_cells, key=lambda cluster: cluster["cell_ids"][0]
-        )
-        logger.debug(
-            "  First cell ids after sorting: "
-            + str([cl["cell_ids"][0] for cl in clusters_with_cells_sorted])
-        )
-        sorted_clusters = clusters_with_cells_sorted + clusters_without_cells
-    else:
-        logger.debug(
-            "Unknown cluster_sort_type: `"
-            + cluster_sort_type
-            + "`, no cluster sorting will happen."
-        )
-
-    if sort_ids:
-        for i, cl in enumerate(sorted_clusters):
-            cl["id"] = i
-    return sorted_clusters
-
-
-## -------------------------------
-## Line Splitting
-
-
-def sort_cells_horizontal(line_cell_ids, raw_cells):
-    ## "line_cells" should be a non-empty list of (raw) cell_ids
-    ## "raw_cells" has the structure of item["raw"]["cells"].
-    ## Sorts the cells in the line by x0 (left start).
-    new_line_cell_ids = sorted(
-        line_cell_ids, key=lambda cell_id: raw_cells[cell_id]["bbox"][0]
-    )
-    return new_line_cell_ids
-
-
-def adapt_bboxes(raw_cells, clusters, orphan_cell_indices):
-    new_clusters = []
-    for ix, cluster in enumerate(clusters):
-        new_cluster = copy.deepcopy(cluster)
-        logger.debug(
-            "Treating cluster " + str(ix) + ", type " + str(new_cluster["type"])
-        )
-        logger.debug("  with cells: " + str(new_cluster["cell_ids"]))
-        if len(cluster["cell_ids"]) == 0 and cluster["type"] != DocItemLabel.PICTURE:
-            logger.debug("  Empty non-picture, removed")
-            continue  ## Skip this former cluster, now without cells.
-        new_bbox = adapt_bbox(raw_cells, new_cluster, orphan_cell_indices)
-        new_cluster["bbox"] = new_bbox
-        new_clusters.append(new_cluster)
-    return new_clusters
-
-
-def adapt_bbox(raw_cells, cluster, orphan_cell_indices):
-    if not (cluster["type"] in [DocItemLabel.TABLE, DocItemLabel.PICTURE]):
-        ## A text-like cluster. The bbox only needs to be around the text cells:
-        logger.debug("    Initial bbox: " + str(cluster["bbox"]))
-        new_bbox = surrounding_list(
-            [raw_cells[cid]["bbox"] for cid in cluster["cell_ids"]]
-        )
-        logger.debug("  New bounding box:" + str(new_bbox))
-    if cluster["type"] == DocItemLabel.PICTURE:
-        ## We only make the bbox completely comprise included text cells:
-        logger.debug("  Picture")
-        if len(cluster["cell_ids"]) != 0:
-            min_bbox = surrounding_list(
-                [raw_cells[cid]["bbox"] for cid in cluster["cell_ids"]]
-            )
-            logger.debug("    Minimum bbox: " + str(min_bbox))
-            logger.debug("    Initial bbox: " + str(cluster["bbox"]))
-            new_bbox = surrounding(min_bbox, cluster["bbox"])
-            logger.debug("    New bbox (initial and text cells): " + str(new_bbox))
-        else:
-            logger.debug("    without text cells, no change.")
-            new_bbox = cluster["bbox"]
-    else:  ## A table
-        ## At least we have to keep the included text cells, and we make the bbox completely comprise them
-        min_bbox = surrounding_list(
-            [raw_cells[cid]["bbox"] for cid in cluster["cell_ids"]]
-        )
-        logger.debug("    Minimum bbox: " + str(min_bbox))
-        logger.debug("    Initial bbox: " + str(cluster["bbox"]))
-        new_bbox = surrounding(min_bbox, cluster["bbox"])
-        logger.debug("    Possibly increased bbox: " + str(new_bbox))
-
-        ## Now we look which non-belonging cells are covered.
-        ## (To decrease dependencies, we don't make use of which cells we actually removed.)
-        ## We don't worry about orphan cells, those could still be added to the table.
