inference.py

#modified from https://github.com/microsoft/table-transformer/blob/main/src/inference.py
from custom import MyStandardROIHeads, MyStandardRPNHead, MyGeneralizedRCNN, MyFastRCNNConvFCHead, MyAnchorGenerator
from collections import OrderedDict, defaultdict
import json
import argparse
import sys
import xml.etree.ElementTree as ET
from tqdm import tqdm
import os
import random
import io

import torch
from torchvision import transforms
from PIL import Image
import cv2
from fitz import Rect
import numpy as np
import pandas as pd
import matplotlib
#matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib.patches import Patch
from detectron2.config import get_cfg
from detectron2.engine import DefaultPredictor
import postprocess
from copy import copy
#from mmocr.utils.ocr import MMOCR

#ocr = MMOCR(det_config="/data/logs/mmocr/lytica_only_fcenet_log_new/fcenet_r50dcnv2_fpn_1500e_lytica.py", det_ckpt="/data/logs/mmocr/lytica_only_fcenet_log_new/latest.pth",  recog_config='/data/logs/mmocr/lytica_syn_sar_log/sar_r31_parallel_decoder_lytica.py', recog_ckpt='/data/logs/mmocr/lytica_syn_sar_log/latest.pth')
#ocr = MMOCR(det="FCE_CTW_DCNv2",  recog_config='/data/logs/mmocr/lytica_syn_sar_log/sar_r31_parallel_decoder_lytica.py', recog_ckpt='/data/logs/mmocr/lytica_syn_sar_log/latest.pth')

def filter_predictions_with_confidence(predictions, confidence_threshold=0.5):
    if "instances" in predictions:
        preds = predictions["instances"]
        keep_idxs = preds.scores > confidence_threshold
        predictions = copy(predictions) # don't modify the original
        predictions["instances"] = preds[keep_idxs]
    return predictions

def build_model(config_path, model_path, device):

    cfg = get_cfg()
    cfg.merge_from_file(config_path)
    cfg.MODEL.WEIGHTS = model_path
    cfg.MODEL.ROI_HEADS.SCORE_THRESH_TEST = 0.5
    #cfg.INPUT.MAX_SIZE_TEST = 1000
    
    predictor = DefaultPredictor(cfg)

    return predictor
    #outputs = predictor(im)

class MaxResize(object):
    def __init__(self, max_size=800):
        self.max_size = max_size

    def __call__(self, image):
        width, height = image.size
        current_max_size = max(width, height)
        scale = self.max_size / current_max_size
        resized_image = image.resize((int(round(scale*width)), int(round(scale*height))))
        
        return resized_image

detection_transform = transforms.Compose([
    MaxResize(800),
    transforms.ToTensor(),
    transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])

structure_transform = transforms.Compose([
    MaxResize(1000),
    transforms.ToTensor(),
    transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])

def get_class_map(data_type):
    if data_type == 'structure':
        class_map = {
            'table': 0,
            'table column': 1,
            'table row': 2,
            'table spanning cell': 3,
            'table projected row header': 4,
            'table column header': 5,
            'no object': 6 
        }
    elif data_type == 'detection':
        class_map = {'table': 0, 'table rotated': 1, 'no object': 2}
    return class_map

detection_class_thresholds = {
    "table": 0.5,
    "table rotated": 0.5,
    "no object": 10
}

structure_class_thresholds = {
    "table": 0.5,
    "table column": 0.5,
    "table row": 0.5,
    "table column header": 0.5,
    "table projected row header": 0.5,
    "table spanning cell": 0.5,
    "no object": 10
}

def get_args():
    parser = argparse.ArgumentParser()

    parser.add_argument('--image_dir',
                        help="Directory for input images")
    parser.add_argument('--words_dir',
                        help="Directory for input words")
    parser.add_argument('--out_dir',
                        help="Output directory")
    parser.add_argument('--mode',
                        help="The processing to apply to the input image and tokens",
                        choices=['detect', 'recognize', 'extract'])
    parser.add_argument('--structure_config_path',
                        help="Filepath to the structure model config file")
    parser.add_argument('--structure_model_path', help="The path to the structure model")
    parser.add_argument('--detection_config_path',
                        help="Filepath to the detection model config file")
    parser.add_argument('--detection_model_path', help="The path to the detection model")                       
    parser.add_argument('--detection_device', default="cuda")
    parser.add_argument('--structure_device', default="cuda")
    parser.add_argument('--crops', '-p', action='store_true',
                        help='Output cropped data from table detections')
    parser.add_argument('--objects', '-o', action='store_true',
                        help='Output objects')
    parser.add_argument('--cells', '-l', action='store_true',
                        help='Output cells list')
    parser.add_argument('--html', '-m', action='store_true',
                        help='Output HTML')
    parser.add_argument('--csv', '-c', action='store_true',
                        help='Output CSV')
    parser.add_argument('--verbose', '-v', action='store_true',
                        help='Verbose output')
    parser.add_argument('--visualize', '-z', action='store_true',
                        help='Visualize output')
    parser.add_argument('--crop_padding', type=int, default=10,
                        help="The amount of padding to add around a detected table when cropping.")

    return parser.parse_args()


# for output bounding box post-processing
def box_cxcywh_to_xyxy(x):
    x_c, y_c, w, h = x.unbind(-1)
    b = [(x_c - 0.5 * w), (y_c - 0.5 * h), (x_c + 0.5 * w), (y_c + 0.5 * h)]
    return torch.stack(b, dim=1)


def rescale_bboxes(out_bbox, size):
    img_w, img_h = size
    b = box_cxcywh_to_xyxy(out_bbox)
    b = b * torch.tensor([img_w, img_h, img_w, img_h], dtype=torch.float32)
    return b


def iob(bbox1, bbox2):
    """
    Compute the intersection area over box area, for bbox1.
    """
    intersection = Rect(bbox1).intersect(bbox2)
    
    bbox1_area = Rect(bbox1).get_area()
    if bbox1_area > 0:
        return intersection.get_area() / bbox1_area
    
    return 0


def align_headers(headers, rows):
    """
    Adjust the header boundary to be the convex hull of the rows it intersects
    at least 50% of the height of.

    For now, we are not supporting tables with multiple headers, so we need to
    eliminate anything besides the top-most header.
    """
    
    aligned_headers = []

    for row in rows:
        row['column header'] = False

    header_row_nums = []
    for header in headers:
        for row_num, row in enumerate(rows):
            row_height = row['bbox'][3] - row['bbox'][1]
            min_row_overlap = max(row['bbox'][1], header['bbox'][1])
            max_row_overlap = min(row['bbox'][3], header['bbox'][3])
            overlap_height = max_row_overlap - min_row_overlap
            if overlap_height / row_height >= 0.5:
                header_row_nums.append(row_num)

    if len(header_row_nums) == 0:
        return aligned_headers

    header_rect = Rect()
    if header_row_nums[0] > 0:
        header_row_nums = list(range(header_row_nums[0]+1)) + header_row_nums

    last_row_num = -1
    for row_num in header_row_nums:
        if row_num == last_row_num + 1:
            row = rows[row_num]
            row['column header'] = True
            header_rect = header_rect.include_rect(row['bbox'])
            last_row_num = row_num
        else:
            # Break as soon as a non-header row is encountered.
            # This ignores any subsequent rows in the table labeled as a header.
            # Having more than 1 header is not supported currently.
            break

    header = {'bbox': list(header_rect)}
    aligned_headers.append(header)

    return aligned_headers


def refine_table_structure(table_structure, class_thresholds):
    """
    Apply operations to the detected table structure objects such as
    thresholding, NMS, and alignment.
    """
    rows = table_structure["rows"]
    columns = table_structure['columns']

    # Process the headers
    column_headers = table_structure['column headers']
    column_headers = postprocess.apply_threshold(column_headers, class_thresholds["table column header"])
    column_headers = postprocess.nms(column_headers)
    column_headers = align_headers(column_headers, rows)

    # Process spanning cells
    spanning_cells = [elem for elem in table_structure['spanning cells'] if not elem['projected row header']]
    projected_row_headers = [elem for elem in table_structure['spanning cells'] if elem['projected row header']]
    spanning_cells = postprocess.apply_threshold(spanning_cells, class_thresholds["table spanning cell"])
    projected_row_headers = postprocess.apply_threshold(projected_row_headers,
                                                        class_thresholds["table projected row header"])
    spanning_cells += projected_row_headers
    # Align before NMS for spanning cells because alignment brings them into agreement
    # with rows and columns first; if spanning cells still overlap after this operation,
    # the threshold for NMS can basically be lowered to just above 0
    spanning_cells = postprocess.align_supercells(spanning_cells, rows, columns)
    spanning_cells = postprocess.nms_supercells(spanning_cells)

    postprocess.header_supercell_tree(spanning_cells)

    table_structure['columns'] = columns
    table_structure['rows'] = rows
    table_structure['spanning cells'] = spanning_cells
    table_structure['column headers'] = column_headers

    return table_structure


def outputs_to_objects(outputs, img_size, class_idx2name):
    #m = outputs['pred_logits'].softmax(-1).max(-1)
    #pred_labels = list(m.indices.detach().cpu().numpy())[0]
    #pred_scores = list(m.values.detach().cpu().numpy())[0]
    pred_bboxes = outputs["pred_boxes"].tensor.detach().cpu()
    pred_labels = outputs["pred_classes"].detach().cpu()
    pred_scores = outputs["scores"].detach().cpu()
    #pred_bboxes = [elem.tolist() for elem in rescale_bboxes(pred_bboxes, img_size)]

    objects = []
    for label, score, bbox in zip(pred_labels, pred_scores, pred_bboxes):
        class_label = class_idx2name[int(label)]
        if not class_label == 'no object':
            objects.append({'label': class_label, 'score': float(score),
                            'bbox': [float(elem) for elem in bbox]})