-        enclosed_cells = compute_enclosed_cells(
-            new_bbox, raw_cells, min_cell_intersection_with_cluster=0.3
-        )[0]
-        additional_cells = set(enclosed_cells) - set(cluster["cell_ids"])
-        logger.debug(
-            "    Additional cells enclosed by Table bbox: " + str(additional_cells)
-        )
-        spurious_cells = additional_cells - set(orphan_cell_indices)
-        logger.debug(
-            "    Spurious cells enclosed by Table bbox (additional minus orphans): "
-            + str(spurious_cells)
-        )
-        if len(spurious_cells) == 0:
-            return new_bbox
-
-        ## Else we want to keep as much as possible, e.g., grid lines, but not the spurious cells if we can.
-        ## We initialize possible cuts with the current bbox.
-        left_cut = new_bbox[0]
-        right_cut = new_bbox[2]
-        upper_cut = new_bbox[3]
-        lower_cut = new_bbox[1]
-
-        for cell_ix in spurious_cells:
-            cell = raw_cells[cell_ix]
-            # logger.debug("     Spurious cell bbox: " + str(cell["bbox"]))
-            is_left = cell["bbox"][2] < min_bbox[0]
-            is_right = cell["bbox"][0] > min_bbox[2]
-            is_above = cell["bbox"][1] > min_bbox[3]
-            is_below = cell["bbox"][3] < min_bbox[1]
-            # logger.debug("      Left, right, above, below? " + str([is_left, is_right, is_above, is_below]))
-
-            if is_left:
-                if cell["bbox"][2] > left_cut:
-                    ## We move the left cut to exclude this cell:
-                    left_cut = cell["bbox"][2]
-            if is_right:
-                if cell["bbox"][0] < right_cut:
-                    ## We move the right cut to exclude this cell:
-                    right_cut = cell["bbox"][0]
-            if is_above:
-                if cell["bbox"][1] < upper_cut:
-                    ## We move the upper cut to exclude this cell:
-                    upper_cut = cell["bbox"][1]
-            if is_below:
-                if cell["bbox"][3] > lower_cut:
-                    ## We move the left cut to exclude this cell:
-                    lower_cut = cell["bbox"][3]
-            # logger.debug("      Current bbox: " + str([left_cut, lower_cut, right_cut, upper_cut]))
-
-            new_bbox = [left_cut, lower_cut, right_cut, upper_cut]
-
-        logger.debug("   Final bbox: " + str(new_bbox))
-    return new_bbox
-
-
-def remove_cluster_duplicates_by_conf(cluster_predictions, threshold=0.5):
-    DuplicateDeletedClusterIDs = []
-    for cluster_1 in cluster_predictions:
-        for cluster_2 in cluster_predictions:
-            if cluster_1["id"] != cluster_2["id"]:
-                if_conf = False
-                if cluster_1["confidence"] > cluster_2["confidence"]:
-                    if_conf = True
-                if if_conf == True:
-                    if bb_iou(cluster_1["bbox"], cluster_2["bbox"]) > threshold:
-                        DuplicateDeletedClusterIDs.append(cluster_2["id"])
-                    elif contains(
-                        cluster_1["bbox"],
-                        [
-                            cluster_2["bbox"][0] + 3,
-                            cluster_2["bbox"][1] + 3,
-                            cluster_2["bbox"][2] - 3,
-                            cluster_2["bbox"][3] - 3,
-                        ],
-                    ):
-                        DuplicateDeletedClusterIDs.append(cluster_2["id"])
-
-    DuplicateDeletedClusterIDs = list(set(DuplicateDeletedClusterIDs))
-
-    for cl_id in DuplicateDeletedClusterIDs:
-        for cluster in cluster_predictions:
-            if cl_id == cluster["id"]:
-                cluster_predictions.remove(cluster)
-    return cluster_predictions
-
-
-# Assign orphan cells by a low confidence prediction that is below the assigned confidence
-def assign_orphans_with_low_conf_pred(
-    cluster_predictions, cluster_predictions_low, raw_cells, orphan_cell_indices
-):
-    for orph_id in orphan_cell_indices:
-        cluster_chosen = {}
-        iou_thresh = 0.05
-        confidence = 0.05
-
-        # Loop over all predictions, and find the one with the highest IOU, and confidence
-        for cluster in cluster_predictions_low:
-            calc_iou = bb_iou(cluster["bbox"], raw_cells[orph_id]["bbox"])
-            cluster_area = (cluster["bbox"][3] - cluster["bbox"][1]) * (