    return objects

def objects_to_crops(img, tokens, objects, class_thresholds, padding=10):
    """
    Process the bounding boxes produced by the table detection model into
    cropped table images and cropped tokens.
    """

    table_crops = []
    for obj in objects:
        if obj['score'] < class_thresholds[obj['label']]:
            continue

        cropped_table = {}

        bbox = obj['bbox']
        bbox = [bbox[0]-padding, bbox[1]-padding, bbox[2]+padding, bbox[3]+padding]

        cropped_img = img.crop(bbox)

        table_tokens = [token for token in tokens if iob(token['bbox'], bbox) >= 0.5]
        for token in table_tokens:
            token['bbox'] = [token['bbox'][0]-bbox[0],
                             token['bbox'][1]-bbox[1],
                             token['bbox'][2]-bbox[0],
                             token['bbox'][3]-bbox[1]]

        # If table is predicted to be rotated, rotate cropped image and tokens/words:
        if obj['label'] == 'table rotated':
            cropped_img = cropped_img.rotate(270, expand=True)
            for token in table_tokens:
                bbox = token['bbox']
                bbox = [cropped_img.size[0]-bbox[3]-1,
                        bbox[0],
                        cropped_img.size[0]-bbox[1]-1,
                        bbox[2]]
                token['bbox'] = bbox

        cropped_table['image'] = cropped_img
        cropped_table['tokens'] = table_tokens

        table_crops.append(cropped_table)

    return table_crops

def objects_to_structures(objects, tokens, class_thresholds):
    """
    Process the bounding boxes produced by the table structure recognition model into
    a *consistent* set of table structures (rows, columns, spanning cells, headers).
    This entails resolving conflicts/overlaps, and ensuring the boxes meet certain alignment
    conditions (for example: rows should all have the same width, etc.).
    """

    tables = [obj for obj in objects if obj['label'] == 'table']
    table_structures = []

    for table in tables:
        table_objects = [obj for obj in objects if iob(obj['bbox'], table['bbox']) >= 0.5]
        table_tokens = [token for token in tokens if iob(token['bbox'], table['bbox']) >= 0.5]
        
        structure = {}

        columns = [obj for obj in table_objects if obj['label'] == 'table column']
        rows = [obj for obj in table_objects if obj['label'] == 'table row']
        column_headers = [obj for obj in table_objects if obj['label'] == 'table column header']
        spanning_cells = [obj for obj in table_objects if obj['label'] == 'table spanning cell']
        for obj in spanning_cells:
            obj['projected row header'] = False
        projected_row_headers = [obj for obj in table_objects if obj['label'] == 'table projected row header']
        for obj in projected_row_headers:
            obj['projected row header'] = True
        spanning_cells += projected_row_headers
        for obj in rows:
            obj['column header'] = False
            for header_obj in column_headers:
                if iob(obj['bbox'], header_obj['bbox']) >= 0.5:
                    obj['column header'] = True

        # Refine table structures
        rows = postprocess.refine_rows(rows, table_tokens, class_thresholds['table row'])
        columns = postprocess.refine_columns(columns, table_tokens, class_thresholds['table column'])

        # Shrink table bbox to just the total height of the rows
        # and the total width of the columns
        row_rect = Rect()
        for obj in rows:
            row_rect.include_rect(obj['bbox'])
        column_rect = Rect() 
        for obj in columns:
            column_rect.include_rect(obj['bbox'])
        table['row_column_bbox'] = [column_rect[0], row_rect[1], column_rect[2], row_rect[3]]
        table['bbox'] = table['row_column_bbox']

        # Process the rows and columns into a complete segmented table
        columns = postprocess.align_columns(columns, table['row_column_bbox'])
        rows = postprocess.align_rows(rows, table['row_column_bbox'])

        structure['rows'] = rows
        structure['columns'] = columns
        structure['column headers'] = column_headers
        structure['spanning cells'] = spanning_cells

        if len(rows) > 0 and len(columns) > 1:
            structure = refine_table_structure(structure, class_thresholds)

        table_structures.append(structure)

    return table_structures

def get_preprocess_shape(oldh: int, oldw: int, long_side_length: int):
    """
    Compute the output size given input size and target long side length.
    """
    scale = long_side_length * 1.0 / max(oldh, oldw)
    newh, neww = oldh * scale, oldw * scale
    neww = int(neww + 0.5)
    newh = int(newh + 0.5)

    return (neww, newh)

def resize_pad(image, target_size):
    if not isinstance(image, Image.Image):
        h, w = image.shape[0], image.shape[1]
    else:
        w, h = image.size

    #target_size = get_preprocess_shape(h, w, target_size)
    #image = cv2.resize(image, target_size)

    # Pad image and mask to form a square
    h, w = image.shape[0], image.shape[1]
    #max_dim = max(w, h)
    max_dim = max(target_size, w, h)
    pad_h = (max_dim - h) // 2
    pad_w = (max_dim - w) // 2
    padding = (pad_w, pad_h, max_dim - w - pad_w, max_dim - h - pad_h)

    image = cv2.copyMakeBorder(image, pad_h, max_dim - h - pad_h, pad_w, max_dim - w - pad_w, cv2.BORDER_CONSTANT, None, value=(255,255,255))

    return image



def extract_text_inside_bbox(image, bbox):

    x1, y1, x2, y2 = int(bbox[0]), int(bbox[1]), int(bbox[2]), int(bbox[3])
    cell_image = image[y1:y2, x1: x2]

    #cell_image = cv2.copyMakeBorder(cell_image, 50, 50, 50, 50, cv2.BORDER_CONSTANT, None, value=(255,255,255))
    cell_image = resize_pad(cell_image, 600)

    #cv2.imwrite("cell_image.jpg", cell_image)
    #exit()


    #ocr_result_list = ocr.readtext(cell_image)
    result_str = ""
    #for ocr_result in ocr_result_list:
    #    text_str_list = ocr_result["text"]
    #    for text_str in text_str_list:
    #        result_str = result_str + " " + text_str.replace("<UKN>", " ")

    return result_str

def structure_to_cells(image, table_structure, tokens):
    """
    Assuming the row, column, spanning cell, and header bounding boxes have
    been refined into a set of consistent table structures, process these
    table structures into table cells. This is a universal representation
    format for the table, which can later be exported to Pandas or CSV formats.
    Classify the cells as header/access cells or data cells
    based on if they intersect with the header bounding box.
    """
    columns = table_structure['columns']
    rows = table_structure['rows']
    spanning_cells = table_structure['spanning cells']
    cells = []
    subcells = []

    # Identify complete cells and subcells
    for column_num, column in enumerate(columns):
        for row_num, row in enumerate(rows):
            column_rect = Rect(list(column['bbox']))
            row_rect = Rect(list(row['bbox']))
            cell_rect = row_rect.intersect(column_rect)
            header = 'column header' in row and row['column header']
            cell = {'bbox': list(cell_rect), 'column_nums': [column_num], 'row_nums': [row_num],
                    'column header': header}

            cell['subcell'] = False
            for spanning_cell in spanning_cells:
                spanning_cell_rect = Rect(list(spanning_cell['bbox']))
                if cell_rect.get_area() != 0 and (spanning_cell_rect.intersect(cell_rect).get_area()
                        / cell_rect.get_area()) > 0.5:
                    cell['subcell'] = True
                    break

            if cell['subcell']:
                subcells.append(cell)
            else:
                #cell_text = extract_text_inside_bbox(image, cell['bbox'])
                #cell['cell text'] = cell_text
                cell['projected row header'] = False
                cells.append(cell)

    for spanning_cell in spanning_cells:
        spanning_cell_rect = Rect(list(spanning_cell['bbox']))
        cell_columns = set()
        cell_rows = set()
        cell_rect = None
        header = True
        for subcell in subcells:
            subcell_rect = Rect(list(subcell['bbox']))
            subcell_rect_area = subcell_rect.get_area()
            if (subcell_rect.intersect(spanning_cell_rect).get_area()
                    / subcell_rect_area) > 0.5:
                if cell_rect is None:
                    cell_rect = Rect(list(subcell['bbox']))
                else:
                    cell_rect.include_rect(Rect(list(subcell['bbox'])))
                cell_rows = cell_rows.union(set(subcell['row_nums']))
                cell_columns = cell_columns.union(set(subcell['column_nums']))
                # By convention here, all subcells must be classified
                # as header cells for a spanning cell to be classified as a header cell;
                # otherwise, this could lead to a non-rectangular header region
                header = header and 'column header' in subcell and subcell['column header']
        if len(cell_rows) > 0 and len(cell_columns) > 0:
            cell = {'bbox': list(cell_rect), 'column_nums': list(cell_columns), 'row_nums': list(cell_rows),
                    'column header': header, 'projected row header': spanning_cell['projected row header']}
            cells.append(cell)

    # Compute a confidence score based on how well the page tokens
    # slot into the cells reported by the model

    #use ocr to extract text
    #for cell in cells:
    #    bbox = cell["bbox"]
    #    cell_text = extract_text_inside_bbox(image, bbox)
    #    cell["cell text"] = cell_text

    _, _, cell_match_scores = postprocess.slot_into_containers(cells, tokens)
    try:
        mean_match_score = sum(cell_match_scores) / len(cell_match_scores)
        min_match_score = min(cell_match_scores)
        confidence_score = (mean_match_score + min_match_score)/2
    except:
        confidence_score = 0