-                cluster["bbox"][2] - cluster["bbox"][0]
-            )
-            cell_area = (
-                raw_cells[orph_id]["bbox"][3] - raw_cells[orph_id]["bbox"][1]
-            ) * (raw_cells[orph_id]["bbox"][2] - raw_cells[orph_id]["bbox"][0])
-
-            if (
-                (iou_thresh < calc_iou)
-                and (cluster["confidence"] > confidence)
-                and (cell_area * 3 > cluster_area)
-            ):
-                cluster_chosen = cluster
-                iou_thresh = calc_iou
-                confidence = cluster["confidence"]
-        # If a candidate is found, assign to it the PDF cell ids, and tag that it was created by this function for tracking
-        if iou_thresh != 0.05 and confidence != 0.05:
-            cluster_chosen["cell_ids"].append(orph_id)
-            cluster_chosen["created_by"] = "orph_low_conf"
-            cluster_predictions.append(cluster_chosen)
-            orphan_cell_indices.remove(orph_id)
-    return cluster_predictions, orphan_cell_indices
-
-
-def remove_ambigous_pdf_cell_by_conf(cluster_predictions, raw_cells, amb_cell_idxs):
-    for amb_cell_id in amb_cell_idxs:
-        highest_conf = 0
-        highest_bbox_iou = 0
-        cluster_chosen = None
-        problamatic_clusters = []
-
-        # Find clusters in question
-        for cluster in cluster_predictions:
-
-            if amb_cell_id in cluster["cell_ids"]:
-                problamatic_clusters.append(amb_cell_id)
-
-                # If the cell_id is in a cluster of high conf, and highest iou score, and smaller in area
-                bbox_iou_val = bb_iou(cluster["bbox"], raw_cells[amb_cell_id]["bbox"])
-
-                if (
-                    cluster["confidence"] > highest_conf
-                    and bbox_iou_val > highest_bbox_iou
-                ):
-                    cluster_chosen = cluster
-                    highest_conf = cluster["confidence"]
-                    highest_bbox_iou = bbox_iou_val
-                    if cluster["id"] in problamatic_clusters:
-                        problamatic_clusters.remove(cluster["id"])
-
-        # now remove the assigning of cell id from lower confidence, and threshold
-        for cluster in cluster_predictions:
-            for prob_amb_id in problamatic_clusters:
-                if prob_amb_id in cluster["cell_ids"]:
-                    cluster["cell_ids"].remove(prob_amb_id)
-        amb_cell_idxs.remove(amb_cell_id)
-
-    return cluster_predictions, amb_cell_idxs
-
-
-def ranges(nums):
-    # Find if consecutive numbers exist within pdf cells
-    # Used to remove line numbers for review manuscripts
-    nums = sorted(set(nums))
-    gaps = [[s, e] for s, e in zip(nums, nums[1:]) if s + 1 < e]
-    edges = iter(nums[:1] + sum(gaps, []) + nums[-1:])
-    return list(zip(edges, edges))
-
-
-def set_orphan_as_text(
-    cluster_predictions, cluster_predictions_low, raw_cells, orphan_cell_indices
-):
-    max_id = -1
-    figures = []
-    for cluster in cluster_predictions:
-        if cluster["type"] == DocItemLabel.PICTURE:
-            figures.append(cluster)
-
-        if cluster["id"] > max_id:
-            max_id = cluster["id"]
-    max_id += 1
-
-    lines_detector = False
-    content_of_orphans = []
-    for orph_id in orphan_cell_indices:
-        orph_cell = raw_cells[orph_id]
-        content_of_orphans.append(raw_cells[orph_id]["text"])
-
-    fil_content_of_orphans = []
-    for cell_content in content_of_orphans:
-        if cell_content.isnumeric():
-            try:
-                num = int(cell_content)
-                fil_content_of_orphans.append(num)
-            except ValueError:  # ignore the cell
-                pass
-
-    # line_orphans = []
-    #  Check if there are more than 2 pdf orphan cells, if there are more than 2,
-    #  then check between the orphan cells if they are numeric
-    # and if they are a consecutive series of numbers (using ranges function) to decide
-
-    if len(fil_content_of_orphans) > 2:
-        out_ranges = ranges(fil_content_of_orphans)
-        if len(out_ranges) > 1:
-            cnt_range = 0
-            for ranges_ in out_ranges:
-                if ranges_[0] != ranges_[1]:
-                    # If there are more than 75 (half the total line number of a review manuscript page)
-                    # decide that there are line numbers on page to be ignored.