    # Dilate rows and columns before final extraction
    #dilated_columns = fill_column_gaps(columns, table_bbox)
    dilated_columns = columns
    #dilated_rows = fill_row_gaps(rows, table_bbox)
    dilated_rows = rows
    for cell in cells:
        column_rect = Rect()
        for column_num in cell['column_nums']:
            column_rect.include_rect(list(dilated_columns[column_num]['bbox']))
        row_rect = Rect()
        for row_num in cell['row_nums']:
            row_rect.include_rect(list(dilated_rows[row_num]['bbox']))
        cell_rect = column_rect.intersect(row_rect)
        cell['bbox'] = list(cell_rect)

    span_nums_by_cell, _, _ = postprocess.slot_into_containers(cells, tokens, overlap_threshold=0.001,
                                                               unique_assignment=True, forced_assignment=False)

    for cell, cell_span_nums in zip(cells, span_nums_by_cell):
        cell_spans = [tokens[num] for num in cell_span_nums]
        # TODO: Refine how text is extracted; should be character-based, not span-based;
        # but need to associate 

        cell['cell text'] = postprocess.extract_text_from_spans(cell_spans, remove_integer_superscripts=False)
        cell['spans'] = cell_spans
        
    # Adjust the row, column, and cell bounding boxes to reflect the extracted text
    num_rows = len(rows)
    rows = postprocess.sort_objects_top_to_bottom(rows)
    num_columns = len(columns)
    columns = postprocess.sort_objects_left_to_right(columns)
    min_y_values_by_row = defaultdict(list)
    max_y_values_by_row = defaultdict(list)
    min_x_values_by_column = defaultdict(list)
    max_x_values_by_column = defaultdict(list)
    for cell in cells:
        min_row = min(cell["row_nums"])
        max_row = max(cell["row_nums"])
        min_column = min(cell["column_nums"])
        max_column = max(cell["column_nums"])
        for span in cell['spans']:
            min_x_values_by_column[min_column].append(span['bbox'][0])
            min_y_values_by_row[min_row].append(span['bbox'][1])
            max_x_values_by_column[max_column].append(span['bbox'][2])
            max_y_values_by_row[max_row].append(span['bbox'][3])
    for row_num, row in enumerate(rows):
        if len(min_x_values_by_column[0]) > 0:
            row['bbox'][0] = min(min_x_values_by_column[0])
        if len(min_y_values_by_row[row_num]) > 0:
            row['bbox'][1] = min(min_y_values_by_row[row_num])
        if len(max_x_values_by_column[num_columns-1]) > 0:
            row['bbox'][2] = max(max_x_values_by_column[num_columns-1])
        if len(max_y_values_by_row[row_num]) > 0:
            row['bbox'][3] = max(max_y_values_by_row[row_num])
    for column_num, column in enumerate(columns):
        if len(min_x_values_by_column[column_num]) > 0:
            column['bbox'][0] = min(min_x_values_by_column[column_num])
        if len(min_y_values_by_row[0]) > 0:
            column['bbox'][1] = min(min_y_values_by_row[0])
        if len(max_x_values_by_column[column_num]) > 0:
            column['bbox'][2] = max(max_x_values_by_column[column_num])
        if len(max_y_values_by_row[num_rows-1]) > 0:
            column['bbox'][3] = max(max_y_values_by_row[num_rows-1])
    for cell in cells:
        row_rect = Rect()
        column_rect = Rect()
        for row_num in cell['row_nums']:
            row_rect.include_rect(list(rows[row_num]['bbox']))
        for column_num in cell['column_nums']:
            column_rect.include_rect(list(columns[column_num]['bbox']))
        cell_rect = row_rect.intersect(column_rect)
        if cell_rect.get_area() > 0:
            cell['bbox'] = list(cell_rect)
            pass

    return cells, confidence_score

def cells_to_csv(cells):
    if len(cells) > 0:
        num_columns = max([max(cell['column_nums']) for cell in cells]) + 1
        num_rows = max([max(cell['row_nums']) for cell in cells]) + 1
    else:
        return

    header_cells = [cell for cell in cells if cell['column header']]
    if len(header_cells) > 0:
        max_header_row = max([max(cell['row_nums']) for cell in header_cells])
    else:
        max_header_row = -1

    table_array = np.empty([num_rows, num_columns], dtype="object")
    if len(cells) > 0:
        for cell in cells:
            for row_num in cell['row_nums']:
                for column_num in cell['column_nums']:
                    table_array[row_num, column_num] = cell["cell text"]

    header = table_array[:max_header_row+1,:]
    flattened_header = []
    for col in header.transpose():
        flattened_header.append(' | '.join(OrderedDict.fromkeys(col)))
    df = pd.DataFrame(table_array[max_header_row+1:,:], index=None, columns=flattened_header)

    return df.to_csv(index=None)

def cells_to_html(cells):
    cells = sorted(cells, key=lambda k: min(k['column_nums']))
    cells = sorted(cells, key=lambda k: min(k['row_nums']))

    table = ET.Element("table")
    current_row = -1

    for cell in cells:
        this_row = min(cell['row_nums'])

        attrib = {}
        colspan = len(cell['column_nums'])
        if colspan > 1:
            attrib['colspan'] = str(colspan)
        rowspan = len(cell['row_nums'])
        if rowspan > 1:
            attrib['rowspan'] = str(rowspan)
        if this_row > current_row:
            current_row = this_row
            if cell['column header']:
                cell_tag = "th"
                row = ET.SubElement(table, "thead")
            else:
                cell_tag = "td"
                row = ET.SubElement(table, "tr")
        tcell = ET.SubElement(row, cell_tag, attrib=attrib)
        #tcell.text = cell['cell text']

    return str(ET.tostring(table, encoding="unicode", short_empty_elements=False))

def visualize_detected_tables(img, det_tables, out_path):
    plt.imshow(img, interpolation="lanczos")
    plt.gcf().set_size_inches(20, 20)
    ax = plt.gca()
    
    for det_table in det_tables:
        bbox = det_table['bbox']

        if det_table['label'] == 'table':
            facecolor = (1, 0, 0.45)
            edgecolor = (1, 0, 0.45)
            alpha = 0.3
            linewidth = 2
            hatch='//////'
        elif det_table['label'] == 'table rotated':
            facecolor = (0.95, 0.6, 0.1)
            edgecolor = (0.95, 0.6, 0.1)
            alpha = 0.3
            linewidth = 2
            hatch='//////'
        else:
            continue
 
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=linewidth, 
                                    edgecolor='none',facecolor=facecolor, alpha=0.1)
        ax.add_patch(rect)
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=linewidth, 
                                    edgecolor=edgecolor,facecolor='none',linestyle='-', alpha=alpha)
        ax.add_patch(rect)
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=0, 
                                    edgecolor=edgecolor,facecolor='none',linestyle='-', hatch=hatch, alpha=0.2)
        ax.add_patch(rect)

    plt.xticks([], [])
    plt.yticks([], [])

    legend_elements = [Patch(facecolor=(1, 0, 0.45), edgecolor=(1, 0, 0.45),
                                label='Table', hatch='//////', alpha=0.3),
                        Patch(facecolor=(0.95, 0.6, 0.1), edgecolor=(0.95, 0.6, 0.1),
                                label='Table (rotated)', hatch='//////', alpha=0.3)]
    plt.legend(handles=legend_elements, bbox_to_anchor=(0.5, -0.02), loc='upper center', borderaxespad=0,
                    fontsize=10, ncol=2)  
    plt.gcf().set_size_inches(10, 10)
    plt.axis('off')
    plt.savefig(out_path, bbox_inches='tight', dpi=150)
    plt.close()

    return

def visualize_cells(img, cells, out_path):
    plt.imshow(img, interpolation="lanczos")
    plt.gcf().set_size_inches(20, 20)
    ax = plt.gca()
    
    for cell in cells:
        bbox = cell['bbox']

        if cell['column header']:
            facecolor = (1, 0, 0.45)
            edgecolor = (1, 0, 0.45)
            alpha = 0.3
            linewidth = 2
            hatch='//////'
        elif cell['projected row header']:
            facecolor = (0.95, 0.6, 0.1)
            edgecolor = (0.95, 0.6, 0.1)
            alpha = 0.3
            linewidth = 2
            hatch='//////'
        else:
            facecolor = (0.3, 0.74, 0.8)
            edgecolor = (0.3, 0.7, 0.6)
            alpha = 0.3
            linewidth = 2
            hatch='\\\\\\\\\\\\'
 
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=linewidth, 
                                    edgecolor='none',facecolor=facecolor, alpha=0.1)
        ax.add_patch(rect)
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=linewidth, 
                                    edgecolor=edgecolor,facecolor='none',linestyle='-', alpha=alpha)
        ax.add_patch(rect)
        rect = patches.Rectangle(bbox[:2], bbox[2]-bbox[0], bbox[3]-bbox[1], linewidth=0, 
                                    edgecolor=edgecolor,facecolor='none',linestyle='-', hatch=hatch, alpha=0.2)
        ax.add_patch(rect)

    plt.xticks([], [])
    plt.yticks([], [])

    legend_elements = [Patch(facecolor=(0.3, 0.74, 0.8), edgecolor=(0.3, 0.7, 0.6),
                                label='Data cell', hatch='\\\\\\\\\\\\', alpha=0.3),
                        Patch(facecolor=(1, 0, 0.45), edgecolor=(1, 0, 0.45),
                                label='Column header cell', hatch='//////', alpha=0.3),
                        Patch(facecolor=(0.95, 0.6, 0.1), edgecolor=(0.95, 0.6, 0.1),
                                label='Projected row header cell', hatch='//////', alpha=0.3)]
    plt.legend(handles=legend_elements, bbox_to_anchor=(0.5, -0.02), loc='upper center', borderaxespad=0,
                    fontsize=10, ncol=3)  
    plt.gcf().set_size_inches(10, 10)
    plt.axis('off')
    plt.savefig(out_path, bbox_inches='tight', dpi=150)
    plt.close()

    return

class TableExtractionPipeline(object):
    def __init__(self, det_device=None, str_device=None,
                 det_model=None, str_model=None,
                 det_model_path=None, str_model_path=None,
                 det_config_path=None, str_config_path=None):

        self.det_device = det_device
        self.str_device = str_device

        self.det_class_name2idx = get_class_map('detection')
        self.det_class_idx2name = {v:k for k, v in self.det_class_name2idx.items()}
        self.det_class_thresholds = detection_class_thresholds

        self.str_class_name2idx = get_class_map('structure')
        self.str_class_idx2name = {v:k for k, v in self.str_class_name2idx.items()}
        self.str_class_thresholds = structure_class_thresholds

        if not det_config_path is None:
            #with open(det_config_path, 'r') as f:
            #    det_config = json.load(f)
            #det_args = type('Args', (object,), det_config)
            #det_args.device = det_device
            self.det_model = build_model(det_config_path, det_model_path, det_device)
            print("Detection model initialized.")