-                    if len(list(range(ranges_[0], ranges_[1]))) > 75:
-                        lines_detector = True
-                        # line_orphans = line_orphans + list(range(ranges_[0], ranges_[1]))
-
-    for orph_id in orphan_cell_indices:
-        orph_cell = raw_cells[orph_id]
-        if bool(orph_cell["text"] and not orph_cell["text"].isspace()):
-            fig_flag = False
-            # Do not assign orphan cells if they are inside a figure
-            for fig in figures:
-                if contains(fig["bbox"], orph_cell["bbox"]):
-                    fig_flag = True
-
-            # if fig_flag == False and raw_cells[orph_id]["text"] not in line_orphans:
-            if fig_flag == False and lines_detector == False:
-                # get class from low confidence detections if not set as text:
-                class_type = DocItemLabel.TEXT
-
-                for cluster in cluster_predictions_low:
-                    intersection = compute_intersection(
-                        orph_cell["bbox"], cluster["bbox"]
-                    )
-                    class_type = DocItemLabel.TEXT
-                    if (
-                        cluster["confidence"] > 0.1
-                        and bb_iou(cluster["bbox"], orph_cell["bbox"]) > 0.4
-                    ):
-                        class_type = cluster["type"]
-                    elif contains(
-                        cluster["bbox"],
-                        [
-                            orph_cell["bbox"][0] + 3,
-                            orph_cell["bbox"][1] + 3,
-                            orph_cell["bbox"][2] - 3,
-                            orph_cell["bbox"][3] - 3,
-                        ],
-                    ):
-                        class_type = cluster["type"]
-                    elif intersection > area(orph_cell["bbox"]) * 0.2:
-                        class_type = cluster["type"]
-
-                new_cluster = {
-                    "id": max_id,
-                    "bbox": orph_cell["bbox"],
-                    "type": class_type,
-                    "cell_ids": [orph_id],
-                    "confidence": -1,
-                    "created_by": "orphan_default",
-                }
-                max_id += 1
-                cluster_predictions.append(new_cluster)
-    return cluster_predictions, orphan_cell_indices
-
-
-def merge_cells(cluster_predictions):
-    # Using graph component creates clusters if orphan cells are touching or too close.
-    G = nx.Graph()
-    for cluster in cluster_predictions:
-        if cluster["created_by"] == "orphan_default":
-            G.add_node(cluster["id"])
-
-    for cluster_1 in cluster_predictions:
-        for cluster_2 in cluster_predictions:
-            if (
-                cluster_1["id"] != cluster_2["id"]
-                and cluster_2["created_by"] == "orphan_default"
-                and cluster_1["created_by"] == "orphan_default"
-            ):
-                cl1 = copy.deepcopy(cluster_1["bbox"])
-                cl2 = copy.deepcopy(cluster_2["bbox"])
-                cl1[0] = cl1[0] - 2
-                cl1[1] = cl1[1] - 2
-                cl1[2] = cl1[2] + 2
-                cl1[3] = cl1[3] + 2
-                cl2[0] = cl2[0] - 2
-                cl2[1] = cl2[1] - 2
-                cl2[2] = cl2[2] + 2
-                cl2[3] = cl2[3] + 2
-                if is_intersecting(cl1, cl2):
-                    G.add_edge(cluster_1["id"], cluster_2["id"])
-
-    component = sorted(map(sorted, nx.k_edge_components(G, k=1)))
-    max_id = -1
-    for cluster_1 in cluster_predictions:
-        if cluster_1["id"] > max_id:
-            max_id = cluster_1["id"]
-
-    for nodes in component:
-        if len(nodes) > 1:
-            max_id += 1
-            lines = []
-            for node in nodes:
-                for cluster in cluster_predictions:
-                    if cluster["id"] == node:
-                        lines.append(cluster)
-                        cluster_predictions.remove(cluster)
-            new_merged_cluster = build_cluster_from_lines(
-                lines, DocItemLabel.TEXT, max_id
-            )
-            cluster_predictions.append(new_merged_cluster)
-    return cluster_predictions
-
-
-def clean_up_clusters(
-    cluster_predictions,
-    raw_cells,
-    merge_cells=False,
-    img_table=False,
-    one_cell_table=False,
-):
-    DuplicateDeletedClusterIDs = []
-
-    for cluster_1 in cluster_predictions:
-        for cluster_2 in cluster_predictions:
-            if cluster_1["id"] != cluster_2["id"]:
-                # remove any artifcats created by merging clusters
-                if merge_cells == True:
-                    if contains(
-                        cluster_1["bbox"],
-                        [
-                            cluster_2["bbox"][0] + 3,
-                            cluster_2["bbox"][1] + 3,
-                            cluster_2["bbox"][2] - 3,
-                            cluster_2["bbox"][3] - 3,
-                        ],
-                    ):
-                        cluster_1["cell_ids"] = (
-                            cluster_1["cell_ids"] + cluster_2["cell_ids"]
-                        )
-                        DuplicateDeletedClusterIDs.append(cluster_2["id"])
-                # remove clusters that might appear inside tables, or images (such as pdf cells in graphs)
-                elif img_table == True:
-                    if (
-                        cluster_1["type"] == DocItemLabel.TEXT
-                        and cluster_2["type"] == DocItemLabel.PICTURE
-                        or cluster_2["type"] == DocItemLabel.TABLE
-                    ):
-                        if bb_iou(cluster_1["bbox"], cluster_2["bbox"]) > 0.5:
-                            DuplicateDeletedClusterIDs.append(cluster_1["id"])
-                        elif contains(
-                            [
-                                cluster_2["bbox"][0] - 3,
-                                cluster_2["bbox"][1] - 3,
-                                cluster_2["bbox"][2] + 3,
-                                cluster_2["bbox"][3] + 3,
-                            ],
-                            cluster_1["bbox"],
-                        ):
-                            DuplicateDeletedClusterIDs.append(cluster_1["id"])
-            # remove tables that have one pdf cell
-            if one_cell_table == True:
-                if (
-                    cluster_1["type"] == DocItemLabel.TABLE
-                    and len(cluster_1["cell_ids"]) < 2
-                ):
-                    DuplicateDeletedClusterIDs.append(cluster_1["id"])
-
-    DuplicateDeletedClusterIDs = list(set(DuplicateDeletedClusterIDs))
-
-    for cl_id in DuplicateDeletedClusterIDs:
-        for cluster in cluster_predictions:
-            if cl_id == cluster["id"]:
-                cluster_predictions.remove(cluster)
-    return cluster_predictions
-
-
-def assigning_cell_ids_to_clusters(clusters, raw_cells, threshold):
-    for cluster in clusters:
-        cells_in_cluster, _ = compute_enclosed_cells(
-            cluster["bbox"], raw_cells, min_cell_intersection_with_cluster=threshold
-        )
-        cluster["cell_ids"] = cells_in_cluster
-        ## These cell_ids are ids of the raw cells.
-        ## They are often, but not always, the same as the "id" or the index of the "cells" list in a prediction.
-    return clusters
-
-
-# Creates a map of cell_id->cluster_id
-def cell_id_state_map(clusters, cell_count):
-    clusters_around_cells = find_clusters_around_cells(cell_count, clusters)
-    orphan_cell_indices = [
-        ix for ix in range(cell_count) if len(clusters_around_cells[ix]) == 0
-    ]  # which cells are assigned no cluster?
-    ambiguous_cell_indices = [
-        ix for ix in range(cell_count) if len(clusters_around_cells[ix]) > 1
-    ]  # which cells are assigned > 1 clusters?
-    return clusters_around_cells, orphan_cell_indices, ambiguous_cell_indices