            #if not det_model_path is None:
            #    self.det_model.load_state_dict(torch.load(det_model_path,
            #                                         map_location=torch.device(det_device)))
            #    self.det_model.to(det_device)
            #    self.det_model.eval()
            #    print("Detection model weights loaded.")
            #else:
            #    self.det_model = None

        if not str_config_path is None:
            #with open(str_config_path, 'r') as f:
            #    str_config = json.load(f)
            #str_args = type('Args', (object,), str_config)
            #str_args.device = str_device
            self.str_model = build_model(str_config_path, str_model_path, str_device)
            print("Structure model initialized.")

            #if not str_model_path is None:
            #    self.str_model.load_state_dict(torch.load(str_model_path,
            #                                         map_location=torch.device(str_device)))
            #    self.str_model.to(str_device)
            #    self.str_model.eval()
            #    print("Structure model weights loaded.")
            #else:
            #    self.str_model = None


    def __call__(self, page_image, page_tokens=None):
        return self.extract(self, page_image, page_tokens)

    def detect(self, img, tokens=None, out_objects=True, out_crops=False, crop_padding=10):
        out_formats = {}
        if self.det_model is None:
            print("No detection model loaded.")
            return out_formats

        # Transform the image how the model expects it
        img_tensor = detection_transform(img)

        # Run input image through the model
        outputs = self.det_model([img_tensor.to(self.det_device)])

        # Post-process detected objects, assign class labels

        #make sure image size is (w, h)
        if isinstance(image, Image.Image):
            image_size = img.size
        else:
            image_size = (img.shape[1], img.shape[0])

        objects = outputs_to_objects(outputs, img.size, self.det_class_idx2name)
        if out_objects:
            out_formats['objects'] = objects
        if not out_crops:
            return out_formats

        # Crop image and tokens for detected table
        if out_crops:
            tables_crops = objects_to_crops(img, tokens, objects, self.det_class_thresholds,
                                            padding=crop_padding)
            out_formats['crops'] = tables_crops

        return out_formats

    def recognize(self, img, tokens=None, out_objects=False, out_cells=False,
                  out_html=False, out_csv=False):
        out_formats = {}
        if self.str_model is None:
            print("No structure model loaded.")
            return out_formats

        if not (out_objects or out_cells or out_html or out_csv):
            print("No output format specified")
            return out_formats

        # Transform the image how the model expects it
        #img_tensor = structure_transform(img)

        # Run input image through the model
        #outputs = self.str_model([img_tensor.to(self.str_device)])
        outputs = self.str_model(img)
        #outputs = filter_predictions_with_confidence(outputs, 0.6)

        output_dict = {}
        output_dict["pred_boxes"] = outputs["instances"].pred_boxes
        output_dict["scores"] = outputs["instances"].scores
        output_dict["pred_classes"] = outputs["instances"].pred_classes

        if isinstance(img, Image.Image):
            image_size = img.size
        else:
            image_size = (img.shape[1], img.shape[0])

        # Post-process detected objects, assign class labels
        objects = outputs_to_objects(output_dict, image_size, self.str_class_idx2name)
        if out_objects:
            out_formats['objects'] = objects
        if not (out_cells or out_html or out_csv):
            return out_formats

        # Further process the detected objects so they correspond to a consistent table 
        tables_structure = objects_to_structures(objects, tokens, self.str_class_thresholds)

        # Enumerate all table cells: grid cells and spanning cells
        tables_cells = [structure_to_cells(img, structure, tokens)[0] for structure in tables_structure]
        if out_cells:
            out_formats['cells'] = tables_cells
        if not (out_html or out_csv):
            return out_formats

        # Convert cells to HTML
        if out_html:
            tables_htmls = [cells_to_html(cells) for cells in tables_cells]
            out_formats['html'] = tables_htmls

        # Convert cells to CSV, including flattening multi-row column headers to a single row 
        if out_csv:
            tables_csvs = [cells_to_csv(cells) for cells in tables_cells]
            out_formats['csv'] = tables_csvs

        return out_formats

    def extract(self, img, tokens=None, out_objects=True, out_crops=False, out_cells=False,
                out_html=False, out_csv=False, crop_padding=10):

        detect_out = self.detect(img, tokens=tokens, out_objects=False, out_crops=True,
                                 crop_padding=crop_padding)
        cropped_tables = detect_out['crops']

        extracted_tables = []
        for table in cropped_tables:
            img = table['image']
            tokens = table['tokens']

            extracted_table = self.recognize(img, tokens=tokens, out_objects=out_objects,
                                       out_cells=out_cells, out_html=out_html, out_csv=out_csv)
            extracted_table['image'] = img
            extracted_table['tokens'] = tokens
            extracted_tables.append(extracted_table)

        return extracted_tables


def output_result(key, val, args, img, img_file):
    if key == 'objects':
        if args.verbose:
            print(val)
        out_file = img_file.replace(".jpg", "_objects.json")
        with open(os.path.join(args.out_dir, out_file), 'w') as f:
            json.dump(val, f)
        if args.visualize:
            out_file = img_file.replace(".jpg", "_fig_tables.jpg")
            out_path = os.path.join(args.out_dir, out_file)
            visualize_detected_tables(img, val, out_path)
    elif not key == 'image' and not key == 'tokens':
        #assert len(val) == 1
        for idx, elem in enumerate(val):
            if key == 'crops':
                for idx, cropped_table in enumerate(val):
                    out_img_file = img_file.replace(".jpg", "_table_{}.jpg".format(idx))
                    cropped_table['image'].save(os.path.join(args.out_dir,
                                                                out_img_file))
                    out_words_file = out_img_file.replace(".jpg", "_words.json")
                    with open(os.path.join(args.out_dir, out_words_file), 'w') as f:
                        json.dump(cropped_table['tokens'], f)
            elif key == 'cells':
                out_file = img_file.replace(".jpg", "_{}_objects.json".format(idx))
                with open(os.path.join(args.out_dir, out_file), 'w') as f:
                    json.dump(elem, f)
                if args.verbose:
                    print(elem)
                if args.visualize:
                    out_file = img_file.replace(".jpg", "_fig_cells.jpg")
                    out_path = os.path.join(args.out_dir, out_file)
                    visualize_cells(img, elem, out_path)
            else:
                out_file = img_file.replace(".jpg", "_{}.{}".format(idx, key))
                with open(os.path.join(args.out_dir, out_file), 'w') as f:
                    if elem is not None:
                        f.write(elem)
                    else:
                        f.write("")
                if args.verbose:
                    print(elem)
                        

def main():
    args = get_args()
    print(args.__dict__)
    print('-' * 100)

    if not args.out_dir is None and not os.path.exists(args.out_dir):
        os.makedirs(args.out_dir)

    # Create inference pipeline
    print("Creating inference pipeline")
    pipe = TableExtractionPipeline(det_device=args.detection_device,
                                   str_device=args.structure_device,
                                   det_config_path=args.detection_config_path, 
                                   det_model_path=args.detection_model_path,
                                   str_config_path=args.structure_config_path, 
                                   str_model_path=args.structure_model_path)

    # Load images
    img_files = os.listdir(args.image_dir)
    num_files = len(img_files)
    random.shuffle(img_files)

    for count, img_file in enumerate(img_files):
        print("({}/{})".format(count+1, num_files))
        img_path = os.path.join(args.image_dir, img_file)
        #img = Image.open(img_path)
        img = cv2.imread(img_path)
        img = cv2.cvtColor(img, cv2.COLOR_BGR2RGB)
        print("Image loaded.")

        if not args.words_dir is None:
            tokens_path = os.path.join(args.words_dir, img_file.replace(".jpg", "_words.json"))
            with open(tokens_path, 'r') as f:
                tokens = json.load(f)

                # Handle dictionary format
                if type(tokens) is dict and 'words' in tokens:
                    tokens = tokens['words']

                # 'tokens' is a list of tokens
                # Need to be in a relative reading order
                # If no order is provided, use current order
                for idx, token in enumerate(tokens):
                    if not 'span_num' in token:
                        token['span_num'] = idx
                    if not 'line_num' in token:
                        token['line_num'] = 0
                    if not 'block_num' in token:
                        token['block_num'] = 0
        else:
            tokens = []

        #padding
        img = cv2.copyMakeBorder(img, 2, 2, 2, 2, cv2.BORDER_CONSTANT, None, value=(255,255,255))

        if args.mode == 'recognize':
            extracted_table = pipe.recognize(img, tokens, out_objects=args.objects, out_cells=args.csv,
                                out_html=args.html, out_csv=args.csv)
            print("Table(s) recognized.")

            for key, val in extracted_table.items():
                output_result(key, val, args, img, img_file)

        if args.mode == 'detect':
            detected_tables = pipe.detect(img, tokens, out_objects=args.objects, out_crops=args.crops)
            print("Table(s) detected.")

            for key, val in detected_tables.items():
                output_result(key, val, args, img, img_file)

        if args.mode == 'extract':
            extracted_tables = pipe.extract(img, tokens, out_objects=args.objects, out_cells=args.csv,
                                            out_html=args.html, out_csv=args.csv,
                                            crop_padding=args.crop_padding)
            print("Table(s) extracted.")

            for table_idx, extracted_table in enumerate(extracted_tables):
                for key, val in extracted_table.items():
                    output_result(key, val, args, extracted_table['image'],
                                  img_file.replace('.jpg', '_{}.jpg'.format(table_idx)))

if __name__ == "__main__":
    main()